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The RFamide peptide family , or the RFamide-related peptides ( RFRPs ), are a family of neuropeptides . [ 1 ] [ 2 ] They are characterized by the possession of an Arg-Phe-NH 2 motif at their C-terminal extremities. [ 1 ] [ 2 ]
Members of the family include: [ 1 ] [ 2 ]
This biochemistry article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/RFamide_peptide_family |
The arginine-glycine or arginine-glycine-glycine ( RG/RGG ) motif is a repeating amino acid sequence motif commonly found in RNA-binding proteins (RBPs). RGG regions in proteins are defined as two or more RG/RGG sequences within a stretch of 30 amino acids. [ 1 ] Initially named the RGG box , it confers a protein with the ability to bind double-stranded mRNA molecules. [ 2 ] The RGG motif has been observed in proteins from at least 12 animal species, including humans. [ 3 ]
RGG motifs are primarily involved in mediating protein-RNA interactions . Positive charges from arginine residues promote electrostatic interactions with mRNA molecules. The composition and structure of the arginine side chain may also allow for specific interactions with other molecules as opposed to the other positively charged amino acids , lysine and histidine. [ 4 ] Glycine residues add flexibility to the peptide structure and promote their tendency to form intrinsically disordered regions . The RGG motif can also drive liquid-lipid phase separation of proteins inside cells as well as in vitro. [ 5 ] [ 6 ]
Researchers have pursued creating condensates with novel functions for use in cellular and metabolic engineering . Synthetically designed proteins containing repeating RGG motifs have been used to form droplets with tunable properties in cells and in vitro. [ 7 ] [ 8 ]
RGG motif-containing proteins are the second most abundant group of RBPs in the human genome. [ 9 ] [ 10 ] They are involved in various RNA metabolism, export, and translation functions. | https://en.wikipedia.org/wiki/RG/RGG_motif |
RG Jones Sound Engineering , or simply RG Jones , is a professional audiovisual , sound reinforcement and live touring production support company. Founded in 1926, RG Jones is the oldest British sound reinforcement company still in operation and one of the oldest in the world. [ 1 ] [ 2 ]
Reginald Geoffrey Jones (1912-1987) worked as a salesman for Milton Products in busy street markets where he could not be heard above the crowd. To solve the problem he built a public address system which he mounted on top the panel van he conducted business out of. The public address system consisted of a microphone connected to an amplifier which fed two large wooden horns he had constructed. Four 12V batteries were used to power a rotary 48V to 23V converter to provide portable electricity for the system. The Milton Products Company asked Jones to build 15 more of these systems, leading to his founding the Magnet Publicity Broadcasting Company, which was later re-named RG Jones. [ 3 ] [ 2 ] [ 4 ]
In 1942 Jones moved his company to Morden in southwest London and began installing sound reinforcement systems in numerous London theatres . Jones also designed the Theatre Panatrope--a system that facilitated precise cueing of a sound effects or music record for theatre productions. [ 3 ]
To further expand his business, Jones built a recording studio. Originally a two-track facility based in two rooms of a house, RG Jones Recording Studios became one of the first 4-track facilities in England. During World War II , RG Jones Recording Studios produced transcription discs used by the armed forces to replay radio programs, [ 5 ] and the company's mobile PA equipment was used by The Home Guard and the Red Cross . RG Jones provided PA systems for the VE Day and VJ Day celebrations in London.
In 1952, RG Jones opened a second studio at Morden, and in 1964, the Rolling Stones first recorded at RG Jones Studios. [ 3 ] In 1969, RG Jones opened a new studio in Wimbledon and closed the Morden studio, whose building was demolished to make way for Merton College . Notable artists who recorded at the studio before its eventual closure in 2001 [ 6 ] included the Moody Blues , The Who , David Bowie , Love Affair , Sonny Boy Williamson , the Rolling Stones , Elton John , the Bee Gees , Leo Sayer , The Police , a-ha , Cliff Richard , and Mark Morrison . [ 3 ] [ 7 ]
In 1971 company founder Ronald passed the company on to his son, Robin, and retired (he would pass away 16 years later in 1987 at the age of 75). [ 3 ]
RG Jones business maintained separate divisions for equipment rental, sales, installation projects, and the recording studio.
In the 1980s, the rental division gained prominence through such high-profile events as Royal Fireworks for the Wedding of Prince Charles and Lady Diana Spencer in 1981, the 1982 visit by Pope John Paul II to the United Kingdom , and the opening of the Thames Barrier the same year. The company also supporting classical open-air concerts at Kenwood House , Marble Hill House , and Crystal Palace Bowl . In 1997, the company provided sound reinforcement at the Funeral of Diana, Princess of Wales . The rental division also experienced an increase in jobs supporting outdoor broadcast events for the BBC, Thames TV , and London Weekend Television . [ 3 ] Outdoor festivals, including the Henley Festival , [ 8 ] Glastonbury Festival , [ 9 ] and Radio 1's Big Weekend became clients for RJ Jones as well. In 2014, the company provided sound reinforcement at the Outlook festival in Croatia. [ 5 ]
The RG Jones installation division completed projects for such high-profile entities and buildings as the Lloyd's building , the Royal Academy of Arts , the BBC , Buckingham Palace , St Paul's Cathedral , Westminster Cathedral , Lord's Cricket Ground , Wimbledon Lawn Tennis Club , and City of London Corporation . In 2012, the company completed work at the Baitul Futuh Mosque . [ 3 ] [ 5 ] The company has been installing, maintaining, and operating AV systems for the Royal Household for more than 30 years, and is the first English sound company to be able to display a Royal Warrant . [ 10 ]
in 1998, with Robin approaching retirement, management buyout (MBO) talks began, with the MBO completed on July 7 2004. [ 3 ] RG Jones continues to provide sound systems for festivals, concerts, sporting and special events, and also has a large installed sound business providing service to churches, businesses and schools. | https://en.wikipedia.org/wiki/RG_Jones_Sound_Engineering |
The RH-32 was a radiation-hardened 32-bit MIPS R3000 based microprocessor chipset developed by the USAF Rome Laboratories [ 1 ] for the Ballistic Missile Defense Agency, and produced by Honeywell (later, TRW) for Aerospace applications. It achieves a throughput of 20 MIPS . It was a three-chip set, consisting of Central Processing Unit , Floating Point Unit , and Cache Memory . [ 2 ]
This computing article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/RH-32 |
RIAA equalization is a specification for the recording and playback of phonograph records , established by the Recording Industry Association of America (RIAA). The purposes of the equalization are to permit greater recording times (by decreasing the mean width of each groove), to improve sound quality, and to reduce the groove damage that would otherwise arise during playback.
The RIAA equalization curve was intended to operate as a de facto global industry standard for records since 1954, but when the change actually took place is difficult to determine. [ 1 ]
Before then, especially from 1940, each record company applied its own equalization; over 100 combinations of turnover and rolloff frequencies were in use, the main ones being Columbia-78, Decca-U.S., European (various), Victor-78 (various), Associated, BBC, NAB, Orthacoustic, World, Columbia LP, FFRR-78 and microgroove, and AES. The obvious consequence was that different reproduction results were obtained if the recording and playback filtering were not matched.
RIAA equalization is a form of pre-emphasis on recording and de-emphasis on playback. A recording is made with the low frequencies reduced and the high frequencies boosted, and on playback, the opposite occurs. The net result is a flat frequency response, but with attenuation of high-frequency noise such as hiss and clicks that arise from the recording medium. Reducing the low frequencies also limits the excursions the cutter needs to make when cutting a groove. Groove width is thus reduced, allowing more grooves to fit into a given surface area, permitting longer recording times. This also reduces physical stresses on the stylus , which might otherwise cause distortion or groove damage during playback.
A potential drawback of the system is that rumble from the playback turntable 's drive mechanism is amplified by the low-frequency boost that occurs on playback. Players must, therefore, be designed to limit rumble, more so than if RIAA equalization did not occur.
RIAA playback equalization is not a simple low-pass filter. It defines transition points in three places: 75 μs, 318 μs and 3180 μs, which correspond to 2122 Hz, 500.5 Hz and 50.05 Hz. [ 2 ] Mathematically, the pre-emphasis transfer function is expressed as follows, where T 1 =3180 μs, T 2 =318 μs, T 3 =75 μs: [ 3 ]
f ( s ) = ( s T 1 + 1 ) ( s T 3 + 1 ) ( s T 2 + 1 ) {\displaystyle f(s)={\frac {(sT_{1}+1)(sT_{3}+1)}{(sT_{2}+1)}}}
Implementing this characteristic is not especially difficult, but is more involved than a simple amplifier. [ 4 ] Practically every 20th century hi-fi preamplifier , integrated amplifier and receiver featured a built-in phono stage with the RIAA characteristic. As more modern designs omitted the phonograph inputs, add-on phono preamplifiers with the RIAA equalization curve have become available. These adapt a magnetic phono cartridge to an unbalanced −10 dBv consumer line-level RCA input. Some modern turntables feature built-in preamplification to the RIAA standard. Special preamplifiers are also available for the various equalization curves used on pre-1954 records.
Digital audio editors often feature the ability to equalize audio samples using standard and custom equalization curves, removing the need for a dedicated hardware preamplifier when capturing audio with a computer. However, this can add an extra step in processing a sample, and may amplify or reduce audio quality deficiencies of the sound card being used to capture the signal.
Equalization practice for electrical recordings dates to the beginning of the art. In 1926, Joseph P. Maxwell and Henry C. Harrison from Bell Telephone Laboratories disclosed that the recording pattern of the Western Electric "rubber line" magnetic disc cutter had a constant-velocity characteristic. This meant that as frequency increased in the treble, recording amplitude decreased. Conversely in the bass, as frequency decreased, recording amplitude increased. Therefore, attenuating the bass frequencies was necessary below about 250 Hz , the bass turnover point, in the amplified microphone signal fed to the recording head. Otherwise, bass modulation became excessive and overcutting took place, with the cutter getting into the next record groove. When played back electrically with a magnetic pickup having a smooth response in the bass region, a complementary boost in amplitude at the bass turnover point was necessary. G. H. Miller in 1934 reported that when complementary boost at the turnover point was used in radio broadcasts of records, the reproduction was more realistic and many of the musical instruments stood out in their true form.
West in 1930 and later P. G. H. Voight (1940) showed that the early Wente-style condenser microphones contributed to a 4- to 6-dB midrange brilliance or pre-emphasis in the recording chain. This meant that the electrical recording characteristics of Western Electric licensees such as Columbia Records and Victor Talking Machine Company had a higher amplitude in the midrange region. Brilliance such as this compensated for dullness in many early magnetic pickups having drooping midrange and treble response [ citation needed ] . As a result, this practice was the empirical beginning of using pre-emphasis above 1,000 Hz in 78 and 33 1 ⁄ 3 rpm records, some 29 years before the RIAA curve.
Over the years, a variety of record equalization practices emerged, with no industry standard. For example, in Europe, for many years recordings required playback with a bass turnover setting of 250 to 300 Hz and a treble rolloff at 10,000 Hz ranging from 0 to −5 dB, or more. In the United States, practices varied and a tendency arose to use higher bass turnover frequencies, such as 500 Hz, as well as a greater treble rolloff such as −8.5 dB, and more. The purpose was to record higher modulation levels on the record.
Evidence from the early technical literature concerning electrical recording suggests that serious efforts to standardize recording characteristics within an industry did not occur until 1942–1949. Before this time, electrical recording technology from company to company was considered a proprietary art all the way back to the 1925 Western Electric licensed method first used by Columbia and Victor. For example, what Brunswick did was different from the practices of Victor .
Broadcasters were faced with having to adapt daily to the varied recording characteristics of many sources - various makers of "home recordings" readily available to the public, European recordings, lateral cut transcriptions, and vertical cut transcriptions. Efforts were started in 1942 to standardize within the National Association of Broadcasters (NAB), later known as the National Association of Radio and Television Broadcasters. The NAB, among other items, issued recording standards in 1942 and 1949 for laterally and vertically cut records, principally transcriptions. A number of 78 rpm record producers, as well as early LP makers, also cut their records to the NAB lateral standard.
The lateral-cut NAB curve was remarkably similar to the NBC Orthacoustic curve, which evolved from practices within the National Broadcasting Company since the mid-1930s. Empirically, and not by any formula, the bass end of the audio spectrum below 100 Hz could be boosted somewhat to override system hum and turntable rumble noises. Likewise at the treble end beginning at 1,000 Hz, if audio frequencies were boosted by 16 dB at 10,000 Hz the delicate sibilant sounds of speech and high overtones of musical instruments could be heard despite the high background noise of shellac discs. When the record was played back using a complementary inverse curve ( de-emphasis ), signal-to-noise ratio was improved and the programming sounded more lifelike.
In a related area, around 1940 treble pre-emphasis similar to that used in the NBC Orthacoustic recording curve was first employed by Edwin Howard Armstrong in his system of frequency modulation ( FM ) radio broadcasting. FM radio receivers using Armstrong circuits and treble de-emphasis would render high-quality, wide-range audio output with low noise levels.
When the Columbia LP was released in June 1948, the developers subsequently published technical information about the 33 1 ⁄ 3 rpm, microgroove, long-playing record. [ 5 ] Columbia disclosed a recording characteristic showing that it was like the NAB curve in the treble, but had more bass boost or pre-emphasis below about 150 Hz. The authors disclosed electrical network characteristics for the Columbia LP curve. Nevertheless, the curve was not yet based on mathematical formulae, at least not explicitly.
In 1951, at the beginning of the post-World War II high fidelity (hi-fi) popularity, the Audio Engineering Society (AES) developed a standard playback curve. [ 6 ] This was intended for use by hi-fi amplifier manufacturers. If records were engineered to sound good on hi-fi amplifiers using the AES curve, this would be a worthy goal towards standardization. This curve was defined by the transition frequencies of audio filters and had a pole at 2.5 kHz (approximately 63.7 μs) and a zero at 400 Hz (approximately 397.9 μs).
RCA Victor and Columbia were in a "market war" concerning which recorded format was going to win: the Columbia LP versus the RCA Victor 45 rpm disc (released in February 1949). Besides also being a battle of disc size and record speed, there was a technical difference in the recording characteristics. RCA Victor was using "New Orthophonic", whereas Columbia was using their own LP curve.
Ultimately, the New Orthophonic curve was disclosed in a publication by R. C. Moyer of RCA Victor in 1953; [ 7 ] additional background information about this evolution can also be found in another article of the same author, published in 1957. [ 8 ] He traced the RCA Victor characteristics back to the Western Electric "rubber line" recorder in 1925 up to the early 1950s laying claim to long-held recording practices and reasons for major changes in the intervening years. The RCA Victor New Orthophonic curve was within the tolerances for the NAB/NARTB, Columbia LP, and AES curves. It eventually became the technical predecessor to the RIAA curve.
Between 1953 and 1956 (before the stereo LP in 1958), several standards bodies around the world adopted the same playback curve—identical to the RCA Victor New Orthophonic curve—which became standard throughout the national and international record markets. [ 9 ] However, although these standards were all identical, no universal name was used. One of the standards was called simply "RIAA", and it is likely that this name was eventually adopted because it was memorable.
Some niche record cutters possibly were still using EQ curves other than the RIAA curve well into the 1970s. As a result, some audio manufacturers today produce phono equalizers with selectable EQ curves, including options for Columbia LP, Decca, CCIR, and TELDEC's Direct Metal Mastering .
The official RIAA standard defines three time-constants with pre-emphasis rising indefinitely above 75 μs, but in practice this is not possible. When the RIAA equalization standard was written the inherent bandwidth limitations of the recording equipment and cutting amplifier imposed their own ultimate upper limit on the pre-emphasis characteristic, so no official upper limit was included in the RIAA definition.
Modern systems have far wider potential bandwidth. An essential feature of all cutting amplifiers—including the Neumann cutting amplifiers—is a forcibly imposed high frequency roll-off above the audio band (>20 kHz). This implies two or more additional time constants to those defined by the RIAA curve. This is not standardized anywhere, but set by the maker of the cutting amplifier and associated electronics.
The so-called "Neumann pole" attempts to provide complementary correction for these unofficial time constants upon playback. However, there is no such pole.
In 1995, an unqualified source erroneously suggested that Neumann cutting amplifiers applied a single high-frequency zero at 3.18 μs (about 50 kHz) and that a complementary zero should therefore be included upon playback. [ 10 ] However, no such zero exists. [ 11 ] [ 2 ]
For example, the RIAA pre-emphasis in the popular Neumann SAB 74B equalizer applies a second-order roll off at 49.9 kHz, implemented by a Butterworth (maximally flat) active filter, plus an additional pole at 482 kHz. [ 2 ] This cannot be compensated for by a simple zero even if it were necessary, and in any case, other amplifiers will differ. Correction upon playback is not, in fact, required, as it is taken into account at the cutting stage when manual equalization is applied while monitoring initial cuts on a standard RIAA playback system. Nevertheless, the use of the erroneous zero, misnamed "pole", remains a subject of some debate among amateur enthusiasts.
Many common phono preamplifier designs using negative feedback equalization include an unintentional zero at high frequencies, caused by using series negative feedback around a non-inverting gain stage, which cannot reduce the gain below 1. This was noted in the Lipshitz JAES paper, [ 4 ] as t6 , with equations and RC networks for a solution: all of which was missed by Wright, who claimed it was not mentioned by Lipshitz. This solution is implemented in some but not all affected phono preamplifiers. [ 11 ]
In 1976, an alternative version of the replay curve (but not the recording curve) was proposed by the International Electrotechnical Commission , differing from the RIAA replay curve only in the addition of a pole at 7950 μs (approximately 20 Hz). [ 12 ] The justification was to reduce the subsonic output of the phono amplifier caused by disk warp and turntable rumble.
This so-called IEC amendment to the RIAA curve is not universally seen as desirable, as it introduces considerable amplitude and—of more concern—phase errors into the low-frequency response during playback. The simple first-order roll-off also provides only very mild reduction of rumble, [ 11 ] and many manufacturers consider that turntables, arm, and cartridge combinations should be of sufficient quality for problems not to arise.
Some manufacturers follow the IEC standard, others do not, while the remainder make this IEC-RIAA option user selectable. It remains subject to debate some 35 years later. [ 2 ] This IEC Amendment was withdrawn in June 2009, though.
Telefunken and Decca founded a record company ( Teldec ) that used a characteristic which was also proposed for German DIN standards in July 1957 ( Entwurf DIN 45533, DIN 45536, and DIN 45537). Incidentally, this proposed standard defined exactly the same characteristic as the intermediate CCIR Recommendation No. 208 of 1956, which was valid until about mid-1959. Nevertheless, the proposed DIN standards were was adopted in April 1959 (DIN 45533:1959, DIN 45536:1959, and DIN 45537:1959): that is, at a time when the RIAA characteristic was already well-established; and it was in effect until November 1962, when the German DIN finally adopted the RIAA characteristic (DIN 45536:1962 and DIN 45537:1962). The extent of usage of the Teldec characteristic is unclear, though.
The time constants of the Teldec characteristic are 3180 μs (approximately 50 Hz), 318 μs (approximately 500 Hz), and 50 μs (approximately 3183 Hz), thus differing only in the third value from the corresponding RIAA values. [ 13 ] Although the Teldec characteristic is close to the RIAA characteristic, it is different enough for recordings recorded with the former and played back with the latter to sound a little dull. [ 14 ] | https://en.wikipedia.org/wiki/RIAA_equalization |
An ICE table or RICE box or RICE chart is a tabular system of keeping track of changing concentrations in an equilibrium reaction . ICE stands for initial, change, equilibrium . It is used in chemistry to keep track of the changes in amount of substance of the reactants and also organize a set of conditions that one wants to solve with. [ 1 ] Some sources refer to a RICE table (or box or chart) where the added R stands for the reaction to which the table refers. [ 2 ] Others simply call it a concentration table (for the acid–base equilibrium). [ 3 ]
To illustrate the processes, consider the case of dissolving a weak acid , HA, in water. The pH can be calculated using an ICE table. Note that in this example, we are assuming that the acid is not very weak, and that the concentration is not very dilute, so that the concentration of [OH − ] ions can be neglected. This is equivalent to the assumption that the final pH will be below about 6 or so. See pH calculations for more details.
First write down the equilibrium expression. HA ↽ − − ⇀ A − + H + {\displaystyle {\ce {HA<=>{A^{-}}+{H+}}}} The columns of the table correspond to the three species in equilibrium.
The first row shows the reaction, which some authors label R and some leave blank.
The second row, labeled I, has the initial conditions: the nominal concentration of acid is C a and it is initially undissociated, so the concentrations of A − and H + are zero.
The third row, labeled C, specifies the change that occurs during the reaction. When the acid dissociates, its concentration changes by an amount − x {\displaystyle -x} , and the concentrations of A − and H + both change by an amount + x {\displaystyle +x} . This follows from consideration of mass balance (the total number of each atom/molecule must remain the same) and charge balance (the sum of the electric charges before and after the reaction must be zero).
Note that the coefficients in front of the " x " correlate to the mole ratios of the reactants to the product. For example, if the reaction equation had 2 H + ions in the product, then the "change" for that cell would be "2 x "
The fourth row, labeled E, is the sum of the first two rows and shows the final concentrations of each species at equilibrium.
It can be seen from the table that, at equilibrium, [H + ] = x .
To find x , the acid dissociation constant (that is, the equilibrium constant for acid-base dissociation ) must be specified.
K a = [ H + ] [ A − ] [ HA ] {\displaystyle K_{\text{a}}={\frac {{\ce {[H^+][A^-]}}}{{\ce {[HA]}}}}}
Substitute the concentrations with the values found in the last row of the ICE table.
K a = x 2 C a − x {\displaystyle K_{\text{a}}={\frac {x^{2}}{C_{a}-x}}}
x 2 + K a x − K a C a = 0 {\displaystyle x^{2}+K_{\text{a}}x-K_{\text{a}}C_{a}=0}
With specific values for C a and K a this quadratic equation can be solved for x . Assuming [ 4 ] that pH = −log 10 [H + ] the pH can be calculated as pH = −log 10 x .
If the degree of dissociation is quite small, C a ≫ x and the expression simplifies to K a = x 2 C a {\displaystyle K_{\text{a}}={\frac {x^{2}}{C_{a}}}} and pH = 1 / 2 (p K a − log C a ). This approximate expression is good for p K a values larger than about 2 and concentrations high enough. | https://en.wikipedia.org/wiki/RICE_chart |
MDGRAPE-3 is an ultra-high performance petascale supercomputer system developed by the Riken research institute in Japan . It is a special purpose system built for molecular dynamics simulations, especially protein structure prediction . [ 1 ]
MDGRAPE-3 consists of 201 units of 24 custom MDGRAPE-3 chips (4,824 total), plus additional dual-core Intel Xeon processors (codename "Dempsey" ) which serve as host machines.
In June 2006 Riken announced its completion, [ 2 ] achieving the petaFLOPS level of floating point arithmetic performance. [ 2 ] This was more than three times faster than the 2006 version of the IBM Blue Gene/L system, which then led the TOP500 list of supercomputers at 0.28 petaFLOPS. Because it's not a general-purpose machine capable of running the LINPACK benchmarks , MDGRAPE-3 does not qualify for the TOP500 list. | https://en.wikipedia.org/wiki/RIKEN_MDGRAPE-3 |
The RIM-900 was one of the first wireless data devices, marketed as a two-way pager . It operated on the Mobitex network. It was a clam shell device that could fit on a belt. It had a small QWERTY keyboard for sending and receiving email and interactive messages.
The product was introduced as Inter@ctive Paging in 1996 by Research in Motion and RAM Mobile Data . [ 1 ]
This article about wireless technology is a stub . You can help Wikipedia by expanding it .
This PDA-related article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/RIM-900 |
In the field of geodesy , Receiver Independent Exchange Format ( RINEX ) is a data interchange format for raw satellite navigation system data. This allows the user to post-process the received data to produce a more accurate result — usually with other data unknown to the original receiver, such as better models of the atmospheric conditions at time of measurement.
The final output of a navigation receiver is usually its position, speed or other related physical quantities. However, the calculation of these quantities are based on a series of measurements from one or more satellite constellations. Although receivers calculate positions in real time, in many cases it is interesting to store intermediate measures for later use. RINEX is the standard format that allows the management and disposal of the measures generated by a receiver, as well as their off-line processing by a multitude of applications, whatever the manufacturer of both the receiver and the computer application.
The RINEX format is designed to evolve over time, adapting to new types of measurements and new satellite navigation systems. The first RINEX version was developed by W. Gurtner in 1989 [ 1 ] and published by W. Gurtner and G. Mader in the CSTG GPS Bulletin of September/October 1990. Since 1993 the RINEX 2 is available, which has been revised and adopted several times. RINEX enables storage of measurements of pseudorange , carrier-phase , Doppler and signal-to-noise from GPS (including GPS modernization signals e.g. L5 and L2C), [ 2 ] GLONASS , Galileo , Beidou , along with data from EGNOS and WAAS satellite based augmentation systems (SBAS), QZSS , simultaneously. RINEX version 3.02 was submitted in April 2013 and contain new observation codes [ 3 ] from GPS or Galileo systems.
Although not part of the RINEX format, the Hatanaka compression scheme is commonly used to reduce the size of RINEX files, resulting in an ASCII-based CompactRINEX or CRINEX [ 4 ] format. [ 5 ] It uses higher-order time differences to reduce the number of characters needed to store time data. [ 6 ]
Ionospheric data in RINEX facilitates the exchange of information regarding the ionosphere , particularly through the IONosphere-map EXchange (IONEX) format. [ 7 ] Developed to standardize the sharing of Total Electron Content (TEC) maps derived from Global Navigation Satellite System (GNSS) signals, [ 7 ] IONEX files are essential for understanding the impact of ionospheric conditions on GNSS signal propagation . [ 8 ]
As GNSS signals traverse the ionosphere , they experience distortion due to the ionised plasma present in this region. [ 8 ] This distortion results in delays and changes in signal direction, influenced by factors such as satellite elevation and solar position. [ 8 ] Consequently, analysis of GNSS signals at ground stations yields critical insights into the ionosphere's state, particularly the density of free electrons , which is a key parameter affecting signal quality. [ 8 ]
IONEX files consist of an ASCII format that includes a comprehensive header with global information, followed by a data section detailing TEC maps. [ 7 ] TEC is measured in terms of the number of free electrons per square meter in a vertical column of the ionosphere , with a standard density of 10 16 electrons representing one unit of TEC. [ 8 ]
In addition to TEC maps, IONEX files also provide Root Mean Square (RMS) error maps and height maps, enhancing the understanding of ionospheric variations. [ 8 ] | https://en.wikipedia.org/wiki/RINEX |
The RISKS Digest or Forum On Risks to the Public in Computers and Related Systems is an online periodical published since 1985 by the Committee on Computers and Public Policy of the Association for Computing Machinery . The editor is Peter G. Neumann .
It is a moderated forum concerned with the security and safety of computers , software , and technological systems. Security, and risk, here are taken broadly; RISKS is concerned not merely with so-called security holes in software, but with unintended consequences and hazards stemming from the design (or lack thereof) of automated systems. Other recurring subjects include cryptography and the effects of technically ill-considered public policies. RISKS also publishes announcements and Calls for Papers from various technical conferences, and technical book reviews (usually by Rob Slade , though occasionally by others).
Although RISKS is a forum of a computer science association, most contributions are readable and informative to anyone with an interest in the subject. It is heavily read by system administrators , and computer security managers, as well as computer scientists and engineers .
The RISKS Digest is published on a frequent but irregular schedule through the moderated Usenet newsgroup comp.risks , which exists solely to carry the Digest.
Summaries of the forum appear as columns edited by Neumann in the ACM SIGSOFT Software Engineering Notes (SEN) and the Communications of the ACM (CACM). | https://en.wikipedia.org/wiki/RISKS_Digest |
RIVPACS (River Invertebrate Prediction and Classification System) is an aquatic biomonitoring system for assessing water quality in freshwater rivers in the United Kingdom . It is based on the macroinvertebrate species (such as freshwater shrimp , freshwater sponges , worms, crayfish , aquatic snails , freshwater mussels , insects , and many others) found at the study site during sampling. Some of these species are tolerant to pollution , low dissolved oxygen, and other stressors, but others are sensitive; organisms vary in their tolerances. Therefore, different species will usually be found, in different proportions, at different river sites of varying quality. Some organisms are especially good indicator species . The species found at the reference sites collectively make up the species assemblage for that site and are the basis for a statistical comparison between reference sites and non-reference sites. The comparison between the expected species and the observed species can then be used to estimate this aspect of the ecological health of a river.
The system is meant to be standardized, easy to use, and relatively low cost. It can complement other types of water quality monitoring such as chemical monitoring. RIVPACS supports the implementation of the Water Framework Directive as its official tool for macroinvertebrate classification [ 1 ]
Reference sites can be chosen and adjusted several ways. Usually they represent the best conditions within the region or area under study, and are a short stretch of river. Sometimes the reference site expectations are adjusted for degradation of the entire region by human impact. 'Pristine' freshwater sites are sampled to collect information on physical characteristics, chemistry, and macroinvertebrates , sometimes several times each year. [ 1 ] This information is then used to predict what invertebrates are present from samples of physiochemistry from other sites.
RIVPACS is used across the UK and supported by Centre for Ecology and Hydrology , Countryside Council for Wales , Department for Environment, Food and Rural Affairs , Natural England , Environment Agency , Northern Ireland Environment Agency , Freshwater Biological Association , Scotland and Northern Ireland Forum for Environmental Research, Scottish Environment Protection Agency , Scottish Government , Scottish Natural Heritage , South West Water , and Welsh Assembly Government . [ 1 ]
This classification of freshwater sites based on the macroinvertebrate fauna was first derived in 1977. Since then it has been developed and updated with addition of a wider range of freshwater sites. It has been adapted into various other versions around the world, [ 1 ] including a Canadian version known as CABIN, [ 2 ] AUSRIVAS in Australia, [ 3 ] MEDPACS in Spain , [ 4 ] and others. [ 1 ]
This ecology -related article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/RIVPACS |
The RK2 Plasmid is a broad-host-range plasmid belonging to the incP incompatibility group [ 1 ] It is notable for its ability to replicate in a wide variety of single-celled organisms , which makes it suitable as a genetic engineering tool. [ 2 ] It is capable of transfer, replication, and maintenance in most genera of Gram-negative bacteria. RK2 may sometimes be referred to as pRK2, which is also the name of another, unrelated plasmid. [ 3 ] [ 4 ] [ 5 ] Other names for RK2 include R18, R68, RP1, and RP4. These were all separate isolates, and later found to be identical plasmids. [ 6 ] The IncP-1 plasmid group (IncP plasmids in Escherichia coli ) of which RK2 is a part has been described as "highly potent, self-transmissible, selfish DNA molecules with a complicated regulatory circuit" [ 7 ]
RK2 was first isolated in connection with an outbreak of antibiotic-resistant Pseudomonas aeruginosa and Klebsiella aerogenes in Birmingham in 1969, as one of a family of plasmids implicated in transfer of Ampicillin resistance between bacterial strains. [ 8 ] Plasmids in the IncP-1 subgroup has been isolated from wastewater, agricultural soil, and hospitals. [ 9 ]
RK2 is approximately 60 kbp long and contains genes for replication , maintenance, conjugation and antibiotic resistance . The resistance genes confer resistance to the antibiotics kanamycin, ampicillin and tetracycline. [ 8 ] In addition, RK2 contains a set of potentially lethal (to the cell) genes, called kil genes, and a set of complementary transcriptional repressor genes, called kor (short for "kil-override") genes, which inactivate the kil genes. The kil and kor genes together are suspected to play a role in the broad host range of RK2. [ 10 ]
The essential replication system in RK2 consists of an origin of replication, oriV , and a gene, trfA , whose gene product, the TrfA protein, binds to and activates oriV . [ 11 ] [ 12 ] In Escherichia coli , replication proceeds unidirectionally from oriV after activation by TrfA. [ 13 ] In E. coli, multiple plasmid copies appear to cluster together, creating a few multiplasmid clusters in each cell. [ 14 ] [ 15 ] The copy number of RK2 is about 4-7 per cell in E. coli and 3 in P. aeruginosa . [ 16 ]
Several minimal derivatives of RK2 have been prepared. In these plasmids most of the genes have been removed, leaving only genes essential for replication and one or more selectable markers . One such "mini-replicon" is the plasmid PFF1, which is 5873 basepairs long.
PFF1 consists of an origin of replication , oriV, an origin of transfer , oriT, a gene coding for plasmid replication proteins, trfA, and two antibiotic resistance genes, bla and cat , which confer resistance to Ampicillin and Chloramphenicol , respectively. Minimal plasmids such as PFF1 are useful for studying the basic mechanisms of plasmid replication and copy number regulation, as there are less superfluous genetic elements which might affect the processes being studied. Several mutants of PFF1 which affect the copy number of the plasmid have been identified. Two such mutants, PFF1cop254D and PFF1cop271C, increase the copy number of PFF1 in E. coli from approximately 39-40 to about 501 and 113 plasmids per cell, respectively. [ 17 ] An increase in copy number is useful for genetic engineering applications to increase the production yield of recombinant protein . [ 18 ] | https://en.wikipedia.org/wiki/RK2_plasmid |
RMG ( Real Space MultiGrid ) is an open source density functional theory electronic structure code distributed under the GNU General Public License . [ 1 ] [ 2 ] It solves Kohn-Sham equations directly on a 3D real space grid without using basis set functions. [ 2 ] RMG is highly scalable; it has been run on supercomputers with thousands of CPU cores.
RMG's main feature is that it uses real-space mesh as a basis, rather plane waves or other types of basis set functions. [ 2 ] This formulation lends itself to a straightforward parallelization, because each processor can be assigned a region of space. This avoids the need for Fourier transforms , and makes RMG highly scalable. The multigrid method is used to solve Poisson equation and to accelerate convergence. Mehrstellen discretization, which is shorter ranged than the commonly used than central difference discretization, is used to represent the kinetic energy operator. [ 2 ] This decreases the cost of processor-to-processor communication, which is advantageous for the use on massively parallel supercomputers.
Domain decomposition is used to assign different regions of space to individual CPU cores or nodes. RMG scales nearly linearly up to 100k processor cores and 20k GPUs on Cray XK6. [ 3 ]
RMG was originally developed in 1993–1994 at North Carolina State University . [ 4 ] It was written in C with small parts being in FORTRAN . The current version uses a mixture of C and C++. MPI is used for inter-node communication and C++11 threads for intra-node parallelization. Other libraries used are Lapack , ScaLAPACK , FFTW , libxc and spglib. [ 3 ]
RMG runs on laptops, desktops, workstations, clusters or supercomputers. It can run on Linux , Unix , Windows and Mac OS X operating systems. [ 3 ]
This free and open-source software article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/RMG_(program) |
RNA-based evolution is a theory that posits that RNA is not merely an intermediate between Watson and Crick model of the DNA molecule and proteins , but rather a far more dynamic and independent role-player in determining phenotype . By regulating the transcription in DNA sequences, the stability of RNA, and the capability of messenger RNA to be translated , RNA processing events allow for a diverse array of proteins to be synthesized from a single gene . Since RNA processing is heritable, it is subject to natural selection suggested by Darwin and contributes to the evolution and diversity of most eukaryotic organisms.
In accordance with the central dogma of molecular biology, RNA passes information between the DNA of a genome and the proteins expressed within an organism. [ 1 ] Therefore, from an evolutionary standpoint, a mutation within the DNA bases results in an alteration of the RNA transcripts, which in turn leads to a direct difference in phenotype.
RNA is also believed to have been the genetic material of the first life on Earth. The role of RNA in the origin of life is best supported by the ease of forming RNA from basic chemical building blocks (such as amino acids , sugars , and hydroxyl acids ) that were likely present 4 billion years ago. [ 2 ] [ 3 ] Molecules of RNA have also been shown to effectively self-replicate, catalyze basic reactions, and store heritable information. [ 4 ] [ 5 ] As life progressed and evolved over time only DNA, which is much more chemically stable than RNA, could support large genomes and eventually took over the role as the major carrier of genetic information. [ 6 ]
Single-stranded RNA molecules can single handedly fold into complex structures. The molecules fold into secondary and tertiary structures by intramolecular base pairing. [ 7 ] There is a fine dynamic of disorder and order that facilitate an efficient structure formation. RNA strands form complementary base pairs. These complementary strands of RNA base pair with another strand, which results in a three-dimensional shape from the paired strands folding in on itself. The formation of the secondary structure results from base pairing by hydrogen bonds between the strands, while tertiary structure results from folding of the RNA. The three-dimensional structure consists of grooves and helices. [ 8 ] The formation of these complex structure gives reason to suspect that early life could have formed by RNA.
Research within the past decade has shown that strands of RNA are not merely transcribed from regions of DNA and translated into proteins. Rather RNA has retained some of its former independence from DNA and is subject to a network of processing events that alter the protein expression from that bounded by just the genomic DNA. [ 9 ] Processing of RNA influences protein expression by managing the transcription of DNA sequences, the stability of RNA, and the translation of messenger RNA.
Splicing is the process by which non-coding regions of RNA are removed. The number and combination of splicing events varies greatly based on differences in transcript sequence and environmental factors. Variation in phenotype caused by alternative splicing is best seen in the sex determination of D. melanogaster . The Tra gene, determinant of sex, in male flies becomes truncated as splicing events fail to remove a stop codon that controls the length of the RNA molecule. In others the stop signal is retained within the final RNA molecule and a functional Tra protein is produced resulting in the female phenotype. [ 10 ] Thus, alternative RNA splicing events allow differential phenotypes, regardless of the identity of the coding DNA sequence.
Phenotype may also be determined by the number of RNA molecules, as more RNA transcripts lead to a greater expression of protein. Short tails of repetitive nucleic acids are often added to the ends of RNA molecules in order to prevent degradation, effectively increasing the number of RNA strands able to be translated into protein. [ 11 ] During mammalian liver regeneration RNA molecules of growth factors increase in number due to the addition of signaling tails. [ 12 ] With more transcripts present the growth factors are produced at a higher rate, aiding the rebuilding process of the organ.
Silencing of RNA occurs when double stranded RNA molecules are processed by a series of enzymatic reactions, resulting in RNA fragments that degrade complementary RNA sequences. [ 13 ] [ 14 ] By degrading transcripts, a lower amount of protein products are translated and the phenotype is altered by yet another RNA processing event.
In Earth's early developmental history RNA was the primary substance of life. RNA served as a blueprint for genetic material and was the catalyst to multiply said blueprint. Currently RNA acts by forming proteins. protein enzymes carry out catalytic reactions. RNAs are critical in gene expression and that gene expression depends on mRNA , rRNA , and tRNA . [ 15 ] There is a relationship between protein and RNAs. This relationship could suggest that there is a mutual transfer of energy or information. [ 16 ] In vitro RNA selection experiments have produced RNA that bind tightly to amino acids. It has been shown that the amino acids recognized by the RNA nucleotide sequences had a disproportionately high frequency of codons for said amino acids. There is a possibility that the direct association of amino acids containing specific RNA sequences yielded a limited genetic code. [ 17 ]
Most RNA processing events work in concert with one another and produce networks of regulating processes that allow a greater variety of proteins to be expressed than those strictly directed by the genome. [ 9 ] These RNA processing events can also be passed on from generation to generation via reverse transcription into the genome. [ 9 ] [ 18 ] Over time, RNA networks that produce the fittest phenotypes will be more likely to be maintained in a population, contributing to evolution. Studies have shown that RNA processing events have especially been critical with the fast phenotypic evolution of vertebrates —large jumps in phenotype explained by changes in RNA processing events. [ 19 ] Human genome searches have also revealed RNA processing events that have provided significant “sequence space for more variability”. [ 20 ] On the whole, RNA processing expands the possible phenotypes of a given genotype and contributes to the evolution and diversity of life.
RNA virus evolution appears to be facilitated by a high mutation rate caused by the lack of a proofreading mechanism during viral genome replication. [ 21 ] In addition to mutation, RNA virus evolution is also facilitated by genetic recombination. [ 21 ] Genetic recombination can occur when at least two RNA viral genomes are present in the same host cell and has been studies in numerous RNA viruses. [ 22 ] RNA recombination appears to be a major driving force in viral evolution among Picornaviridae ( (+)ssRNA ) (e.g. poliovirus ). [ 23 ] In the Retroviridae ((+)ssRNA)(e.g. HIV ), damage in the RNA genome appears to be avoided during reverse transcription by strand switching, a form of genetic recombination. [ 24 ] [ 25 ] [ 26 ] Recombination also occurs in the Coronaviridae ((+)ssRNA) (e.g. SARS ). [ 27 ] Recombination in RNA viruses appears to be an adaptation for coping with genome damage. [ 22 ] Recombination can occur infrequently between animal viruses of the same species but of divergent lineages. The resulting recombinant viruses may sometimes cause an outbreak of infection in humans. [ 27 ] | https://en.wikipedia.org/wiki/RNA-based_evolution |
RNA-binding proteins (often abbreviated as RBPs ) are proteins that bind to the double or single stranded RNA [ 1 ] in cells and participate in forming ribonucleoprotein complexes.
RBPs contain various structural motifs , such as RNA recognition motif (RRM), dsRNA binding domain , zinc finger and others. [ 2 ] [ 3 ] They are cytoplasmic and nuclear proteins. However, since most mature RNA is exported from the nucleus relatively quickly, most RBPs in the nucleus exist as complexes of protein and pre-mRNA called heterogeneous ribonucleoprotein particles (hnRNPs).
RBPs have crucial roles in various cellular processes such as: cellular function, transport and localization. They especially play a major role in post-transcriptional control of RNAs, such as: splicing , polyadenylation , mRNA stabilization, mRNA localization and translation . Eukaryotic cells express diverse RBPs with unique RNA-binding activity and protein–protein interaction . According to the Eukaryotic RBP Database (EuRBPDB), there are 2961 genes encoding RBPs in humans . During evolution , the diversity of RBPs greatly increased with the increase in the number of introns . Diversity enabled eukaryotic cells to utilize RNA exons in various arrangements, giving rise to a unique RNP (ribonucleoprotein) for each RNA. Although RBPs have a crucial role in post-transcriptional regulation in gene expression, relatively few RBPs have been studied systematically. It has now become clear that RNA–RBP interactions play important roles in many biological processes among organisms. [ 4 ] [ 5 ] [ 6 ]
Many RBPs have modular structures and are composed of multiple repeats of just a few specific basic domains that often have limited sequences. Different RBPs contain these sequences arranged in varying combinations. A specific protein's recognition of a specific RNA has evolved through the rearrangement of these few basic domains. Each basic domain recognizes RNA, but many of these proteins require multiple copies of one of the many common domains to function. [ 2 ]
As nuclear RNA emerges from RNA polymerase , RNA transcripts are immediately covered with RNA-binding proteins that regulate every aspect of RNA metabolism and function including RNA biogenesis, maturation, transport, cellular localization and stability. All RBPs bind RNA, however they do so with different RNA-sequence specificities and affinities, which allows the RBPs to be as diverse as their targets and functions. [ 5 ] These targets include mRNA , which codes for proteins, as well as a number of functional non-coding RNAs . NcRNAs almost always function as ribonucleoprotein complexes and not as naked RNAs. These non-coding RNAs include microRNAs , small interfering RNAs (siRNA), as well as spliceosomal small nuclear RNAs (snRNA). [ 7 ]
Alternative splicing is a mechanism by which different forms of mature mRNAs (messengers RNAs) are generated from the same gene . It is a regulatory mechanism by which variations in the incorporation of the exons into mRNA leads to the production of more than one related protein, thus expanding possible genomic outputs. RBPs function extensively in the regulation of this process. Some binding proteins such as neuronal specific RNA-binding proteins, namely NOVA1 , control the alternative splicing of a subset of hnRNA by recognizing and binding to a specific sequence in the RNA (YCAY where Y indicates pyrimidine, U or C). [ 5 ] These proteins then recruit splicesomal proteins to this target site. SR proteins are also well known for their role in alternative splicing through the recruitment of snRNPs that form the splicesome , namely U1 snRNP and U2AF snRNP. However, RBPs are also part of the splicesome itself. The splicesome is a complex of snRNA and protein subunits and acts as the mechanical agent that removes introns and ligates the flanking exons. [ 7 ] Other than core splicesome complex, RBPs also bind to the sites of Cis -acting RNA elements that influence exons inclusion or exclusion during splicing. These sites are referred to as exonic splicing enhancers (ESEs), exonic splicing silencers (ESSs), intronic splicing enhancers (ISEs) and intronic splicing silencers (ISSs) and depending on their location of binding, RBPs work as splicing silencers or enhancers. [ 8 ]
The most extensively studied form of RNA editing involves the ADAR protein. This protein functions through post-transcriptional modification of mRNA transcripts by changing the nucleotide content of the RNA. This is done through the conversion of adenosine to inosine in an enzymatic reaction catalyzed by ADAR. This process effectively changes the RNA sequence from that encoded by the genome and extends the diversity of the gene products. The majority of RNA editing occurs on non-coding regions of RNA; however, some protein-encoding RNA transcripts have been shown to be subject to editing resulting in a difference in their protein's amino acid sequence. An example of this is the glutamate receptor mRNA where glutamine is converted to arginine leading to a change in the functionality of the protein. [ 5 ]
Polyadenylation is the addition of a "tail" of adenylate residues to an RNA transcript about 20 bases downstream of the AAUAAA sequence within the three prime untranslated region . Polyadenylation of mRNA has a strong effect on its nuclear transport , translation efficiency, and stability. All of these as well as the process of polyadenylation depend on binding of specific RBPs. All eukaryotic mRNAs with few exceptions are processed to receive 3' poly (A) tails of about 200 nucleotides. One of the necessary protein complexes in this process is CPSF . CPSF binds to the 3' tail (AAUAAA) sequence and together with another protein called poly(A)-binding protein , recruits and stimulates the activity of poly(A) polymerase . Poly(A) polymerase is inactive on its own and requires the binding of these other proteins to function properly. [ 5 ]
After processing is complete, mRNA needs to be transported from the cell nucleus to cytoplasm . This is a three-step process involving the generation of a cargo-carrier complex in the nucleus followed by translocation of the complex through the nuclear pore complex and finally release of the cargo into cytoplasm. The carrier is then subsequently recycled. TAP/NXF1:p15 heterodimer is thought to be the key player in mRNA export. Over-expression of TAP in Xenopus laevis frogs increases the export of transcripts that are otherwise inefficiently exported. However TAP needs adaptor proteins because it is unable interact directly with mRNA. Aly/REF protein interacts and binds to the mRNA recruiting TAP. [ 5 ]
mRNA localization is critical for regulation of gene expression by allowing spatially regulated protein production. Through mRNA localization proteins are translated in their intended target site of the cell. This is especially important during early development when rapid cell cleavages give different cells various combinations of mRNA which can then lead to drastically different cell fates. RBPs are critical in the localization of this mRNA that insures proteins are only translated in their intended regions. One of these proteins is ZBP1 . ZBP1 binds to beta-actin mRNA at the site of transcription and moves with mRNA into the cytoplasm. It then localizes this mRNA to the lamella region of several asymmetric cell types where it can then be translated. [ 5 ] In 2008 it was proposed that FMRP was involved in the stimulus-induced localization of several dendritic mRNAs in the neuronal dendrites of cultured hippocampal neurons. [ 9 ] More recent studies of FMRP-bound RNAs present in microdissected dendrites of CA1 hippocampal neurons revealed no changes in localization in wild type versus FMRP-null mouse brains. [ 10 ]
Translational regulation provides a rapid mechanism to control gene expression. Rather than controlling gene expression at the transcriptional level, mRNA is already transcribed but the recruitment of ribosomes is controlled. This allows rapid generation of proteins when a signal activates translation. ZBP1 in addition to its role in the localization of B-actin mRNA is also involved in the translational repression of beta-actin mRNA by blocking translation initiation. ZBP1 must be removed from the mRNA to allow the ribosome to properly bind and translation to begin. [ 5 ]
RNA-binding proteins exhibit highly specific recognition of their RNA targets by recognizing their sequences, structures, motifs and RNA modifications. [ 11 ] Specific binding of the RNA-binding proteins allow them to distinguish their targets and regulate a variety of cellular functions via control of the generation, maturation, and lifespan of the RNA transcript. This interaction begins during transcription as some RBPs remain bound to RNA until degradation whereas others only transiently bind to RNA to regulate RNA splicing , processing, transport, and localization. [ 12 ] Cross-linking immunoprecipitation (CLIP) methods are used to stringently identify direct RNA binding sites of RNA-binding proteins in a variety of tissues and organisms. In this section, three classes of the most widely studied RNA-binding domains (RNA-recognition motif, double-stranded RNA-binding motif, zinc-finger motif) will be discussed.
The RNA recognition motif , which is the most common RNA-binding motif, is a small protein domain of 75–85 amino acids that forms a four-stranded β-sheet against the two α-helices. This recognition motif exerts its role in numerous cellular functions, especially in mRNA/rRNA processing, splicing, translation regulation, RNA export, and RNA stability. Ten structures of an RRM have been identified through NMR spectroscopy and X-ray crystallography . These structures illustrate the intricacy of protein–RNA recognition of RRM as it entails RNA–RNA and protein–protein interactions in addition to protein–RNA interactions. Despite their complexity, all ten structures have some common features. All RRMs' main protein surfaces' four-stranded β-sheet was found to interact with the RNA, which usually contacts two or three nucleotides in a specific manner. In addition, strong RNA binding affinity and specificity towards variation are achieved through an interaction between the inter-domain linker and the RNA and between RRMs themselves. This plasticity of the RRM explains why RRM is the most abundant domain and why it plays an important role in various biological functions. [ 12 ]
The double-stranded RNA-binding motif (dsRM, dsRBD), a 70–75 amino-acid domain, plays a critical role in RNA processing , RNA localization , RNA interference , RNA editing , and translational repression. All three structures of the domain solved as of 2005 possess uniting features that explain how dsRMs only bind to dsRNA instead of dsDNA. The dsRMs were found to interact along the RNA duplex via both α-helices and β1-β2 loop. Moreover, all three dsRBM structures make contact with the sugar-phosphate backbone of the major groove and of one minor groove, which is mediated by the β1-β2 loop along with the N-terminus region of the alpha helix 2. This interaction is a unique adaptation for the shape of an RNA double helix as it involves 2'-hydroxyls and phosphate oxygen. Despite the common structural features among dsRBMs, they exhibit distinct chemical frameworks, which permits specificity for a variety for RNA structures including stem-loops, internal loops, bulges or helices containing mismatches. [ 12 ]
CCHH-type zinc-finger domains are the most common DNA-binding domain within the eukaryotic genome . In order to attain high sequence-specific recognition of DNA, several zinc fingers are utilized in a modular fashion. Zinc fingers exhibit ββα protein fold in which a β-hairpin and a α-helix are joined via a Zn 2+ ion. Furthermore, the interaction between protein side-chains of the α-helix with the DNA bases in the major groove allows for the DNA-sequence-specific recognition. Despite its wide recognition of DNA, there has been recent discoveries that zinc fingers also have the ability to recognize RNA. In addition to CCHH zinc fingers, CCCH zinc fingers were recently discovered to employ sequence-specific recognition of single-stranded RNA through an interaction between intermolecular hydrogen bonds and Watson-Crick edges of the RNA bases. CCHH-type zinc fingers employ two methods of RNA binding. First, the zinc fingers exert non-specific interaction with the backbone of a double helix whereas the second mode allows zinc fingers to specifically recognize the individual bases that bulge out. Differing from the CCHH-type, the CCCH-type zinc finger displays another mode of RNA binding, in which single-stranded RNA is identified in a sequence-specific manner. Overall, zinc fingers can directly recognize DNA via binding to dsDNA sequence and RNA via binding to ssRNA sequence. [ 12 ]
RNA-binding proteins' transcriptional and post-transcriptional regulation of RNA has a role in regulating the patterns of gene expression during development. [ 13 ] Extensive research on the nematode C. elegans has identified RNA-binding proteins as essential factors during germline and early embryonic development. Their specific function involves the development of somatic tissues ( neurons , hypodermis , muscles and excretory cells) as well as providing timing cues for the developmental events. Nevertheless, it is exceptionally challenging to discover the mechanism behind RBPs' function in development due to the difficulty in identifying their RNA targets. This is because most RBPs usually have multiple RNA targets. [ 14 ] However, it is indisputable that RBPs exert a critical control in regulating developmental pathways in a concerted manner.
In Drosophila melanogaster , Elav, Sxl and tra-2 are RNA-binding protein encoding genes that are critical in the early sex determination and the maintenance of the somatic sexual state. [ 15 ] These genes impose effects on the post-transcriptional level by regulating sex-specific splicing in Drosophila . Sxl exerts positive regulation of the feminizing gene tra to produce a functional tra mRNA in females. In C. elegans , RNA-binding proteins including FOG-1, MOG-1/-4/-5 and RNP-4 regulate germline and somatic sex determination. Furthermore, several RBPs such as GLD-1, GLD-3, DAZ-1, PGL-1 and OMA-1/-2 exert their regulatory functions during meiotic prophase progression, gametogenesis , and oocyte maturation . [ 14 ]
In addition to RBPs' functions in germline development, post-transcriptional control also plays a significant role in somatic development. Differing from RBPs that are involved in germline and early embryo development, RBPs functioning in somatic development regulate tissue-specific alternative splicing of the mRNA targets. For instance, MEC-8 and UNC-75 containing RRM domains localize to regions of hypodermis and nervous system, respectively. [ 14 ] Furthermore, another RRM-containing RBP, EXC-7, is revealed to localize in embryonic excretory canal cells and throughout the nervous system during somatic development.
ZBP1 was shown to regulate dendritogenesis ( dendrite formation) in hippocampal neurons. [ 16 ] Other RNA-binding proteins involved in dendrite formation are Pumilio and Nanos, [ 17 ] FMRP , CPEB and Staufen 1 [ 18 ]
RBPs are emerging to play a crucial role in tumor development. [ 19 ] Hundreds of RBPs are markedly dysregulated across human cancers and showed predominant downregulation in tumors related to normal tissues. [ 19 ] Many RBPs are differentially expressed in different cancer types for example KHDRBS1(Sam68), [ 20 ] [ 21 ] ELAVL1(HuR), [ 22 ] [ 23 ] FXR1 [ 24 ] and UHMK1 . [ 25 ] For some RBPs, the change in expression are related with Copy Number Variations (CNV), for example CNV gains of BYSL in colorectal cancer cells [ 19 ] and ESRP1, CELF3 in breast cancer, RBM24 in liver cancer, IGF2BP2, IGF2BP3 in lung cancer or CNV losses of KHDRBS2 in lung cancer. [ 26 ] Some expression changes are cause due to protein affecting mutations on these RBPs for example NSUN6, ZC3H13, ELAC1, RBMS3 , and ZGPAT, SF3B1, SRSF2, RBM10, U2AF1, SF3B1, PPRC1, RBMXL1, HNRNPCL1 etc. [ 19 ] [ 26 ] [ 27 ] [ 28 ] [ 29 ] Several studies have related this change in expression of RBPs to aberrant alternative splicing in cancer. [ 26 ] [ 30 ] [ 31 ]
As RNA-binding proteins exert significant control over numerous cellular functions, they have been a popular area of investigation for many researchers. Due to its importance in the biological field, numerous discoveries regarding RNA-binding proteins' potentials have been recently unveiled. [ 12 ] Recent development in experimental identification of RNA-binding proteins has extended the number of RNA-binding proteins significantly [ 32 ] [ 33 ] [ 34 ]
RNA-binding protein Sam68 controls the spatial and temporal compartmentalization of RNA metabolism to attain proper synaptic function in dendrites . Loss of Sam68 results in abnormal posttranscriptional regulation and ultimately leads to neurological disorders such as fragile X-associated tremor/ataxia syndrome . Sam68 was found to interact with the mRNA encoding β-actin , which regulates the synaptic formation of the dendritic spines with its cytoskeletal components. Therefore, Sam68 plays a critical role in regulating synapse number via control of postsynaptic β-actin mRNA metabolism. [ 35 ]
Neuron-specific CELF family RNA-binding protein UNC-75 specifically binds to the UUGUUGUGUUGU mRNA stretch via its three RNA recognition motifs for the exon 7a selection in C. elegans' neuronal cells. As exon 7a is skipped due to its weak splice sites in non-neuronal cells, UNC-75 was found to specifically activate splicing between exon 7a and exon 8 only in the neuronal cells. [ 36 ]
The cold inducible RNA binding protein CIRBP plays a role in controlling the cellular response upon confronting a variety of cellular stresses, including short wavelength ultraviolet light , hypoxia , and hypothermia . This research yielded potential implications for the association of disease states with inflammation. [ 37 ]
Serine-arginine family of RNA-binding protein Slr1 was found exert control on the polarized growth in Candida albicans . Slr1 mutations in mice results in decreased filamentation and reduces damage to epithelial and endothelial cells that leads to extended survival rate compared to the Slr1 wild-type strains. Therefore, this research reveals that SR-like protein Slr1 plays a role in instigating the hyphal formation and virulence in C. albicans . [ 38 ] | https://en.wikipedia.org/wiki/RNA-binding_protein |
RNA-dependent RNA polymerase ( RdRp ) or RNA replicase is an enzyme that catalyzes the replication of RNA from an RNA template. Specifically, it catalyzes synthesis of the RNA strand complementary to a given RNA template. This is in contrast to typical DNA-dependent RNA polymerases , which all organisms use to catalyze the transcription of RNA from a DNA template.
RdRp is an essential protein encoded in the genomes of most RNA-containing viruses that lack a DNA stage, [ 1 ] [ 2 ] including SARS-CoV-2 . Some eukaryotes also contain RdRps, which are involved in RNA interference and differ structurally from viral RdRps.
Viral RdRps were discovered in the early 1960s from studies on mengovirus and polio virus when it was observed that these viruses were not sensitive to actinomycin D , a drug that inhibits cellular DNA-directed RNA synthesis. This lack of sensitivity suggested the action of a virus-specific enzyme that could copy RNA from an RNA template. [ 3 ]
RdRps are highly conserved in viruses and are related to telomerase , though the reason for this was an ongoing question as of 2009. [ 4 ] The similarity led to speculation that viral RdRps are ancestral to human telomerase. [ 5 ]
The most famous example of RdRp is in the polio virus . The viral genome is composed of RNA, which enters the cell through receptor-mediated endocytosis . From there, the RNA acts as a template for complementary RNA synthesis. The complementary strand acts as a template for the production of new viral genomes that are packaged and released from the cell ready to infect more host cells. The advantage of this method of replication is that no DNA stage complicates replication. The disadvantage is that no 'back-up' DNA copy is available. [ 6 ]
Many RdRps associate tightly with membranes making them difficult to study. The best-known RdRps are polioviral 3Dpol, vesicular stomatitis virus L, [ 7 ] and hepatitis C virus NS5B protein.
Many eukaryotes have RdRps that are involved in RNA interference : these amplify microRNAs and small temporal RNAs and produce double-stranded RNA using small interfering RNAs as primers. [ 8 ] These RdRps are used in the defense mechanisms and can be appropriated by RNA viruses. [ 9 ] Their evolutionary history predates the divergence of major eukaryotic groups. [ 10 ]
RdRp differs from DNA dependent RNA polymerase as it catalyzes RNA synthesis of strands complementary to a given RNA template. The RNA replication process is a four-step mechanism:
RNA synthesis can be performed by a primer -independent ( de novo ) or a primer-dependent mechanism that utilizes a viral protein genome-linked (VPg) primer. [ 13 ] The de novo initiation consists in the addition of a NTP to the 3'-OH of the first initiating NTP. [ 13 ] During the following elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product. Termination of the nascent RNA chain produced by RdRp is not completely known, however, RdRp termination is sequence-independent. [ 14 ]
One major drawback of RNA-dependent RNA polymerase replication is the transcription error rate. [ 13 ] RdRps lack fidelity on the order of 10 4 nucleotides, which is thought to be a direct result of inadequate proofreading. [ 13 ] This variation rate is favored in viral genomes as it allows for the pathogen to overcome host defenses trying to avoid infection, allowing for evolutionary growth. [ 15 ]
Viral/prokaryotic RdRp, along with many single-subunit DdRp, employ a fold whose organization has been linked to the shape of a right hand with three subdomains termed fingers, palm, and thumb. [ 16 ] Only the palm subdomain, composed of a four-stranded antiparallel beta sheet with two alpha helices , is well conserved. In RdRp, the palm subdomain comprises three well-conserved motifs (A, B, and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the aspartic acid residues of these motifs are implied in the binding of Mg 2+ and/or Mn 2+ . The asparagine residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and, thus, determines whether RNA rather than DNA is synthesized. [ 17 ] The domain organization [ 18 ] and the 3D structure of the catalytic centre of a wide range of RdRps, even those with a low overall sequence homology, are conserved. The catalytic center is formed by several motifs containing conserved amino acid residues. [ citation needed ]
Eukaryotic RNA interference requires a cellular RdRp (c RdRp). Unlike the "hand" polymerases, they resemble simplified multi-subunit DdRPs, specifically in the catalytic β/β' subunits, in that they use two sets of double-psi β-barrels in the active site. QDE1 ( Q9Y7G6 ) in Neurospora crassa , which has both barrels in the same chain, [ 19 ] is an example of such a c RdRp enzyme. [ 20 ] Bacteriophage homologs of c RdRp, including the similarly single-chain DdRp yonO ( O31945 ), appear to be closer to c RdRps than DdRPs are. [ 8 ] [ 21 ]
Four superfamilies of viruses cover all RNA-containing viruses with no DNA stage:
Flaviviruses produce a polyprotein from the ssRNA genome. The polyprotein is cleaved to a number of products, one of which is NS5, an RdRp. It possesses short regions and motifs homologous to other RdRps. [ 22 ]
RNA replicase found in positive-strand ssRNA viruses are related to each other, forming three large superfamilies. [ 23 ] Birnaviral RNA replicase is unique in that it lacks motif C (GDD) in the palm. [ 24 ] Mononegaviral RdRp (PDB 5A22) has been automatically classified as similar to (+)−ssRNA RdRps, specifically one from Pestivirus and one from Leviviridae . [ 25 ] Bunyaviral RdRp monomer (PDB 5AMQ) resembles the heterotrimeric complex of Orthomyxoviral (Influenza; PDB 4WSB) RdRp. [ 26 ]
Since it is a protein universal to RNA-containing viruses, RdRp is a useful marker for understanding their evolution. [ 27 ] [ 28 ]
When replicating its (+)ssRNA genome , the poliovirus RdRp is able to carry out recombination . Recombination appears to occur by a copy choice mechanism in which the RdRp switches (+)ssRNA templates during negative strand synthesis. [ 29 ] Recombination frequency is determined in part by the fidelity of RdRp replication. [ 30 ] RdRp variants with high replication fidelity show reduced recombination, and low fidelity RdRps exhibit increased recombination. [ 30 ] Recombination by RdRp strand switching occurs frequently during replication in the (+)ssRNA plant carmoviruses and tombusviruses . [ 31 ]
Sendai virus (family Paramyxoviridae ) has a linear, single-stranded, negative-sense, nonsegmented RNA genome. The viral RdRp consists of two virus-encoded subunits, a smaller one P and a larger one L. Testing different inactive RdRp mutants with defects throughout the length of the L subunit in pairwise combinations, restoration of viral RNA synthesis was observed in some combinations. [ 32 ] This positive L–L interaction is referred to as intragenic complementation and indicates that the L protein is an oligomer in the viral RNA polymerase complex. [ citation needed ]
The use of RdRp plays a major role in RNA interference in eukaryotes, a process used to silence gene expression via small interfering RNAs ( siRNAs ) binding to mRNA rendering them inactive. [ 36 ] Eukaryotic RdRp becomes active in the presence of dsRNA, and is less widely distributed than other RNAi components as it lost in some animals, though still found in C. elegans , P. tetraurelia , [ 37 ] and plants . [ 38 ] This presence of dsRNA triggers the activation of RdRp and RNAi processes by priming the initiation of RNA transcription through the introduction of siRNAs. [ 37 ] In C. elegans , siRNAs are integrated into the RNA-induced silencing complex, RISC , which works alongside mRNAs targeted for interference to recruit more RdRps to synthesize more secondary siRNAs and repress gene expression. [ 39 ] | https://en.wikipedia.org/wiki/RNA-dependent_RNA_polymerase |
RNA-induced transcriptional silencing ( RITS ) is a form of RNA interference by which short RNA molecules – such as small interfering RNA (siRNA) – trigger the downregulation of transcription of a particular gene or genomic region. This is usually accomplished by posttranslational modification of histone tails (e.g. methylation of lysine 9 of histone H3) which target the genomic region for heterochromatin formation. The protein complex that binds to siRNAs and interacts with the methylated lysine 9 residue of histones H3 ( H3K9me2 ) is the RITS complex.
RITS was discovered in the fission yeast Schizosaccharomyces pombe , and has been shown to be involved in the initiation and spreading of heterochromatin in the mating-type region and in centromere formation. The RITS complex in S. pombe contains at least a piwi domain -containing RNase H -like argonaute , a chromodomain protein Chp1, and an argonaute interacting protein Tas3 which can also bind to Chp1, [ 1 ] while heterochromatin formation has been shown to require at least argonaute and an RNA-dependent RNA polymerase . [ 2 ] Loss of these genes in S. pombe results in abnormal heterochromatin organization and impairment of centromere function, [ 3 ] resulting in lagging chromosomes on anaphase during cell division . [ 4 ]
The maintenance of heterochromatin regions by RITS complexes has been described as a self-reinforcing feedback loop , in which RITS complexes stably bind the methylated histones of a heterochromatin region using the Chp1 protein and induce co-transcriptional degradation of any nascent messenger RNA (mRNA) transcripts, which are then used as RNA-dependent RNA polymerase substrates to replenish the complement of siRNA molecules to form more RITS complexes. [ 5 ] The RITS complex localizes to heterochromatic regions through the base pairing of the nascent heterochromatic transcripts as well as through the Chp chromodomain which recognizes methylated histones found in heterochromatin. [ 6 ] Once incorporated into the heterochromatin, the RITS complex is also known to play a role in the recruitment of other RNAi complexes as well as other chromatin modifying enzymes to specific genomic regions. [ 7 ] Heterochromatin formation, but possibly not maintenance, is dependent on the ribonuclease protein dicer , which is used to generate the initial complement of siRNAs. [ 8 ]
The relevance of observations from fission yeast mating-type regions and centromeres to mammals is not clear, as some evidence suggests that heterochromatin maintenance in mammalian cells is independent of the components of the RNAi pathway. [ 9 ] It is known, however, that plants and animals have analogous mechanism for small RNA-guided heterochromatin formation, and it is believed that the mechanisms described above for S. pombe are highly conserved and play some role in heterochromatin formation in mammals as well. In higher eukaryotes, RNAi-dependent heterochromatic silencing appears to play a larger role in germline cells than in primary cells or cell lines, and is only one of the many different forms of gene silencing used throughout the genome, making it more difficult to study. [ 10 ]
The role of RNAi in transcriptional gene silencing in plants has been characterized fairly well, and functions primarily through DNA methylation via the RdDM pathway. In this process, which is distinct from the process described above, argonaut-bound siRNA recognizes nascent RNA transcripts or the target DNA to guide the methylation and silencing of the target genomic region. [ 11 ] | https://en.wikipedia.org/wiki/RNA-induced_transcriptional_silencing |
RNA-targeting small molecules represent a class of small molecules , organic compounds with traditional drug properties (e.g., Lipinski's rule of five ) that can bind to RNA secondary or tertiary structures and alter translation patterns, localization, and degradation.
