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of DNA allows researchers to visualize the "footprint" as a region lacking cleaved fragments. This approach is particularly useful when studying protein-DNA interactions in native conditions, as it preserves the integrity of complex formations. Additionally, combining electrophoretic mobility shift assays (EMSA) with footprinting enhances the specificity and resolution of detecting less stable protein-DNA complexes. == Advanced applications == === In vivo footprinting === In vivo footprinting is a technique used to analyze the protein-DNA interaction occurring within a cell at a given time point. This method helps identify regions of DNA occupied by proteins, revealing insights into in vivo gene regulation with the cell. Cleavage agents are used to degrade the unbound DNA while preserving protein-bound DNA. DNase I is commonly used as a cleavage agent when the cellular membrane has been permeabilized, making it more porous to allow better penetration of external substances. However, the most common cleavage agent used is UV-irradiation, because it penetrates the cell membrane without disrupting the cell and can thus capture interactions that are sensitive to cellular changes. However, this comes with the drawback that DNase I provides higher specificity and accuracy. DNase I is capable of cleaving unprotected DNA regions, leaving a footprint where proteins are bound. This allows for precise identification of protein-DNA interactions, while UV radiation induces widespread damage, such that, it can be difficult to find the exact binding sites. Once the DNA has been cleaved or damaged by UV, the cells can be lysed and DNA purified for analysis of a region of interest. Ligation-mediated PCR is an alternative method to footprint in vivo. Following DNA cleavage and isolation, linker proteins are attached at the breakpoints. A region of interest is amplified between the linker and a gene-specific primer, and when run on a polyacrylamide gel, will have a
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"page_id": 5638621,
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"title": "DNA footprinting"
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footprint, a gap, where a protein was bound. In vivo footprinting can be combined with immunoprecipitation to assess protein specificity at particular locations throughout the genome. This assay involves either using chemical crosslinkers or UV light to cross-link DNA to its associated proteins. After digesting unbound DNA, the DNA-protein complexes will remain. The protein of interest can be then selectively immunoprecipitated when detected by a complimentary antibody. Once detected, the immunoprecipitated DNA can be purified, released from crosslink and analyzed using DNA footprinting techniques like PCR or sequencing the region of interest. The DNA bound to a protein of interest can be immunoprecipitated with an antibody to that protein, and then specific region binding can be assessed using the DNA footprinting technique. === Quantitative footprinting === The DNA footprinting technique can be modified to assess the binding strength of a protein to specific regions of DNA. By using a range of protein concentrations in the footprinting experiment, the intensity of banding and the footprint can be tracked. This concentration-dependent technique investigates the affinity between DNA and the protein of interest by testing it under a range of protein concentrations. After DNase I treatment, the resulting fragments will be visualized on a PAGE gel and computationally analyzed. The intensity of banding and presence of the footprint will reflect the binding affinity between the protein of interest and a specific region of DNA. It is expected that with lower protein concentration, the gaps that signify the protein-DNA interactions will disappear, because fewer proteins are bound to the DNA, leading to more random cleavage. === Detection by capillary electrophoresis === To adapt the footprinting technique to updated detection methods, the labelled DNA fragments are detected by a capillary electrophoresis device instead of being run on a polyacrylamide gel. If the DNA fragment to
|
{
"page_id": 5638621,
"source": null,
"title": "DNA footprinting"
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be analyzed is produced by polymerase chain reaction (PCR), it is straightforward to couple a fluorescent molecule such as carboxyfluorescein (FAM) to the primers. This way, the fragments produced by DNase I digestion will contain FAM, and will be detectable by the capillary electrophoresis machine. Typically, carboxytetramethyl-rhodamine (ROX)-labelled size standards are also added to the mixture of fragments to be analyzed. Binding sites of transcription factors have been successfully identified this way. Capillary electrophoresis can be used to detect length differences of DNA fragments of interest within a sample. Additionally, this technique offers high resolution, allowing for the detection of even minor variations in fragment length. The automation and high-throughput capabilities of capillary electrophoresis make it a valuable tool