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blocks of atom records, such as TER and MODEL. Protein and nucleic acid chains are specified by the TER keyword, as well as a one-letter designation in the coordinate records. The chains are included one after another in the file, separated by a TER record to indicate that the chains |
are not physically connected to each other. Most molecular graphics programs look for this TER record so that they don't draw a bond to connect different chains. PDB format files use the MODEL keyword to indicate multiple molecules in a single file. This was initially created to archive coordinate sets |
that include several different models of the same structure, like the structural ensembles obtained in NMR analysis. When you view these files, you will see dozens of similar molecules all superimposed. The MODEL keyword is now also used in biological assembly files to separate the many symmetrical copies of the |
molecule that are generated from the asymmetric unit (For more information, see the tutorial on biological assemblies). Two useful coloring schemes allow you to explore the different chains in any given PDB file. First, you may color each chain differently to show the packing of different chains in the molecule |
as shown in the bottom image. Then, you can color each chain using a rainbow of colors from one end of the chain to the other to highlight its folding characteristics as shown at the top. Both of these methods are available in most molecular graphics programs. The molecule shown |
here is hemolysin from PDB entry 7ahl. If we were able to hold an atom rigidly fixed in one place, we could observe its distribution of electrons in an ideal situation. The image would be dense towards the center with the density falling off further from the nucleus. When you |
look at experimental electron density distributions, however, the electrons usually have a wider distribution than this ideal. This may be due to vibration of the atoms, or differences between the many different molecules in the crystal lattice. The observed electron density will include an average of all these small m... |
yielding a slightly smeared image of the molecule. These motions, and the resultant smearing of the electron density, are incorporated into the atomic model by a B-value or temperature factor. The amount of smearing is proportional to the magnitude of the B-value. Values under 10 create a model of the |
atom that is very sharp, indicating that the atom is not moving much and is in the same position in all of the molecules in the crystal. Values greater than 50 or so indicate that the atom is moving so much that it can barely been seen. This is often |
the case for atoms at the surface of proteins, where long sidechains are free to wag in the surrounding water. The example shown is from a myoglobin structure solved at a 2.0 Å resolution (PDB entry 1mbi). Two histidine amino acids are shown. On the left is HIS93, which coordinates |
with the iron atom and thus, is held firmly in place. It has B-values in the range of 15-20 -- notice how the contours nicely surround the whole amino acid, revealing a sharp electron density. On the right is HIS81, which is exposed on the surface of the protein and |
has higher B-values in the range of 22-74. Notice how the contours enclose a smaller space, showing a smaller region with high electron density for this amino acid because the overall electron density is weakly smeared in the space around the contours. These pictures are created using the Astex viewer, |
which is available on the Structure Summary page for this PDB entry (just click the "EDS" link in the "Experimental Method" section). The picture shows the whole molecule, with the atoms colored by the temperature factors. High values, indicating lots of motion, are in red and yellow, and low values |
are in blue. Notice that the interior of the protein has low B-values and the amino acids on the surface have higher values. You can click on the picture for an interactive Jmol view. Tip: Temperature factors are a measure of our confidence in the location of each atom. If |
you find an atom on the surface of a protein with a high temperature factor, keep in mind that this atom is probably moving a lot, and that the coordinates specified in the PDB file are only one possible snapshot of its location. Occupancy and Multiple Conformations Macromolecular crystals are |
composed of many individual molecules packed into a symmetrical arrangement. In some crystals, there are slight differences between each of these molecules. For instance, a sidechain on the surface may wag back and forth between several conformations, or a substrate may bind in two orientations in an active site, or |
a metal ion may be bound to only a few of the molecules. When researchers build the atomic model of these portions, they can use the occupancy to estimate the amount of each conformation that is observed in the crystal. For most atoms, the occupancy is given a value of |
1, indicating that the atom is found in all of the molecules in the same place in the crystal. However, if a metal ion binds to only half of the molecules in the crystal, the researcher will see a weak image of the ion in the electron density map, and |