Recent discoveries implicating RNA in the pathogenesis of several forms of cancer and neuromuscular diseases have created a paradigm shift in drug discovery . This work combined with advances in structural characterization techniques such as NMR spectroscopy , X-ray crystallography , Cryogenic electron microscopy [ 1 ] together with computational modeling , [ 2 ] has pushed forward the realization that RNA is a dynamic yet viable drug target . Traditionally, RNA was thought to be a mediator between DNA sequence-encoded instructions and functional protein . However, recent reports have shown that there are a large number of non-coding RNAs (ncRNAs) that are not translated into protein. Whereas 85% of the human genome is transcribed into RNA only 3% of the transcripts code for functional protein. [ 3 ] Although, ncRNAs do affect gene expression [ 4 ] levels by a variety of mechanisms. [ 5 ] Further, RNA can adopt discrete secondary or tertiary structures which play a pivotal role in many biological processes and disease pathology. For these reasons, RNA is being recognized as an attractive drug target for small molecules . [ citation needed ]
The earliest attempts to target RNA led to the discovery that aminoglycosides could bind to human RNA. In an early report, Noller discovered that several classes of antibiotics ( streptomycin , tetracycline , spectinomycin , edeine, hygromycin, and the neomycins ) could "protect" nucleotides in 16S ribosomal RNA by binding to this RNA. [ 6 ] [ 7 ] Subsequent studies by Schroeder and Green began to plant the seed that RNA could be targeted. Schroeder uncovered that aminoglycosides could inhibit protein synthesis by interacting with the ribosome through interactions with the 3’ end of the 16S RNA of E. coli taking advantage of RNA conformational changes. [ 8 ] Green and coworkers further confirmed this idea, discovering that aminoglycosides blocked the interaction of HIV-1 Rev protein and its viral RNA-binding site. [ 9 ]
David Wilson and David Draper were the first to suggest that RNA structures could be targeted by small molecules. They hypothesized that RNA could be "druggable" by targeting the 3D structure in the same way as protein 3D structures are used as drug targets and furthered the idea that targeting RNA could be used to treat diseases. [ 10 ] Czarnik and co-workers at Parke-Davis completed a screen on HIV Tat. [ 11 ] They found multiple small molecule inhibitors of the HIV-1 Tat—TAR system that recognized the bulge, lower stem, or loop region of the TAR RNA. One of the compounds discovered, 2,4,5,6-tetraaminoquinozaline, binds to the loop region of TAR, downregulates cellular Tat transactivation, and ultimately inhibits HIV-1 replication. [ 12 ]
The use of aminoglycosides, while an early start to RNA-targeting, came with some challenges. These molecules were only modestly selective and showed unfavorable toxicity levels at relevant therapeutic concentrations. [ 3 ] As another strategy for targeting RNA, antisense oligonucleotides were developed which have been pushed forward through the clinic for several diseases. By this principle, if one can identify an RNA involved in disease then the sequence can be used to design a complementary antisense oligonucleotide , and that agent can be introduced into cells to treat the disease. [ 5 ] But, this approach in its basic form has been met with several challenges. The most obvious are their large size and propensity to degradation by nucleases. In order for cellular RNA to be effective it must enter the cells intact. While backbone modifications to antisense oligonucleotides in order to prevent nuclease degradation have been shown to work, this approach is still somewhat limited. Small molecules may present a better way to target RNA and subsequently DNA because they can be designed to be more "drug-like" and have a better chance of reaching their target, most by oral administration. For this reason, there is an emerging interest in designing and discovering small molecules to target RNA secondary and tertiary structures to ultimately treat new diseases. [ citation needed ]
There are limited examples of small molecules that target RNA and are approved drugs for the treatment of human disease. Ribavirin was approved in 2002 to treat Hepatitis C and viral hemorrhagic fever . As a nucleoside inhibitor, the guanosine analog prodrug is used to stop viral RNA synthesis and viral mRNA capping by incorporating into RNA and pairing to uracil or cytosine. Branaplam is currently in phase I/II clinical trial for the treatment of Spinal Muscular Atrophy (SMA). This molecule is from a class of pyridazine small molecules and enhances the inclusion of exon 7, resulting in a full-length and functional protein product. [ citation needed ]
Branaplam represents the first mechanistic study of splicing modulation using a sequence-selective small molecule. The drug stabilizes the transient double-stranded RNA (dsRNA) structure formed between the SMN2 pre-mRNA and U1 snRNP complex, a key component of the splicesome . Further, this compound acts by increasing the binding affinity of U1 snRNP to the 5’ splice site (5’ss) in a sequence-selective manner that is discrete from constitutive recognition. [ 13 ] Ataluren is in clinical trials for the treatment of Duchenne Muscular Dystrophy (DMD). It is believed that Ataluren acts by promoting insertion of near-cognate tRNAs at the site of the nonsense codon without affecting transcription , mRNA processing, mRNA stability, or protein stability to give nonsense suppression. This drug would be effective for ~10% of patients with DMD who have a single mutation in the DMD gene causing a stop codon to appear prematurely ( nonsense mutation ). [ 14 ]
Compared to the number of drug candidates that have successfully made it to the clinical trial phase, there are many more lead compounds which have been tested in vivo using various animal models. Much of the current work that has progressed to in vivo testing has been directed to the RNA repeat expansions implicated in genetic neuromuscular diseases. In myotonic dystrophy type 1 (DM1), r(CUG)exp mRNAs sequester proteins including the alternative splicing regulator MBNL1 into the nucleus causing missplicing. Several groups have developed compounds which bind the toxic RNA and dissolve nuclear foci. In 2011, Artero and coworkers discovered that a peptide could reduce the toxicity associated with r(CUG) repeats in Drosophila and mouse models. [ 15 ] Disney and colleagues provided the first small molecules that targeted r(CUG) repeats in animals models by using rational designing to identify many small molecules directly targeting this toxic RNA and the compounds improved disease defects in a DM1 mouse model. [ 16 ]
Other works by the Disney group has shown that in cellular models of various RNA-mediated diseases that are causes by RNA repeats such as r(CAG) in Huntington's disease [ 17 ] and r(CCUG) repeats in Myotonic Dystrophy Types 2 [ 18 ] [ 19 ] could also be targeted with small molecules. Nakamori and colleagues also reported in 2012 that erythromycin could be orally dosed in DM1 mouse models to restore missplicing defects and inhibit the complex formed between r(CUG) and MBNL1 . [ 20 ] In that same year, Miller and coworkers screened a library of compounds to find a small molecule drug that could improve splicing defects in a mouse model. [ 21 ] The Zimmerman group has taken a rational design approach to discovering small molecule drugs that target r(CUG). One such compound contains a selective triaminotriazine recognition motif which binds to the UU mismatches in r(CUG) selectively most likely in a base triplet combined with an amidinium RNA groove binding unit. Studies using a Drosophila model for DM1 showed an influence on related phenotypic outcomes such as eye morphology and climbing distance. [ 22 ]
Aside from studies involved r(CUG) repeats, other complex RNA structures have also been targeted. Pearson and coworkers discovered that a cationic porphyrin (TMPyP4) bound a G-quadruplex r(G 4 C 2 ) and inhibited the binding of proteins to r(G 4 C 2 ). [ 23 ] Work by Disney and Petrucelli rationally identified small molecules that can target this repeat and affect disease biology in model cellular systems and also in patient-derive iNeurons. [ 24 ] Further studies by Rothstein and colleagues determined that TMPyP4 could suppress r(G 4 C 2 )-mediated neurodegeneration in a Drosophila model. [ 25 ] Additionally targets have been rationally identified by using a powerful seqecune-based design approach termed informal to identify dozens of bioactive small molecules that target disease causing non-coding RNA termed INFORNA. [ 26 ] This study important showed for the first time that small molecules appear to have selectivities that are competitive with oligonucleotides with cell-permeable and medicinally optimizable small molecules. Additionally, compounds have been shown to be bioactive in diverse disease settings that ranged from breast cancer. [ 26 ] [ 27 ] and hepatocellular carcinoma. [ 28 ] More recently, the Disney group further used their prediction database INFORNA to design Targaprimir-96 to target miRNA precursors in animal models of cancer, the first small molecules to do so. This compound has a nanomolar affinity for the miRNA hairpin precursor selectively over other sequences. Targaprimir-96 was further tested in cells and in mice, inhibiting tumor growth in a xenograft mouse model of triple negative breast cancer upon i.p. injection. [ 29 ]
RNA-targeting small molecule drug discovery has greatly benefitted from the available cellular models for disease. The use of cell culture in early development has become a requirement for assessing the basic efficacy of a drug candidate. Thus, more research groups have implemented these techniques in their programs. In a leading example, Al-Hashimi and coworkers identified six small molecules with high affinity for TAR of HIV-1 through a computational approach. They docked a library of small molecules onto RNA dynamic structures generated by NMR and Molecular Dynamics (MD) simulations. The hit molecules inhibited the Tat—TAR interaction in vitro . They arrived at lead molecule, netilmicin , that had the best selectivity for HIV-1 TAR and inhibited HIV-1 replication in cells with a low IC50. [ 30 ] The Disney group has studied aminoglycoside derivatives in 2009 for their ability to inhibit interactions between repeat RNA and proteins. Using their prediction database INFORNA, they discovered that a compound could bind to 1 x 1 UU internal loops on an N-methyl peptide backbone. They confirmed that like other compounds that target DM1 r(CUG), they could inhibit the complex between r(CUG)-MBNL1, disrupt nuclear foci, and increase nucleocytoplasmic transport of the gene in patient-derived DM1 fibroblasts . [ 31 ] In that study the Disney group also described several approaches to validate the RNA targets of small molecules. In the first approach termed chemical cross-linking and isolation by pull down (Chem-CLIP) and chemical cross-linking and isolation by pull down to map binding sites (Chem-CLIP-Map). [ 32 ] [ 33 ] [ 31 ]
These studies showed in cells that small molecules can direct target disease-causing r(CUG) repeats in DM1 and that impressively the compound can discriminate against other RNAs with shorter repeats and also between the mutant and wild type allele of the DMPK mRNA that contains r(CUG) disease-causing repeats. In an additional approach, dubbed small–molecule nucleic acid profiling by cleavage applied to RNA (Ribo-SNAP) [ 31 ] [ 34 ] showed that small molecules can be used to cleave RNA targets in cells and also importantly demonstrated that designer small molecules target precisely disease causing RNA repeats and discriminate against RNAs that are not disease causing but have short repeats of r(CUG). Thus, targeting RNA structure with small molecules can have important selectively discrimination implications in cells. [ citation needed ]
In 2014, Chenowith and colleagues reported a cationic triptycene scaffold that targets RNA and DNA three-way junctions. Subsequent studies showed that these molecules exhibited favorable cellular uptake and cytotoxicity in human ovarian cancer cell lines. [ 35 ] In 2017, the Xodo group reported anthrafurandione and anthrathiophenedione small molecules with aminoethyl side chains could bind to RNA G-quadraplexes at the 5’-UTR of certain mRNAs. Further, these compounds were shown to suppress the KRAS oncogene in pancreatic cancer cells and induce apoptosis by reducing the metabolic activity of the cells. [ 36 ]
In 2009, the Zimmerman group discovered a compound to target the trinucleotide repeat expanded RNA and DNA that cause DM1. Through rational design, they utilized a triaminotriazine recognition unit to target TT or UU mismatches through a Janus Wedge type binding mode, creating a base triplet with the mismatch. The combined use of an acridine intercalator to pi-pi stack on the target gave a nanomolar binding affinity for TT or UU mismatches over others. Along with high binding affinity, this molecule was shown to displace MBNL from the complex with r(CUG) with a micromolar K i. [ 37 ] Additionally, HIV-1 RNA has been targeted extensively in vitro by RNA-binding small molecules. In 2007, Miller and coworkers used dynamic combinatorial chemistry to screen a compound library against HIV-1 frameshift regulatory stem-loop RNA. They identified a hit compound that was selective for the regulatory sequence with micromolar binding affinity. [ 38 ]
In 2011, Butcher and colleagues discovered a frameshifting stimulator (DB213) which bound to HIV-1 FS RNA with moderate binding affinity. An NMR structure of the RNA in complex with DB213, showed that the small molecule bound to the major groove of the RNA duplex. [ 39 ] Schneekloth and Hargrove have taken a different approach by targeting the HIV-1 TAR RNA hairpin. In a small molecule microarray screening, the Schneekloth group identified a thienopyridine derivative that interacts with HIV-1 TAR RNA hairpin. Further SAR studies provided more information on the structure and binding mode. The lead analogue was found to bind to the 5’-UTR of HIV with an IC 50 of 40 μM for displacing a Tat-derived peptide. [ 40 ] The Hargrove group developed a small library of amiloride derivatives with changes at the C(5) and C(6) positions to improve the binding affinity of amiloride to the loop and bulge of the HIV-1 TAR RNA. Using in vitro studies and modeling, they found a hit compound whose inhibition activity was increased by more than 100x compared to the parent amiloride. This compound is reported to be one of the tightest non- aminoglycoside TAR ligands reported to date. [ 41 ] | https://en.wikipedia.org/wiki/RNA-targeting_small_molecule_drugs |
RNA Automation , a member of Rhein-Nadel Automation, was established in Birmingham UK, in 1986, and has progressed into becoming the major supplier of parts handling equipment in the UK . [ citation needed ] The company operates in the area of specialized Automation Engineering , providing automatic parts handling equipment for high volume production in the cosmetics , pharmaceutical , electronics , food and metal working industries, with seven manufacturing facilities across Europe and North America and a network of sales and service outlets across the globe.
Founded in 1972, Rhein-Nadel Automation or RNA operates worldwide in parts handling technology. Rhein-Nadel Automation is a member of the Rheinnadel Group, which has been based since 1898 in the city of Aachen , Germany. Rhein-Nadel Automation have four manufacturing sites in Germany and individual manufacturing plants in the UK, Spain and Switzerland, together with a world-wide, decentralized distribution and service network with 28 subsidiaries. [ citation needed ]
1968 — The department of the needle factory, so far only responsible for the internal construction of operating materials and machines, trades under the name Rheinnadel Maschinenbau and begins working for external customers.
1972 — Rheinnadel Maschinenbau now also uses the firm name Rhein-Nadel Automation GmbH and concentrates exclusively on the area of Feeding Technology.
1980–1989 — Rhein-Nadel Automation expands. The permanent establishment in Ergolding and the subsidiaries in Switzerland and Great Britain are found.
1990–1999 — Rhein-Nadel Automation continues to grow. The Spanish company Vibrant S.A. is purchased.
2000 — With RNA Automated Systems Inc., the first subsidiary outside of Europe to take up its commercial activities in Canada.
2004 — The Rheinnadel Group concentrates its activities on the area of Automation. RNA broadens its range with the components and continues to extend its development capacities.
RNA Automation specializes in automated feeder and specialist handling systems, offering vibratory bowl feeders, Linear Feeders, Centrifugal Feeders and Step Feeder systems. RNA also supplies a range of specialist handling equipment, including Vision Guided Robots, Tablet Inspection, Vision Inspection, Tray Loading, and Bottle Handling.
RNA supplies a range of vibratory, centrifugal feeders, linear and conveyor feed systems, and hopper elevator systems in different formats.
In association with Hoppmann Corporation, RNA offers a full range of tooled centrifugal feeders. The centrifugal feeder systems can be interfaced and supplied as a complete packaging line with further production transportation via downstream conveyor systems to subsequent packaging operations such as capping, labelling, flow wrapping, and cartoning machines .
RNA are the sole agents in the UK and Ireland for the SVIA range of Vision Guided Robotic Systems . All systems have a Robotic arm for handling and manipulating the product, a camera system, and share the same PC-based control system and are, in most cases, integrated with a standard ABB robot controller.
RNA, alongside camera specialists Machine Vision Technology, has developed a tablet inspection system to inspect and sort tablets up to and over 1000 parts per minute. The specification of a tablet inspection system is as follows:
A 600mm diameter vibratory bowl feeder in stainless steel and a variable speed controller. A speed of 800–1000 tablets per minute Outputs onto a conveyor with a reject sort facility. With up to four double-speed progressive scan cameras and lighting mounted along the conveyor, A high-speed PC with a 17-inch LCD display mounted in a SS enclosure. The system is designed to meet pharmaceutical standards The software complies with FDA requirements. All documentation is to CFR 21 pt. 11, with the fully validated version option. [ citation needed ] | https://en.wikipedia.org/wiki/RNA_Automation |
Graham A. Hudson
The RNA Characterization of Secondary Structure Motifs database ( RNA CoSSMos ) is a repository of three-dimensional nucleic acid PDB structures containing secondary structure motifs ( loops, hairpin loops ...). [ 1 ]
This Biological database -related article is a stub . You can help Wikipedia by expanding it .
This biophysics -related article is a stub . You can help Wikipedia by expanding it .
This stereochemistry article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/RNA_CoSSMos |
The RNA Tie Club was an informal scientific club, meant partly to be humorous, [ 1 ] of select scientists who were interested in how proteins were synthesised from genes, specifically the genetic code . [ 2 ] It was created by George Gamow upon a suggestion by James Watson in 1954 [ 2 ] when the relationship between nucleic acids and amino acids in genetic information was unknown. The club consisted of 20 full members, each representing an amino acid, and four honorary members, representing the four nucleotides . The function of the club members was to think up possible solutions and share with the other members.
The first important document of the RNA Tie Club was Francis Crick 's adaptor hypothesis in 1955. Experimental work on the hypothesis led to the discovery of transfer RNA , a molecule that carries the key to genetic code. Most of the theoretical groundwork and preliminary experiments on the genetic code were done by the club members within a decade. However, the specific code was discovered by Marshall Nirenberg , a non-member, who received Nobel Prize in Physiology or Medicine in 1968 for the discovery.
In 1953, English biophysicist Francis Crick and American biologist James Watson , working together at the Cavendish Laboratory of the University of Cambridge, deduced the structure of DNA , the principal genetic material of organisms, [ 3 ] thought to link genetic information in DNA to proteins. [ 4 ] By 1954, it was becoming understood that the genetic information pathway involved DNA , RNA and proteins. However, the structure and nature of RNA were still a mystery (specific RNA molecules were not known until 1960 [ 5 ] ), especially how RNA is involved in protein synthesis. [ 6 ] Watson called this problem "the mystery of life" in his letter to Crick. [ 5 ]
Soviet-American physicist George Gamow at George Washington University suggested the first scheme for protein synthesis from DNA. [ 7 ] [ 8 ] In early 1954, he spent several days at Woods Hole on Cape Cod with Crick, Watson and Sydney Brenner , discussing genetics. [ 2 ] Based on the Watson-Crick model , he proposed a "direct DNA template hypothesis" stating that proteins are synthesised directly from the double-stranded grooves of DNA. [ 9 ] The four bases of DNA were assumed to synthesise 20 different amino acids as triplets with overlapping nucleotide sequences. [ 10 ] He published the hypothesis in the 13 February 1954 issue of Nature , explaining:
It seems to me that such translation procedure can be easily established by considering the ' key-and-lock ' relation between various amino-acids, and the rhomb-shaped 'holes' formed by various nucleotides in the deoxyribonucleic acid chain... One can speculate that free amino-acids from the surrounding medium get caught into the 'holes' of deoxyribonucleic acid molecules, and thus unite into the corresponding peptide chains. [ 11 ]
In May 1954, Watson visited Gamow, who was on sabbatical at the University of California, Berkeley . While discussing Gamow's hypothesis, he suggested that they form a 20-member club to work out the genetic code. [ 2 ] Gamow instantly came up with the RNA Tie Club to "solve the riddle of the RNA structure and to understand how it built proteins", adding the motto "do or die; or don't try." [ 12 ]
The club thus consisted of 20 eminent scientists, each of whom corresponded to an amino acid, plus four honorary members (S. Brenner, VAL. F. Lipmann, A. Szent-Gyorgyi , and another individual), one for each nucleotide . [ 12 ]
Each member received a woolen necktie having an embroidered helix, hence the name "RNA Tie Club". [ 12 ]
Members of the RNA Tie Club received a black wool-knit tie with a green and yellow RNA helix emblazoned on it. The original design of the tie came from Orgel, with the final pattern re-imagined by Gamow. [ 12 ] Gamow's tie pattern was delivered to a Los Angeles haberdasher on Colorado Avenue by Watson, with the shop tailor promising to make the ties for $4 each. [ 13 ] Along with each tie, members of the club were to receive a golden tiepin with the three letter abbreviation of their club amino acid designation. Not all members may have received their pin. Gamow, however, wore his pin on several occasions, often causing confusion and questioning of why he was wearing the "wrong initials". [ 13 ]
The RNA Tie Club never had a formal meeting of all its members. [ 2 ] Members visited each other to discuss the scientific developments, usually involving cigars and alcohol. This allowed bonding and close friendships to develop among this scientific elite, and it turned out to be a breeding ground for creative ideas. The members mailed letters and preprints of articles to each other suggesting new concepts and ideas. [ 14 ]
Using mathematics, Gamow postulated that a nucleotide code consisting of three letters (triplets) would be enough to define all 20 amino acids. [ 11 ] This concept is the basis of " codons ", and set an upper and lower limit on their size. Gamow had simply estimated that the number of bases and their complementary pairs in a DNA strand could create 20 cavities for amino acids, meaning that 20 different amino acids could be involved in protein synthesis. [ 15 ] He named this DNA–protein interaction the "diamond code." [ 16 ] Although Gamow's premise that DNA directly synthesized proteins was proven wrong, [ 10 ] the triplet code became the foundation of genetic code. [ 16 ]
Sydney Brenner proposed the concept of the codon, the idea that three non-overlapping nucleotides could code for one amino acid. [ 17 ] His proof involved statistics and experimental evidence from amino acid protein sequences.
Francis Crick proposed the " adaptor hypothesis " (a name given by Brenner [ 18 ] ) suggesting that some molecule ferried the amino acids around, and put them in the correct order corresponding to the nucleic acid sequence. [ 19 ] The hypothesis contradicted Gamow's direct DNA template hypothesis, positing that DNA could not synthesise proteins directly, but instead requires other molecules, adaptors to convert the DNA sequences to amino acid sequences. He also suggested that there were such 20 separate adaptor molecules. [ 20 ] [ 21 ] This was later confirmed by Robert Holley and the adaptor molecules were named transfer RNAs (tRNAs). [ 22 ]
The typed paper distributed to the members of the RNA Tie Club in January 1955 as "On Degenerate Templates and the Adaptor Hypothesis: A Note for the RNA Tie Club" is described as "one of the most important unpublished articles in the history of science", [ 23 ] [ 24 ] and "the most famous unpublished paper in the annals of molecular biology." [ 24 ] Watson recalled, "The most famous of these [unpublished] notes, by Francis, in time would totally change the way we thought about protein synthesis. [ 2 ]
Six members of the RNA Tie Club became Nobel laureates: Richard Feynman, Melvin Calvin, James Watson, Max Delbruck, Francis Crick and Sydney Brenner. However, the ultimate goal of understanding and deciphering the code linking nucleic acids and amino acids was achieved by Marshall Nirenberg , who was not a member of the RNA Tie Club, [ 25 ] and received the Nobel Prize in Physiology or Medicine in 1968 with Holley and Har Gobind Khorana . [ 26 ] | https://en.wikipedia.org/wiki/RNA_Tie_Club |
RNA activation (RNAa) is a small RNA-guided and Argonaute (Ago)-dependent gene regulation phenomenon in which promoter-targeted short double-stranded RNAs (dsRNAs) induce target gene expression at the transcriptional/epigenetic level. RNAa was first reported in a 2006 PNAS paper by Li et al . [ 1 ] who also coined the term "RNAa" [ 1 ] as a contrast to RNA interference ( RNAi ) to describe such gene activation phenomenon. dsRNAs that trigger RNAa have been termed small activating RNA (saRNA) . [ 2 ] Unlike RNAi, where small RNAs typically lead to gene silencing, RNAa demonstrates that small RNAs can also act as activators of gene expression.
The phenomenon of RNAa was first reported in 2006 by Long-Cheng Li and colleagues at University of California, San Francisco (UCSF). [ 1 ] They demonstrated that synthetic dsRNAs, termed saRNAs, could target gene promoters and induce potent and sustained upregulation of gene expression in human cells. This discovery challenged the prevailing view of small RNAs as solely negative regulators of gene expression. The Li group coined the term " small activating RNA " (saRNA) to distinguish these RNAs from those that mediate gene silencing. [ 1 ]
Shortly after, in 2007, Janowski et al . independently confirmed RNAa, showing that dsRNAs could activate the expression of the progesterone receptor gene. [ 3 ] Subsequent research revealed that endogenous miRNAs, traditionally known for gene silencing, could also activate gene expression through a process termed miRNA-mediated RNAa (mi-RNAa). [ 4 ] [ 5 ] Since the initial discovery of RNAa in human cells, many other groups have made similar observations in different mammalian species including human, non-human primates, rat and mice, [ 6 ] [ 7 ] [ 8 ] plant [ 9 ] and C. elegans. [ 10 ] [ 11 ]
The molecular mechanism of RNAa is not fully understood. Similar to RNAi, it has been shown that
mammalian RNAa requires members of the Ago clade of Argonaute proteins, particularly Ago2, [ 1 ] [ 12 ] [ 13 ] but possesses kinetics distinct from RNAi, characterized by a delayed
onset and sustained activity over multiple cell divisions. [ 14 ] [ 15 ] [ 16 ] In contrast to RNAi, promoter-targeted saRNAs induce prolonged activation of gene expression associated with epigenetic
changes. [ 1 ] [ 3 ] [ 16 ]
The mechanism of saRNA-mediated RNAa centers around the RNA-induced transcriptional activation (RITA) complex. [ 17 ] This complex includes:
The RITA complex assembly at the target gene promoter leads to a shift in the transcriptional machinery, promoting the transition from paused to elongating RNAP II. This is evidenced by changes in phosphorylation patterns at the transcriptional start site (TSS): a decrease in Ser5-phosphorylated RNAP II (pausing) and an increase in Ser2-phosphorylated RNAP II (elongating). [ 17 ] Histone H2B monoubiquitination is also an early epigenetic event associated with RNAa, promoting further histone modifications that enhance active transcription. [ 17 ]
Endogenous miRNAs, typically known for their role in post-transcriptional gene silencing, can also activate gene expression. The mechanisms of mi-RNAa are diverse. Several models have been proposed:
A critical aspect of RNAa is the nuclear import of saRNAs and miRNAs. While the exact mechanisms are still under investigation, several pathways have been implicated:
RNAa has been observed in a wide range of organisms, suggesting its evolutionary conservation and fundamental biological importance. It has been documented in:
RNAa has been used as a convenient tool by many scientists to study gene function in lieu of vector-based gene overexpression. [ 34 ] [ 35 ] [ 36 ]
RNAa offers promising therapeutic potential because of its ability to increase gene expression. This provides a different approach for treating diseases caused by gene underexpression or loss-of-function mutations. saRNAs for a number of genes have been tested in various cell and animal disease models for therapeutic efficacy. [ 37 ]
Several saRNA therapeutics have entered clinical trials: | https://en.wikipedia.org/wiki/RNA_activation |
RNA editing (also RNA modification ) is a molecular process through which some cells can make discrete changes to specific nucleotide sequences within an RNA molecule after it has been generated by RNA polymerase . It occurs in all living organisms and is one of the most evolutionarily conserved properties of RNAs . [ 1 ] [ 2 ] [ 3 ] RNA editing may include the insertion, deletion, and base substitution of nucleotides within the RNA molecule. RNA editing is relatively rare, with common forms of RNA processing (e.g. splicing , 5'- capping , and 3'- polyadenylation ) not usually considered as editing. It can affect the activity, localization as well as stability of RNAs, and has been linked with human diseases. [ 1 ] [ 2 ] [ 3 ] [ 4 ]
RNA editing has been observed in some tRNA , rRNA , mRNA , or miRNA molecules of eukaryotes and their viruses , archaea , and prokaryotes . [ 5 ] RNA editing occurs in the cell nucleus, as well as within mitochondria and plastids . In vertebrates, editing is rare and usually consists of a small number of changes to the sequence of the affected molecules. In other organisms, such as squids , [ 6 ] extensive editing ( pan-editing ) can occur; in some cases the majority of nucleotides in an mRNA sequence may result from editing. More than 160 types of RNA modifications have been described so far. [ 7 ]
RNA-editing processes show great molecular diversity, and some appear to be evolutionarily recent acquisitions that arose independently. The diversity of RNA editing phenomena includes nucleobase modifications such as cytidine (C) to uridine (U) and adenosine (A) to inosine (I) deaminations , as well as non-template nucleotide additions and insertions. RNA editing in mRNAs effectively alters the amino acid sequence of the encoded protein so that it differs from that predicted by the genomic DNA sequence. [ 8 ]
To identify diverse post-transcriptional modifications of RNA molecules and determine the transcriptome-wide landscape of RNA modifications by means of next generation RNA sequencing, recently many studies have developed conventional [ 9 ] or specialised sequencing methods. [ 1 ] [ 2 ] [ 3 ] Examples of specialised methods are MeRIP-seq , [ 10 ] m6A-seq, [ 11 ] PA-m 5 C-seq [ 12 ] , methylation-iCLIP, [ 13 ] m6A-CLIP, [ 14 ] Pseudo-seq, [ 15 ] Ψ-seq, [ 16 ] CeU-seq, [ 17 ] Aza-IP [ 18 ] and RiboMeth-seq [ 19 ] ). Many of these methods are based on specific capture of the RNA species containing the specific modification, for example through antibody binding coupled with sequencing of the captured reads. After the sequencing these reads are mapped against the whole transcriptome to see where they originate from. [ 20 ] Generally with this kind of approach it is possible to see the location of the modifications together with possible identification of some consensus sequences that might help identification and mapping further on. One example of the specialize methods is PA-m 5 C-seq. This method was further developed from PA-m 6 A-seq method to identify m 5 C modifications on mRNA instead of the original target N6-methyladenosine. The easy switch between different modifications as target is made possible with a simple change of the capturing antibody form m6A specific to m 5 C specific. [ 12 ] Application of these methods have identified various modifications (e.g. pseudouridine, m 6 A , m5C, 2′-O-Me) within coding genes and non-coding genes (e.g. tRNA, lncRNAs, microRNAs) at single nucleotide or very high resolution. [ 4 ]
Mass spectrometry is a way to quantify RNA modifications. [ 21 ] More often than not, modifications cause an increase in mass for a given nucleoside. This gives a characteristic readout for the nucleoside and the modified counterpart. [ 21 ] Moreover, mass spectrometry allows the investigation of modification dynamics by labelling RNA molecules with stable (non-radioactive) heavy isotopes in vivo . Due to the defined mass increase of heavy isotope labeled nucleosides they can be distinguished from their respective unlabelled isotopomeres by mass spectrometry. This method, called NAIL-MS (nucleic acid isotope labelling coupled mass spectrometry), enables a variety of approaches to investigate RNA modification dynamics. [ 22 ] [ 23 ] [ 24 ]
Recently, functional experiments have revealed many novel functional roles of RNA modifications. Most of the RNA modifications are found on transfer-RNA and ribosomal-RNA, but also eukaryotic mRNA has been shown to be modified with multiple different modifications. 17 naturally occurring modifications on mRNA have been identified, from which the N6-methyladenosine is the most abundant and studied. [ 25 ] mRNA modifications are linked to many functions in the cell. They ensure the correct maturation and function of the mRNA, but also at the same time act as part of cell's immune system. [ 26 ] Certain modifications like 2’O-methylated nucleotides has been associated with cells ability to distinguish own mRNA from foreign RNA. [ 27 ] For example, m 6 A has been predicted to affect protein translation and localization, [ 1 ] [ 2 ] [ 3 ] mRNA stability, [ 28 ] alternative polyA choice [ 14 ] and stem cell pluripotency. [ 29 ] Pseudouridylation of nonsense codons suppresses translation termination both in vitro and in vivo , suggesting that RNA modification may provide a new way to expand the genetic code. [ 30 ] 5-methylcytosine on the other hand has been associated with mRNA transport from the nucleus to the cytoplasm and enhancement of translation. These functions of m 5 C are not fully known and proven but one strong argument towards these functions in the cell is the observed localization of m 5 C to translation initiation site. [ 31 ] Importantly, many modification enzymes are dysregulated and genetically mutated in many disease types. [ 1 ] For example, genetic mutations in pseudouridine synthases cause mitochondrial myopathy, sideroblastic anemia (MLASA) [ 32 ] and dyskeratosis congenital. [ 33 ]
Compared to the modifications identified from other RNA species like tRNA and rRNA, the amount of identified modifications on mRNA is very small. One of the biggest reasons why mRNA modifications are not so well known is missing research techniques. In addition to the lack of identified modifications, the knowledge of associated proteins is also behind other RNA species. Modifications are results of specific enzyme interactions with the RNA molecule. [ 25 ] Considering mRNA modifications most of the known related enzymes are the writer enzymes that add the modification on the mRNA. The additional groups of enzymes readers and erasers are for most of the modifications either poorly known of not known at all. [ 34 ] For these reasons there has been during the past decade huge interest in studying these modifications and their function. [ 20 ]
Transfer RNA or tRNA is the most abundantly modified type of RNA. [ 35 ] Modifications in tRNA play crucial roles in maintaining translation efficiency through supporting structure, anticodon-codon interactions, and interactions with enzymes. [ 36 ]
Anticodon modifications are important for proper decoding of mRNA. Since the genetic code is degenerate, anticodon modifications are necessary to properly decode mRNA. Particularly, the wobble position of the anticodon determines how the codons are read. For example, in eukaryotes an adenosine at position 34 of the anticodon can be converted to inosine. Inosine is a modification that is able to base-pair with cytosine, adenine, and uridine. [ 37 ]
Another commonly modified base in tRNA is the position adjacent to the anticodon. Position 37 is often hypermodified with bulky chemical modifications. These modifications prevent frameshifting and increase anticodon-codon binding stability through stacking interactions. [ 37 ]
Ribosomal RNA (rRNA) is essential to the makeup of ribosomes and peptide transfer during translation processes. [ 38 ] Ribosomal RNA modifications are made throughout ribosome synthesis, and often occur during and/or after translation. Modifications primarily play a role in the structure of the rRNA in order to protect translational efficiency. [ 38 ] Chemical modification in rRNA consists of methylation of ribose sugars , isomerization of uridines, and methylation and acetylation of individual bases. [ 39 ]
Methylation of rRNA upholds structural rigidity by blocking base pair stacking and surrounds the 2’-OH group to block hydrolysis. It occurs at specific parts of eukaryotic rRNA. The template for methylation consists of 10-21 nucleotides. [ 38 ] 2'-O-methylation of the ribose sugar is one of the most common rRNA modifications. [ 40 ] Methylation is primarily introduced by small nucleolar RNA's, referred to as snoRNPs. There are two classes of snoRNPs that target methylation sites, and they are referred to box C/D and box H/ACA. [ 39 ] [ 40 ] One type of methylation, 2′-O-methylation, contributes to helical stabilization. [ 38 ]
The isomerization of uridine to pseudouridine is the second most common rRNA modification. These pseudouridines are also introduced by the same classes of snoRNPs that participate in methylation. Pseudouridine synthases are the major participating enzymes in the reaction. [ 41 ] The H/ACA box snoRNPs introduce guide sequences that are about 14-15 nucleotides long. [ 39 ] Pseudouridylation is triggered in numerous places of rRNAs at once to preserve the thermal stability of RNA. [ 39 ] Pseudouridine allows for increased hydrogen bonding and alters translation in rRNA and tRNA. [ 40 ] [ 41 ] It alters translation by increasing the affinity of the ribosome subunit to specific mRNAs. [ 38 ]
Base Editing:
Base editing is the third major class of rRNA modification, specifically in eukaryotes. There are 8 categories of base edits that can occur at the gap between the small and large ribosomal subunits. [ 38 ] RNA methyltransferases are the enzymes that introduce base methylation. [ 38 ] Acetyltransferases are the enzymes responsible for acetylation of cytosine in rRNA. Base methylation plays a role in translation. These base modifications all work in conjunction with the two other main classes of modification to contribute to RNA structural stability. An example of this occurs in N7-methylation, which increases the nucleotide's charge to increase ionic interactions of proteins attaching to the RNA before translation.
RNA editing through the addition and deletion of uracil has been found in kinetoplasts from the mitochondria of Trypanosoma brucei . [ 42 ] Because this may involve a large fraction of the sites in a gene, it is sometimes called "pan-editing" to distinguish it from topical editing of one or a few sites.
Pan-editing starts with the base-pairing of the unedited primary transcript with a guide RNA (gRNA), which contains complementary sequences to the regions around the insertion/deletion points. The newly formed double-stranded region is then enveloped by an editosome, a large multi-protein complex that catalyzes the editing. [ 43 ] [ 44 ] The editosome opens the transcript at the first mismatched nucleotide and starts inserting uridines. The inserted uridines will base-pair with the guide RNA, and insertion will continue as long as A or G is present in the guide RNA and will stop when a C or U is encountered. [ 45 ] [ 46 ] The inserted nucleotides cause a frameshift , and result in a translated protein that differs from its gene.
The mechanism of the editosome involves an endonucleolytic cut at the mismatch point between the guide RNA and the unedited transcript. The next step is catalyzed by one of the enzymes in the complex, a terminal U-transferase, which adds Us from UTP at the 3' end of the mRNA. [ 47 ] The opened ends are held in place by other proteins in the complex. Another enzyme, a U-specific exoribonuclease, removes the unpaired Us. After editing has made mRNA complementary to gRNA, an RNA ligase rejoins the ends of the edited mRNA transcript. [ 48 ] [ 49 ] As a consequence, the editosome can edit only in a 3' to 5' direction along the primary RNA transcript. The complex can act on only a single guide RNA at a time. Therefore, a RNA transcript requiring extensive editing will need more than one guide RNA and editosome complex.
The editing involves cytidine deaminase that deaminates a cytidine base into a uridine base. An example of C-to-U editing is with the apolipoprotein B gene in humans. Apo B100 is expressed in the liver and apo B48 is expressed in the intestines. In the intestines, the mRNA has a CAA sequence edited to be UAA, a stop codon, thus producing the shorter B48 form.
C-to-U editing often occurs in the mitochondrial RNA of flowering plants. Different plants have different degrees of C-to-U editing; for example, eight editing events occur in mitochondria of the moss Funaria hygrometrica , whereas over 1,700 editing events occur in the lycophytes Isoetes engelmanii . [ 50 ] C-to-U editing is performed by members of the pentatricopeptide repeat (PPR) protein family. Angiosperms have large PPR families, acting as trans -factors for cis -elements lacking a consensus sequence; Arabidopsis has around 450 members in its PPR family. There have been a number of discoveries of PPR proteins in both plastids and mitochondria. [ 51 ]
Adenosine-to-inosine (A-to-I) modifications contribute to nearly 90% of all editing events in RNA. The deamination of adenosine is catalyzed by the double-stranded RNA-specific adenosine deaminase ( ADAR ), which typically acts on pre-mRNAs. The deamination of adenosine to inosine disrupts and destabilizes the dsRNA base pairing, therefore rendering that particular dsRNA less able to produce siRNA , which interferes with the RNAi pathway.
The wobble base pairing causes deaminated RNA to have a unique but different structure, which may be related to the inhibition of the initiation step of RNA translation. Studies have shown that I-RNA (RNA with many repeats of the I-U base pair) recruits methylases that are involved in the formation of heterochromatin and that this chemical modification heavily interferes with miRNA target sites. [ 52 ] There is active research into the importance of A-to-I modifications and their purpose in the novel concept of epitranscriptomics , in which modifications are made to RNA that alter their function. [ 53 ] [ 54 ] A long established consequence of A-to-I in mRNA is the interpretation of I as a G, therefore leading to functional A-to-G substitution, e.g. in the interpretation of the genetic code by ribosomes. Newer studies, however, have weakened this correlation by showing that inosines can also be decoded by the ribosome (although in a lesser extent) as adenosines or uracils. Furthermore, it was shown that I's lead to the stalling of ribosomes on the I-rich mRNA. [ 55 ]
The development of high-throughput sequencing in recent years has allowed for the development of extensive databases for different modifications and edits of RNA. RADAR (Rigorously Annotated Database of A-to-I RNA editing) was developed in 2013 to catalog the vast variety of A-to-I sites and tissue-specific levels present in humans, mice , and flies . The addition of novel sites and overall edits to the database are ongoing. [ 56 ] The level of editing for specific editing sites, e.g. in the filamin A transcript, is tissue-specific. [ 57 ] The efficiency of mRNA-splicing is a major factor controlling the level of A-to-I RNA editing. [ 58 ] [ 59 ] Interestingly, ADAR1 and ADAR2 also affect alternative splicing via both A-to-I editing ability and dsRNA binding ability. [ 60 ] [ 61 ]
Alternative U-to-C mRNA editing was first reported in WT1 (Wilms Tumor-1) transcripts, [ 62 ] and non-classic G-A mRNA changes were first observed in HNRNPK (heterogeneous nuclear ribonucleoprotein K) transcripts in both malignant and normal colorectal samples. [ 63 ] The latter changes were also later seen alongside non-classic U-to-C alterations in brain cell TPH2 (tryptophan hydroxylase 2) transcripts. [ 64 ] Although the reverse amination might be the simplest explanation for U-to-C changes, transamination and transglycosylation mechanisms have been proposed for plant U-to-C editing events in mitochondrial transcripts. [ 65 ] A recent study reported novel G-to-A mRNA changes in WT1 transcripts at two hotspots, proposing the APOBEC3A (apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3A) as the enzyme implicated in this class of alternative mRNA editing. [ 66 ] It was also shown that alternative mRNA changes were associated with canonical WT1 splicing variants, indicating their functional significance.
It has been shown in previous studies that the only types of RNA editing seen in the plants' mitochondria and plastids are conversion of C-to-U and U-to-C (very rare). [ 67 ] [ 68 ] [ 69 ] [ 70 ] [ 71 ] [ 72 ] [ 73 ] [ 74 ] [ 75 ] [ 76 ] [ 77 ] [ 78 ] [ 79 ] RNA-editing sites are found mainly in the coding regions of mRNA, introns , and other non-translated regions. [ 69 ] In fact, RNA editing can restore the functionality of tRNA molecules. [ 71 ] [ 72 ] The editing sites are found primarily upstream of mitochondrial or plastid RNAs. While the specific positions for C to U RNA editing events have been fairly well studied in both the mitochondrion and plastid, [ 80 ] the identity and organization of all proteins comprising the editosome have yet to be established. Members of the expansive PPR protein family have been shown to function as trans -acting factors for RNA sequence recognition. [ 81 ] Specific members of the MORF (Multiple Organellar RNA editing Factor) family are also required for proper editing at several sites. As some of these MORF proteins have been shown to interact with members of the PPR family, it is possible MORF proteins are components of the editosome complex. [ 82 ] An enzyme responsible for the trans- or deamination of the RNA transcript remains elusive, though it has been proposed that the PPR proteins may serve this function as well.
RNA editing is essential for the normal functioning of the plant's translation and respiration activity. Editing can restore the essential base-pairing sequences of tRNAs, restoring functionality. [ 83 ] It has also been linked to the production of RNA-edited proteins that are incorporated into the polypeptide complexes of the respiration pathway. Therefore, it is highly probable that polypeptides synthesized from unedited RNAs would not function properly and hinder the activity of both mitochondria and plastids.
C-to-U RNA editing can create start and stop codons , but it cannot destroy existing start and stop codons. A cryptic start codon is created when the codon ACG is edited to be AUG.
Viruses (i.e., measles , mumps , or parainfluenza ), especially viruses that have an RNA genome, have been shown to have evolved to utilize RNA modifications in many ways when taking over the host cell. Viruses are known to utilize the RNA modifications in different parts of their infection cycle from immune evasion to protein translation enhancement. [ 27 ] RNA editing is used for stability and generation of protein variants. [ 84 ] [ 85 ] Viral RNAs are transcribed by a virus-encoded RNA-dependent RNA polymerase , which is prone to pausing and "stuttering" at certain nucleotide combinations. In addition, up to several hundred non-templated A's are added by the polymerase at the 3' end of nascent mRNA. [ 86 ] These As help stabilize the mRNA. Furthermore, the pausing and stuttering of the RNA polymerase allows the incorporation of one or two Gs or As upstream of the translational codon. [ 86 ] The addition of the non-templated nucleotides shifts the reading frame, which generates a different protein.
Additionally, the RNA modifications are shown to have both positive and negative effects on the replication and translation efficiency depending on the virus. For example, Courtney et al. [ 12 ] showed that an RNA modification called 5-methylcytosine is added to the viral mRNA in infected host cells in order to enhance the protein translation of HIV-1 virus. The inhibition of the m 5 C modification on viral mRNA results in significant reduction in viral protein translation, but interestingly it has no effect on the expression of viral mRNAs in the cell. On the other hand, Lichinchi et al. [ 87 ] showed that the N6-methyladenosine modification on ZIKV mRNA inhibits the viral replication.
The RNA-editing system seen in the animal may have evolved from mononucleotide deaminases, which have led to larger gene families that include the apobec-1 and adar genes. These genes share close identity with the bacterial deaminases involved in nucleotide metabolism. The adenosine deaminase of E. coli cannot deaminate a nucleoside in the RNA; the enzyme's reaction pocket is too small for the RNA strand to bind to. However, this active site is widened by amino acid changes in the corresponding human analog genes, APOBEC1 and ADAR , allowing deamination. [ 88 ] [ 89 ] The gRNA-mediated pan-editing in trypanosome mitochondria, involving templated insertion of U residues, is an entirely different biochemical reaction. The enzymes involved have been shown in other studies to be recruited and adapted from different sources. [ 43 ] [ 90 ] But the specificity of nucleotide insertion via the interaction between the gRNA and mRNA is similar to the tRNA editing processes in the animal and Acanthamoeba mitochondria. [ 91 ] Eukaryotic ribose methylation of rRNAs by guide RNA molecules is a similar form of modification. [ 92 ]
Thus, RNA editing evolved more than once. Several adaptive rationales for editing have been suggested. [ 93 ] Editing is often described as a mechanism of correction or repair to compensate for defects in gene sequences. However, in the case of gRNA-mediated editing, this explanation does not seem possible because if a defect happens first, there is no way to generate an error-free gRNA-encoding region, which presumably arises by duplication of the original gene region. A more plausible alternative for the evolutionary origins of this system is through constructive neutral evolution , where the order of steps is reversed, with the gratuitous capacity for editing preceding the "defect". [ 94 ]
Directing edits to correct mutated sequences was first proposed and demonstrated in 1995. [ 95 ] This initial work used synthetic RNA antisense oligonucleotides complementary to a pre-mature stop codon mutation in a dystrophin sequence to activate A-to-I editing of the stop codon to a read through codon in a model xenopus cell system. [ 95 ] While this also led to nearby inadvertent A-to-I transitions, A to I (read as G) transitions can correct all three stop codons, but cannot create a stop codon. Therefore, the changes led >25% correction of the targeted stop codon with read through to a downstream luciferase reporter sequence. Follow on work by Rosenthal achieved editing of mutated mRNA sequence in mammalian cell culture by directing an oligonucleotide linked to a cytidine deaminase to correct a mutated cystic fibrosis sequence. [ 96 ] More recently, CRISPR-Cas13 fused to deaminases has been employed to direct mRNA editing. [ 97 ]
In 2022, therapeutic RNA editing for Cas7-11 was reported. [ 98 ] [ 99 ] It enables sufficiently targeted cuts and an early version of it was used for in vitro editing in 2021. [ 100 ]
Unlike DNA editing, which is permanent, the effects of RNA editing − including potential off-target mutations in RNA − are transient and are not inherited. RNA editing is therefore considered to be less risky. Furthermore, it may only require a guide RNA by using the ADAR protein already found in humans and many other eukaryotes' cells instead of needing to introduce a foreign protein into the body. [ 101 ] | https://en.wikipedia.org/wiki/RNA_editing |
RNA extraction is the purification of RNA from biological samples. This procedure is complicated by the ubiquitous presence of ribonuclease enzymes in cells and tissues, which can rapidly degrade RNA. [ 1 ] Several methods are used in molecular biology to isolate RNA from samples, the most common of these is guanidinium thiocyanate-phenol-chloroform extraction . [ 2 ] [ 3 ] Usually, the phenol-chloroform solution used for RNA extraction has lower pH, this aids in separating DNA from RNA and leads to a more pure RNA preparation. The filter paper based lysis and elution method features high throughput capacity. [ 4 ]
RNA extraction in liquid nitrogen, commonly using a mortar and pestle (or specialized steel devices known as tissue pulverizers) is also useful in preventing ribonuclease activity.
The extraction of RNA in molecular biology experiments is greatly complicated by the presence of ubiquitous and hardy RNases that degrade RNA samples. Certain RNases can be extremely hardy and inactivating them is difficult compared to neutralizing DNases . In addition to the cellular RNases that are released there are several RNases that are present in the environment. RNases have evolved to have many extracellular functions in various organisms. [ 5 ] [ 6 ] [ 7 ] For example, RNase 7, a member of the RNase A superfamily, is secreted by human skin and serves as a potent antipathogen defence. [ 8 ] [ 9 ] For these secreted RNases, enzymatic activity may not even be necessary for the RNase's exapted function. For example, immune RNases act by destabilizing the cell membranes of bacteria. [ 10 ] [ 11 ]
To counter this, equipment used for RNA extraction is usually cleaned thoroughly, kept separate from common lab equipment and treated with various harsh chemicals that destroy RNases. This includes solutions that are used for RNA extraction, which can be treated with chemicals such as DEPC. [ 12 ] For the same reason, experimenters take special care not to let their bare skin touch the equipment, to avoid contaminating the sample with RNAses that are present on human skin. Broad RNAse inhibitors are also commercially available and sometimes added to in vitro transcription (RNA synthesis) reactions. [ 13 ]
Two-phase wash to solve the ubiquitous contaminant-carryover problem in commercial nucleic-acid extraction kits ; by Erik Jue, Daan Witters & Rustem F. Ismagilov; Nature, Scientific reports, 2020. | https://en.wikipedia.org/wiki/RNA_extraction |
RIP-chip (RNA immunoprecipitation chip) is a molecular biology technique which combines RNA immunoprecipitation with a microarray . The purpose of this technique is to identify which RNA sequences interact with a particular RNA binding protein of interest in vivo . [ 1 ] [ 2 ] [ 3 ] [ 4 ] It can also be used to determine relative levels of gene expression , to identify subsets of RNAs which may be co-regulated, or to identify RNAs that may have related functions. [ 4 ] [ 5 ] This technique provides insight into the post-transcriptional gene regulation which occurs between RNA and RNA binding proteins. [ 5 ]
The genes fluorescently identified by the chip analysis are the genes whose RNA interacts with the original protein of interest. The strength of the fluorescent signal for a particular gene can indicate how much of that particular RNA was present in the original sample, which indicates the expression level of that gene.
Previous techniques aiming to understand protein-RNA interactions included RNA Electrophoretic Mobility Shift Assays and UV-crosslinking followed by RT-PCR, [ 9 ] however such selective analysis cannot be used when the bound RNAs are not yet known. [ 1 ] To resolve this, RIP-chip combines RNA immunoprecipitation to isolate RNA molecules interacting with specific proteins with a microarray which can elucidate the identity of the RNAs participating in this interaction. [ 5 ] [ 1 ] Alternatives to RIP-chip include: | https://en.wikipedia.org/wiki/RNA_immunoprecipitation_chip |
The RNA integrity number (RIN) is an algorithm for assigning integrity values to RNA measurements.
The integrity of RNA is a major concern for gene expression studies and traditionally has been evaluated using the 28S to 18S rRNA ratio, a method that has been shown to be inconsistent. [ 1 ] This inconsistency arises because subjective, human interpretation is necessary to compare the 28S and 18S gel images. The RIN algorithm was devised to overcome this issue. The RIN algorithm is applied to electrophoretic RNA measurements, typically obtained using capillary gel electrophoresis, and based on a combination of different features that contribute information about the RNA integrity to provide a more universal measure. RIN has been demonstrated to be robust and reproducible in studies comparing it to other RNA integrity calculation algorithms, cementing its position as a preferred method of determining the quality of RNA to be analyzed. [ 2 ]
A major criticism to RIN is when using with plants or in studies of eukaryotic-prokaryotic cells interactions. The RIN algorithm is unable to differentiate eukaryotic / prokaryotic / chloroplastic ribosomal RNA, creating serious quality index underestimation in such situations.
Electrophoresis is the process of separating nucleic acid species based on their length by applying an electric field to them. As nucleic acids are negatively charged, they are pushed by an electric field through a matrix, usually an agarose gel, with the smaller molecules being pushed farther, faster. [ 3 ] Capillary electrophoresis is a technique whereby small amounts of a nucleic acid sample can be run on a gel in a very thin tube. There is a detector in the machine that can tell when nucleic acid samples pass through a specific point in the tube, with smaller samples passing through first. This can produce an electropherogram such as the one in Figure 1, where length is related to time at which the samples pass the detector.
A marker is a sample of known size run along with the sample so that the actual size of the rest of the sample can be known by comparing their running distance/time to be relative to this marker.
RNA is a biological macromolecule made of sugars and nitrogenous bases that plays a number of crucial roles in all living cells. There are several subtypes of RNA, with the most prominent in the cell being tRNA (transfer RNA), rRNA (ribosomal RNA), and mRNA (messenger RNA). All three of these are involved in the process of translation , with the most prominent species (~85%) of cellular RNA being rRNA. As a result, this is the most immediately visible species when RNA is analyzed via electrophoresis and is thus used for determining RNA quality (see Computation, below). rRNA comes in various sizes, with those in mammals belonging to the sizes 5S, 18S, and 28S. The 28S and 5S rRNAs form the large subunit and the 18S forms the small subunit of the ribosome , the molecular machinery responsible for synthesizing proteins. [ 4 ]
RNases are ubiquitous and can often contaminate and subsequently degrade RNA samples in the laboratory, so RNA integrity can very easily be compromised, leading to a number of laboratory techniques designed to eliminate their impact. [ 5 ] [ 6 ] However, these methods are not fool-proof, and so samples can still be degraded, necessitating a method of measuring RNA integrity to ensure the trustworthiness and reproducibility of molecular assays, as RNA integrity is critical for proper results in gene expression studies, such as microarray analysis, Northern blots, or quantitative real-time PCR (qPCR). [ 7 ] [ 8 ] RNA that has been degraded has a direct impact on calculated expression levels, often leading to significantly decreased apparent expression. [ 9 ]
qPCR and similar techniques are very expensive, taking a good deal of both time and money, so continuing research being undertaken to decrease the cost while maintaining qPCR's accuracy and reproducibility for gene expression and other applications. [ 10 ] RIN assessment allows a scientist to evaluate an experiment's trustworthiness and reproducibility before incurring substantial costs in performing the gene expression studies.
RIN is a standard method of measuring RNA integrity and can be used to evaluate the quality of RNA produced by new RNA isolation techniques. [ 11 ]
As RNA integrity has long been known to be a problem in molecular biology studies, there are a few methods that have been used historically to determine the integrity of RNA. The most popular has long been agarose gel electrophoresis with ethidium bromide staining, allowing one to visualize the bands from the rRNA peaks. The height of the 28S and 18S bands can be compared to each other, with a 2:1 ratio indicating non-degraded RNA. [ 1 ] While this method is very cheap and easy, there are several issues with this method, primarily its subjectivity, leading to inconsistent, non-standardized RNA quality assessments, and the large amounts of RNA that are needed to visualize it on an agarose gel, which can be problematic if there is not much RNA to work with. [ 1 ] [ 12 ] There are also a number of different problems that can arise from agarose gel electrophoresis, such as poor loading, uneven running, and uneven staining that lead to increased variability in the accuracy of using agarose gel electrophoresis to determine RNA integrity. [ 13 ]
The RNA Integrity Number was developed by Agilent Technologies in 2005. [ 1 ] The algorithm was generated by taking hundreds of samples and having specialists manually assign them all a value of 1 to 10 based on their integrity, with 10 being the highest. Adaptive learning tools using a Bayesian learning technique were used to generate an algorithm that could predict the RIN, predominantly by using the features listed below under "Computation". [ 1 ] [ 14 ] This allows for all Agilent software to produce the same RIN for a given RNA sample, standardizing the measurement and making it much less subjective than earlier methods [ citation needed ] .
RIN for a sample is computed using several characteristics of an RNA electropherogram trace, with the first two listed below being most significant. RIN assigns an electropherogram a value of 1 to 10, with 10 being the least degraded. All the following descriptions apply to mammalian RNA because RNAs in other species have different rRNA sizes: [ 1 ] The total RNA ratio is calculated by taking the ratio of the area under the 18S and 28S rRNA peaks to the total area under the graph, a large number here is desired, indicating much of the rRNA is still at these sizes and thus little to no degradation has occurred. An ideal ratio can be seen in figure 1, where almost all of the RNA is in the 18S and 28S RNA peaks.
For the height of 28S peak, a large value is desired. 28S, the most prominent rRNA species, is used in RIN calculation as it is typically degraded more quickly than 18S rRNA, and so measuring its peak height allows for detection of the early stages of degradation. Again, this is seen in figure 1, where the 28S peak is the largest, and so this is good.
The fast region is the area between the 18S and 5S rRNA peaks on an electropherogram. Initially, as the fast area ratio value increases, it indicates degradation of the 18S and 28S rRNA to an intermediate size, though the ratio subsequently decreases as RNA degrades further, to even smaller sizes. Thus, a low value doesn't necessarily indicate either good or bad RNA integrity.
A small marker height is desired, indicating only small amounts of RNA have been degraded and proceeded to the smallest lengths, indicated by the short marker. If a large number is found here, that indicates that large amounts of the rRNAs have been degraded to small pieces that would be found closer to this marker. This situation can be seen in the 'poor quality' RNA electropherogram found in figure 2, where the height of the peak over the marker (far left) is very large, so the RNA has been greatly degraded.
In prokaryotic samples, the algorithm is somewhat different, but the Agilent 2100 Bioanalyzer Expert software is able to calculate RIN for prokaryotic samples now as well. [ 15 ] The difference likely arises from the fact that, while mammalian samples have 28S and 18S ribosomal RNAs as their predominant species, prokaryotic RNAs have the sizes shifted slightly smaller, to 23S and 16S, so the algorithm must be shifted to accommodate that. Another crucial fact about calculating prokaryotic RNA integrity numbers is that RIN has not been validated to the extent that it has for eukaryotic RNA. [ 15 ] It has been shown that higher RIN values correlate with better downstream results in eukaryotes, but this hasn't been done as extensively for prokaryotes, so it may mean less in prokaryotes.
These electropherograms for calculating RIN are done using the Agilent Bioanalyzer machine, which is capable of performing electrophoresis and generating the electropherograms. [ 14 ] The Agilent 2100 software is uniquely able to perform the RIN software, as the exact algorithm is proprietary, so there are additional important RNA electropherogram features that are used in its calculation that are not publicly available. | https://en.wikipedia.org/wiki/RNA_integrity_number |
RNA origami is the nanoscale folding of RNA , enabling the RNA to create particular shapes to organize these molecules. [ 1 ] It is a new method that was developed by researchers from Aarhus University and California Institute of Technology . [ 2 ] RNA origami is synthesized by enzymes that fold RNA into particular shapes. The folding of the RNA occurs in living cells under natural conditions. RNA origami is represented as a DNA gene , which within cells can be transcribed into RNA by RNA polymerase . Many computer algorithms are present to help with RNA folding, but none can fully predict the folding of RNA of a singular sequence. [ 2 ]
In nucleic acids nanotechnology, artificial nucleic acids are designed to form molecular components that can self-assemble into stable structures for use ranging from targeted drug delivery to programmable biomaterials. [ 3 ] DNA nanotechnology uses DNA motifs to build target shapes and arrangements. It has been used in a variety of situations, including nanorobotics, algorithmic arrays, and sensor applications. The future of DNA nanotechnology is filled with possibilities for applications. [ 4 ]
The success of DNA nanotechnology has allowed designers to develop RNA nanotechnology as a growing discipline. RNA nanotechnology combines the simplistic design and manipulation characteristic of DNA, with the additional flexibility in structure and diversity in function similar to that of proteins. [ 5 ] RNA's versatility in structure and function, favorable in vivo attributes, and bottom-up self-assembly is an ideal avenue for developing biomaterial and nanoparticle drug delivery. Several techniques were developed to construct these RNA nanoparticles, including RNA cubic scaffold, [ 6 ] templated and non-templated assembly, and RNA origami.
The first work in RNA origami appeared in Science , published by Ebbe S. Andersen of Aarhus University. [ 7 ] Researchers at Aarhus University used various 3D models and computer software to design individual RNA origami. Once encoded as a synthetic DNA gene, adding RNA polymerase resulted in the formation of RNA origami. Observation of RNA was primarily done through atomic force microscopy , a technique that allows researchers to look at molecules a thousand times closer than would normally be possible with a conventional light microscope. They were able to form honeycomb shapes, but determined other shapes are also possible.
Cody Geary, a scholar in the field of RNA origami, described the uniqueness of the method of RNA origami. He stated that its folding recipe is encoded in the molecule itself, and determine by its sequence. The sequence gives the RNA origami both its final shape and movements of the structure as it folds. The primary challenge associated with RNA origami stems from the fact RNA folds on its own and can thus easily tangle itself. [ 2 ]
Computer-aided design of the RNA origami structure requires three main processes; creating the 3D model, writing the 2D structure, and designing the sequence. First, a 3D model is constructed using tertiary motifs from existing databases. This is necessary to ensure the created structure has feasible geometry and strain. The next process is creating the 2D structure describing the strand path and base pairs from the 3D model. This 2D blueprint introduces sequence constraints, creating primary, secondary, and tertiary motifs. The final step is designing sequences compatible with designed structure. Design algorithms can be used to create sequences that can fold into various structures. [ 8 ]
To produce a desired shape, the RNA origami method uses double-crossovers (DX) to arrange the RNA helices in parallel to each other to form a building block. While DNA origami requires the construction of DNA molecules from multiple strands, researchers were able to devise a method in making DX molecules from only one strand for RNA. This was done through adding hairpin motifs to the edges and kissing-loop complexes on internal helices. The addition of more DNA molecules on top of one another creates a junction known as the dovetail seam. This dovetail seam has base pairs that cross between adjacent junctions; thus, the structural seam along the junction becomes sequence-specific. An important aspect of these folding interactions is its folding; the order that interactions form can potentially create a situation in which one interaction blocks another, creating a knot. Because the kissing-loop interactions and dovetail interactions are a half-turn or shorter, they do not create these topological issues. [ 8 ]
RNA and DNA nanostructures are used for the organization and coordination of important molecular processes. However, there exist several distinct differences between the fundamental structure and applications between the two. Although inspired by the DNA origami techniques established by Paul Rothemund , [ 9 ] the process for RNA origami is vastly different. RNA origami is a much newer process than DNA origami; DNA origami has been studied for approximately a decade now, while the study of RNA origami has only recently begun.
In contrast to DNA origami, which involves chemically synthesizing the DNA strands and arranging the strands to form any shape desired with the aid of "staple strands", RNA origami is made by enzymes and subsequently folds into pre-rendered shapes. RNA is able to fold into unique ways in complex structures due to a number of secondary structural motifs, such as conserved motifs and short structural elements. A major determinant for RNA topology is the secondary-structure interaction, which include motifs such as pseudoknots and kissing loops, adjacent helices stacking on one another, hairpin loops with bulge content, and coaxial stacks. This is largely a result of four different nucleotides: adenine (A), cytosine (C), guanine (G) and uracil (U), and ability to form non-canonical base pairs .
There also exist more complex and longer-range RNA tertiary interactions. DNA are unable to forms these tertiary motifs and thereby cannot match the functional capacity of RNA in performing more versatile tasks. RNA molecules that are correctly folded can serve as enzymes, due to positioning metal ions at their active sites; this gives the molecules a diverse array of catalytic abilities. [ 10 ] Because of this relationship to enzymes, RNA structures can potentially be grown within living cells and used to organize cellular enzymes into distinct groups.
Additionally, the DNA origami's molecular breakup is not easily incorporated into the genetic material of an organism. However, RNA origami is capable of being written directly as a DNA gene and transcribed using RNA polymerase. Therefore, while DNA origami requires expensive culturing outside of a cell, RNA origami can be produced in mass, cheap quantities directly within cells just by growing bacteria. [ 11 ] The feasibility and cost effectiveness of manufacturing RNA in living cells and combined with the extra functionality of RNA structure is promising for the development of RNA origami.
RNA origami is a new concept and has great potential for applications in nanomedicine and synthetic biology. The method was developed to allow new creations of large RNA nanostructures that create defined scaffolds for combining RNA based functionalities. Because of the infancy of RNA origami, many of its potential applications are still in the process of discovery. Its structures are able to provide a stable basis to allow functionality for RNA components. These structures include riboswitches , ribozymes , interaction sites, and aptamers . Aptamer structures allow the binding of small molecules which gives possibilities for construction of future RNA based nanodevices. RNA origami is further useful in areas such as cell recognition and binding for diagnosis. Additionally, targeted delivery and blood-brain barrier passing have been studied. [ 6 ] Perhaps the most important future application for RNA origami is building scaffolds to arrange other microscopic proteins and allow them to work with one another. [ 8 ]
Using RNA origami techniques, researchers have created nanotubular structures that replicate the cytoskeleton, an important element of living cells. These artificial cytoskeletal structures offer essential structural stability and organization, key to developing artificial cells. The technology does away with protein synthesis, thus streamlining synthetic cellular entity assembly. The ability to design and manipulate these structures raises new questions in synthetic biology, such as creating artificial cells for use in medical and industrial contexts. [ 12 ] [ 13 ] [ 14 ] | https://en.wikipedia.org/wiki/RNA_origami |
In molecular biology , RNA polymerase (abbreviated RNAP or RNApol ), or more specifically DNA-directed/dependent RNA polymerase ( DdRP ), is an enzyme that catalyzes the chemical reactions that synthesize RNA from a DNA template.
Using the enzyme helicase , RNAP locally opens the double-stranded DNA so that one strand of the exposed nucleotides can be used as a template for the synthesis of RNA, a process called transcription . A transcription factor and its associated transcription mediator complex must be attached to a DNA binding site called a promoter region before RNAP can initiate the DNA unwinding at that position. RNAP not only initiates RNA transcription, it also guides the nucleotides into position, facilitates attachment and elongation , has intrinsic proofreading and replacement capabilities, and termination recognition capability. In eukaryotes , RNAP can build chains as long as 2.4 million nucleotides.
RNAP produces RNA that, functionally, is either for protein coding , i.e. messenger RNA (mRNA); or non-coding (so-called "RNA genes"). Examples of four functional types of RNA genes are:
RNA polymerase is essential to life, and is found in all living organisms and many viruses . Depending on the organism, a RNA polymerase can be a protein complex (multi-subunit RNAP) or only consist of one subunit (single-subunit RNAP, ssRNAP), each representing an independent lineage. The former is found in bacteria , archaea , and eukaryotes alike, sharing a similar core structure and mechanism. [ 1 ] The latter is found in phages as well as eukaryotic chloroplasts and mitochondria , and is related to modern DNA polymerases . [ 2 ] Eukaryotic and archaeal RNAPs have more subunits than bacterial ones do, and are controlled differently.
Bacteria and archaea only have one RNA polymerase. Eukaryotes have multiple types of nuclear RNAP, each responsible for synthesis of a distinct subset of RNA:
The 2006 Nobel Prize in Chemistry was awarded to Roger D. Kornberg for creating detailed molecular images of RNA polymerase during various stages of the transcription process. [ 3 ] [ 4 ]
In most prokaryotes , a single RNA polymerase species transcribes all types of RNA. RNA polymerase "core" from E. coli consists of five subunits: two alpha (α) subunits of 36 kDa , a beta (β) subunit of 150 kDa, a beta prime subunit (β′) of 155 kDa, and a small omega (ω) subunit. A sigma (σ) factor binds to the core, forming the holoenzyme. After transcription starts, the factor can unbind and let the core enzyme proceed with its work. [ 5 ] [ 6 ] The core RNA polymerase complex forms a "crab claw" or "clamp-jaw" structure with an internal channel running along the full length. [ 7 ] Eukaryotic and archaeal RNA polymerases have a similar core structure and work in a similar manner, although they have many extra subunits. [ 8 ]
All RNAPs contain metal cofactors , in particular zinc and magnesium cations which aid in the transcription process. [ 9 ] [ 10 ]
Control of the process of gene transcription affects patterns of gene expression and, thereby, allows a cell to adapt to a changing environment, perform specialized roles within an organism, and maintain basic metabolic processes necessary for survival. Therefore, it is hardly surprising that the activity of RNAP is long, complex, and highly regulated. In Escherichia coli bacteria, more than 100 transcription factors have been identified, which modify the activity of RNAP. [ 11 ]
RNAP can initiate transcription at specific DNA sequences known as promoters . It then produces an RNA chain, which is complementary to the template DNA strand. The process of adding nucleotides to the RNA strand is known as elongation; in eukaryotes, RNAP can build chains as long as 2.4 million nucleotides (the full length of the dystrophin gene). RNAP will preferentially release its RNA transcript at specific DNA sequences encoded at the end of genes, which are known as terminators .
Products of RNAP include:
RNAP accomplishes de novo synthesis . It is able to do this because specific interactions with the initiating nucleotide hold RNAP rigidly in place, facilitating chemical attack on the incoming nucleotide. Such specific interactions explain why RNAP prefers to start transcripts with ATP (followed by GTP, UTP, and then CTP). In contrast to DNA polymerase , RNAP includes helicase activity, therefore no separate enzyme is needed to unwind DNA.
RNA polymerase binding in bacteria involves the sigma factor recognizing the core promoter region containing the −35 and −10 elements (located before the beginning of sequence to be transcribed) and also, at some promoters, the α subunit C-terminal domain recognizing promoter upstream elements. [ 12 ] There are multiple interchangeable sigma factors, each of which recognizes a distinct set of promoters. For example, in E. coli , σ 70 is expressed under normal conditions and recognizes promoters for genes required under normal conditions (" housekeeping genes "), while σ 32 recognizes promoters for genes required at high temperatures (" heat-shock genes "). In archaea and eukaryotes, the functions of the bacterial general transcription factor sigma are performed by multiple general transcription factors that work together. The RNA polymerase-promoter closed complex is usually referred to as the " transcription preinitiation complex ." [ 13 ] [ 14 ]
After binding to the DNA, the RNA polymerase switches from a closed complex to an open complex. This change involves the separation of the DNA strands to form an unwound section of DNA of approximately 13 bp, referred to as the " transcription bubble ". Supercoiling plays an important part in polymerase activity because of the unwinding and rewinding of DNA. Because regions of DNA in front of RNAP are unwound, there are compensatory positive supercoils. Regions behind RNAP are rewound and negative supercoils are present. [ 14 ]
RNA polymerase then starts to synthesize the initial DNA-RNA heteroduplex, with ribonucleotides base-paired to the template DNA strand according to Watson-Crick base-pairing interactions. As noted above, RNA polymerase makes contacts with the promoter region. However these stabilizing contacts inhibit the enzyme's ability to access DNA further downstream and thus the synthesis of the full-length product. In order to continue RNA synthesis, RNA polymerase must escape the promoter. It must maintain promoter contacts while unwinding more downstream DNA for synthesis, "scrunching" more downstream DNA into the initiation complex. [ 15 ] During the promoter escape transition, RNA polymerase is considered a "stressed intermediate." Thermodynamically the stress accumulates from the DNA-unwinding and DNA-compaction activities. Once the DNA-RNA heteroduplex is long enough (~10 bp), RNA polymerase releases its upstream contacts and effectively achieves the promoter escape transition into the elongation phase. The heteroduplex at the active center stabilizes the elongation complex.
However, promoter escape is not the only outcome. RNA polymerase can also relieve the stress by releasing its downstream contacts, arresting transcription. The paused transcribing complex has two options: (1) release the nascent transcript and begin anew at the promoter or (2) reestablish a new 3′-OH on the nascent transcript at the active site via RNA polymerase's catalytic activity and recommence DNA scrunching to achieve promoter escape. Abortive initiation , the unproductive cycling of RNA polymerase before the promoter escape transition, results in short RNA fragments of around 9 bp in a process known as abortive transcription. The extent of abortive initiation depends on the presence of transcription factors and the strength of the promoter contacts. [ 16 ]
The 17-bp transcriptional complex has an 8-bp DNA-RNA hybrid, that is, 8 base-pairs involve the RNA transcript bound to the DNA template strand. [ 17 ] As transcription progresses, ribonucleotides are added to the 3′ end of the RNA transcript and the RNAP complex moves along the DNA. The characteristic elongation rates in prokaryotes and eukaryotes are about 10–100 nts/sec. [ 18 ]
Aspartyl ( asp ) residues in the RNAP will hold on to Mg 2+ ions, which will, in turn, coordinate the phosphates of the ribonucleotides. The first Mg 2+ will hold on to the α-phosphate of the NTP to be added. This allows the nucleophilic attack of the 3′-OH from the RNA transcript, adding another NTP to the chain. The second Mg 2+ will hold on to the pyrophosphate of the NTP. [ 19 ] The overall reaction equation is:
Unlike the proofreading mechanisms of DNA polymerase those of RNAP have only recently been investigated. Proofreading begins with separation of the mis-incorporated nucleotide from the DNA template. This pauses transcription. The polymerase then backtracks by one position and cleaves the dinucleotide that contains the mismatched nucleotide. In the RNA polymerase this occurs at the same active site used for polymerization and is therefore markedly different from the DNA polymerase where proofreading occurs at a distinct nuclease active site. [ 20 ]
The overall error rate is around 10 −4 to 10 −6 . [ 21 ]
In bacteria, termination of RNA transcription can be rho-dependent or rho-independent. The former relies on the rho factor , which destabilizes the DNA-RNA heteroduplex and causes RNA release. [ 22 ] The latter, also known as intrinsic termination , relies on a palindromic region of DNA. Transcribing the region causes the formation of a "hairpin" structure from the RNA transcription looping and binding upon itself. This hairpin structure is often rich in G-C base-pairs, making it more stable than the DNA-RNA hybrid itself. As a result, the 8 bp DNA-RNA hybrid in the transcription complex shifts to a 4 bp hybrid. These last 4 base pairs are weak A-U base pairs, and the entire RNA transcript will fall off the DNA. [ 23 ]
Transcription termination in eukaryotes is less well understood than in bacteria, but involves cleavage of the new transcript followed by template-independent addition of adenines at its new 3′ end, in a process called polyadenylation . [ 24 ]
Given that DNA and RNA polymerases both carry out template-dependent nucleotide polymerization, it might be expected that the two types of enzymes would be structurally related. However, x-ray crystallographic studies of both types of enzymes reveal that, other than containing a critical Mg 2+ ion at the catalytic site, they are virtually unrelated to each other; indeed template-dependent nucleotide polymerizing enzymes seem to have arisen independently twice during the early evolution of cells. One lineage led to the modern DNA polymerases and reverse transcriptases, as well as to a few single-subunit RNA polymerases (ssRNAP) from phages and organelles. [ 2 ] The other multi-subunit RNAP lineage formed all of the modern cellular RNA polymerases. [ 25 ] [ 1 ]
In bacteria , the same enzyme catalyzes the synthesis of mRNA and non-coding RNA (ncRNA) .
RNAP is a large molecule. The core enzyme has five subunits (~400 kDa ): [ 26 ]
In order to bind promoters, RNAP core associates with the transcription initiation factor sigma (σ) to form RNA polymerase holoenzyme. Sigma reduces the affinity of RNAP for nonspecific DNA while increasing specificity for promoters, allowing transcription to initiate at correct sites. The complete holoenzyme therefore has 6 subunits: β′βα I and α II ωσ (~450 kDa).
Eukaryotes have multiple types of nuclear RNAP, each responsible for synthesis of a distinct subset of RNA. All are structurally and mechanistically related to each other and to bacterial RNAP:
Eukaryotic chloroplasts contain a multi-subunit RNAP ("PEP, plastid-encoded polymerase"). Due to its bacterial origin, the organization of PEP resembles that of current bacterial RNA polymerases: It is encoded by the RPOA, RPOB, RPOC1 and RPOC2 genes on the plastome, which as proteins form the core subunits of PEP, respectively named α, β, β′ and β″. [ 35 ] Similar to the RNA polymerase in E. coli , PEP requires the presence of sigma (σ) factors for the recognition of its promoters, containing the -10 and -35 motifs. [ 36 ] Despite the many commonalities between plant organellar and bacterial RNA polymerases and their structure, PEP additionally requires the association of a number of nuclear encoded proteins, termed PAPs (PEP-associated proteins), which form essential components that are closely associated with the PEP complex in plants. Initially, a group consisting of 10 PAPs was identified through biochemical methods, which was later extended to 12 PAPs. [ 37 ] [ 38 ]
Chloroplast also contain a second, structurally and mechanistically unrelated, single-subunit RNAP ("nucleus-encoded polymerase, NEP"). Eukaryotic mitochondria use POLRMT (human), a nucleus-encoded single-subunit RNAP. [ 2 ] Such phage-like polymerases are referred to as RpoT in plants. [ 39 ]
Archaea have a single type of RNAP, responsible for the synthesis of all RNA. Archaeal RNAP is structurally and mechanistically similar to bacterial RNAP and eukaryotic nuclear RNAP I-V, and is especially closely structurally and mechanistically related to eukaryotic nuclear RNAP II. [ 8 ] [ 40 ] The history of the discovery of the archaeal RNA polymerase is quite recent. The first analysis of the RNAP of an archaeon was performed in 1971, when the RNAP from the extreme halophile Halobacterium cutirubrum was isolated and purified. [ 41 ] Crystal structures of RNAPs from Sulfolobus solfataricus and Sulfolobus shibatae set the total number of identified archaeal subunits at thirteen. [ 8 ] [ 42 ]
Archaea has the subunit corresponding to Eukaryotic Rpb1 split into two. There is no homolog to eukaryotic Rpb9 ( POLR2I ) in the S. shibatae complex, although TFS (TFIIS homolog) has been proposed as one based on similarity. There is an additional subunit dubbed Rpo13; together with Rpo5 it occupies a space filled by an insertion found in bacterial β′ subunits (1,377–1,420 in Taq ). [ 8 ] An earlier, lower-resolution study on S. solfataricus structure did not find Rpo13 and only assigned the space to Rpo5/Rpb5. Rpo3 is notable in that it's an iron–sulfur protein . RNAP I/III subunit AC40 found in some eukaryotes share similar sequences, [ 42 ] but does not bind iron. [ 43 ] This domain, in either case, serves a structural function. [ 44 ]
Archaeal RNAP subunit previously used an "RpoX" nomenclature where each subunit is assigned a letter in a way unrelated to any other systems. [ 1 ] In 2009, a new nomenclature based on Eukaryotic Pol II subunit "Rpb" numbering was proposed. [ 8 ]
Orthopoxviruses and some other nucleocytoplasmic large DNA viruses synthesize RNA using a virally encoded multi-subunit RNAP. They are most similar to eukaryotic RNAPs, with some subunits minified or removed. [ 45 ] Exactly which RNAP they are most similar to is a topic of debate. [ 46 ] Most other viruses that synthesize RNA use unrelated mechanics.