for large-scale studies and applications where rapid and accurate results are required. Furthermore, the use of fluorescent labelling enhances sensitivity and allows for multiplexing, enabling the simultaneous analysis of multiple samples or target regions within a single run. === Cell-free fragmentomics === Cell-free (Cf) DNA fragmentomics analyzes the fragmentation patterns of cfDNA. DNA footprinting is applied to cfDNA to study the binding sites of DNA-binding proteins. This allows researchers to identify and analyze protein-DNA interactions non-invasively. This is specifically used for early cancer detection by assessing disease-associated fragmentation patterns. This is done by extracting DNA from a body fluid sample, undergo sequencing and analysis, where specific features like fragment size, end motifs, and fragment distribution across different genomic regions to detect disease in a non-invasive manner. == Genome-wide assays == Next-generation sequencing has enabled a genome-wide approach to identify DNA footprints. Open chromatin assays such as DNase-Seq and FAIRE-Seq have proven to provide a robust regulatory landscape for many cell types. However, these assays require some downstream bioinformatics analyses in order to provide genome-wide DNA footprints. The computational tools proposed can
|
{
"page_id": 5638621,
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"title": "DNA footprinting"
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be categorized in two classes: segmentation-based and site-centric approaches. Segmentation-based methods are based on the application of Hidden Markov models or sliding window methods to segment the genome into open/closed chromatin region. Examples of such methods are: HINT, Boyle method and Neph method. Site-centric methods, on the other hand, find footprints given the open chromatin profile around motif-predicted binding sites, i.e., regulatory regions predicted using DNA-protein sequence information (encoded in structures such as position weight matrix). Examples of these methods are CENTIPEDE and Cuellar-Partida method. == See also == DNase footprinting Protein footprinting Toeprinting assay == References == == External links == HINT Website CENTIPEDE Website
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{
"page_id": 5638621,
"source": null,
"title": "DNA footprinting"
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Lattice Miner is a formal concept analysis software tool for the construction, visualization and manipulation of concept lattices. It allows the generation of formal concepts and association rules as well as the transformation of formal contexts via apposition, subposition, reduction and object/attribute generalization, and the manipulation of concept lattices via approximation, projection and selection. Lattice Miner allows also the drawing of nested line diagrams. == Introduction == Formal concept analysis (FCA) is a branch of applied mathematics based on the formalization of concept and concept hierarchy and mainly used as a framework for conceptual clustering and rule mining. Over the last two decades, a collection of tools have emerged to help FCA users visualize and analyze concept lattices. They range from the earliest DOS-based implementations (e.g., ConImp and GLAD) to more recent implementations in Java like ToscanaJ, Galicia, ConExp and Coron. A main issue in the development of FCA tools is to visualize large concept lattices and provide efficient mechanisms to highlight patterns (e.g., concepts, associations) that could be relevant to the user. The initial objective of the FCA tool called Lattice Miner was to focus on visualization mechanisms for the representation of concept lattices, including nested line diagrams. Later on, many other interesting features were integrated into the tool. == Functional architecture of Lattice Miner == Lattice Miner is a Java-based platform whose functions are articulated around a core. The Lattice Miner core provides all low-level operations and structures for the representation and manipulation of contexts, lattices and association rules. Mainly, the core of Lattice Miner consists of three modules: context, concept and association rule modules. The user interface offers a context editor and concept lattice manipulator to assist the user in a set of tasks. The architecture of Lattice Miner is open and modular enough to allow the
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{
"page_id": 27593182,
"source": null,
"title": "Lattice Miner"