can assign an occupancy of 0.5 in the PDB structure file for this atom. Occupancies are also commonly used to identify sidechains or ligands that are observed in multiple conformations. The occupancy value is used to indicate the fraction of molecules that have each of the conformations. Two (or more) |
atom records are included for each atom, with occupancies like 0.5 and 0.5, or 0.4 and 0.6, or other fractional occupancies that sum to a total of 1. The two images shown are taken from the high-resolution structure of myoglobin in entry 1a6m: glutamine 8 is on the left, and |
tyrosine 151 on the right. In both cases, the depositors interpreted the experimental data as showing two conformations of the amino acid, with occupancies of 0.57 and 0.43 for the glutamine, and 0.5 for each of the tyrosine conformations. The blue contours surround the regions with high electron density, and |
the atomic model is shown in sticks. These pictures are created using the Astex viewer, which is available on the Structure Summary page for this PDB entry (just click the "EDS" link in the "Experimental Method" section). The picture below of the whole myoglobin molecule is shown with all of |
the amino acids that have two conformations in the file. You can click on the picture for an interactive Jmol version. Tip: When dealing with PDB entries with multiple coordinates, you often need to pay close attention. It is not always possible to select just the "A" conformations and throw |
Thinking and Reasoning 2 (1):33 – 49 (1996) |Abstract||We postulate the Testing Principle : that individuals ''act like statisticians'' when they face uncertainty in a decision problem, ranking alternatives to the extent that available evidence allows. The Testing Principle implies that completeness of preferences, rat... |
uncertain acts in modified Ellsberg-type urn problems, with sample information about the uncertain urn. Our results show, consistent with the Testing Principle, that the uncertain urn is chosen more often when the sample size is larger, holding constant a measure of ambiguity (proportion of balls of unknown colour in t... |
42 (1):21-36. Ronald N. Giere (1970). An Orthodox Statistical Resolution of the Paradox of Confirmation. Philosophy of Science 37 (3):354-362. Patrick Maher (1999). Inductive Logic and the Ravens Paradox. Philosophy of Science 66 (1):50-70. Horacio Arlo-Costa & Jeffrey Helzner, Iterated Random Selection as Intermediate... |
Decision 66 (4):301-315. Katie Steele (2007). Distinguishing Indeterminate Belief From “Risk-Averse” Preferences. Synthese 158 (2):189 - 205. Horacio Arló-Costa & Jeffrey Helzner (2010). Ambiguity Aversion: The Explanatory Power of Indeterminate Probabilities. Synthese 172 (1). Jürgen Eichberger & David Kelsey (1999). ... |
the Biennial Meeting of the Philosophy of Science Association 1994:260 - 269. Added to index2009-02-11 Total downloads29 ( #42,416 of 549,122 ) Recent downloads (6 months)0 How can I increase my downloads? |
Like brush strokes on a canvas, ridges of color seem to flow across the Lagoon Nebula, a canvas nearly 3 light-years wide. The colors map emission from ionized gas in the nebula were recorded by the Hubble Space Telescope's Advanced Camera for Surveys. Also known as M8, the nebula is |
a star-forming region in the constellation Sagittarius. Hubble's remarkably sharp, close-up view reveals undulating shapes sculpted by the energetic light and winds from the region's new born stars. Of course, the Lagoon Nebula is a popular target for earthbound skygazers, too. Explore further: Collisions of coronal ma... |
An important discovery has been made with respect to the mystery of “handedness” in biomolecules. Researchers led by Sandra Pizzarello, a research professor at Arizona State University, found that some of the possible abiotic precursors to the origin of life on Earth have been shown to carry “handedness” in a larger nu... |
in this week’s Early Edition of the Proceedings of the National Academy of Sciences. The paper is titled, “Molecular asymmetry in extraterrestrial chemistry: Insights from a pristine meteorite,” and is co-authored by Pizzarello and Yongsong Huang and Marcelo Alexandre, of Brown University. Pizzarello, in ASU’s Departme... |
of a special group of meteorites that contain among a variety of compounds, amino acids that have identical counterparts in terrestrial biomolecules. These meteorites are fragments of asteroids that are about the same age as the solar system (roughly 4.5 billion years.) Scientists have long known that most compounds in... |
of DNA and RNA are “right-handed.” The mystery as to why this is the case, “parallels in many of its queries those that surround the origin of life,” said Pizzarello. Years ago Pizzarello and ASU professor emeritus John Cronin analyzed amino acids from the Murchison meteorite (which landed in Australia in 1969) that we... |
PNAS work was made possible by the finding in Antarctica of an exceptionally pristine meteorite. Antarctic ices are good “curators” of meteorites. After a meteorite falls -- and meteorites have been falling throughout the history of Earth -- it is quickly covered by snow and buried in the ice. Because these ices are in... |