Many viruses use a single-subunit DNA-dependent RNAP (ssRNAP) that is structurally and mechanistically related to the single-subunit RNAP of eukaryotic chloroplasts (RpoT) and mitochondria ( POLRMT ) and, more distantly, to DNA polymerases and reverse transcriptases . Perhaps the most widely studied such single-subunit RNAP is bacteriophage T7 RNA polymerase . ssRNAPs cannot proofread. [ 2 ]
B. subtilis prophage SPβ uses YonO, a homolog of the β+β′ subunits of msRNAPs to form a monomeric (both barrels on the same chain) RNAP distinct from the usual "right hand" ssRNAP. It probably diverged very long ago from the canonical five-unit msRNAP, before the time of the last universal common ancestor . [ 47 ] [ 48 ]
Other viruses use an RNA-dependent RNAP (an RNAP that employs RNA as a template instead of DNA). This occurs in negative strand RNA viruses and dsRNA viruses , both of which exist for a portion of their life cycle as double-stranded RNA. However, some positive strand RNA viruses , such as poliovirus , also contain RNA-dependent RNAP. [ 49 ]
RNAP was discovered independently by Sam Weiss, Audrey Stevens , and Jerard Hurwitz in 1960. [ 50 ] By this time, one half of the 1959 Nobel Prize in Medicine had been awarded to Severo Ochoa for the discovery of what was believed to be RNAP, [ 51 ] but instead turned out to be polynucleotide phosphorylase .
RNA polymerase can be isolated in the following ways:
And also combinations of the above techniques.
( Wayback Machine copy) | https://en.wikipedia.org/wiki/RNA_polymerase |
RNA polymerase 1 (also known as Pol I ) is, in higher eukaryotes , the polymerase that only transcribes ribosomal RNA (but not 5S rRNA , which is synthesized by RNA polymerase III ), a type of RNA that accounts for over 50% of the total RNA synthesized in a cell . [ 1 ]
Pol I is a 590 kDa enzyme that consists of 14 protein subunits ( polypeptides ), and its crystal structure in the yeast Saccharomyces cerevisiae was solved at 2.8Å resolution in 2013. [ 2 ] Twelve of its subunits have identical or related counterparts in RNA polymerase II (Pol II) and RNA polymerase III (Pol III). The other two subunits are related to Pol II initiation factors and have structural homologues in Pol III.
Ribosomal DNA transcription is confined to the nucleolus , where about 400 copies of the 42.9-kb rDNA gene are present, arranged as tandem repeats in nucleolus organizer regions . Each copy contains a ~13.3 kb sequence encoding the 18S , the 5.8S , and the 28S RNA molecules, interlaced with two internal transcribed spacers , ITS1 and ITS2, and flanked upstream by a 5' external transcribed spacer and a downstream 3' external transcribed spacer. [ 3 ] [ 4 ] These components are transcribed together to form the 45S pre-rRNA . [ 5 ] The 45S pre-rRNA is then post-transcriptionally cleaved by C/D box and H/ACA box snoRNAs , [ 6 ] removing the two spacers and resulting in the three rRNAs by a complex series of steps. [ 7 ] The 5S ribosomal RNA is transcribed by Pol III. Because of the simplicity of Pol I transcription, it is the fastest-acting polymerase and contributes up to 60% of cellular transcription levels in exponentially growing cells.
In Saccharomyces cerevisiae , the 5S rDNA has the unusual feature of lying inside the rDNA repeat. It is flanked by non-transcribed spacers NTS1 and NTS2, and is transcribed backwards by Pol III, separately from the rest of the rDNA. [ 7 ]
The rate of cell growth is directly dependent on the rate of protein synthesis, which is itself intricately linked to ribosome synthesis and rRNA transcription. Thus, intracellular signals must coordinate the synthesis of rRNA with that of other components of protein translation. Myc is known to bind to human ribosomal DNA in order to stimulate rRNA transcription by RNA polymerase I. [ 8 ] Two specific mechanisms have been identified, ensuring proper control of rRNA synthesis and Pol I-mediated transcription.
Given the large numbers of rDNA genes (several hundreds) available for transcription, the first mechanism involves adjustments in the number of genes being transcribed at a specific time. In mammalian cells, the number of active rDNA genes varies between cell types and level of differentiation . In general, as a cell becomes more differentiated, it requires less growth and, therefore, will have a decrease in rRNA synthesis and a decrease in rDNA genes being transcribed. When rRNA synthesis is stimulated, SL1 (selectivity factor 1) will bind to the promoters of rDNA genes that were previously silent, and recruit a pre-initiation complex to which Pol I will bind and start transcription of rRNA.
Changes in rRNA transcription can also occur via changes in the rate of transcription. While the exact mechanism through which Pol I increases its rate of transcription is as yet unknown, evidence has shown that rRNA synthesis can increase or decrease without changes in the number of actively transcribed rDNA.
In the process of transcription (by any polymerase), there are three main stages:
Pol I requires no TATA box in the promoter, instead relying on an upstream control element (UCE) located between −200 and −107, and a core element located between −45 and +20. [ 9 ] [ 10 ]
Note that this process is variable in different organisms. [ 10 ]
As Pol I escapes and clears the promoter, UBF and SL1 remain-promoter bound, ready to recruit another Pol I. Indeed, each active rDNA gene can be transcribed multiple times simultaneously, as opposed to Pol II-transcribed genes, which associate with only one complex at a time. While elongation proceeds unimpeded in vitro, it is unclear at this point whether this process happens in a cell, given the presence of nucleosomes . Pol I does seem to transcribe through nucleosomes, either bypassing or disrupting them, perhaps assisted by chromatin-remodeling activities. In addition, UBF might also act as positive feedback, enhancing Pol I elongation through an anti-repressor function. An additional factor, TIF-IC, can also stimulate the overall rate of transcription and suppress pausing of Pol I. As Pol I proceeds along the rDNA, supercoils form both ahead of and behind the complex. These are unwound by topoisomerase I or II at regular intervals, similar to what is seen in Pol II-mediated transcription. [ citation needed ]
Elongation is likely to be interrupted at sites of DNA damage. Transcription-coupled repair occurs similarly to Pol II-transcribed genes and requires the presence of several DNA repair proteins, such as TFIIH, CSB, and XPG.
In higher eukaryotes, TTF-I binds and bends the termination site at the 3' end of the transcribed region. This will force Pol I to pause. TTF-I, with the help of transcript-release factor PTRF and a T-rich region, will induce Pol I into terminating transcription and dissociating from the DNA and the new transcript. Evidence suggests that termination might be rate-limiting in cases of high rRNA production. TTF-I and PTRF will then indirectly stimulate the reinitiation of transcription by Pol I at the same rDNA gene.
In organisms such as budding yeast the process seems to be much more complicated and is still not completely elucidated. [ citation needed ]
Recombination hotspots are DNA sequences that increase local recombination . The HOT1 sequence in yeast is one of the most well studied mitotic recombination hotspots. The HOT1 sequence includes an RNA polymerase I transcription promoter . In a yeast mutant strain defective in RNA polymerase I the HOT1 activity in promoting recombination is abolished. The level of RNA polymerase I transcription activity that is dependent on the promoter in the HOT1 sequence appears to determine the level of nearby mitotic recombination. [ 13 ] | https://en.wikipedia.org/wiki/RNA_polymerase_I |
RNA polymerase II ( RNAP II and Pol II ) is a multiprotein complex that transcribes DNA into precursors of messenger RNA (mRNA) and most small nuclear RNA (snRNA) and microRNA . [ 1 ] [ 2 ] It is one of the three RNAP enzymes found in the nucleus of eukaryotic cells. [ 3 ] A 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNA polymerase . A wide range of transcription factors are required for it to bind to upstream gene promoters and begin transcription.
Early studies suggested a minimum of two RNAPs: one which synthesized rRNA in the nucleolus , and one which synthesized other RNA in the nucleoplasm , part of the nucleus but outside the nucleolus. [ 5 ] In 1969, biochemists Robert G. Roeder and William Rutter discovered there are total three distinct nuclear RNA polymerases , an additional RNAP that was responsible for transcription of some kind of RNA in the nucleoplasm. [ 6 ] The finding was obtained by the use of ion-exchange chromatography via DEAE coated Sephadex beads. The technique separated the enzymes by the order of the corresponding elutions, Ι,ΙΙ,ΙΙΙ, by increasing the concentration of ammonium sulfate. The enzymes were named according to the order of the elutions, RNAP I , RNAP II, RNAP IΙI . [ 3 ] This discovery demonstrated that there was an additional enzyme present in the nucleoplasm, which allowed for the differentiation between RNAP II and RNAP III. [ 7 ]
RNA polymerase II (RNAP2) undergoes regulated transcriptional pausing during early elongation. Various studies has shown that disruption of transcription elongation is implicated in cancer , neurodegeneration , HIV latency etc. [ 8 ]
The eukaryotic core RNA polymerase II was first purified using transcription assays. [ 10 ] The purified enzyme has typically 10–12 subunits (12 in humans and yeast) and is incapable of specific promoter recognition. [ 11 ] Many subunit-subunit interactions are known. [ 12 ]
RPB3 is involved in RNA polymerase II assembly. [ 21 ] A subcomplex of RPB2 and RPB3 appears soon after subunit synthesis. [ 21 ] This complex subsequently interacts with RPB1. [ 21 ] RPB3, RPB5, and RPB7 interact with themselves to form homodimers, and RPB3 and RPB5 together are able to contact all of the other RPB subunits, except RPB9. [ 12 ] Only RPB1 strongly binds to RPB5. [ 12 ] The RPB1 subunit also contacts RPB7, RPB10, and more weakly but most efficiently with RPB8. [ 12 ] Once RPB1 enters the complex, other subunits such as RPB5 and RPB7 can enter, where RPB5 binds to RPB6 and RPB8 and RPB3 brings in RPB10, RPB 11, and RPB12. [ 12 ] RPB4 and RPB9 may enter once most of the complex is assembled. RPB4 forms a complex with RPB7. [ 12 ]
Enzymes can catalyze up to several million reactions per second. Enzyme rates depend on solution conditions and substrate concentration. Like other enzymes POLR2 has a saturation curve and a maximum velocity ( V max ). It has a K m (substrate concentration required for one-half V max ) and a k cat (the number of substrate molecules handled by one active site per second). The specificity constant is given by k cat / K m . The theoretical maximum for the specificity constant is the diffusion limit of about 10 8 to 10 9 ( M −1 s −1 ), where every collision of the enzyme with its substrate results in catalysis. In yeast, mutation in the Trigger-Loop domain of the largest subunit can change the kinetics of the enzyme. [ 22 ]
Bacterial RNA polymerase, a relative of RNA Polymerase II, switches between inactivated and activated states by translocating back and forth along the DNA. [ 23 ] Concentrations of [NTP] eq = 10 μM GTP, 10 μM UTP, 5 μM ATP and 2.5 μM CTP, produce a mean elongation rate, turnover number, of ~1 bp (NTP) −1 for bacterial RNAP, a relative of RNA polymerase II. [ 23 ]
RNA polymerase II undergoes extensive co-transcriptional pausing during transcription elongation. [ 24 ] [ 25 ] This pausing is especially pronounced at nucleosomes, and arises in part through the polymerase entering a transcriptionally incompetent backtracked state. [ 24 ] The duration of these pauses ranges from seconds to minutes or longer, and exit from long-lived pauses can be promoted by elongation factors such as TFIIS. [ 26 ] In turn, the transcription rate influences whether the histones of transcribed nucleosomes are evicted from chromatin, or reinserted behind the transcribing polymerase. [ 27 ]
RNA polymerase II is inhibited by α-Amanitin [ 28 ] and other amatoxins . α-Amanitin is a highly poisonous substance found in many mushrooms. [ 5 ] The mushroom poison has different effects on each of the RNA Polymerases: I, II, III. RNAP I is completely unresponsive to the substance and will function normally while RNAP III has a moderate sensitivity. RNAP II, however, is completely inhibited by the toxin. Alpha-Amanitin inhibits RNAP II by strong interactions in the enzyme's "funnel", "cleft", and the key "bridge α-helix " regions of the RPB-1 subunit. [ 29 ]
RNA polymerase II holoenzyme is a form of eukaryotic RNA polymerase II that is recruited to the promoters of protein -coding genes in living cells. [ 11 ] It consists of RNA polymerase II, a subset of general transcription factors , and regulatory proteins known as SRB proteins.
Part of the assembly of the holoenzyme is referred to as the preinitiation complex , because its assembly takes place on the gene promoter before the initiation of transcription . The mediator complex acts as a bridge between RNA polymerase II and the transcription factors.
This is an outline of an example mechanism of yeast cells by which chromatin structure and histone post-translational modification help regulate and record the transcription of genes by RNA polymerase II.
This pathway gives examples of regulation at these points of transcription:
This refers to various stages of the process as regulatory steps. It has not been proven that they are used for regulation, but is very likely they are.
RNA Pol II elongation promoters can be summarised in 3 classes.
The C-terminus of RPB1 is appended to form the C-terminal domain (CTD). The carboxy-terminal domain of RNA polymerase II typically consists of up to 52 repeats of the sequence Tyr-Ser-Pro-Thr-Ser-Pro-Ser. [ 32 ] The domain stretches from the core of the RNAPII enzyme to the exit channel, this placement is effective due to its inductions of "RNA processing reactions, through direct or indirect interactions with components of the RNA processing machinery". [ 33 ] The CTD domain does not exist in RNA Polymerase I or RNA Polymerase III. [ 3 ] The RNA Polymerase CTD was discovered first in the laboratory of C. J. Ingles at the University of Toronto and also in the laboratory of J Corden at Johns Hopkins University during the processes of sequencing the DNA encoding the RPB1 subunit of RNA polymerase from yeast and mice respectively. Other proteins often bind the C-terminal domain of RNA polymerase in order to activate polymerase activity. It is the protein domain that is involved in the initiation of transcription, the capping of the RNA transcript , and attachment to the spliceosome for RNA splicing . [ 13 ]
RNA Polymerase II exists in two forms unphosphorylated and phosphorylated, IIA and IIO respectively. [ 5 ] [ 3 ] The transition between the two forms facilitates different functions for transcription. The phosphorylation of CTD is catalyzed by one of the six general transcription factors , TFIIH . TFIIH serves two purposes: one is to unwind the DNA at the transcription start site and the other is to phosphorylate. The form polymerase IIA joins the preinitiation complex, this is suggested because IIA binds with higher affinity to the TBP ( TATA-box binding protein ), the subunit of the general transcription factor TFIID , than polymerase IIO form. The form polymerase IIO facilitates the elongation of the RNA chain. [ 5 ] The method for the elongation initiation is done by the phosphorylation of serine at position 5 (Ser5), via TFIIH. The newly phosphorylated Ser5 recruits enzymes to cap the 5' end of the newly synthesized RNA and the "3' processing factors to poly(A) sites". [ 33 ] Once the second serine is phosphorylated, Ser2, elongation is activated. In order to terminate elongation dephosphorylation must occur. Once the domain is completely dephosphorylated the RNAP II enzyme is "recycled" and catalyzes the same process with another initiation site. [ 33 ]
Oxidative DNA damage may block RNA polymerase II transcription and cause strand breaks. An RNA templated transcription-associated recombination process has been described that can protect against DNA damage. [ 34 ] During the G1/G0 stages of the cell cycle , cells exhibit assembly of homologous recombination factors at double-strand breaks within actively transcribed regions. It appears that transcription is coupled to repair of DNA double-strand breaks by RNA templated homologous recombination. This repair process efficiently and accurately rejoins double-strand breaks in genes being actively transcribed by RNA polymerase II. | https://en.wikipedia.org/wiki/RNA_polymerase_II |
In eukaryote cells, RNA polymerase III (also called Pol III ) is a protein that transcribes DNA to synthesize 5S ribosomal RNA , tRNA , and other small RNAs.
The genes transcribed by RNA Pol III fall in the category of "housekeeping" genes whose expression is required in all cell types and most environmental conditions. Therefore, the regulation of Pol III transcription is primarily tied to the regulation of cell growth and the cell cycle and thus requires fewer regulatory proteins than RNA polymerase II . Under stress conditions, however, the protein Maf1 represses Pol III activity. [ 1 ] Rapamycin is another Pol III inhibitor via its direct target TOR. [ 2 ]
The process of transcription (by any polymerase) involves three main stages:
Pol III is unusual (compared to Pol II) by requiring no control sequences upstream of the gene, instead normally relying on internal control sequences - sequences within the transcribed section of the gene (although upstream sequences are occasionally seen, e.g. U6 snRNA gene has an upstream TATA box as seen in Pol II Promoters).
There are three classes of Pol III initiation, corresponding to 5S rRNA, tRNA, and U6 snRNA initiation. In all cases, the process starts with transcription factors binding to control sequences and ends with TFIIIB ( T ranscription F actor for polymerase III B ) being recruited to the complex and assembling Pol III. TFIIIB consists of three subunits: TATA binding protein (TBP), a TFIIB-related factor ( BRF1 , or BRF2 for transcription of a subset of Pol III-transcribed genes in vertebrates), and a B-double-prime ( BDP1 ) unit. The overall architecture bears similarities to that of Pol II. [ 3 ]
Typical stages in 5S rRNA (also termed class I) gene initiation:
Typical stages in a tRNA (also termed class II) gene initiation:
Typical stages in a U6 snRNA (also termed class III) gene initiation (documented in vertebrates only):
TFIIIB remains bound to DNA following the initiation of transcription by Pol III, unlike bacterial σ factors and most of the basal transcription factors for Pol II transcription. This leads to a high rate of transcriptional reinitiation of Pol III-transcribed genes. One study conducted on Saccharomyces cerevisiae found the average rate of chain elongation was 21 to 22 nucleotides per second, with the fastest being 29 nucleotides per second. These rates were comparable to elongation rates of RNA polymerase II found by an in vivo study conducted on Drosophila. The analysis of the individual steps of RNA chain elongation depicted that adding U and A to U-terminated RNA chains was slow. [ 5 ]
Polymerase III terminates transcription at small polyUs stretch (5-6). In eukaryotes, a hairpin loop is not required, but may enhance termination efficiency in humans. [ 6 ] In Saccharomyces cerevisiae, it was found that termination of transcription occurred in the sequence T7GT6 and was progressive. The presence of transcripts with five, six, and seven U residues and the slow readthrough of the T7 stretch suggest that the incorporation of a single G into the RNA chain served to reset elongation rates either entirely or substantially. [ 5 ]
The types of RNAs transcribed from RNA polymerase III include: [ 7 ]
RNA polymerase III appears to be essential for homologous recombinational repair of DNA double-strand breaks . [ 10 ] RNA polymerase III catalyzes the formation of a transient RNA-DNA hybrid at double strand breaks, an essential intermediate step in homologous recombination mediated double-strand break repair. [ 10 ] This step protects the 3’ overhanging DNA strand from degradation. [ 10 ] After the transient RNA-DNA hybrid intermediate is formed, the RNA strand is replaced by the RAD51 protein, which then catalyzes the ssDNA invasion step of homologous recombination. | https://en.wikipedia.org/wiki/RNA_polymerase_III |
RNA polymerase II holoenzyme is a form of eukaryotic RNA polymerase II that is recruited to the promoters of protein -coding genes in living cells. [ 1 ] [ 2 ] It consists of RNA polymerase II , a subset of general transcription factors , and regulatory proteins known as SRB proteins [ clarification needed ] .
RNA polymerase II (also called RNAP II and Pol II ) is an enzyme found in eukaryotic cells. It catalyzes the transcription of DNA to synthesize precursors of mRNA and most snRNA and microRNA . [ 3 ] [ 4 ] In humans, RNAP II consists of seventeen protein molecules (gene products encoded by POLR2A-L, where the proteins synthesized from POLR2C , POLR2E , and POLR2F form homodimers).
General transcription factors (GTFs) or basal transcription factors are protein transcription factors that have been shown to be important in the transcription of class II genes to mRNA templates. [ 5 ] Many of them are involved in the formation of a preinitiation complex , which, together with RNA polymerase II , bind to and read the single-stranded DNA gene template. [ 6 ] The cluster of RNA polymerase II and various transcription factors is known as a basal transcriptional complex (BTC).
The preinitiation complex (PIC) is a large complex of proteins that is necessary for the transcription of protein-coding genes in eukaryotes and archaea . The PIC helps position RNA polymerase II over gene transcription start sites , denatures the DNA, and positions the DNA in the RNA polymerase II active site for transcription. [ 5 ]
The typical PIC is made up of six general transcription factors: TFIIA ( GTF2A1 , GTF2A2 ), TFIIB ( GTF2B ), B-TFIID ( BTAF1 , TBP ), TFIID ( BTAF1 , BTF3 , BTF3L4 , EDF1 , TAF1-15, 16 total), TFIIE , TFIIF , TFIIH and TFIIJ .
The construction of the polymerase complex takes place on the gene promoter . The TATA box is one well-studied example of a promoter element that occurs in approximately 10% of genes. It is conserved in many (though not all) model eukaryotes and is found in a fraction of the promoters in these organisms. The sequence TATA (or variations) is located at approximately 25 nucleotides upstream of the Transcription Start Point (TSP). In addition, there are also some weakly conserved features including the TFIIB-Recognition Element (BRE), approximately 5 nucleotides upstream (BRE u ) and 5 nucleotides downstream (BRE d ) of the TATA box. [ 7 ]
Although the sequence of steps involved in the assembly of the PIC can vary, in general, they follow step 1, binding to the promoter .
The formation of the preinitiation complex (PIC) is analogous to the mechanism seen in bacterial initiation. In bacteria, the sigma factor recognizes and binds to the promoter sequence. In eukaryotes , the transcription factors perform this role. [ 9 ]
Mediator is a multiprotein complex that functions as a transcriptional coactivator . The Mediator complex is required for the successful transcription of nearly all class II gene promoters in yeast. [ 11 ] It works in the same manner in mammals.
The mediator functions as a coactivator and binds to the C-terminal domain (CTD) of RNA polymerase II holoenzyme , acting as a bridge between this enzyme and transcription factors . [ 12 ]
The carboxy-terminal domain (CTD) of RNA polymerase II is that portion of the polymerase that is involved in the initiation of DNA transcription , the capping of the RNA transcript , and attachment to the spliceosome for RNA splicing . [ 13 ] The CTD typically consists of up to 52 repeats (in humans) of the sequence Tyr-Ser-Pro-Thr-Ser-Pro-Ser. [ 14 ] The carboxy-terminal repeat domain (CTD) is essential for life. Cells containing only RNAPII with none or only up to one-third of its repeats are inviable. [ 15 ]
The CTD is an extension appended to the C terminus of RPB1, the largest subunit of RNA polymerase II. It serves as a flexible binding scaffold for numerous nuclear factors, determined by the phosphorylation patterns on the CTD repeats. Each repeat contains an evolutionary conserved and repeated heptapeptide, Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7, which is subjected to reversible phosphorylations during each transcription cycle. [ 16 ] This domain is inherently unstructured yet evolutionarily conserved, and in eukaryotes it comprises from 25 to 52 tandem copies of the consensus repeat heptad. [ 15 ] As the CTD is frequently not required for general transcription factor (GTF)-mediated initiation and RNA synthesis, it does not form a part of the catalytic essence of RNAPII, but performs other functions. [ 16 ]
RNAPII can exist in two forms: RNAPII0, with a highly phosphorylated CTD, and RNAPIIA, with a nonphosphorylated CTD. [ 16 ] Phosphorylation occurs principally on Ser2 and Ser5 of the repeats, although these positions are not equivalent. The phosphorylation state changes as RNAPII progresses through the transcription cycle: The initiating RNAPII is form IIA, and the elongating enzyme is form II0. While RNAPII0 does consist of RNAPs with hyperphosphorylated CTDs, the pattern of phosphorylation on individual CTDs can vary due to differential phosphorylation of Ser2 versus Ser5 residues and/or to differential phosphorylation of repeats along the length of the CTD. [ 16 ] The PCTD (phosphoCTD of an RNAPII0) physically links pre-mRNA processing to transcription by tethering processing factors to elongating RNAPII, e.g., 5′-end capping, 3′-end cleavage, and polyadenylation . [ 16 ]
Ser5 phosphorylation (Ser5PO 4 ) near the 5′ ends of genes depends principally on the kinase activity of TFIIH (Kin28 in yeast ; CDK7 in metazoans ). [ 16 ] The transcription factor TFIIH is a kinase and will hyperphosphorylate the CTD of RNAP, and in doing so, causes the RNAP complex to move away from the initiation site. Subsequent to the action of TFIIH kinase, Ser2 residues are phosphorylated by CTDK-I in yeast ( CDK9 kinase in metazoans). Ctk1 (CDK9) acts in complement to phosphorylation of serine 5 and is, thus, seen in middle to late elongation.
CDK8 and cyclin C (CCNC) are components of the RNA polymerase II holoenzyme that phosphorylate the carboxy-terminal domain (CTD). CDK8 regulates transcription by targeting the CDK7 / cyclin H subunits of the general transcription initiation factor IIH ( TFIIH ), thereby providing a link between the mediator and the basal transcription machinery. [ 17 ]
The gene CTDP1 encodes a phosphatase that interacts with the carboxy-terminus of transcription initiation factor TFIIF , a transcription factor that regulates elongation as well as initiation by RNA polymerase II . [ 18 ]
Also involved in the phosphorylation and regulation of the RPB1 CTD is cyclin T1 ( CCNT1 ). [ 19 ] Cyclin T1 tightly associates and forms a complex with CDK9 kinase , both of which are involved in the phosphorylation and regulation.
TFIIF and FCP1 cooperate for RNAPII recycling. FCP1, the CTD phosphatase, interacts with RNA polymerase II. Transcription is regulated by the state of phosphorylation of a heptapeptide repeat. [ 20 ] The nonphosphorylated form, RNAPIIA, is recruited to the initiation complex, whereas the elongating polymerase is found with RNAPII0. RNAPII cycles during transcription. CTD phosphatase activity is regulated by two GTFs ( TFIIF and TFIIB ). The large subunit of TFIIF (RAP74) stimulates the CTD phosphatase activity, whereas TFIIB inhibits TFIIF-mediated stimulation. Dephosphorylation of the CTD alters the migration of the largest subunit of RNAPII (RPB1).
The carboxy-terminal domain is also the binding site of the cap-synthesizing and cap-binding complex. In eukaryotes, after transcription of the 5' end of an RNA transcript, the cap-synthesizing complex on the CTD will remove the gamma-phosphate from the 5'-phosphate and attach a GMP, forming a 5',5'-triphosphate linkage. The synthesizing complex falls off and the cap then binds to the cap-binding complex (CBC), which is bound to the CTD.
The 5'cap of eukaryotic RNA transcripts is important for binding of the mRNA transcript to the ribosome during translation, to the CTD of RNAP, and prevents RNA degradation.
The carboxy-terminal domain is also the binding site for spliceosome factors that are part of RNA splicing . These allow for the splicing and removal of introns (in the form of a lariat structure) during RNA transcription.
Major studies in which knockout of particular amino acids was achieved in the CTD have been carried out. The results indicate that RNA polymerase II CTD truncation mutations affect the ability to induce transcription of a subset of genes in vivo , and the lack of response to induction maps to the upstream activating sequences of these genes.
Several protein members of the BRCA1 -associated genome surveillance complex (BASC) associate with RNA polymerase II and play a role in transcription. [ 21 ]
The transcription factor TFIIH is involved in transcription initiation and DNA repair. MAT1 (for 'ménage à trois-1') is involved in the assembly of the CAK complex. CAK is a multisubunit protein that includes CDK7 , cyclin H ( CCNH ), and MAT1 . CAK is an essential component of the transcription factor TFIIH that is involved in transcription initiation and DNA repair .
The nucleotide excision repair (NER) pathway is a mechanism to repair damage to DNA. ERCC2 is involved in transcription-coupled NER and is an integral member of the basal transcription factor BTF2/TFIIH complex. ERCC3 is an ATP-dependent DNA helicase that functions in NER. It also is a subunit of basal transcription factor 2 (TFIIH) and, thus, functions in class II transcription. XPG ( ERCC5 ) forms a stable complex with TFIIH , which is active in transcription and NER. [ 22 ] ERCC6 encodes a DNA-binding protein that is important in transcription-coupled excision repair. ERCC8 interacts with Cockayne syndrome type B ( CSB ) protein, with p44 ( GTF2H2 ), a subunit of the RNA polymerase II transcription factor IIH, and ERCC6. It is involved in transcription-coupled excision repair.
Higher error ratios in transcription by RNA polymerase II are observed in the presence of Mn 2+ compared to Mg 2+ . [ 23 ]
The EDF1 gene encodes a protein that acts as a transcriptional coactivator by interconnecting the general transcription factor TATA element-binding protein ( TBP ) and gene-specific activators. [ 24 ]
TFIID and human mediator coactivator ( THRAP3 ) complexes (mediator complex, plus THRAP3 protein) assemble cooperatively on promoter DNA, from which they become part of the RNAPII holoenzyme.
The completed assembly of the holoenzyme with transcription factors and RNA polymerase II bound to the promoter forms the eukaryotic transcription initiation complex. Transcription in the archaea domain is similar to transcription in eukaryotes . [ 25 ]
Transcription begins with matching of NTPs to the first and second in the DNA sequence. This, like most of the remainder of transcription, is an energy -dependent process, consuming adenosine triphosphate (ATP) or other NTP.
After the first bond is synthesized, the RNA polymerase must clear the promoter. During this time, there is a tendency to release the RNA transcript and produce truncated transcripts. This is called abortive initiation and is common for both eukaryotes and prokaryotes. [ 26 ] Abortive initiation continues to occur until the σ factor rearranges, resulting in the transcription elongation complex (which gives a 35 bp-moving footprint). The σ factor is released before 80 nucleotides of mRNA are synthesized. [ 27 ] Once the transcript reaches approximately 23 nucleotides, it no longer slips and elongation can occur.
Due to the range of genes that Pol II transcribes, this is the polymerase that experiences the most regulation by a range of factors at each stage of transcription. It is also one of the most complex in terms of polymerase cofactors involved.
Initiation is regulated by many mechanisms. These can be separated into two main categories:
Protein interference is the process where in some signaling protein interacts, either with the promoter or with some stage of the partially constructed complex, to prevent further construction of the polymerase complex, so preventing initiation. In general, this is a very rapid response and is used for fine level, individual gene control and for 'cascade' processes for a group of genes useful under a specific conditions (for example, DNA repair genes or heat shock genes).
Chromatin structure inhibition is the process wherein the promoter is hidden by chromatin structure. Chromatin structure is controlled by post-translational modification of the histones involved and leads to gross levels of high or low transcription levels. See: chromatin , histone , and nucleosome .
These methods of control can be combined in a modular method, allowing very high specificity in transcription initiation control.
The largest subunit of Pol II (Rpb1) has a domain at its C-terminus called the CTD (C-terminal domain). This is the target of kinases and phosphatases . The phosphorylation of the CTD is an important regulation mechanism, as this allows attraction and rejection of factors that have a function in the transcription process. The CTD can be considered as a platform for transcription factors .
The CTD consists of repetitions of an amino acid motif, YSPTSPS, of which Serines and Threonines can be phosphorylated . The number of these repeats varies; the mammalian protein contains 52, while the yeast protein contains 26. Site-directed-mutagenesis of the yeast protein has found at least 10 repeats are needed for viability. There are many different combinations of phosphorylations possible on these repeats and these can change rapidly during transcription. The regulation of these phosphorylations and the consequences for the association of transcription factors plays a major role in the regulation of transcription.
During the transcription cycle, the CTD of the large subunit of RNAP II is reversibly phosphorylated. RNAP II containing unphosphorylated CTD is recruited to the promoter, whereas the hyperphosphorylated CTD form is involved in active transcription. Phosphorylation occurs at two sites within the heptapeptide repeat, at Serine 5 and Serine 2. Serine 5 phosphorylation is confined to promoter regions and is necessary for the initiation of transcription, whereas Serine 2 phosphorylation is important for mRNA elongation and 3'-end processing.
The process of elongation is the synthesis of a copy of the DNA into messenger RNA. RNA Pol II matches complementary RNA nucleotides to the template DNA by Watson-Crick base pairing . These RNA nucleotides are ligated, resulting in a strand of messenger RNA .
Unlike DNA replication, mRNA transcription can involve multiple RNA polymerases on a single DNA template and multiple rounds of transcription (amplification of particular mRNA), so many mRNA molecules can be rapidly produced from a single copy of a gene.
Elongation also involves a proofreading mechanism that can replace incorrectly incorporated bases. In eukaryotes, this may correspond with short pauses during transcription that allow appropriate RNA editing factors to bind. These pauses may be intrinsic to the RNA polymerase or due to chromatin structure.
RNA Pol II elongation promoters can be summarised in three classes:
As for initiation, protein interference, seen as the "drug/sequence-dependent arrest affected factors" and "RNA Pol II catalysis improving factors" provide a very rapid response and is used for fine level individual gene control. Elongation downregulation is also possible, in this case usually by blocking polymerase progress or by deactivating the polymerase.
Chromatin structure-oriented factors are more complex than for initiation control. Often the chromatin-altering factor becomes bound to the polymerase complex, altering the histones as they are encountered and providing a semi-permanent 'memory' of previous promotion and transcription.
Termination is the process of breaking up the polymerase complex and ending the RNA strand. In eukaryotes using RNA Pol II, this termination is very variable (up to 2000 bases), relying on post transcriptional modification.
Little regulation occurs at termination, although it has been proposed newly transcribed RNA is held in place if proper termination is inhibited, allowing very fast expression of genes given a stimulus. This has not yet been demonstrated in eukaryotes .
Active RNA Pol II transcription holoenzymes can be clustered in the nucleus, in discrete sites called transcription factories . There are ~8,000 such factories in the nucleoplasm of a HeLa cell , but only 100–300 RNAP II foci per nucleus in erythroid cells, as in many other tissue types. [ 28 ] The number of transcription factories in tissues is far more restricted than indicated by previous estimates from cultured cells. [ 28 ] As an active transcription unit is usually associated with only one Pol II holoenzyme, a polymerase II factory may contain on average ~8 holoenzymes. Colocalization of transcribed genes has not been observed when using cultured fibroblast-like cells. [ 29 ] Differentiated or committed tissue types have a limited number of available transcription sites. [ 28 ] Estimates show that erythroid cells express at least 4,000 genes, so many genes are obliged to seek out and share the same factory. [ 28 ]
The intranuclear position of many genes is correlated with their activity state. During transcription in vivo , distal active genes are dynamically organized into shared nuclear subcompartments and colocalize to the same transcription factory at high frequencies. [ 28 ] Movement into or out of these factories results in activation (On) or abatement (Off) of transcription, rather than by recruiting and assembling a transcription complex. [ 28 ] Usually, genes migrate to preassembled factories for transcription. [ 28 ]
An expressed gene is preferentially located outside of its chromosome territory , but a closely linked, inactive gene is located inside. [ 30 ]
RNA polymerase II holoenzyme stability determines the number of base pairs that can be transcribed before the holoenzyme loses its ability to transcribe. The length of the CTD is essential for RNA polymerase II stability. [ 31 ] RNA polymerase II stability has been shown to be regulated by post-translation proline hydroxylation. [ 32 ] The von Hippel–Lindau tumor suppressor protein (pVHL, human GeneID: 7428 [ 33 ] ) complex binds the hyperphosphorylated large subunit of the RNA polymerase II complex, in a proline hydroxylation- and CTD phosphorylation-dependent manner, targeting it for ubiquitination. [ 32 ] | https://en.wikipedia.org/wiki/RNA_polymerase_II_holoenzyme |
RNA silencing or RNA interference refers to a family of gene silencing effects by which gene expression is negatively regulated by non-coding RNAs such as microRNAs . RNA silencing may also be defined as sequence-specific regulation of gene expression triggered by double-stranded RNA ( dsRNA ). [ 1 ] RNA silencing mechanisms are conserved among most eukaryotes . [ 2 ] The most common and well-studied example is RNA interference ( RNAi ), in which endogenously expressed microRNA ( miRNA ) or exogenously derived small interfering RNA ( siRNA ) induces the degradation of complementary messenger RNA . Other classes of small RNA have been identified, including piwi-interacting RNA ( piRNA ) [ 3 ] and its subspecies repeat associated small interfering RNA ( rasiRNA ). [ 4 ]
RNA silencing describes several mechanistically related pathways which are involved in controlling and regulating gene expression. [ 5 ] [ 6 ] [ 7 ] RNA silencing pathways are associated with the regulatory activity of small non-coding RNAs (approximately 20–30 nucleotides in length) that function as factors involved in inactivating homologous sequences, promoting endonuclease activity, translational arrest, and/or chromatic or DNA modification. [ 8 ] [ 9 ] [ 10 ] In the context in which the phenomenon was first studied, small RNA was found to play an important role in defending plants against viruses. For example, these studies demonstrated that enzymes detect double-stranded RNA ( dsRNA ) not normally found in cells and digest it into small pieces that are not able to cause disease. [ 11 ] [ 12 ] [ 13 ] [ 14 ] [ 2 ]
While some functions of RNA silencing and its machinery are understood, many are not. For example, RNA silencing has been shown to be important in the regulation of development and in the control of transposition events. [ 15 ] RNA silencing has been shown to play a role in antiviral protection in plants as well as insects. [ 16 ] Also in yeast, RNA silencing has been shown to maintain heterochromatin structure. [ 17 ] However, the varied and nuanced role of RNA silencing in the regulation of gene expression remains an ongoing scientific inquiry. A range of diverse functions have been proposed for a growing number of characterized small RNA sequences—e.g., regulation of developmental, neuronal cell fate, cell death, proliferation, fat storage, haematopoietic cell fate, insulin secretion. [ 18 ]
RNA silencing functions by repressing translation or by cleaving messenger RNA ( mRNA ), depending on the amount of complementarity of base-pairing. RNA has been largely investigated within its role as an intermediary in the translation of genes into proteins. [ 19 ] More active regulatory functions, however, only began to be addressed by researchers beginning in the late-1990s. [ 20 ] The landmark study providing an understanding of the first identified mechanism was published in 1998 by Fire et al., [ 1 ] demonstrating that double-stranded RNA could act as a trigger for gene silencing. [ 20 ] Since then, various other classes of RNA silencing have been identified and characterized. [ 5 ] Presently, the therapeutic potential of these discoveries is being explored, for example, in the context of targeted gene therapy. [ 21 ] [ 22 ]
While RNA silencing is an evolving class of mechanisms, a common theme is the fundamental relationship between small RNAs and gene expression. [ 9 ] It has also been observed that the major RNA silencing pathways currently identified have mechanisms of action which may involve both post-transcriptional gene silencing (PTGS) [ 23 ] as well as chromatin-dependent gene silencing (CDGS) pathways. [ 5 ] CDGS involves the assembly of small RNA complexes on nascent transcripts and is regarded as encompassing mechanisms of action which implicate transcriptional gene silencing (TGS) and co-transcriptional gene silencing (CTGS) events. [ 24 ] This is significant at least because the evidence suggests that small RNAs play a role in the modulation of chromatin structure and TGS. [ 25 ] [ 26 ]
Despite early focus in the literature on RNA interference ( RNAi ) as a core mechanism which occurs at the level of messenger RNA translation, others have since been identified in the broader family of conserved RNA silencing pathways acting at the DNA and chromatin level. [ 27 ] RNA silencing refers to the silencing activity of a range of small RNAs and is generally regarded as a broader category than RNAi. While the terms have sometimes been used interchangeably in the literature, RNAi is generally regarded as a branch of RNA silencing. To the extent it is useful to craft a distinction between these related concepts, RNA silencing may be thought of as referring to the broader scheme of small RNA related controls involved in gene expression and the protection of the genome against mobile repetitive DNA sequences, retroelements, and transposons to the extent that these can induce mutations. [ 28 ] The molecular mechanisms for RNA silencing were initially studied in plants [ 13 ] but have since broadened to cover a variety of subjects, from fungi to mammals, providing strong evidence that these pathways are highly conserved. [ 29 ]
At least three primary classes of small RNA have currently been identified, namely: small interfering RNA ( siRNA ), microRNA ( miRNA ), and piwi-interacting RNA ( piRNA ).
siRNAs act in the nucleus and the cytoplasm and are involved in RNAi as well as CDGS. [ 5 ] siRNAs come from long dsRNA precursors derived from a variety of single-stranded RNA (ssRNA) precursors, such as sense and antisense RNAs. siRNAs also come from hairpin RNAs derived from transcription of inverted repeat regions. siRNAs may also arise enzymatically from non-coding RNA precursors. [ 30 ] The volume of literature on siRNA within the framework of RNAi is extensive. One of the potent applications of siRNAs is the ability to distinguish the target versus non-target sequence with a single-nucleotide difference. This approach has been considered as therapeutically crucial for the silencing dominant gain-of-function (GOF) disorders, where mutant allele causing disease is differed from wt-allele by a single nucleotide (nt). This type of siRNAs with capability to distinguish a single-nt difference are termed as allele-specific siRNAs. [ 31 ]
The majority of miRNAs act in the cytoplasm and mediate mRNA degradation or translational arrest. [ 32 ] However, some plant miRNAs have been shown to act directly to promote DNA methylation. [ 33 ] miRNAs come from hairpin precursors generated by the RNaseIII enzymes Drosha and Dicer . [ 34 ] Both miRNA and siRNA form either the RNA-induced silencing complex ( RISC ) or the nuclear form of RISC known as RNA-induced transcriptional silencing complex ( RITS ). [ 35 ] The volume of literature on miRNA within the framework of RNAi is extensive.
Three prime untranslated regions (3'UTRs) of messenger RNAs (mRNAs) often contain regulatory sequences that post-transcriptionally cause RNA interference. Such 3'-UTRs often contain both binding sites for microRNAs (miRNAs) as well as for regulatory proteins. By binding to specific sites within the 3'-UTR, miRNAs can decrease gene expression of various mRNAs by either inhibiting translation or directly causing degradation of the transcript. The 3'-UTR also may have silencer regions that bind repressor proteins that inhibit the expression of a mRNA.
The 3'-UTR often contains microRNA response elements (MREs) . MREs are sequences to which miRNAs bind. These are prevalent motifs within 3'-UTRs. Among all regulatory motifs within the 3'-UTRs (e.g. including silencer regions), MREs make up about half of the motifs.
As of 2014, the miRBase web site, [ 36 ] an archive of miRNA sequences and annotations, listed 28,645 entries in 233 biologic species. Of these, 1,881 miRNAs were in annotated human miRNA loci. miRNAs were predicted to have an average of about four hundred target mRNAs (affecting expression of several hundred genes). [ 37 ] Freidman et al. [ 37 ] estimate that >45,000 miRNA target sites within human mRNA 3'UTRs are conserved above background levels, and >60% of human protein-coding genes have been under selective pressure to maintain pairing to miRNAs.
Direct experiments show that a single miRNA can reduce the stability of hundreds of unique mRNAs. [ 38 ] Other experiments show that a single miRNA may repress the production of hundreds of proteins, but that this repression often is relatively mild (less than 2-fold). [ 39 ] [ 40 ]
The effects of miRNA dysregulation of gene expression seem to be important in cancer. [ 41 ] For instance, in gastrointestinal cancers, nine miRNAs have been identified as epigenetically altered and effective in down regulating DNA repair enzymes. [ 42 ]
The effects of miRNA dysregulation of gene expression also seem to be important in neuropsychiatric disorders, such as schizophrenia, bipolar disorder, major depression, Parkinson's disease, Alzheimer's disease and autism spectrum disorders. [ 43 ] [ 44 ] [ 45 ]
piRNAs represent the largest class of small non-coding RNA molecules expressed in animal cells, deriving from a large variety of sources, including repetitive DNA and transposons. [ 46 ] However, the biogenesis of piRNAs is also the least well understood. [ 47 ] piRNAs appear to act both at the post-transcriptional and chromatin levels. They are distinct from miRNA due to at least an increase in terms of size and complexity. Repeat associated small interfering RNA ( rasiRNAs ) are considered to be a subspecies of piRNA. [ 4 ]
The most basic mechanistic flow for RNA Silencing is as follows:
(For a more detailed explanation of the mechanism, refer to the RNAi:Cellular mechanism article.)
1: RNA with inverted repeats hairpin/panhandle constructs --> 2: dsRNA --> 3: miRNAs / siRNAs --> 4: RISC --> 5: Destruction of target mRNA
RNA silencing is the mechanism that our cells (and cells from all kingdoms ) use to fight RNA viruses and transposons (which originate from our own cells as well as from other vehicles). [ 2 ] In the case of RNA viruses, these get destroyed immediately by the mechanism cited above. In the case of transposons, it's a little more indirect. Since transposons are located in different parts of the genome, the different transcriptions from the different promoters produce complementary mRNAs that can hybridize with each other. When this happens, the RNAi machinery goes into action, debilitating the mRNAs of the proteins that would be required to move the transposons themselves. [ 48 ]
For a detailed explanation of the down-regulation of genes, see RNAi:downregulation of genes
For a detailed explanation of the up-regulation of genes, see RNAi:upregulation of genes
The same way that RNA silencing regulates downstream target mRNAs , RNA silencing itself is regulated. For example, silencing signals get spread between cells by a group of enzymes called RdRPs ( RNA-dependent RNA polymerases ) or RDRs. [ 2 ]
Growing understanding of small RNA gene-silencing mechanisms involving dsRNA-mediated sequence-specific mRNA degradation has directly impacted the fields of functional genomics, biomedicine, and experimental biology. The following section describes various applications involving the effects of RNA silencing. These include uses in biotechnology, therapeutics, and laboratory research. Bioinformatics techniques are also being applied to identify and characterize large numbers of small RNAs and their targets.
Artificial introduction of long dsRNAs or siRNAs has been adopted as a tool to inactivate gene expression, both in cultured cells and in living organisms. [ 2 ] Structural and functional resolution of small RNAs as the effectors of RNA silencing has had a direct impact on experimental biology. For example, dsRNA may be synthesized to have a specific sequence complementary to a gene of interest. Once introduced into a cell or biological system, it is recognized as exogenous genetic material and activates the corresponding RNA silencing pathway. This mechanism can be used to effect decreases in gene expression with respect to the target, useful for investigating loss of function for genes relative to a phenotype. That is, studying the phenotypic and/or physiologic effects of expression decreases can reveal the role of a gene product. The observable effects can be nuanced, such that some methods can distinguish between “knockdown” (decrease expression) and “knockout” (eliminate expression) of a gene. [ 49 ] RNA interference technologies have been noted recently as one of the most widely utilized techniques in functional genomics. [ 50 ] Screens developed using small RNAs have been used to identify genes involved in fundamental processes such as cell division, apoptosis and fat regulation.
Since at least the mid-2000s, there has been intensifying interest in developing short interfering RNAs for biomedical and therapeutic applications. [ 51 ] Bolstering this interest is a growing number of experiments which have successfully demonstrated the clinical potential and safety of small RNAs for combatting diseases ranging from viral infections to cancer as well as neurodegenerative disorders. [ 52 ] In 2004, the first Investigational New Drug applications for siRNA were filed in the United States with the Food and Drug Administration ; it was intended as a therapy for age-related macular degeneration . [ 50 ] RNA silencing in vitro and in vivo has been accomplished by creating triggers (nucleic acids that induce RNAi) either via expression in viruses or synthesis of oligonucleotides. [ 53 ] Optimistically many studies indicate that small RNA-based therapies may offer novel and potent weapons against pathogens and diseases where small molecule/pharmacologic and vaccine/biologic treatments have failed or proved less effective in the past. [ 51 ] However, it is also warned that the design and delivery of small RNA effector molecules should be carefully considered in order to ensure safety and efficacy.
The role of RNA silencing in therapeutics, clinical medicine, and diagnostics is a fast developing area and it is expected that in the next few years some of the compounds using this technology will reach market approval. A report has been summarized below to highlight the many clinical domains in which RNA silencing is playing an increasingly important role, chief among them are ocular and retinal disorders, cancer, kidney disorders, LDL lowering, and antiviral. [ 53 ] The following table displays a listing of RNAi based therapy currently in various phases of clinical trials. The status of these trials can be monitored on the ClinicalTrials.gov website, a service of the National Institutes of Health ( NIH ). [ 54 ] Of note are treatments in development for ocular and retinal disorders, that were among the first compounds to reach clinical development. AGN211745 (sirna027) (Allergan) and bevasiranib (Cand5) (Opko) underwent clinical development for the treatment of age-related macular degeneration, but trials were terminated before the compounds reached the market. Other compounds in development for ocular conditions include SYL040012 (Sylentis) and QPI-007 (Quark). SYL040012 (bamosinan) is a drug candidate under clinical development for glaucoma, a progressive optic neurdegeneration frequently associated to increased intraocular pressure; QPI-007 is a candidate for the treatment of angle-closure glaucoma and Non-arteritic anterior ischaemic optic neuropathy; both compounds are currently undergoing phase II clinical trials. Several compounds are also under development for conditions such as cancer and rare diseases.
As with conventional manufactured drugs, the main challenge in developing successful offshoots of the RNAi-based drugs is the precise delivery of the RNAi triggers to where they are needed in the body. The reason that the ocular macular degeneration antidote was successful sooner than the antidote with other diseases is that the eyeball is almost a closed system, and the serum can be injected with a needle exactly where it needs to be. The future successful drugs will be the ones who are able to land where needed, probably with the help of nanobots. Below is a rendition of a table [ 53 ] that shows the existing means of delivery of the RNAi triggers.
The scientific community has been quick to harness RNA silencing as a research tool. The strategic targeting of mRNA can provide a large amount of information about gene function and its ability to be turned on and off. Induced RNA silencing can serve as a controlled method for suppressing gene expression. Since the machinery is conserved across most eukaryotes, these experiments scale well to a range of model organisms. [ 55 ] In practice, expressing synthetic short hairpin RNAs can be used to reach stable knock-down. [ 56 ] If promoters can be made to express these designer short hairpin RNAs, the result is often potent, stable, and controlled gene knock-down in both in vitro and in vivo contexts. [ 57 ] Short hairpin RNA vector systems can be seen as roughly analogous in scope to using cDNA overexpression systems. [ 58 ] Overall, synthetic and natural small RNAs have proven to be an important tool for studying gene function in cells as well as animals. [ 59 ]
Bioinformatics approaches to identify small RNAs and their targets have returned several hundred, if not thousands of, small RNA candidates predicted to affect gene expression in plants, C. elegans, D. melanogaster, zebrafish, mouse, rat, and human. [ 60 ] These methods are largely directed to identifying small RNA candidates for knock-out experiments but may have broader applications. One bioinformatics approach evaluated sequence conservation criteria by filtering seed complementary target-binding sites. The cited study predicted that approximately one third of mammalian genes were to be regulated by, in this case, miRNAs. [ 61 ]
One aspect of RNA silencing to consider is its possible off-target affects, toxicity, and delivery methods. If RNA silencing is to become a conventional drug, it must first pass the typical ethical issues of biomedicine. [ 62 ] Using risk-benefit analysis, researchers can determine whether RNA silencing conforms to ethical ideologies such as nonmaleficence, beneficence, and autonomy. [ 63 ]
There is a risk of creating infection-competent viruses that could infect non-consenting people. [ 64 ] There is also a risk of affecting future generations based on these treatments. These two scenarios, in respect to autonomy, is possible unethical. At this moment, unsafe delivery methods and unintended aspects of vector viruses add to the argument against RNA silencing. [ 63 ]
In terms of off-target effects, siRNA can induce innate interferon responses, inhibit endogenous miRNAs through saturation, and may have complementary sequences to other non-target mRNAs. These off-targets could also have target up-regulations such as oncogenes and antiapoptotic genes. The toxicity of RNA silencing is still under review as there are conflicting reports. [ 63 ] [ 64 ] [ 65 ]
RNA silencing is quickly developing, because of that, the ethical issues need to be discussed further. With the knowledge of general ethical principles, we must continuously perform risk-benefit analysis. [ 63 ] | https://en.wikipedia.org/wiki/RNA_silencing |
An RNA spike-in is an RNA transcript of known sequence and quantity used to calibrate measurements in RNA hybridization assays , such as DNA microarray experiments , RT-qPCR , and RNA-Seq . [ 1 ]
A spike-in is designed to bind to a DNA molecule with a matching sequence , known as a control probe . [ 2 ] [ 3 ] [ 4 ] This process of specific binding is called hybridization . A known quantity of RNA spike-in is mixed with the experiment sample during preparation. [ 2 ] The degree of hybridization between the spike-ins and the control probes is used to normalize the hybridization measurements of the sample RNA. [ 2 ]
Nucleic acid hybridization assays have been used for decades to detect specific sequences of DNA or RNA, [ 5 ] with a DNA microarray precursor used as early as 1965. [ 6 ] In such assays, positive control oligonucleotides are necessary to provide a standard for comparison of target sequence concentration, and to check and correct for nonspecific binding ; that is, incidental binding of the RNA to non- complementary DNA sequences. [ 7 ] These controls became known as "spike-ins". [ 1 ] With the advent of DNA microarray chips in the 1990s [ 8 ] and the commercialization of high-throughput methods for sequencing and RNA detection assays, manufacturers of hybridization assay "kits" started to provide pre-developed spike-ins. [ 1 ] In the case of gene expression assay microarrays or RNA sequencing (RNA-seq), RNA spike-ins are used.
RNA spike-ins can be synthesized by any means of creating RNA synthetically , or by using cells to transcribe DNA to RNA in vivo (in cells). [ 1 ] RNA can be produced in vitro (cell free) using RNA polymerase and DNA with the desired sequence. [ 1 ] Large scale biotech manufacturers produce RNA synthetically via high-throughput techniques and provide solutions of RNA spike-ins at predetermined concentration. [ 1 ] Bacteria containing DNA (usually on plasmids ) for transcription to spike-ins are also commercially available. [ 1 ] The purified RNA can be stored long-term in a buffered solution at low temperature. [ 1 ]
DNA microarrays are solid surfaces, usually a small chip, to which short DNA polymers of known sequence are covalently bound . [ 6 ] When a sample of unknown RNA is flowed over the array, the RNA base pairs with and binds to complementary DNA . [ 6 ] Bound transcripts can be detected, indicating the presence of RNA with the corresponding sequence. [ 6 ] DNA microarray assays are useful in studies of gene expression , because many of the mRNA transcripts present in a cell can be detected at the same time. [ 6 ] RNA spike-ins of known quantity can provide a baseline signal for comparison with the signal from transcripts of unknown quantity, such that the data can be normalized within an array and between different arrays. [ 2 ]
RNA sequencing (RNA-Seq) is performed by reverse transcribing RNA to complementary DNA (cDNA) and high-throughput sequencing the cDNA. [ 9 ] Such high-throughput methods can be error prone, and known controls are necessary to detect and correct for levels of error. [ 9 ] RNA spike-in controls can provide a measure of sensitivity and specificity of an RNA-Seq experiment. [ 9 ] | https://en.wikipedia.org/wiki/RNA_spike-in |
RNA splicing is a process in molecular biology where a newly-made precursor messenger RNA (pre- mRNA ) transcript is transformed into a mature messenger RNA ( mRNA ). It works by removing all the introns (non-coding regions of RNA) and splicing back together exons (coding regions). For nuclear-encoded genes , splicing occurs in the nucleus either during or immediately after transcription . For those eukaryotic genes that contain introns, splicing is usually needed to create an mRNA molecule that can be translated into protein . For many eukaryotic introns, splicing occurs in a series of reactions which are catalyzed by the spliceosome , a complex of small nuclear ribonucleoproteins ( snRNPs ). There exist self-splicing introns , that is, ribozymes that can catalyze their own excision from their parent RNA molecule. The process of transcription, splicing and translation is called gene expression , the central dogma of molecular biology .
Several methods of RNA splicing occur in nature; the type of splicing depends on the structure of the spliced intron and the catalysts required for splicing to occur.
The word intron is derived from the terms intragenic region , [ 1 ] and intracistron , [ 2 ] that is, a segment of DNA that is located between two exons of a gene . The term intron refers to both the DNA sequence within a gene and the corresponding sequence in the unprocessed RNA transcript. As part of the RNA processing pathway, introns are removed by RNA splicing either shortly after or concurrent with transcription . [ 3 ] Introns are found in the genes of most organisms and many viruses. They can be located in a wide range of genes, including those that generate proteins , ribosomal RNA (rRNA), and transfer RNA (tRNA). [ 4 ]
Within introns, a donor site (5' end of the intron), a branch site (near the 3' end of the intron) and an acceptor site (3' end of the intron) are required for splicing. The splice donor site includes an almost invariant sequence GU at the 5' end of the intron, within a larger, less highly conserved region. The splice acceptor site at the 3' end of the intron terminates the intron with an almost invariant AG sequence. Upstream (5'-ward) from the AG there is a region high in pyrimidines (C and U), or polypyrimidine tract . Further upstream from the polypyrimidine tract is the branchpoint, which includes an adenine nucleotide involved in lariat formation. [ 5 ] [ 6 ] The consensus sequence for an intron (in IUPAC nucleic acid notation ) is: G-G-[cut]-G-U-R-A-G-U (donor site) ... intron sequence ... Y-U-R-A-C (branch sequence 20-50 nucleotides upstream of acceptor site) ... Y-rich-N-C-A-G-[cut]-G (acceptor site). [ 7 ] However, it is noted that the specific sequence of intronic splicing elements and the number of nucleotides between the branchpoint and the nearest 3' acceptor site affect splice site selection. [ 8 ] [ 9 ] Also, point mutations in the underlying DNA or errors during transcription can activate a cryptic splice site in part of the transcript that usually is not spliced. This results in a mature messenger RNA with a missing section of an exon. In this way, a point mutation , which might otherwise affect only a single amino acid, can manifest as a deletion or truncation in the final protein. [ citation needed ]
Splicing is catalyzed by the spliceosome , a large RNA-protein complex composed of five small nuclear ribonucleoproteins ( snRNPs ). Assembly and activity of the spliceosome occurs during transcription of the pre-mRNA. The RNA components of snRNPs interact with the intron and are involved in catalysis. Two types of spliceosomes have been identified (major and minor) which contain different snRNPs .
In most cases, splicing removes introns as single units from precursor mRNA transcripts. However, in some cases, especially in mRNAs with very long introns, splicing happens in steps, with part of an intron removed and then the remaining intron is spliced out in a following step. This has been found first in the Ultrabithorax ( Ubx ) gene of the fruit fly, Drosophila melanogaster , and a few other Drosophila genes, but cases in humans have been reported as well. [ 17 ] [ 18 ]
Trans-splicing is a form of splicing that removes introns or outrons , and joins two exons that are not within the same RNA transcript. [ 19 ] Trans-splicing can occur between two different endogenous pre-mRNAs or between an endogenous and an exogenous (such as from viruses) or artificial RNAs. [ 20 ]
Self-splicing occurs for rare introns that form a ribozyme , performing the functions of the spliceosome by RNA alone. There are three kinds of self-splicing introns, Group I , Group II and Group III . Group I and II introns perform splicing similar to the spliceosome without requiring any protein. This similarity suggests that Group I and II introns may be evolutionarily related to the spliceosome. Self-splicing may also be very ancient, and may have existed in an RNA world present before protein. [ citation needed ]
Two transesterifications characterize the mechanism in which group I introns are spliced: [ citation needed ]
The mechanism in which group II introns are spliced (two transesterification reaction like group I introns) is as follows:
tRNA (also tRNA-like) splicing is another rare form of splicing that usually occurs in tRNA. The splicing reaction involves a different biochemistry than the spliceosomal and self-splicing pathways.
In the yeast Saccharomyces cerevisiae , a yeast tRNA splicing endonuclease heterotetramer, composed of TSEN54 , TSEN2 , TSEN34 , and TSEN15 , cleaves pre-tRNA at two sites in the acceptor loop to form a 5'-half tRNA, terminating at a 2',3'-cyclic phosphodiester group, and a 3'-half tRNA, terminating at a 5'-hydroxyl group, along with a discarded intron. [ 21 ] Yeast tRNA kinase then phosphorylates the 5'-hydroxyl group using adenosine triphosphate . Yeast tRNA cyclic phosphodiesterase cleaves the cyclic phosphodiester group to form a 2'-phosphorylated 3' end. Yeast tRNA ligase adds an adenosine monophosphate group to the 5' end of the 3'-half and joins the two halves together. [ 22 ] NAD-dependent 2'-phosphotransferase then removes the 2'-phosphate group. [ 23 ] [ 24 ]
Splicing occurs in all the kingdoms or domains of life, however, the extent and types of splicing can be very different between the major divisions. Eukaryotes splice many protein-coding messenger RNAs and some non-coding RNAs . Prokaryotes , on the other hand, splice rarely and mostly non-coding RNAs. Another important difference between these two groups of organisms is that prokaryotes completely lack the spliceosomal pathway.
Because spliceosomal introns are not conserved in all species, there is debate concerning when spliceosomal splicing evolved. Two models have been proposed: the intron late and intron early models (see intron evolution ).
Spliceosomal splicing and self-splicing involve a two-step biochemical process. Both steps involve transesterification reactions that occur between RNA nucleotides. tRNA splicing, however, is an exception and does not occur by transesterification. [ 25 ]
Spliceosomal and self-splicing transesterification reactions occur via two sequential transesterification reactions. First, the 2'OH of a specific branchpoint nucleotide within the intron, defined during spliceosome assembly, performs a nucleophilic attack on the first nucleotide of the intron at the 5' splice site, forming the lariat intermediate . Second, the 3'OH of the released 5' exon then performs a nucleophilic attack at the first nucleotide following the last nucleotide of the intron at the 3' splice site, thus joining the exons and releasing the intron lariat. [ 26 ]
In many cases, the splicing process can create a range of unique proteins by varying the exon composition of the same mRNA. This phenomenon is then called alternative splicing . Alternative splicing can occur in many ways. Exons can be extended or skipped, or introns can be retained. It is estimated that 95% of transcripts from multiexon genes undergo alternative splicing, some instances of which occur in a tissue-specific manner and/or under specific cellular conditions. [ 27 ] Development of high throughput mRNA sequencing technology can help quantify the expression levels of alternatively spliced isoforms. Differential expression levels across tissues and cell lineages allowed computational approaches to be developed to predict the functions of these isoforms. [ 28 ] [ 29 ] Given this complexity, alternative splicing of pre-mRNA transcripts is regulated by a system of trans-acting proteins (activators and repressors) that bind to cis-acting sites or "elements" (enhancers and silencers) on the pre-mRNA transcript itself. These proteins and their respective binding elements promote or reduce the usage of a particular splice site. The binding specificity comes from the sequence and structure of the cis-elements, e.g. in HIV-1 there are many donor and acceptor splice sites. Among the various splice sites, ssA7, which is 3' acceptor site, folds into three stem loop structures, i.e. Intronic splicing silencer (ISS), Exonic splicing enhancer (ESE), and Exonic splicing silencer (ESSE3). Solution structure of Intronic splicing silencer and its interaction to host protein hnRNPA1 give insight into specific recognition. [ 30 ] However, adding to the complexity of alternative splicing, it is noted that the effects of regulatory factors are many times position-dependent. For example, a splicing factor that serves as a splicing activator when bound to an intronic enhancer element may serve as a repressor when bound to its splicing element in the context of an exon, and vice versa. [ 31 ] In addition to the position-dependent effects of enhancer and silencer elements, the location of the branchpoint (i.e., distance upstream of the nearest 3' acceptor site) also affects splicing. [ 8 ] The secondary structure of the pre-mRNA transcript also plays a role in regulating splicing, such as by bringing together splicing elements or by masking a sequence that would otherwise serve as a binding element for a splicing factor. [ 32 ] [ 33 ]
The location of pre-mRNA splicing is throughout the nucleus, and once mature mRNA is generated, it is transported to the cytoplasm for translation. In both plant and animal cells, nuclear speckles are regions with high concentrations of splicing factors. These speckles were once thought to be mere storage centers for splicing factors. However, it is now understood that nuclear speckles help concentrate splicing factors near genes that are physically located close to them. Genes located farther from speckles can still be transcribed and spliced, but their splicing is less efficient compared to those closer to speckles. Cells can vary their genomic positions of genes relative to nuclear speckles as a mechanism to modulate the expression of genes via splicing. [ 34 ]
The process of splicing is linked with HIV integration , as HIV-1 targets highly spliced genes. [ 35 ]
DNA damage affects splicing factors by altering their post-translational modification , localization, expression and activity. [ 36 ] Furthermore, DNA damage often disrupts splicing by interfering with its coupling to transcription . DNA damage also has an impact on the splicing and alternative splicing of genes intimately associated with DNA repair . [ 36 ] For instance, DNA damages modulate the alternative splicing of the DNA repair genes Brca1 and Ercc1 .
Splicing events can be experimentally altered [ 37 ] [ 38 ] by binding steric-blocking antisense oligos , such as Morpholinos or Peptide nucleic acids to snRNP binding sites, to the branchpoint nucleotide that closes the lariat, [ 39 ] or to splice-regulatory element binding sites. [ 40 ]
The use of antisense oligonucleotides to modulate splicing has shown great promise as a therapeutic strategy for a variety of genetic diseases caused by splicing defects. [ 41 ]
Recent studies have shown that RNA splicing can be regulated by a variety of epigenetic modifications, including DNA methylation and histone modifications. [ 42 ]
It has been suggested that one third of all disease-causing mutations impact on splicing . [ 31 ] Common errors include:
Although many splicing errors are safeguarded by a cellular quality control mechanism termed nonsense-mediated mRNA decay (NMD), [ 43 ] a number of splicing-related diseases also exist, as suggested above. [ 44 ]
Allelic differences in mRNA splicing are likely to be a common and important source of phenotypic diversity at the molecular level, in addition to their contribution to genetic disease susceptibility. Indeed, genome-wide studies in humans have identified a range of genes that are subject to allele-specific splicing.
In plants, variation for flooding stress tolerance correlated with stress-induced alternative splicing of transcripts associated with gluconeogenesis and other processes. [ 45 ]
In addition to RNA, proteins can undergo splicing. Although the biomolecular mechanisms are different, the principle is the same: parts of the protein, called inteins instead of introns, are removed. The remaining parts, called exteins instead of exons, are fused together.
Protein splicing has been observed in a wide range of organisms, including bacteria, archaea , plants, yeast and humans. [ 46 ]
The existence of backsplicing was first suggested in 2012. [ 47 ] This backsplicing explains the genesis of circular RNAs resulting from the exact junction between the 3' boundary of an exon with the 5' boundary of an exon located upstream. [ 48 ] In these exonic circular RNAs, the junction is a classic 3'-5'link.
The exclusion of intronic sequences during splicing can also leave traces, in the form of circular RNAs. [ 49 ] In some cases, the intronic lariat is not destroyed and the circular part remains as a lariat-derived circRNA [ 50 ] .In these lariat-derived circular RNAs, the junction is a 2'-5'link. | https://en.wikipedia.org/wiki/RNA_splicing |
RNA therapeutics are a new class of medications based on ribonucleic acid (RNA) . Research has been working on clinical use since the 1990s, with significant success in cancer therapy in the early 2010s. [ 1 ] In 2020 and 2021, mRNA vaccines have been developed globally for use in combating the coronavirus disease (COVID-19 pandemic). [ 2 ] The Pfizer–BioNTech COVID-19 vaccine was the first mRNA vaccine approved by a medicines regulator , followed by the Moderna COVID-19 vaccine , and others.
The main types of RNA therapeutics are those based on messenger RNA (mRNA), antisense RNA (asRNA), RNA interference (RNAi), RNA activation (RNAa) and RNA aptamers . Of the four types, mRNA-based therapy is the only type which is based on triggering synthesis of proteins within cells, making it particularly useful in vaccine development. [ 3 ] Antisense RNA is complementary to coding mRNA and is used to trigger mRNA inactivation to prevent the mRNA from being used in protein translation. [ 4 ] RNAi-based systems use a similar mechanism, and involve the use of both small interfering RNA (siRNA) and micro RNA (miRNA) to prevent mRNA translation and/or degrade mRNA. [ 5 ] [ 6 ] Small activating RNA (saRNA) represents a novel class of RNA therapeutics that upregulates gene expression via the RNAa mechanism, offering a unique mechanism compared to other RNA-based therapies. [ 7 ] However, RNA aptamers are short, single stranded RNA molecules produced by directed evolution to bind to a variety of biomolecular targets with high affinity thereby affecting their normal in vivo activity. [ 8 ] [ 9 ] [ 10 ]
RNA is synthesized from template DNA by RNA polymerase with messenger RNA (mRNA) serving as the intermediary biomolecule between DNA expression and protein translation . Because of its unique properties (such as its typically single-stranded nature and its 2' OH group) and its ability to adopt many different secondary/tertiary structures, both coding and noncoding RNAs have attracted attention in medicine. Research has begun to explore RNAs potential to be used for therapeutic benefit, and unique challenges have occurred during drug discovery and implementation of RNA therapeutics. [ 11 ]
Messenger RNA ( mRNA ) is a single-stranded RNA molecule that is complementary to one of the DNA strands of a gene . [ 12 ] An mRNA molecule transfers a portion of the DNA code to other parts of the cell for making proteins. [ 13 ] DNA therapeutics needs access to the nucleus to be transcribed into RNA, and its functionality depends on nuclear envelope breakdown during cell division. However, mRNA therapeutics do not need to enter into the nucleus to be functional since it will be translated immediately once it has reached to the cytoplasm . [ 14 ] Moreover, unlike plasmids and viral vectors , mRNAs do not integrate into the genome and therefore do not have the risk of insertional mutagenesis , [ 15 ] making them suitable for use in cancer vaccines, tumor immunotherapy and infectious disease prevention. [ 16 ]
In 1953, Alfred Day Hershey reported that soon after infection with phage , bacteria produced a form of RNA at a high level and this RNA was also broken down rapidly. [ 17 ] However, the first clear indication of mRNA was from the work of Elliot Volkin and Lazarus Astrachan in 1956 by infecting E.coli with T2 bacteriophages and putting them into the medium with 32 P . [ 18 ] [ 19 ] They found out that the protein synthesis of E.coli was stopped and phage proteins were synthesized. [ 20 ] Then, in May 1961, their collaborated researchers Sydney Brenner, François Jacob, and Jim Watson announced the isolation of mRNA. [ 21 ] [ 22 ] For a few decades after mRNA discovery, people focused on understanding the structural, functional, and metabolism pathway aspects of mRNAs. However, in 1990, Jon A. Wolff demonstrated the idea of nucleic acid-encoded drugs by direct injecting in vitro transcribed (IVT) mRNA or plasmid DNA (pDNA) into the skeletal muscle of mice which expressed the encoded protein in the injected muscle. [ 23 ] [ 24 ] [ 25 ]
Once IVT mRNA has reached the cytoplasm, the mRNA is translated instantly. Thus, it does not need to enter the nucleus to be functional. [ 26 ] Also, it does not integrate into the genome and therefore does not have the risk of insertional mutagenesis. [ 27 ] Moreover, IVT mRNA is only transiently active and is completely degraded via physiological metabolic pathways. [ 28 ] Due to these reasons, IVT mRNA has undergone extensive preclinical investigation.