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integration of new features and facilities in each one of its components. === Context module === The context module offers all the basic operations and structures to manipulate binary and valued contexts as well as context decomposition to produce nested line diagrams. Basic context operations include apposition, subposition, generalization, clarification, reduction as well as the complementary context computation. The module provides also the arrow relations (for context reduction and decomposition) [2]. The tool has an input LMB format and recognizes the binary format SLF found in Galicia and the format CEX produced by ConExp. === Concept module === The main function of the concept module is to generate the concepts of the current binary context and construct the corresponding lattice and nested structure (see Figures 2 and 3). It provides the user with basic operators such as projection, selection, and exact search as well as advanced features like pair approximation. Some known algorithms are included in this module such as Bordat’s procedure, Godin’s algorithm and NextClosure algorithm. The approximation feature implemented in Lattice Miner is based on the following idea: given a pair (X,Y) where X ⊆ G, and Y ⊆ M, is there a set of formal concepts (Ai,Bi) which are “close to” (X,Y)? To answer this question, The tool starts to identify the type of couple that the pair (X,Y) represents. It can be a formal concept, a protoconcept, a semiconcept or a preconcept. In the last case, the approximation is given by the interval [(X",X′),(Y′,Y")] and highlighted in the line diagram. === Association rule module === This module includes procedures for computing the (stem) Guigues–Duquenne base using NextClosure algorithm [3], as well as the generic and informative bases. Implications with negation can be obtained using the apposition of a context and its complementary. This module embeds also
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{
"page_id": 27593182,
"source": null,
"title": "Lattice Miner"
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procedures for the computation of a non-redundant family C of implications and the closure of a set Y of attributes for the given implication set C. === User interface === The initial objective of Lattice Miner was to focus on lattice drawing and visualization either as a flat or nested structure by taking into account the cognitive process of human beings and known principles for lattice drawing (e.g., reducing the number of edge intersections, ensuring diagram symmetry). Some well-known visualization techniques were implemented such as focus & context and fisheye view. The basic idea behind focus & context visualization paradigm is to allow a viewer to see key (important) objects in full detail in the foreground (focus) while at the same time an overview of all the surrounding information (context) remains available in the background. Lattice Miner translates the focus & context paradigm into clear and blurred elements while the size of nodes and the intensity of their color were used to indicate their importance. Various forms of highlighting, labelling and animation are also provided. In order to better handle the display of large lattices, nested line diagrams are offered in the tool. Figure 3 shows the third level of the nested line diagram corresponding to the binary context of Figure 1 where three levels of nesting are defined. Each one of the inner nodes of this diagram represents a combination of attributes from the previous two (outer) levels. Real inner concepts (see the node on the left hand-side of the diagram) are identified by colored nodes while void elements are in grey color. Each node of levels 1 and 2 can be expanded to exhibit its internal line diagram. Both flat and nested diagrams can be saved as an image. Simple (flat) lattices can also be saved as an
|
{
"page_id": 27593182,
"source": null,
"title": "Lattice Miner"
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XML format file. == References == == External links == https://github.com/LarimUQO/lattice-miner https://sourceforge.net/projects/lattice-miner/ https://upriss.github.io/fca/fca.html http://w3.uqo.ca/icfca10/
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{
"page_id": 27593182,
"source": null,
"title": "Lattice Miner"
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Formiminoglutamic acid (FIGLU; conjugate base, formiminoglutamate) is an intermediate in the catabolism of L-histidine to L-glutamic acid. It thus is also a biomarker for intracellular levels of folate. The FIGLU test is used to identify vitamin B₁₂ deficiency, folate deficiency, and liver failure or liver disease. It is elevated with folate trapping, where it is accompanied by decreased methylmalonic acid, increased folate and a decrease in homocysteine. == See also == Formiminotransferase cyclodeaminase Glutamate-1-semialdehyde Glutamic acid Imidazol-4-one-5-propionic acid == References ==
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{
"page_id": 11471325,
"source": null,
"title": "Formiminoglutamic acid"