a mountain, they will flow over the hill and bring meteorites to the surface. “Thanks to the pristine nature of this meteorite, we were able to demonstrate that other extraterrestrial amino acids carry the left-handed excesses in meteorites and, above all, that these excesses appear to signify that their precursor mole... |
other words, a molecular trait that defines life seems to have broader distribution as well as a long cosmic lineage.” “This study may provide an important clue to the origin of molecular asymmetry,” added Brown associate professor and co-author Huang. Source: Arizona State University Explore further: University of Ill... |
Industrial pipe systems are inaccessible and narrow. The pipes can be vertical and have junctions. Just as challenging, leakage points in the water system must be located, the condition of oil and gas pipelines must be checked and ventilation systems need to be cleaned. In the main, today’s robots are not that clever. ... |
few have active joints. Cybernetics and optical measurement scientists at SINTEF are working on a solution. Navigation by light and image With experience and knowledge acquired with snake robots Anna Konda and AiKo as a starting point, a team is now developing an intelligent pipe inspection robot on wheels that will be... |
location in the pipe system. The inspection robot will be able to move in pipes of various diameters, right down to 20 cm. Cybernetics scientists are developing the propulsion system while a team of optics scientists is working on the new robot’s visual system. “We are currently developing the vision system than will e... |
“In the meantime, we are using the lego robot Mindstormer to collect the data to train the vision system. This lego robot has a camera attached and moves around the pipe following a pre-programmed map. The next step will be to utilise the vision system as input to control the actual snake robot we are going to develop.... |
new robot’s vision is an off the shelf time-of-flight camera that provides a bathymetric chart of the pipe system using inflected light. “Combined with our algorithms, the robot will be able to navigate and move forward on its own,” says Thielemann. “The robot knows when a left or right turn is approaching and also con... |
carry out in different situations. Functions as a train “Given our previous work on snake robots, we have become good at controlling mechanisms that are linked,” says SINTEF cybernetics scientist Erik Kyrkjebø. “We now want to develop a robot with 10-11 joint modules, each with an identical pair of wheels cast in plast... |
can we put the camera and accelerator motor in two different joint modules? The robot will function as a train when operating horizontally. Such robots already exist, but we want to develop a robot that can climb too.” The scientists have designed several versions of the pipe inspection robot and have tested different ... |
compact. They have now come up with a design they have faith in. When the robot enters a vertical pipe, it lifts its head in the pipe and meets the pipe wall. It can then either move sideways with its abdomen against the pipe and twist itself upwards or it can topple backwards, attach itself to the pipe wall, in the sa... |
we would put our feet against a shaft wall to hold on, and then roll upwards. The scientists emphasise that the project is at the design stage. In June, two of the 11 joint modules will be tested to verify the concept and they hope to demonstrate a prototype model by the end of the year. This comprises just phase one o... |
development, but the enthusiastic scientists are confident of succeeding in the foreseeable future. The final version of the robot will be constructed of aluminium and is planned to be 1.5 m long. Source: Aase Dragland Explore further: NASA: Austin, calling Austin. 3-D pizzas to go |
A schematic of a blind quantum computer that could protect user's privacy. Image credit: Phillip Walther et al./Vienna University. Researchers worry that if quantum computers are realized in the next few years, only a few specialized facilities will be able to host them. This may leave users' privacy vulnerable. To |
This summer, Mount Diablo Unified School District's governing board will make sure district policies on bullying comply with state legislation known as Seth's Law, which went into effect on July |
1. Named for Seth Walsh, a 13-year-old in Tehachapi, Calif. who hanged himself in 2010 after being bullied for being gay, AB 9 requires public schools to have clear rules |
about preventing and punishing bullying. Here's the definition of bullying Mt. Diablo Unified staff shared with the school board in June: No student or group of students shall through physical, |
written, verbal, or other means harass, sexually harass, threaten, intimidate, cyberbully, cause bodily injury to, or commit hate violence against any other student or school personnel. Unwilling to force new |
costs on cash-strapped school districts, state lawmakers nixed language in the original bill that would have required staff to attend trainings on bullying. It falls on the California Department of |