In vitro transcription (IVT) is performed on a linearized DNA plasmid template containing the targeted coding sequence. Then, naked mRNA or mRNA complexed in a nanoparticle will be delivered systemically or locally. Subsequently, a part of the exogenous naked mRNA or complexed mRNA will go through cell-specific mechanisms. Once in the cytoplasm, the IVT mRNA is translated by the protein synthesis machinery. [ 29 ] [ 30 ]
There are two identified RNA sensors, toll-like receptors (TLRs) and the RIG-I-like receptor family. TLRs are localized in the endosomal compartment of cells, such as DCs and macrophages. [ 31 ] RIG-I-like family is as a pattern recognition receptor (PRR). [ 32 ] However, the immune response mechanisms and process of mRNA vaccine recognition by cellular sensors and the mechanism of sensor activation are still unclear. [ 30 ]
In 1995, Robert Conry demonstrated that intramuscular injection of naked RNA encoding carcinoembryonic antigen elicited antigen-specific antibody responses. [ 33 ] Then, it was elaborated by demonstrating that dendritic cells (DCs) exposed to mRNA coding for specific antigens or to total mRNA extracted from tumor cells and injected into tumor-bearing mice induced T cell immune responses and inhibited the growth of tumors. [ 34 ] Then, researchers started to approach mRNA transfected DCs using vaccines based on ex vivo IVT mRNA-transfected DCs. [ 35 ] Meanwhile, Argos Therapeutics had initiated a Phase III clinical trial using DCs with advanced renal cell carcinoma in 2015 (NCT01582672) but it was terminated due to the lack of efficacy. [ 36 ]
For further application, IVT mRNA was optimized for in situ transfections of DCs in vivo . It improved the translation efficiency and stability of IVT mRNA and enhanced the presentation of the mRNA-encoded antigen on MHC class I and II molecules. [ 37 ] [ 38 ] Then, they found out that the direct injection of naked IVT mRNA into lymph nodes was the most effective way to induce T cell responses. [ 39 ] Based on this discovery, first-in-human testing of the injection of naked IVT mRNA encoding cancer antigens by BioNTech has started with patients with melanoma (NCT01684241). [ 40 ]
Recently, the new cancer immunotherapy, the combining of self-delivering RNA(sd-rxRNA) and adoptive cell transfer (ACT) therapy, was invented by RXi Pharmaceuticals and the Karolinska Institute . In this therapy, the sd-rxRNA eliminated the expression of immunosuppressive receptors and proteins in therapeutic immune cells so it improved the ability of immune cells to destroy the tumor cells. Then, the PD-1 targeted sd-rxRNA helped increasing the anti-tumor activity of tumor-infiltrating lymphocytes (TIL) against melanoma cells. [ 41 ] [ 42 ] Based on this idea, the mRNA-4157 has been tested and passed phase I clinical trial. [ 43 ]
Cytosolic nucleic acid-sensing pathways can enhance immune response to cancer. RIG-I agonist, stem loop RNA (SLR) 14. Tumor growth was significantly delayed and extended survival in mice. SLR14 improved antitumor efficacy of anti- PD1 antibody over single-agent treatment. SLR14 was absorbed by CD11b+ myeloid cells in the tumor microenvironment . Genes associated with immune defense were significantly up-regulated, along with increased CD8+ T lymphocytes , NK cells , and CD11b+ cells. SLR14 inhibited nonimmunogenic B16 tumor growth, leaving immune memory. [ 44 ]
In 1993, the first success of an mRNA vaccine was reported in mice , by using liposome -encapsulated IVT mRNA which is encoding the nucleoprotein of influenza that induced virus-specific T cells. [ 45 ] Then, IVT mRNA was formulated with synthetic lipid nanoparticles and it induced protective antibody responses against the respiratory syncytial virus (RSV) and influenza virus in mice. [ 46 ]
There are a few different types of IVT mRNA-based vaccine development for infectious diseases. One of the successful types is using self-amplifying IVT mRNA that has sequences of positive-stranded RNA viruses. It was originally developed for a flavivirus and it was workable with intradermal injection. One of the other ways is injecting a two-component vaccine which is containing an mRNA adjuvant and naked IVT mRNA encoding influenza hemagglutinin antigen only or in combination with neuraminidase encoding IVT mRNA. [ 47 ]
For example, for the HIV treatment, vaccines are using DCs transfected with IVT mRNA that is encoding HIV proteins. There are a few phase I and II clinical trials using IVT mRNA encoding combinations and it shows that antigen-specific CD8+ and CD4+ T cell responses can be induced. However, no antiviral effects have been observed in the clinical trial. [ 48 ] [ 49 ]
One of the other mRNA vaccines is for COVID-19 . The Severe Acute Respiratory Syndrome CoronaVirus 2 ( SARS-CoV-2 ) outbreaks in December 2019 and spread all over the world, causing a pandemic of respiratory illness designated coronavirus disease 2019 (COVID-19). [ 50 ] The Moderna COVID-19 vaccine , manufactured by Moderna since 2020, is a lipid nanoparticle (LNP) encapsulated mRNA-based vaccine that encodes for a full-length, prefusion stabilized spike(S)-2P antigen of SARS-CoV-2 with a transmembrane anchor. [ 51 ] [ 52 ]
In 2021, SLR14 was reported to prevent infection in the lower respiratory tract and severe disease in an interferon type I (IFN-I)–dependent manner in mice. Immunodeficient mice with chronic SARS-CoV-2 infection experienced near-sterilizing innate immunity with no help from the adaptive immune system . [ 53 ]
A 2022 study by researchers from the Mayo Clinic , Maastricht University , and Ethris GmBH, a biotech company that focuses on RNA therapeutics, found that chemically modified mRNA encoding BMP-2 promoted dosage-dependent healing of femoral osteotomies in male rats. The mRNA molecules were complexed within nonviral lipid particles , loaded onto sponges, and surgically implanted into the bone defects. They remained localized around the site of application. Compared to receiving rhBMP-2 directly, bony tissues regenerated after mRNA treatment displayed superior strength and less formation of massive callus. [ 54 ]
There are many challenges for the successful translation of mRNA into drugs because mRNA is a very large and heavy molecule(10^5 ~ 10^6 Da). Moreover, mRNA is unstable and easily degraded by nucleases, and it also activates the immune systems. [ 55 ] Furthermore, mRNA has a high negative charge density and it reduces the permeation of mRNA across cellular membranes. [ 56 ] Due to these reasons, without the appropriate delivery system, mRNA is degraded easily and the half-life of mRNA without a delivery system is only around 7 hours. [ 57 ] Even though some degrees of challenges could be overcome by chemical modifications , delivery of mRNA remains an obstacle. The methods that have been researched to improve the delivery system of mRNA are using microinjection , RNA patches (mRNA loaded in a dissolving micro-needle), gene gun , protamine condensation, RNA adjuvants , and encapsulating mRNA in nanoparticles with lipids. [ 55 ] [ 58 ] [ 59 ]
Even though In Vitro Translated (IVT) mRNA with delivery agents showed improved resistance against degradation, it needs more studies on how to improve the efficiency of the delivery of naked mRNA in vivo . [ 24 ]
Antisense RNA is the non-coding and single-stranded RNA that is complementary to a coding sequence of mRNA. It inhibits the ability of mRNA to be translated into proteins. [ 65 ] Short antisense RNA transcripts are produced within the nucleus by the action of the enzyme Dicer, which cleaves double-stranded RNA precursors into 21–26 nucleotide long RNA species. [ 4 ]
There is an antisense-based discovery strategy, rationale and design of screening assays, and the application of such assays for screening of natural product extracts and the discovery of fatty acid condensing enzyme inhibitors. [ 66 ] Antisense RNA is used for treating cancer and inhibition of metastasis and vectors for antisense sequestration. Particularly MicroRNAs (miRs) 15 and 16 to a patient in need of the treatment for diagnosis and prophylaxis of cancer. [ 67 ] Antisense drugs are based on the fact that antisense RNA hybridizes with and inactivates mRNA. These drugs are short sequences of RNA that attach to mRNA and stop a particular gene from producing the protein for which it encodes. Antisense drugs are being developed to treat lung cancer, diabetes and diseases such as arthritis and asthma with a major inflammatory component. [ 68 ] It shows that the decreased expression of MLLT4 antisense RNA 1 (MLLT4‑AS1) is a potential biomarker and a predictor of a poor prognosis for gastric cancer. So far, applications of antisense RNAs in antivirus and anticancer treatments and in regulating the expression of related genes in plants and microorganisms have been explored. [ 69 ] [ 70 ]
Non-viral vectors, virus vectors and liposomes have been used to deliver the antisense RNA through the cell membrane into the cytoplasm and nucleus. [ citation needed ] It has been found that the viral vector based delivery is the most advantageous among different delivery systems because it has a high transfection efficacy. [ 71 ] However, it is difficult to deliver antisense RNA only to the targeted sites. Also, due to the size and the stability issues of antisense RNA, there are some limitations to its use. To improve the delivery issues, chemical modifications, and new oligonucleotide designs have been studied to enhance the drug distribution, side effects, and tolerability. [ 72 ] [ 73 ]
Interfering RNA are a class of short, noncoding RNA that act to translationally or post-translationally repress gene expression. [ 74 ] [ 5 ] Their discovery and subsequent identification as key effectors of post-transcriptional gene regulation have made small interfering RNA ( siRNA ) and micro RNA ( miRNA ) potential therapeutics for systemic diseases. [ 74 ] [ 5 ] [ 75 ] The RNAi system was originally discovered in 1990 by Jorgensen et al., who were doing research involving the introduction of coloration genes into petunias, [ 75 ] [ 76 ] and it is thought that this system originally developed as a means of innate immunity against double-stranded RNA viruses. [ 77 ]
Small interfering ( siRNA ) are short, 19-23 base-pair (with a 3' overhang of two nucleotides), double-stranded pieces of RNA that participate in the RNA-induced silencing complex (RISC) for gene silencing. [ 5 ] [ 75 ] Specifically, siRNA is bound by the RISC complex where it is unwound using ATP hydrolysis. [ 75 ] [ 78 ] [ 79 ] It is then used as a guide by the enzyme "Slicer" to target mRNAs for degradation based on complementary base-pairing to the target mRNA. [ 75 ] [ 78 ] [ 79 ] As a therapeutic, siRNA is able to be delivered locally, through the eye or nose, to treat various diseases. [ 5 ] Local delivery benefits from simple formulation and drug delivery and high bioavailability of the drug. [ 5 ] Systemic delivery is necessary to target cancers and other diseases. [ 5 ] Targeting the siRNA when delivered locally is one of the main challenges in siRNA therapeutics. [ 5 ] While it is possible to use intravenous injection to deliver siRNA therapies, concerns have been raised about the large volumes used in the injection, as these must often be ~20-30% of the total blood volume. [ 75 ] Other methods of delivery include liposome packaging, conjugation to membrane-permeable peptides , and direct tissue/organ electroporation . [ 75 ] Additionally, it has been found that exogeneous siRNAs only last a few days (a few weeks at most in non-dividing cells) in vivo . [ 80 ] [ 81 ] If siRNA is able to successfully reach its target, it has the potential to therapeutically regulate gene expression through its ability to base-pair to mRNA targets and promote their degradation through the RISC system [ 5 ] [ 75 ] Currently, siRNA-based therapy is in a phase I clinical trial for the treatment of age-related macular degeneration , [ 75 ] although it is also being explored for use in cancer therapy. For instance, siRNA can be used to target mRNAs that code for proteins that promote tumor growth such as the VEGF receptor and telomerase enzyme. [ 75 ]
Micro RNAs ( miRNAs ) are short, ~19-23 base pair long RNA oligonucleotides that are involved in the microRNA-induced silencing complex. [ 75 ] [ 6 ] Specifically, once loaded onto the ARGONAUTE enzyme, miRNAs work with mRNAs to repress translation and post-translationally destabilize mRNA . [ 6 ] While they are functionally similar to siRNAs, miRNAs do not require extensive base-pairing for mRNA silencing (can require as few as seven base-pairs with target), [ 82 ] [ 83 ] thus allowing them to broadly affect a wider range of mRNA targets. [ 84 ] In the cell, miRNA uses switch, tuning, and neutral interactions to finely regulate gene repression. [ 6 ] As a therapeutic, miRNA has the potential to affect biochemical pathways throughout the organism. [ 74 ]
With more than 400 miRNA identified in humans, discerning their target gene for repression is the first challenge. [ 6 ] Multiple databases have been built, for example TargetScan , using miRNA seed matching. [ 74 ] In vitro assays assist in determining the phenotypic effects of miRNAs, [ 74 ] but due to the complex nature of gene regulation not all identified miRNAs have the expected effect. [ 6 ] Additionally, several miRNAs have been found to act as either tumor suppressors or oncogenes in vivo , such as the oncogenic miR-155 and miR-17-92. [ 84 ]
In clinical trials , miRNA are commonly used as biomarkers for a variety of diseases, potentially providing earlier diagnosis as well as disease progression, stage, and genetic links. [ 74 ] Phase 1 and 2 trials currently test miRNA mimics (to express genes) and miRNA (to repress genes) in patients with cancers and other diseases. [ 74 ] In particular, mimic miRNAs are used to introduce miRNAs that act as tumor suppressors into cancerous tissues, while miRNA antagonists are used to target oncogenic miRNAs to prevent their cancer-promoting activity. [ 84 ] Therapeutic miRNA is also used in addition to common therapies (such as cancer therapies) that are known to overexpress or destabilize the patient miRNA levels. [ 74 ] An example of one mimic miRNA therapy that demonstrated efficacy in impeding lung cancer tumor growth in mouse studies is miR-34a. [ 84 ] [ 85 ]
One concerning aspect of miRNA-based therapies is the potential for the exogeneous miRNA to affect miRNA silencing mechanisms within normal body cells, thereby affecting normal cellular biochemical pathways. [ 84 ] However, in vivo studies have indicated that miRNAs display little to no effect in non-target tissues/organs. [ 85 ] [ 86 ]
Small activating RNAs (saRNAs) are short double-stranded RNA molecules (typically 19–21 nucleotides in length) that induce transcriptional activation of target genes through a process known as RNA activation (RNAa). [ 7 ] Unlike RNA interference (RNAi), which silences gene expression, saRNAs upregulate gene expression by targeting promoter regions of DNA and recruiting transcriptional machinery. [ 87 ]
The mechanism of RNAa involves the formation of an RNA-induced transcriptional activation (RITA) complex. This complex includes Argonaute proteins (particularly Ago2), RNA helicase A (RHA), and other transcriptional coactivators, which facilitate the activation of RNA polymerase II at the targeted promoter. This process is often associated with epigenetic changes, such as histone modifications, that promote active transcription. [ 87 ]
saRNAs have demonstrated potential in preclinical studies for treating diseases caused by insufficient gene expression, such as cancer and metabolic disorders. For example, saRNAs have been used to reactivate tumor suppressor genes in cancer cells, offering a promising therapeutic approach. [ 88 ] Additionally, saRNAs are being explored for their ability to upregulate genes involved in metabolic regulation, neurodegenerative diseases, and other conditions. [ 89 ]
An example of an saRNA therapeutic in clinical development is MTL-CEBPA, which targets the CEBPA gene to treat liver cancer. This drug, developed by MiNA Therapeutics, has shown promise in early-phase clinical trials. [ 90 ] Another saRNA therapeutic, RAG-01, developed by Ractigen Therapeutics, is being investigated for the treatment of non-muscle invasive bladder cancer (NMIBC) [ 91 ] and has shown promising early complete responses (CRs) in Phase I trial for BCG-unresponsive patients. [ 92 ]
saRNAs represent a significant advancement in RNA therapeutics, expanding the scope of RNA-based therapies to include gene activation in addition to gene silencing. [ 7 ]
Broadly, aptamers are small molecules composed of either single-stranded DNA or RNA and are typically 20-100 nucleotides in length, [ 8 ] [ 9 ] [ 94 ] or ~3-60 kDa . [ 94 ] [ 95 ] Because of their single-stranded nature, aptamers are capable of forming many secondary structures, including pseudoknots , stem loops, and bulges, through intra-strand base pairing interactions. [ 94 ] The combinations of secondary structures present in an aptamer confer it a particular tertiary structure which in turn dictates the specific target the aptamer will selectively bind to. [ 94 ] [ 96 ] Because of the selective binding ability of aptamers, they are considered a promising biomolecule for use in pharmaceuticals. [ 8 ] [ 9 ] [ 94 ] Additionally, aptamers exhibit tight binding to targets, with dissociation constants often in the pM to nM range. [ 8 ] [ 10 ] Besides their strong binding ability, aptamers are also valued because they can be used on targets that are not capable of being bound by small peptides generated by phage display or by antibodies , and they are able to differentiate between conformational isomers and amino acid substitutions. [ 94 ] [ 97 ] [ 98 ] Also, because aptamers are nucleic-acid based, they can be directly synthesized, eliminating the need for cell-based expression and extraction as is the case in antibody production. [ 9 ] [ 99 ] RNA aptamers in particular are capable of producing a myriad of different structures, leading to speculations that they are more discriminating in their target affinity compared to DNA aptamers. [ 94 ] [ 100 ]
Aptamers were originally discovered in 1990 when Lary Gold and Craig Tuerk utilized a method of directed evolution known as SELEX to isolate a small single stranded RNA molecule that was capable of binding to T4 bacteriophage DNA polymerase. [ 9 ] [ 101 ] Additionally, the term “aptamer” was coined by Andrew Ellington, who worked with Jack Szostak to select an RNA aptamer that was capable of tight binding to certain organic dye molecules. [ 94 ] [ 102 ] The term itself is a conglomeration of the Latin “aptus” or “to fit” and the Greek “meros” or “part." [ 94 ] [ 102 ]
RNA aptamers are not so much “created” as “selected.” To develop an RNA aptamer capable of selective binding to a molecular target, a method known as Systematic Evolution of Ligands by EXponential Enrichment (SELEX) is used to isolate a unique RNA aptamer from a pool of ~10^13 to 10^16 different aptamers, otherwise known as a library. [ 8 ] [ 9 ] [ 94 ] [ 101 ] [ 102 ] The library of potential aptamer oligonucleotides is then incubated with a non-target species so as to remove aptamers that exhibit non-specific binding. [ 8 ] After subsequent removal of the non-specific aptamers, the remaining library members are then exposed to the desired target, which can be a protein, peptide, cell type, or even an organ (in the case of live animal-based SELEX). [ 8 ] [ 94 ] [ 103 ] [ 104 ] [ 105 ] [ 106 ] [ 107 ] [ 108 ] From there, the RNA aptamers which were bound to the target are transcribed to cDNA which then is amplified through PCR , and the PCR products are then re-transcribed to RNA. [ 94 ] These new RNA transcripts are then used to repeat the selection cycle many times, thus eventually producing a homogeneous pool of RNA aptamers capable of highly specific, high-affinity target binding. [ 8 ]
RNA aptamers can be designed to act as antagonists , agonists , or so-called ”RNA decoy aptamers." [ 94 ] [ 109 ] In the case of antagonists, the RNA aptamer is used either to prevent binding of a certain protein to its cell membrane receptor or to prevent the protein from performing its activity by binding to the protein's target. [ 94 ] Currently, the only RNA aptamer-based therapies that have advanced to clinical trials act as antagonists. [ 94 ] When RNA aptamers are designed to act as agonists, they promote immune cell activation as a co-stimulatory molecule, thus aiding in the mobilization of the body's own defense system. [ 94 ] [ 110 ] For RNA decoy aptamers, the synthetic RNA aptamer resembles a native RNA molecule. [ 94 ] [ 109 ] As such, proteins(s) which bind to the native RNA target instead bind to the RNA aptamer, possibly interfering with the biomolecular pathway of a particular disease. [ 94 ] [ 109 ] In addition to their utility as direct therapeutic agents, RNA aptamers are also being considered for other therapeutic roles. For instance, by conjugating the RNA aptamer to a drug compound, the RNA aptamer can act as a targeted delivery system for that drug. [ 8 ] Such RNA aptamers are known as ApDCs. [ 8 ] Additionally, through conjugation to radioisotope or a fluorescent dye molecule, RNA aptamers may be useful in diagnostic imaging. [ 8 ] [ 111 ] [ 112 ]
Because of the SELEX process utilized to select RNA aptamers, RNA aptamers can be generated for many potential targets. By directly introducing the RNA aptamers to the target during SELEX, a very selective, high-affinity, homogeneous pool of RNA aptamers can be produced. As such, RNA aptamers can be made to target small peptides and proteins, as well as cell fragments, whole cells, and even specific tissues. [ 8 ] [ 94 ] [ 113 ] [ 114 ] [ 106 ] [ 115 ] Examples of RNA aptamer molecular targets and potential targets include vascular endothelial growth factor , [ 116 ] osteoblasts , [ 117 ] and C-X-C Chemokine Ligand 12 ( CXCL2 ). [ 8 ] [ 9 ] [ 118 ]
An example of an RNA aptamer therapy includes Pegaptanib (aka Macugen ® ), the only FDA-approved RNA aptamer treatment. [ 8 ] [ 9 ] [ 94 ] Originally approved in 2004 to treat age-related macular degeneration , Pegaptanib is a 28 nucleotide RNA aptamer that acts as a VEGF antagonist. [ 8 ] [ 9 ] [ 94 ] However, it is not as effective as antibody-based treatments such as bevacizumab and ranibizumab . [ 94 ] [ 119 ] [ 120 ] Another example of an RNA aptamer therapeutic is NOX-A12, a 45 nucleotide RNA aptamer that is in clinical trials for chronic lymphocytic leukemia , pancreatic cancer , as well as other cancers. [ 9 ] NOX-A12 acts as antagonist for CXCL12/SDF-1, a chemokine involved in tumor growth. [ 9 ]
While the high-selectivity and tight-binding of RNA aptamers have generated interest in their use as pharmaceuticals, there are many problems which have prevented them from being successful in vivo . For one, without modifications RNA aptamers are degraded after being introduced into the body by nucleases in the span of a few minutes. [ 9 ] [ 94 ] [ 121 ] [ 122 ] Also, due to their small size, RNA aptamers can be removed from the bloodstream by the renal system. [ 9 ] [ 94 ] [ 95 ] [ 121 ] [ 122 ] Because of their negative charge, RNA aptamers are additionally known to bind proteins in the bloodstream, leading to non-target tissue delivery and toxicity. [ 94 ] [ 123 ] [ 124 ] Care must also be taken when isolating the RNA aptamers, as aptamers which contain repeated Cytosine-Phosphate-Guanine (CpG) sequences will cause immune system activation through the Toll-like receptor pathway. [ 9 ] [ 125 ] [ 126 ]
In order to combat some of the in vivo limitations of RNA aptamers, various modifications can be added to the nucleotides to aid in efficacy of the aptamer. For instance, a polyethylene glycol (PEG) moiety can be attached to increase the size of the aptamer, thereby preventing its removal from the bloodstream by the renal glomerulus . [ 127 ] [ 128 ] However, PEG has been implicated in allergic reactions during in vivo testing. [ 94 ] [ 129 ] [ 130 ] Furthermore, modifications can be added to prevent nuclease degradation, such as a 2’ fluoro or amino group as well as a 3’ inverted thymidine. [ 9 ] [ 94 ] [ 131 ] [ 132 ] Additionally, the aptamer can be synthesized so that the ribose sugar is in the L-form instead of the D-form , further preventing nuclease recognition. [ 8 ] [ 94 ] [ 133 ] [ 134 ] Such aptamers are known as Spiegelmers . [ 8 ] [ 134 ] In order to prevent Toll-like receptor pathway activation, the cytosine nucleobases within the aptamer can be methylated. [ 9 ] Nevertheless, despite these potential solutions to reduced in vivo efficacy, it is possible that chemically modifying the aptamer may weaken its binding affinity towards its target. [ 94 ] [ 135 ] | https://en.wikipedia.org/wiki/RNA_therapeutics |
An RNA timestamp is a technology that enables the age of any given RNA transcript to be inferred by exploiting RNA editing . [ 1 ] In this technique, the RNA of interest is tagged to an adenosine rich reporter motif that consists of multiple MS2 binding sites. These MS2 binding sites recruit a complex composed of ADAR2 (adenosine deaminase acting on RNA catalytic 2 domain) and MCP (MS2 capsid protein). The binding of the ADAR2 enzyme to the RNA timestamp initiates the gradual conversion of adenosine to inosine molecules. Over time, these edits accumulate and are then read through RNA-seq. This technology allows us to glean cell-type specific temporal information associated with RNA-seq data, that until now, has not been accessible. [ 1 ]
The advent of RNA-sequencing (RNA-seq) in 2009 allowed for a deeper look into the biology of unique cell types by allowing researchers to examine the presence and quantity of RNA in a sample at any given time. [ 2 ] The ability for analysis of the transcriptome has revealed valuable information about cellular differences and transcriptional changes between cell types. Further, RNA-seq has provided insights into examining alternative gene splicing , post-transcriptional modification and fusion genes – all of which would go undetected with genome analysis alone. [ 3 ] [ 4 ] The missing piece of the puzzle is understanding temporally when genes are expressed in a cell. RNA-seq requires the destruction of the cell, thus only revealing the transcriptome at a single moment. [ 1 ] Understanding expression times and patterns of genes transcription would create a deeper understanding of the roles of genes and how regulation of expression timing could be affecting cellular processes and possible dysregulation could be contributing to disease development.
In recent years, there have been other technologies created with the end goal of determining the age of RNA transcripts within a given cell. For example, TimeLapse-seq, [ 5 ] SLAM-seq [ 6 ] as well as measuring RNA velocity which is the instantaneous change in cell state from unspliced transcripts. [ 7 ] However, these methods were only able to reveal the age of transcripts at a fixed time point and failed to measure transcript age from more than one transcriptional pulse. While this information has importance, the ability to capture the dynamic transcriptional changes within a cell remained elusive.
The research groups of Edward Boyden at MIT and Fei Chen at Harvard , both in Cambridge, Massachusetts, U.S.A, developed RNA timestamps, a new (2020) method that allows the age chosen transcripts in a cell to be inferred. [ 1 ] This technology provides the means to understand cellular biology at a new level and deepen our understanding of cellular processes and transcriptional regulation. Further, the use of RNA timestamps does not require lysis of the cell which is an undeniable advantage. This allows timestamps to have the unique availability to suggest information from multiple transcriptional pulses throughout the cellular development rather than being limited to a fixed time point. [ 1 ]
Since multiple timestamped RNA transcripts are produced in the cells by a specific promoter, a transcriptional program was developed that uses a gradient descent algorithm to describe the number of timestamps generated as a function of time. [ 1 ] This helps with determining the source of the time point for the RNA timestamps and the accuracy of the algorithm increased with the number of RNAs. Further, this reveals the time point at which the specific promoter was active. [ 1 ]
RNA timestamp experiments were first experimentally validated in HEK293T cells that expressed the ADAR variant along with time stamped RNA under the control of tetracycline response element (TRE) induced by doxycycline. From these experiments, it was shown that the age of multiple RNA transcripts can be accurately determined (with a 95% confidence interval of 2.7±0.4h). [ 1 ]
As part of their proof of concept experiments, the researchers showed that timestamps can be used in primary hippocampal neuron cell culture to infer the c-fos response from KCl activation of neural activity. [ 1 ]
This technology was also shown to have the potential to determine transcriptional events in individual cells. Timestamps can be read out when used in combination with high throughput single-cell droplet based methods thus allowing RNA timestamps to be used for applications like ordering of mRNAs based on the timing of transcriptional processes based on cell type, and determining whether a specific promoter was active. [ 1 ]
RNA timestamp technology provides a novel means to understand cellular transcription. Only a few months after this technology was described, Dr. Michael Gilhooey and colleagues in England discussed RNA timestamps as an interesting new perspective to apply to their research on inherited optic neuropathies. [ 12 ] This suggests diverse potential applications of RNA timestamps, and perhaps it will be beneficial to better understanding transcriptional changes in human diseases, as alluded to by Dr. Gilhooey.
Further, the researchers suggested that perhaps timestamps could be calibrated to be used in in vivo experiments. The researchers have also suggested a potential mechanism using a virus to deliver the RNA reporter to target cells in vivo . [ 13 ] This could provide a revolutionary mechanism to track expression dynamics during development or recording responses to stimuli in vivo . However, for now, timestamps are limited to in vitro experiments.
Despite the many advantages of this method, there are some caveats of RNA timestamping worth mentioning: | https://en.wikipedia.org/wiki/RNA_timestamp |
RNA velocity is based on bridging measurements to an underlying mechanism, mRNA splicing, with two modes indicating the current and future state. [ 1 ] It is a method used to predict the future gene expression of a cell based on the measurement of both spliced and unspliced transcripts of mRNA. [ 2 ]
RNA velocity could be used to infer the direction of gene expression changes in single-cell RNA sequencing (scRNA-seq) data. It provides insights into the future state of individual cells by using the abundance of unspliced to spliced RNA transcripts. This ratio can indicate the transcriptional dynamics and potential fate of a cell, such as whether it is transitioning from one cell type to another or undergoing differentiation. [ 3 ]
There are several software tools available for RNA velocity analysis.Each of these tools has its own strengths and applications, so the choice of tool would depend on the specific requirements of your analysis:
Velocyto is a package for the analysis of expression dynamics in single cell RNA seq data. In particular, it enables estimations of RNA velocities of single cells by distinguishing unspliced and spliced mRNAs in standard single-cell RNA sequencing protocols. It is the first paper proposed the concept of RNA velocity. velocyto predicted RNA velocity by solving the proposed differential equations for each gene. The authors envision future manifold learning algorithms that simultaneously fit a manifold and the kinetics on that manifold, on the basis of RNA velocity. [ 3 ]
scVelo is a method that solves the full transcriptional dynamics of splicing kinetics using a likelihood-based dynamical model. This generalizes RNA velocity to systems with transient cell states, which are common in development and in response to perturbations. scVelo was applied to disentangling subpopulation kinetics in neurogenesis and pancreatic endocrinogenesis. scVelo demonstrate the capabilities of the dynamical model on various cell lineages in hippocampal dentate gyrus neurogenesis and pancreatic endocrinogenesis. [ 4 ]
cellDancer is a scalable deep neural network that locally infers velocity for each cell from its neighbors and then relays a series of local velocities to provide single-cell resolution inference of velocity kinetics. cellDancer improved the extisting hypothesis of kinetic rates of velocyto and scVelo, transcription rate was either a constant (velocyto model) or binary values (scVelo model), splicing and degradation rates were shared by all the genes and cells, which may have unpredictable performance, while cellDancer can predict the specific transcription, splicing and degradation rates of each gene in each cell through deep learning. [ 5 ]
MultiVelo is a differential equation model of gene expression that extends the RNA velocity framework to incorporate epigenomic data. MultiVelo uses a probabilistic latent variable model to estimate the switch time and rate parameters of chromatin accessibility and gene expression . [ 6 ]
DeepVelo is a neural network–based ordinary differential equation that can model complex transcriptome dynamics by describing continuous-time gene expression changes within individual cells. DeepVelo has been applied to public datasets from different sequencing platforms to (i) formulate transcriptome dynamics on different time scales, (ii) measure the instability of cell states, and (iii) identify developmental driver genes via perturbation analysis. [ 7 ]
UnitVelo is a statistical framework of RNA velocity that models the dynamics of spliced and unspliced RNAs via flexible transcription activities. UnitVelo supports the inference of a unified latent time across the transcriptome. [ 8 ] | https://en.wikipedia.org/wiki/RNA_velocity |
The RNA world is a hypothetical stage in the evolutionary history of life on Earth in which self-replicating RNA molecules proliferated before the evolution of DNA and proteins . [ 1 ] The term also refers to the hypothesis that posits the existence of this stage. Alexander Rich first proposed the concept of the RNA world in 1962, [ 2 ] and Walter Gilbert coined the term in 1986. [ 3 ]
Among the characteristics of RNA that suggest its original prominence are that:
Although alternative chemical paths to life have been proposed, [ 8 ] and RNA-based life may not have been the first life to exist, [ 3 ] [ 9 ] the RNA world hypothesis seems to be the most favored abiogenesis paradigm. However, even proponents agree that there is still not conclusive evidence to completely falsify other paradigms and hypotheses. [ 2 ] [ 10 ] [ 11 ] Regardless of its plausibility in a prebiotic scenario, the RNA world can serve as a model system for studying the origin of life. [ 12 ]
If the RNA world existed, it was probably followed by an age characterized by the evolution of ribonucleoproteins ( RNP world ), [ 3 ] which in turn ushered in the era of DNA and longer proteins. DNA has greater stability and durability than RNA, which may explain why it became the predominant information storage molecule. [ 13 ] Protein enzymes may have replaced RNA-based ribozymes as biocatalysts because the greater abundance and diversity of the monomers of which they are built makes them more versatile. As some cofactors contain both nucleotide and amino-acid characteristics, it may be that amino acids, peptides, and finally proteins initially were cofactors for ribozymes. [ 7 ]
One of the challenges in studying abiogenesis is that the system of reproduction and metabolism utilized by all extant life involves three distinct types of interdependent macromolecules ( DNA , RNA , and proteins ), none of which can function and reproduce without the others, the classic chicken-and-egg paradox . This suggests that life could not have arisen in its current form, which has led researchers to hypothesize mechanisms whereby the current system might have arisen from a simpler precursor system. [ 14 ] American molecular biologist Alexander Rich was the first to posit a coherent hypothesis on the origin of nucleotides as precursors of life. [ 15 ] In an article he contributed to a volume issued in honor of Nobel-laureate physiologist Albert Szent-Györgyi , he explained that the primitive Earth's environment could have produced RNA molecules (polynucleotide monomers) that eventually acquired enzymatic and self-replicating functions. [ 16 ]
Other mentions of RNA as a primordial molecule can be found in papers by Francis Crick [ 17 ] and Leslie Orgel , [ 18 ] as well as in Carl Woese 's 1967 book The Genetic Code . [ 19 ] Hans Kuhn in 1972 laid out a possible process by which the modern genetic system might have arisen from a nucleotide-based precursor, and this led Harold White in 1976 to observe that many of the cofactors essential for enzymatic function are either nucleotides or could have been derived from nucleotides. He proposed a scenario whereby the critical electrochemistry of enzymatic reactions would have necessitated retention of the specific nucleotide moieties of the original RNA-based enzymes carrying out the reactions, while the remaining structural elements of the enzymes were gradually replaced by protein, until all that remained of the original RNAs were these nucleotide cofactors, "fossils of nucleic acid enzymes". [ 7 ]
The properties of RNA make the idea of the RNA world hypothesis conceptually plausible, though its general acceptance as an explanation for the origin of life requires further evidence. [ 20 ] RNA is known to form efficient catalysts, and its similarity to DNA makes clear its ability to store information. Opinions differ, however, as to whether RNA constituted the first autonomous self-replicating system or was a derivative of a still-earlier system. [ 3 ] One version of the hypothesis is that a different type of nucleic acid , termed pre-RNA , was the first one to emerge as a self-reproducing molecule, to be replaced by RNA only later. On the other hand, the discovery in 2009 that activated pyrimidine ribonucleotides can be synthesized under plausible prebiotic conditions [ 21 ] suggests that it is premature to dismiss the RNA-first scenarios. [ 3 ] Suggestions for 'simple' pre-RNA nucleic acids have included peptide nucleic acid (PNA), threose nucleic acid (TNA) or glycol nucleic acid (GNA). [ 22 ] [ 23 ] Despite their structural simplicity and possession of properties comparable with RNA, the chemically plausible generation of "simpler" nucleic acids under prebiotic conditions has yet to be demonstrated. [ 24 ]
In the 1980s, RNA structures capable of self-processing were discovered, [ 25 ] with the RNA moiety of ribonuclease P acting as its catalytic subunit. [ 26 ] These catalytic RNAs – referred to as RNA enzymes , or ribozymes – are found in today's DNA-based life and could be examples of living fossils . Ribozymes play vital roles, such as that of the ribosome . The large subunit of the ribosome includes an rRNA responsible for the peptide bond-forming peptidyl transferase activity of protein synthesis. Many other ribozyme activities exist; for example, the hammerhead ribozyme performs self-cleavage [ 27 ] and an RNA polymerase ribozyme can synthesize a short RNA strand from a primed RNA template. [ 28 ]
Among the enzymatic properties important for the beginning of life are:
RNA is a very similar molecule to DNA, with only two significant chemical differences (the backbone of RNA uses ribose instead of deoxyribose and its nucleobases include uracil instead of thymine ). The overall structure of RNA and DNA are immensely similar—one strand of DNA and one of RNA can bind to form a double helical structure. This makes the storage of information in RNA possible in a very similar way to the storage of information in DNA. However, RNA is less stable, being more prone to hydrolysis due to the presence of a hydroxyl group at the ribose 2' position.
The major difference between RNA and DNA is the presence of a hydroxyl group at the 2'-position of the ribose sugar in RNA (illustration, right). [ 20 ] This group makes the molecule less stable because, when not constrained in a double helix, the 2' hydroxyl can chemically attack the adjacent phosphodiester bond to cleave the phosphodiester backbone. The hydroxyl group also forces the ribose into the C3'- endo sugar conformation unlike the C2'- endo conformation of the deoxyribose sugar in DNA. This forces an RNA double helix to change from a B-DNA structure to one more closely resembling A-DNA .
RNA also uses a different set of bases than DNA— adenine , guanine , cytosine and uracil , instead of adenine, guanine, cytosine and thymine . Chemically, uracil is similar to thymine, differing only by a methyl group , and its production requires less energy. [ 49 ] In terms of base pairing, this has no effect. Adenine readily binds uracil or thymine. Uracil is, however, one product of damage to cytosine that makes RNA particularly susceptible to mutations that can replace a GC base pair with a GU ( wobble ) or AU base pair .
RNA is thought to have preceded DNA, because of their ordering in the biosynthetic pathways. [ 9 ] The deoxyribonucleotides used to make DNA are made from ribonucleotides, the building blocks of RNA, by removing the 2'-hydroxyl group. As a consequence, a cell must have the ability to make RNA before it can make DNA.
The chemical properties of RNA make large RNA molecules inherently fragile, and they can easily be broken down into their constituent nucleotides through hydrolysis . [ 50 ] [ 51 ] These limitations do not make use of RNA as an information storage system impossible, simply energy intensive (to repair or replace damaged RNA molecules) and prone to mutation. While this makes it unsuitable for current 'DNA optimised' life, it may have been acceptable for more primitive life.
Riboswitches have been found to act as regulators of gene expression, particularly in bacteria, but also in plants and archaea . Riboswitches alter their secondary structure in response to the binding of a metabolite . Riboswitch classes have highly conserved aptamer domains, even among diverse organisms. When a target metabolite is bound to this aptamer, conformational changes occur, modulating the expression of genes carried by mRNA. These changes occur in an expression platform, located downstream from the aptamer. [ 52 ] This change in structure can result in the formation or disruption of a terminator , truncating or permitting transcription respectively. [ 53 ] Alternatively, riboswitches may bind or occlude the Shine–Dalgarno sequence , affecting translation. [ 54 ] It has been suggested that these originated in an RNA-based world. [ 55 ] In addition, RNA thermometers regulate gene expression in response to temperature changes. [ 56 ]
The RNA world hypothesis is supported by RNA's ability to do all three of to store, to transmit, and to duplicate genetic information, as DNA does, and to perform enzymatic reactions, like protein-based enzymes. Because it can carry out the types of tasks now performed by proteins and DNA, RNA is believed to have once been capable of supporting independent life on its own. [ 20 ] Some viruses use RNA as their genetic material, rather than DNA. [ 57 ] Further, while nucleotides were not found in experiments based on Miller-Urey experiment , their formation in prebiotically plausible conditions was reported in 2009; [ 21 ] a purine base, adenine, is merely a pentamer of hydrogen cyanide , and it happens that this particular base is used as omnipresent energy vehicle in the cell: adenosine triphosphate is used everywhere in preference to guanosine triphosphate , cytidine triphosphate , uridine triphosphate or even deoxythymidine triphosphate , which could serve just as well but are practically never used except as building blocks for nucleic acid chains. Experiments with basic ribozymes, like Bacteriophage Qβ RNA, have shown that simple self-replicating RNA structures can withstand even strong selective pressures (e.g., opposite-chirality chain terminators). [ 58 ]
Since there were no known chemical pathways for the abiogenic synthesis of nucleotides from pyrimidine nucleobases cytosine and uracil under prebiotic conditions, it is thought by some that nucleic acids did not contain these nucleobases seen in life's nucleic acids. [ 59 ] The nucleoside cytosine has a half-life in isolation of 19 days at 100 °C (212 °F) and 17,000 years in freezing water, which some argue is too short on the geologic time scale for accumulation. [ 60 ] Others have questioned whether ribose and other backbone sugars could be stable enough to be found in the original genetic material, [ 61 ] and have raised the issue that all ribose molecules would have had to be the same enantiomer , as any nucleotide of the wrong chirality acts as a chain terminator . [ 62 ]
Pyrimidine ribonucleosides and their respective nucleotides have been prebiotically synthesised by a sequence of reactions that by-pass free sugars and assemble in a stepwise fashion by including nitrogenous and oxygenous chemistries. In a series of publications, John Sutherland and his team at the School of Chemistry, University of Manchester , have demonstrated high yielding routes to cytidine and uridine ribonucleotides built from small 2- and 3-carbon fragments such as glycolaldehyde , glyceraldehyde or glyceraldehyde-3-phosphate, cyanamide , and cyanoacetylene . One of the steps in this sequence allows the isolation of enantiopure ribose aminooxazoline if the enantiomeric excess of glyceraldehyde is 60% or greater, of possible interest toward biological homochirality. [ 63 ] This can be viewed as a prebiotic purification step, where the said compound spontaneously crystallised out from a mixture of the other pentose aminooxazolines. Aminooxazolines can react with cyanoacetylene in a mild and highly efficient manner, controlled by inorganic phosphate, to give the cytidine ribonucleotides. Photoanomerization with UV light allows for inversion about the 1' anomeric centre to give the correct beta stereochemistry; one problem with this chemistry is the selective phosphorylation of alpha-cytidine at the 2' position. [ 64 ] However, in 2009, they showed that the same simple building blocks allow access, via phosphate controlled nucleobase elaboration, to 2',3'-cyclic pyrimidine nucleotides directly, which are known to be able to polymerise into RNA. [ 21 ] Organic chemist Donna Blackmond described this finding as "strong evidence" in favour of the RNA world. [ 65 ] However, John Sutherland said that while his team's work suggests that nucleic acids played an early and central role in the origin of life, it did not necessarily support the RNA world hypothesis in the strict sense, which he described as a "restrictive, hypothetical arrangement". [ 66 ]
The Sutherland group's 2009 paper also highlighted the possibility for the photo-sanitization of the pyrimidine-2',3'-cyclic phosphates. [ 21 ] A potential weakness of these routes is the generation of enantioenriched glyceraldehyde, or its 3-phosphate derivative (glyceraldehyde prefers to exist as its keto tautomer dihydroxyacetone). [ citation needed ]
On August 8, 2011, a report, based on NASA studies with meteorites found on Earth , was published suggesting building blocks of RNA (adenine, guanine, and related organic molecules ) may have been formed in outer space . [ 67 ] [ 68 ] [ 69 ] In 2017, research using a numerical model suggested that a RNA world may have emerged in warm ponds on the early Earth, and that meteorites were a plausible and probable source of the RNA building blocks ( ribose and nucleic acids) to these environments. [ 70 ] On August 29, 2012, astronomers at Copenhagen University reported the detection of a specific sugar molecule, glycolaldehyde , in a distant star system. The molecule was found around the protostellar binary IRAS 16293-2422 , which is located 400 light years from Earth. [ 71 ] [ 72 ] Because glycolaldehyde is needed to form RNA, this finding suggests that complex organic molecules may form in stellar systems prior to the formation of planets, eventually arriving on young planets early in their formation. [ 73 ] Nitriles , key molecular precursors of the RNA World scenario, are among the most abundant chemical families in the universe and have been found in molecular clouds in the center of the Milky Way, protostars of different masses, meteorites and comets, and also in the atmosphere of Titan, the largest moon of Saturn. [ 74 ] [ 75 ]
A study in 2001 shows that nicotinic acid and its precursor, quinolinic acid can be "produced in yields as high as 7% in a six-step nonenzymatic sequence from aspartic acid and dihydroxyacetone phosphate (DHAP). The biosynthesis of ribose phosphate could have produced DHAP and other three carbon compounds. Aspartic acid could have been available from prebiotic synthesis or from the ribozyme synthesis of pyrimidines." This supports that NAD could have originated in the RNA world. [ 76 ] RNA sequences at lengths of 30 nucleotides, 60 nucleotides, 100 nucleotides, and 140 nucleotides, were capable of catalysis of "the synthesis of three common coenzymes, CoA, NAD, and FAD, from their precursors, 4‘-phosphopantetheine , NMN , and FMN , respectively". [ 77 ]
Nucleotides are the fundamental molecules that combine in series to form RNA. They consist of a nitrogenous base attached to a sugar-phosphate backbone. RNA is made of long stretches of specific nucleotides arranged so that their sequence of bases carries information. The RNA world hypothesis holds that in the primordial soup (or sandwich ), there existed free-floating nucleotides. These nucleotides regularly formed bonds with one another, which often broke because the change in energy was so low. However, certain sequences of base pairs have catalytic properties that lower the energy of their chain being created, enabling them to stay together for longer periods of time. As each chain grew longer, it attracted more matching nucleotides faster, causing chains to now form faster than they were breaking down.
These chains have been proposed by some as the first, primitive forms of life. In an RNA world, different sets of RNA strands would have had different replication outputs, which would have increased or decreased their frequency in the population, i.e., natural selection . As the fittest sets of RNA molecules expanded their numbers, novel catalytic properties added by mutation, which benefitted their persistence and expansion, could accumulate in the population. Such an autocatalytic set of ribozymes, capable of self-replication in about an hour, has been identified. It was produced by molecular competition ( in vitro evolution ) of candidate enzyme mixtures. [ 78 ]
Competition between RNA may have favored the emergence of cooperation between different RNA chains, opening the way for the formation of the first protocell . Eventually, RNA chains developed with catalytic properties that help amino acids bind together (a process called peptide-bonding ). These amino acids could then assist with RNA synthesis, giving those RNA chains that could serve as ribozymes the selective advantage. The ability to catalyze one step in protein synthesis, aminoacylation of RNA, has been demonstrated in a short (five-nucleotide) segment of RNA. [ 79 ]
In March 2015, NASA scientists reported that, for the first time, complex DNA and RNA organic compounds of life , including uracil, cytosine, and thymine, have been formed in the laboratory under conditions found only in outer space , using starting chemicals, like pyrimidine , found in meteorites . Pyrimidine, like polycyclic aromatic hydrocarbons (PAHs), may have been formed in red giant stars or in interstellar dust and gas clouds, according to the scientists. [ 80 ]
In 2018, researchers at Georgia Institute of Technology identified three molecular candidates for the bases that might have formed an earliest version of proto-RNA: barbituric acid , melamine , and 2,4,6-triaminopyrimidine (TAP). These three molecules are simpler versions of the four bases in current RNA, which could have been present in larger amounts and could still be forward-compatible with them but may have been discarded by evolution in exchange for more optimal base pairs. [ 81 ] Specifically, TAP can form nucleotides with a large range of sugars. [ 82 ] Both TAP and melamine base pair with barbituric acid. All three spontaneously form nucleotides with ribose. [ 83 ]
One of the challenges posed by the RNA world hypothesis is to discover the pathway by which an RNA-based system transitioned to one based on DNA. Geoffrey Diemer and Ken Stedman, at Portland State University in Oregon, may have found a solution. While conducting a survey of viruses in a hot acidic lake in Lassen Volcanic National Park, California, they uncovered evidence that a simple DNA virus had acquired a gene from a completely unrelated RNA-based virus . Virologist Luis Villareal of the University of California Irvine also suggests that viruses capable of converting an RNA-based gene into DNA and then incorporating it into a more complex DNA-based genome might have been common in the virus world during the RNA to DNA transition some 4 billion years ago. [ 84 ] [ 85 ] This finding bolsters the argument for the transfer of information from the RNA world to the emerging DNA world before the emergence of the last universal common ancestor . From the research, the diversity of this virus world is still with us.
Additional evidence supporting the concept of an RNA world has resulted from research on viroids , the first representatives of a novel domain of "subviral pathogens". [ 86 ] [ 87 ] Viroids infect plants, where most are pathogens, and consist of short stretches of highly complementary, circular, single-stranded and non-coding RNA without a protein coat. They are extremely small, ranging from 246 to 467 nucleobases, compared to the smallest known viruses capable of causing an infection, with genomes about 2,000 nucleobases in length. [ 88 ]
Based on their characteristic properties, in 1989 plant biologist Theodor Diener argued that viroids are more plausible living relics of the RNA world than introns and other RNAs considered candidates at the time. [ 89 ] Diener's hypothesis would be expanded by the research group of Ricardo Flores, [ 90 ] [ 91 ] and gained a broader audience when in 2014, a New York Times science writer published a popularized version of the proposal. [ 92 ]
The characteristics of viroids highlighted as consistent with an RNA world were their small size, high guanine and cytosine content, circular structure, structural periodicity, the lack of protein-coding ability and, in some cases, ribozyme-mediated replication. [ 91 ] One aspect critics of the hypothesis have focused on is that the exclusive hosts of all known viroids, angiosperms , did not evolve until billions of years after the RNA world was replaced, making viroids more likely to have arisen through later evolutionary mechanisms unrelated to the RNA world than to have survived via a cryptic host over that extended period. [ 93 ] Whether they are relics of that world or of more recent origin, their function as autonomous naked RNA is seen as analogous to that envisioned for an RNA world.
Eigen et al . [ 94 ] and Woese [ 95 ] proposed that the genomes of early protocells were composed of single-stranded RNA, and that individual genes corresponded to separate RNA segments, rather than being linked end-to-end as in present-day DNA genomes. A protocell that was haploid (one copy of each RNA gene) would be vulnerable to damage, since a single lesion in any RNA segment would be potentially lethal to the protocell (e.g., by blocking replication or inhibiting the function of an essential gene).
Vulnerability to damage could be reduced by maintaining two or more copies of each RNA segment in each protocell, i.e., by maintaining diploidy or polyploidy. Genome redundancy would allow a damaged RNA segment to be replaced by an additional replication of its homolog. However, for such a simple organism, the proportion of available resources tied up in the genetic material would be a large fraction of the total resource budget. Under limited resource conditions, the protocell reproductive rate would likely be inversely related to ploidy number. The protocell's fitness would be reduced by the costs of redundancy. Consequently, coping with damaged RNA genes while minimizing the costs of redundancy would likely have been a fundamental problem for early protocells.
A cost-benefit analysis was carried out in which the costs of maintaining redundancy were balanced against the costs of genome damage. [ 96 ] This analysis led to the conclusion that, under a wide range of circumstances, the selected strategy would be for each protocell to be haploid, but to periodically fuse with another haploid protocell to form a transient diploid. The retention of the haploid state maximizes the growth rate. The periodic fusions permit mutual reactivation of otherwise lethally damaged protocells. If at least one damage-free copy of each RNA gene is present in the transient diploid, viable progeny can be formed. For two, rather than one, viable daughter cells to be produced would require an extra replication of the intact RNA gene homologous to any RNA gene that had been damaged prior to the division of the fused protocell. The cycle of haploid reproduction, with occasional fusion to a transient diploid state, followed by splitting to the haploid state, can be considered to be the sexual cycle in its most primitive form. [ 96 ] [ 97 ] In the absence of this sexual cycle, haploid protocells with damage in an essential RNA gene would simply die.
This model for the early sexual cycle is hypothetical, but it is very similar to the known sexual behavior of the segmented RNA viruses, which are among the simplest organisms known. Influenza virus , whose genome consists of 8 physically separated single-stranded RNA segments, [ 98 ] is an example of this type of virus. In segmented RNA viruses, "mating" can occur when a host cell is infected by at least two virus particles. If these viruses each contain an RNA segment with a lethal damage, multiple infection can lead to reactivation providing that at least one undamaged copy of each virus gene is present in the infected cell. This phenomenon is known as "multiplicity reactivation". Multiplicity reactivation has been reported to occur in influenza virus infections after induction of RNA damage by UV-irradiation , [ 99 ] and ionizing radiation. [ 100 ]
Patrick Forterre has been working on a novel hypothesis, called "three viruses, three domains": [ 101 ] that viruses were instrumental in the transition from RNA to DNA and the evolution of Bacteria , Archaea , and Eukaryota . He believes the last universal common ancestor [ 101 ] was RNA-based and evolved RNA viruses. Some of the viruses evolved into DNA viruses to protect their genes from attack. Through the process of viral infection into hosts the three domains of life evolved. [ 101 ] [ 102 ]
Another interesting proposal is the idea that RNA synthesis might have been driven by temperature gradients, in the process of thermosynthesis . [ 103 ] Single nucleotides have been shown to catalyze organic reactions. [ 104 ]
Steven Benner has argued that chemical conditions on the planet Mars , such as the presence of boron , molybdenum , and oxygen , may have been better for initially producing RNA molecules than those on Earth . If so, life-suitable molecules, originating on Mars, may have later migrated to Earth via mechanisms of panspermia or similar process. [ 105 ] [ 106 ]
The hypothesized existence of an RNA world does not exclude a "Pre-RNA world", where a metabolic system based on a different nucleic acid is proposed to pre-date RNA. A candidate nucleic acid is peptide nucleic acid ( PNA ), which uses simple peptide bonds to link nucleobases. [ 107 ] PNA is more stable than RNA, but its ability to be generated under prebiological conditions has yet to be demonstrated experimentally. [ citation needed ]
Threose nucleic acid ( TNA ) or glycol nucleic acid ( GNA ) have also been proposed as a starting point, and like PNA, also lack experimental evidence for their respective abiogenesis. [ citation needed ]
An alternative—or complementary—theory of RNA origin is proposed in the PAH world hypothesis , whereby polycyclic aromatic hydrocarbons ( PAHs ) mediate the synthesis of RNA molecules. [ 108 ] PAHs are the most common and abundant of the known polyatomic molecules in the visible Universe and are a likely constituent of the primordial sea . [ 109 ] PAHs and fullerenes (also implicated in the origin of life ) [ 110 ] have been detected in nebulae . [ 111 ]
The iron-sulfur world theory proposes that simple metabolic processes developed before genetic materials did, and these energy-producing cycles catalyzed the production of genes. [ citation needed ]
Some of the difficulties of producing the precursors on earth are bypassed by another alternative or complementary theory for their origin, panspermia . It discusses the possibility that the earliest life on this planet was carried here from somewhere else in the galaxy, possibly on meteorites similar to the Murchison meteorite . [ 112 ] Sugar molecules , including ribose , have been found in meteorites . [ 113 ] [ 114 ] Panspermia does not invalidate the concept of an RNA world, but posits that this world or its precursors originated not on Earth but rather another, probably older, planet. [ citation needed ]
The relative chemical complexity of the nucleotide and the unlikelihood of it spontaneously arising, along with the limited number of combinations possible among four base forms, as well as the need for RNA polymers of some length before seeing enzymatic activity, have led some to reject the RNA world hypothesis in favor of a metabolism-first hypothesis, where the chemistry underlying cellular function arose first, along with the ability to replicate and facilitate this metabolism. [ citation needed ]
Another proposal is that the dual-molecule system we see today, where a nucleotide-based molecule is needed to synthesize protein, and a peptide-based (protein) molecule is needed to make nucleic acid polymers, represents the original form of life. [ 115 ] This theory is called RNA-peptide coevolution, [ 116 ] or the Peptide-RNA world, and offers a possible explanation for the rapid evolution of high-quality replication in RNA (since proteins are catalysts), with the disadvantage of having to postulate the coincident formation of two complex molecules, an enzyme (from peptides) and a RNA (from nucleotides). In this Peptide-RNA World scenario, RNA would have contained the instructions for life, while peptides (simple protein enzymes) would have accelerated key chemical reactions to carry out those instructions. [ 117 ] The study leaves open the question of exactly how those primitive systems managed to replicate themselves — something neither the RNA World hypothesis nor the Peptide-RNA World theory can yet explain, unless polymerases (enzymes that rapidly assemble the RNA molecule) played a role. [ 117 ]
A research project completed in March 2015 by the Sutherland group found that a network of reactions beginning with hydrogen cyanide and hydrogen sulfide , in streams of water irradiated by UV light, could produce the chemical components of proteins and lipids, alongside those of RNA. [ 118 ] [ 119 ] The researchers used the term "cyanosulfidic" to describe this network of reactions. [ 118 ] In November 2017, a team at the Scripps Research Institute identified reactions involving the compound diamidophosphate which could have linked the chemical components into short peptide and lipid chains as well as short RNA-like chains of nucleotides. [ 120 ] [ 121 ]
The RNA world hypothesis, if true, has important implications for the definition of life and the origin of life . For most of the time that followed Franklin , Watson and Crick 's elucidation of DNA structure in 1953, life was largely defined in terms of DNA and proteins: DNA and proteins seemed the dominant macromolecules in the living cell, with RNA only aiding in creating proteins from the DNA blueprint.
The RNA world hypothesis places RNA at center-stage when life originated. The RNA world hypothesis is supported by the observations that ribosomes are ribozymes: [ 122 ] [ 123 ] the catalytic site is composed of RNA, and proteins hold no major structural role and are of peripheral functional importance. This was confirmed with the deciphering of the 3-dimensional structure of the ribosome in 2001. Specifically, peptide bond formation, the reaction that binds amino acids together into proteins , is now known to be catalyzed by an adenine residue in the rRNA .
RNAs are known to play roles in other cellular catalytic processes, specifically in the targeting of enzymes to specific RNA sequences. In eukaryotes, the processing of pre-mRNA and RNA editing take place at sites determined by the base pairing between the target RNA and RNA constituents of small nuclear ribonucleoproteins (snRNPs) . Such enzyme targeting is also responsible for gene down regulation through RNA interference (RNAi), where an enzyme-associated guide RNA targets specific mRNA for selective destruction. Likewise, in eukaryotes the maintenance of telomeres involves copying of an RNA template that is a constituent part of the telomerase ribonucleoprotein enzyme. Another cellular organelle, the vault , includes a ribonucleoprotein component, although the function of this organelle remains to be elucidated. | https://en.wikipedia.org/wiki/RNA_world |
The Route Network Definition File (RNDF) specifies accessible road segments and provides information such as waypoints , stop sign locations, lane widths, checkpoint locations, and parking spot locations. The route network has no implied start or end point. In addition to road segments, the RNDF specifies free-travel ‘zones’ that have a defined perimeter, but for which no waypoints are provided. Zones are used to represent parking lots and areas with moving or stationary obstacles or vehicles. It is used by DARPA for its Grand Challenge program. [ 1 ] [ 2 ]
This computing article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/RNDF |
9604
56736
ENSG00000013561
ENSMUSG00000060450
Q9UBS8
Q9JI90
NM_183401
NM_001361266 NM_001361267 NM_001361268 NM_001361269
NP_899648
NP_001348195 NP_001348196 NP_001348197 NP_001348198
E3 ubiquitin-protein ligase RNF14 is an enzyme that in humans is encoded by the RNF14 gene . [ 5 ] [ 6 ] [ 7 ]
The protein encoded by this gene contains a RING zinc finger, a motif known to be involved in protein-protein interactions. This protein interacts with androgen receptor (AR) and may function as a coactivator that induces AR target gene expression in prostate. A dominant negative mutant of this gene has been demonstrated to inhibit the AR-mediated growth of prostate cancer. This protein also interacts with class III ubiquitin-conjugating enzymes (E2s) and may act as a ubiquitin-ligase (E3) in the ubiquitination of certain nuclear proteins. Five alternatively spliced transcript variants encoding two distinct isoforms have been reported. [ 7 ] Another function of RNF14 protein relates to its regulation of the inter-relationship between bioenergetic status and inflammation. It influences the expression of mitochondrial and immune-related genes in skeletal muscle including cytokines and interferon regulatory factors. [ 8 ]
RNF14 has been shown to interact with the Androgen receptor . [ 5 ] [ 9 ] [ 10 ] [ 11 ]
This article incorporates text from the United States National Library of Medicine , which is in the public domain .
This article on a gene on human chromosome 5 is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/RNF14 |
In chemistry , amines ( / ə ˈ m iː n , ˈ æ m iː n / , [ 1 ] [ 2 ] UK also / ˈ eɪ m iː n / [ 3 ] ) are compounds and functional groups that contain a basic nitrogen atom with a lone pair . Formally, amines are derivatives of ammonia ( NH 3 in which the bond angle between the nitrogen and hydrogen is 107°), wherein one or more hydrogen atoms have been replaced by a substituent such as an alkyl or aryl group [ 4 ] (these may respectively be called alkylamines and arylamines; amines in which both types of substituent are attached to one nitrogen atom may be called alkylarylamines). Important amines include amino acids , biogenic amines , trimethylamine , and aniline . Inorganic derivatives of ammonia are also called amines, such as monochloramine ( NClH 2 ). [ 5 ]
The substituent −NH 2 is called an amino group. [ 6 ]
The chemical notation for amines contains the letter "R", where "R" is not an element, but an "R-group", which in amines could be a single hydrogen or carbon atom, or could be a hydrocarbon chain.
Compounds with a nitrogen atom attached to a carbonyl group , thus having the structure R−C(=O)−NR′R″ , are called amides and have different chemical properties from amines.
Amines can be classified according to the nature and number of substituents on nitrogen . Aliphatic amines contain only H and alkyl substituents. Aromatic amines have the nitrogen atom connected to an aromatic ring.
Amines, alkyl and aryl alike, are organized into three subcategories (see table) based on the number of carbon atoms adjacent to the nitrogen (how many hydrogen atoms of the ammonia molecule are replaced by hydrocarbon groups): [ 6 ] [ 7 ]
A fourth subcategory is determined by the connectivity of the substituents attached to the nitrogen:
It is also possible to have four organic substituents on the nitrogen. These species are not amines but are quaternary ammonium cations and have a charged nitrogen center. Quaternary ammonium salts exist with many kinds of anions .
Amines are named in several ways. Typically, the compound is given the prefix "amino-" or the suffix "-amine". The prefix " N -" shows substitution on the nitrogen atom. An organic compound with multiple amino groups is called a diamine , triamine , tetraamine and so forth.
Lower amines are named with the suffix -amine .
Higher amines have the prefix amino as a functional group. IUPAC however does not recommend this convention, [ 8 ] but prefers the alkanamine form, e.g. butan-2-amine.
Hydrogen bonding significantly influences the properties of primary and secondary amines. For example, methyl and ethyl amines are gases under standard conditions, whereas the corresponding methyl and ethyl alcohols are liquids. Amines possess a characteristic ammonia smell, liquid amines have a distinctive "fishy" and foul smell.
The nitrogen atom features a lone electron pair that can bind H + to form an ammonium ion R 3 NH + . The lone electron pair is represented in this article by two dots above or next to the N. The water solubility of simple amines is enhanced by hydrogen bonding involving these lone electron pairs. Typically salts of ammonium compounds exhibit the following order of solubility in water: primary ammonium ( RNH + 3 ) > secondary ammonium ( R 2 NH + 2 ) > tertiary ammonium (R 3 NH + ). Small aliphatic amines display significant solubility in many solvents , whereas those with large substituents are lipophilic. Aromatic amines, such as aniline , have their lone pair electrons conjugated into the benzene ring, thus their tendency to engage in hydrogen bonding is diminished. Their boiling points are high and their solubility in water is low.
Typically the presence of an amine functional group is deduced by a combination of techniques, including mass spectrometry as well as NMR and IR spectroscopies. 1 H NMR signals for amines disappear upon treatment of the sample with D 2 O. In their infrared spectrum primary amines exhibit two N-H bands, whereas secondary amines exhibit only one. [ 6 ] In their IR spectra, primary and secondary amines exhibit distinctive N-H stretching bands near 3300 cm −1 . Somewhat less distinctive are the bands appearing below 1600 cm −1 , which are weaker and overlap with C-C and C-H modes. For the case of propyl amine , the H-N-H scissor mode appears near 1600 cm −1 , the C-N stretch near 1000 cm −1 , and the R 2 N-H bend near 810 cm −1 . [ 9 ]
Alkyl amines characteristically feature tetrahedral nitrogen centers. C-N-C and C-N-H angles approach the idealized angle of 109°. C-N distances are slightly shorter than C-C distances. The energy barrier for the nitrogen inversion of the stereocenter is about 7 kcal/mol for a trialkylamine. The interconversion has been compared to the inversion of an open umbrella into a strong wind.
Amines of the type NHRR' and NRR′R″ are chiral : the nitrogen center bears four substituents counting the lone pair. Because of the low barrier to inversion, amines of the type NHRR' cannot be obtained in optical purity. For chiral tertiary amines, NRR′R″ can only be resolved when the R, R', and R″ groups are constrained in cyclic structures such as N -substituted aziridines ( quaternary ammonium salts are resolvable).
In aromatic amines ("anilines"), nitrogen is often nearly planar owing to conjugation of the lone pair with the aryl substituent. The C-N distance is correspondingly shorter. In aniline, the C-N distance is the same as the C-C distances. [ 10 ]
Like ammonia, amines are bases . [ 11 ] Compared to alkali metal hydroxides, amines are weaker.
The basicity of amines depends on:
Owing to inductive effects, the basicity of an amine might be expected to increase with the number of alkyl groups on the amine. Correlations are complicated owing to the effects of solvation which are opposite the trends for inductive effects. Solvation effects also dominate the basicity of aromatic amines (anilines). For anilines, the lone pair of electrons on nitrogen delocalizes into the ring, resulting in decreased basicity. Substituents on the aromatic ring, and their positions relative to the amino group, also affect basicity as seen in the table.
Solvation significantly affects the basicity of amines. N-H groups strongly interact with water, especially in ammonium ions. Consequently, the basicity of ammonia is enhanced by 10 11 by solvation. The intrinsic basicity of amines, i.e. the situation where solvation is unimportant, has been evaluated in the gas phase. In the gas phase, amines exhibit the basicities predicted from the electron-releasing effects of the organic substituents. Thus tertiary amines are more basic than secondary amines, which are more basic than primary amines, and finally ammonia is least basic. The order of pK b 's (basicities in water) does not follow this order. Similarly aniline is more basic than ammonia in the gas phase, but ten thousand times less so in aqueous solution. [ 14 ]
In aprotic polar solvents such as DMSO , DMF , and acetonitrile the energy of solvation is not as high as in protic polar solvents like water and methanol. For this reason, the basicity of amines in these aprotic solvents is almost solely governed by the electronic effects.
Industrially significant alkyl amines are prepared from ammonia by alkylation with alcohols: [ 5 ]
Unlike the reaction of amines with alcohols the reaction of amines and ammonia with alkyl halides is used for synthesis in the laboratory:
In such reactions, which are more useful for alkyl iodides and bromides, the degree of alkylation is difficult to control such that one obtains mixtures of primary, secondary, and tertiary amines, as well as quaternary ammonium salts. [ 5 ]
Selectivity can be improved via the Delépine reaction , although this is rarely employed on an industrial scale. Selectivity is also assured in the Gabriel synthesis , which involves organohalide reacting with potassium phthalimide .
Aryl halides are much less reactive toward amines and for that reason are more controllable. A popular way to prepare aryl amines is the Buchwald-Hartwig reaction .
Disubstituted alkenes react with HCN in the presence of strong acids to give formamides, which can be decarbonylated. This method, the Ritter reaction , is used industrially to produce tertiary amines such as tert -octylamine . [ 5 ]
Hydroamination of alkenes is also widely practiced. The reaction is catalyzed by zeolite-based solid acids . [ 5 ]
Via the process of hydrogenation , unsaturated N-containing functional groups are reduced to amines using hydrogen in the presence of a nickel catalyst. Suitable groups include nitriles , azides , imines including oximes , amides, and nitro . In the case of nitriles, reactions are sensitive to acidic or alkaline conditions, which can cause hydrolysis of the −CN group. LiAlH 4 is more commonly employed for the reduction of these same groups on the laboratory scale.
Many amines are produced from aldehydes and ketones via reductive amination , which can either proceed catalytically or stoichiometrically.
Aniline ( C 6 H 5 NH 2 ) and its derivatives are prepared by reduction of the nitroaromatics. In industry, hydrogen is the preferred reductant, whereas, in the laboratory, tin and iron are often employed.
Many methods exist for the preparation of amines, many of these methods being rather specialized.
Aside from their basicity, the dominant reactivity of amines is their nucleophilicity . [ 16 ] Most primary amines are good ligands for metal ions to give coordination complexes . Amines are alkylated by alkyl halides. Acyl chlorides and acid anhydrides react with primary and secondary amines to form amides (the " Schotten–Baumann reaction ").
Similarly, with sulfonyl chlorides, one obtains sulfonamides . This transformation, known as the Hinsberg reaction , is a chemical test for the presence of amines.
Because amines are basic, they neutralize acids to form the corresponding ammonium salts R 3 NH + . When formed from carboxylic acids and primary and secondary amines, these salts thermally dehydrate to form the corresponding amides .
Amines undergo sulfamation upon treatment with sulfur trioxide or sources thereof:
Amines reacts with nitrous acid to give diazonium salts. The alkyl diazonium salts are of little importance because they are too unstable. The most important members are derivatives of aromatic amines such as aniline ("phenylamine") (A = aryl or naphthyl):
Anilines and naphthylamines form more stable diazonium salts, which can be isolated in the crystalline form. [ 17 ] Diazonium salts undergo a variety of useful transformations involving replacement of the N 2 group with anions. For example, cuprous cyanide gives the corresponding nitriles:
Aryldiazoniums couple with electron-rich aromatic compounds such as a phenol to form azo compounds . Such reactions are widely applied to the production of dyes. [ 18 ]
Imine formation is an important reaction. Primary amines react with ketones and aldehydes to form imines . In the case of formaldehyde (R' = H), these products typically exist as cyclic trimers : RNH 2 + R 2 ′ C = O ⟶ R 2 ′ C = NR + H 2 O {\displaystyle {\ce {RNH2 + R'_2C=O -> R'_2C=NR + H2O}}} Reduction of these imines gives secondary amines: R 2 ′ C = NR + H 2 ⟶ R 2 ′ CH − NHR {\displaystyle {\ce {R'_2C=NR + H2 -> R'_2CH-NHR}}}
Similarly, secondary amines react with ketones and aldehydes to form enamines : R 2 NH + R ′ ( R ″ CH 2 ) C = O ⟶ R ″ CH = C ( NR 2 ) R ′ + H 2 O {\displaystyle {\ce {R2NH + R'(R''CH2)C=O -> R''CH=C(NR2)R' + H2O}}}
Mercuric ions reversibly oxidize tertiary amines with an α hydrogen to iminium ions: [ 19 ] Hg 2 + + R 2 NCH 2 R ′ ↽ − − ⇀ Hg + [ R 2 N = CHR ′ ] + + H + {\displaystyle {\ce {Hg^2+ + R2NCH2R' <=> Hg + [R2N=CHR']+ + H+}}}
An overview of the reactions of amines is given below:
Amines are ubiquitous in biology. The breakdown of amino acids releases amines, famously in the case of decaying fish which smell of trimethylamine . Many neurotransmitters are amines, including epinephrine , norepinephrine , dopamine , serotonin , and histamine . Protonated amino groups ( –NH + 3 ) are the most common positively charged moieties in proteins , specifically in the amino acid lysine . [ 20 ] The anionic polymer DNA is typically bound to various amine-rich proteins. [ 21 ] Additionally, the terminal charged primary ammonium on lysine forms salt bridges with carboxylate groups of other amino acids in polypeptides , which is one of the primary influences on the three-dimensional structures of proteins. [ 22 ]
Hormones derived from the modification of amino acids are referred to as amine hormones. Typically, the original structure of the amino acid is modified such that a –COOH, or carboxyl, group is removed, whereas the –NH + 3 , or amine, group remains. Amine hormones are synthesized from the amino acids tryptophan or tyrosine . [ 23 ]
Primary aromatic amines are used as a starting material for the manufacture of azo dyes . It reacts with nitrous acid to form diazonium salt, which can undergo coupling reaction to form an azo compound. As azo-compounds are highly coloured, they are widely used in dyeing industries, such as:
Most drugs and drug candidates contain amine functional groups: [ 24 ]
Aqueous monoethanolamine (MEA), diglycolamine (DGA), diethanolamine (DEA), diisopropanolamine (DIPA) and methyldiethanolamine (MDEA) are widely used industrially for removing carbon dioxide (CO 2 ) and hydrogen sulfide (H 2 S) from natural gas and refinery process streams. They may also be used to remove CO 2 from combustion gases and flue gases and may have potential for abatement of greenhouse gases . Related processes are known as sweetening . [ 26 ]
Amines are often used as epoxy resin curing agents. [ 27 ] [ 28 ] These include dimethylethylamine , cyclohexylamine , and a variety of diamines such as 4,4-diaminodicyclohexylmethane. [ 5 ] Multifunctional amines such as tetraethylenepentamine and triethylenetetramine are also widely used in this capacity. [ 29 ] The reaction proceeds by the lone pair of electrons on the amine nitrogen attacking the outermost carbon on the oxirane ring of the epoxy resin. This relieves ring strain on the epoxide and is the driving force of the reaction. [ 30 ] Molecules with tertiary amine functionality are often used to accelerate the epoxy-amine curing reaction and include substances such as 2,4,6-Tris(dimethylaminomethyl)phenol . It has been stated that this is the most widely used room temperature accelerator for two-component epoxy resin systems. [ 31 ] [ 32 ]
Low molecular weight simple amines, such as ethylamine , are toxic with LD 50 between 100 and 1000 mg/kg. They are skin irritants, especially as some are easily absorbed through the skin. [ 5 ] Amines are a broad class of compounds, and more complex members of the class can be extremely bioactive, for example strychnine . | https://en.wikipedia.org/wiki/RNH2 |
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RNR2 ( RNA, ribosomal 45S cluster 2 [ 2 ] ) is a human ribosomal DNA gene located on Chromosome 14 . Tandem copies of this gene form one of five nucleolus organizer regions in the human genome, they are located on the chromosomes 13 ( RNR1 ), 14 ( RNR2 ), 15 ( RNR3 ), 21 ( RNR4 ), 22 ( RNR5 ). [ 3 ] [ 2 ] Each gene cluster contains 30–40 copies and encodes a 45S RNA product that is then processed to form 18S, 5.8S and 28S rRNA . [ 2 ]
This protein -related article is a stub . You can help Wikipedia by expanding it .
This article on a gene on human chromosome 14 is a stub . You can help Wikipedia by expanding it .
This catalysis article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/RNR2 |
RNU2-2 syndrome is a neurodevelopmental disorder caused by de novo variants in the human gene RNU2-2 , which encodes an RNA component of the major spliceosome . It is characterized by epilepsy , intellectual disability, autistic behavior, microcephaly , hypotonia and hyperventilation . [ 1 ]
The syndrome is an autosomal dominant genetic disorder caused by de novo variants in RNU2-2 , a gene on chromosome 11 , which encodes the small nuclear RNA (snRNA) U2. U2 is a component of the major spliceosome, a complex of proteins and non-coding RNAs that is necessary for RNA splicing . Most cases of RNU2-2 syndrome are explained by the single nucleotide variants n.4G>A, n.35A>G, in roughly equal proportions. n.4G>A is thought to disrupt the interactions of snRNA U2 with the snRNA U6. n.35A>G is thought to disrupt the interaction of snRNA U2 with the 3′ branch sites of introns .