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Two-dimensional chromatography is a type of chromatographic technique in which the injected sample is separated by passing through two different separation stages. Two different chromatographic columns are connected in sequence, and the effluent from the first system is transferred onto the second column. Typically the second column has a different separation mechanism, so that bands that are poorly resolved from the first column may be completely separated in the second column. (For instance, a C18 reversed-phase chromatography column may be followed by a phenyl column.) Alternately, the two columns might run at different temperatures. During the second stage of separation the rate at which the separation occurs must be faster than the first stage, since there is still only a single detector. The plane surface is amenable to sequential development in two directions using two different solvents. == History == Modern two-dimensional chromatographic techniques are based on the results of the early developments of paper chromatography and thin-layer chromatography (TLC) which involved liquid mobile phases and solid stationary phases. These techniques would later generate modern gas chromatography (GC) and liquid chromatography (LC) analysis. Different combinations of one-dimensional GC and LC produced the analytical chromatographic technique that is known as two-dimensional chromatography. The earliest form of 2D-chromatography came in the form of a multi-step TLC separation in which a thin sheet of cellulose is used first with one solvent in one direction, then, after the paper has been dried, another solvent is run in a direction at right angles to the first. This methodology first appeared in the literature with a 1944 publication by A. J. P. Martin and coworkers detailing an efficient method for separating amino acids – "...but the two-dimensional chromatogram is especially convenient, in that it shows at a glance information that can be gained otherwise only as
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"page_id": 17828319,
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the result of numerous experiments" (Biochem J., 1944, 38, 224). == Examples == Two-dimensional separations can be carried out in gas chromatography or liquid chromatography. Various different coupling strategies have been developed to "resample" from the first column into the second. Some important hardware for two-dimensional separations are Deans' switch and Modulator, which selectively transfer the first dimension eluent to second dimension column. The chief advantage of two-dimensional techniques is that they offer a large increase in peak capacity, without requiring extremely efficient separations in either column. (For instance, if the first column offers a peak capacity (k1)of 100 for a 10-minute separation, and the second column offers a peak capacity of 5 (k2) in a 5-second separation, then the combined peak capacity may approach k1 × k2=500, with the total separation time still ~ 10 minutes). 2D separations have been applied to the analysis of gasoline and other petroleum mixtures, and more recently to protein mixtures. === Tandem mass spectrometry === Tandem mass spectrometry (Tandem MS or MS/MS) uses two mass analyzers in sequence to separate more complex mixtures of analytes. The advantage of tandem MS is that it can be much faster than other two-dimensional methods, with times ranging from milliseconds to seconds. Because there is no dilution with solvents in MS, there is less probability of interference, so tandem MS can be more sensitive and have a higher signal-to-noise ratio compared to other two-dimensional methods. The main disadvantage associated with tandem MS is the high cost of the instrumentation needed. Prices can range from $500,000 to over $1 million. Many form of tandem MS involve a mass selection step and a fragmentation step. The first mass analyzer can be programmed to only pass molecules of a specific mass-to-charge ratio. Then the second mass analyzer can fragment the
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{
"page_id": 17828319,
"source": null,
"title": "Two-dimensional chromatography"
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molecule to determine its identity. This can be especially useful for separating molecules of the same mass (i.e. proteins of the same mass or molecular isomers). Different types of mass analyzers can be coupled to achieve varying effects. One example would be a TOF-Quadrupole system. Ions can be sequentially fragmented and/or analyzed in a quadrupole as they leave the TOF in order of increasing m/z. Another prevalent tandem mass spectrometer is the quadrupole-quadrupole-quadrupole (Q-Q-Q) analyzer. The first quadrupole separates by mass, collisions take place in the second quadrupole, and the fragments are separated by mass in the third quadrupole. === Gas chromatography-mass spectrometry === Gas chromatography-mass spectrometry (GC-MS) is a two-dimensional chromatography technique that combines the separation technique of gas chromatography with the identification technique of mass spectrometry. GC-MS is the single most important analytical tool for the analysis of volatile and semi-volatile organic compounds in complex mixtures. It works by first injecting the sample into the GC inlet where it is vaporized and pushed through a column by a carrier gas, typically helium. The analytes in the sample are separated based upon their interaction with the coating of the column, or the stationary phase, and the carrier gas, or the mobile phase. The compounds eluted from the column are converted into ions via electron impact (EI) or chemical ionization (CI) before traveling through the mass analyzer. The mass analyzer serves to separate the ions on a mass-to-charge basis. Popular choices perform the same function but differ in the way that they accomplish the separation. The analyzers typically used with GC-MS are the time-of-flight mass analyzer and the quadrupole mass analyzer. After leaving the mass analyzer, the analytes reach the detector and produce a signal that is read by a computer and used to create a gas chromatogram and mass