Education to make sure school districts are following the new law, but with resources scarce, it will likely be difficult for the CDE to do much in the way of |
enforcement. That means administrators, teachers, parents and students will ultimately be responsible for addressing the problem of bullying in individual schools. What do you think about the culture in Pleasant |
Hill's secondary schools? Does school staff take bullying seriously? Do gay and lesbian students feel respected and safe? Tell us in the comments below.Suspensions for bullying, violence, intimidation or sexual |
harassment in 2010-2011 Total suspensions in 2010-2011 57 113 Source: California Department of Education During the 2010-2011 school year, researchers for the California Healthy Kids Survey asked around 5,600 secondary |
students in Mount Diablo Unified how they feel about their schools. The findings below are from the questions related to bullying.Mean rumors spread about you 2 or more times Sexual |
comments or jokes directed at you 2 or more times Been made fun of for the way you look or talk 2 or more times 7th Graders 23 percent 28 |
percent 27 percent 9th Graders 33 percent 34 percent 25 percent 11th Graders 20 percent 36 percent 24 percent Been pushed shoved or hit 2 or more times Been afraid |
of being beaten up 2 or more times Been in a physical fight 2 or more times 7th Graders 24 percent 12 percent 12 percent 9th Graders 15 percent 9 |
percent 9 percent 11th Graders 9 percent 7 percent 8 percent Source: California Healthy Kids Survey, 2010-2011 Want Pleasant Hill news delivered straight to your inbox? Sign up for our |
Railroads and ferries brought prosperity |A. B. Safford Memorial Museum in Cairo, Illinois, built in 1883| Cairo, Illinois, is at the extreme southern tip of Illinois, at the point where the Ohio and Mississippi Rivers converge. I always have mixed feelings as I drive through Cairo (pronounced "Kay-roh".) Sadly, the to... |
business district, empty lots suggest that many deteriorated buildings have been bulldozed and hauled away. Some old buildings, still standing, are candidates for the next demolition list. |I'm not sure if this church is in use.| Cairo became an important railroad hub after the Civil War, and the town enjoyed several d... |
rivers, and the ferry business was as important to local fortunes as the railroad and river-shipping businesses. |The Riverlore in Cairo, Illinois| Then in 1889, the Illinois Central Railroad completed the Cairo Rail Bridge across the Ohio River (image, another image). It was a masterpiece of engineering. The metal bri... |
was almost 4 miles long. Freight from Chicago could travel directly to New Orleans via the Cairo Rail Bridge -- a revolution in rail shipping, but a blow to Cairo. |More mansions in Cairo| Vehicles traveling in the Cairo area still used the ferries until two highway bridges were built -- the Mississippi River bridge (l... |
bridge (leading to Kentucky) in 1937. The bridges and roads connected a short distance south of Cairo, so travelers could quickly cross both rivers without even entering town. The loss of the railroad and ferry industries was significant, but it alone did not kill the town. By the early 1900s, other serious problems (r... |
century, these evils had a slow-but-deadly effect on the town. You can read about the darker side of Cairo's history at "Cairo, Illinois, Death by Racism." |Overgrowth and disrepair, too!| A photo I took inside the Customs House some years ago Seen at Wickliffe, Kentucky |Ohio River bridge, just south of Cairo| |
This page is being updated... | Finedust | House dust mites and especially their pellets are held responsible for certain allergies and asthma. What is known ? Claims that carpets were breeding grounds for dust mites have proven false. In |
carpets, dust mites can easily be kept under control with regular ventilation and proper cleaning. Carpet is not the ideal habitat for mites. Carpet prevents the allergic material from being released into the atmosphere by holding the fine allergen particles |
in the pile until next vacuuming. Hard surfaces, on the contrary, allow the allergens to become easily airborne with the slightest draught or vibration. Thus, carpet improves the quality of life of allergic persons. It is not the floor covering, |
but the temperature and humidity that make the difference. The map on the next page shows that conditions in northern Europe do not favour mite growth, and yet, that’s where carpet has been considered wrongly a problem. In southern countries |
mites do survive, even on hard floors and tiles. Despite this, no problems have been reported. (Source: Bronswijk J.E.M.H. van, Schober G. Geoklimatische Verteilung von Innenraumallergenen. In: Jorde W., Schata M., eds. Mönchengladbacher Allergieseminar Band 5. Innenraumallergene. Dustri-Verlag, München-Deisenhofen. 19... |
69-84.) Distribution of mites in houses of mite-allergic patients Bedding offers ideal living conditions for dust mites, because they are not dependant upon the relative humidity of the bedroom itself: bedding is warm, dark, and damp after sleep and contains |