RNU2-2 syndrome was discovered by the statisticians Daniel Greene and Ernest Turro at the Icahn School of Medicine at Mount Sinai , using a Bayesian approach applied to data generated by Genomics England . [ 2 ] The same team were one of two groups to previously discover ReNU syndome , a related disorder caused by de novo variants in RNU4-2, that is 5 times more prevalent, using the same approach. [ 3 ] [ 1 ] | https://en.wikipedia.org/wiki/RNU2-2_syndrome |
RNU4-2 Syndrome or ReNU syndrome is a neurodevelopmental disorder caused by de novo variants in the human gene RNU4-2 , which encodes an RNA component of the major spliceosome . It is characterized by hypotonia , global developmental delay , severely impaired intellectual development with poor or absent speech, delayed walking or inability to walk, feeding difficulties with poor overall growth, dysmorphic facial features, and brain anomalies, including ventriculomegaly . [ 1 ] [ 2 ] [ 3 ] [ 4 ]
The syndrome is an autosomal dominant genetic disorder caused by de novo variants in RNU4-2 , a gene on chromosome 12 , which encodes the small nuclear RNA (snRNA) U4. U4 is a component of the major spliceosome, a complex of proteins and non-coding RNAs that is necessary for RNA splicing . Most cases of RNU4-2 / ReNU syndrome are explained by a 1-bp insertion (n.64_65insT, NR_003137.2), which is thought to disrupt the interactions of snRNA U4 with the snRNA U6, affecting the stability of the ACAGAGA loop of U6 sRNA which binds 5' splice sites and induces splicing after U4-U6 unwinding. [ 1 ] [ 2 ] [ 3 ] Disrupted splicing, in particular a change in 5' splice site usage, has been reported in individuals with variants in RNU4-2 . [ 2 ]
The genetic etiology of RNU4-2 / ReNU syndrome was identified independently by two research groups, both of which used data collected by Genomics England . The statisticians Daniel Greene and Ernest Turro at the Icahn School of Medicine at Mount Sinai , used a Bayesian approach to identify the genetic association. [ 5 ] [ 3 ] [ 6 ] The other team involved a global collaboration led by Yuyang Chen and Nicola Whiffin of the University of Oxford . [ 2 ]
Neurodevelopmental disorder with hypotonia, brain anomalies, distinctive facies, and absent language (NEDHAFA) was a suggested name for this syndrome, however, ReNU syndrome (pronounced 'renew') was chosen through a collaboration between researchers and the families of those impacted by variants in RNU4-2 . The name symbolises that this diagnosis “renews” hope for a brighter future for all those affected. [ 7 ]
An etiologically related disorder RNU2-2 syndrome has been identified by Greene and Turro. [ 8 ] RNU2-2 syndrome is a major spliceosome disorder with similar symptoms to RNU4-2 / ReNU syndrome but it is five times less prevalent. | https://en.wikipedia.org/wiki/RNU4-2_syndrome |
RNase H-dependent PCR (rhPCR) [ 1 ] is a modification of the standard PCR technique. In rhPCR, the primers are designed with a removable amplification block on the 3’ end. Amplification of the blocked primer is dependent on the cleavage activity of a hyperthermophilic archaeal Type II RNase H enzyme during hybridization to the complementary target sequence. This RNase H enzyme possesses several useful characteristics that enhance the PCR. First, it has very little enzymatic activity at low temperature, enabling a “ hot start PCR ” without modifications to the DNA polymerase . Second, the cleavage efficiency of the enzyme is reduced in the presence of mismatches near the RNA residue. This allows for reduced primer dimer formation, [ 1 ] detection of alternative splicing variants, [ 2 ] [ 3 ] ability to perform multiplex PCR with higher numbers of PCR primers, and the ability to detect single-nucleotide polymorphisms . [ 4 ]
rhPCR primers consist of three sections. 1) The 5’ DNA section, equivalent in length and melting temperature (Tm) requirements to a standard PCR primer, is extended after cleavage by the RNase HII enzyme. 2) A single RNA base provides the cleavage site for the RNase HII. 3) A short 3’ extension of four or five bases followed by a blocker (usually a short, non-extendable molecule like a propanediol ) prevents extension by a DNA polymerase until removal. A rhPCR reaction begins with the primers and template free in solution (Figure 1). While free in solution, these primers are not deblocked by the RNase HII enzyme, as they must be in an RNA:DNA heteroduplex with the template to be cleaved. Once bound to the template, the rhPCR primers are cleaved by the thermostable RNase HII enzyme. This removes the block, allowing for the DNA polymerase to extend off of the primers. The cycling of the PCR reaction continues the process. rhPCR primers are designed so that after cleavage by the RNase H2 enzyme, the Tm of the primers are still greater than the annealing temperature of PCR reaction. These primers can be used in both 5’ nuclease Taqman and SYBR Green types of quantitative PCR .
rhPCR can be used for quantitative PCR and medical or environmental laboratories: | https://en.wikipedia.org/wiki/RNase_H-dependent_PCR |
ROMeo [ 1 ] [ 2 ] Rigorous Online Modelling and Equation Based Optimization is an advanced online chemical process optimizer of SimSci, a brand of Aveva software [ 3 ] It is mainly used by process engineers in the chemical , petroleum and natural gas industries.
It includes a chemical component library , thermodynamic property prediction methods, and unit operations such as distillation columns , heat exchangers , compressors , and reactors as found in the chemical processing industries.
It can perform steady state mass and energy balance calculations for modeling, simulating and optimizing continuous processes. [ 4 ] [ 5 ]
ROMeo 6.0 has been released with increased access to native Refinery Process Models based on technology from ExxonMobil.
From ROMeo 7.0, ROMeo changed from 32 bit to 64bit.
ROMeo changed the name to AVEVA Process Optimization from 2020 version. | https://en.wikipedia.org/wiki/ROMeo_(process_optimizer) |
Rho-related GTPases from plants, otherwise known as ROPs, are involved in cell polarity through the regulation of cytoskeleton components like actin and microtubules . [ 1 ] [ 2 ] Unlike mammalian cells, plant cells do not contain heterotrimeric G proteins like Cdc42 , Rac, and Rho that are known to regulate cellular polarity. [ 2 ]
ROP proteins are a type of monomeric G proteins found in plants belonging to the Rho family. [ 1 ] ROP binding to GTP or GDP determines its activity due to conformational changes within its structure. [ 1 ] Within the G-domain of the structure are the G-box motifs G1-5. These motifs are formed during protein folding and are composed of conserved sequences that are responsible for nucleotide and magnesium binding as well as hydrolysis of GTP. [ 1 ] Motifs G2 (switch I loop) and G3 (switch II loop) possess distinct conformations depending on GTP binding state. [ 1 ] In addition, the G-domain contains a unique and conserved helical domain commonly found in Rho family proteins called αi. [ 1 ]
Specific locations within the 3D ROP protein structure, including the amino acids 13-20, 60-64, and 118-121, act as binding sites during protein activity. [ 3 ] The serine residue at amino acid 74 has been shown to be a potential protein activity regulation site through phosphorylation. [ 4 ]
This plant physiology article is a stub . You can help Wikipedia by expanding it .
This protein -related article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/ROP_GTPase |
ROSAT (short for Röntgensatellit ; in German X-rays are called Röntgenstrahlen, in honour of Wilhelm Röntgen ) was a German Aerospace Center -led satellite X-ray telescope , with instruments built by West Germany , the United Kingdom and the United States. It was launched on 1 June 1990, on a Delta II rocket from Cape Canaveral , on what was initially designed as an 18-month mission, with provision for up to five years of operation. ROSAT operated for over eight years, finally shutting down on 12 February 1999.
In February 2011, it was reported that the 2,400 kg (5,291 lb) satellite was unlikely to burn up entirely while re-entering the Earth's atmosphere due to the large amount of ceramics and glass used in construction. Parts as heavy as 400 kg (882 lb) could impact the surface. [ 2 ] ROSAT eventually re-entered the Earth's atmosphere on 23 October 2011 over the Bay of Bengal . [ 3 ]
The Roentgensatellit (ROSAT) was a joint German, U.S. and British X-ray astrophysics project. [ 4 ] ROSAT carried a German-built imaging X-ray Telescope (XRT) with three focal plane instruments: two German Position Sensitive Proportional Counters (PSPC) and the US-supplied High Resolution Imager (HRI). The X-ray mirror assembly was a grazing incidence four-fold nested Wolter I telescope with an 84-cm diameter aperture and 240-cm focal length. The angular resolution was less than 5 arcsecond at half energy width (the "angle within which half of the electromagnetic radiation" [ 5 ] is focused). The XRT assembly was sensitive to X-rays between 0.1 and 2 keV (one thousand Electronvolt ).
In addition, a British-supplied extreme ultraviolet (XUV) telescope, the Wide Field Camera (WFC), was coaligned with the XRT and covered the energy band from 0.042 to 0.21 keV (30 to 6 nm ).
ROSAT's unique strengths were high spatial resolution, low-background, soft X-ray imaging for the study of the structure of low surface brightness features, and for low-resolution spectroscopy.
The ROSAT spacecraft was a three-axis stabilized satellite which can be used for pointed observations, for slewing between targets, and for performing scanning observations on great circles perpendicular to the plane of the ecliptic . ROSAT was capable of fast slews (180 deg. in ~15 min.) which makes it possible to observe two targets on opposite hemispheres during each orbit. The pointing accuracy was 1 arcminute with stability less than 5 arcsec per sec and jitter radius of ~10 arcsec. Two CCD star sensors were used for optical position sensing of guide stars and attitude determination of the spacecraft. The post facto attitude determination accuracy was 6 arcsec.
The ROSAT mission was divided into two phases:
The main assembly was a German-built imaging X-ray Telescope (XRT) with three focal plane instruments: two German Position Sensitive Proportional Counters (PSPC) and the US-supplied High Resolution Imager (HRI). The X-ray mirror assembly was a grazing incidence four-fold nested Wolter I telescope with an 84 cm (33 in) diameter aperture and 240 cm (94 in) focal length. The angular resolution was less than 5 arcsec at half energy width. The XRT assembly was sensitive to X-rays between 0.1 and 2 keV. [ 4 ]
There are two Position Sensitive Proportional Counters (PSPC), PSPC-B and PSPC-C, mounted on a carousel within the focal plane turret of ROSAT. PSPC-C was intended to be the primary detector for the mission and was used for the bulk of the All-Sky Survey until it was destroyed during the AMCS glitch on 25 January 1991. After the glitch, PSPC-B was used for all further observations. Two more PSPCs(PSPC-A and PSPC-D) were mounted on ROSAT for ground calibration. [ 6 ]
Each PSPC is a thin-window gas counter. Each incoming X-ray photon produces an electron cloud whose position and charge are detected using two wire grids. The photon position is determined with an accuracy of about 120 micrometers. The electron cloud's charge corresponds to the photon energy, [ 7 ] with a nominal spectral bandpass 0.1-2.4 keV.
The US-supplied High Resolution Imager used a crossed grid detector with a position accuracy to 25 micrometers. [ 8 ] The instrument was damaged by solar exposure on 20 September 1998.
The Wide Field Camera (WFC) was a UK-supplied extreme ultraviolet (XUV) telescope co-aligned with the XRT and covered the wave band between 300 and 60 angstroms (0.042 to 0.21 keV). [ 4 ]
ROSAT was originally planned to be launched on the Space Shuttle but the Challenger disaster caused it to be moved to the Delta platform. This move made it impossible to recapture ROSAT with a Shuttle and bring it back to Earth. [ citation needed ]
Originally designed for a five-year mission, ROSAT continued in its extended mission for a further four years before equipment failure forced an end to the mission. For some months after this, ROSAT completed its very last observations before being finally switched off on 12 February 1999. [ 9 ]
On 25 April 1998, failure of the primary star tracker on the X-ray Telescope led to pointing errors that in turn had caused solar overheating. [ 10 ] A contingency plan and the necessary software had already been developed to utilise an alternative star tracker attached to the Wide Field Camera .
ROSAT was soon operational again, but with some restrictions to the effectiveness of its tracking and thus its control. [ 11 ] It was severely damaged on 20 September 1998 when a reaction wheel in the spacecraft's Attitude Measuring and Control System reached its maximum rotational speed, [ note 1 ] losing control of a slew, damaging the High Resolution Imager by exposure to the sun. [ 11 ] This failure was initially attributed to the difficulties of controlling the satellite under these difficult circumstances outside its initial design parameters. [ 11 ]
In 2008, NASA investigators were reported to have found that the ROSAT failure was linked to a cyber-intrusion at Goddard Space Flight Center . [ 12 ] The root of this allegation is a 1999 advisory report by Thomas Talleur, senior investigator for cyber-security at NASA. [ 12 ] This advisory [ 13 ] is reported to describe a series of attacks from Russia that reached computers in the X-ray Astrophysics Section (i.e. ROSAT's) at Goddard , and took control of computers used for the control of satellites, not just a passive "snooping" attack. The advisory stated:
"Hostile activities compromised [NASA] computer systems that directly and indirectly deal with the design, testing, and transferring of satellite package command-and-control codes." [ 13 ]
The advisory is further reported as claiming that the ROSAT incident was "coincident with the intrusion" [ 12 ] and that, "Operational characteristics and commanding of the ROSAT were sufficiently similar to other space assets to provide intruders with valuable information about how such platforms are commanded,". [ 12 ] Without public access to the advisory, it is obviously impossible to comment in detail. Even if it did describe a real intrusion, there is a plausible "no attack" explanation for ROSAT's failure, and the report is claimed to link the two incidents as no more than "coincident." [ original research? ] However, NASA officials in charge of the day-to-day operations of the ROSAT mission at Goddard, including GSFC Rosat Project Scientist Rob Petre, say definitively that no such incident occurred. Talleur's information appears to have come from one of his interns who exaggerated a hacking incident on an office computer not related to flight operations. [ 14 ]
IT security remains a significant issue for NASA. Other systems including the Earth Observing System have also been attacked. [ 15 ]
In 1990, the satellite was put in an orbit at an altitude of 580 km (360 mi) and inclination of 53°. [ 16 ] Due to atmospheric drag, the satellite slowly lost height until, in September 2011, the satellite was orbiting approximately 270 km (168 mi) above the Earth. On 23 October 2011 ROSAT re-entered the Earth's atmosphere sometime between 1:45 UTC and 2:15 UTC over the Bay of Bengal , east of India. There was no confirmation if pieces of debris had reached the Earth's surface. [ 17 ] [ 18 ] [ 19 ]
eROSITA launched on board the Russian-German Spektr-RG space observatory in 2019. [ 20 ] It will provide an updated all-sky survey of the X-ray sky, extending the energy range to 10keV, increase the sensitivity by a factor of 25 and improve the spatial and spectral resolution. | https://en.wikipedia.org/wiki/ROSAT |
The resistivity of solvent extract ( ROSE ) test is a test for the presence and average concentration of soluble ionic contaminants, for example on a printed circuit board (PCB). [ 1 ] [ 2 ] [ 3 ] [ 4 ] It was developed in the early 1970s. [ 5 ] Some manufacturers use it as part of Six Sigma processes. [ 3 ]
Some modern fluxes have low solubility in traditional ROSE solvents such as water and isopropyl alcohol , and therefore require the use of different solvents. [ 6 ] [ 7 ]
This article about analytical chemistry is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/ROSE_test |
Reliable Quantum Operations Per Second (rQOPS) is a metric that measures the capabilities and error rates of a quantum computer . It combines several key factors to measure how many reliable operations a computer can execute in a single second: logical error rates, clock speed , and number of reliable qubits . [ 1 ] [ 2 ] [ 3 ]
The quantities included in rQOPS can be measured in all quantum computer architectures, allowing different architectures to be compared with one standard metric. A larger rQOPS measurement indicates a faster and more accurate device capable of solving more complex problems.
Microsoft suggest that a machine with 1 million rQOPS qualifies as a quantum supercomputer. [ 3 ] [ 1 ] [ 4 ]
Alternative benchmarks include quantum volume , cross-entropy benchmarking , Circuit Layer Operations Per Second (CLOPS) proposed by IBM and IonQ 's Algorithmic Qubits. [ 5 ] [ 6 ] [ 7 ] However, as opposed to considering qubit performance alone, rQOPS measures how capable a quantum system is at solving tangible problems.
rQOPS is calculated as rQOPS=Q x f, at a corresponding logical error rate pL., where Q is the number of logical qubits and f is the hardware's logical clock speed. Microsoft has selected this metric for the higher quantum computing implementation levels as it encompasses scale, speed, and reliability. [ 1 ]
rQOPS =[Q][f] | https://en.wikipedia.org/wiki/RQOPS |
The Rice–Ramsperger–Kassel–Marcus ( RRKM ) theory is a theory of chemical reactivity . [ 1 ] [ 2 ] [ 3 ] It was developed by Rice and Ramsperger in 1927 [ 4 ] and Kassel in 1928 [ 5 ] (RRK theory [ 6 ] ) and generalized (into the RRKM theory) in 1952 by Marcus [ 7 ] who took the transition state theory developed by Eyring in 1935 into account. These methods enable the computation of simple estimates of the unimolecular reaction rates from a few characteristics of the potential energy surface .
Assume that the molecule consists of harmonic oscillators , which are connected and can exchange energy with each other.
Assume that A * is an excited molecule:
where P stands for product, and A ‡ for the critical atomic configuration with the maximum energy E 0 along the reaction coordinate .
The unimolecular rate constant k u n i {\displaystyle k_{\mathrm {uni} }} is obtained as follows: [ 8 ]
where k ( E , J ) {\displaystyle k(E,J)} is the microcanonical transition state theory rate constant, G ‡ {\displaystyle G^{\ddagger }} is the sum of states for the active degrees of freedom in the transition state, J {\displaystyle J} is the quantum number of angular momentum, ω {\displaystyle \omega } is the collision frequency between A ∗ {\displaystyle A^{*}} molecule and bath molecules, Q r {\displaystyle Q_{r}} and Q v {\displaystyle Q_{v}} are the molecular vibrational and external rotational partition functions. | https://en.wikipedia.org/wiki/RRKM_theory |
RRT Global is an international company that specializes in the development of technologies for oil refining process. The company's CEO , Douglas Harris, is a former vice president of TNK-BP . [ 3 ] [ 4 ] The company is a resident of the Energy Efficient Technologies cluster of the Skolkovo Foundation . [ 5 ] [ 6 ] [ 7 ] RRT Global is the first company to implement the conversion of light gasoline fractions in a combined process. [ 4 ]
The company was founded in St. Petersburg by chemical engineers Oleg Parputs ( Russian : Олег Парпуц ) and Oleg Giiazov ( Russian : Олег Гиязов ), [ 4 ] [ 8 ] who had previously worked in an engineering company that served the oil refining sector. [ 1 ] Startup financing was provided by Foresight Ventures, Bright Capital [ 4 ] and the Skolkovo Foundation. [ 1 ]
The first laboratory was established on the campus of the Saint Petersburg State Institute of Technology . [ 4 ] The laboratory was unheated, which meant that researchers had to work there for 6–8 hours in padded jackets. [ 9 ]
The company became a resident of the Energy Efficient Technologies cluster of the Skolkovo Foundation in 2011. [ 3 ] Douglas Harris, the former Vice President of Refining at BP and TNK-BP , became the company’s CEO in the same year. [ 1 ] The company has patented the PRIS technology in Russia, Europe and the United States. [ 10 ]
The Prime Minister of the Russian Federation , Dmitry Medvedev , met with the company’s management team in October 2011, [ 10 ] [ 11 ] and visited the company’s laboratory in September 2012 [ 5 ] [ 6 ] during his official visit to Saint Petersburg.
The company was rated one of the Top 10 Startups of the Year in 2012 by the Russian Startup Rating. [ 11 ]
After conducting a company audit in 2012, PricewaterhouseCoopers awarded the company an AAA rating. [ 11 ]
In 2015-2016 RRT Global formed technology alliances with American engineering company KBR and Russian IT company Yandex . [ 12 ] [ 13 ]
The company is headquartered in the United States . [ 1 ] RRT Global has subsidiary operating in the Russian Federation [ 5 ] [ 1 ]
RRT Global’s R&D center is located in St. Petersburg. [ 14 ] [ 15 ] The center includes a pilot plant park, laboratory facilities for studying catalytic systems , an analytical laboratory, and an administrative and logistics center.
The company’s senior management includes Dmitry Shalupkin ( CTO ), Douglas Harris ( CEO ), Oleg Giiazov (Director in Russia). [ 16 ]
One of the company’s areas of focus is to improve the technology to obtain MSAT-2 gasoline components based on combining catalytic systems and refining in a single unit. [ 17 ] The company is making extensive use of 3D printing for the production of certain equipment components. [ 18 ]
PRIS is a technology developed by the company for converting light gasoline fractions in a combined process. [ 19 ] Papers on this technology have been published in the journal Chemical Engineering and Processing , as well as other specialized scientific journals. Worldwide Refinery Processing Review Included the technology in four of the State-of-the-Art commercial isomerization technologies, together with international providers of advanced technologies: UOP, Axens, GTC. [ 4 ] Rossiyskaya Gazeta called the technology “revolutionary”. [ 10 ]
According to this technology, refining and catalytic systems are combined in a single unit, reducing capital and energy costs [ 20 ] [ 21 ] and reducing environmental pollution. [ 3 ] [ 22 ] A similar combination principle had previously been used primarily in the pharmaceutical industry . [ 3 ] The PRIS technology allows the use of a low-octane straight-run gasoline fraction with a benzole -containing fraction as raw materials. [ 23 ] The technology allows the production of high-octane gasoline components meeting the EURO 5 standard. [ 23 ]
IС7 is a technology developed by the company for isomerization product of oil refining, heptanes. Earlier heptanes not found practical applications and have been used as solvents. The technology helps to increase production of high-octane gasoline. [ 24 ] | https://en.wikipedia.org/wiki/RRT_Global |
The Xbox 360 video game console was subject to a number of technical problems and failures, some as a result of design flaws. Some issues could be identified by a pattern of red lights on the front face of the console; these colloquially became known as the " Red Ring of Death " or the " RRoD ". [ 1 ] [ 2 ] There were also other issues, such as discs becoming scratched in the drive and " bricking " of consoles due to dashboard updates.
There were many conflicting estimates of the console's unusually high failure rate . [ 3 ] [ 4 ] [ 5 ] The warranty provider SquareTrade estimated it at 23.7% in 2009, [ 6 ] while a Game Informer survey reported 54.2%. [ 7 ] Among the consoles owned by employees of Joystiq , which saw heavy use for games journalism purposes, the failure rate had reached 90% by the end of 2007. [ 8 ] The crisis was ultimately abated from 2009 by design revisions to the later-produced Xbox models; the S model in particular was far more resilient. By 2012 the failure rate for the Xbox 360 family was comparable to the PS3 failure rate. [ 9 ]
The issues proved extremely damaging for Microsoft . Repairs and shipping of replacement hardware cost the company $1.15bn. The issues triggered multiple lawsuits , [ 10 ] cost the Xbox ground in the console wars and threatened the long term viability of the Xbox brand. [ 11 ]
The design of the Xbox 360 was a hurried process subject to a number of late changes. This included the addition of a hard disk drive, which compromised airflow in the machine. The holes in the case were added to try and ameliorate this airflow issue. Time pressures also resulted in insufficient testing. Microsoft were aware of a myriad of technical challenges as early as August 2005, including "overheating graphics chips, cracking heat sinks, cosmetic issues with the hard disk and the front of the box, underperforming graphics memory chips from Infineon , a problem with the DVD drive - and more". Thermal issues with the GPU were ultimately what caused the infamous "Red Ring" issues, while the DVD drive issue was later responsible for scratching discs. An engineer requested a shut down of the production line that month, but this did not occur out of fear of a delay to console delivery in some regions. [ 12 ]
The console launched in November 2005 in North America, swiftly followed by other regions. However, consoles began failing "almost immediately". Microsoft initially dismissed these concerns as "isolated reports", that were within the normal range of failure (around 2%). [ 12 ] [ 13 ] [ 14 ] [ 15 ] [ 16 ] In late 2005, Microsoft's internal data was reporting a failure rate during manufacturing of around 6-7%. These consoles were not shipped to consumers but remained in warehouses. By March 2006, around 30% of consoles manufactured were either returned or had failed checks at the factory. At one point Microsoft's yield was as low as 32% (meaning a failure rate of 68%) [ 17 ]
Peter Moore , the Vice President of Microsoft's Interactive Entertainment Business division in 2015 detailed a conversation he had with Microsoft CEO Steve Ballmer on his planned response to the incident in the mid 2000s. He stated:
"...here's what we have to do: we need to FedEx an empty box to a customer who had a problem - they would call us up - with a FedEx return label to send your box, and then we would FedEx it back to them and fix it. ... I always remember $240m of that was FedEx. ... It was sickening. I was doing a lot of interviews. ... We couldn't figure it out. ... There was a theory. We had changed our solder, which is the way you put the GPU and the fans, to lead-free. ... We think it was somehow the heat coming off the GPU was drying out some of the solder, and it wasn't the normal stuff we'd used, because we had to meet European Standards and take the lead out. ... He said, 'what's it going to cost?' I remember taking a deep breath, looking at Robbie, and saying, 'we think it's $1.15bn, Steve.' He said, 'do it.' There was no hesitation. ... If we hadn't made that decision there and then, and tried to fudge over this problem, then the Xbox brand and Xbox One wouldn't exist today." [ 11 ]
In July 2007 Moore published an open letter recognizing the console's problems, as well as announcing a three-year warranty from the original date of purchase for every Xbox 360 console that experienced the "general hardware failure" (Red Ring) issue. [ 18 ] That October a class action lawsuit was brought against Microsoft due to the problems the console had with disc scratching, which could render games unplayable. [ 19 ] The case was lengthy and worked through the court system over the following decade, with litigation focusing on the validity of class certification. In 2017 the matter was decided by the United States Supreme Court in Microsoft Corp. v. Baker , which settled in favour of Microsoft.
During the Game Developers Conference in February 2008, Microsoft announced that the failure rate had "dropped", but did not mention any specifics. [ 20 ] The same month, electronics warranty provider SquareTrade published an examination of 1040 Xbox 360s and said that they suffered from a failure rate of 16.4%. Of the 171 failures, 60% were due to a general hardware failure (and thus fell under the 3 year extended warranty). And of the remaining 40% which were not covered by the extended warranty, 18% were disc read errors, 13% were video card failures, 13% were hard drive freezes, 10% were power issues and 7% were disc tray malfunctions. [ 21 ] [ 22 ] SquareTrade also stated that its estimates are likely significantly lower than reality due to the time span of the sample (six to ten months), the eventual failure of many consoles that did not occur within this time span and the fact that most owners did not deal with SquareTrade and had their consoles repaired directly through Microsoft via the extended RROD warranty.
From 2009 the crisis began to abate due to design revisions. The Jasper models sold that year had a failure rate of under 4%, with the overall product family rate at around 12% in the first quarter. [ 23 ] The Xbox 360 S launched in 2010 and had a far lower failure rate. The S models did not include segmented outer ring lights like the launch model, and were not included in the extended warranty. [ 24 ] The 360 family as a whole was discontinued in 2016, but Microsoft continued to offer repairs for a time after that. [ 25 ]
Microsoft did not reveal the full technical details of the problem until a 2021 documentary on the history of Xbox, though earlier independant investigations had correctly indentified the issues with the GPU and soldering. [ 26 ] In a nod to the incident, Microsoft sold Red Ring holiday sweaters in December 2024. The item was popular among Microsoft employees. [ 27 ]
The launch model of the Xbox 360 includes four lights in a ring around the power button, on the front face of the console. Green indicated normal operation, while red lights were used for error codes. Most famously, three red lights indicated a "general hardware failure". [ 28 ] The error was coined the "Red Ring of Death" after Windows ' Blue Screen of Death error. The error was sometimes preceded by freeze-ups, graphical problems in the middle of gameplay, such as checkerboard or pinstripe patterns on the screen, and sound errors; mostly consisting of extremely loud noises that couldn't be affected by the volume control, and the console only responding when the power button was pressed to turn it off. [ 29 ] The problem was most prevalent in early models.
This error code was usually caused by the failure of one or more hardware components, although it could indicate that the console is not receiving enough power from the power supply. This coould be caused by a faulty or improperly connected power supply. The three flashing lights could also be caused by power surges. Unplugging and restarting the console fixed this issue in some cases. [ 30 ] [ 31 ]
On the Xbox 360 S and E models, the power button utilizes a different design that does not incorporate the same style of lighting that past models used. [ 32 ] A flashing red light means that the console is overheating, similar to the two-light error code on the original model Xbox 360; however, an on-screen message also appears, telling the user that the console will automatically power off to protect itself from overheating. A solid red light is similar to the one-light error if an "E XX" error message is displayed and a three-light error code if the error message is absent.
The related E74 error caused only a single of the red ring quadrants to illuminate, and the screen to display an error message in multiple languages: "System Error. Contact Xbox Customer Support", with the code E74 at the bottom. Much like the infamous Red Ring issue, the error was related to connection issues with the GPU, but could also be caused by a more general GPU failure or failing eDRAM. The E74 issue was covered by the three-year extended warranty from 2009 as Microsoft considered it part of the same issue as the Red Ring, and customers who previously paid Microsoft for out-of-warranty service to correct the E74 error received a refund. [ 33 ] [ 34 ] [ 35 ]
The console would illuminate all four lights if it could not detect an AV cable. This was not triggered by later revisions of the console which included an HDMI port. In some cases the four lights indicated a more serious problem with the console, followed by a 2-digit error code. [ 36 ] The four lights would also be illuminated briefly by power issues such as surges or brief outages.
Microsoft did not reveal the cause of the issues publicly until 2021, when a 6-part documentary on the history of Xbox was released. The Red Ring issue was caused by the cracking of solder joints inside the GPU flip chip package, connecting the GPU to the substrate interposer, as a result of thermal stress from heating up and cooling back down when the system is power cycled. [ 37 ] Microsoft had switched to lead-free solder due to regulations in the European Union , but using the incorrect alternative resulted in fracturing. [ 12 ]
While the cause was not confirmed by Microsoft until 2021, many independant investigations came to similar conclusions at the time, identifying thermal stress on the GPU and the solder as the culprit. The German computer magazine c't blamed the problem primarily on the use of the wrong type of lead-free solder, a type that when exposed to elevated temperatures for extended periods of time becomes brittle and can develop hair-line cracks that are almost irreparable. [ 38 ] Microsoft designed the chip in-house to cut out the traditional ASIC vendor with the goal of saving money in ASIC design costs. After multiple product failures, Microsoft went back to an ASIC vendor and had the chip redesigned so it would dissipate more heat. [ 39 ] [ 40 ]
The Guardian also claimed that using Xbox Kinect with an old Xenon generation Xbox would cause the Red Ring, but this was denied by Microsoft. [ 41 ]
The design of the disc drive was flawed, and could cause scratches on discs, particularly if the console was moved while the disc was spinning. Unlike the Red Ring issues, the disc scratching was not resolved by hardware revisions and was present in the S and E models. Those versions shipped with a sticker informing users that moving the console while powered on posed a risk. [ 42 ] Even on static footing however, normal floor vibrations that would occur in a household environment were enough to cause disc scratches. [ 43 ] The issue was particularly prevalent in 2006 models.
The issue was subject to multiple independant investigations, initially by the Dutch television program Kassa and later by the European Commissioner for Consumer Protection and the BBC . The BBC investigation in particular involved laboratory conditions for testing. [ 44 ] The issue ultimately led to a Supreme Court case which was ruled in favour of Microsoft in 2017. [ 45 ] [ 46 ]
Although discs scratched by the Xbox 360 were not covered under its warranty, [ 47 ] Microsoft's Xbox Disc Replacement Program [ 48 ] sold customers a new copy of discs scratched by the Xbox 360, if they were published in countries where the Xbox was originally sold, at a cost of $20. [ 49 ] The published list of games that qualify, however, was limited. [ 50 ] Third party games were only ever replaced at the discretion of the publishers. Electronic Arts for example offered replacements made within 90 days of purchase. [ 51 ]
Independant investigations concluded that the disc drives lacked a mechanism to secure the disc solidly in place. [ 52 ] Tilting or moving the console, when operating with a disc spinning inside, can potentially cause damage to the disc and in some cases render the disc unplayable as a result. [ 53 ] Microsoft engineers were aware of the issue ahead of launch, around September or October of 2005. However, installing "bumpers" to prevent the discs moving out of alignment would have added 50 cents to the production cost of each console, and was not implemented. An alternative would have been to slow the disc rotation speed but this would have led to increased loading times, and magnetic adjustments would not have been possible due to the disc tray locking mechanism. [ 54 ]
Several Xbox 360 system updates caused major issues for users.
An update patch released on November 1, 2006 was reported to " brick " consoles, rendering them useless. [ 55 ] The most obvious issue occurs after the installation of the patch, after which the console immediately reboots and shows an error message. Usually, error code E71 is shown during or directly after the booting animation.
In response to the November 2006 update error that "bricked" his console, a California man filed a class action lawsuit against Microsoft in Washington federal court in early December 2006. [ 56 ] The lawsuit seeks $5 million in damages and the free repair of any console rendered unusable by the update. This was the second such lawsuit filed against Microsoft, the first having been filed in December 2005, shortly after the 360's launch. Following Microsoft's extension of the Xbox 360 warranty to a full year, from the previous 90 days, the California man's attorney confirmed to the Seattle Post Intelligencer that the lawsuit had been resolved under confidential terms. [ 57 ]
On November 19, 2008, Microsoft released the " New Xbox Experience " (NXE). This update provided streaming Netflix capability and avatars; however, some users have reported the update has caused their consoles to not properly read optical media. [ 1 ] Others have reported that the update has disabled audio through HDMI connections. [ 58 ] A Microsoft spokesperson stated the company is "aware that a handful of Xbox LIVE users are experiencing audio issues, and are diligently monitoring this issue and working towards a solution." Microsoft released a patch on February 3, 2009 for the HDMI audio issues. [ 59 ]
A patch released in May 2011 prevented some users from playing games from discs. The update involved "a change in the disc reading algorithms", but would simply inform users that the disc was unreadable and ask them to clean it with a cloth. [ 60 ]
In 2007, the official steering wheel peripheral faced issues with overheating and releasing smoke, prompting the "Hotwheels" nickname. Microsoft encouraged users to only use the steering wheel in battery mode rather than while plugged in. [ 61 ] That August a product recall was issued, with Microsoft retrofitting the existing steering wheels to remedy the problem. [ 62 ]
The Nyko Intercooler was a popular aftermarket cooler, purchased by users who wished to improve air flow in an attempt to avoid the red-ring issue. While the exact cause of red-ring was not yet public in the late 2000s, it was known that temperature was an issue. [ 63 ] [ 64 ] Unfortunately, the Nyko Intercooler itself had issues and its usage could cause the red-ring or damage the power DC input. [ 64 ] The Intercooler could also melt itself onto the 360, melt the powercord, or make itself extremely hard to remove. [ 65 ]
Microsoft stated that the peripheral drained too much power from the console (the Intercooler power cord was installed between the Xbox 360 power supply and the console itself), could cause faults to occur, and stated that consoles fitted with the peripheral would have their warranties voided. Nyko released an updated Intercooler that used its own power source, and claimed the problem no longer occurred, but this did not affect Microsoft's stance on the warranty. | https://en.wikipedia.org/wiki/RRoD |
The blue screen of death ( BSoD ) – or blue screen error , blue screen , fatal error , bugcheck , and officially known as a stop error [ 1 ] [ 2 ] [ 3 ] – is a critical error screen displayed by the Microsoft Windows operating systems to indicate a system crash , in which the operating system reaches a critical condition where it can no longer operate safely.
The name comes from the blue colored background used predominately on the error screens found in the majority of Windows releases. Possible issues contributing to a BSoD may include hardware failures, an issue with or without a device driver, viruses , malware , and other factors such as intentional user action.
Blue screen errors have been around since the first beta release of Windows 1.0 ; if Windows detects a newer DOS version than the one it expected, the boot screen would have the text "Incorrect DOS version" alongside other messages detailing what check failed to pass appended into it before starting normally. [ 4 ] This was retained in the final release (version 1.01), however it mostly prints out random characters instead due to the remaining text messages being removed during development. [ 4 ] However, this is not a screen of death; upon crashing, Windows 1.0 locks up or terminates and the user is returned to DOS. This behavior is also present in Windows 2.0 and Windows 2.1 .
Windows 3.0 uses a text-mode screen for displaying important system messages, usually from digital device drivers in 386 Enhanced Mode or other situations where a program could not run. Windows 3.1 changed the color of this screen from black to blue. It also displays a blue screen when the user presses the Ctrl+Alt+Delete key combination to bring up a rudimentary task manager , reserved for quitting any unresponsive programs if they are available. Like previous versions of Windows before 3.0, Windows 3.x exits to DOS if an error condition is severe enough.
The first BSoD to indicate a critical system error appeared in Windows NT 3.1 (the first version of the Windows NT family, released in 1993). [ 5 ] The error screens initially started with *** STOP: in its earlier iterations, hence it became known as a "stop error." This format was used on all Windows operating systems released afterwards, with various differences in later versions. Despite popular belief, there are no known equivalents of a BSoD in the Windows Embedded Compact (formerly known as Windows CE) line of embedded operating systems. [ 6 ]
BSoDs can be caused by poorly written device drivers or malfunctioning hardware, [ 7 ] such as faulty memory , power supply problems, overheating of components, or hardware running beyond its specification limits. In the Windows 9x line of operating systems, incompatible DLLs or bugs in the operating system kernel could also cause BSoDs. [ 8 ] Because of the general instability and lack of memory protection in Windows 9x, BSoDs were much more common.
On September 4, 2014, several online journals such as Business Insider , DailyTech , Engadget , Gizmodo , Lifehacker , Neowin , Softpedia , TechSpot , Boy Genius Report ( BGR ), The Register , and The Verge , [ 9 ] as well as print and non-English sources like PC Authority and Austrian tech site FutureZone [ 10 ] all attributed the creation of the Blue Screen of Death to Steve Ballmer , the former CEO of Microsoft. The articles specifically cited a blog post by Microsoft employee Raymond Chen entitled "Who wrote the text for the Ctrl+Alt+Del dialog in Windows 3.1?", [ 11 ] which focused on the creation of the first rudimentary task manager in Windows 3.x. The aforementioned task manager shared some visual similarities with a BSOD, with Ballmer writing the messages that appeared on the screen. [ 11 ]
Chen had to address this widespread misinformation himself in a blog post on September 9, 2014. According to his post, he was scathing on his evaluation of major tech news sites that had picked up on the incorrect story and performed poor or non-existent research that demonstrated complete ignorance of his original account. He indicated that, in addition to the faulty base story, over half a dozen significant sites had included other embellished or invented details in their stories, including incorrectly naming Chen as a Microsoft executive, treating Chen as an "official company spokesperson", and using unrelated images from Windows NT or Windows 95 as illustrations. In addition, he also pointed out a very special mention for the worst single distortion out of any misinformations, which belonged to BGR (Boy Genius Report), who "fabricated a scenario and posited it as real" in a rhetorical question to readers. He also found that several sources had conflated the creation of the BSoD with the fact that they occur, thus inverting cause and effect by implying that the invention of BSoDs caused fatal errors to occur instead of their actual, helpful function of giving the user information about a fatal error after the system has already become unrecoverable (such incorrect sources transitively blamed Ballmer for the existence of all fatal crashes in Windows). [ 12 ] A day after his initial complaint, Chen would follow this up with another blog post on September 10, 2014, claiming responsibility for revising the BSoD in Windows 95 . His post said in detail that he was the one who "sort of" created the BSoD in its first modern incarnation in Windows 95. [ 13 ]
According to former Microsoft employee Dave Plummer , the BSoD in the Windows NT family was not based on the rudimentary task manager screen of Windows 3.x, but was actually designed by Microsoft developer John Vert. [ 14 ] Additionally, Vert has also stated that the reason why the error screens were given the color blue was because the universal color palette of the video hardware at that time was very rudimentary, and he personally used a MIPS OS box and SlickEdit for programming so that both the firmware and editor displayed white text on a blue background, making for a more consistent programming experience. [ 14 ]
BSoDs originally showed silver text on a royal blue background with information about current memory values and register values. Starting with Windows Server 2012 (released in September 2012), Windows adopted a cerulean background. Earlier versions of Windows 11 used a black background, [ 15 ] which was changed to dark blue starting with build 22000.348 [ 16 ] and then back to black with build 26120.3653. [ 17 ] Preview builds of Windows 10, Windows 11, and Windows Server (available from the Windows Insider program) feature a dark green background instead of a blue one. [ 18 ] [ 19 ] [ 15 ] Windows 3.1, 95, and 98 supports customizing the color of the screen [ 20 ] whereas the color is hard-coded in the Windows NT family . [ 20 ]
Windows 95, 98, and Me render their BSoDs in the 80×25 text mode with a 720×400 screen resolution . BSoDs in the Windows NT family initially used the 80×50 text mode with a 720×400 screen resolution, but changed to use the 640×480 screen resolution starting with Windows 2000 up to 7. BSoDs on Windows 8 and Windows Server 2012 are rendered in higher resolutions than previous versions of Windows, where it uses the highest screen resolution available on UEFI machines. On legacy BIOS machines, they use the 1024×768 resolution by default, but they can also be configured to use the highest resolution available (via the ' highestmode ' parameter in Boot Configuration Data ). [ 21 ] Windows 95, 98, Me, and NT versions prior to Windows 2000 used text mode fonts provided by the graphics adapter, Windows 2000 used its built-in kernel mode font, Windows XP, Vista, and 7 use the Lucida Console font, and Windows 8 and Windows Server 2012 onwards use the Segoe UI font.
Windows 10 builds 14316 and up uses the same format as Windows 8, but has a QR code which leads to a Microsoft Support web page that tries to help users troubleshoot the issue step-by-step. This format was retained in Windows 11, however build 26120.3653 changes the layout to be more consistent with that of Windows 11's UI, removing the QR code among other changes. [ 17 ]
In the Windows NT family of operating systems, the blue screen of death (referred to as " bug check " in the Windows software development kit and driver development kit documentation) occurs when the kernel or a driver running in kernel mode encounters an error from which it cannot recover. This is usually caused by an illegal operation being performed. The only safe action the operating system can take in this situation is to restart the computer . Because of this, data loss may occur since the restart is unplanned, and the user is not given an opportunity to save their work.
The text on the error screen contains the code of the error and its symbolic name (e.g. "0x0000001E, KMODE_EXCEPTION_NOT_HANDLED") along with four error-dependent values in parentheses that are there to help software engineers fix the problem that occurred. Depending on the error code, it may display the address where the problem occurred, along with the driver which is loaded at that address. Under Windows NT, the second and third sections of the screen may contain information on all loaded drivers and a stack dump, respectively. The driver information is in three columns; the first lists the base address of the driver, the second lists the driver's creation date (as a Unix timestamp ), and the third lists the name of the driver. [ 22 ] By default, Windows will create a memory dump file when a stop error occurs. Depending on the OS version, there may be several formats this can be saved in, ranging from a 64kB "minidump" (introduced in Windows 2000) to a "complete dump" which is effectively a copy of the entire contents of physical memory ( RAM ). The resulting memory dump file may be debugged later, using a kernel debugger . For Windows, WinDBG or KD debuggers from Debugging Tools for Windows are used. [ 23 ] A debugger is necessary to obtain a stack trace, and may be required to ascertain the true cause of the problem; as the information on-screen is limited and thus possibly misleading, it may hide the true source of the error. By default, Windows XP is configured to save only a 64kB minidump when it encounters a stop error, and to then automatically reboot the computer. Because this process happens very quickly, the blue screen may be seen only for an instant or not at all. Users have sometimes noted this as a random reboot rather than a traditional stop error, and are only aware of an issue after Windows reboots and displays a notification that it has recovered from a serious error. This happens only when the computer has a function called "Auto Restart" enabled, which can be disabled in the Control Panel which in turn shows the stop error.
Microsoft Windows can also be configured to send live debugging information to a kernel debugger running on a separate computer . If a stop error is encountered while a live kernel debugger is attached to the system, Windows will halt execution and cause the debugger to break in, rather than displaying the BSoD. The debugger can then be used to examine the contents of memory and determine the source of the problem.
A BSoD can also be caused by a critical boot loader error, where the operating system is unable to access the boot partition due to incorrect storage drivers, a damaged file system or similar problems. The error code in this situation is STOP: 0x0000007B (INACCESSIBLE_BOOT_DEVICE). [ 24 ] In such cases, there is no memory dump saved. Since the system is unable to boot from the hard drive in this situation, correction of the problem often requires using the repair tools found on the Windows installation disc.
BSoDs in the Windows NT family before the release of Windows 8 and Windows Server 2012 displayed the error name in uppercase (e.g. APC_INDEX_MISMATCH) and its respective hexadecimal error number (e.g. 0x00000001), along with four parameters. This is shown together in the following format: [ 25 ]
error code (parameter 1, parameter 2, parameter 3, parameter 4) error name
Depending on the error number and its nature, all, some, or even none of the parameters contain data pertaining to what went wrong, and/or where it happened. In addition, starting with Windows 2000 onwards, the error screens showed up to four paragraphs of general explanation and advice and may have included other technical data such the file name of the culprit and memory addresses.
In rare cases, the BSOD would be truncated, sometimes not showing the error name, codes, or the four paragraphs of advice. Instead, it would often show different formats of the error screen depending on the type of error that occurred. For instance, BSoDs related to the termination of the Winlogon process (e.g. "0xC000021A, WINLOGON_FATAL_ERROR") displayed the following message in this format:
STOP: c000021a {Fatal System Error} The Windows Logon Process/SubSystem system process terminated unexpectedly with a status of parameter 1 (parameter 2 parameter 3). The system has been shut down.
On Windows 2000, the above message is sometimes displayed alongside the four paragraphs of general instructions and advice, the latter of which are absent on Windows XP to Windows 7.
Another example is that when Windows finds a corrupt registry file that is critical to the operating system (e.g. "0xC0000218, STATUS_CANNOT_LOAD_REGISTRY_FILE"), it would display the following message:
STOP: c0000218 {Registry File Failure} The registry cannot load the hive (file):\SystemRoot\System\Config\SOFTWARE or its log or alternate. It is corrupt, absent, or not writable.
Also, hardware errors that can prevent Windows from booting properly will also display this rare message (This example is 0x00000080 (NMI_HARDWARE_FAILURE); note that the error code is not shown in this example below):
Hardware Malfunction Call your hardware vendor for support. NMI: Parity Check / Memory Parity Error The system has halted.
Additionally, when the system is performing a memory dump on the BSoD, the following message is displayed after the memory dump is done (after the "Physical memory dump complete" sentence):
Contact your system administrator/admin or technical support group for further assistance.
From Windows XP to Windows 7 , the layout of the BSoD was slightly altered, specifically the hexadecimal error number and the four parameters were moved to the bottom of the screen after the four paragraphs under the label "Technical information:". The error screens also began with the following infamous message:
A problem has been detected and Windows has been shut down to prevent damage to your computer.
On BSoDs with error code 0x000000F4 (CRITICAL_OBJECT_TERMINATION), which determines that a critical process has been exited or terminated unexpectedly by various factors (including intentional action by the user), the following message would be displayed in place of the error name:
A process or thread crucial to system operation has unexpectedly exited or been terminated.
Additionally, on 64-bit versions of Windows XP, Vista and 7, the BSoD would oftentimes have the four parameters extended, where the parameters are extended to about 16 characters long ("0x0000000000000000") instead of 8 ("0x00000000").
With the release of Windows 8 and Windows Server 2012, the BSoD was changed. It removed all of the above in favor of the error name and a concise description. Windows 8 also adds a sad emoticon to the error screen, which is absent from Japanese releases or its Windows Server counterparts. The hexadecimal error code and parameters can still be found in the Windows Event Log or in memory dumps , however some BSoDs which used a truncated format from previous BSoDs such as those relating to Winlogon termination may have the aforementioned hexadecimal error code in place of the error name. Hardware errors causing an BSoD also uses the same format as the normal BSoD, including the use of the error name instead of an error code. One such example are BSoDs with the error name "NMI_HARDWARE_FAILURE" (error code 0x00000080).
This format was retained in Windows 10 and Windows 11 (as well as its Server counterparts). Windows 10 build 14316 adds a QR code to the screen for quick troubleshooting, and all references to "PC" were changed to the word "device" starting from Windows 10 v2004 onwards. The BSoD was once again changed starting with Windows 11 build 26120.3653, which included the removal of the QR code and the sad emoticon from the error screen as well as changes to the layout to be more consistent with that of Windows 11. [ 17 ]
The Windows 9x line of operating systems used the Blue Screen of Death as the main way for virtual device drivers to report errors to the user. This version of the BSoD, internally referred to as " _VWIN32_FaultPopup ", gives the user the option either to restart the computer or to continue using Windows, allowing the user to save their work before any data could be lost. Depending on the type of situation it may have occurred, however, the options to either continue or restart may or may not work at all. This is in contrast to the Windows NT version of BSoDs, which prevented the user from using the computer until it has been powered off or restarted (usually automatic for the latter).
The most common BSoD is displayed on an 80×25 text-mode screen, which is the operating system's way of reporting an interrupt caused by a processor exception; it is a more serious form of the general protection fault dialog boxes. The memory address of the error is given and the error type is a hexadecimal number from 00 to 11 (0 to 17 decimal). The error codes are as follows: [ 26 ]
Reasons for BSoDs include:
In Windows 95 and 98, a BSoD occurs when the system attempts to access the file " c:\con\con ", " c:\aux\aux ", or " c:\prn\prn " on the hard drive. This could be inserted on a website to crash visitors' machines as a prank. In reality, however, they are reserved device names for DOS systems; attempting to access them from Windows causes a crash, which in turn brings up said BSoD. Creating the aforementioned directories within Windows will also not work and may cause the same BSOD to occur. On March 16, 2000, Microsoft released a security update to resolve this issue. [ 27 ]
One famous instance of a Windows 9x BSoD occurred during a presentation of a Windows 98 beta given by Bill Gates at COMDEX on April 20, 1998: The demo PC crashed with a BSoD when his assistant, Chris Capossela , connected a scanner to the PC to demonstrate Windows 98's support for Plug and Play devices. This event brought thunderous applause from the crowd and Gates replied (after a nervous pause): "That must be why we're not shipping Windows 98 yet." [ 28 ]
Stop errors are comparable to kernel panics in macOS , Linux , and other Unix-like systems, and to bugchecks in OpenVMS .
A black screen of death can occur upon hardware or software failures. Windows 3.1 displays a black screen of death instead of a blue one. [ 12 ] Some versions of macOS (notably OS X Lion ) display a black screen of death instead of a kernel panic, usually pointed to a graphics card or sleep/wake issue, [ 29 ] it may also display a black screen when the operating system fails to boot properly. [ 30 ] The Xbox series of consoles (which includes the original Xbox , Xbox 360 , Xbox One and the Xbox Series X/S ) also display a black screen when a hardware or software error occurs. [ 31 ]
In some cases, a differently-colored error screen is used. Beta versions of Windows 98 display a red error screen raised by the Advanced Configuration and Power Interface (ACPI) when the host computer's BIOS encounters a problem. [ 32 ] The bootloader of the first beta version of Windows Vista originally displayed a red screen background in the event of a boot failure, [ 33 ] [ 34 ] [ 35 ] which was changed to black afterwards. As mentioned earlier, the insider builds of Windows 10 and later, as well as Windows Server 2016 and later, display a green screen instead of blue. [ 18 ] [ 19 ] [ 15 ] Windows 10 and later (and Windows Server 2016 and later) also display an orange screen in an extremely rare case where a hardware issue with the GPU or a graphics driver problem is encountered. [ 36 ]
ReactOS , an open-source operating system designed to achieve binary compatibility with Windows, implements a version of the Blue Screen of Death similar to that used in Windows NT operating systems. systemd , a software suite providing system components for Linux operating systems, also implements a version of the Blue Screen of Death similar to that of Windows, albeit not as a replacement to the kernel panic in Linux (see above), but rather was used in the event of a bootup failure. This iteration uses systemd-bsod, which was added on December 6, 2023 starting with version 255 of systemd. [ 37 ] [ 38 ] | https://en.wikipedia.org/wiki/RSOD |
The RSPB Medal is awarded annually by the Royal Society for the Protection of Birds . [ 1 ]
According to the RSPB:
The RSPB Medal is the Society's most prestigious award. It is presented to an individual in recognition of wild bird protection and countryside conservation. It is usually awarded annually to one or occasionally two people. [ 1 ]
The medal was first awarded in 1908. [ 2 ] | https://en.wikipedia.org/wiki/RSPB_Medal |
The blue screen of death ( BSoD ) – or blue screen error , blue screen , fatal error , bugcheck , and officially known as a stop error [ 1 ] [ 2 ] [ 3 ] – is a critical error screen displayed by the Microsoft Windows operating systems to indicate a system crash , in which the operating system reaches a critical condition where it can no longer operate safely.
The name comes from the blue colored background used predominately on the error screens found in the majority of Windows releases. Possible issues contributing to a BSoD may include hardware failures, an issue with or without a device driver, viruses , malware , and other factors such as intentional user action.
Blue screen errors have been around since the first beta release of Windows 1.0 ; if Windows detects a newer DOS version than the one it expected, the boot screen would have the text "Incorrect DOS version" alongside other messages detailing what check failed to pass appended into it before starting normally. [ 4 ] This was retained in the final release (version 1.01), however it mostly prints out random characters instead due to the remaining text messages being removed during development. [ 4 ] However, this is not a screen of death; upon crashing, Windows 1.0 locks up or terminates and the user is returned to DOS. This behavior is also present in Windows 2.0 and Windows 2.1 .
Windows 3.0 uses a text-mode screen for displaying important system messages, usually from digital device drivers in 386 Enhanced Mode or other situations where a program could not run. Windows 3.1 changed the color of this screen from black to blue. It also displays a blue screen when the user presses the Ctrl+Alt+Delete key combination to bring up a rudimentary task manager , reserved for quitting any unresponsive programs if they are available. Like previous versions of Windows before 3.0, Windows 3.x exits to DOS if an error condition is severe enough.
The first BSoD to indicate a critical system error appeared in Windows NT 3.1 (the first version of the Windows NT family, released in 1993). [ 5 ] The error screens initially started with *** STOP: in its earlier iterations, hence it became known as a "stop error." This format was used on all Windows operating systems released afterwards, with various differences in later versions. Despite popular belief, there are no known equivalents of a BSoD in the Windows Embedded Compact (formerly known as Windows CE) line of embedded operating systems. [ 6 ]
BSoDs can be caused by poorly written device drivers or malfunctioning hardware, [ 7 ] such as faulty memory , power supply problems, overheating of components, or hardware running beyond its specification limits. In the Windows 9x line of operating systems, incompatible DLLs or bugs in the operating system kernel could also cause BSoDs. [ 8 ] Because of the general instability and lack of memory protection in Windows 9x, BSoDs were much more common.
On September 4, 2014, several online journals such as Business Insider , DailyTech , Engadget , Gizmodo , Lifehacker , Neowin , Softpedia , TechSpot , Boy Genius Report ( BGR ), The Register , and The Verge , [ 9 ] as well as print and non-English sources like PC Authority and Austrian tech site FutureZone [ 10 ] all attributed the creation of the Blue Screen of Death to Steve Ballmer , the former CEO of Microsoft. The articles specifically cited a blog post by Microsoft employee Raymond Chen entitled "Who wrote the text for the Ctrl+Alt+Del dialog in Windows 3.1?", [ 11 ] which focused on the creation of the first rudimentary task manager in Windows 3.x. The aforementioned task manager shared some visual similarities with a BSOD, with Ballmer writing the messages that appeared on the screen. [ 11 ]
Chen had to address this widespread misinformation himself in a blog post on September 9, 2014. According to his post, he was scathing on his evaluation of major tech news sites that had picked up on the incorrect story and performed poor or non-existent research that demonstrated complete ignorance of his original account. He indicated that, in addition to the faulty base story, over half a dozen significant sites had included other embellished or invented details in their stories, including incorrectly naming Chen as a Microsoft executive, treating Chen as an "official company spokesperson", and using unrelated images from Windows NT or Windows 95 as illustrations. In addition, he also pointed out a very special mention for the worst single distortion out of any misinformations, which belonged to BGR (Boy Genius Report), who "fabricated a scenario and posited it as real" in a rhetorical question to readers. He also found that several sources had conflated the creation of the BSoD with the fact that they occur, thus inverting cause and effect by implying that the invention of BSoDs caused fatal errors to occur instead of their actual, helpful function of giving the user information about a fatal error after the system has already become unrecoverable (such incorrect sources transitively blamed Ballmer for the existence of all fatal crashes in Windows). [ 12 ] A day after his initial complaint, Chen would follow this up with another blog post on September 10, 2014, claiming responsibility for revising the BSoD in Windows 95 . His post said in detail that he was the one who "sort of" created the BSoD in its first modern incarnation in Windows 95. [ 13 ]
According to former Microsoft employee Dave Plummer , the BSoD in the Windows NT family was not based on the rudimentary task manager screen of Windows 3.x, but was actually designed by Microsoft developer John Vert. [ 14 ] Additionally, Vert has also stated that the reason why the error screens were given the color blue was because the universal color palette of the video hardware at that time was very rudimentary, and he personally used a MIPS OS box and SlickEdit for programming so that both the firmware and editor displayed white text on a blue background, making for a more consistent programming experience. [ 14 ]
BSoDs originally showed silver text on a royal blue background with information about current memory values and register values. Starting with Windows Server 2012 (released in September 2012), Windows adopted a cerulean background. Earlier versions of Windows 11 used a black background, [ 15 ] which was changed to dark blue starting with build 22000.348 [ 16 ] and then back to black with build 26120.3653. [ 17 ] Preview builds of Windows 10, Windows 11, and Windows Server (available from the Windows Insider program) feature a dark green background instead of a blue one. [ 18 ] [ 19 ] [ 15 ] Windows 3.1, 95, and 98 supports customizing the color of the screen [ 20 ] whereas the color is hard-coded in the Windows NT family . [ 20 ]
Windows 95, 98, and Me render their BSoDs in the 80×25 text mode with a 720×400 screen resolution . BSoDs in the Windows NT family initially used the 80×50 text mode with a 720×400 screen resolution, but changed to use the 640×480 screen resolution starting with Windows 2000 up to 7. BSoDs on Windows 8 and Windows Server 2012 are rendered in higher resolutions than previous versions of Windows, where it uses the highest screen resolution available on UEFI machines. On legacy BIOS machines, they use the 1024×768 resolution by default, but they can also be configured to use the highest resolution available (via the ' highestmode ' parameter in Boot Configuration Data ). [ 21 ] Windows 95, 98, Me, and NT versions prior to Windows 2000 used text mode fonts provided by the graphics adapter, Windows 2000 used its built-in kernel mode font, Windows XP, Vista, and 7 use the Lucida Console font, and Windows 8 and Windows Server 2012 onwards use the Segoe UI font.
Windows 10 builds 14316 and up uses the same format as Windows 8, but has a QR code which leads to a Microsoft Support web page that tries to help users troubleshoot the issue step-by-step. This format was retained in Windows 11, however build 26120.3653 changes the layout to be more consistent with that of Windows 11's UI, removing the QR code among other changes. [ 17 ]
In the Windows NT family of operating systems, the blue screen of death (referred to as " bug check " in the Windows software development kit and driver development kit documentation) occurs when the kernel or a driver running in kernel mode encounters an error from which it cannot recover. This is usually caused by an illegal operation being performed. The only safe action the operating system can take in this situation is to restart the computer . Because of this, data loss may occur since the restart is unplanned, and the user is not given an opportunity to save their work.
The text on the error screen contains the code of the error and its symbolic name (e.g. "0x0000001E, KMODE_EXCEPTION_NOT_HANDLED") along with four error-dependent values in parentheses that are there to help software engineers fix the problem that occurred. Depending on the error code, it may display the address where the problem occurred, along with the driver which is loaded at that address. Under Windows NT, the second and third sections of the screen may contain information on all loaded drivers and a stack dump, respectively. The driver information is in three columns; the first lists the base address of the driver, the second lists the driver's creation date (as a Unix timestamp ), and the third lists the name of the driver. [ 22 ] By default, Windows will create a memory dump file when a stop error occurs. Depending on the OS version, there may be several formats this can be saved in, ranging from a 64kB "minidump" (introduced in Windows 2000) to a "complete dump" which is effectively a copy of the entire contents of physical memory ( RAM ). The resulting memory dump file may be debugged later, using a kernel debugger . For Windows, WinDBG or KD debuggers from Debugging Tools for Windows are used. [ 23 ] A debugger is necessary to obtain a stack trace, and may be required to ascertain the true cause of the problem; as the information on-screen is limited and thus possibly misleading, it may hide the true source of the error. By default, Windows XP is configured to save only a 64kB minidump when it encounters a stop error, and to then automatically reboot the computer. Because this process happens very quickly, the blue screen may be seen only for an instant or not at all. Users have sometimes noted this as a random reboot rather than a traditional stop error, and are only aware of an issue after Windows reboots and displays a notification that it has recovered from a serious error. This happens only when the computer has a function called "Auto Restart" enabled, which can be disabled in the Control Panel which in turn shows the stop error.
Microsoft Windows can also be configured to send live debugging information to a kernel debugger running on a separate computer . If a stop error is encountered while a live kernel debugger is attached to the system, Windows will halt execution and cause the debugger to break in, rather than displaying the BSoD. The debugger can then be used to examine the contents of memory and determine the source of the problem.
A BSoD can also be caused by a critical boot loader error, where the operating system is unable to access the boot partition due to incorrect storage drivers, a damaged file system or similar problems. The error code in this situation is STOP: 0x0000007B (INACCESSIBLE_BOOT_DEVICE). [ 24 ] In such cases, there is no memory dump saved. Since the system is unable to boot from the hard drive in this situation, correction of the problem often requires using the repair tools found on the Windows installation disc.
BSoDs in the Windows NT family before the release of Windows 8 and Windows Server 2012 displayed the error name in uppercase (e.g. APC_INDEX_MISMATCH) and its respective hexadecimal error number (e.g. 0x00000001), along with four parameters. This is shown together in the following format: [ 25 ]
error code (parameter 1, parameter 2, parameter 3, parameter 4) error name
Depending on the error number and its nature, all, some, or even none of the parameters contain data pertaining to what went wrong, and/or where it happened. In addition, starting with Windows 2000 onwards, the error screens showed up to four paragraphs of general explanation and advice and may have included other technical data such the file name of the culprit and memory addresses.
In rare cases, the BSOD would be truncated, sometimes not showing the error name, codes, or the four paragraphs of advice. Instead, it would often show different formats of the error screen depending on the type of error that occurred. For instance, BSoDs related to the termination of the Winlogon process (e.g. "0xC000021A, WINLOGON_FATAL_ERROR") displayed the following message in this format:
STOP: c000021a {Fatal System Error} The Windows Logon Process/SubSystem system process terminated unexpectedly with a status of parameter 1 (parameter 2 parameter 3). The system has been shut down.
On Windows 2000, the above message is sometimes displayed alongside the four paragraphs of general instructions and advice, the latter of which are absent on Windows XP to Windows 7.
Another example is that when Windows finds a corrupt registry file that is critical to the operating system (e.g. "0xC0000218, STATUS_CANNOT_LOAD_REGISTRY_FILE"), it would display the following message:
STOP: c0000218 {Registry File Failure} The registry cannot load the hive (file):\SystemRoot\System\Config\SOFTWARE or its log or alternate. It is corrupt, absent, or not writable.
Also, hardware errors that can prevent Windows from booting properly will also display this rare message (This example is 0x00000080 (NMI_HARDWARE_FAILURE); note that the error code is not shown in this example below):
Hardware Malfunction Call your hardware vendor for support. NMI: Parity Check / Memory Parity Error The system has halted.
Additionally, when the system is performing a memory dump on the BSoD, the following message is displayed after the memory dump is done (after the "Physical memory dump complete" sentence):
Contact your system administrator/admin or technical support group for further assistance.
From Windows XP to Windows 7 , the layout of the BSoD was slightly altered, specifically the hexadecimal error number and the four parameters were moved to the bottom of the screen after the four paragraphs under the label "Technical information:". The error screens also began with the following infamous message:
A problem has been detected and Windows has been shut down to prevent damage to your computer.
On BSoDs with error code 0x000000F4 (CRITICAL_OBJECT_TERMINATION), which determines that a critical process has been exited or terminated unexpectedly by various factors (including intentional action by the user), the following message would be displayed in place of the error name:
A process or thread crucial to system operation has unexpectedly exited or been terminated.
Additionally, on 64-bit versions of Windows XP, Vista and 7, the BSoD would oftentimes have the four parameters extended, where the parameters are extended to about 16 characters long ("0x0000000000000000") instead of 8 ("0x00000000").
With the release of Windows 8 and Windows Server 2012, the BSoD was changed. It removed all of the above in favor of the error name and a concise description. Windows 8 also adds a sad emoticon to the error screen, which is absent from Japanese releases or its Windows Server counterparts. The hexadecimal error code and parameters can still be found in the Windows Event Log or in memory dumps , however some BSoDs which used a truncated format from previous BSoDs such as those relating to Winlogon termination may have the aforementioned hexadecimal error code in place of the error name. Hardware errors causing an BSoD also uses the same format as the normal BSoD, including the use of the error name instead of an error code. One such example are BSoDs with the error name "NMI_HARDWARE_FAILURE" (error code 0x00000080).
This format was retained in Windows 10 and Windows 11 (as well as its Server counterparts). Windows 10 build 14316 adds a QR code to the screen for quick troubleshooting, and all references to "PC" were changed to the word "device" starting from Windows 10 v2004 onwards. The BSoD was once again changed starting with Windows 11 build 26120.3653, which included the removal of the QR code and the sad emoticon from the error screen as well as changes to the layout to be more consistent with that of Windows 11. [ 17 ]
The Windows 9x line of operating systems used the Blue Screen of Death as the main way for virtual device drivers to report errors to the user. This version of the BSoD, internally referred to as " _VWIN32_FaultPopup ", gives the user the option either to restart the computer or to continue using Windows, allowing the user to save their work before any data could be lost. Depending on the type of situation it may have occurred, however, the options to either continue or restart may or may not work at all. This is in contrast to the Windows NT version of BSoDs, which prevented the user from using the computer until it has been powered off or restarted (usually automatic for the latter).
The most common BSoD is displayed on an 80×25 text-mode screen, which is the operating system's way of reporting an interrupt caused by a processor exception; it is a more serious form of the general protection fault dialog boxes. The memory address of the error is given and the error type is a hexadecimal number from 00 to 11 (0 to 17 decimal). The error codes are as follows: [ 26 ]
Reasons for BSoDs include:
In Windows 95 and 98, a BSoD occurs when the system attempts to access the file " c:\con\con ", " c:\aux\aux ", or " c:\prn\prn " on the hard drive. This could be inserted on a website to crash visitors' machines as a prank. In reality, however, they are reserved device names for DOS systems; attempting to access them from Windows causes a crash, which in turn brings up said BSoD. Creating the aforementioned directories within Windows will also not work and may cause the same BSOD to occur. On March 16, 2000, Microsoft released a security update to resolve this issue. [ 27 ]
One famous instance of a Windows 9x BSoD occurred during a presentation of a Windows 98 beta given by Bill Gates at COMDEX on April 20, 1998: The demo PC crashed with a BSoD when his assistant, Chris Capossela , connected a scanner to the PC to demonstrate Windows 98's support for Plug and Play devices. This event brought thunderous applause from the crowd and Gates replied (after a nervous pause): "That must be why we're not shipping Windows 98 yet." [ 28 ]
Stop errors are comparable to kernel panics in macOS , Linux , and other Unix-like systems, and to bugchecks in OpenVMS .
A black screen of death can occur upon hardware or software failures. Windows 3.1 displays a black screen of death instead of a blue one. [ 12 ] Some versions of macOS (notably OS X Lion ) display a black screen of death instead of a kernel panic, usually pointed to a graphics card or sleep/wake issue, [ 29 ] it may also display a black screen when the operating system fails to boot properly. [ 30 ] The Xbox series of consoles (which includes the original Xbox , Xbox 360 , Xbox One and the Xbox Series X/S ) also display a black screen when a hardware or software error occurs. [ 31 ]
In some cases, a differently-colored error screen is used. Beta versions of Windows 98 display a red error screen raised by the Advanced Configuration and Power Interface (ACPI) when the host computer's BIOS encounters a problem. [ 32 ] The bootloader of the first beta version of Windows Vista originally displayed a red screen background in the event of a boot failure, [ 33 ] [ 34 ] [ 35 ] which was changed to black afterwards. As mentioned earlier, the insider builds of Windows 10 and later, as well as Windows Server 2016 and later, display a green screen instead of blue. [ 18 ] [ 19 ] [ 15 ] Windows 10 and later (and Windows Server 2016 and later) also display an orange screen in an extremely rare case where a hardware issue with the GPU or a graphics driver problem is encountered. [ 36 ]
ReactOS , an open-source operating system designed to achieve binary compatibility with Windows, implements a version of the Blue Screen of Death similar to that used in Windows NT operating systems. systemd , a software suite providing system components for Linux operating systems, also implements a version of the Blue Screen of Death similar to that of Windows, albeit not as a replacement to the kernel panic in Linux (see above), but rather was used in the event of a bootup failure. This iteration uses systemd-bsod, which was added on December 6, 2023 starting with version 255 of systemd. [ 37 ] [ 38 ] | https://en.wikipedia.org/wiki/RSoD |
The plug flow reactor model ( PFR , sometimes called continuous tubular reactor , CTR , or piston flow reactors ) is a model used to describe chemical reactions in continuous, flowing systems of cylindrical geometry. The PFR model is used to predict the behavior of chemical reactors of such design, so that key reactor variables, such as the dimensions of the reactor, can be estimated.
Fluid going through a PFR may be modeled as flowing through the reactor as a series of infinitely thin coherent "plugs", each with a uniform composition, traveling in the axial direction of the reactor, with each plug having a different composition from the ones before and after it. The key assumption is that as a plug flows through a PFR, the fluid is perfectly mixed in the radial direction but not in the axial direction (forwards or backwards). Each plug of differential volume is considered as a separate entity, effectively an infinitesimally small continuous stirred tank reactor , limiting to zero volume. As it flows down the tubular PFR, the residence time ( τ {\displaystyle \tau } ) of the plug is a function of its position in the reactor. In the ideal PFR, the residence time distribution is therefore a Dirac delta function with a value equal to τ {\displaystyle \tau } .
The stationary PFR is governed by ordinary differential equations , the solution for which can be calculated providing that appropriate boundary conditions are known.
The PFR model works well for many fluids: liquids, gases, and slurries. Although turbulent flow and axial diffusion cause a degree of mixing in the axial direction in real reactors, the PFR model is appropriate when these effects are sufficiently small that they can be ignored.
In the simplest case of a PFR model, several key assumptions must be made in order to simplify the problem, some of which are outlined below. Note that not all of these assumptions are necessary, however the removal of these assumptions does increase the complexity of the problem. The PFR model can be used to model multiple reactions as well as reactions involving changing temperatures, pressures and densities of the flow. Although these complications are ignored in what follows, they are often relevant to industrial processes.
Assumptions:
A material balance on the differential volume of a fluid element, or plug, on species i of axial length dx between x and x + dx gives:
Accumulation is 0 under steady state; therefore, the above mass balance can be re-written as follows:
1. F i ( x ) − F i ( x + d x ) + A t d x ν i r = 0 {\displaystyle F_{i}(x)-F_{i}(x+dx)+A_{t}dx\nu _{i}r=0} . [ 1 ]
where:
The flow linear velocity, u (m/s) and the concentration of species i , C i (mol/m 3 ) can be introduced as:
where v ˙ {\displaystyle {\dot {v}}} is the volumetric flow rate.
On application of the above to Equation 1, the mass balance on i becomes:
2. A t u [ C i ( x ) − C i ( x + d x ) ] + A t d x ν i r = 0 {\displaystyle A_{t}u[C_{i}(x)-C_{i}(x+dx)]+A_{t}dx\nu _{i}r=0\,} . [ 1 ]
When like terms are cancelled and the limit dx → 0 is applied to Equation 2 the mass balance on species i becomes
3. u d C i d x = ν i r {\displaystyle u{\frac {dC_{i}}{dx}}=\nu _{i}r} , [ 1 ]
The temperature dependence of the reaction rate, r , can be estimated using the Arrhenius equation . Generally, as the temperature increases so does the rate at which the reaction occurs. Residence time, τ {\displaystyle \tau } , is the average amount of time a discrete quantity of reagent spends inside the tank.
Assume:
After integration of Equation 3 using the above assumptions, solving for C A (x) we get an explicit equation for the concentration of species A as a function of position:
4. C A ( x ) = C A 0 e − k τ {\displaystyle C_{A}(x)=C_{A0}e^{-k\tau }\,} ,
where C A0 is the concentration of species A at the inlet to the reactor, appearing from the integration boundary condition.