|
{
"page_id": 17828319,
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"title": "Two-dimensional chromatography"
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spectrum. Sometimes GC-MS utilizes two gas chromatographers in particularly complex samples to obtain considerable separation power and be able to unambiguously assign the specific species to the appropriate peaks in a technique known as GCxGC-(MS). Ultimately, GC-MS is a technique utilized in many analytical laboratories and is a very effective and adaptable analytical tool. === Liquid chromatography-mass spectrometry === Liquid chromatography-mass spectrometry (LC/MS) couples high resolution chromatographic separation with MS detection. As the system adopts the high separation of HPLC, analytes which are in the liquid mobile phase are often ionized by various soft ionization methods including atmospheric pressure chemical ionization (APCI), electrospray ionization (ESI) or matrix-assisted laser desorption/ionization (MALDI), which attains the gas phase ionization required for the coupling with MS. These ionization methods allow the analysis of a wider range of biological molecules, including those with larger masses, thermally unstable or nonvolatile compounds where GC-MS is typically incapable of analyzing. LC-MS provides high selectivity as unresolved peaks can be isolated by selecting a specific mass. Furthermore, better identification is also attained by mass spectra and the user does not have to rely solely on the retention time of analytes. As a result, molecular mass and structural information as well as quantitative data can all be obtained via LC-MS. LC-MS can therefore be applied to various fields, such as impurity identification and profiling in drug development and pharmaceutical manufacturing, since LC provides efficient separation of impurities and MS provides structural characterization for impurity profiling. Common solvents used in normal or reversed phase LC such as water, acetonitrile, and methanol are all compatible with ESI, yet a LC grade solvent may not be suitable for MS. Furthermore, buffers containing inorganic ions should be avoided as they may contaminate the ion source. Nonetheless, the problem can be resolved by 2D LC-MS,
|
{
"page_id": 17828319,
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"title": "Two-dimensional chromatography"
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as well as other various issues including analyte coelution and UV detection responses. === Liquid chromatography-liquid chromatography === Two-dimensional liquid chromatography (2D-LC) combines two separate analyses of liquid chromatography into one data analysis. Modern 2D liquid chromatography has its origins in the late 1970s to early 1980s. During this time, the hypothesized principles of 2D-LC were being proven via experiments conducted along with supplementary conceptual and theoretical work. It was shown that 2D-LC could offer quite a bit more resolving power compared to the conventional techniques of one-dimensional liquid chromatography. In the 1990s, the technique of 2D-LC played an important role in the separation of extremely complex substances and materials found in the proteomics and polymer fields of study. Unfortunately, the technique had been shown to have a significant disadvantage when it came to analysis time. Early work with 2D-LC was limited to small portion of liquid phase separations due to the long analysis time of the machinery. Modern 2D-LC techniques tackled that disadvantage head on, and have significantly reduced what was once a damaging feature. Modern 2D-LC has an instrumental capacity for high resolution separations to be completed in an hour or less. Due to the growing need for instrumentation to perform analysis on substances of growing complexity with better detection limits, the development of 2D-LC pushes forward. Instrumental parts have become a mainstream industry focus and are much easier to attain then before. Prior to this, 2D-LC was performed using components from 1D-LC instruments, and would lead to results of varying degrees in both accuracy and precision. The reduced stress on instrumental engineering has allowed for pioneering work in the field and technique of 2D-LC. The purpose of employing this technique is to separate mixtures that one-dimensional liquid chromatography otherwise cannot separate effectively. Two-dimensional liquid chromatography is better
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{
"page_id": 17828319,
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"title": "Two-dimensional chromatography"