discarded skin scales. Dust mite allergen in mattresses can be 1.5 times greater than in dust from bedrooms placed carpet. Dust mites are almost not found in offices. In a study comparing carpets in 27 randomly selected offices with 30 |
bedrooms in homes, mite allergen levels were found to be 0.32 μ/g in offices vs. 18.4 μ/g in bedrooms. It was concluded that mite exposure in offices does not seem to be a risk for neither allergic (atopic) nor for |
two — chromosomes 18 in a fetus or baby's cells. The additional chromosome usually occurs before conception. A healthy egg or sperm cell contains 23 individual chromosomes - one to |
contribute to each of the 23 pairs of chromosomes needed to form a normal cell with 46 chromosomes. Numerical errors arise at either of the two meiotic divisions and cause |
the failure of segregation of a chromosome into the daughter cells (non-disjunction). This results in an extra chromosome making the haploid number 24 rather than 23. Fertilization of these eggs |
or sperm that contain an extra chromosome results in trisomy, or three copies of a chromosome rather than two. It is this extra genetic information that causes all the abnormalities |
characteristic of individuals with Edwards Syndrome. As each and every cell in their body contains extra information, the ability to grow and develop appropriately is delayed or impaired. This results |
in characteristic physical abnormalities such as low birth weight; a small, abnormally shaped head; small jaw; small mouth; low-set ears; and clenched fists with overlapping fingers. Babies with Edwards syndrome |
also have heart defects, and other organ malformations such that most systems of the body are affected. Edwards Syndrome also results in significant developmental delays. For this reason a full-term |
Edwards syndrome baby may well exhibit the breathing and feeding difficulties of a premature baby. Given the assistance offered to premature babies, some of these infants are able to overcome |
these initial difficulties, but most eventually succumb. The survival rate for Edwards Syndrome is very low. About half die in utero. Of liveborn infants, only 50% live to 2 months, |
and only 5 - 10% will survive their first year of life. Major causes of death include apnea and heart abnormalities. It is impossible to predict the exact prognosis of |
an Edwards Syndrome child during pregnancy or the neonatal period. As major medical interventions are routinely withheld from these children, it is also difficult to determine what the survival rate |
or prognosis would be for the condition if they were treated with the same aggressiveness as their genetically normal peers. They are typically severely to profoundly developmentally delayed. The rate |
of occurrence for Edwards Syndrome is ~ 1:3000 conceptions and 1:6000 live births, as 50% of those diagnosed prenatally with the condition will not survive the prenatal period. Although women |
in their 20's and 30's may conceive Edwards Syndrome babies, there is an increased risk of conceiving a child with Edwards Syndrome as a woman's age increases. A small percentage |
of cases occur when only some of the body's cells have an extra copy of chromosome 18, resulting in a mixed population of cells with a differing number of chromosomes. |
Such cases are sometimes called mosaic Edwards syndrome. Very rarely, a piece of chromosome 18 becomes attached to another chromosome (translocated) before or after conception. Affected people have two copies |
of chromosome 18, plus extra material from chromosome 18 attached to another chromosome. With a translocation, the person has a partial trisomy for chromosome 18 and the abnormalities are often |
less than for the typical Edwards syndrome. Features and characteristicsEdit Symptoms and findings may be extremely variable from case to case. However, in many affected infants, the following may be |
found: - Growth deficiency - Feeding difficulties - Breathing difficulties - Developmental delays - Mental retardation - Undescended testicles in males - Prominent back portion of the head - Small |
head (microcephaly) - Low-set, malformed ears - Abnormally small jaw (micrognathia) - Small mouth - Cleft lip/palate - Upturned nose - Narrow eyelid folds (palpebral fissures) - Widely-spaced eyes (ocular |
hypertelorism) - Dropping of the upper eyelids (ptosis) - Overlapped, flexed fingers - Underdeveloped or absent thumbs - Underdeveloped nails - Absent radius - Webbing of the second and third |
toes - Clubfeet or Rocker bottom feet - Small pelvis with limited movements of the hips - Short breastbone - Kidney malformations - Structural heart defects at birth (i.e., ventricular |
septal defect, atrial septal defect, patent ductus arteriosus) - Stenson, Carol M. (1999). Trisomy 18: A Guidebook for Families. University of Nebraska Medical Center. ISBN 1-889843-29-6. - Barnes, Ann M. |
(2000). Care of the infant and child with trisomy 18 or 13: medical problems, reported treatments and milestones. University of Nebraska Medical Center. ISBN 1-889843-58-X. - Trisomy 18 Support Foundation |
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