PFRs are used to model the chemical transformation of compounds as they are transported in systems resembling "pipes". The "pipe" can represent a variety of engineered or natural conduits through which liquids or gases flow. (e.g. rivers, pipelines, regions between two mountains, etc.)
An ideal plug flow reactor has a fixed residence time: Any fluid (plug) that enters the reactor at time t {\displaystyle t} will exit the reactor at time t + τ {\displaystyle t+\tau } , where τ {\displaystyle \tau } is the residence time of the reactor. The residence time distribution function is therefore a Dirac delta function at τ {\displaystyle \tau } . A real plug flow reactor has a residence time distribution that is a narrow pulse around the mean residence time distribution.
A typical plug flow reactor could be a tube packed with some solid material (frequently a catalyst ). Typically these types of reactors are called packed bed reactors or PBR's. Sometimes the tube will be a tube in a shell and tube heat exchanger .
When a plug flow model can not be applied, the dispersion model is usually employed. [ 2 ] [ 3 ]
The residence-time distribution (RTD) of a reactor is a characteristic of the mixing that occurs in the chemical reactor. There is no axial mixing in a plug-flow reactor, and this omission is reflected in the RTD which is exhibited by this class of reactors. [ 4 ]
Real plug flow reactors do not satisfy the idealized flow patterns, back mix flow or plug flow deviation from ideal behavior can be due to channeling of fluid through the vessel, recycling of fluid within the vessel or due to the presence of stagnant region or dead zone of fluid in the vessel. [ 5 ] Real plug flow reactors with non-ideal behavior have also been modelled. [ 6 ] To predict the exact behavior of a vessel as a chemical reactor , RTD or stimulus response technique is used. The tracer technique , the most widely used method for the study of axial dispersion, is usually used in the form of: [ 7 ]
The RTD is determined experimentally by injecting an inert chemical, molecule, or atom, called a tracer, into the reactor at some time t = 0 and then measuring the tracer concentration, C, in the effluent stream as a function of time. [ 4 ]
The RTD curve of fluid leaving a vessel is called the E-Curve. This curve is normalized in such a way that the area under it is unity:
The mean age of the exit stream or mean residence time is:
When a tracer is injected into a reactor at a location more than two or three particle diameters downstream from the entrance and measured some distance upstream from the exit, the system can be described by the dispersion model with combinations of open or close boundary conditions. [ 3 ] For such a system where there is no discontinuity in type of flow at the point of tracer injection or at the point of tracer measurement, the variance for open-open system is:
Where,
which represents the ratio of rate of transport by convection to rate of transport by diffusion or dispersion.
Vessel dispersion number is defined as:
The variance of a continuous distribution measured at a finite number of equidistant locations is given by:
Where mean residence time τ is given by:
Thus (σ θ ) 2 can be evaluated from the experimental data on C vs. t and for known values of ( σ θ ) 2 {\displaystyle (\sigma _{\theta })^{2}} , the dispersion number ( 1 / P e ) {\displaystyle (1/P_{e})} can be obtained from eq. (3) as:
Thus axial dispersion coefficient D L can be estimated (L = packed height) [ 5 ]
As mentioned before, there are also other boundary conditions that can be applied to the dispersion model giving different relationships for the dispersion number. [ 8 ] [ 9 ] [ 3 ]
From the safety technical point of view the PFR has the advantages that [ 10 ]
The main problems lies in difficult and sometimes critical start-up and shut down operations. [ 10 ]
Plug flow reactors are used for some of the following applications: | https://en.wikipedia.org/wiki/RTD_studies_of_plug_flow_reactor |
RTL 24 started as a mobile TV news channel on 5 June 2008. It was available through KPN DVB-H . [ 1 ] Its broadcast as a mobile TV channel stopped when KPN ceased its DVB-H services on 1 June 2011. [ 2 ]
After a short break, RTL 24 re-launched as a mobile app for smart phones , tablet computers and other mobile devices in November 2011. [ 3 ] On 19 January 2012 the app changed into RTL Nieuws 365 and therefore the brand RTL 24 discontinued. [ 4 ]
This mobile computing related article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/RTL_24 |
RTMI ( Radio Telefono Mobile Integrato ) was the first mobile communication service in Italy , started in 1973. It operated on the 160 MHz frequency band and was used by a few people working in the public sector (public administrations and defense officials). In the 1980s, the Radio Telephone Mobile (RTM) emerged, which operated on the 450 MHz frequency band and attracted 100,000 customers.
The cellular standard RTMS was launched in 1985. In 1989 the SIP (Società Italiana per l'Esercizio delle Telecomunicazioni) adopted the TACS standard. RTMS services were switched off in 1996. [ 1 ]
This article about wireless technology is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/RTMI |
RVT-802 ( allogeneic cultured postnatal thymus-derived tissue ) is a medication being developed by Enzyvant Therapeutics Ireland Limited for the treatment of congenital athymia (absence of a thymus gland), especially in the context of DiGeorge syndrome .
Enzyvant licensed the technology underlying RVT-802 from Duke University in 2017. [ 1 ] In the same year, the Food and Drug Administration granted Regenerative Medicine Advanced Therapy – the second such approval ever to be granted – status to RVT-802. [ 2 ] In December 2019, the Food and Drug Administration raised concerns about the manufacturing of RVT-802, and declined to approve it, instead issuing a Complete Response Letter . [ 3 ] In April 2021, Enzyvant resubmitted its Biologics License Application . [ 4 ] It is expected that the review of RVT-802 will conclude in October 2021 ( PDUFA date ).
RVT-802 is an investigational treatment for congenital athymia, primarily associated with DiGeorge syndrome . It is a tissue-based therapy that consists of cultured donor thymus-derived tissue. RVT-802 consists of donor thymus-derived tissue that is cultured and surgically implanted into the recipient
In patients with congenital athymia, the thymus gland is absent. Because of the crucial role the thymus gland plays in the maturation and differentiation of T cells , athymia results in severe immunodeficiency, typically resulting in death within the first two years of life. [ 5 ]
RVT-802 is manufactured by extracting thymus tissue from infants undergoing cardiac surgery , depleting it of immature T cells to prevent graft-versus-host disease , then implanting the processed tissue into the recipient's leg, where it fulfils the immunological role of the thymus. [ 6 ] | https://en.wikipedia.org/wiki/RVT-802 |
RV Rachel Carson is a research vessel owned and operated by the University of Maryland 's Center for Environmental Science, named in honor of the marine biologist and writer Rachel Carson .
The 81-foot aluminum-hulled vessel is an extended and modified Challenger class fast research vessel, designed by marine architect Roger Long. [ 2 ] It is equipped with twin 1,200 horsepower diesel engines and water jet drives which give a maximum speed of 24 knots. A dynamic positioning system automatically maintains the vessel's position. [ 3 ]
The ship was built by Hike Metal Products of Wheatley, Ontario , [ 3 ] at a cost of $4.6 million, and christened by Katie O'Malley on November 16, 2008, at Annapolis . [ 4 ]
The Rachel Carson has operated in Chesapeake Bay since early 2009, teaching estuarine sampling techniques, carrying out water quality surveys, plankton collection, box coring operations, and deploying instrument packages. [ 3 ] | https://en.wikipedia.org/wiki/RV_Rachel_Carson_(2008) |
R/V Rachel Carson is a research vessel owned and operated by the University of Washington 's School of Oceanography, named in honor of the marine biologist and writer Rachel Carson . The vessel is part of the UNOLS fleet. It is capable of conducting operations within the Salish Sea and coastal waters of the western United States and British Columbia. She can accommodate up to 28 persons, including the crew, for day operations, while up to 13 can be accommodated for multi-day operations. [ 3 ] [ 4 ]
The ship was originally launched in May 2003 at the Macduff Shipyard in Macduff , Scotland, as the
R/V Aora , a fisheries research vessel . [ 3 ] She was based at the University Marine Biological Station Millport in the Firth of Clyde , [ 5 ] until the station was closed in 2013. [ 6 ]
In 2015 the University of Washington's School of Oceanography wanted to replace the fifty-year old RV Clifford A. Barnes , but were unable to raise the funds required to design and build a replacement. In December 2016 they found the Aora for sale on a yacht-trading website. [ 4 ] [ 7 ] After an inspection in March 2017, the ship was purchased for $1.07m on 8 August 2017, [ 7 ] with the aid of a $1m gift. [ 8 ] A programme of maintenance and some modifications at the MacDuff yard were completed in October, and the Rachel Carson was transported by ship from Rotterdam to West Palm Beach, Florida by early November. [ 7 ] [ 9 ] She was then transported to the University of Washington, arriving on 28 December. After further preparations and modifications the ship entered service on 7 April 2018, [ 7 ] with a five-day cruise in Puget Sound to collect samples for monitoring by the Washington Ocean Acidification Center. [ 8 ] She was accepted as a UNOLS vessel in the U.S. Academic Research Fleet on 24 July. [ 7 ] | https://en.wikipedia.org/wiki/RV_Rachel_Carson_(2017) |
RV Song of the Whale is a research vessel owned by Marine Conservation Research International and operated by Marine Conservation Research Ltd. The 70-foot vessel was designed specifically to carry out research on cetaceans (and other marine fauna) using benign research techniques such as passive acoustic monitoring.
Song of the Whale is a cutter-rigged steel-hulled research vessel commissioned by the International Fund for Animal Welfare (IFAW) and built in 2004. The vessel was designed by Rogers Yacht Design of Lymington and built to Lloyd's Special Service Craft Rules for world-wide service – the first sailing vessel to meet those standards for 30 years. [ 2 ] Ordered from Blondecell Ltd, the subcontracted steel hull was fabricated by Corus Steel and assembled by Riverside Fabrication at Falmouth, Cornwall . The addition of the composite superstructure and the full outfitting was carried out at Blondecell's facility at Cracknore Hard, Marchwood , Hampshire. [ 3 ] The vessel cost £1.5 million. [ 2 ]
The design minimises acoustic emissions to facilitate the benign research techniques favoured by her former owners IFAW and the engine-room is encased in a Faraday cage to contain electrical fields. [ 4 ] [ 5 ] [ 6 ] The outfit of Song of the Whale includes the latest computerised recording and tracking devices to ensure that best and most advanced acoustic research can be carried out. To assist physical observation, there is a two-person crow's nest . [ 2 ]
The new vessel was launched in St Katharine Docks, London, on 6 June 2004 by Pierce and Keely Brosnan . [ 2 ] [ 6 ] [ 7 ]
Song of the Whale was formerly owned by IFAW until 14 March 2014 when the vessel was granted to Marine Conservation Research International of Kelvedon , UK. [ 8 ] She is based at Ipswich and continues to carry out the research for which she designed, using benign techniques. She replaced a smaller vessel of the same name, a converted 46-foot luxury yacht, which had been in service for 17 years. [ 2 ] [ 6 ]
Song of the Whale carries out most of its research under sail to reduce the impact on the whales and other marine mammals being researched. The focus of projects is on their presence, distribution, movements and behaviour. Noise suppression is particularly important when assessing populations of whales as the researchers can listen to their sounds up to 20 miles away using hydrophone arrays , not relying solely on surface sightings. [ 6 ] Research undertaken is focused on the conservation of threatened species and habitats and includes work on the problems of underwater noise, whales becoming entangled in fishing gear or in collisions with ships. [ 9 ] [ 10 ] | https://en.wikipedia.org/wiki/RV_Song_of_the_Whale |
RW3 Technologies is a software company that provides SaaS Intelligent in store execution, data driven field sales, survey, Dashboard/reporting consumer packaged goods (CPG) industryand Online — Instore Competitive Pricing to Retailers. It is headquartered in Austin Texas .
RW3 Technologies was founded in the Bay Area by Bruce Nagle in 1992. [ 1 ] The company's primary focus was to streamline daily data entry processes for the sales industry.
In 1992, RW3 introduced one of the first Land-Line CPG broker sales systems that allowed for mobile data entry. [ 2 ] It was initially used in food brokerage, though eventually expanded to include functionality for the consumer packaged goods industry. [ 3 ]
In 2000, the company expanded its business model to include business-to-business account management. [ 4 ]
In 2010, the company began development of their first general SaaS product application since the late 1990s; the SaaS application called InStore Mobile (now MarketCheck) was released in 2011. The in-store survey application allows for two-way communication between the account rep and broker, allowing organizations to improve and track retail conditions. [ 5 ]
In 2013, RW3 released the BI Suite, a business intelligence environment that enables organizations to create views across departments and utilize multiple data sources to align sales strategies. [ 6 ]
In 2014 Smartcall was launched and marketed to the CPG industry. The application enables field sales reps to conduct traditional store calls and manage sales routes. It is packaged with MarketCheck into their InStore Execution Suite, providing retail execution and monitoring applications for the consumer goods industry. [ 7 ]
RW3 offers four SaaS products for the retail, wholesale, and B2B industries:
RW3 serves three primary markets: | https://en.wikipedia.org/wiki/RW3_Technologies |
An RX meter is used to measure the separate resistive and reactive components of reactive parallel Z network.
The two variable frequency oscillators track each other at frequencies 100 kHz apart. The output of a 0.5-250 MHz oscillator, [ 1 ] F1, is fed into a bridge. When the impedance network to be measured is connected one arm across the bridge, the equivalent parallel resistance and reactance (capacitive or inductive) unbalances the bridge and the resulting voltage is fed to the mixer. The output of the 0.6-250.1 MHz oscillator F 2 , tracking 100 kHz above F 1 , is also fed to the mixer. This results in a 100 kHz difference frequency proportional in level to the bridge unbalance. The difference frequency signal is amplified by a filter amplifier combination and is applied to a null meter. When the bridge resistive and reactive controls are nulled, their respective dials accurately indicate the parallel impedance components of the network under test.
The best-known RX meter was the RX250-A, developed in the early 1950s by Boonton Radio Corporation (BRC). After acquiring BRC, Hewlett-Packard continued to sell versions of the meter (both the original and the improved 250B) into the late 1960s. [ 2 ] | https://en.wikipedia.org/wiki/RX_meter |
R is the ratio of the hadronic cross section to the muon cross section in electron – positron collisions :
where the superscript (0) indicates that the cross section has been corrected for initial state radiation. R is an important input in the calculation of the anomalous magnetic dipole moment . [ 1 ] Experimental values have been measured for center-of-mass energies from 400 MeV to 150 GeV. [ 2 ]
R also provides experimental confirmation of the electric charge of quarks , in particular the charm quark and bottom quark, and the existence of three quark colors. [ 3 ] A simplified calculation of R yields
where the sum is over all quark flavors with mass less than the beam energy. e q is the electric charge of the quark, and the factor of 3 accounts for the three colors of the quarks. QCD corrections to this formula have been calculated. [ 4 ]
Usually, the denominator in R is not the actual experimental μμ cross section, but the off-resonance theoretical QED cross-section: this makes resonances more visibly dramatic than normalization by the μμ cross section, which is also greatly enhanced at these resonances (hadronic states, and Z boson).
This scattering –related article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/R_(cross_section_ratio) |
R bodies (from refractile bodies , also R-bodies ) are polymeric protein inclusions formed inside the cytoplasm of bacteria . [ 1 ] Initially discovered in kappa particles , bacterial endosymbionts of the ciliate Paramecium , R bodies (and genes encoding them) have since been discovered in a variety of taxa. [ 2 ]
At neutral pH , type 51 R bodies resemble a coil of ribbon approximately 500 nm in diameter and approximately 400 nm deep. [ 1 ] Encoded by a single operon containing four open reading frames , [ 3 ] [ 4 ] R bodies are formed from two small structural proteins, RebA and RebB. [ 5 ] A third protein, RebC, is required for the covalent assembly of these two structural proteins into higher-molecular weight products, visualized as a ladder on an SDS-PAGE gel. [ 5 ]
At low pH, Type 51 R bodies undergo a dramatic structural rearrangement. Much like a paper yo-yo , the ribbon extends (from the center) to form hollow tube with pointed ends that can reach up to 20μm in length. [ 6 ]
Other types of R bodies from different bacterial species vary in their size, ribbon morphology, and triggers for extension. [ 1 ]
When kappa particles shed from a killer paramecium are ingested, R bodies extend within the acidic food vacuole of the predatory paramecium, distending and rupturing the membrane. [ 7 ] This liberates the contents of the food vacuole into the cytoplasm of the paramecium. [ 7 ] While feeding kappa particles to sensitive paramecium results in the death of paramecium, feeding purified R bodies or R bodies recombinantly expressed in E. coli is not toxic. [ 3 ] [ 8 ] Thus, R bodies are thought to function as a toxin delivery system.
R bodies are also capable of rupturing E. coli spheroplasts , demonstrating that they can rupture membranes in a foreign context, and they can be engineered to extend at a variety of different pH levels. [ 9 ] | https://en.wikipedia.org/wiki/R_bodies |
Radium bromide is the bromide salt of radium , with the formula RaBr 2 . It is produced during the process of separating radium from uranium ore . This inorganic compound was discovered by Pierre and Marie Curie in 1898, and the discovery sparked a huge interest in radiochemistry and radiotherapy . Since elemental radium oxidizes readily in air and water, radium salts are the preferred chemical form of radium to work with. [ 3 ] Even though it is more stable than elemental radium, radium bromide is still extremely toxic, and can explode under certain conditions. [ 4 ]
After the Curies discovered radium (in the form of radium chloride ) in 1898, scientists began to isolate radium on an industrial scale, with the intent of using it for radiotherapy treatments. Radium salts, including radium bromide, were most often used by placing the chemical in a tube that was then passed over or inserted into diseased tissue in the body. Many of the first scientists to try to determine radium's uses were affected by their exposure to the radioactive material. Pierre Curie went so far as to self-inflict a severe chemical skin reaction by applying a radium source directly to his forearm, which ultimately created a skin lesion. [ 5 ] All types of therapeutic tests were performed for different skin diseases including eczema , lichen and psoriasis . Later, it was hypothesized that radium could be used to treat cancerous diseases.
However, during this time frame, radium also gained popularity among pseudoscientific "health remedy" industries, which promoted radium as an essential element that could "heal" and "reinvigorate" cells in the human body and remove poisonous substances. As a result, radium gained popularity as a "health trend" in the 1920s and radium salts were added to food, drinks, clothing, toys, and even toothpaste. [ 6 ] Furthermore, many respectable journals and newspapers in the early 1900s published statements claiming that radium posed no health hazard.
The main problem with the growth of interest in radium was the lack of radium on earth itself. In 1913, it was reported that the Radium Institute had four grams of radium total, which at the time was more than half the world supply. [ 6 ] Numerous countries and institutions across the world set out to extract as much radium as possible, a time-consuming and expensive task. It was reported in Science magazine in 1919 that the United States had produced approximately 55 grams of radium since 1913, which was also more than half the radium produced in the world at the time. [ 7 ] A principal source for radium is pitchblende , which holds a total of 257 mg of radium per ton of U 3 O 8 . [ 3 ] With so little product recovered from such a large amount of material, it was difficult to extract a large quantity of radium. This was the reason radium bromide became one of the most expensive materials on earth. In 1921, it was stated in Time magazine that one ton of radium cost 17,000,000,000 Euros, whereas one ton of gold cost 208,000 Euros and one ton of diamond cost 400,000,000 Euros. [ 6 ]
Radium bromide was also found to induce phosphorescence at normal temperatures. [ 8 ] This led to the US army manufacturing and supplying luminous watches and gun sights to soldiers. It also allowed for the invention of the spinthariscope , which soon became a popular household item. [ 9 ]
Radium bromide is a luminous salt that causes the air surrounding it, even when encased in a tube, to glow a brilliant green and demonstrate all bands of the nitrogen spectrum. It is possible that the effect of the alpha radiation on the nitrogen in the air causes this luminescence . Radium bromide is highly reactive and crystals can sometimes explode, especially if heated. Helium gas evolved from alpha particles can accumulate within the crystals, which can cause them to weaken and rupture.
Radium bromide will crystallize when separated from aqueous solution. It forms a dihydrate , very similar to barium bromide . [ 4 ]
Radium is obtained from uranium or pitchblende ores by the "Curie method", which involves two major stages. In the first stage the ore is treated with sulfuric acid dissolves many components. The residue contains, barium, radium, and lead sulfates. The mixture will then be treated with sodium chloride and sodium carbonate to remove the lead. The second stage involves separation of the barium from the radium. [ 3 ] [ 4 ]
Radium bromide can be obtained from radium chloride by reaction with a stream of hydrogen bromide . [ 4 ]
Radium bromide, like all radium compounds, is highly radioactive and very toxic. Due to its chemical similarity to calcium , radium tends to accumulate in the bones, where it irradiates the bone marrow and can cause anemia , leukemia , sarcoma , bone cancer , genetic defects, infertility , ulcers, and necrosis . Symptoms of poisoning can take years to develop, by which time it is usually too late for any effective medical treatment. Radium bromide also poses a severe environmental hazard , amplified due to its high solubility in water, and it can bioaccumulate and cause long-lasting damage to organisms. [ citation needed ]
Radium bromide is highly reactive, and crystals can explode if violently shocked or heated. This is, in part, due to self-damage of the crystals by alpha radiation, which weakens the lattice structure. [ dubious – discuss ]
Radium and radium salts were commonly used for treating cancer ; however, these treatments have been mostly phased out in favor of less toxic chemicals such as technetium or strontium-89 . [ 6 ] Radium bromide was also used in luminous paint on watches, but its use was ultimately phased out in the 1960-1970s in favor of less dangerous chemicals like promethium and tritium . | https://en.wikipedia.org/wiki/RaBr2 |
Radium chloride is an inorganic compound with the chemical formula Ra Cl 2 . It is a radium salt of hydrogen chloride . It was the first radium compound isolated in a pure state. Marie Curie and André-Louis Debierne used it in their original separation of radium from barium . The first preparation of radium metal was by the electrolysis of a solution of this salt using a mercury cathode. [ 2 ] [ 1 ] : 3
Radium chloride crystallises from aqueous solution as the dihydrate . The dihydrate is dehydrated by heating to 100 °C in air for one hour followed by 5.5 hours at 520 °C under argon . [ 3 ] If the presence of other anions is suspected, the dehydration may be effectuated by fusion under hydrogen chloride . [ 4 ]
Radium chloride can also be prepared by heating radium bromide in a flow of dry hydrogen chloride gas. It can be produced by treating radium carbonate with hydrochloric acid.
Radium chloride is a colorless salt with a blue-green luminescence , especially when heated. Its color gradually changes to yellow with aging, whereas contamination by barium may impart a rose tint. [ 1 ] : 5 It is less soluble in water than other alkaline earth metal chlorides – at 25 °C its solubility is 245 g/L whereas that of barium chloride is 307 g/L, and the difference is even larger in hydrochloric acid solutions. This property is used in the first stages of the separation of radium from barium by fractional crystallization . [ 1 ] : 6 Radium chloride is only sparingly soluble in azeotropic hydrochloric acid and virtually insoluble in concentrated hydrochloric acid. [ 5 ]
Gaseous RaCl 2 shows strong absorptions in the visible spectrum at 676.3 nm and 649.8 nm (red): the dissociation energy of the radium–chlorine bond is estimated as 2.9 eV , [ 6 ] and its length as 292 pm . [ 7 ]
Contrary to diamagnetic barium chloride, radium chloride is weakly paramagnetic with a magnetic susceptibility of 1.05 × 10 6 . Its flame color is red. [ 1 ] : 5
Radium chloride is still used for the initial stages of the separation of radium from barium during the extraction of radium from pitchblende . The large quantities of material involved (to extract a gram of pure radium metal, about 7 tonnes of pitchblende is required) favour this less costly (but less efficient) method over those based on radium bromide or radium chromate (used for the later stages of the separation).
It was also used in medicine to produce radon gas which in turn was used as a brachytheraputic cancer treatment. [ 8 ] [ 9 ]
Radium-223 dichloride ( USP , radium chloride Ra 223), tradename Xofigo (formerly Alpharadin), is an alpha-emitting radiopharmaceutical . Bayer received FDA approval for this drug to treat prostate cancer osteoblastic bone metastases in May 2013. Radium-223 chloride is one of the most potent ((antineoplastic drugs)) known. [ citation needed ] One dose (50 kBq/kg) in an adult is about 60 nanograms; this amount is 1/1000 the weight of an eyelash (75 micrograms). | https://en.wikipedia.org/wiki/RaCl2 |
Rabatment of the rectangle is a compositional technique used as an aid for the placement of objects or the division of space within a rectangular frame, or as an aid for the study of art.
Every rectangle contains two implied squares, each consisting of a short side of the rectangle, an equal length along each longer side, and an imaginary fourth line parallel to the short side. The process of mentally rotating the short sides onto the long ones is called "rabatment", and often the imaginary fourth line is called "the rabatment".
There is no absolute explanation of the mechanism of this method, but there are various theories. [ 1 ] One argument is that squares are such a simple, primal geometric shape that the brain automatically looks for them, mentally completing this rabatment whether it is made explicit or not. When a composition uses elements of the scene to match, the square feels complete in itself, producing a feeling of harmony. [ 1 ]
Renaissance artists used rabatment as a foundation to art and architectural works, [ 2 ] [ 3 ] but the rabatment can be observed in art taken from almost any period. [ 4 ]
As one of many composition techniques, rabatment of the rectangle can be used to inform the positioning of elements within the rectangle. There is no hard and fast rule regarding such positioning; a composition can have a sense of dynamic unrest or a sense of equilibrium relative to important lines such as ones taken from rabatment or from the rule of thirds, or from nodal points such as the "eyes of a rectangle"—the four intersections derived from the rule of thirds. [ 5 ] Primary image elements can be positioned within one of the two rabatment squares to define the center of interest, and secondary image elements can be placed outside of a rabatment square. [ 6 ]
The concept of rabatment can be applied to rectangles of any proportion. [ 7 ] For rectangles with a 3:2 ratio (as in 35mm film in still photography), it happens that the rabatment lines are exactly matched to the rule of thirds lines. [ 8 ]
In a horizontally-aligned rectangle, there is one implied square for the left side and one for the right; for a vertically-aligned rectangle, there are upper and lower squares. [ 1 ] If the long sides of the rectangle are exactly twice the length of the short, this line is right in the middle. With longer-proportioned rectangles, the squares don't overlap, but with shorter-proportioned ones, they do. In Western cultures that read left to right, attention is often focused inside the left-hand rabatment, or on the line it forms at the right-hand side of the image. [ 9 ]
When rabatment is used with one side of a golden rectangle , and then iteratively applied to the left-over rectangle, the resulting "whirling rectangles" describe the golden spiral . [ 10 ] | https://en.wikipedia.org/wiki/Rabatment_of_the_rectangle |
Rabattement (also rabatment ) is a rotation of a planar object around a folding line (using the line like a hinge ) in order to align the object with another plane. [ 1 ] [ 2 ] [ 3 ] Rabattement is used in technical drawings to produce developments (patterns, templates). In these drawings the object is "unfolded" to lay flat on a plane so it can be represented in entirety. [ 4 ] The term originates from French rabbatement ' an act of lowering ' , due to the typical alignment plane being the horizontal one, [ 5 ] although a vertical plane is sometimes used in elevation . [ 6 ]
The technique of rabattement is very old: the archaic paintings that predate Antiquity used similar methods to achieve "intellectual realism" (as opposed to " visual realism " of later times) by unfolding the object to represent its hidden sides. [ 4 ]
Rabattement was extensively used by stonemasons in the construction drawings, and, together with projection plane , evolved into a method of descriptive geometry. Descriptive geometry manuals sometimes use the term "rotation" when discussing moving points and lines, reserving "rabattement" for shapes and planes, but in practice both operations are identical. [ 7 ]
The goal of the rabattement operation is to represent the true shape and size of a face of an object [ 2 ] (this is impossible to do with orthographic projection if the shape of interest is inclined with respect to all planes of projection [ 8 ] ).
This geometry-related article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Rabattement_(drafting) |
Rabbi Nehemiah was a rabbi who lived circa 150 AD (fourth generation of tannaim ).
He was one of the great students of Rabbi Akiva , and one of the rabbis who received semicha from R' Judah ben Baba
The Talmud equated R' Nechemiah with Rabbi Nehorai : "His name was not Rabbi Nehorai, but Rabbi Meir." [ 1 ]
His son, R' Yehudah BeRabi Nechemiah, studied before Rabbi Tarfon , but died at a young age after damaging R' Tarfon's honor, after R' Akiva predicted his death. [ 2 ]
In the Talmud , all anonymous sayings in the Tosefta are attributed to R' Nechemiah. [ 3 ] However, Sherira Gaon said that this does not mean they were said by R' Nechemiah, but that the laws in question were transmitted by R' Nechemiah. [ 4 ]
In the Talmud, many times he disagrees with R' Judah bar Ilai on matters of halacha.
He is attributed as the author of the Mishnat ha-Middot (ca. AD 150), making it the earliest known Hebrew text on geometry , although some historians assign the text to a later period by an unknown author.
The Mishnat ha-Middot argues against the common belief that the Bible defines the geometric ratio π (pi) as being exactly equal to 3, based on the description in 1 Kings 7:23 (and 2 Chronicles 4:2) of the great bowl situated outside the Temple of Jerusalem as having a diameter of 10 cubits and a circumference of 30 cubits. He maintained that the diameter of the bowl was measured from the outside brim, while the circumference was measured along the inner brim, which with a brim that is one handbreadth wide (as described in the subsequent verses 1 Kings 7:24 and 2 Chronicles 4:3) yields a ratio from the circular rim closer to the actual value of π . [ 5 ]
This biographical article about a rabbi from the Middle East is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Rabbi_Nehemiah |
The State Barrier Fence of Western Australia , [ 1 ] formerly known as the Rabbit-Proof Fence , the State Vermin Fence , and the Emu Fence , is a pest-exclusion fence constructed between 1901 and 1907 to keep rabbits , and other agricultural pests from the east, out of Western Australian pastoral areas. [ 2 ]
There are three fences in Western Australia: the original No. 1 Fence crosses the state from north to south, No. 2 Fence is smaller and further west, and No. 3 Fence is smaller still and runs east–west. The fences took six years to build. When completed, the rabbit-proof fence (including all three fences) stretched 3,256 kilometres (2,023 mi). The cost to build each kilometre of fence at the time was about $250 (equivalent to $42,000 in 2022). [ 3 ]
When it was completed in 1907, the 1,833-kilometre (1,139 mi) No. 1 Fence was the longest unbroken fence in the world. [ 4 ]
Rabbits were introduced to Australia by the First Fleet in 1788. [ 5 ] They became a problem after October 1859, when Thomas Austin released 24 wild rabbits from England for hunting purposes, believing "The introduction of a few rabbits could do little harm and might provide a touch of home, in addition to a spot of hunting." [ 6 ]
With virtually no local predators, the rabbits became extremely prolific and spread rapidly across the southern parts of the country. Australia had ideal conditions for an explosion in the rabbit population, which constituted an invasive species .
By 1887, agricultural losses from rabbit damage compelled the New South Wales Government to offer a £25,000 reward (equivalent to $3,900,000 in 2022) for "any method of success not previously known in the Colony for the effectual extermination of rabbits". [ 7 ] A Royal Commission was held in 1901 to investigate the situation. It determined to build a pest-exclusion fence.
The fence posts are placed 12 ft (3.7 m) apart and have a minimum diameter of 4 in (100 mm). There were initially three wires of 12 + 1 ⁄ 2 gauge , strung 4 in (102 mm), 1 ft 8 in (0.5 m), and 3 ft (0.9 m) above ground, with a barbed wire added later at 3 ft 4 in (1.02 m) and a plain wire at 3 ft 7 in (1.1 m), to make the fence a barrier against dingoes and foxes as well. Wire netting, extending 6 in (150 mm) below ground, was attached to the wire.
The fence was constructed with a variety of materials, according to the local climate and availability of wood . At first, fence posts were made from salmon gum and gimlet , but they attracted termites (locally known as white ants) and had to be replaced. Split white gum was one of the best types of wood used in the fence. Other timbers used were mulga , wodjil , native pine , and tea-tree , depending on what could be found close to where the fence was to be built. Iron posts were used where there was no wood. Most materials had to be hauled hundreds of kilometres from rail heads and ports by bullock, mule and camel teams. [ 8 ]
From 1901, the fence was constructed by private contractors. In 1904, the project became the responsibility of the Public Works Department of Western Australia, under the supervision of Richard John Anketell. [ 3 ] With a workforce of 120 men, 350 camels, 210 horses and 41 donkeys, Anketell was responsible for the construction of the greater part of No. 1 Fence and the survey of its last 70 miles (110 km). [ 4 ]
Alexander Crawford took over the maintenance of the fence from Anketell as each section was finished; he was in charge until he retired in 1922. [ 4 ] The area inside the fence to the west became known as "Crawford's Paddock". The fence was maintained at first by boundary riders riding bicycles and later by riders astride camels . However, fence inspection was difficult from atop the tall animal. In 1910, a car was bought for fence inspection, but it was subject to punctured tyres. It was found the best way to inspect the fence was using buckboard buggies, pulled by two camels.
The camels were also used as pack animals , especially in the north. In the east, camels were used to pull drays with supplies for the riders. Camels were ideal for this as they could go for a long time without water. They were considered critical to the building and maintenance of the fence.
Crawford supervised four sub-inspectors, each responsible for about 500 miles (800 km) of fence, and 25 boundary riders, who regularly patrolled 100-mile (160 km) sections of fence. Due to frontier violence in the north of the state, a 300-mile (480 km) section of No. 1 Fence was patrolled by riders who traveled in pairs. [ 9 ]
Crawford also was responsible for eliminating rabbits that had breached the fence. In the first year following the fence's completion, rabbit colonies were found and all members killed at several locations inside the fence. These included sites near Coorow , Mullewa , and Northampton . [ 9 ]
Following the introduction of myxomatosis to control rabbits in the 1950s, the importance of the rabbit-proof fence diminished.
By 1902, rabbits had already been found west of the fence line that had been initially constructed. The Number 2 Rabbit Proof Fence was built in 1905 in order to stem their advance. [ 10 ] It held back the rabbits for many years, to such an extent that the Government Scheme for supplying rabbit netting, by extending long-term loans to farmers, was never applied to farmers west of that fence. The farmers between the two fences suffered from the ravages of the rabbits for many years, before they bred into plague form to spread out over the agricultural districts to the west of the No. 2 fence. [ 11 ]
Overall, as a long-term barrier to rabbits, the fences were a failure; even while construction was underway, rabbits were hopping into regions that the fences were intended to protect. [ 12 ]
No. 1 Fence intersected railway lines at:
No. 2 Fence intersected with most of the Wheatbelt railway lines of Western Australia .
The Darling Downs–Moreton Rabbit Board fence is a rabbit fence that extends along part of the Queensland–New South Wales border. [ 13 ]
In 1907, Arthur Upfield , an Australian writer who had previously worked on the construction of No. 1 Fence, began writing a fictional story that explored a way of disposing of a body in the desert. Before the book was published, stockman Snowy Rowles, an acquaintance of the writer, carried out at least two murders and disposed of the bodies using the method described in the book.
The 1932 trial that followed the arrest of Rowles for murder was one of the most sensational in the history of Western Australia. Decades later, Terry Walker wrote a book about this called Murder on the Rabbit Proof Fence: The Strange Case of Arthur Upfield and Snowy Rowles (1993). [ 14 ] The events are now referred to as the Murchison Murders .
Doris Pilkington Garimara 's book, Follow the Rabbit-Proof Fence (1996), describes how three Indigenous Australian girls used the fence to guide their route back home from Moore River Native Settlement to Jigalong . The girls, taken from their families in Western Australia as part of the Stolen Generations , escaped from the mission settlement. Two sisters were successful in walking hundreds of kilometers back to their family at Jigalong by following the rabbit-proof fence. Garmimara is the daughter of Molly, one of the girls.
The dramatic film Rabbit-Proof Fence (2002) is based on the book. In 2016, Englishwoman Lindsey Cole walked the fence from Moore River Settlement, 1,600 kilometres (990 mi) through to Jigalong. She was met by Doris Garimara's daughter at the end of the walk in September 2016. [ 15 ] | https://en.wikipedia.org/wiki/Rabbit-proof_fence |
A rabbit hybridoma is a hybrid cell line formed by the fusion of an antibody producing rabbit B cell with a cancerous B-cell ( myeloma ).
The rabbit immune system has been documented as a vehicle for developing antibodies with higher affinity and more diverse recognition of many molecules including phospho-peptides, carbohydrates and immunogens that are not otherwise immunogenic in mouse. [ 1 ] However, until recently, the type of antibodies available from rabbit had been limited in scope to polyclonal antibodies . Several efforts were made to generate rabbit monoclonal antibodies after the development of mouse hybridoma technology in the 1970s. [ 2 ] Research was conducted into mouse-rabbit hetero-hybridomas to make rabbit monoclonal antibodies. [ 1 ] [ 3 ] However, these hetero-hybridomas were ultimately difficult to clone, and the clones, generally unstable, and did not secrete antibody over a prolonged period of time.
In 1995, Katherine Knight and her colleagues, at Loyola University of Chicago, succeeded in developing a double transgenic rabbit over-expressing the oncogenes v-abl and c-myc under the control of the immunoglobulin heavy and light chain enhancers. The rabbit formed a myeloma-like tumor, allowing the isolation of a plasmacytoma cell line, named 240E-1. Fusion of 240E-1 cells with rabbit lymphocytes produced hybridomas that secreted rabbit monoclonal antibodies in a consistent manner. [ 4 ] However, like the early mouse myeloma lines developed in the 1970s, stability was a concern. A number of laboratories which had received the 240E-1 cell line from Dr. Knight’s laboratory reported stability problems with the fusion cell line 240E-1. [ 5 ]
In 1996, Weimin Zhu and Robert Pytela, at the University of California San Francisco (UCSF), obtained 240E-1 from Dr. Knight’s laboratory and attempted to develop an improved rabbit hybridoma. [ 4 ] Improvements in the characteristics of 240E-1 were accomplished by repeated subcloning, selection for high fusion efficiency, robust growth, and morphological characteristics such as a bright appearance under a phase-contrast microscope . Selected subclones were further tested for their ability to produce a stable hybridoma and monoclonal antibody secretion. After multiple rounds of subcloning and selection processes, a new cell line named 240E-W, was identified and which expressed better fusion efficiency and stability. Cell line 240E-W has since been further developed and optimized for production of rabbit monoclonal antibodies for research and commercial applications.
The process of hybridoma formation in a rabbit first entails obtaining B-cells from a rabbit that has been immunized. There are numerous immunization protocols for rabbit, notably for the generation of polyclonal antibodies. [ 6 ] [ 7 ] [ 8 ] After immunization, B-cells are fused with a candidate rabbit fusion partner cell line to form hybridomas. Resulting antibodies from hybridomas are screened for an antigen which meets criteria of interest by diagnostic tests such as ELISA , western blot , immunohistochemistry , and FACS. The resulting hybrdomas may be subcloned to ensure monoclonal characteristics.
Mitchell Ho and Ira Pastan at National Cancer Institute (Bethesda, USA) isolated a group of rabbit monoclonal antibodies (e.g. YP218, YP223) that recognize rare epitopes of mesothelin , including poorly immunogenic sites close to the C terminal end, for cancer therapy. [ 9 ] Dr. Ho's laboratory analyzed the complex structures of rabbit antibodies with their antigens from the Protein Data Bank, and identified antigen-contacting residues on the rabbit Fv within the 6 Angstrom distance to its antigen. [ 10 ] They named "HV4" and "LV4", non-complementarity-determining region (CDR) loops that are structurally close to the antigen and located in framework 3 of the rabbit heavy chain and light chain, respectively. Based on computational structural modeling, Ho and Zhang designed a humanization strategy by grafting the combined Kabat/IMGT/Paratome CDRs into a human germline framework sequence. The immunotoxins composed of the humanized rabbit Fvs (e.g. hYP218) fused to a clinically used toxin showed stronger cytotoxicity against tumor cells than the immunotoxins derived from their original rabbit Fvs. The CAR T cells based on the hYP218 antibody also show effective inhibition of tumor growth in mice. [ 11 ] The method (i.e. grafting combined Kabat/IMGT/Paratome rabbit CDRs to a stable human germline framework) has been suggested as a general approach to humanizing rabbit antibodies. [ 10 ] | https://en.wikipedia.org/wiki/Rabbit_hybridoma |
In 1617 a treatise in Latin titled Rabdologiæ and written by John Napier was published in Edinburgh. Printed three years after his treatise on the discovery of logarithms and in the same year as his death, it describes three devices to aid arithmetic calculations.
The devices themselves don't use logarithms, rather they are tools to reduce multiplication and division of natural numbers to simple addition and subtraction operations.
The first device, which by then was already popularly used and known as Napier's bones , was a set of rods inscribed with the multiplication table. Napier coined the word rabdology (from Greek ῥάβδος [rhabdos], rod and λόγoς [logos] calculation or reckoning) to describe this technique. The rods were used to multiply, divide and even find the square roots and cube roots of numbers.
The second device was a promptuary (Latin promptuarium meaning storehouse) and consisted of a large set of strips that could multiply multidigit numbers more easily than the bones. In combination with a table of reciprocals, it could also divide numbers.
The third device used a checkerboard like grid and counters moving on the board to perform binary arithmetic. Napier termed this technique location arithmetic from the way in which the locations of the counters on the board represented and computed numbers. Once a number is converted into a binary form, simple movements of counters on the grid could multiply, divide and even find square roots of numbers.
Of these devices, Napier's bones were the most popular and widely known. In fact, part of his motivation to publish the treatise was to establish credit for his invention of the technique. The bones were easy to manufacture and simple to use, and several variations on them were published and used for many years.
The promptuary was never widely used, perhaps because it was more complex to manufacture, and it took nearly as much time to lay out the strips to find the product of numbers as to find the answer with pen and paper.
Location arithmetic was an elegant insight into the simplicity of binary arithmetic, but remained a curiosity probably because it was never clear that the effort to convert numbers in and out of binary form was worth the trouble.
An interesting tidbit is this treatise contains the earliest written reference to the decimal point (though its usage would not come into general use for another century).
The computing devices in Rabdology were overshadowed by Napier's seminal work on logarithms as they proved more useful and more widely applicable. Nevertheless, these devices (as indeed are logarithms) are examples of Napier's ingenious attempts to discover easier ways to multiply, divide and find roots of numbers. Location arithmetic in particular foreshadowed the ease of and power of mechanizing binary arithmetic, but was never fully appreciated. | https://en.wikipedia.org/wiki/Rabdology |
The Rabi frequency is the frequency at which the probability amplitudes of two atomic energy levels fluctuate in an oscillating electromagnetic field. It is proportional to the transition dipole moment of the two levels and to the amplitude ( not intensity ) of the electromagnetic field . Population transfer between the levels of such a 2-level system illuminated with light exactly resonant with the difference in energy between the two levels will occur at the Rabi frequency; when the incident light is detuned from this energy difference (detuned from resonance) then the population transfer occurs at the generalized Rabi frequency . The Rabi frequency is a semiclassical concept since it treats the atom as an object with quantized energy levels and the electromagnetic field as a continuous wave.
In the context of a nuclear magnetic resonance experiment, the Rabi frequency is the nutation frequency of a sample's net nuclear magnetization vector about a radio-frequency field. (Note that this is distinct from the Larmor frequency , which characterizes the precession of a transverse nuclear magnetization about a static magnetic field.)
Consider two energy eigenstates of a quantum system with Hamiltonian H ^ 0 {\displaystyle {\hat {H}}_{0}} (for example, this could be the Hamiltonian of a particle in a 1 r {\displaystyle {\frac {1}{r}}} potential, like the Hydrogen atom or the Alkali atoms):
ψ 1 ( r , t ) = e − i ω 1 t | 1 ⟩ ψ 2 ( r , t ) = e − i ω 2 t | 2 ⟩ {\displaystyle {\begin{aligned}\psi _{1}(\mathbf {r} ,t)&=e^{-i\omega _{1}t}|1\rangle \\\psi _{2}(\mathbf {r} ,t)&=e^{-i\omega _{2}t}|2\rangle \end{aligned}}}
We want to consider the time dependent Hamiltonian
H ^ = H ^ 0 + V ^ ( t ) {\displaystyle {\hat {\mathcal {H}}}={\hat {H}}_{0}+{\hat {V}}(t)}
where V ^ ( t ) = e r ⋅ E 0 cos ( ω t ) {\displaystyle {\hat {V}}(t)=e\mathbf {r} \cdot \mathbf {E} _{0}\cos(\omega t)} is the potential energy of the electromagnetic field. Treating the potential energy as a perturbation , we can expect the eigenstates of the perturbed Hamiltonian to be some mixture of the eigenstates of the original Hamiltonian with time dependent coefficients:
Ψ ( r , t ) = c 1 ( t ) e − i ω 1 t | 1 ⟩ + c 2 ( t ) e − i ω 2 t | 2 ⟩ {\displaystyle \Psi (\mathbf {r} ,t)=c_{1}(t)e^{-i\omega _{1}t}|1\rangle +c_{2}(t)e^{-i\omega _{2}t}|2\rangle }
Plugging this into the time dependent Schrödinger equation
i ℏ ∂ Ψ ( r , t ) ∂ t = H ^ Ψ ( r , t ) {\displaystyle i\hbar {\frac {\partial \Psi (\mathbf {r} ,t)}{\partial t}}={\hat {\mathcal {H}}}\Psi (\mathbf {r} ,t)}
taking the inner product with each of e i ω 1 t ⟨ 1 | {\displaystyle e^{i\omega _{1}t}\langle 1|} and e i ω 2 t ⟨ 2 | {\displaystyle e^{i\omega _{2}t}\langle 2|} , and using the orthogonality condition of eigenstates ⟨ i | j ⟩ = δ i , j {\displaystyle \langle i|j\rangle =\delta _{i,j}} , we arrive at two equations in the coefficients c 1 ( t ) {\displaystyle c_{1}(t)} and c 2 ( t ) {\displaystyle c_{2}(t)} :
i c ˙ 1 ( t ) = c 1 ( t ) cos ( ω t ) ℏ ⟨ 1 | e r ⋅ E 0 | 1 ⟩ + e i ω 0 t c 2 ( t ) cos ( ω t ) ℏ ⟨ 1 | e r ⋅ E 0 | 2 ⟩ i c ˙ 2 ( t ) = c 2 ( t ) cos ( ω t ) ℏ ⟨ 2 | e r ⋅ E 0 | 2 ⟩ + e − i ω 0 t c 1 ( t ) cos ( ω t ) ℏ ⟨ 2 | e r ⋅ E 0 | 1 ⟩ {\displaystyle {\begin{aligned}i{\dot {c}}_{1}(t)&={\frac {c_{1}(t)\cos(\omega t)}{\hbar }}\langle 1|e\mathbf {r} \cdot \mathbf {E} _{0}|1\rangle +{\frac {e^{i\omega _{0}t}c_{2}(t)\cos(\omega t)}{\hbar }}\langle 1|e\mathbf {r} \cdot \mathbf {E} _{0}|2\rangle \\i{\dot {c}}_{2}(t)&={\frac {c_{2}(t)\cos(\omega t)}{\hbar }}\langle 2|e\mathbf {r} \cdot \mathbf {E} _{0}|2\rangle +{\frac {e^{-i\omega _{0}t}c_{1}(t)\cos(\omega t)}{\hbar }}\langle 2|e\mathbf {r} \cdot \mathbf {E} _{0}|1\rangle \end{aligned}}}
where ω 0 = ω 1 − ω 2 {\displaystyle \omega _{0}=\omega _{1}-\omega _{2}} . The two terms in parentheses are dipole matrix elements dotted into the polarization vector of the electromagnetic field. In considering the spherically symmetric spatial eigenfunctions | i ⟩ {\displaystyle |i\rangle } of the Hydrogen atom potential, the diagonal matrix elements go to zero, leaving us with
i c ˙ 1 ( t ) = c 2 ( t ) cos ( ω t ) ℏ ⟨ 1 | e r ⋅ E 0 | 2 ⟩ e i ω 0 t i c ˙ 2 ( t ) = c 1 ( t ) cos ( ω t ) ℏ ⟨ 2 | e r ⋅ E 0 | 1 ⟩ e − i ω 0 t {\displaystyle {\begin{aligned}i{\dot {c}}_{1}(t)&={\frac {c_{2}(t)\cos(\omega t)}{\hbar }}\langle 1|e\mathbf {r} \cdot \mathbf {E} _{0}|2\rangle e^{i\omega _{0}t}\\i{\dot {c}}_{2}(t)&={\frac {c_{1}(t)\cos(\omega t)}{\hbar }}\langle 2|e\mathbf {r} \cdot \mathbf {E} _{0}|1\rangle e^{-i\omega _{0}t}\end{aligned}}}
or
i c ˙ 1 ( t ) = Ω c 2 ( t ) cos ( ω t ) e i ω 0 t i c ˙ 2 ( t ) = Ω ∗ c 1 ( t ) cos ( ω t ) e − i ω 0 t {\displaystyle {\begin{aligned}i{\dot {c}}_{1}(t)&=\Omega c_{2}(t)\cos(\omega t)e^{i\omega _{0}t}\\i{\dot {c}}_{2}(t)&=\Omega ^{*}c_{1}(t)\cos(\omega t)e^{-i\omega _{0}t}\end{aligned}}}
Here Ω := Ω 1 , 2 {\displaystyle \Omega :=\Omega _{1,2}} , where Ω i , j = ⟨ i | e r ⋅ E 0 | j ⟩ ℏ {\displaystyle \Omega _{i,j}={\frac {\langle i|e\mathbf {r} \cdot \mathbf {E} _{0}|j\rangle }{\hbar }}} is the Rabi Frequency.
In the numerator we have the transition dipole moment for the i → j {\displaystyle i\to j} transition, whose squared amplitude represents the strength of the interaction between the electromagnetic field and the atom, and E 0 = ϵ ^ E 0 {\displaystyle \mathbf {E} _{0}={\hat {\epsilon }}E_{0}} is the vector electric field amplitude , which includes the polarization . The numerator has dimensions of energy, so dividing by ℏ {\displaystyle \hbar } gives an angular frequency .
By analogy with a classical dipole , it is clear that an atom with a large dipole moment will be more susceptible to perturbation by an electric field. The dot product includes a factor of cos θ {\displaystyle \cos \theta } , where θ {\displaystyle \theta } is the angle between the polarization of the light and the transition dipole moment. When they are parallel the interaction is strongest, when they are perpendicular there is no interaction at all.
If we rewrite the differential equations found above:
i c ˙ 1 ( t ) = Ω c 2 ( t ) cos ( ω t ) e i ω 0 t → Ω c 2 2 ( e i ( ω − ω 0 ) t + e − i ( ω + ω 0 ) t ) i c ˙ 2 ( t ) = Ω ∗ c 1 ( t ) cos ( ω t ) e − i ω 0 t → Ω ∗ c 1 2 ( e i ( ω + ω 0 ) t + e − i ( ω − ω 0 ) t ) {\displaystyle {\begin{aligned}i{\dot {c}}_{1}(t)=\Omega c_{2}(t)\cos(\omega t)e^{i\omega _{0}t}&\to {\frac {\Omega c_{2}}{2}}(e^{i(\omega -\omega _{0})t}+e^{-i(\omega +\omega _{0})t})\\i{\dot {c}}_{2}(t)=\Omega ^{*}c_{1}(t)\cos(\omega t)e^{-i\omega _{0}t}&\to {\frac {\Omega ^{*}c_{1}}{2}}(e^{i(\omega +\omega _{0})t}+e^{-i(\omega -\omega _{0})t})\end{aligned}}}
and apply the rotating-wave approximation , which assumes that ω + ω 0 >> ω − ω 0 {\displaystyle \omega +\omega _{0}>>\omega -\omega _{0}} , such that we can discard the high frequency oscillating terms, we have
i c ˙ 1 ( t ) = Ω c 2 2 e i δ t i c ˙ 2 ( t ) = Ω ∗ c 1 2 e − i δ t {\displaystyle {\begin{aligned}i{\dot {c}}_{1}(t)&={\frac {\Omega c_{2}}{2}}e^{i\delta t}\\i{\dot {c}}_{2}(t)&={\frac {\Omega ^{*}c_{1}}{2}}e^{-i\delta t}\end{aligned}}}
where δ = ω − ω 0 {\displaystyle \delta =\omega -\omega _{0}} is called the detuning between the laser and the atomic frequencies.
We can solve these equations, assuming at time t = 0 {\displaystyle t=0} the atom is in | 1 ⟩ {\displaystyle |1\rangle } (i.e. c 1 ( 0 ) = 1 {\displaystyle c_{1}(0)=1} ) to find
| c 2 ( t ) | 2 = Ω 2 sin 2 ( Ω 2 + δ 2 t 2 ) Ω 2 + δ 2 {\displaystyle |c_{2}(t)|^{2}={\frac {\Omega ^{2}\sin ^{2}{\bigg (}{\frac {{\sqrt {\Omega ^{2}+\delta ^{2}}}t}{2}}{\bigg )}}{\Omega ^{2}+\delta ^{2}}}}
This is the probability as a function of detuning and time of the population of state | 2 ⟩ {\displaystyle |2\rangle } . A plot as a function of detuning and ramping the time from 0 to t = π Ω {\displaystyle t={\frac {\pi }{\Omega }}} gives:
We see that for δ = 0 {\displaystyle \delta =0} the population will oscillate between the two states at the Rabi frequency.
The quantity Ω 2 + δ 2 {\displaystyle {\sqrt {\Omega ^{2}+\delta ^{2}}}} is commonly referred to as the "generalized Rabi frequency." For cases in which δ ≠ 0 {\displaystyle \delta \neq 0} , Rabi flopping actually occurs at this frequency, where δ {\displaystyle \delta } is the detuning , a measure of how far the light is off-resonance relative to the transition. For instance, examining the above animation at an offset frequency of ±1.73, one can see that during the 1/2 Rabi cycle (at resonance) shown during the animation, the oscillation instead undergoes one full cycle, thus at twice the (normal) Rabi frequency Ω i , j {\displaystyle \Omega _{i,j}} , just as predicted by this equation. Also note that as the incident light frequency shifts further from the transition frequency, the amplitude of the Rabi oscillation decreases, as is illustrated by the dashed envelope in the above plot.
Coherent Rabi oscillations may also be driven by two-photon transitions . In this case we consider a system with three atomic energy levels, | 1 ⟩ {\displaystyle |1\rangle } , | i ⟩ {\displaystyle |i\rangle } , and | 2 ⟩ {\displaystyle |2\rangle } , where | i ⟩ {\displaystyle |i\rangle } is an intermediate state with corresponding frequency ω i {\displaystyle \omega _{i}} , and an electromagnetic field with two frequency components:
V ^ ( t ) = e r ⋅ E L 1 cos ( ω L 1 t ) + e r ⋅ E L 2 cos ( ω L 2 t ) {\displaystyle {\hat {V}}(t)=e\mathbf {r} \cdot \mathbf {E} _{L1}\cos(\omega _{L1}t)+e\mathbf {r} \cdot \mathbf {E} _{L2}\cos(\omega _{L2}t)}
A two-photon transition is not the same as excitation from the ground to intermediate state, and then out of the intermediate state to the excited state. Instead, the atom absorbs two photons simultaneously and is promoted directly between the initial and final states. The beat note of the two photons must be resonant with the two-photon transition (difference between initial and final state frequencies):
| ω L 1 − ω L 2 | = ω 2 − ω 1 Δ = | ω L 1 − ( ω i − ω 1 ) | ≫ 0 {\displaystyle {\begin{aligned}&|\omega _{L1}-\omega _{L2}|=\omega _{2}-\omega _{1}\\&\Delta =|\omega _{L1}-(\omega _{i}-\omega _{1})|\gg 0\end{aligned}}}
Delta determines the rate of scattering off of the intermediate state. The greater it is the longer the coherence time.
We may derive the two-photon Rabi frequency by returning to the equations
i c ˙ 1 ( t ) = Ω 1 i c i 2 e i Δ t i c ˙ i ( t ) = Ω 1 i ∗ c 1 2 e − i Δ t {\displaystyle {\begin{aligned}i{\dot {c}}_{1}(t)&={\frac {\Omega _{1i}c_{i}}{2}}e^{i\Delta t}\\i{\dot {c}}_{i}(t)&={\frac {\Omega _{1i}^{*}c_{1}}{2}}e^{-i\Delta t}\end{aligned}}}
which now describe excitation between the ground and intermediate states. We know we have the solution
c i ( t ) = Ω 1 i sin ( Ω ~ 1 i t 2 ) Ω ~ 1 i {\displaystyle c_{i}(t)={\frac {\Omega _{1i}\sin {\bigg (}{\frac {{\tilde {\Omega }}_{1i}t}{2}}{\bigg )}}{{\tilde {\Omega }}_{1i}}}}
where Ω ~ 1 i {\displaystyle {\tilde {\Omega }}_{1i}} is the generalized Rabi frequency for the transition from the initial to intermediate state. Similarly for the intermediate to final state transition we have the equations
i c ˙ i ( t ) = Ω i 2 c 2 2 e i Δ t i c ˙ 2 ( t ) = Ω i 2 ∗ c i 2 e − i Δ t {\displaystyle {\begin{aligned}i{\dot {c}}_{i}(t)&={\frac {\Omega _{i2}c_{2}}{2}}e^{i\Delta t}\\i{\dot {c}}_{2}(t)&={\frac {\Omega _{i2}^{*}c_{i}}{2}}e^{-i\Delta t}\end{aligned}}}
Now we plug c i ( t ) {\displaystyle c_{i}(t)} into the above equation for c ˙ 2 ( t ) {\displaystyle {\dot {c}}_{2}(t)}
i c ˙ 2 ( t ) = Ω i 2 ∗ Ω 1 i sin ( Ω ~ 1 i t 2 ) 2 Ω ~ 1 i e − i Δ t {\displaystyle i{\dot {c}}_{2}(t)={\frac {\Omega _{i2}^{*}\Omega _{1i}\sin {\bigg (}{\frac {{\tilde {\Omega }}_{1i}t}{2}}{\bigg )}}{2{\tilde {\Omega }}_{1i}}}e^{-i\Delta t}}
The coefficient is proportional to:
c 2 ( t ) ∝ Ω i 2 Ω 1 i 2 Δ {\displaystyle c_{2}(t)\propto {\frac {\Omega _{i2}\Omega _{1i}}{2\Delta }}}
This is the two-photon Rabi frequency. [ 1 ] It is the product of the individual Rabi frequencies for the | 1 ⟩ → | i ⟩ {\displaystyle |1\rangle \to |i\rangle } and | i ⟩ → | 2 ⟩ {\displaystyle |i\rangle \to |2\rangle } transitions, divided by the detuning from the intermediate state | i ⟩ {\displaystyle |i\rangle } . | https://en.wikipedia.org/wiki/Rabi_frequency |
Rabi resonance method is a technique developed by Isidor Isaac Rabi for measuring the nuclear spin, in which an atom is placed in a static magnetic field and a perpendicular rotating magnetic field.
When only the static magnetic field (B 0 ) is turned on, the spin will precess around it with Larmor frequency ν 0 and the corresponding angular frequency is ω 0 .
According to mechanics, the equation of motion of the spin J is:
where μ is the magnetic moment .
g is g-factor , which is dimensionless and reflecting the environmental effect on the spin.
Solving gives the angular frequency ( Larmor frequency ) with the magnetic field pointing on z-axis:
The minus sign is necessary. It reflects that the J is rotating in left-hand when the thumb is pointing as the H field.
when turned on the rotating magnetic field (B R ), with angular frequency ω. In the rotating frame of the rotating field, the equation of motion is:
or
if γ B 0 = ω 0 {\displaystyle \gamma B_{0}=\omega _{0}} , the static field is cancelled, and the spin now precesses around H R with angular frequency Rabi frequency
Since the rotating field is perpendicular to the static field, the spin in rotating frame is now able to flip between up and down.
By sweeping ω R , one can obtain a maximum flipping and determine the magnetic moment.
The experiment setup contains 3 parts: an inhomogeneous magnetic field in front, the rotating field at the middle, and another inhomogeneous magnetic field at the end.
Atoms after passing the first inhomogeneous field will split into 2 beams corresponding the spin up and spin down state. Select one beam (spin up state, for example) and let it pass the rotating field. If the rotating field has frequency (ω) equal to the Larmor frequency, it will produce a high intensity of the other beam (spin down state). By sweeping the frequency to obtain a maximum intensity, one can find out the Larmor frequency and the magnetic moment of the atom.
https://web.archive.org/web/20160325004825/https://www.colorado.edu/physics/phys7550/phys7550_sp07/extras/Ramsey90_RMP.pdf | https://en.wikipedia.org/wiki/Rabi_resonance_method |
The Rabinovich–Fabrikant equations are a set of three coupled ordinary differential equations exhibiting chaotic behaviour for certain values of the parameters . They are named after Mikhail Rabinovich and Anatoly Fabrikant , who described them in 1979.
The equations are: [ 1 ]
where α , γ are constants that control the evolution of the system. For some values of α and γ , the system is chaotic, but for others it tends to a stable periodic orbit.
Danca and Chen [ 2 ] note that the Rabinovich–Fabrikant system is difficult to analyse (due to the presence of quadratic and cubic terms) and that different attractors can be obtained for the same parameters by using different step sizes in the integration, see on the right an example of a solution obtained by two different solvers for the same parameter values and initial conditions. Also, recently, a hidden attractor was discovered in the Rabinovich–Fabrikant system. [ 3 ]
The Rabinovich–Fabrikant system has five hyperbolic equilibrium points , one at the origin and four dependent on the system parameters α and γ : [ 2 ]
where
These equilibrium points only exist for certain values of α and γ > 0.
An example of chaotic behaviour is obtained for γ = 0.87 and α = 1.1 with initial conditions of (−1, 0, 0.5), [ 4 ] see trajectory on the right. The correlation dimension was found to be 2.19 ± 0.01. [ 5 ] The Lyapunov exponents, λ are approximately 0.1981, 0, −0.6581 and the Kaplan–Yorke dimension , D KY ≈ 2.3010 [ 4 ]
Danca and Romera [ 6 ] showed that for γ = 0.1, the system is chaotic for α = 0.98, but progresses on a stable limit cycle for α = 0.14. | https://en.wikipedia.org/wiki/Rabinovich–Fabrikant_equations |
The Racah parameters are a set of parameters used in atomic and molecular spectroscopy to describe the amount of total electrostatic repulsion in an atom that has multiple electrons .
When an atom has more than one electron, there will be some electrostatic repulsion between the electrons. The amount of repulsion varies from atom to atom, depending upon the number of electrons, their spin , and the orbitals that they occupy. The total repulsion can be expressed in terms of three parameters A , B and C which are known as the Racah parameters after Giulio Racah , who first described them. They are generally obtained empirically from gas-phase spectroscopic studies of atoms. [ 1 ]
They are often used in transition-metal chemistry to describe the repulsion energy associated with an electronic term . For example, the interelectronic repulsion of a 3 P term is A + 7 B , and of a 3 F term is A - 8 B , and the difference between them is therefore 15 B .
The Racah parameters are defined as
( A B C ) = ( 1 0 − 49 0 1 − 5 0 0 35 ) ( F 0 F 2 F 4 ) {\displaystyle {\begin{pmatrix}A\\B\\C\\\end{pmatrix}}={\begin{pmatrix}1&0&-49\\0&1&-5\\0&0&35\\\end{pmatrix}}{\begin{pmatrix}F_{0}\\F_{2}\\F_{4}\\\end{pmatrix}}}
where F k {\displaystyle F_{k}} are Slater integrals
( F 0 F 2 F 4 ) = ( F 0 1 49 F 2 1 441 F 4 ) {\displaystyle {\begin{pmatrix}F_{0}\\F_{2}\\F_{4}\\\end{pmatrix}}={\begin{pmatrix}F^{0}\\{\frac {1}{49}}F^{2}\\{\frac {1}{441}}F^{4}\\\end{pmatrix}}}
and F k {\displaystyle F^{k}} are the Slater-Condon parameters
F k := ∫ 0 ∞ r 1 2 d r 1 ∫ 0 ∞ r 2 2 d r 2 R 2 ( r 1 ) R 2 ( r 2 ) r < k r > k + 1 {\displaystyle F^{k}:=\int _{0}^{\infty }r_{1}^{2}dr_{1}\int _{0}^{\infty }r_{2}^{2}dr_{2}R^{2}(r_{1})R^{2}(r_{2}){\frac {r_{<}^{k}}{r_{>}^{k+1}}}}
where R ( r ) {\displaystyle R(r)} is the normalized radial part of an electron orbital , r > = max { r 1 , r 2 } {\displaystyle r_{>}=\max\{r_{1},r_{2}\}} and r < = min { r 1 , r 2 } {\displaystyle r_{<}=\min\{r_{1},r_{2}\}} . [ 2 ]
This spectroscopy -related article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Racah_parameter |
In mathematics , Racah polynomials are orthogonal polynomials named after Giulio Racah , as their orthogonality relations are equivalent to his orthogonality relations for Racah coefficients .
The Racah polynomials were first defined by Wilson (1978) and are given by
There are three generating functions for x ∈ { 0 , 1 , 2 , . . . , N } {\displaystyle x\in \{0,1,2,...,N\}}
When α = a + b − 1 , β = c + d − 1 , γ = a + d − 1 , δ = a − d , x → − a + i x , {\displaystyle \alpha =a+b-1,\beta =c+d-1,\gamma =a+d-1,\delta =a-d,x\rightarrow -a+ix,}
Askey & Wilson (1979) introduced the q -Racah polynomials defined in terms of basic hypergeometric functions by
They are sometimes given with changes of variables as
This algebra -related article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Racah_polynomials |
The Racah seniority number (seniority quantum number) ν {\displaystyle \nu } was introduced by Giulio Racah for the classification of electrons in an atomic configuration. [ 1 ] The "seniority number", in a loosing statement, is quantum number additional to the total angular momentum L {\displaystyle L} and total spin S {\displaystyle S} , which gives the degree of unpaired particles.
A spin-independent interaction V ^ {\displaystyle {\hat {V}}} is assumed with the property [ 2 ]
where L {\displaystyle L} is the combined angular momentum, M L {\displaystyle M_{L}} magnetic quantum number, l {\displaystyle l} is electrons' orbital angular momenta, and g {\displaystyle g} is the dimensionless magnetic moment. The equation above shows there is no interaction unless the two electrons' orbital angular momenta are coupled to L = 0 {\displaystyle L=0} . The eigenvalue is the "seniority number" ν {\displaystyle \nu } . | https://en.wikipedia.org/wiki/Racah_seniority_number |
Race and health refers to how being identified with a specific race influences health. Race is a complex concept that has changed across chronological eras and depends on both self-identification and social recognition. [ 1 ] In the study of race and health, scientists organize people in racial categories depending on different factors such as: phenotype , ancestry , social identity , genetic makeup and lived experience . Race and ethnicity often remain undifferentiated in health research. [ 2 ] [ 3 ]
Differences in health status , health outcomes , life expectancy , and many other indicators of health in different racial and ethnic groups are well documented. [ 4 ] Epidemiological data indicate that racial groups are unequally affected by diseases, in terms of morbidity and mortality. [ 5 ] Some individuals in certain racial groups receive less care, have less access to resources, and live shorter lives in general. [ 6 ] Overall, racial health disparities appear to be rooted in social disadvantages associated with race such as implicit stereotyping and average differences in socioeconomic status . [ 7 ] [ 8 ] [ 9 ]
Health disparities are defined as "preventable differences in the burden of disease, injury, violence, or opportunities to achieve optimal health that are experienced by socially disadvantaged populations". [ 10 ] According to the U.S. Centers for Disease Control and Prevention , they are intrinsically related to the "historical and current unequal distribution of social, political, economic and environmental resources". [ 10 ]
The relationship between race and health has been studied from multidisciplinary perspectives, with increasing focus on how racism influences health disparities, and how environmental and physiological factors respond to one another and to genetics . [ 7 ] [ 8 ] Research highlights a need for more race-conscious approaches in addressing social determinants, as current social needs interventions show limited adaptation to racial and ethnic disparities. [ 11 ] [ 12 ]
Health disparities refer to gaps in the quality of health and health care across racial and ethnic groups . [ 13 ] The US Health Resources and Services Administration defines health disparities as "population-specific differences in the presence of disease, health outcomes, or access to health care". [ 14 ] Health is measured through variables such as life expectancy and incidence of diseases. [ 15 ]
For racial and ethnic minorities in the United States, health disparities take on many forms, including higher rates of chronic disease, premature death, and maternal mortality compared to the rates among whites. For example, African Americans are 2–3 times more likely to die as a result of pregnancy-related complications than white Americans. [ 16 ] It is important to note that this pattern is not universal. Some minority groups—most notably, Hispanic immigrants—may have better health outcomes than whites when they arrive in the United States. However this appears to diminish with time spent in the United States. [ 17 ] For other indicators, disparities have shrunk, not because of improvements among minorities but because of declines in the health of majority groups.
In the U.S., more than 133 million Americans (45% of the population) have one or more chronic diseases. One study has shown that between the ages of 60 and 70, racial/ethnic minorities are 1.5 to 2.0 times more likely than whites (Hispanic and non Hispanic) to have one of the four major chronic diseases specifically Diabetes, cancer, cardiovascular disease (CVD), and chronic lung disease. However, the greatest differences only occurred among people with single chronic diseases. Racial/ethnic differences were less distinct for some conditions including multiple diseases. Non-Hispanic whites trended toward a high prevalence for dyads of cardiovascular disease (CVD) with cancer or lung disease. Hispanics and African Americans had the greatest prevalence of diabetes, while non-Hispanic blacks had higher odds of having heart disease with cancer or chronic lung disease than non-Hispanic whites. Among non-Hispanic whites the prevalence of multimorbidities that include diabetes was low; however, non-Hispanic whites had a very high prevalence of multimorbidities that exclude diabetes. Non-Hispanic whites had the highest prevalence of cancer only or lung disease only. [ 18 ] Black Americans have an increased risk of death from COVID-19 compared to white Americans. In a study in Michigan in 2020 regarding COVID-19, it is shown that Black people are 3.6 times more likely to die due to COVID-19. [ 19 ]
In the United States, the mental health of African Americans has been shown to be negatively impacted by systemic racism, contributing to increased risk of mortality from substance use disorders. This negative mental health can lead to reaching for substances to cope with the mental effects of systemic racism. [ 20 ] Structural racism, as outlined by Bailey et al., is a key driver of these disparities. It encompasses interconnected systems such as housing, healthcare, education, employment, and criminal justice that perpetuate racial discrimination and the unequal distribution of resources. For instance, housing discrimination and limited access to quality healthcare facilities in predominantly Black neighborhoods create barriers to effective care. These inequities, coupled with racially biased medical practices, result in higher rates of chronic diseases, greater mortality, and poorer health outcomes among African Americans. Addressing these structural issues is crucial for improving health equity and reducing the systemic disadvantages faced by racial and ethnic minorities. [ 21 ]
Macias-Konstantopoulos et al. (2023) highlight how these factors disproportionately affect Black, Indigenous, and People of Color (BIPOC), leading to significant health-care inequities. Emergency medicine (EM) serves as a critical domain for examining these disparities, particularly in the treatment of infectious diseases such as HIV and COVID-19, noncommunicable diseases like diabetes and hypertension, and trauma cases like gunshot injuries. Systemic imbalances, rather than genetic differences, create longer wait times for Black patients in emergency departments and less effective pain management compared to their white counterparts. Such inequalities highlight the pervasive impact of institutional biases in health care. [ citation needed ]
The study also emphasizes actionable steps for addressing these inequities, including fostering culturally sensitive practices and enhancing access to quality care for minority communities. This underscores the need for health-care professionals to understand the interplay between race, systemic determinants of health, and outcomes to foster equitable health care for all populations. [ 22 ]
Between 1960 and 2005 the percentage of children with a chronic disease in the United States quadrupled with minority having higher likelihood for these disease. The most common major chronic biases of youth in the United States are asthma , diabetes mellitus , obesity , hypertension , dental disease , attention deficit hyperactivity disorder (ADHD) , mental illness , cancers and others. This results in Black and Latin adult patients facing a disproportionate amount of health concerns, such as asthma, with treatment and management guidelines not developed with studies based on their populations and healthcare needs. [ 1 ]
Although individuals from different environmental, continental, socioeconomic, and racial groups etc. have different levels of health, yet not all of these differences are always categorized or defined as health disparities. Some researchers separate definitions of health inequality from health disparity by preventability. Health inequalities are often categorized as being unavoidable i.e. due to age, while preventable unfair health outcomes are categorized as health inequities. These are seen as preventable because they are usually associated with income, education, race, ethnicity, gender, and more. [ 23 ]
Definitions of race are ambiguous due to the various paradigms used to discuss race. These definitions are a direct result of biological and social views. Definitions have changed throughout history to yield a modern understanding of race that is complex and fluid. Moreover, there is no one definition that stands, as there are many competing and interlocking ways to look at race. [ 24 ] Due to its ambiguity, terms such as race, genetic population, ethnicity, geographic population, and ancestry are used interchangeably in everyday discourse involving race. Some researchers critique this interchangeability noting that the conceptual differences between race and ethnicity are not widely agreed upon. [ 25 ]
Even though there is a broad scientific agreement that essentialist and typological conceptions of race are untenable, [ 26 ] [ 27 ] [ 28 ] [ 29 ] [ 30 ] [ 31 ] scientists around the world continue to conceptualize race in widely differing ways. [ 32 ] Historically, biological definitions of race have encompassed both essentialist and anti-essentialist views. Essentialists have sought to show that racial groups are genetically distinct populations, describing "races as groups of people who share certain innate, inherited biological traits". [ 33 ] In contrast, anti-essentialists have used biological evidence to demonstrate that "race groupings do not reflect patterns of human biological variation, countering essentialist claims to the contrary". [ 34 ]
Over the past 20 years, a consensus has emerged that, while race is partially based on physical similarities within groups, it does not have an inherent physical or biological meaning. [ 35 ] [ 36 ] [ 37 ] In response, researchers and social scientists have begun examining notions of race as constructed. [ 38 ] Racial groups are "constructed" from differing historical, political, and economic contexts, rather than corresponding to inherited, biological variations. Proponents of the constructionist view claim that biological definitions have been used to justify racism in the past and still have the potential to be used to encourage racist thinking in the future. [ 33 ] Since race is changing and often so loosely characterized on arbitrary phenotypes, and because it has no genetic basis, the only working definition we can assign it is a social construct. This is not to say race is imaginary or non-existent. It is an important social reality. However to say that the concept of race has any scientific merit or has a scientific foundation can lead to many issues in scientific research, and it may also lead to inherent racial bias. [ 39 ]
Social interpretations of race explains that social views also better explain the ambiguity of racial definitions. An individual may self-identify as one race based on one set of determinants (for example, phenotype, culture, ancestry) while society may ascribe the person otherwise based on external forces and discrete racial standards. Dominant racial conceptions influence how individuals label both themselves and others within society. [ citation needed ] Modern human populations are becoming more difficult to define within traditional racial boundaries due to racial admixture. Most scientific studies, applications, and government documents ask individuals to self-identify race from a limited assortment of common racial categories. [ 40 ] The conflict between self-identification and societal ascription further complicates biomedical research and public health policies. However complex its sociological roots, race has real biological ramifications; the intersection of race, science, and society permeates everyday life and influences human health via genetics, access to medical care, diagnosis, and treatment.