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suited to analyzing complex mixtures samples such as urine, environmental substances and forensic evidence such as blood. Difficulties in separating mixtures can be attributed to the complexity of the mixture in the sense that separation cannot occur due to the number of different effluents in the compound. Another problem associated with one-dimensional liquid chromatography involves the difficulty associated to resolving closely related compounds. Closely related compounds have similar chemical properties that may prove difficult to separate based on polarity, charge, etc. Two-dimensional liquid chromatography provides separation based on more than one chemical or physical property. Using an example from Nagy and Vekey, a mixture of peptides can be separated based on their basicity, but similar peptides may not elute well. Using a subsequent LC technique, the similar basicity between the peptides can be further separated by employing differences in apolar character. As a result, to be able to separate mixtures more efficiently, a subsequent LC analysis must employ very different separation selectivity relative to the first column. Another requirement to effectively use 2D liquid chromatography, according to Bushey and Jorgenson, is to employ highly orthogonal techniques which means that the two separation techniques must be as different as possible. There are two major classifications of 2D liquid chromatography. These include: Comprehensive 2D liquid chromatography (LCxLC) and Heart-cutting 2D liquid chromatography (LC-LC). In comprehensive 2D-LC, all the peaks from a column elution are fully sampled, but it has been deemed unnecessary to transfer the entire sample from the first to the second column. A portion of the sample is sent to waste while the rest is sent to the sampling valve. In heart-cutting 2D-LC specific peaks are targeted with only a small portion of the peak being injected onto a second column. Heart-cutting 2D-LC has proven to be quite useful for
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{
"page_id": 17828319,
"source": null,
"title": "Two-dimensional chromatography"
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sample analysis of substances that are not very complex provided they have similar retention behavior. Compared to comprehensive 2D-LC, heart-cutting 2D-LC provides an effective technique with much less system setup and a much lower operating cost. Multiple heart-cutting (mLC-LC) may be utilized to sample multiple peaks from first dimensional analysis without risking temporary overlap of second dimensional analysis. Multiple heart-cutting (mLC-LC) utilizes a setup of multiple sampling loops. For 2D-LC, peak capacity is a very important issue. This can be generated using gradient elution separation with much greater efficiency than an isocratic separation given a reasonable amount of time. While isocratic elution is much easier on a fast time scale, it is preferable to perform a gradient elution separation in the second dimension. The mobile phase strength is varied from a weak eluent composition to a stronger one. Based on linear solvent strength theory (LSST) of gradient elution for reversed phase chromatography, the relationship between retention time, instrumental variables and solute parameters is shown below. tR=t0 +tD + t0/b*ln(b*(k0-td/t0) + 1) While a lot of pioneering work has been completed in the years since 2D-LC became a major analytical chromatographic technique, there are still many modern problems to be considered. Large amounts of experimental variables have yet to be decided on, and the technique is constantly in a state of development. === Gas chromatography – gas chromatography === Comprehensive two-dimensional gas chromatography is an analytical technique that separates and analyzes complex mixtures. It has been utilized in fields such as: flavor, fragrance, environmental studies, pharmaceuticals, petroleum products and forensic science. GCxGC provides a high range of sensitivity and produces a greater separation power due to the increased peak capacity. == See also == Two-dimensional gel electrophoresis == References ==
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{
"page_id": 17828319,
"source": null,
"title": "Two-dimensional chromatography"
}
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Site-specific recombination, also known as conservative site-specific recombination, is a type of genetic recombination in which DNA strand exchange takes place between segments possessing at least a certain degree of sequence homology. Enzymes known as site-specific recombinases (SSRs) perform rearrangements of DNA segments by recognizing and binding to short, specific DNA sequences (sites), at which they cleave the DNA backbone, exchange the two DNA helices involved, and rejoin the DNA strands. In some cases the presence of a recombinase enzyme and the recombination sites is sufficient for the reaction to proceed; in other systems a number of accessory proteins and/or accessory sites are required. Many different genome modification strategies, among these recombinase-mediated cassette exchange (RMCE), an advanced approach for the targeted introduction of transcription units into predetermined genomic loci, rely on SSRs. Site-specific recombination systems are highly specific, fast, and efficient, even when faced with complex eukaryotic genomes. They are employed naturally in a variety of cellular processes, including bacterial genome replication, differentiation and pathogenesis, and movement of mobile genetic elements. For the same reasons, they present a potential basis for the development of genetic engineering tools. Recombination sites are typically between 30 and 200 nucleotides in length and consist of two motifs with a partial inverted-repeat symmetry, to which the recombinase binds, and which flank a central crossover sequence at which the recombination takes place. The pairs of sites between which the recombination occurs are usually identical, but there are exceptions (e.g. attP and attB of λ integrase). == Classification: tyrosine- vs. serine- recombinases == Based on amino acid sequence homologies and mechanistic relatedness, most site-specific recombinases are grouped into one of two families: the tyrosine (Tyr) recombinase family or serine (Ser) recombinase family. The names stem from the conserved nucleophilic amino acid residue present in each class of
|
{
"page_id": 10095073,
"source": null,
"title": "Site-specific recombination"
}
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recombinase which is used to attack the DNA and which becomes covalently linked to it during strand exchange. The earliest identified members of the serine recombinase family were known as resolvases or DNA invertases, while the founding member of the tyrosine recombinases, lambda phage integrase (using attP/B recognition sites), differs from the now well-known enzymes such as Cre (from the P1 phage) and FLP (from the yeast Saccharomyces cerevisiae). Famous serine recombinases include enzymes such as gamma-delta resolvase (from the Tn1000 transposon), Tn3 resolvase (from the Tn3 transposon), and φC31 integrase (from the φC31 phage). There are several classes of serine recombinases, consisting of the small serine recombinase, the ISXc5 resolvase, the serine transposase, and the large serine recombinase. Although the individual members of the two recombinase families can perform reactions with the same practical outcomes, the families are unrelated to each other, having different protein structures and reaction mechanisms. Unlike tyrosine recombinases, serine recombinases are highly modular, as was first hinted by biochemical studies and later shown by crystallographic structures. Knowledge of these protein structures could prove useful when attempting to re-engineer recombinase proteins as tools for genetic manipulation. == Mechanism == Recombination between two DNA sites begins by the recognition and binding of these sites – one site on each of two separate double-stranded DNA molecules, or at least two distant segments of the same molecule – by the recombinase enzyme. This is followed by synapsis, i.e. bringing the sites together to form the synaptic complex. It is within this synaptic complex that the strand exchange takes place, as the DNA is cleaved and rejoined by controlled transesterification reactions. During strand exchange, each double-stranded DNA molecule is cut at a fixed point within the crossover region of the recognition site, releasing a deoxyribose hydroxyl group, while the recombinase
|
{
"page_id": 10095073,
"source": null,
"title": "Site-specific recombination"
}
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enzyme forms a transient covalent bond to a DNA backbone phosphate. This phosphodiester bond between the hydroxyl group of the nucleophilic serine or tyrosine residue conserves the energy that was expended in cleaving the DNA. Energy stored in this bond is subsequently used for the rejoining of the DNA to the corresponding deoxyribose hydroxyl group on the other DNA molecule. The entire reaction therefore proceeds without the need for external energy-rich cofactors such as ATP. Although the basic chemical reaction is the same for both tyrosine and serine recombinases, there are some differences between them. Tyrosine recombinases, such as Cre or FLP, cleave one DNA strand at a time at points that are staggered by 6–8bp, linking the 3' end of the strand to the hydroxyl group of the tyrosine nucleophile (Fig. 1). Strand exchange then proceeds via a crossed strand intermediate analogous to the Holliday junction in which only one pair of strands has been exchanged. The mechanism and control of serine recombinases is much less well understood. This group of enzymes was only discovered in the mid-1990s and is still relatively small. The now classical members gamma-delta and Tn3 resolvase, but also new additions like φC31-, Bxb1-, and R4 integrases, cut all four DNA strands simultaneously at points that are staggered by 2 bp (Fig. 2). During cleavage, a protein–DNA bond is formed via a transesterification reaction, in which a phosphodiester bond is replaced by a phosphoserine bond between a 5' phosphate at the cleavage site and the hydroxyl group of the conserved serine residue (S10 in resolvase). It is still not entirely clear how the strand exchange occurs after the DNA has been cleaved. However, it has been shown that the strands are exchanged while covalently linked to the protein, with a resulting net rotation of 180°.