Diseases affect racial groups differently, especially when they are co-related with class disparities. [ 4 ] As socioeconomic factors influence the access to care, [ citation needed ] the barriers to access healthcare systems can perpetuate different biological effects of diseases among racial groups that are not pre-determined by biology.
Some researchers advocate for the use of self-reported race as a way to trace socioeconomic disparities and its effects in health. [ 41 ] For instance, a study conducted by the National Health Service checks program in the United Kingdom, which aims to increase diagnosis across demographics, noted that "the reported lower screening in specific black and minority ethnic communities... may increase inequalities in health." [ 42 ] In this specific case, the lack of attention to certain demographics can be seen as a cause of increased instances of disease from this lack of proper, equal preventive care. One must consider these external factors when evaluating statistics on the prevalence of disease in populations, even though genetic components can play a role in predispositions to contracting some illnesses.
Individuals who share a similar genetic makeup can also share certain propensity or resistance to specific diseases. However, there are confronted positions in relation to the utility of using 'races' to talk about populations sharing a similar genetic makeup. Some geneticists argued that human variation is geographically structured and that genetic differences correlate with general conceptualizations of racial groups. [ 43 ] Others claimed that this correlation is too unstable and that the genetic differences are minimal and they are "distributed over the world in a discordant manner". [ 44 ] Therefore, race is regarded by some as a useful tool for the assessment of genetic epidemiological risk, [ 45 ] while others consider it can lead to an increased underdiagnosis in 'low risk' populations. [ 46 ]
There are many autosomal recessive single gene genetic disorders that differ in frequency between different populations due to the region and ancestry as well as the founder effect . Some examples of these disorders include:
Many diseases differ in frequency between different populations. However, complex diseases are affected by multiple factors, including genetic and environmental. There is controversy over the extent to which some of these conditions are influenced by genes, and ongoing research aims to identify which genetic loci, if any, are linked to these diseases. "Risk is the probability that an event will occur. In epidemiology, it is most often used to express the probability that a particular outcome will occur following a particular exposure." [ 50 ] [ 51 ] Different populations are considered "high-risk" or "low-risk" groups for various diseases due to the probability of that particular population being more exposed to certain risk factors. Beyond genetic factors, history and culture, as well as current environmental and social conditions, influence a certain population's risk for specific diseases.
Racial groups may differ in how a disease progresses. Different access to healthcare services, different living and working conditions influence how a disease progresses within racial groups. [ 52 ] However, the reasons for these differences are multiple, and should not be understood a consequence of genetic differences between races, but rather as effects of social and environmental factors affecting. [ 52 ]
Genetics has been proven to be a strong predictor for common diseases such as cancer, cardiovascular disease (CVD), diabetes, autoimmune disorders, and psychiatric illnesses. [ 53 ] Some geneticists have determined that " human genetic variation is geographically structured" and that different geographic regions correlate with different races. [ 54 ] Meanwhile, others have claimed that the human genome is characterized by clinal changes across the globe, in relation with the "Out of Africa" theory and how migration to new environments cause changes in populations' genetics over time.
Some diseases are more prevalent in some populations identified as races due to their common ancestry. Thus, people of African and Mediterranean descent are found to be more susceptible to sickle-cell disease while cystic fibrosis and hemochromatosis are more common among European populations. [ 54 ] Some physicians claim that race can be used as a proxy for the risk that the patient may be exposed to in relation to these diseases. However, racial self-identification only provides fragmentary information about the person's ancestry. Thus, racial profiling in medical services would also lead to the risk of underdiagnosis.
While genetics plays a role in determining how susceptible a person is to specific diseases, environmental, structural, cultural, and communication messaging factors play a large role as well. [ 55 ] [ 56 ] For this reason, it is impossible to discern exactly what causes a person to acquire a disease, but it is important to observe how many inter-related factors relate to each other. Each person's health is unique, as they have different genetic compositions and life histories.
Racial groups, especially when defined as minorities or ethnic groups, often face structural and cultural barriers to access healthcare services. The development of culturally and structurally competent services and research that meet the specific health care needs of racial groups is still in its infancy. [ 57 ] In the United States, the Office of Minority Health The NIH (National institutes of health) and The WHO are organizations that provide useful links and support research that is targeted at the development of initiatives around minority communities and the health disparities they face. Similarly, In the United Kingdom, the National Health Service established a specialist collection on Ethnicity & Health. [ 58 ] This resource was supported by the National Institute for Health and Clinical Excellence (NICE) as part of the UK NHS Evidence initiative NHS Evidence . [ citation needed ] Similarly, there are growing numbers of resource and research centers which are seeking to provide this service for other national settings, such as Multicultural Mental Health Australia. [ 59 ] However, cultural competence has also been criticized for having the potential to create stereotypes.
Scientific studies have shown the lack of efficacy of adapting pharmaceutical treatment to racial categories. "Race-based medicine" is the term for medicines that are targeted at specific racial clusters which are shown to have a propensity for a certain disorder. The first example of this in the U.S. was when BiDil , a medication for congestive heart failure, was licensed specifically for use in American patients that self-identify as black. [ 60 ] Previous studies had shown that African American patients with congestive heart failure generally respond less effectively to traditional treatments than white patients with similar conditions. [ 61 ]
After two trials, BiDil was licensed exclusively for use in African American patients. Critics have argued that this particular licensing was unwarranted, since the trials did not in fact show that the drug was more effective in African Americans than in other groups, but merely that it was more effective in African Americans than other similar drugs. It was also only tested in African American males, but not in any other racial groups or among women. This peculiar trial and licensing procedure has prompted suggestions that the licensing was in fact used as a race-based advertising scheme. [ 62 ]
Critics are concerned that the trend of research on race-specific pharmaceutical treatments will result in inequitable access to pharmaceutical innovation and smaller minority groups may be ignored. This has led to a call for regulatory approaches to be put in place to ensure scientific validity of racial disparity in pharmacological treatment. [ 63 ]
Similarly, sexual orientation-based discrimination in healthcare has been shown to negatively impact health behaviors and outcomes, as demonstrated in a scoping review by Gioia and Rosenberger. The study highlights significant gaps in current data and illustrates how discrimination affects healthcare utilization behaviors, such as delaying care for cervical cancer screenings and contributing to poor health behaviors like substance abuse. The authors also emphasize the indirect effects of prejudice on health through medical distrust and poor patient-provider interactions. Recommendations include implementing LGBTQ-focused sensitivity training for healthcare personnel, addressing healthcare inequality through policy changes, and reducing medical mistrust to ensure equitable access to care for sexual minorities. These findings underscore that healthcare biases extend beyond race, encompassing sexual orientation and gender as significant factors influencing treatment outcomes. [ 64 ]
An alternative to "race-based medicine" is personalized or precision medicine. [ 65 ] Precision medicine is a medical model that proposes the customization of healthcare , with medical decisions, treatments, practices, or products being tailored to the individual patient. It involves identifying genetic, genomic (i.e., genomic sequencing), and clinical information—as opposed to using race as a proxy for these data—to better predict a patient's predisposition to certain diseases. [ 66 ]
In addition to issues surrounding race-based medications, discrimination in healthcare settings also plays a significant role in health outcomes. For example, a study by Turan et al. (2017) [ 67 ] demonstrated that perceived discrimination in healthcare settings negatively affected adherence to antiretroviral therapy (ART) among HIV-positive individuals. This was mediated by stigma and depressive symptoms, emphasizing the need for culturally competent care and efforts to address racism in healthcare to improve outcomes. This finding highlights the complex interplay between systemic racism, psychological factors, and treatment adherence in healthcare.
A positive correlation between minorities and a socioeconomic status of being low-income in industrialized and rural regions of the U.S. depict how low-income communities tend to include more individuals that have a lower educational background, most importantly in health . Income status, diet, and education all construct a higher burden for low-income minorities, to be conscious about their health. Research conducted by medical departments at universities in San Diego, Miami, Pennsylvania, and North Carolina suggested that minorities in regions where lower socioeconomic status is common, there was a direct relationship with unhealthy diets and greater distance of supermarkets. [ 68 ] Therefore, in areas where supermarkets are less accessible ( food deserts ) to impoverished areas, the more likely these groups are to purchase inexpensive fast food or just follow an unhealthy diet. [ 68 ] As a result, because food deserts are more prevalent in low income communities, minorities that reside in these areas are more prone to obesity , which can lead to diseases such as chronic kidney disease , hypertension , or diabetes. [ 68 ] [ 69 ]
Furthermore, this can also occur when minorities living in rural areas undergoing urbanization are introduced to fast food . A study completed in Thailand focused on urbanized metropolitan areas: students who participated were diagnosed as "non-obese" in their early life according to their BMI, however were increasingly at risk of developing type 2 diabetes , or obesity as adults, as opposed to young adults who lived in more rural areas during their early life. [ 70 ] Therefore, early exposure to urbanized regions can encourage unhealthy eating due to widespread presence of inexpensive fast food. Different racial populations that originate from more rural areas and then immigrate to the urbanized metropolitan areas can develop a fixation for a more westernized diet; this change in lifestyle typically occurs due to loss of traditional values when adapting to a new environment. For example, a 2009 study named CYKIDS was based on children from Cyprus , a country east of the Mediterranean Sea, who were evaluated by the KIDMED index to test their adherence to a Mediterranean diet after changing from a rural residence to an urban residence. [ 71 ] It was found that children in urban areas swapped their traditional dietary patterns for a diet favoring fast food.
The fact that every human has a unique genetic code is the key to techniques such as genetic fingerprinting. Versions of genetic markers, known as alleles, occur at different frequencies in different human populations; populations that are more geographically and ancestrally remote tend to differ more.
A phenotype is the "outward, physical manifestation" of an organism." [ This quote needs a citation ] For humans, phenotypic differences are most readily seen via skin color, eye color, hair color, or height; however, any observable structure, function, or behavior can be considered part of a phenotype. A genotype is the "internally coded, inheritable information" carried by all living organisms. The human genome is encoded in DNA. [ citation needed ]
For any trait of interest, observed differences among individuals "may be due to differences in the genes" coding for a trait and "the result of variation in environmental condition". This variability is due to gene-environment interactions that influence genetic expression patterns and trait heritability. [ 72 ]
For humans, there is "more genetic variation among individual people than between larger racial groups". [ 15 ] In general, an average of 80% of genetic variation exists within local populations, around 10% is between local populations within the same continent, and approximately 8% of variation occurs between large groups living on different continents. [ 73 ] [ 74 ] [ 75 ] Studies have found evidence of genetic differences between populations, but the distribution of genetic variants within and among human populations is impossible to describe succinctly because of the difficulty of defining a "population", the clinal nature of variation, and heterogeneity across the genome. [ 76 ] Thus, the racialization of science and medicine can lead to controversy when the term population and race are used interchangeably.
Genes may be under strong selection in response to local diseases. For example, people who are duffy negative tend to have higher resistance to malaria. Most Africans are duffy negative and most non-Africans are duffy positive due to endemic transmission of malaria in Africa. [ 77 ] A number of genetic diseases more prevalent in malaria-affected areas may provide some genetic resistance to malaria including sickle cell disease , thalassaemias , glucose-6-phosphate dehydrogenase , and possibly others.
Many theories about the origin of the cystic fibrosis have suggested that it provides a heterozygote advantage by giving resistance to diseases earlier common in Europe.
In earlier research, a common theory was the " common disease-common variant " model. It argues that for common illnesses, the genetic contribution comes from the additive or multiplicative effects of gene variants that each one is common in the population. Each such gene variant is argued to cause only a small risk of disease and no single variant is sufficient or necessary to cause the disease. An individual must have many of these common gene variants in order for the risk of disease to be substantial. [ 78 ]
More recent research indicates that the "common disease-rare variant" may be a better explanation for many common diseases. In this model, rare but higher-risk gene variants cause common diseases. [ 79 ] This model may be relevant for diseases that reduces fertility. [ 80 ] In contrast, for common genes associated with common disease to persist they must either have little effect during the reproductive period of life (like Alzheimer's disease ) or provide some advantage in the original environment (like genes causing autoimmune diseases also providing resistance against infections). In either case varying frequencies of genes variants in different populations may be an explanation for health disparities. [ 78 ] Genetic variants associated with Alzheimer's disease, deep venous thrombosis , Crohn disease , and type 2 diabetes appear to adhere to "common disease-common variant" model. [ 81 ]
Gene flow and admixture can also have an effect on relationships between race and race-linked disorders. Multiple sclerosis, for example, is typically associated with people of European descent, but due to admixture African Americans have elevated levels of the disorder relative to Africans. [ 82 ]
Some diseases and physiological variables vary depending upon their admixture ratios. Examples include measures of insulin functioning [ 83 ] and obesity . [ 84 ]
The same gene variant, or group of gene variants, may produce different effects in different populations depending on differences in the gene variants, or groups of gene variants, they interact with. One example is the rate of progression to AIDS and death in HIV –infected patients. In whites and Hispanics, HHC haplotypes were associated with disease retardation, particularly a delayed progression to death, while for African Americans, possession of HHC haplotypes was associated with disease acceleration. In contrast, while the disease-retarding effects of the CCR2-641 allele were found in African Americans, they were not found in whites. [ 85 ]
Public health researchers and policy makers are working to reduce health disparities. Health effects of racism are now a major area of research. In fact, these seem to be the primary research focus in biological and social sciences. [ 23 ] Interdisciplinary methods have been used to address how race affects health. according to published studies, many factors combine to affect the health of individuals and communities. [ 38 ] Whether people are healthy or not, is determined by their circumstances and environment. Factors that need to be addressed when looking at health and race include income and social status, education, physical environment, social support networks, genetics, health services, targeted instruction, and gender. [ 23 ] [ 86 ] [ 87 ] [ 88 ] These determinants are often cited in public health, anthropology, and other social science disciplines. The WHO categorizes these determinants into three broader topics: the social and economic environment, the physical environment, and the person's individual characteristics and behaviors. Due to the diversity of factors that often attribute to health disparities outcomes, interdisciplinary approaches are often implemented. [ 86 ] For instance, Donna L. Washington and colleagues emphasize the importance of applying theoretical frameworks to reduce racial and ethnic disparities in healthcare. Their work highlights the ongoing inequalities in preventive, diagnostic, and therapeutic healthcare services for minority groups compared to white individuals, which contribute significantly to higher morbidity and mortality rates among these populations. [ 89 ]
To address these disparities, the authors recommend practical solutions such as improving communication between healthcare professionals and patients, adopting culturally and linguistically sensitive practices, implementing flexible payment options, and enrolling patients in financial assistance programs. These approaches align with interdisciplinary methods by combining cultural, economic, and social considerations to create actionable strategies that can be integrated into clinical practice. Such strategies exemplify how theoretical approaches can be translated into practical interventions to promote health equity. [ 90 ]
Interdisciplinarity or interdisciplinary studies involves the combining of two or more academic disciplines into one activity (e.g., a research project) The term interdisciplinary is applied within education and training pedagogies to describe studies that use methods and insights of several established disciplines or traditional fields of study. Interdisciplinarity involves researchers, students, and teachers in the goals of connecting and integrating several academic schools of thought, professions, or technologies—along with their specific perspectives—in the pursuit of a common task.
Biocultural evolution was introduced and first used in the 1970s. [ 91 ] Biocultural methods focus on the interactions between humans and their environment to understand human biological adaptation and variation . These studies:
"research on questions of human biology and medical ecology that specifically includes social, cultural, or behavioral variables in the research design, offer valuable models for studying the interface between biological and cultural factors affecting human well-being" [ citation needed ]
This approach is useful in generating holistic viewpoints on human biological variation. There are two biocultural approach models. The first approach fuses biological, environmental, and cultural data. The second approach treats biological data as primary data and culture and environmental data as secondary.
The salt sensitivity hypothesis is an example of implementing biocultural approaches in order to understand cardiovascular health disparities among African American populations. This theory, founded by Wilson and Grim, stems from the disproportional rates of salt sensitive high blood pressure seen between U.S. African American and White populations and between U.S. African American and West Africans as well. The researchers hypothesized that the patterns were in response to two events. One the trans-Atlantic slave trade, which resulted in massive death totals of Africans who were forced over, those who survived and made to the United States were more likely able to withstand the harsh conditions because they retained salt and water better. The selection continued once they were in the United States. African Americans who were able to withstand hard working conditions had better survival rates due to high water and salt retention. Second, today, because of different environmental conditions and increased salt intake with diets, water and salt retention are disadvantageous, leaving U.S. African Americans at disproportional risks because of their biological descent and culture. [ 92 ]
Similar to the biocultural approach, the bio social inheritance model also looks at biological and social methods in examining health disparities. Hoke et al. define Biosocial inheritance as "the process whereby social adversity in one generation is transmitted to the next through reinforcing biological and social mechanisms that impair health, exacerbating social and health disparities." [ 93 ]
There is a controversy regarding race as a method for classifying humans. Different sources argue it is purely social construct [ 94 ] or a biological reality reflecting average genetic group differences. New interest in human biological variation has resulted in a resurgence of the use of race in biomedicine. [ 95 ]
The main impetus for this development is the possibility of improving the prevention and treatment of certain diseases by predicting hard-to-ascertain factors, such as genetically conditioned health factors, based on more easily ascertained characteristics such as phenotype and racial self-identification. Since medical judgment often involves decision making under uncertain conditions, [ 96 ] many doctors consider it useful to take race into account when treating disease because diseases and treatment responses tend to cluster by geographic ancestry. [ 97 ] The discovery that more diseases than previously thought correlate with racial identification have further sparked the interest in using race as a proxy for bio-geographical ancestry and genetic buildup.
Race in medicine is used as an approximation for more specific genetic and environmental risk factors. Race is thus partly a surrogate for environmental factors such as differences in socioeconomic status that are known to affect health. It is also an imperfect surrogate for ancestral geographic regions and differences in gene frequencies between different ancestral populations and thus differences in genes that can affect health. This can give an approximation of probability for disease or for preferred treatment, although the approximation is less than perfect. [ 15 ]
Taking the example of sickle-cell disease , in an emergency room , knowing the geographic origin of a patient may help a doctor doing an initial diagnosis if a patient presents with symptoms compatible with this disease. This is unreliable evidence with the disease being present in many different groups as noted above with the trait also present in some Mediterranean European populations. Definitive diagnosis comes from examining the blood of the patient. In the US, screening for sickle cell anemia is done on all newborns regardless of race. [ 96 ]
The continued use of racial categories has been criticized. Apart from the general controversy regarding race, some argue that the continued use of racial categories in health care and as risk factors could result in increased stereotyping and discrimination in society and health services. [ 15 ] [ 98 ] [ 99 ] Some of those who are critical of race as a biological concept see race as socially meaningful group that is important to study epidemiologically in order to reduce disparities. [ 100 ] For example, some racial groups are less likely than others to receive adequate treatment for osteoporosis, even after risk factors have been assessed. Since the 19th century, blacks have been thought to have thicker bones than whites have and to lose bone mass more slowly with age. [ 101 ] In a recent study, African Americans were shown to be substantially less likely to receive prescription osteoporosis medications than whites. Men were also significantly less likely to be treated compared with women. This discrepancy may be due to physicians' knowledge that, on average, African Americans are at lower risk for osteoporosis than whites. It may be possible that these physicians generalize this data to high-risk African-Americans, leading them to fail to appropriately assess and manage these individuals' osteoporosis. [ 101 ] On the other hand, some of those who are critical of race as a biological concept see race as socially meaningful group that is important to study epidemiologically in order to reduce disparities. Black Americans also have the highest mortality rate related to cardiovascular diseases, at about 30 percent higher than white Americans, even after the American Heart Association (AHA) has attempted to lower all risks. [ 102 ]
David Williams (1994) argued, after an examination of articles in the journal Health Services Research during the 1966–90 period, that how race was determined and defined was seldom described. At a minimum, researchers should describe if race was assessed by self-report, proxy report, extraction from records, or direct observation. Race was also often used questionable, such as an indicator of socioeconomic status. [ 103 ] Racial genetic explanations may be overemphasized, ignoring the interaction with and the role of the environment. [ 104 ]
There is general agreement that a goal of health-related genetics should be to move past the weak surrogate relationships of racial health disparity and get to the root causes of health and disease. This includes research which strives to analyze human genetic variation in smaller groups than races across the world. [ 15 ]
One such method is called ethnogenetic layering. It works by focusing on geographically identified microethnic groups. For example, in the Mississippi Delta region ethnogenetic layering might include such microethnic groups as the Cajun (as a subset of European Americans), the Creole and Black groups [with African origins in Senegambia, Central Africa and Bight of Benin] (as a subset of African Americans), and Choctaw, Houmas, Chickasaw, Coushatta, Caddo, Atakapa, Karankawa and Chitimacha peoples (as subsets of Native Americans). [ 105 ] [ 106 ]
Better still may be individual genetic assessment of relevant genes. [ 54 ] As genotyping and sequencing have become more accessible and affordable, avenues for determining individual genetic makeup have opened dramatically. [ 107 ] Even when such methods become commonly available, race will continue to be important when looking at groups instead of individuals such as in epidemiologic research. [ 54 ]
Some doctors and scientists such as geneticist Neil Risch argue that using self-identified race as a proxy for ancestry is necessary to be able to get a sufficiently broad sample of different ancestral populations, and in turn to be able to provide health care that is tailored to the needs of minority groups. [ 43 ]
One area in which population categories can be important considerations in genetics research is in controlling for confounding between population genetic substructure, environmental exposures, and health outcomes. Association studies can produce spurious results if cases and controls have differing allele frequencies for genes that are not related to the disease being studied, [ 108 ] [ 109 ] although the magnitude of its problem in genetic association studies is subject to debate. [ 110 ] [ 111 ] Various techniques detect and account for population substructure, [ 112 ] [ 113 ] but these methods can be difficult to apply in practice. [ 114 ]
Population genetic substructure also can aid genetic association studies. For example, populations that represent recent mixtures of separated ancestral groups can exhibit longer-range linkage disequilibrium between susceptibility alleles and genetic markers than is the case for other populations. [ 115 ] [ 116 ] [ 117 ] [ 118 ] Genetic studies can use this disequilibrium to search for disease alleles with fewer markers than would be needed otherwise. Association studies also can take advantage of the contrasting experiences of racial or ethnic groups, including migrant groups, to search for interactions between particular alleles and environmental factors that might influence health. [ 119 ] [ 120 ]
Historically, race has been utilized in medicine in various ways, which continue to have enduring impacts today. The imposition of race on pulmonary function and the machinery used to conduct testing is a noteworthy example. Samuel Cartwright was a 19th-century physician and scientist who is known for his work on spirometry and respiratory physiology. Spirometry is a medical test that measures how much air a person can breathe in and out of their lungs, and how quickly they can do so. Cartwright used spirometry to compare Black enslaved people's lung function to white people's. [ 121 ] Cartwright, drawing on Thomas Jefferson's beliefs on pulmonary dysfunction, saw a 20% quantitative difference between Black and White people as proof of deficiency that necessitated the enslavement of Black individuals. [ 121 ]
These findings of lower lung capacity by race are present in modern medicine through the correction of race in modern spirometry machines and within most textbooks for medical school. [ 122 ] When inputting race into the machine, patients either provide their self-identified race or it is determined by the provider. Spirometers in the US utilize population-specific standards or correction factors of 10% to 15% for Black persons and 4% to 6% for Asian people. [ 123 ] Thus, equations derived from Black populations will yield a higher percentage of predicted lung function values than those derived from White populations, which may underestimate lung disease severity and delay detection. However, applying an equation developed from White populations to other racial groups may lead to overdiagnosis and limited eligibility for treatment due to the increased perception of risk. [ 124 ] Research regarding the efficacy of race-based spirometry found that the race correction was only accurate for Black patients when their African ancestry was above the median between 81 and 100%. [ 125 ] As a result, opponents of race correction say it may cause misdiagnosis and perpetuate racial prejudices by encouraging biological race. [ 124 ] [ 123 ] These race-based clinical decision support tools, such as pulmonary function testing with spirometry, were ended by a report published by the US House of Representatives Ways and Means Committee in October 2021. [ 126 ]
In a report by the Institute of Medicine called Unequal Treatment, three major source categories are put forth as potential explanations for disparities in health care: patient-level variables, healthcare system-level factors, and care process-level variables. [ 127 ]
There are many individual factors that could explain the established differences in health care between different racial and ethnic groups. First, attitudes and behaviors of minority patients are different. They are more likely to refuse recommended services, adhere poorly to treatment regimens, and delay seeking care, yet despite this, these behaviors and attitudes are unlikely to explain the differences in health care. [ 127 ] In addition to behaviors and attitudes, biological based racial differences have been documented, but these also seem unlikely to explain the majority of observed disparities in care. [ 127 ]
Health system-level factors include any aspects of health systems that can have different effects on patient outcomes. Some of these factors include different access to services, access to insurance or other means to pay for services, access to adequate language and interpretation services, and geographic availability of different services. [ 127 ] Many studies assert that these factors explain portions of the existing disparities in health of racial and ethnic minorities in the United States when compared to their white counterparts.
Three major mechanisms are suggested by the Institute of Medicine that may contribute to healthcare disparities from the provider's side: bias (or prejudice) against racial and ethnic minorities; greater clinical uncertainty when interacting with minority patients; and beliefs held by the provider about the behavior or health of minorities. [ 127 ] While research in this area is ongoing, some exclusions within clinical trials themselves are also present. A recent systematic review of the literature relating to hearing loss in adults demonstrated that many studies fail to include aspects of racial or ethnic diversity, resulting in studies that do not necessarily represent the US population. [ 128 ]
A 2023 scoping review of the literature found that in studies conducted in multiracial or multiethnic populations, the inclusion of race or ethnicity variables lacked thoughtful conceptualization and informative analysis regarding race or ethnicity as indicators of exposure to racialized social disadvantage, the systemic and structural barriers, discrimination, and social exclusion faced by individuals and communities based on their race or ethnicity, leading to disparities in access to resources, opportunities, and health outcomes. [ 12 ] [ 11 ]
United States: | https://en.wikipedia.org/wiki/Race_and_health |
Racemic acid is an old name for an optically inactive or racemic form of tartaric acid . It is an equal mixture of two mirror-image isomers ( enantiomers ), optically active in opposing directions. Racemic acid does not occur naturally in grape juice, although L-tartaric acid does.
Tartaric acid's sodium-ammonium salt is unusual among racemic mixtures in that during crystallization it can separate out into two kinds of crystals, each composed of one isomer, and whose macroscopic crystalline shapes are mirror images of each other. Thus, Louis Pasteur was able in 1848 to isolate each of the two enantiomers by laboriously separating the two kinds crystals using delicate tweezers and a hand lens. [ 1 ] Pasteur announced his intention to resolve racemic acid in:
while he presented his resolution of racemic acid into separate optical isomers in:
In the latter paper, Pasteur sketches from natural concrete reality chiral polytopes quite possibly for the first time. The optical property of tartaric acid was first observed in 1832 by Jean Baptiste Biot , who observed its ability to rotate polarized light . [ 4 ] [ 5 ] It remains unknown whether Arthur Cayley or Ludwig Schläfli , or other contemporary mathematicians who studied polytopes, knew of the French work.
In two modern-day re-enactments performed in Japan of the Pasteur experiment, [ 6 ] [ 7 ] it was established that the preparation of crystals was not very reproducible. The crystals deformed, but they were large enough to inspect with the naked eye (microscope not required). | https://en.wikipedia.org/wiki/Racemic_acid |
Racemic crystallography is a technique used in structural biology where crystals of a protein molecule are developed from an equimolar mixture of an L-protein molecule of natural chirality and its D-protein mirror image. [ 1 ] [ 2 ] L-protein molecules consist of 'left-handed' L- amino acids and the achiral amino acid glycine, whereas the mirror image D-protein molecules consist of 'right-handed' D-amino acids and glycine. Typically, both the L-protein and the D-protein are prepared by total chemical synthesis.
Native chemical ligation of unprotected peptide segments is used to prepare the protein's polypeptide chain, which is then folded to form a protein molecule. [ 1 ] In native chemical ligation, a peptide C-terminal thioester reacts with a second peptide that has a cysteine residue at its N-terminus, to give a product with a peptide bond at the ligation site. [ 3 ] Multiple unprotected peptide segments can be linked in this way to give the full length polypeptide chain, which is folded to give the target protein molecule. Once the chemical synthesis of an L-protein is achieved, the D-protein enantiomer can be manufactured using synthetic peptide building blocks made from D-amino acids and Gly. [ 1 ] Convergent synthesis is most effective in preparing long polypeptide chains, by using peptide-hydrazides, where the hydrazide can be converted to a thioester for use in native chemical ligation. The hydrazide is stable to native chemical ligation reaction conditions, and can be converted in situ to a reactive peptide-thioester for the next native chemical ligation condensation reaction. [ 4 ]
There are just 230 different ways of arranging objects in regular three-dimensional arrays. In molecular crystallography, these arrangements are called 'space groups'. However, only 65 of these arrangements are accessible to chiral objects or chiral molecules. The remaining 165 space groups contain either a center of symmetry or a mirror plane and are thus not accessible to natural globular proteins, which are chiral molecules. Wukowitz and Yeates developed a mathematical theory to explain the preference of globular proteins to crystallize in certain space groups. They suggested the preferred space group was determined by the number of degrees of freedom (D) or dimensionality as a measure of the ease with which a given symmetry can be formed. They analyzed the number of degrees of freedom for both chiral and achiral space groups where it was found that the space group P1(bar) with D=8 is theoretically the most dominant space group. Since the achiral space group had a higher degree of freedom compared to the chiral space groups, they predicted that racemic mixtures of protein enantiomers would crystallize more readily compared to the natural L-proteins alone by forming achiral {L-protein plus D-protein} pairs. While space group P1(bar) is most preferred, P21/c and C2/c are also highly preferred, whereas the other achiral space groups are expected to appear less frequently. Hence, P1(bar), P21/c, and C2/c are considered common centrosymmetric space groups in racemic mixtures. [ 1 ]
In 1989, Alan Mackay suggested that if chemical synthesis could be used to make L-protein and D-protein enantiomers, it would enable the use of racemic mixtures to crystallize proteins in centrosymmetric space groups. He stated that, because in the X-ray diffraction data obtained from a centrosymmetric crystal the off-diagonal phases would cancel giving phases that differ by 180 degrees, this would facilitate solving the phase problem in protein structure determination through X-ray crystallography. [ 4 ]
In 1993, Laura Zawadzke and Jeremy Berg first used the small (45 amino acids) protein rubredoxin to synthesize it in racemic form. This was done since the structural determination would potentially be easier and more robust by using diffraction data from a centrosymmetric crystal, which requires growth from a racemic mixture . By having a centre of symmetry formed by the racemic protein pairs, the steps of phasing diffraction in data analysis would be further simplified. [ 5 ] As mentioned above, in 1995 Stephanie Wukovitz and Todd Yeates had developed a mathematical theory to explain why protein molecules tend to crystallize more frequently in certain space groups than in others; they predicted that the most favored protein space group would be P1<bar>, and predicted that globular proteins would crystallize more easily as racemates, from a racemic protein mixture. [ 6 ]
With the development of native chemical ligation in 1994, total chemical synthesis of pairs of D-protein and L-protein enantiomers became feasible. In the first practical application to solving an unknown structure, racemic and quasi-racemic X-ray crystallography were used to determine the structure of snow flea anti-freeze protein. In the course of that work it was observed that racemic and even quasi-racemic protein mixtures dramatically facilitated the formation of diffraction quality, centrosymmetric crystals. Quasi-racemates are formed by mirror image protein molecules that are not true enantiomers but which are sufficiently similar mirror image objects to form ordered pseudo-centrosymmetric arrays. [ 4 ]
Subsequently, pairs of racemic and quasi-racemic protein molecules prepared by total chemical synthesis have been shown to dramatically increase the rate of success in forming diffraction-quality crystals from a wide range of globular protein molecules. [ 7 ]
Rv1738, a protein of Mycobacterium tuberculosis is the most up-regulated gene product when M. tb enters persistent dormancy. Preparations of recombinantly expressed Rv1738 L-protein resisted extensive attempts to form crystals. A racemic mixture of the chemically synthesized D-protein and L-protein forms of Rv1738 gave crystals in the centrosymmetric space group C2/c. The structure, containing L-protein and D-protein dimers in a centrosymmetric space group, revealed structural similarity to 'hibernation-promoting factors' that can bind to ribosomes and suppress translation. [ 8 ]
Crystallization of ubiquitin protein was successfully done using racemic crystallography. Crystallization of either D-ubiquitin or L-ubiquitin alone is difficult, whereas a racemic mixture of D-ubiquitin and L-ubiquitin was readily crystallized and diffraction quality crystals were obtained overnight in almost half the conditions tested in a standard commercial crystallization screen. [ 4 ]
Crystallization of racemates of disulfide-containing microprotein molecules was used to determine the structure of trypsin inhibitor SFTI-1 (14 amino acids,1 disulfide), conotoxin cVc1.1 (22 amino acids, 2 disul-fides) and cyclotide kB1 (29 amino acids, 3 disulfides). Using X-ray diffraction, it was found that the racemates crystallized in the centrosymmetric spacegroups P3(bar), Pbca and P1(bar). [ 4 ]
Interestingly, achiral "'peptoid'" chains were found to fold as racemic pairs and crystallize in highly preferred centrosymmetric space groups.
A high-resolution crystal structure of the racemate of a heterochiral D-protein complex with vascular endothelial growth factor A (VEGF-A). The mirror image D-protein form of VEGF-A was used in phage display to identify a 56 residue L-protein binder with nanomolar affinity; the chemically synthesized D-protein binder had the same affinity for the L-protein form of VEGF-A. A mixture of chemically synthesized proteins consisting of D-VEGF-A, L-VEGF-A, and two equivalents each of the D-protein binder and L-protein binder, gave racemic crystals in the centrosymmetric space group P21/n. The structure of this 71kDa heterochiral protein complex was solved at a resolution of 1.6 Å [ 4 ] | https://en.wikipedia.org/wiki/Racemic_crystallography |
In chemistry , a racemic mixture or racemate ( / r eɪ ˈ s iː m eɪ t , r ə -, ˈ r æ s ɪ m eɪ t / [ 1 ] ) is a mixture that has equal amounts (50:50) of left- and right-handed enantiomers of a chiral molecule or salt. Racemic mixtures are rare in nature, but many compounds are produced industrially as racemates.
The first known racemic mixture was racemic acid , which Louis Pasteur found to be a mixture of the two enantiomeric isomers of tartaric acid . He manually separated the crystals of a mixture, starting from an aqueous solution of the sodium ammonium salt of racemate tartaric acid. Pasteur benefited from the fact that ammonium tartrate salt gives enantiomeric crystals with distinct crystal forms (at 77 °F). Reasoning from the macroscopic scale down to the molecular, he reckoned that the molecules had to have non-superimposable mirror images. [ 2 ] A sample with only a single enantiomer is an enantiomerically pure or enantiopure compound. [ 3 ]
The word racemic derives from Latin racemus , meaning pertaining to a bunch of grapes . [ 4 ] Racemic acid , when naturally produced in grapes, is only the right-handed version of the molecule, better known as tartaric acid . In many Germanic languages racemic acid is called "grape acid", e.g. German Traubensäure and Swedish druvsyra . Carl von Linné gave red elderberry the scientific name Sambucus racemosa as the Swedish name, druvfläder , means 'grape elder', so called because its berries grow in a grape-like cluster.
A racemic mixture is denoted by the prefix (±)- or dl- (for sugars the prefix dl - may be used), indicating an equal (1:1) mixture of dextro and levo isomers. Also the prefix rac- (or racem- ) or the symbols RS and SR (all in italic letters) are used.
If the ratio is not 1:1 (or is not known), the prefix (+)/(−) , d/l - or d/l- (with a slash) is used instead.
The usage of d and l is discouraged by IUPAC . [ 5 ] [ 6 ]
A racemate is optically inactive ( achiral ), meaning that such materials do not rotate the polarization of plane- polarized light. Although the two enantiomers rotate plane-polarized light in opposite directions, the rotations cancel each other out because they are present in equal amounts of negative (-) counterclockwise ( levorotatory ) and positive (+) clockwise ( dextrorotatory ) enantiomers. [ 7 ]
In contrast to the two pure enantiomers, which have identical physical properties except for the direction of rotation of plane-polarized light, a racemate sometimes has different properties from either of the pure enantiomers. Different melting points are most common, but different solubilities and boiling points are also possible.
Pharmaceuticals may be available as a racemate or as the pure enantiomer, which might have different potencies. Because biological systems have many chiral asymmetries, pure enantiomers frequently have very different biological effects; examples include glucose and methamphetamine .
There are four ways to crystallize a racemate; three of which H. W. B. Roozeboom had distinguished by 1899:
The separation of a racemate into its components, the individual enantiomers, is called a chiral resolution . Various methods exist for this separation, including crystallization, chromatography , and the use of various reagents.
Without a chiral influence (for example a chiral catalyst , solvent or starting material), a chemical reaction that makes a chiral product will always yield a racemate. That can make the synthesis of a racemate cheaper and easier than making the pure enantiomer, because it does not require special conditions. This fact also leads to the question of how biological homochirality evolved on what is presumed to be a racemic primordial earth.
The reagents of, and the reactions that produce, racemic mixtures are said to be "not stereospecific " or "not stereoselective ", for their indecision in a particular stereoisomerism . A frequent scenario is that of a planar species (such as an sp 2 carbon atom or a carbocation intermediate) acting as an electrophile. The nucleophile will have a 50% probability of 'hitting' either of the two sides of the planar grouping, thus producing a racemic mixture:
Some drug molecules are chiral, and the enantiomers have different effects on biological entities. They can be sold as one enantiomer or as a racemic mixture. Examples include thalidomide , ibuprofen , cetirizine and salbutamol . A well known drug that has different effects depending on its ratio of enantiomers is amphetamine . Adderall is an unequal mixture of both amphetamine enantiomers. A single Adderall dose combines the neutral sulfate salts of dextroamphetamine and amphetamine, with the dextro isomer of amphetamine saccharate and D/L-amphetamine aspartate monohydrate. The original Benzedrine was a racemic mixture, and isolated dextroamphetamine was later introduced to the market as Dexedrine. The prescription analgesic tramadol is also a racemate.
In some cases (e.g., ibuprofen and thalidomide ), the enantiomers interconvert or racemize in vivo . This means that preparing a pure enantiomer for medication is largely pointless. However, sometimes samples containing pure enantiomers may be made and sold at a higher cost in cases where the use requires specifically one isomer (e.g., for a stereospecific reagent); compare omeprazole and esomeprazole . Moving from a racemic drug to a chiral specific drug may be done for a better safety profile or an improved therapeutic index. This process is called chiral switching and the resulting enantiopure drug is called a chiral switch . [ 11 ] As examples, esomeprazole is a chiral switch of (±)-omeprazole and levocetirizine is a chiral switch of (±)-cetirizine.
While often only one enantiomer of the drug may be active, there are cases in which the other enantiomer is harmful, like salbutamol [ 12 ] and thalidomide . The (R) enantiomer of thalidomide is effective against morning sickness, while the (S) enantiomer is teratogenic, causing birth defects. Since the drug racemizes, the drug cannot be considered safe for use by women of child-bearing age, [ 13 ] and its use is tightly controlled when used for treating other illness. [ 14 ]
Methamphetamine is available by prescription under the brand name Desoxyn . The active component of Desoxyn is dextromethamphetamine hydrochloride . This is the right-handed isomer of methamphetamine. The left-handed isomer of methamphetamine, levomethamphetamine , is an OTC drug that is less centrally-acting and more peripherally-acting. Methedrine during the 20th century was a 50:50 racemic mixture of both methamphetamine isomers (levo and dextro).
Wallach's rule (first proposed by Otto Wallach ) states that racemic crystals tend to be denser than their chiral counterparts. [ 15 ] This rule has been substantiated by crystallographic database analysis. [ 16 ] | https://en.wikipedia.org/wiki/Racemic_mixture |
In chemistry , racemization is a conversion, by heat or by chemical reaction, of an optically active compound into a racemic (optically inactive) form. This creates a 1:1 molar ratio of enantiomers and is referred to as a racemic mixture (i.e. contain equal amount of (+) and (−) forms). Plus and minus forms are called Dextrorotation and levorotation . [ 1 ] The D and L enantiomers are present in equal quantities, the resulting sample is described as a racemic mixture or a racemate. Racemization can proceed through a number of different mechanisms, and it has particular significance in pharmacology inasmuch as different enantiomers may have different pharmaceutical effects.
Chiral molecules have two forms (at each point of asymmetry), which differ in their optical characteristics: The levorotatory form (the (−)-form ) will rotate counter-clockwise on the plane of polarization of a beam of light, whereas the dextrorotatory form (the (+)-form ) will rotate clockwise on the plane of polarization of a beam of light. [ 1 ] The two forms, which are non-superposable when rotated in 3-dimensional space, are said to be enantiomers . The notation is not to be confused with D and L naming of molecules which refers to the similarity in structure to D -glyceraldehyde and L -glyceraldehyde. Also, ( R )- and ( S )- refer to the chemical structure of the molecule based on Cahn–Ingold–Prelog priority rules of naming rather than rotation of light. R/S notation is the primary notation used for +/- now because D and L notation are used primarily for sugars and amino acids. [ 2 ]
Racemization occurs when one pure form of an enantiomer is converted into equal proportion of both enantiomers, forming a racemate . When there are both equal numbers of dextrorotating and levorotating molecules, the net optical rotation of a racemate is zero. Enantiomers should also be distinguished from diastereomers which are a type of stereoisomer that have different molecular structures around a stereocenter and are not mirror images.
Partial to complete racemization of stereochemistry in solutions are a result of SN1 mechanisms . However, when complete inversion of stereochemistry configuration occurs in a substitution reaction , an SN2 reaction is responsible. [ 3 ]
In the solid state, racemic mixtures may have different physical properties from either of the pure enantiomers because of the differential intermolecular interactions (see Biological Significance section). The change from a pure enantiomer to a racemate can change its density, melting point, solubility, heat of fusion, refractive index, and its various spectra. Crystallization of a racemate can result in separate (+) and (−) forms, or a single racemic compound. However, in liquid and gaseous states, racemic mixtures will behave with physical properties that are identical, or near identical, to their pure enantiomers . [ 4 ]
In general, most biochemical reactions are stereoselective, so only one stereoisomer will produce the intended product while the other simply does not participate or can cause side-effects. Of note, the L form of amino acids and the D form of sugars (primarily glucose) are usually the biologically reactive form. This is due to the fact that many biological molecules are chiral and thus the reactions between specific enantiomers produce pure stereoisomers. [ 5 ] Also notable is the fact that all amino acid residues exist in the L form. However, bacteria produce D -amino acid residues that polymerize into short polypeptides which can be found in bacterial cell walls. These polypeptides are less digestible by peptidases and are synthesized by bacterial enzymes instead of mRNA translation which would normally produce L -amino acids. [ 5 ]
The stereoselective nature of most biochemical reactions meant that different enantiomers of a chemical may have different properties and effects on a person. Many psychotropic drugs show differing activity or efficacy between isomers, e.g. amphetamine is often dispensed as racemic salts while the more active dextroamphetamine is reserved for refractory cases or more severe indications; another example is methadone , of which one isomer has activity as an opioid agonist and the other as an NMDA antagonist . [ 6 ]
Racemization of pharmaceutical drugs can occur in vivo . Thalidomide as the ( R ) enantiomer is effective against morning sickness , while the ( S ) enantiomer is teratogenic , causing birth defects when taken in the first trimester of pregnancy. If only one enantiomer is administered to a human subject, both forms may be found later in the blood serum. [ 7 ] The drug is therefore not considered safe for use by women of child-bearing age, and while it has other uses, its use is tightly controlled. [ 8 ] [ 9 ] Thalidomide can be used to treat multiple myeloma . [ 10 ]
Another commonly used drug is ibuprofen which is only anti-inflammatory as one enantiomer while the other is biologically inert. Likewise, the ( S ) stereoisomer is much more reactive than the ( R ) enantiomer in citalopram (Celexa), an antidepressant which inhibits serotonin reuptake, is active. [ 11 ] [ 5 ] [ 12 ] The configurational stability of a drug is therefore an area of interest in pharmaceutical research. [ 13 ] The production and analysis of enantiomers in the pharmaceutical industry is studied in the field of chiral organic synthesis.
Racemization can be achieved by simply mixing equal quantities of two pure enantiomers. Racemization can also occur in a chemical interconversion. For example, when ( R )-3-phenyl-2- butanone is dissolved in aqueous ethanol that contains NaOH or HCl , a racemate is formed. The racemization occurs by way of an intermediate enol form in which the former stereocenter becomes planar and hence achiral. [ 14 ] : 373 An incoming group can approach from either side of the plane, so there is an equal probability that protonation back to the chiral ketone will produce either an R or an S form, resulting in a racemate.
Racemization can occur through some of the following processes:
The rate of racemization (from L -forms to a mixture of L -forms and D -forms) has been used as a way of dating biological samples in tissues with slow rates of turnover, forensic samples, and fossils in geological deposits. This technique is known as amino acid dating .
In 1843, Louis Pasteur discovered optical activity in paratartaric, or racemic, acid found in grape wine. He was able to separate two enantiomer crystals that rotated polarized light in opposite directions. [ 11 ] | https://en.wikipedia.org/wiki/Racemization |
In calculus ,
the racetrack principle describes the movement and growth of two functions in terms of their derivatives .
This principle is derived from the fact that if a horse named Frank Fleetfeet always runs faster than a horse named Greg Gooseleg, then if Frank and Greg start a race from the same place and the same time, then Frank will win. More briefly, the horse that starts fast and stays fast wins.
In symbols:
or, substituting ≥ for > produces the theorem
which can be proved in a similar way
This principle can be proven by considering the function h ( x ) = f ( x ) − g ( x ) {\displaystyle h(x)=f(x)-g(x)} . If we were to take the derivative we would notice that for x > 0 {\displaystyle x>0} ,
Also notice that h ( 0 ) = 0 {\displaystyle h(0)=0} . Combining these observations, we can use the mean value theorem on the interval [ 0 , x ] {\displaystyle [0,x]} and get
By assumption, x > 0 {\displaystyle x>0} , so multiplying both sides by x {\displaystyle x} gives f ( x ) − g ( x ) > 0 {\displaystyle f(x)-g(x)>0} . This implies f ( x ) > g ( x ) {\displaystyle f(x)>g(x)} .
The statement of the racetrack principle can slightly generalized as follows;
as above, substituting ≥ for > produces the theorem
This generalization can be proved from the racetrack principle as follows:
Consider functions f 2 ( x ) = f ( x + a ) {\displaystyle f_{2}(x)=f(x+a)} and g 2 ( x ) = g ( x + a ) {\displaystyle g_{2}(x)=g(x+a)} .
Given that f ′ ( x ) > g ′ ( x ) {\displaystyle f'(x)>g'(x)} for all x > a {\displaystyle x>a} , and f ( a ) = g ( a ) {\displaystyle f(a)=g(a)} ,
f 2 ′ ( x ) > g 2 ′ ( x ) {\displaystyle f_{2}'(x)>g_{2}'(x)} for all x > 0 {\displaystyle x>0} , and f 2 ( 0 ) = g 2 ( 0 ) {\displaystyle f_{2}(0)=g_{2}(0)} , which by the proof of the racetrack principle above means f 2 ( x ) > g 2 ( x ) {\displaystyle f_{2}(x)>g_{2}(x)} for all x > 0 {\displaystyle x>0} so f ( x ) > g ( x ) {\displaystyle f(x)>g(x)} for all x > a {\displaystyle x>a} .
The racetrack principle can be used to prove a lemma necessary to show that the exponential function grows faster than any power function. The lemma required is that
for all real x {\displaystyle x} . This is obvious for x < 0 {\displaystyle x<0} but the racetrack principle can be used for x > 0 {\displaystyle x>0} . To see how it is used we consider the functions
and
Notice that f ( 0 ) = g ( 0 ) {\displaystyle f(0)=g(0)} and that
because the exponential function is always increasing ( monotonic ) so f ′ ( x ) > g ′ ( x ) {\displaystyle f'(x)>g'(x)} . Thus by the racetrack principle f ( x ) > g ( x ) {\displaystyle f(x)>g(x)} . Thus,
for all x > 0 {\displaystyle x>0} . | https://en.wikipedia.org/wiki/Racetrack_principle |
A racetrack problem is a specific instance of a type of race condition . A racetrack problem is a flaw in a system or process whereby the output and/or result of the process is unexpectedly and critically dependent on the sequence or timing of other events that run in a circular pattern. This problem is semantically different from a race condition because of the circular nature of the problem.
The term originates with the idea of two signals racing each other in a circular motion to influence the output first. [ citation needed ] Racetrack problems can occur in electronics systems, especially logic circuits, and in computer software, especially multithreaded or distributed programs. | https://en.wikipedia.org/wiki/Racetrack_problem |
Racewood is a British company that specialises in creating horse riding simulators. It was established in 1990.
Racewood simulators are seen in riding schools as well as gyms and tack shops. [ 1 ] They are also sometimes brought in to horse expeditions and shows such as the Grand National , Horse Of The Year Show and the Badminton Horse Trials . [ citation needed ]
A popular nationwide festival, The National Riding Festival, also uses a Racewood cantering simulator called "Trigger", who appears at every date on the festival tour and at some primary and secondary schools to encourage children to take up horse riding. [ citation needed ]
In 2023, Scotland's Rural College purchased a £100,000 Racewood simulator for students to practice riding to improve their equestrian performance and safety. [ 2 ]
This article about equestrian sports or equestrianism is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Racewood |
Rachna Malayalam is considered as the first computer operating system in Malayalam language and the first such system in a regional language in India . It was launched on February 16, 2006. [ 1 ]
The operating system, developed by four people in Kerala , is in the Linux platform and is an open software .
This software article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Rachana_Malayalam |
The Rachel Carson Prize is awarded annually by the Society for Social Studies of Science , an international academic association based in the United States. It is given for a book "of social or political relevance" in the field of science and technology studies . This prize was created in 1996. [ 1 ] | https://en.wikipedia.org/wiki/Rachel_Carson_Prize_(academic_book_prize) |
Moulay Rachid Idrissi ( Arabic : مولاي رشيد الإدريسي ; 1939 – October 18, 1971) was a Moroccan nuclear chemist and engineer. Idrissi gained notoriety after his work on the recovery of uranium from phosphates , where he discovered a significant amount of uranium in Moroccan phosphates. Shortly after this discovery, he died in a traffic accident near Rabat, the circumstances of which remain contested.
Moulay Rachid Idrissi was born in 1939 in the Douar Oulad Belhlou near the town of Outat El Haj , near Taza . [ 1 ] [ 2 ] [ 3 ] His family claimed descendance from the Idrisid dynasty . [ 1 ] [ 3 ]
He studied in the town throughout primary school where he obtained his Certificate of Primary Education before studying at the prestigious Collège d'Azrou . [ 4 ] [ 2 ] [ 5 ] After obtaining his scientific baccalaureate from the collège, he moved to Rabat and continued his studies in chemistry. [ 6 ] [ 1 ] [ 7 ]
As a young man, Idrissi worked on development projects in his hometown of Outat El Haj, coordinating with UNESCO to build a youth house in the village. [ 6 ] [ 3 ] He had also worked to establish an agricultural cooperative near the Moulouya River and a preparatory high school in the village. [ 1 ] [ 7 ] In 1970, Idrissi held a ceremony and handed out prizes to outstanding students from his hometown. [ 7 ]
With the help of classmate Mohamed Chafik , Idrissi pursued his studies in France. [ 2 ] He obtained a Doctorate of Science in nuclear chemistry in 1970 from the Faculty of Science at the University of Paris after doing research regarding electrophilic fluorination of uranium dioxide at the Zoé reactor in Fontenay-aux-Roses . [ 6 ] [ 8 ] [ 9 ] He also obtained a degree in chemical engineering from the National Institute for Nuclear Science and Technology in Saclay . [ 6 ] [ 3 ]
Throughout his career, he rejected offers made to him by foreign laboratories and other parties. [ 6 ] [ 1 ] [ 7 ] After returning to Morocco, Idrissi gained an interest in politics and was an ardent trade unionist and adopted Third-Worldism . [ 6 ] [ 1 ] [ 10 ] He became a community activist and a politician under the banner of the Socialist Union of Popular Forces . [ 2 ] [ 3 ]
He became a professor at the Mohammadia School of Engineering and moved to Safi , where he conducted research in a number of laboratories in the late 1960s. [ 4 ] [ 6 ] Idrissi's field of research focused on the recovery of uranium from phosphates, which was Morocco's biggest export. [ 6 ] [ 11 ] During his research, he mapped the Ganntour basin and its uranium repartition. [ 12 ]
In 1968, he discovered a significant amount of uranium in Moroccan phosphates, which he announced to local press. [ 6 ] [ 10 ] [ 3 ] Idrissi had estimated that about 72 thousand tons of uranium could be extracted annually as a low-cost byproduct from Moroccan phosphates. [ 6 ] [ 1 ] [ 10 ] The media praised his discovery, and he supplied data regarding his findings to the IAEA . [ 6 ] [ 1 ] [ 10 ]
Rachid Idrissi died on October 18, 1971, in Salé in a car accident after being hit by a truck on National Road 15 while crossing a bridge on Bou Regreg from Rabat on his way to his hometown of Outat El Haj. [ 1 ] [ 4 ] [ 2 ] His sudden death immediately raised suspicion of a political assassination from his entourage. [ 6 ] [ 1 ] [ 11 ] He was buried in the cemetery in Douar El Kchahda, near Outat El Haj. [ 7 ]
During a speech at his funeral, engineer Mohamed Ait Kaddour , a colleague of Idrissi, stated that he fell victim to "his involvement in establishing a defense project in the Arab world based on his possession of science, knowledge, and ability". [ 10 ] A scholar in Idrissi's hometown, Hajj Mohamed Harmouche, blamed his death on "external parties". [ 6 ] Newspaper Al Ittihad Al Ichtiraki claimed that Idrissi had been surveilled by foreign intelligence agencies prior to his death, but this remains unconfirmed. [ 10 ]
A posthumous Rachid Idrissi El Ouatati Prize for Criticism was created in May 2023 by the Oboure Cultural Publishing Association in Rabat, the prize crowns works of literary criticism in Morocco and commemorates Idrissi. [ 13 ] [ 14 ] In December 2023, a synopsium was held by the Moulay Rachid Idrissi Center for Studies and Research in Outat El Haj regarding Idrissi's life. [ 7 ] | https://en.wikipedia.org/wiki/Rachid_Idrissi |
According to the National Science Foundation (NSF), women and racial minorities are underrepresented in science, technology, engineering, and mathematics (STEM). [ 1 ] Scholars, governments, and scientific organizations from around the world have noted a variety of explanations contributing to this lack of racial diversity, including higher levels of discrimination , implicit bias , microaggressions , chilly climate, lack of role models and mentors, and less academic preparation. [ 2 ] [ 3 ] [ 4 ]
Racial minorities , with the exception of Asian Americans , are underrepresented through every stage of the STEM pipeline . [ 1 ]
Racial disparities in high school completion are a prominent reason for racial imbalances in STEM fields. While only 1.8% of Asian and 4.1% of White students drop out of high school, 5.6% of Black, 7.7% of Hispanic , 8.0% of Pacific Islander, and 9.6% of American Indian/Alaskan Native students drop out of high school. [ 6 ] Among those that graduate high school, 67% of Whites, 62% of Blacks, and 69% of Hispanics enroll in a “degree granting college.” [ 7 ] While there is no measurable difference in college enrollment of White, Black, and Hispanic STEM students, only 15% of Black students who initially enrolled in a STEM major received a STEM bachelor's degree at graduation, compared to 30% of White and Asian students. [ 8 ]
According to the National Science Board , which provides statistical data on the U.S. labor force, Asians represent 9%, Whites 65%, Hispanics 14%, and Blacks 9% of the STEM labor force. [ 5 ] In particular, white men are 49% of the STEM labor force. [ 1 ] Among different STEM fields, Blacks make up only 4% of life science , 5% of engineering , 6% of physical sciences , 7% of the computer science , 9% of math and 11% of health-related sciences. [ 9 ] There are also significant wage gaps between women, men, and people of color , especially in STEM jobs. An example of this disadvantage is the gender pay gap and racial pay gap in computer science fields, where women earn about 74% of what men earn and the median income for White workers is approximately 23.3% more than the median income for Blacks. [ 9 ] The gender and racial pay gaps in STEM fields are significantly greater than all regular non-STEM jobs with an even greater pay gap between these gender, racial, and ethnic groups. When first being hired, 35% of women of color reported negotiating their salaries, but nearly 50% wished that they had negotiated their salary after starting the job. Many of these women reported being initially satisfied with the salary they had been offered when being hired, but later learned that they were earning much less than other workers at their same level. [ 10 ]
Among Black workers in STEM fields, 57% feel that there too little attention being directed toward adding more racial and ethnic diversity in the workplace. [ 11 ] This lack of diversity contributes to isolation and a lack of social support in the workplace which can increase anxiety and depression for many people of color in STEM. [ 12 ]
Recently, scholars have begun applying the framework of systemic racism to explain the experiences of racial minorities in STEM. [ 13 ] Specifically, research indicates that people of color, especially blacks, experience higher levels of discrimination , incur various microaggressions , and a lack of overall mentorship and support in STEM. [ 11 ]
Scientific racism of the late 19th and early 20th centuries attempted to identify biological, intellectual, and physiological differences among races. Lasting effects of the scientific racism include racial stereotypes about students of color and preconceived notions of STEM as predominantly a white, male field. [ 14 ] A study highlighting the underrepresentation of women and racial minorities in STEM found that Asian and White candidates were viewed as more competent and hirable than Black and Latino/a candidates. Similarly, survey results from this study show that students were much more likely to recognize and name white male STEM professionals than Black or women STEM professionals. [ 15 ] Additionally, students of color on college campus often face prevailing societal misconceptions and assumptions that they are affirmative action beneficiaries, on sport scholarships, and/or “at-risk” students . Students of color additionally must contend with stereotype threat that has been found to lower academic achievement. In particular, high-achieving Black students, attempting to combat prevailing stereotypes about their lack of intelligence, while Asian students combat the prevailing model minority stereotype presuming they are biologically predisposed to mathematical ability.
The development of a STEM identity increases the overall likelihood that a student will continue to develop scientific literacy and pursue a STEM career. The National Research Council's 2009 report describes students developing STEM identities as learning to “think about themselves as science learners and develop[ing] an identity as someone who knows about, uses and sometime[s] contributes to science.” [ 16 ] Black girls are less likely to develop STEM identities in middle school because they have fewer science-related experiences outside of school and less confidence in their scientific ability than Asian-American, Latina, and White middle school girls, making them less likely to enter STEM fields in the future. [ 17 ] Additionally, research demonstrates that beyond first-hand experience with science, societal norms, stereotypes, and interactions with peers, teachers, and family contribute to the development of a STEM identity. [ 18 ]
People of color and underrepresented minority groups in science, technology, engineering and math are more likely than whites to experience racial microaggressions . [ 19 ] Studies show racial microaggressions that occur on college campus weaken students sense of belonging, make it difficult to form relationships with faculty, and contribute to less cultural alignment with STEM. [ 19 ] [ 20 ] At predominantly white institutions (PWI) environmental microaggressions are common in shared laboratory spaces among students and during meetings with faculty and advisors. [ 21 ] Black female students are especially likely to feel alienated and isolated from their peers in STEM departments. [ 22 ] [ 23 ]
Research on implicit bias demonstrates that as early as preschool teachers are likely to hold implicit bias against students of color, especially Black boys. While Black children make up 19% of preschool enrollment, they account for about half of preschool suspension. [ 24 ] Implicit biases among teachers, faculty, and colleagues makes it more difficult for students of color to form relationships, network with professionals in their fields, and find valuable mentors. [ 25 ] Judgements placed upon people of color based on implicit biases are incredibly damaging and contribute to stereotype threat , which affects their overall performances. For instance, Black women are often assumed to be underqualified forcing them to prove that they deserve to be in those spaces as was the case of Katherine Johnson depicted in Disney's " Hidden Figures ".
When people do not feel welcome in a place, environment, or institution, they are less likely to feel they belong and more likely to withdraw. [ 26 ] In particular, women and people of color often adopt individual strategies of assimilation or patriarchal bargaining in their attempt to gain acceptance. [ 13 ] For example, Black male scientists adopt coping strategies to endure racialized interactions with colleagues and managers. [ 27 ] Similarly, Black female undergraduates students describe coping with racism on campus by gravitating toward same-race peers, faculty, and staff. [ 22 ] When underrepresented groups are forced to adapt or leave the field altogether, it costs STEM valuable talent and perspectives that could be used to advance scientific discoveries and advancements.
The STEM pipeline starts to narrow early as students of color face additional barriers to STEM participation in school. The following are some examples of these barriers.
Research indicates that racial disparities in science achievement test scores begin as early as third grade. [ 28 ] These test score disparities were attributed to both socioeconomic status gaps between races and school qualities. In particular, Black and Hispanic students are more than double as likely to live in low-income neighborhoods compared to White students which directly contributes to less money for local public schools and indirectly less funding for STEM programs. [ 7 ] Black and Latino/a may not always have the same access to higher level high school courses that are building blocks for success in College STEM fields. [ 29 ] For example, those who have not taken high school trigonometry, calculus, or physics, are put at a disadvantage in terms of graduating with a STEM degree. [ 26 ] Beyond academic preparation, experiences with STEM across various settings, including school, home, and out-of-school, help students of color see STEM careers as more possible. [ 17 ]
While Black males are twice as likely as their white peers to declare a STEM major upon entering college, they are less likely to graduate with a STEM degree. [ 30 ] [ 7 ] Scholars point to microaggressions, a chilly climate, and lack of role models and mentors as contributing to students of color being "weeded out” of STEM majors. [ 7 ] [ 25 ] Additionally, one study examining Black male engineering graduate students found that microaggressions from counselors, mentors, and fellow students resulted non-normative role strain. [ 27 ] These actors increase the likelihood that people of color leave STEM majors.
Because white men are still overrepresented in STEM fields there is a lack of available mentorship from faculty and scientists of color. As a result, students of color in STEM feel unheard, excluded, and lose opportunities to make connections with peers. Research does indicate that students of color at HBCU's are much more likely to perceive their mentors to be supportive and describe more positive interactions with peers. [ 25 ]
Underrepresented minorities, including women, people of color , and LGBT individuals are more vulnerable to experience discrimination, isolation, and/or harassment in their workplaces. [ 31 ] A Pew survey of men and women in STEM indicates that 50% of women in STEM experienced gender-related discrimination at work and about 62% of Black people in STEM jobs stated they experienced racial discrimination at work. [ 11 ] Additionally, 72% of Black STEM workers believe that facing racial discrimination is a major reason why there are not more people of color in STEM fields. [ 11 ]
Underrepresentation of people of color in STEM is a problem that is rooted to white supremacy and racism .
Many scholars and organization recommend elimination of bias as a means to increase representation in STEM. [ 2 ] Specifically, implicit bias , training of students, managers, faculty, and even students is seen as one way to combat stereotypes and reduce microaggressions targeting people of color. [ 32 ] Additionally, incorporating implicit bias statements and policies can strengthen a commitment to diversity and inclusion within institutions. [ 33 ]
Those in STEM fields have recognized that there is an extensive history of poor representation of women and people of color in STEM and are working to close the gap. Addressing this issue requires a coherent and sustained effort across multiple fronts. Many would argue that single intervention does not work, but that sustainable and strategic reform in education, work place, and within our communities would put our theory in to practice. Transforming our perception of STEM in the early education years for students of color necessitates celebration of the distinct contribution that women and people of color bring to science, technology, engineering, and mathematics. [ 3 ]
While many teachers are highly dedicated to reducing the race gap and actively striving to create equal opportunities in their classrooms, they can actually contribute to the STEM race gap. It is important that teachers understand that their actions impact students’ futures more than they may realize. [ 34 ]
One of the most promoted solutions is the need for role models. While both female and male role models can be effective in recruiting women in STEM fields there is a lack of role models of color to mentor POC in STEM fields. When individuals have someone to look up to that looks like them, they are more willing to stay in the field and develop a sense of belonging. [ 35 ] Opportunities to engage and connect with individuals in STEM allows for excitement to be a part of this community and the development of a stronger STEM identity. [ 36 ]
Mentors provide students the academic and social support they need to succeed in STEM, however, having same-race mentorship is an important step in retaining students of color in STEM. Not only do students of color report more positive interactions with same-race faculty, they are also more likely to develop stronger STEM identities. [ 22 ]
There is a growing number of organizations whose goal is to increase diversity in STEM fields by encouraging girls and women to thrive in STEM environments. An example of one of these organizations is Girls Who Code . Their mission is to successfully close the gender gap in new entry-level tech jobs by 2030. Girls Who Code focuses their work not only on gender diversity but also on young women who are historically underrepresented in computer science fields, including African American/Black, Hispanic or Latina, Bi/ Multiracial, Native American/Alaskan, and Native Hawaiian/Pacific Islander, those who come from low-income backgrounds, specifically free and/or reduced lunch eligible, and those who have had a lack of exposure or access to computer science. Girls Who Code acknowledges and values the intersections of race/ethnicity, gender identity and expression, class, sexual orientation, ability, age, national origin, and religious/spiritual identities.
Similarly, Black girls who participated in I AM STEM , a community nonprofit organization designed to increase STEM participation among underrepresented groups, engaged directly in first-hand scientific research which contributed to stronger connections to STEM. [ 37 ]
Another great example of organizations for the underrepresented is the Society for advancement of Chicanos/Hispanics and Native Americans in Science (SACNAS). SACNAS's mission is to advance the success of Chicanos/Hispanics and Native Americans in securing advanced degrees, careers, and positions of leadership in STEM fields. The organization has been working to make sure that those most underrepresented in STEM have the support they need to attain advanced degrees, careers, and positions of leadership. SACNAS also often points out that diverse voices bring creative solutions to our world's most pressing scientific problems and that building a national network that is innovative, powerful, and inclusive is necessary. | https://en.wikipedia.org/wiki/Racial_diversity_and_discrimination_in_STEM_fields |
Ractopamine ( / r æ k ˈ t ɒ p ə m aɪ n , - m iː n / ) is an animal feed additive used to promote leanness and increase food conversion efficiency in farmed animals in several countries, but banned in others. Pharmacologically, it is a phenol -based TAAR1 agonist and β adrenoreceptor agonist that stimulates β 1 and β 2 adrenergic receptors. [ 1 ] [ 2 ] It is most commonly administered to animals for meat production as ractopamine hydrochloride . [ 3 ] It is the active ingredient in products marketed in the US as Paylean for swine, Optaflexx for cattle, and Topmax [ 4 ] for turkeys. [ 5 ] It was developed by Elanco Animal Health , a former division of Eli Lilly and Company .
As of 2014, according to the Humane Society, the use of ractopamine was “banned or restricted” in 160 countries, [ 6 ] including the European Union , China and Russia , [ 7 ] [ 8 ] while it is legal in 27 other countries, such as Japan , the United States , South Korea , and New Zealand . [ 9 ] [ 10 ] [ 11 ]
Commercial ractopamine is a mixture of all four possible stereoisomers . [ 12 ] It is also a positional isomer of dobutamine , a related drug.
When used as a food additive , ractopamine added to feed can be distributed by the blood to the muscle tissues, where it serves as a full agonist to murine (mouse or rat) TAAR1 , a receptor protein (not necessarily in humans). [ 1 ] It is also an agonist to beta-adrenergic receptors [ 2 ] and a dopamine releasing agent . [ 13 ] A cascade of events will then be initiated to increase protein synthesis , which results in increased muscle fiber size. Ractopamine is known to increase the rate of weight gain, improve feed efficiency, and increase carcass leanness in finishing swine. Its use in finishing swine yields about 3 kg (6.6 lb) of additional lean pork per animal, and improves feed efficiency by 10%. [ 14 ] In cattle on 28 January 2004 Elanco Animal Health made Optaflexx commercially available in the US. Optaflexx is a "medicated feed additive that is labeled only for use in steers or market heifers (not breeding heifers or bulls) during the last 28–42 days on feed." [ 15 ]
On 6 July 2012, the international reference standard Codex Alimentarius Commission narrowly approved the adoption of a maximum residue limit (MRL) of 10 parts per billion (ppb) for muscle cuts of beef and pork. [ 16 ] Setting any limit was a controversial move. Countries with major meat export markets had been lobbying for the establishment of such a standard for several years to use it as leverage to erode individual national-level bans in World Trade Organization disputes. [ 16 ] Consumers International , a world federation of consumer groups that represents 220 consumer organizations in 115 countries, strongly opposed the move. [ 16 ]
Ractopamine use in food animals is banned in over 160 countries. [ 17 ] [ 18 ]
Ractopamine has not been allowed in the European Union , based on the 2009 EU's Food Safety Authority 's opinion on its safety evaluation, which concluded that available data were insufficient to derive a maximum residue limit as a 'safe residue level for human consumption'. The uncertainty was particularly great for people who might be thought to be more susceptible than most to an increase in β adrenergic stimulation from consuming the additive, such as children or people with cardiovascular disease , and that simply increasing the "uncertainty factor" built into the calculation as a safety factor would rapidly become arbitrary. [ 19 ] [ 20 ]
Ractopamine use as a feed additive is authorized in the United States, Canada, and Mexico. [ 19 ] In the US, ractopamine is allowed to be used at a feed concentration of 5–20 mg/kg feed for finishing pigs and in dosages of 5–10 mg/kg feed for finishing pigs heavier than 109 kg. The maximum residue limit for ractopamine for meat in the USA is 50 parts per billion (ppb), or five times the standard set by the Codex Alimentarius . Ractopamine was approved by the FDA in 1999 for use in swine, in 2003 for use in cattle, and in 2008 for use in turkeys. [ 21 ]
In 2015, the USDA approved of a new label, "No ractopamine — a beta-agonist growth promotant" to be used. [ 22 ]
The Canadian Food Inspection Agency (CFIA) maintains the Canadian Ractopamine-Free Pork Certification Program (CRFPCP) so that Canadian exports to Asian countries are not disallowed by their authorities. [ 23 ] [ 24 ] [ 25 ] Hundreds of commercial feed facilities, including some from overseas, are enrolled in the CRFPCP, a programme that is essentially based on self-certification and backed up by a randomized testing policy. [ 26 ]
Currently, the label for USDA organic means no synthetic compounds can be used other than those on the list of allowed synthetics ; therefore, ractopamine would not be allowed in certified organic production. [ 27 ]
For Canadian domestic consumption of non-CRFPCP pork, ractopamine hydrochloride is permitted to be sold over the counter with applications in meal or pellet feed for finishing barrows and gilts (up to 10 mg/kg for last six weeks), confined finishing cattle (up to 30 mg/kg for last 42 days), and finishing heavy turkeys (up to 9 mg/kg for 14 days). The withdrawal period was set to 0 days. [ 28 ]
Japan , which had permitted its feed additive use at least until 2009, [ 19 ] : 1 and South Korea only allow import of meat with ractopamine residues up to the maximum residue limit (MRL), but do not permit its use in beef production. [ 29 ]
In October 2006, Taiwan banned ractopamine along with other beta-adrenergic agonists . [ 30 ] In a 2012 climb-down, its legislature passed amendments to its Act Governing Food Sanitation , authorising government agencies to set safety standards for ractopamine. [ 31 ] The Taiwanese Department of Health ultimately established an MRL of 10 ppb for ractopamine in beef on 31 July 2012. [ 32 ] The American Institute in Taiwan , which represents US interests in Taiwan, states that these "and many other countries have determined that meat from animals fed ractopamine is safe for human consumption"; [ 9 ] this is in the context of an ongoing trade dispute between Taiwan and the US on this subject, which threatened to prevent Taiwan's entry to the Trans-Pacific Partnership trade pact. [ 33 ]
In 2020, restrictions on imports of US pork with ractopamine were relaxed, leading to protests. [ 34 ] A referendum took place on December 18, 2021 , deciding whether to ban the import of pork with ractopamine, and the ban was rejected. [ 35 ]
In 2013, Russia and China banned ractopamine in pork, [ 36 ] and Russia also in beef, [ 17 ] deeming it unfit for human consumption. Because the traditional Chinese diet embraces pig offal , and because ractopamine is concentrated by the gastro-intestinal system of animals, Chinese officials have banned ractopamine. Other countries in Asia, whose traditional diet is similar to that of the Chinese, have had similar concerns, but the American use of tied trade access as a proxy for conflict has somewhat mitigated their reactions. [ 23 ] [ 37 ] [ 38 ]
In 2017, Russia banned imports of beef from New Zealand after finding ractopamine in New Zealand beef. [ 39 ] Ractopamine is not registered for use in cattle in New Zealand.
In 2015, an 18-year-old female karateka (martial arts practitioner) from Egypt gave a urine sample in order for her drugs test to be administered. It was found that the urine contained too much ractopamine and the athlete was sanctioned with ineligibility for four years. The sole arbitrator from the Court of Arbitration for Sport said that ractopamine "is not specifically mentioned by name in the World Anti-Doping Code ("WADC"), but is an Other Anabolic Agent prohibited under S1.2 of the 2015 Prohibited List under the WADC... Athlete did not fulfil her burden of proof to establish the origin of the prohibited substance, [and thus] she has committed an anti-doping rule violation". [ 40 ]
In October 2017 at a World Anti-Doping Agency conference, it was suggested in relation with ractopamine: [ 41 ]
One conclusion reached in October 2017 was that there was a "clear risk for athletes to be tested positive" when consuming meat with residues at the MRL concentration. [ 5 ]
In the late 1990s, the World Trade Organization authorized the United States and Canada to impose retaliatory tariffs of US$116.8 million per year on the European Union after it found the EU beef hormone ban to be in violation of the WTO Agreement on the Application of Sanitary and Phytosanitary Measures (SPS Agreement). [ 42 ] [ 43 ] In September 2009, the trade representatives from the US and EU signed a memorandum of understanding, which established a new duty-free import quota in the European Union for grain-fed, high-quality beef as part of a compromise solution. [ 43 ]
In July 2007, officials of the People's Republic of China seized US-produced pork for containing ractopamine residues. [ 44 ] Further shipments of Canadian ractopamine-fed pork were seized in September 2007. [ 45 ]
In June 2019, customs inspectors in China detected ractopamine in a shipment of Canadian pork products destined for Chinese consumption. The Chinese government thereupon suspended not only pork, but also beef imports from Canada. [ 46 ] Canadian Agriculture Minister Marie-Claude Bibeau stated that the CRFPCP certificate was a forgery and called in the RCMP , while Canadian Public Safety Minister Ralph Goodale stressed that the federal government would vigorously defend Canadian meat producers. [ 46 ] It was also revealed that the Canadian Cattlemen's Association said in a statement that "We are fully confident in our meat production systems in Canada and the safeguards we have in place." [ 46 ] Meanwhile, holes were found in the CRFPCP programme because the meat packer at the centre of the controversy was a chilled butcher shop only.<what> [ 47 ] It was disclosed on 3 July that the Chinese authorities had discovered 188 falsified CRFPCP certificates. [ 48 ]
Ractopamine has been banned in Taiwan since 2006. [ 49 ] In the summer of 2007, two US shipments including ractopamine-laced pork were rejected by Taiwan's health authorities, while the Taiwan government had been considering lifting the ban on such imports. [ 50 ] This resulted in mass protests in the capital city, Taipei , by swine farmers insisting that the ban remain in place. Health Minister Hou Sheng-mou (侯勝茂) declared no lifting of the ban would occur unless related laws were amended. Although the use of ractopamine in livestock is still banned and enforced on the domestic industry, and the government has maintained a "zero tolerance" policy on pork imports that contain it, Taiwan's legislature amended the food safety act in August 2012 to allow the import of beef products containing up to a maximum residue level of 10 parts per billion of the additive. [ 51 ] The remaining restrictions have been an obstacle to the two nations signing a free-trade agreement, and the Office of the United States Trade Representative (USTR)'s 2018 Trade Policy Agenda and 2017 Annual Report assert that these remaining restrictions "...are not based upon science..." and highlights their removal as among the main priorities for the US in its trade with Taiwan. [ 51 ] However, Taiwan plans to ease the import restrictions on US pork commencing January 1, 2021 [ 52 ]
According to the Malaysian Food Act 1983 and Regulations (as of 5 January 2010), ractopamine is allowed in pig muscle and fat (MRL of 10 ppb), pig liver (MRL of 40 ppb), and pig kidney (MRL of 90 ppb). [ 53 ] Ractopamine is allowed as its half-life is lower, leading to reduced residues in the food, and the dose required to affect humans is much higher than other beta agonists. [ 54 ] On 30 December 2008, the Malaysian Veterinary Services Department quarantined 10 of the 656 pig farms in Malaysia , as the livestock were found to contain the banned chemical. [ 55 ] [ 56 ]
The use of ractopamine in Russia is prohibited. On 6 June 2011, the Russian Ministry of Agriculture notified key meat import/exporters in Russia of a future prohibition of ractopamine in meat imported to Russia. [ 57 ]
On 7 December 2012, the prohibition went into force, and pork and beef export to Russia required submission of compliance certificates confirming absence of ractopamine in exported meat. [ 57 ]
A study was conducted to define the pharmacological response of humans to ractopamine. A single oral dose of 40 mg of ractopamine hydrochloride was given to human volunteers. The drug was rapidly absorbed; the mean blood plasma half-life was around 4 hrs and it was not detected in plasma 24 hrs after dosing. Less than 5% of total ractopamine excreted represented the parent drug, while the urinary metabolites were monoglucuronide and monosulfate conjugates , with ractopamine monosulfate being the major metabolite present. [ 58 ]
The metabolic fate of ractopamine hydrochloride is similar in the target species (pigs and cattle), laboratory animals, and humans. Besides the pharmacology effect, ractopamine may cause intoxication effect; therefore, any consumption by humans of a meat and/or byproducts of animals that consumed ractopamine with feed for growth stimulation, may result in such clinical effects as tachycardia and other heart rate increases, tremor, headache , muscle spasm , or high arterial blood pressure . [ 59 ]
In swine, ractopamine is correlated with adverse effects, especially hyperactivity , trembling, and broken limbs, leading to censure by animal rights groups. [ 60 ]
In a conversation with Boulder Weekly newspaper, Colorado State University Professor of Animal Science Temple Grandin , an expert on animal welfare, described harmful effects of ractopamine on feedlot animals, such as cattle with stiff, sore, and lame limbs, and increased heat stress. [ 61 ] In the same column, she also opines that meat from ractopamine-treated animals may be tougher. [ 61 ]
Ractopamine use is a factor in the incidence of downer pigs, animals that are unable to move or stand. [ 62 ] [ 63 ]
Oral LD 50 levels in mice and rats are 3547–2545 mg/kg body weight (male and female) and 474–365 (male and female), respectively. [ 64 ]
Mutation studies in prokaryotes and eukaryotes show that ractopamine is not mutagenic . However, the results of several in vitro studies, including chromosome aberration tests in human lymphocytes, are positive. The positive genotoxic results are explained with limited evidence to be due to a secondary auto-oxidative mechanism from ractopamine-catechol-producing reactive intermediates. [ 65 ]
Ractopamine is not considered to be a carcinogen and not listed by IARC , NTP , ACGIH , or OSHA . [ citation needed ]
Dose-dependent changes of heart rate and cardiac output are observed within the first hour after administration of ractopamine and gradually return to baseline values. The systolic blood pressure will also increase in a dose-dependent manner, while the diastolic pressure remains unchanged. [ 66 ]
Skeletal muscle tremor is the most common adverse effect of beta-agonists, and is more likely to be seen after oral administration than after inhalation. Tremor results from an imbalance between fast- and slow-twitch muscle groups of the extremities, and its severity varies greatly between individuals. [ citation needed ]
Restlessness, apprehension, and anxiety were reported effects after the use of various beta-agonists, particularly after oral or parenteral treatment . In pilot clinical trials with ractopamine, four patients showed little evidence for central nervous system stimulation. Whether long-term treatment with these drugs results in the development of tolerance to these adverse effects is unclear. [ 65 ]
In cattle and swine tissue, it was found in 2007 that a procedure for the analysis of ractopamine residues in liver or muscle can be performed by high performance liquid chromatography (HPLC) with fluorescence detection. The confirmatory method include reversed-phase HPLC/electrospray ionization triple tandem quadrupole mass spectrometry. The limit of quantification of the drug using this LC/MS instrument was shown to be 1 ng/g (1 ppb). [ 67 ] In cattle, a 2018 Chinese study promoted the use of hair as an indelible test of feed containing ractopamine. [ 68 ]
Stuntman and comedian Steve-O has publicly spoken of his involvement as a test subject in an early ractopamine study whose aim was to determine the stress limits of ractopamine saturation in humans. Glover says "Based on how dangerous the study was, the more money you get." [ 69 ] | https://en.wikipedia.org/wiki/Ractopamine |
The RadBall is a 140-millimetre (5.5-inch) diameter deployable, passive, non-electrical gamma hot-spot imaging device that offers a 360 degree view of the deployment area. The device is particularly useful in instances where the radiation fields inside a nuclear facility are unknown but required in order to plan a suitable nuclear decommissioning strategy. The device has been developed by the UK's National Nuclear Laboratory and consists of an inner spherical core made of a radiation sensitive material and an outer tungsten based collimation sheath. The device does not require any electrical supply or communication link and can be deployed remotely thus eliminating the need for radiation exposure to personnel. In addition to this, the device has a very wide target dose range of between 2 and 5,000 rads (20 mGy to 50 Gy ) which makes the technology widely applicable to nuclear decommissioning applications.
The device consists of two constituent parts, a gamma radiation sensitive inner core which fits inside the spherical tungsten outer collimation sheath. The outside diameter of the device is 140 mm (approx 5 ½ inch) which allows deployment in to hard to reach areas whilst providing a 360 degree view of the area. The inner core is made up of material which changes colour when it is exposed to gamma radiation. Therefore, when the device is deployed inside a radioactive environment the collimation device preferentially allows gamma radiation to pass through the collimation holes which deposits tracks within the inner core. These tracks can then be analysed to provide a 3D visualisation of the radioactive environment predicting both source location and intensity.
The overall radiation mapping service based on the device consists of six individual steps. Step 1 involves placing the device inside the given contaminated area with a known position and orientation. This can be achieved in a number of ways including deployment by crane , robot , by an operator or (as in most cases) by a remotely operated manipulator arm. The device can be orientated either upright or upside down. Once the device has been placed in position, Step 2 involves leaving the device in-situ to enable dose uptake. Once the device has been left in-situ and has achieved a suitable dose uptake (between 2 and 5,000 rads), Step 3 involves removing the device from the contaminated area. Once clearance has been given, Step 4 involves removing the radiation sensitive core from within the collimation device, ensuring that it has not rotated or moved during the deployment period.
Step 5 involves scanning the radiation sensitive core using an optical technique which digitises the information captured by the inner core. Step 6 involves the interpretation of this data set to produce a final visualisation . For each detected track within the inner core special software creates a line of best fit for the data points provided and chooses the direction of the track by using the intensity values. This line of best fit is extrapolated until it intersects with a wall of the deployment volume. This indicates that the radiation source is on the wall at this location or anywhere along the line of sight between the device and the point on the wall. If two devices are deployed in different locations within the same deployment area, triangulation can be used to predict where along the extrapolated line the radiation source is.
A number of alternative technologies and approaches do exist ranging from the use of GM based detectors mounted on a manipulator and moved around a radioactive cell to heavily shielded and collimated gamma-based camera. The technology tested here does have a number of advantages over the aforementioned. With regards to the GM / manipulator approach, the technology has directional awareness, an ability to distinguish separate sources which are in close proximity, there is no need for a power or data umbilical and the technology can be used in areas where a manipulator is not present. With regards to the heavily collimated gamma camera technology, the technology also has a number of advantages including a much more compact size, less weight, no power and data umbilical as well as offering a lower financial risk should the equipment become contaminated.
The technology has been successfully deployed a number of times throughout the US and the UK as described below.
The earliest lab based tests undertaken on the original version of the technology was performed at the Savannah River Site (SRS) Health Physics Instrument Calibration Laboratory (HPICL) using various gamma-ray sources and an x-ray machine with known radiological characteristics. The objective of these preliminary tests was to identify the optimal target dose and collimator thickness of the device. The second set of tests involved the deployment of device in a contaminated Hot Cell in order to characterise the radiation sources within. This work is described in a number of previous publications, primarily in a report commissioned by the US Department of Energy , [ 1 ] but also in a number of journal publications. [ 2 ] [ 3 ] [ 4 ] and general industrial news outlets. [ 5 ]
Further testing of the original device was undertaken in order to demonstrate that the technology could locate submerged radiological hazards. This study involved, for the first time, underwater deployments at the US Department of Energy Hanford Site . This study represents the first successful underwater deployment of technology and a further step in demonstrating that the technology has the ability to be remotely deployed with no electrical supplies into difficult to access areas and locate radiation hazards. This study was part of ongoing work to investigate whether the technology is able to characterize more complex radiation environments as described previously. [ 6 ]
A number of trials took place at the US Department of Energy Oak Ridge National Laboratory (ORNL) during December 2010 as described previously. [ 7 ] The overall objective for these trials was to demonstrate that a newly developed technology could be used to locate, quantify and characterise the radiological hazards within two separate Hot Cells (B and C). For Hot Cell B, the primary objective of demonstrating that the technology could be used to locate, quantify and characterise 3 radiological sources has been met with 100% success. Despite more challenging conditions in Hot Cell C, two sources were detected and accurately located. To summarise, the technology performed extremely well with regards to detecting and locating radiation sources and, despite the challenging conditions, moderately well when assessing the relative energy and intensity of those sources.
More recently during Winter 2011 the technology was successfully deployed on the UK's Sellafield Site in order to map the whereabouts of numerous radioactive containers within a Shielded Cell Facility. This particular project involved the deployment of three devices and represents the first instance in which triangulation was demonstrated. Overall the technology performed well by locating and quantifying around a dozen sources. This work package was undertaken in partnership with Sellafield Ltd . | https://en.wikipedia.org/wiki/RadBall |
Radappertization is a form of food irradiation which applies a dose of ionizing radiation sufficient to reduce the number and activity of viable microorganisms to such an extent that very few, if any, are detectable in the treated food by any recognized method ( viruses being excepted).
No microbial spoilage or toxicity should become detectable in a food so treated, regardless of the conditions under which it is stored, provided the packaging remains undamaged. The required dose is usually in the range of 25-45 kiloGrays . [ 1 ] The shelf life of radappertized foods correctly packaged will mainly depend on the service life of the packaging material and its barrier properties.
Radappertization is derived from the combination of rad iation and Appert , the name of the French scientist and engineer who invented sterilized food for the troops of Napoleon .
This cooking article about preparation methods for food and drink is a stub . You can help Wikipedia by expanding it .
This nuclear technology article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Radappertization |
Radar is a system that uses radio waves to determine the distance ( ranging ), direction ( azimuth and elevation angles ), and radial velocity of objects relative to the site. It is a radiodetermination method [ 1 ] used to detect and track aircraft , ships , spacecraft , guided missiles , motor vehicles , map weather formations , and terrain . The term RADAR was coined in 1940 by the United States Navy as an acronym for "radio detection and ranging". [ 2 ] [ 3 ] [ 4 ] [ 5 ] [ 6 ] The term radar has since entered English and other languages as an anacronym , a common noun, losing all capitalization .
A radar system consists of a transmitter producing electromagnetic waves in the radio or microwaves domain, a transmitting antenna , a receiving antenna (often the same antenna is used for transmitting and receiving) and a receiver and processor to determine properties of the objects. Radio waves (pulsed or continuous) from the transmitter reflect off the objects and return to the receiver, giving information about the objects' locations and speeds. This device was developed secretly for military use by several countries in the period before and during World War II . A key development was the cavity magnetron in the United Kingdom , which allowed the creation of relatively small systems with sub-meter resolution.
The modern uses of radar are highly diverse, including air and terrestrial traffic control, radar astronomy , air-defense systems , anti-missile systems , marine radars to locate landmarks and other ships, aircraft anti-collision systems, ocean surveillance systems, outer space surveillance and rendezvous systems, meteorological precipitation monitoring, radar remote sensing , altimetry and flight control systems , guided missile target locating systems, self-driving cars , and ground-penetrating radar for geological observations. Modern high tech radar systems use digital signal processing and machine learning and are capable of extracting useful information from very high noise levels.
Other systems which are similar to radar make use of other parts of the electromagnetic spectrum . One example is lidar , which uses predominantly infrared light from lasers rather than radio waves. With the emergence of driverless vehicles, radar is expected to assist the automated platform to monitor its environment, thus preventing unwanted incidents. [ 7 ]
As early as 1886, German physicist Heinrich Hertz showed that radio waves could be reflected from solid objects. In 1895, Alexander Popov , a physics instructor at the Imperial Russian Navy school in Kronstadt , developed an apparatus using a coherer tube for detecting distant lightning strikes. The next year, he added a spark-gap transmitter . In 1897, while testing this equipment for communicating between two ships in the Baltic Sea , he took note of an interference beat caused by the passage of a third vessel. In his report, Popov wrote that this phenomenon might be used for detecting objects, but he did nothing more with this observation. [ 8 ]
The German inventor Christian Hülsmeyer was the first to use radio waves to detect "the presence of distant metallic objects". In 1904, he demonstrated the feasibility of detecting a ship in dense fog, but not its distance from the transmitter. [ 9 ] He obtained a patent [ 10 ] for his detection device in April 1904 and later a patent [ 11 ] for a related amendment for estimating the distance to the ship. He also obtained a British patent on 23 September 1904 [ 12 ] for a full radar system, that he called a telemobiloscope . It operated on a 50 cm wavelength and the pulsed radar signal was created via a spark-gap. His system already used the classic antenna setup of horn antenna with parabolic reflector and was presented to German military officials in practical tests in Cologne and Rotterdam harbour but was rejected. [ 13 ]
In 1915, Robert Watson-Watt used radio technology to provide advance warning of thunderstorms to airmen [ 14 ] [ 15 ] and during the 1920s went on to lead the U.K. research establishment to make many advances using radio techniques, including the probing of the ionosphere and the detection of lightning at long distances. Through his lightning experiments, Watson-Watt became an expert on the use of radio direction finding before turning his inquiry to shortwave transmission. Requiring a suitable receiver for such studies, he told the "new boy" Arnold Frederic Wilkins to conduct an extensive review of available shortwave units. Wilkins would select a General Post Office model after noting its manual's description of a "fading" effect (the common term for interference at the time) when aircraft flew overhead.
By placing a transmitter and receiver on opposite sides of the Potomac River in 1922, U.S. Navy researchers A. Hoyt Taylor and Leo C. Young discovered that ships passing through the beam path caused the received signal to fade in and out. Taylor submitted a report, suggesting that this phenomenon might be used to detect the presence of ships in low visibility, but the Navy did not immediately continue the work. Eight years later, Lawrence A. Hyland at the Naval Research Laboratory (NRL) observed similar fading effects from passing aircraft; this revelation led to a patent application [ 16 ] as well as a proposal for further intensive research on radio-echo signals from moving targets to take place at NRL, where Taylor and Young were based at the time. [ 17 ]
Similarly, in the UK, L. S. Alder took out a secret provisional patent for Naval radar in 1928. [ 18 ] W.A.S. Butement and P. E. Pollard developed a breadboard test unit, operating at 50 cm (600 MHz) and using pulsed modulation which gave successful laboratory results. In January 1931, a writeup on the apparatus was entered in the Inventions Book maintained by the Royal Engineers. This is the first official record in Great Britain of the technology that was used in coastal defence and was incorporated into Chain Home as Chain Home (low) . [ 19 ] [ 20 ]
Before the Second World War , researchers in the United Kingdom, France , Germany , Italy , Japan , the Netherlands , [ 21 ] the Soviet Union , and the United States, independently and in great secrecy, developed technologies that led to the modern version of radar. Australia, Canada, New Zealand, and South Africa followed prewar Great Britain's radar development, Hungary and Sweden generated its radar technology during the war. [ citation needed ]
In France in 1934, following systematic studies on the split-anode magnetron , the research branch of the Compagnie générale de la télégraphie sans fil (CSF) headed by Maurice Ponte with Henri Gutton, Sylvain Berline and M. Hugon, began developing an obstacle-locating radio apparatus, aspects of which were installed on the ocean liner Normandie in 1935. [ 22 ] [ 23 ]
During the same period, Soviet military engineer P.K. Oshchepkov , in collaboration with the Leningrad Electrotechnical Institute , produced an experimental apparatus, RAPID, capable of detecting an aircraft within 3 km of a receiver. [ 24 ] The Soviets produced their first mass production radars RUS-1 and RUS-2 Redut in 1939 but further development was slowed following the arrest of Oshchepkov and his subsequent gulag sentence. In total, only 607 Redut stations were produced during the war. The first Russian airborne radar, Gneiss-2 , entered into service in June 1943 on Pe-2 dive bombers. More than 230 Gneiss-2 stations were produced by the end of 1944. [ 25 ] The French and Soviet systems, however, featured continuous-wave operation that did not provide the full performance ultimately synonymous with modern radar systems.
Full radar evolved as a pulsed system, and the first such elementary apparatus was demonstrated in December 1934 by the American Robert M. Page , working at the Naval Research Laboratory . [ 26 ] The following year, the United States Army successfully tested a primitive surface-to-surface radar to aim coastal battery searchlights at night. [ 27 ] This design was followed by a pulsed system demonstrated in May 1935 by Rudolf Kühnhold and the firm GEMA [ de ] in Germany and then another in June 1935 by an Air Ministry team led by Robert Watson-Watt in Great Britain.
In 1935, Watson-Watt was asked to judge recent reports of a German radio-based death ray and turned the request over to Wilkins. Wilkins returned a set of calculations demonstrating the system was basically impossible. When Watson-Watt then asked what such a system might do, Wilkins recalled the earlier report about aircraft causing radio interference. This revelation led to the Daventry Experiment of 26 February 1935, using a powerful BBC shortwave transmitter as the source and their GPO receiver setup in a field while a bomber flew around the site. When the plane was clearly detected, Hugh Dowding , the Air Member for Supply and Research , was very impressed with their system's potential and funds were immediately provided for further operational development. [ 28 ] Watson-Watt's team patented the device in patent GB593017. [ 29 ] [ 30 ] [ 31 ]
Development of radar greatly expanded on 1 September 1936, when Watson-Watt became superintendent of a new establishment under the British Air Ministry , Bawdsey Research Station located in Bawdsey Manor , near Felixstowe, Suffolk. Work there resulted in the design and installation of aircraft detection and tracking stations called " Chain Home " along the East and South coasts of England in time for the outbreak of World War II in 1939. This system provided the vital advance information that helped the Royal Air Force win the Battle of Britain ; without it, significant numbers of fighter aircraft, which Great Britain did not have available, would always have needed to be in the air to respond quickly. The radar formed part of the " Dowding system " for collecting reports of enemy aircraft and coordinating the response.
Given all required funding and development support, the team produced working radar systems in 1935 and began deployment. By 1936, the first five Chain Home (CH) systems were operational and by 1940 stretched across the entire UK including Northern Ireland. Even by standards of the era, CH was crude; instead of broadcasting and receiving from an aimed antenna, CH broadcast a signal floodlighting the entire area in front of it, and then used one of Watson-Watt's own radio direction finders to determine the direction of the returned echoes. This fact meant CH transmitters had to be much more powerful and have better antennas than competing systems but allowed its rapid introduction using existing technologies.
A key development was the cavity magnetron in the UK, which allowed the creation of relatively small systems with sub-meter resolution. Britain shared the technology with the U.S. during the 1940 Tizard Mission . [ 32 ] [ 33 ]
In April 1940, Popular Science showed an example of a radar unit using the Watson-Watt patent in an article on air defence. [ 34 ] Also, in late 1941 Popular Mechanics had an article in which a U.S. scientist speculated about the British early warning system on the English east coast and came close to what it was and how it worked. [ 35 ] Watson-Watt was sent to the U.S. in 1941 to advise on air defense after Japan's attack on Pearl Harbor . [ 36 ] Alfred Lee Loomis organized the secret MIT Radiation Laboratory at Massachusetts Institute of Technology , Cambridge, Massachusetts which developed microwave radar technology in the years 1941–45. Later, in 1943, Page greatly improved radar with the monopulse technique that was used for many years in most radar applications. [ 37 ]
The war precipitated research to find better resolution, more portability, and more features for radar, including small, lightweight sets to equip night fighters ( aircraft interception radar ) and maritime patrol aircraft ( air-to-surface-vessel radar ), and complementary navigation systems like Oboe used by the RAF's Pathfinder .
The information provided by radar includes the bearing and range (and therefore position) of the object from the radar scanner. It is thus used in many different fields where the need for such positioning is crucial. The first use of radar was for military purposes: to locate air, ground and sea targets. This evolved in the civilian field into applications for aircraft, ships, and automobiles. [ 38 ] [ 39 ]
In aviation , aircraft can be equipped with radar devices that warn of aircraft or other obstacles in or approaching their path, display weather information, and give accurate altitude readings. The first commercial device fitted to aircraft was a 1938 Bell Lab unit on some United Air Lines aircraft. [ 35 ] Aircraft can land in fog at airports equipped with radar-assisted ground-controlled approach systems in which the plane's position is observed on precision approach radar screens by operators who thereby give radio landing instructions to the pilot, maintaining the aircraft on a defined approach path to the runway. Military fighter aircraft are usually fitted with air-to-air targeting radars, to detect and target enemy aircraft. In addition, larger specialized military aircraft carry powerful airborne radars to observe air traffic over a wide region and direct fighter aircraft towards targets. [ 40 ]
Marine radars are used to measure the bearing and distance of ships to prevent collision with other ships, to navigate, and to fix their position at sea when within range of shore or other fixed references such as islands, buoys, and lightships. In port or in harbour, vessel traffic service radar systems are used to monitor and regulate ship movements in busy waters. [ 41 ]
Meteorologists use radar to monitor precipitation and wind. It has become the primary tool for short-term weather forecasting and watching for severe weather such as thunderstorms , tornadoes , winter storms , precipitation types, etc. Geologists use specialized ground-penetrating radars to map the composition of Earth's crust . Police forces use radar guns to monitor vehicle speeds on the roads. Automotive radars are used for adaptive cruise control and emergency braking on vehicles by ignoring stationary roadside objects that could cause incorrect brake application and instead measuring moving objects to prevent collision with other vehicles. As part of Intelligent Transport Systems , fixed-position stopped vehicle detection (SVD) radars are mounted on the roadside to detect stranded vehicles, obstructions and debris by inverting the automotive radar approach and ignoring moving objects. [ 42 ] Smaller radar systems are used to detect human movement . Examples are breathing pattern detection for sleep monitoring [ 43 ] and hand and finger gesture detection for computer interaction. [ 44 ] Automatic door opening, light activation and intruder sensing are also common.
A radar system has a transmitter that emits radio waves known as radar signals in predetermined directions. When these signals contact an object they are usually reflected or scattered in many directions, although some of them will be absorbed and penetrate into the target. Radar signals are reflected especially well by materials of considerable electrical conductivity —such as most metals, seawater , and wet ground. This makes the use of radar altimeters possible in certain cases. The radar signals that are reflected back towards the radar receiver are the desirable ones that make radar detection work. If the object is moving either toward or away from the transmitter, there will be a slight change in the frequency of the radio waves due to the Doppler effect .
Radar receivers are usually, but not always, in the same location as the transmitter. The reflected radar signals captured by the receiving antenna are usually very weak. They can be strengthened by electronic amplifiers . More sophisticated methods of signal processing are also used in order to recover useful radar signals.
The weak absorption of radio waves by the medium through which they pass is what enables radar sets to detect objects at relatively long ranges—ranges at which other electromagnetic wavelengths, such as visible light , infrared light , and ultraviolet light , are too strongly attenuated. Weather phenomena, such as fog, clouds, rain, falling snow, and sleet, that block visible light are usually transparent to radio waves. Certain radio frequencies that are absorbed or scattered by water vapour, raindrops, or atmospheric gases (especially oxygen) are avoided when designing radars, except when their detection is intended.
Radar relies on its own transmissions rather than light from the Sun or the Moon, or from electromagnetic waves emitted by the target objects themselves, such as infrared radiation (heat). This process of directing artificial radio waves towards objects is called illumination , although radio waves are invisible to the human eye as well as optical cameras.
If electromagnetic waves travelling through one material meet another material, having a different dielectric constant or diamagnetic constant from the first,
the waves will reflect or scatter from the boundary between the materials. This means that a solid object in air or in a vacuum , or a significant change in atomic density between the object and what is surrounding it, will usually scatter radar (radio) waves from its surface. This is particularly true for electrically conductive materials such as metal and carbon fibre, making radar well-suited to the detection of aircraft and ships. Radar absorbing material , containing resistive and sometimes magnetic substances, is used on military vehicles to reduce radar reflection . This is the radio equivalent of painting something a dark colour so that it cannot be seen by the eye at night.
Radar waves scatter in a variety of ways depending on the size (wavelength) of the radio wave and the shape of the target. If the wavelength is much shorter than the target's size, the wave will bounce off in a way similar to the way light is reflected by a mirror . If the wavelength is much longer than the size of the target, the target may not be visible because of poor reflection. Low-frequency radar technology is dependent on resonances for detection, but not identification, of targets. This is described by Rayleigh scattering , an effect that creates Earth's blue sky and red sunsets. When the two length scales are comparable, there may be resonances . Early radars used very long wavelengths that were larger than the targets and thus received a vague signal, whereas many modern systems use shorter wavelengths (a few centimetres or less) that can image objects as small as a loaf of bread.
Short radio waves reflect from curves and corners in a way similar to glint from a rounded piece of glass. The most reflective targets for short wavelengths have 90° angles between the reflective surfaces . A corner reflector consists of three flat surfaces meeting like the inside corner of a cube. The structure will reflect waves entering its opening directly back to the source. They are commonly used as radar reflectors to make otherwise difficult-to-detect objects easier to detect. Corner reflectors on boats, for example, make them more detectable to avoid collision or during a rescue. For similar reasons, objects intended to avoid detection will not have inside corners or surfaces and edges perpendicular to likely detection directions, which leads to "odd" looking stealth aircraft . These precautions do not totally eliminate reflection because of diffraction , especially at longer wavelengths. Half wavelength long wires or strips of conducting material, such as chaff , are very reflective but do not direct the scattered energy back toward the source. The extent to which an object reflects or scatters radio waves is called its radar cross-section .
The power P r returning to the receiving antenna is given by the equation:
where
In the common case where the transmitter and the receiver are at the same location, R t = R r and the term R t ² R r ² can be replaced by R 4 , where R is the range.
This yields:
This shows that the received power declines as the fourth power of the range, which means that the received power from distant targets is relatively very small.
Additional filtering and pulse integration modifies the radar equation slightly for pulse-Doppler radar performance , which can be used to increase detection range and reduce transmit power.
The equation above with F = 1 is a simplification for transmission in a vacuum without interference. The propagation factor accounts for the effects of multipath and shadowing and depends on the details of the environment. In a real-world situation, pathloss effects are also considered.
Frequency shift is caused by motion that changes the number of wavelengths between the reflector and the radar. This can degrade or enhance radar performance depending upon how it affects the detection process. As an example, moving target indication can interact with Doppler to produce signal cancellation at certain radial velocities, which degrades performance.
Sea-based radar systems, semi-active radar homing , active radar homing , weather radar , military aircraft, and radar astronomy rely on the Doppler effect to enhance performance. This produces information about target velocity during the detection process. This also allows small objects to be detected in an environment containing much larger nearby slow moving objects.
Doppler shift depends upon whether the radar configuration is active or passive. Active radar transmits a signal that is reflected back to the receiver. Passive radar depends upon the object sending a signal to the receiver.
The Doppler frequency shift for active radar is as follows, where F D {\displaystyle F_{D}} is Doppler frequency, F T {\displaystyle F_{T}} is transmit frequency, V R {\displaystyle V_{R}} is radial velocity, and C {\displaystyle C} is the speed of light: [ 46 ]
Passive radar is applicable to electronic countermeasures and radio astronomy as follows:
Only the radial component of the velocity is relevant. When the reflector is moving at right angle to the radar beam, it has no relative velocity. Objects moving parallel to the radar beam produce the maximum Doppler frequency shift.
When the transmit frequency ( F T {\displaystyle F_{T}} ) is pulsed, using a pulse repeat frequency of F R {\displaystyle F_{R}} , the resulting frequency spectrum will contain harmonic frequencies above and below F T {\displaystyle F_{T}} with a distance of F R {\displaystyle F_{R}} . As a result, the Doppler measurement is only non-ambiguous if the Doppler frequency shift is less than half of F R {\displaystyle F_{R}} , called the Nyquist frequency , since the returned frequency otherwise cannot be distinguished from shifting of a harmonic frequency above or below, thus requiring:
Or when substituting with F D {\displaystyle F_{D}} :
As an example, a Doppler weather radar with a pulse rate of 2 kHz and transmit frequency of 1 GHz can reliably measure weather speed up to at most 150 m/s (340 mph), thus cannot reliably determine radial velocity of aircraft moving 1,000 m/s (2,200 mph).
In all electromagnetic radiation , the electric field is perpendicular to the direction of propagation, and the electric field direction is the polarization of the wave. For a transmitted radar signal, the polarization can be controlled to yield different effects. Radars use horizontal, vertical, linear, and circular polarization to detect different types of reflections. For example, circular polarization is used to minimize the interference caused by rain. Linear polarization returns usually indicate metal surfaces. Random polarization returns usually indicate a fractal surface, such as rocks or soil, and are used by navigation radars.
A radar beam follows a linear path in vacuum but follows a somewhat curved path in atmosphere due to variation in the refractive index of air, which is called the radar horizon . Even when the beam is emitted parallel to the ground, the beam rises above the ground as the curvature of the Earth sinks below the horizon. Furthermore, the signal is attenuated by the medium the beam crosses, and the beam disperses.
The maximum range of conventional radar can be limited by a number of factors:
Signal noise is an internal source of random variations in the signal, which is generated by all electronic components.
Reflected signals decline rapidly as distance increases, so noise introduces a radar range limitation. The noise floor and signal-to-noise ratio are two different measures of performance that affect range performance. Reflectors that are too far away produce too little signal to exceed the noise floor and cannot be detected. Detection requires a signal that exceeds the noise floor by at least the signal-to-noise ratio.
Noise typically appears as random variations superimposed on the desired echo signal received in the radar receiver. The lower the power of the desired signal, the more difficult it is to discern it from the noise. The noise figure is a measure of the noise produced by a receiver compared to an ideal receiver, and this needs to be minimized.
Shot noise is produced by electrons in transit across a discontinuity, which occurs in all detectors. Shot noise is the dominant source in most receivers. There will also be flicker noise caused by electron transit through amplification devices, which is reduced using heterodyne amplification. Another reason for heterodyne processing is that for fixed fractional bandwidth, the instantaneous bandwidth increases linearly in frequency. This allows improved range resolution. The one notable exception to heterodyne (downconversion) radar systems is ultra-wideband radar. Here a single cycle, or transient wave, is used similar to UWB communications, see List of UWB channels .
Noise is also generated by external sources, most importantly the natural thermal radiation of the background surrounding the target of interest. In modern radar systems, the internal noise is typically about equal to or lower than the external noise. An exception is if the radar is aimed upwards at clear sky, where the scene is so "cold" that it generates very little thermal noise . The thermal noise is given by k B T B , where T is temperature, B is bandwidth (post matched filter) and k B is the Boltzmann constant . There is an appealing intuitive interpretation of this relationship in a radar. Matched filtering allows the entire energy received from a target to be compressed into a single bin (be it a range, Doppler, elevation, or azimuth bin). On the surface it appears that then within a fixed interval of time, perfect, error free, detection could be obtained. This is done by compressing all energy into an infinitesimal time slice. What limits this approach in the real world is that, while time is arbitrarily divisible, current is not. The quantum of electrical energy is an electron, and so the best that can be done is to match filter all energy into a single electron. Since the electron is moving at a certain temperature ( Planck spectrum ) this noise source cannot be further eroded. Ultimately, radar, like all macro-scale entities, is profoundly impacted by quantum theory.
Noise is random and target signals are not. Signal processing can take advantage of this phenomenon to reduce the noise floor using two strategies. The kind of signal integration used with moving target indication can improve noise up to 2 {\displaystyle {\sqrt {2}}} for each stage. The signal can also be split among multiple filters for pulse-Doppler signal processing , which reduces the noise floor by the number of filters. These improvements depend upon coherence .
Radar systems must overcome unwanted signals in order to focus on the targets of interest. These unwanted signals may originate from internal and external sources, both passive and active. The ability of the radar system to overcome these unwanted signals defines its signal-to-noise ratio (SNR). SNR is defined as the ratio of the signal power to the noise power within the desired signal; it compares the level of a desired target signal to the level of background noise (atmospheric noise and noise generated within the receiver). The higher a system's SNR the better it is at discriminating actual targets from noise signals.
Clutter refers to radio frequency (RF) echoes returned from targets which are uninteresting to radar operators. Such targets include man-made objects such as buildings and — intentionally — by radar countermeasures such as chaff . Such targets also include natural objects such as ground, sea, and — when not being tasked for meteorological purposes — precipitation , hail spike , dust storms , animals (especially birds), turbulence in the atmospheric circulation , and meteor trails. Radar clutter can also be caused by other atmospheric phenomena, such as disturbances in the ionosphere caused by geomagnetic storms or other space weather events. This phenomenon is especially apparent near the geomagnetic poles , where the action of the solar wind on the earth's magnetosphere produces convection patterns in the ionospheric plasma . [ 47 ] Radar clutter can degrade the ability of over-the-horizon radar to detect targets. [ 47 ] [ 48 ]
Some clutter may also be caused by a long radar waveguide between the radar transceiver and the antenna. In a typical plan position indicator (PPI) radar with a rotating antenna, this will usually be seen as a "sun" or "sunburst" in the center of the display as the receiver responds to echoes from dust particles and misguided RF in the waveguide. Adjusting the timing between when the transmitter sends a pulse and when the receiver stage is enabled will generally reduce the sunburst without affecting the accuracy of the range since most sunburst is caused by a diffused transmit pulse reflected before it leaves the antenna. Clutter is considered a passive interference source since it only appears in response to radar signals sent by the radar.
Clutter is detected and neutralized in several ways. Clutter tends to appear static between radar scans; on subsequent scan echoes, desirable targets will appear to move, and all stationary echoes can be eliminated. Sea clutter can be reduced by using horizontal polarization, while rain is reduced with circular polarization (meteorological radars wish for the opposite effect, and therefore use linear polarization to detect precipitation). Other methods attempt to increase the signal-to-clutter ratio.
Clutter moves with the wind or is stationary. Two common strategies to improve measures of performance in a clutter environment are:
The most effective clutter reduction technique is pulse-Doppler radar . Doppler separates clutter from aircraft and spacecraft using a frequency spectrum , so individual signals can be separated from multiple reflectors located in the same volume using velocity differences. This requires a coherent transmitter. Another technique uses a moving target indicator that subtracts the received signal from two successive pulses using phase to reduce signals from slow-moving objects. This can be adapted for systems that lack a coherent transmitter, such as time-domain pulse-amplitude radar .
Constant false alarm rate , a form of automatic gain control (AGC), is a method that relies on clutter returns far outnumbering echoes from targets of interest. The receiver's gain is automatically adjusted to maintain a constant level of overall visible clutter. While this does not help detect targets masked by stronger surrounding clutter, it does help to distinguish strong target sources. In the past, radar AGC was electronically controlled and affected the gain of the entire radar receiver. As radars evolved, AGC became computer-software-controlled and affected the gain with greater granularity in specific detection cells.
Clutter may also originate from multipath echoes from valid targets caused by ground reflection, atmospheric ducting or ionospheric reflection / refraction (e.g., anomalous propagation ). This clutter type is especially bothersome since it appears to move and behave like other normal (point) targets of interest. In a typical scenario, an aircraft echo is reflected from the ground below, appearing to the receiver as an identical target below the correct one. The radar may try to unify the targets, reporting the target at an incorrect height, or eliminating it on the basis of jitter or a physical impossibility. Terrain bounce jamming exploits this response by amplifying the radar signal and directing it downward. [ 49 ] These problems can be overcome by incorporating a ground map of the radar's surroundings and eliminating all echoes which appear to originate below ground or above a certain height. Monopulse can be improved by altering the elevation algorithm used at low elevation. In newer air traffic control radar equipment, algorithms are used to identify the false targets by comparing the current pulse returns to those adjacent, as well as calculating return improbabilities.
Radar jamming refers to radio frequency signals originating from sources outside the radar, transmitting in the radar's frequency and thereby masking targets of interest. Jamming may be intentional, as with an electronic warfare tactic, or unintentional, as with friendly forces operating equipment that transmits using the same frequency range. Jamming is considered an active interference source, since it is initiated by elements outside the radar and in general unrelated to the radar signals.
Jamming is problematic to radar since the jamming signal only needs to travel one way (from the jammer to the radar receiver) whereas the radar echoes travel two ways (radar-target-radar) and are therefore significantly reduced in power by the time they return to the radar receiver in accordance with inverse-square law . Jammers therefore can be much less powerful than their jammed radars and still effectively mask targets along the line of sight from the jammer to the radar ( mainlobe jamming ). Jammers have an added effect of affecting radars along other lines of sight through the radar receiver's sidelobes ( sidelobe jamming ).
Mainlobe jamming can generally only be reduced by narrowing the mainlobe solid angle and cannot fully be eliminated when directly facing a jammer which uses the same frequency and polarization as the radar. Sidelobe jamming can be overcome by reducing receiving sidelobes in the radar antenna design and by using an omnidirectional antenna to detect and disregard non-mainlobe signals. Other anti-jamming techniques are frequency hopping and polarization .
One way to obtain a distance measurement (ranging) is based on the time-of-flight : transmit a short pulse of radio signal (electromagnetic radiation) and measure the time it takes for the reflection to return. The distance is one-half the round trip time multiplied by the speed of the signal. The factor of one-half comes from the fact that the signal has to travel to the object and back again. Since radio waves travel at the speed of light , accurate distance measurement requires high-speed electronics.
In most cases, the receiver does not detect the return while the signal is being transmitted. Through the use of a duplexer, the radar switches between transmitting and receiving at a predetermined rate.
A similar effect imposes a maximum range as well. In order to maximize range, longer times between pulses should be used, referred to as a pulse repetition time, or its reciprocal, pulse repetition frequency.
These two effects tend to be at odds with each other, and it is not easy to combine both good short range and good long range in a single radar. This is because the short pulses needed for a good minimum range broadcast have less total energy, making the returns much smaller and the target harder to detect. This could be offset by using more pulses, but this would shorten the maximum range. So each radar uses a particular type of signal. Long-range radars tend to use long pulses with long delays between them, and short range radars use smaller pulses with less time between them. As electronics have improved many radars now can change their pulse repetition frequency, thereby changing their range. The newest radars fire two pulses during one cell, one for short range (about 10 km (6.2 miles)) and a separate signal for longer ranges (about 100 km (62 miles)).
Distance may also be measured as a function of time. The radar mile is the time it takes for a radar pulse to travel one nautical mile , reflect off a target, and return to the radar antenna. Since a nautical mile is defined as 1,852 m, then dividing this distance by the speed of light (299,792,458 m/s), and then multiplying the result by 2 yields a result of 12.36 μs in duration.
Another form of distance measuring radar is based on frequency modulation. In these systems, the frequency of the transmitted signal is changed over time. Since the signal takes a finite time to travel to and from the target, the received signal is a different frequency than what the transmitter is broadcasting at the time the reflected signal arrives back at the radar. By comparing the frequency of the two signals the difference can be easily measured. This is easily accomplished with very high accuracy even in 1940s electronics. A further advantage is that the radar can operate effectively at relatively low frequencies. This was important in the early development of this type when high-frequency signal generation was difficult or expensive.
This technique can be used in continuous wave radar and is often found in aircraft radar altimeters . In these systems a "carrier" radar signal is frequency modulated in a predictable way, typically varying up and down with a sine wave or sawtooth pattern at audio frequencies. The signal is then sent out from one antenna and received on another, typically located on the bottom of the aircraft, and the signal can be continuously compared using a simple beat frequency modulator that produces an audio frequency tone from the returned signal and a portion of the transmitted signal.
The modulation index riding on the receive signal is proportional to the time delay between the radar and the reflector. The frequency shift becomes greater with greater time delay. The frequency shift is directly proportional to the distance travelled. That distance can be displayed on an instrument, and it may also be available via the transponder . This signal processing is similar to that used in speed detecting Doppler radar. Example systems using this approach are AZUSA , MISTRAM , and UDOP .
Terrestrial radar uses low-power FM signals that cover a larger frequency range. The multiple reflections are analyzed mathematically for pattern changes with multiple passes creating a computerized synthetic image. Doppler effects are used which allows slow moving objects to be detected as well as largely eliminating "noise" from the surfaces of bodies of water.
The two techniques outlined above both have their disadvantages. The pulse timing technique has an inherent tradeoff in that the accuracy of the distance measurement is inversely related to the length of the pulse, while the energy, and thus direction range, is directly related. Increasing power for longer range while maintaining accuracy demands extremely high peak power, with 1960s early warning radars often operating in the tens of megawatts. The continuous wave methods spread this energy out in time and thus require much lower peak power compared to pulse techniques, but requires some method of allowing the sent and received signals to operate at the same time, often demanding two separate antennas.
The introduction of new electronics in the 1960s allowed the two techniques to be combined. It starts with a longer pulse that is also frequency modulated. Spreading the broadcast energy out in time means lower peak energies can be used, with modern examples typically on the order of tens of kilowatts. On reception, the signal is sent into a system that delays different frequencies by different times. The resulting output is a much shorter pulse that is suitable for accurate distance measurement, while also compressing the received energy into a much higher energy peak and thus improving the signal-to-noise ratio. The technique is largely universal on modern large radars.
Speed is the change in distance to an object with respect to time. Thus the existing system for measuring distance, combined with a memory capacity to see where the target last was, is enough to measure speed. At one time the memory consisted of a user making grease pencil marks on the radar screen and then calculating the speed using a slide rule . Modern radar systems perform the equivalent operation faster and more accurately using computers.
If the transmitter's output is coherent (phase synchronized), there is another effect that can be used to make almost instant speed measurements (no memory is required), known as the Doppler effect . Most modern radar systems use this principle into Doppler radar and pulse-Doppler radar systems ( weather radar , military radar). The Doppler effect is only able to determine the relative speed of the target along the line of sight from the radar to the target. Any component of target velocity perpendicular to the line of sight cannot be determined by using the Doppler effect alone, but it can be determined by tracking the target's azimuth over time.
It is possible to make a Doppler radar without any pulsing, known as a continuous-wave radar (CW radar), by sending out a very pure signal of a known frequency. CW radar is ideal for determining the radial component of a target's velocity. CW radar is typically used by traffic enforcement to measure vehicle speed quickly and accurately where the range is not important.
When using a pulsed radar, the variation between the phase of successive returns gives the distance the target has moved between pulses, and thus its speed can be calculated.
Other mathematical developments in radar signal processing include time-frequency analysis (Weyl Heisenberg or wavelet ), as well as the chirplet transform which makes use of the change of frequency of returns from moving targets ("chirp").
Pulse-Doppler signal processing includes frequency filtering in the detection process. The space between each transmit pulse is divided into range cells or range gates. Each cell is filtered independently much like the process used by a spectrum analyzer to produce the display showing different frequencies. Each different distance produces a different spectrum. These spectra are used to perform the detection process. This is required to achieve acceptable performance in hostile environments involving weather, terrain, and electronic countermeasures.
The primary purpose is to measure both the amplitude and frequency of the aggregate reflected signal from multiple distances. This is used with weather radar to measure radial wind velocity and precipitation rate in each different volume of air. This is linked with computing systems to produce a real-time electronic weather map. Aircraft safety depends upon continuous access to accurate weather radar information that is used to prevent injuries and accidents. Weather radar uses a low PRF . Coherency requirements are not as strict as those for military systems because individual signals ordinarily do not need to be separated. Less sophisticated filtering is required, and range ambiguity processing is not normally needed with weather radar in comparison with military radar intended to track air vehicles.
The alternate purpose is " look-down/shoot-down " capability required to improve military air combat survivability. Pulse-Doppler is also used for ground based surveillance radar required to defend personnel and vehicles. [ 50 ] [ 51 ] Pulse-doppler signal processing increases the maximum detection distance using less radiation close to aircraft pilots, shipboard personnel, infantry, and artillery. Reflections from terrain, water, and weather produce signals much larger than aircraft and missiles, which allows fast moving vehicles to hide using nap-of-the-earth flying techniques and stealth technology to avoid detection until an attack vehicle is too close to destroy. Pulse-Doppler signal processing incorporates more sophisticated electronic filtering that safely eliminates this kind of weakness. This requires the use of medium pulse-repetition frequency with phase coherent hardware that has a large dynamic range. Military applications require medium PRF which prevents range from being determined directly, and range ambiguity resolution processing is required to identify the true range of all reflected signals. Radial movement is usually linked with Doppler frequency to produce a lock signal that cannot be produced by radar jamming signals. Pulse-Doppler signal processing also produces audible signals that can be used for threat identification. [ 50 ]
Signal processing is employed in radar systems to reduce the radar interference effects . Signal processing techniques include moving target indication , Pulse-Doppler signal processing , moving target detection processors, correlation with secondary surveillance radar targets, space-time adaptive processing , and track-before-detect . Constant false alarm rate and digital terrain model processing are also used in clutter environments.
A track algorithm is a radar performance enhancement strategy. Tracking algorithms provide the ability to predict the future position of multiple moving objects based on the history of the individual positions being reported by sensor systems.
Historical information is accumulated and used to predict future position for use with air traffic control, threat estimation, combat system doctrine, gun aiming, and missile guidance. Position data is accumulated by radar sensors over the span of a few minutes.
There are four common track algorithms: [ 52 ]
Radar video returns from aircraft can be subjected to a plot extraction process whereby spurious and interfering signals are discarded. A sequence of target returns can be monitored through a device known as a plot extractor.
The non-relevant real time returns can be removed from the displayed information and a single plot displayed. In some radar systems, or alternatively in the command and control system to which the radar is connected, a radar tracker is used to associate the sequence of plots belonging to individual targets and estimate the targets' headings and speeds.
A radar's components are:
Radio signals broadcast from a single antenna will spread out in all directions, and likewise a single antenna will receive signals equally from all directions. This leaves the radar with the problem of deciding where the target object is located.
Early systems tended to use omnidirectional broadcast antennas , with directional receiver antennas which were pointed in various directions. For instance, the first system to be deployed, Chain Home, used two straight antennas at right angles for reception, each on a different display. The maximum return would be detected with an antenna at right angles to the target, and a minimum with the antenna pointed directly at it (end on). The operator could determine the direction to a target by rotating the antenna so one display showed a maximum while the other showed a minimum.
One serious limitation with this type of solution is that the broadcast is sent out in all directions, so the amount of energy in the direction being examined is a small part of that transmitted. To get a reasonable amount of power on the "target", the transmitting aerial should also be directional.
More modern systems use a steerable parabolic "dish" to create a tight broadcast beam, typically using the same dish as the receiver. Such systems often combine two radar frequencies in the same antenna in order to allow automatic steering, or radar lock .
Parabolic reflectors can be either symmetric parabolas or spoiled parabolas:
Symmetric parabolic antennas produce a narrow "pencil" beam in both the X and Y dimensions and consequently have a higher gain. The NEXRAD Pulse-Doppler weather radar uses a symmetric antenna to perform detailed volumetric scans of the atmosphere. Spoiled parabolic antennas produce a narrow beam in one dimension and a relatively wide beam in the other. This feature is useful if target detection over a wide range of angles is more important than target location in three dimensions. Most 2D surveillance radars use a spoiled parabolic antenna with a narrow azimuthal beamwidth and wide vertical beamwidth. This beam configuration allows the radar operator to detect an aircraft at a specific azimuth but at an indeterminate height. Conversely, so-called "nodder" height finding radars use a dish with a narrow vertical beamwidth and wide azimuthal beamwidth to detect an aircraft at a specific height but with low azimuthal precision.
Applied similarly to the parabolic reflector, the slotted waveguide is moved mechanically to scan and is particularly suitable for non-tracking surface scan systems, where the vertical pattern may remain constant. Owing to its lower cost and less wind exposure, shipboard, airport surface, and harbour surveillance radars now use this approach in preference to a parabolic antenna.
Another method of steering is used in a phased array radar.
Phased array antennas are composed of evenly spaced similar antenna elements, such as aerials or rows of slotted waveguide. Each antenna element or group of antenna elements incorporates a discrete phase shift that produces a phase gradient across the array. For example, array elements producing a 5 degree phase shift for each wavelength across the array face will produce a beam pointed 5 degrees away from the centerline perpendicular to the array face. Signals travelling along that beam will be reinforced. Signals offset from that beam will be cancelled. The amount of reinforcement is antenna gain . The amount of cancellation is side-lobe suppression. [ 53 ]
Phased array radars have been in use since the earliest years of radar in World War II ( Mammut radar ), but electronic device limitations led to poor performance. Phased array radars were originally used for missile defence (see for example Safeguard Program ). They are the heart of the ship-borne Aegis Combat System and the Patriot Missile System . The massive redundancy associated with having a large number of array elements increases reliability at the expense of gradual performance degradation that occurs as individual phase elements fail. To a lesser extent, phased array radars have been used in weather surveillance . As of 2017, NOAA plans to implement a national network of multi-function phased array radars throughout the United States within 10 years, for meteorological studies and flight monitoring. [ 54 ]
Phased array antennas can be built to conform to specific shapes, like missiles, infantry support vehicles, ships, and aircraft.
As the price of electronics has fallen, phased array radars have become more common. Almost all modern military radar systems are based on phased arrays, where the small additional cost is offset by the improved reliability of a system with no moving parts. Traditional moving-antenna designs are still widely used in roles where cost is a significant factor such as air traffic surveillance and similar systems.
Phased array radars are valued for use in aircraft since they can track multiple targets. The first aircraft to use a phased array radar was the B-1B Lancer . The first fighter aircraft to use phased array radar was the Mikoyan MiG-31 . The MiG-31M's SBI-16 Zaslon passive electronically scanned array radar was considered to be the world's most powerful fighter radar, [ citation needed ] until the AN/APG-77 active electronically scanned array was introduced on the Lockheed Martin F-22 Raptor .
Phased-array interferometry or aperture synthesis techniques, using an array of separate dishes that are phased into a single effective aperture, are not typical for radar applications, although they are widely used in radio astronomy . Because of the thinned array curse , such multiple aperture arrays, when used in transmitters, result in narrow beams at the expense of reducing the total power transmitted to the target. In principle, such techniques could increase spatial resolution, but the lower power means that this is generally not effective.
Aperture synthesis by post-processing motion data from a single moving source, on the other hand, is widely used in space and airborne radar systems .
Antennas generally have to be sized similar to the wavelength of the operational frequency, normally within an order of magnitude . This provides a strong incentive to use shorter wavelengths as this will result in smaller antennas. Shorter wavelengths also result in higher resolution due to diffraction, meaning the shaped reflector seen on most radars can also be made smaller for any desired beamwidth.
Opposing the move to smaller wavelengths are a number of practical issues. For one, the electronics needed to produce high power very short wavelengths were generally more complex and expensive than the electronics needed for longer wavelengths or did not exist at all. Another issue is that the radar equation 's effective aperture figure means that for any given antenna (or reflector) size will be more efficient at longer wavelengths. Additionally, shorter wavelengths may interact with molecules or raindrops in the air, scattering the signal. Very long wavelengths also have additional diffraction effects that make them suitable for over the horizon radars . For this reason, a wide variety of wavelengths are used in different roles.
The traditional band names originated as code-names during World War II and are still in military and aviation use throughout the world. They have been adopted in the United States by the Institute of Electrical and Electronics Engineers and internationally by the International Telecommunication Union . Most countries have additional regulations to control which parts of each band are available for civilian or military use.
Other users of the radio spectrum, such as the broadcasting and electronic countermeasures industries, have replaced the traditional military designations with their own systems.
Modulators act to provide the waveform of the RF-pulse. There are two different radar modulator designs:
Coherent microwave amplifiers operating above 1,000 watts microwave output, like travelling wave tubes and klystrons , require liquid coolant . The electron beam must contain 5 to 10 times more power than the microwave output, which can produce enough heat to generate plasma. This plasma flows from the collector toward the cathode. The same magnetic focusing that guides the electron beam forces the plasma into the path of the electron beam but flowing in the opposite direction. This introduces FM modulation which degrades Doppler performance. To prevent this, liquid coolant with minimum pressure and flow rate is required, and deionized water is normally used in most high power surface radar systems that use Doppler processing. [ 57 ]
Coolanol ( silicate ester ) was used in several military radars in the 1970s. However, it is hygroscopic , leading to hydrolysis and formation of highly flammable alcohol. The loss of a U.S. Navy aircraft in 1978 was attributed to a silicate ester fire. [ 58 ] Coolanol is also expensive and toxic. The U.S. Navy has instituted a program named Pollution Prevention (P2) to eliminate or reduce the volume and toxicity of waste, air emissions, and effluent discharges. Because of this, Coolanol is used less often today.
Radar (also: RADAR ) is defined by article 1.100 of the International Telecommunication Union's (ITU) ITU Radio Regulations (RR) as: [ 59 ]
A radiodetermination system based on the comparison of reference signals with radio signals reflected, or retransmitted, from the position to be determined. Each radiodetermination system shall be classified by the radiocommunication service in which it operates permanently or temporarily. Typical radar utilizations are primary radar and secondary radar , these might operate in the radiolocation service or the radiolocation-satellite service .
Radar come in a variety of configurations in the emitter, the receiver, the antenna, wavelength, scan strategies, etc. | https://en.wikipedia.org/wiki/Radar |
A radar altimeter ( RA ), also called a radio altimeter ( RALT ), electronic altimeter , reflection altimeter , or low-range radio altimeter ( LRRA ), measures altitude above the terrain presently beneath an aircraft or spacecraft by timing how long it takes a beam of radio waves to travel to ground, reflect, and return to the craft. This type of altimeter provides the distance between the antenna and the ground directly below it, in contrast to a barometric altimeter which provides the distance above a defined vertical datum , usually mean sea level .
As the name implies, radar ( ra dio d etection a nd r anging) is the underpinning principle of the system. The system transmits radio waves down to the ground and measures the time it takes them to be reflected back up to the aircraft. The altitude above the ground is calculated from the radio waves' travel time and the speed of light . [ 1 ] Radar altimeters required a simple system for measuring the time-of-flight that could be displayed using conventional instruments, as opposed to a cathode ray tube normally used on early radar systems.
To do this, the transmitter sends a frequency modulated signal that changes in frequency over time, ramping up and down between two frequency limits, F min and F max over a given time, T. In the first units, this was accomplished using an LC tank with a tuning capacitor driven by a small electric motor. The output is then mixed with the radio frequency carrier signal and sent out the transmission antenna. [ 1 ]
Since the signal takes some time to reach the ground and return, the frequency of the received signal is slightly delayed relative to the signal being sent out at that instant. The difference in these two frequencies can be extracted in a frequency mixer , and because the difference in the two signals is due to the delay reaching the ground and back, the resulting output frequency encodes the altitude. The output is typically on the order of hundreds of cycles per second, not megacycles, and can easily be displayed on analog instruments. [ 2 ] This technique is known as Frequency Modulated Continuous-wave radar .
Radar altimeters normally work in the E band , K a band , or, for more advanced sea-level measurement, S band . Radar altimeters also provide a reliable and accurate method of measuring height above water, when flying long sea-tracks. These are critical for use when operating to and from oil rigs. [ clarification needed ] [ citation needed ]
The altitude specified by the device is not the indicated altitude of the standard barometric altimeter. A radar altimeter measures absolute altitude : the height " Above Ground Level " (AGL).
As of 2010 [update] , all commercial radar altimeters use linear frequency-modulated continuous-wave (LFMCW or FMCW) and about 25,000 aircraft in the US have at least one radio altimeter. [ 3 ] [ 4 ]
The underlying concept of the radar altimeter was developed independent of the wider radar field, and originates in a study of long-distance telephony at Bell Labs . During the 1910s, Bell Telephone was struggling with the reflection of signals caused by changes in impedance in telephone lines, typically where equipment connected to the wires. This was especially significant at repeater stations, where poorly matched impedances would reflect large amounts of the signal and made long-distance telephony difficult. [ 5 ]
Engineers noticed that the reflections appeared to have a "humpy" pattern to them; for any given signal frequency, the problem would only be significant if the devices were located at specific points in the line. This led to the idea of sending a test signal into the line and then changing its frequency until significant echos were seen. This would reveal the approximate distance to the device, allowing it to be identified and fixed. [ 5 ]
Lloyd Espenschied was working at Bell Labs when he conceived using this same phenomenon to measure distances in a wire. One of his first developments in this field was a 1919 patent (granted 1924) [ 6 ] on the idea of sending a signal into railway tracks and measuring the distance to discontinuities. These could be used to detect broken tracks, or if the distance was changing more rapidly than the speed of the train, other trains on the same line. [ 5 ]
During this same period there was a great debate in physics over the nature of radio propagation. Guglielmo Marconi 's successful trans-Atlantic transmissions appeared to be impossible. Studies of radio signals demonstrated they travelled in straight lines, at least over long distances, so the broadcast from Cornwall should have disappeared into space instead of being received in Newfoundland . In 1902, Oliver Heaviside in the UK and Arthur Kennelly in the USA independently postulated the existence of an ionized layer in the upper atmosphere that was bouncing the signal back to the ground so it could be received. This became known as the Heaviside layer . [ 7 ]
While an attractive idea, direct evidence was lacking. In 1924, Edward Appleton and Miles Barnett were able to demonstrate the existence of such a layer in a series of experiments carried out in partnership with the BBC . After scheduled transmissions had ended for the day, a BBC transmitter in Bournemouth sent out a signal that slowly increased in frequency. This was picked up by Appleton's receiver in Oxford , where two signals appeared. One was the direct signal from the station, the groundwave, while the other was received later in time after it travelled to the Heaviside layer and back again, the skywave. [ 7 ]
Accurately measuring the distance travelled by the skywave, proving it was actually in the sky, was necessary for the demonstration. This was the purpose of the changing frequency. Since the ground signal travelled a shorter distance, it was more recent and thus closer to the frequency being sent at that instant. The skywave, having to travel a longer distance, was delayed, and was thus the frequency as it was some time ago. By mixing the two in a frequency mixer, a third signal is produced that has its own unique frequency that encodes the difference in the two inputs. Since in this case the difference is due to the longer path, the resulting frequency directly reveals the path length. Although technically more challenging, this was ultimately the same basic technique being used by Bell to measure the distance to the reflectors in the wire. [ 7 ]
In 1929, William Littell Everitt , a professor at Ohio State University , began considering the use of Appleton's basic technique as the basis for an altimeter system. He assigned the work to two seniors, Russell Conwell Newhouse and M. W. Havel. Their experimental system was more in common with the earlier work at Bell, using changes in frequency to measure the distance to the end of wires. The two used it as the basis for a joint senior thesis in 1929. [ 8 ]
Everitt disclosed the concept to the US Patent Office , but did not file a patent at that time. He then approached the Daniel Guggenheim Fund for the Promotion of Aeronautics for development funding. Jimmy Doolittle , secretary of the Foundation, approached Vannevar Bush of Bell Labs to pass judgment. Bush was skeptical that the system could be developed at that time, but nevertheless suggested the Foundation fund development of a working model. This allowed Newhouse to build an experimental machine which formed the basis of his 1930 Master's thesis, in partnership with J. D. Corley. [ 8 ] [ 9 ]
The device was taken to Wright Field where it was tested by Albert Francis Hegenberger , a noted expert in aircraft navigation. Hegenberger found that the system worked as advertised, but stated that it would have to work at higher frequencies to be practical. [ 8 ] [ a ]
Espenschied had also been considering the use of Appleton's idea for altitude measurement. In 1926 he suggested the idea both as a way to measure altitude as well as a forward-looking system for terrain avoidance and collision detection. However, at that time the frequency of available radio systems even in what was known as shortwave was calculated to be fifty times lower than what would be needed for a practical system. [ 5 ] [ 9 ]
Espenschied eventually filed a patent on the idea in 1930. [ 9 ] By this time, Newhouse had left Ohio State and taken a position at Bell Labs. Here he met Peter Sandretto , who was also interested in radio navigation topics. Sandretto left Bell in 1932 to become the Superintendent of Communications at United Air Lines (UAL), where he led the development of commercial radio systems. [ 8 ]
Espenschied's patent was not granted until 1936, [ 10 ] and its publication generated intense interest. Around the same time, Bell Labs had been working on new tube designs that were capable of delivering between 5 and 10 Watts at up to 500 MHz, perfect for the role. [ 9 ] This led Sandretto to contact Bell about the idea, and in 1937 a partnership between Bell Labs and UAL was formed to build a practical version. Led by Newhouse, a team had a working model in testing in early 1938, and Western Electric (Bell's manufacturing division) was already gearing up for a production model. Newhouse also filed several patents on improvements in technique based on this work. [ 11 ]
The system was publicly announced on 8 and 9 October 1938. [ 12 ] During World War II , mass production was taken up by RCA , who produced them under the names ABY-1 and RC-24. In the post-war era, many companies took up production and it became a standard instrument on many aircraft as blind landing became commonplace. [ 11 ]
A paper describing the system was published jointly by Espenschied and Newhouse the next year. The paper explores sources of error and concludes that the worst-case built-in scenario was on the order of 9%, [ 13 ] but this might be as high as 10% when flying over rough terrain like the built-up areas of cities. [ 13 ]
During early flights of the system, it was noticed that the pattern of the returns as seen on an oscilloscope was distinct for different types of terrain below the aircraft. This opened the possibility of all sorts of other uses for the same technology, including ground-scanning and navigation. However, these concepts were not able to be explored by Bell at the time. [ 12 ]
It had been known since the late 1800s that metal and water made excellent reflectors of radio signals, and there had been many attempts to build ship, train and iceberg detectors over the years since that time. Most of these had significant practical limitations due to the use of low-frequency signals that demanded large antennas to provide reasonable performance. The Bell unit, operating at a base frequency of 450 MHz, was among the highest frequency systems of its era which made it much more useful. [ 13 ] [ b ]
In Canada, the National Research Council (NRC) began working on an airborne radar system using the Bell altimeter as its basis. This came as a great surprise to British researchers when they visited in October 1940 as part of the Tizard Mission , as the British believed at that time that they were the only ones working on the concept. Seeing that the idea was already not a secret, the Mission introduced the NRC to its production quality designs. The Bell-based design was abandoned in favour of building the fully developed British ASV Mark II design, which operated at much higher power levels. [ 14 ]
In France, researchers at IT&T 's French division were carrying out similar experiments on radar when the German invasion approached the labs in Paris. The labs were deliberately destroyed to prevent the research from falling into German hands. The German teams found the antennas in the rubble and demanded an explanation. The IT&T director of research deflected suspicion by showing them the altimeter unit on the cover of a magazine and admonishing them for not being up-to-date on the latest navigation techniques. [ 11 ]
Radar altimeters are frequently used by commercial aircraft for approach and landing, especially in low-visibility conditions (see instrument flight rules ) and automatic landings while they are in the glideslope capture mode below 200–300 ft (61–91 m) above ground level (AGL), [ 15 ] allowing the autopilot to know when to begin the flare maneuver . Radar altimeters give data to the autothrottle which is a part of the Flight Computer .
Radar altimeters generally only give readings up to 2,500 feet (760 m) (AGL).
Frequently, the weather radar can be directed downwards to give a reading from a longer range, up to 60,000 feet (18,000 m) AGL.
As of 2012 [update] , all airliners are equipped with at least two and possibly more radar altimeters, as they are essential to autoland capabilities. (As of 2012 [update] , determining height through other methods such as GPS is not permitted by regulations.) Older airliners from the 1960s (such as the British Aircraft Corporation BAC 1-11 ) and smaller airliners in the sub-50 seat class (such as the ATR 42 and BAe Jetstream series) are equipped with them.
Radar altimeters are an essential part in ground proximity warning systems (GPWS), warning the pilot if the aircraft is flying too low or descending too quickly. However, radar altimeters cannot see terrain directly ahead of the aircraft, only that below it; such functionality requires either knowledge of position and the terrain at that position or a forward looking terrain radar. Radar altimeter antennas have a fairly large main lobe of about 80° so that at bank angles up to about 40°, the radar detects the range from the aircraft to the ground (specifically to the nearest large reflecting object). This is because range is calculated based on the first signal return from each sampling period. It does not detect slant range until beyond about 40° of bank or pitch. This is not an issue for landing as pitch and roll do not normally exceed 20°.
Radio altimeters used in civil aviation operate in the IEEE C-band between 4.2 and 4.4 GHz. [ 16 ]
In early 2022, potential interference from 5G cell phone towers caused some flight delays and a few flight cancellations in the United States.
Radar altimeters are also used in military aircraft to fly quite low over the land and the sea to avoid radar detection and targeting by anti-aircraft guns or surface-to-air missiles . A related use of radar altimeter technology is terrain-following radar , which allows fighter bombers to fly at very low altitudes.
The F-111s of the Royal Australian Air Force and the U.S. Air Force have a forward-looking, terrain-following radar (TFR) system connected via digital computer to their automatic pilots . Beneath the nose radome are two separate TFR antennae, each providing individual information to the dual-channel TFR system. In case of a failure in that system, the F-111 has a back-up radar altimeter system, also connected to the automatic pilot. Then, if the F-111 ever dips below the preset minimum altitude (for example, 15 meters) for any reason, its automatic pilot is commanded to put the F-111 into a 2G fly-up (a steep nose-up climb ) to avoid crashing into terrain or water. Even in combat, the hazard of a collision is far greater than the danger of being detected by an enemy. Similar systems are used by F/A-18 Super Hornet aircraft operated by Australia and the United States.
The International Telecommunication Union (ITU) defines radio altimeters as “radionavigation equipment, on board an aircraft or spacecraft, used to determine the height of the aircraft or the spacecraft above the Earth's surface or another surface" in article 1.108 of the ITU Radio Regulations (RR). [ 17 ] Radionavigation equipment shall be classified by the radiocommunication service in which it operates permanently or temporarily. The use of radio altimeter equipment is categorised as a safety-of-life service , must be protected for interferences , and is an essential part of navigation . | https://en.wikipedia.org/wiki/Radar_altimeter |
Radar ornithology is the use of radar technology in studies of bird migration and in approaches to prevent bird strikes particularly to aircraft. The technique was developed from the observations of pale wisps seen moving on radar during the Second World War. These were termed as "angels", "ghosts", or "phantoms" in Britain and were later identified as being caused by migrating birds. Over time, the technology has been vastly improved with Doppler weather radars that allow the detection of birds, bats, as well as insects with resolution and sensitivity that is sufficient to quantify the speed of flaps that can sometimes aid in the identification of species.
According to David Lack , the earliest recorded use of radar in detecting birds came in 1940. The movements of gulls, herons and lapwings that caused some of the detentions was visually confirmed. It was however only in the 1950s through the work of Ernst Sutter at Zurich airport that more elusive "angels" were confirmed to be caused by small passerines. [ 1 ] David Lack was one of the pioneers of radar ornithology in England. [ 2 ]
Early radar ornithology mainly focused, due to limitations of the equipment, on the seasonality, timing, intensity, and direction of flocks of birds in migration. Modern weather radars can detect the wing area of the flying, the speed of flight, the frequency of wing beat, the direction, distance and altitude. [ 3 ] The sensitivity and modern analytical techniques now allows detection of flying insects as well. [ 4 ]
Radar has been used to study seasonal variations in starling roosting behaviour. [ 5 ] It has also been used to identify risks to aircraft operations at airports. [ 6 ] The technique has been in conservation applications such as being used to assess the risk to birds by proposed wind energy installations, to quantify the number of birds at roost or nesting sites. [ 7 ] | https://en.wikipedia.org/wiki/Radar_ornithology |
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