|
{
"page_id": 10095073,
"source": null,
"title": "Site-specific recombination"
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The most quoted (but not the only) model accounting for these facts is the "subunit rotation model" (Fig. 2). Independent of the model, DNA duplexes are situated outside of the protein complex, and large movement of the protein is needed to achieve the strand exchange. In this case the recombination sites are slightly asymmetric, which allows the enzyme to tell apart the left and right ends of the site. When generating products, left ends are always joined to the right ends of their partner sites, and vice versa. This causes different recombination hybrid sites to be reconstituted in the recombination products. Joining of left ends to left or right to right is avoided due to the asymmetric "overlap" sequence between the staggered points of top and bottom strand exchange, which is in stark contrast to the mechanism employed by tyrosine recombinases. The reaction catalysed by Cre-recombinase, for instance, may lead to excision of the DNA segment flanked by the two sites (Fig. 3A), but may also lead to integration or inversion of the orientation of the flanked DNA segment (Fig. 3B). What the outcome of the reaction will be is dictated mainly by the relative locations and orientations of the sites that are to be recombined, but also by the innate specificity of the site-specific system in question. Excisions and inversions occur if the recombination takes place between two sites that are found on the same molecule (intramolecular recombination), and if the sites are in the same (direct repeat) or in an opposite orientation (inverted repeat), respectively. Insertions, on the other hand, take place if the recombination occurs on sites that are situated on two different DNA molecules (intermolecular recombination), provided that at least one of these molecules is circular. Most site-specific systems are highly specialised, catalysing only one of
|
{
"page_id": 10095073,
"source": null,
"title": "Site-specific recombination"
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|
these different types of reaction, and have evolved to ignore the sites that are in the "wrong" orientation. == See also == Cre recombinase Cre-Lox recombination FLP-FRT recombination Genetic recombination Homologous recombination Recombinase-mediated cassette exchange Site-specific recombinase technology == References ==
|
{
"page_id": 10095073,
"source": null,
"title": "Site-specific recombination"
}
|
A timeline of events related to information theory, quantum information theory and statistical physics, data compression, error correcting codes and related subjects. 1872 – Ludwig Boltzmann presents his H-theorem, and with it the formula Σpi log pi for the entropy of a single gas particle 1878 – J. Willard Gibbs defines the Gibbs entropy: the probabilities in the entropy formula are now taken as probabilities of the state of the whole system 1924 – Harry Nyquist discusses quantifying "intelligence" and the speed at which it can be transmitted by a communication system 1927 – John von Neumann defines the von Neumann entropy, extending the Gibbs entropy to quantum mechanics 1928 – Ralph Hartley introduces Hartley information as the logarithm of the number of possible messages, with information being communicated when the receiver can distinguish one sequence of symbols from any other (regardless of any associated meaning) 1929 – Leó Szilárd analyses Maxwell's demon, showing how a Szilard engine can sometimes transform information into the extraction of useful work 1940 – Alan Turing introduces the deciban as a measure of information inferred about the German Enigma machine cypher settings by the Banburismus process 1944 – Claude Shannon's theory of information is substantially complete 1947 – Richard W. Hamming invents Hamming codes for error detection and correction (to protect patent rights, the result is not published until 1950) 1948 – Claude E. Shannon publishes A Mathematical Theory of Communication 1949 – Claude E. Shannon publishes Communication in the Presence of Noise – Nyquist–Shannon sampling theorem and Shannon–Hartley law 1949 – Claude E. Shannon's Communication Theory of Secrecy Systems is declassified 1949 – Robert M. Fano publishes Transmission of Information. M.I.T. Press, Cambridge, Massachusetts – Shannon–Fano coding 1949 – Leon G. Kraft discovers Kraft's inequality, which shows the limits of prefix codes 1949
|
{
"page_id": 3475938,
"source": null,
"title": "Timeline of information theory"
}
|
– Marcel J. E. Golay introduces Golay codes for forward error correction 1951 – Solomon Kullback and Richard Leibler introduce the Kullback–Leibler divergence 1951 – David A. Huffman invents Huffman encoding, a method of finding optimal prefix codes for lossless data compression 1953 – August Albert Sardinas and George W. Patterson devise the Sardinas–Patterson algorithm, a procedure to decide whether a given variable-length code is uniquely decodable 1954 – Irving S. Reed and David E. Muller propose Reed–Muller codes 1955 – Peter Elias introduces convolutional codes 1957 – Eugene Prange first discusses cyclic codes 1959 – Alexis Hocquenghem, and independently the next year Raj Chandra Bose and Dwijendra Kumar Ray-Chaudhuri, discover BCH codes 1960 – Irving S. Reed and Gustave Solomon propose Reed–Solomon codes 1962 – Robert G. Gallager proposes low-density parity-check codes; they are unused for 30 years due to technical limitations 1965 – Dave Forney discusses concatenated codes 1966 – Fumitada Itakura (Nagoya University) and Shuzo Saito (Nippon Telegraph and Telephone) develop linear predictive coding (LPC), a form of speech coding 1967 – Andrew Viterbi reveals the Viterbi algorithm, making decoding of convolutional codes practicable 1968 – Elwyn Berlekamp invents the Berlekamp–Massey algorithm; its application to decoding BCH and Reed–Solomon codes is pointed out by James L. Massey the following year 1968 – Chris Wallace and David M. Boulton publish the first of many papers on Minimum Message Length (MML) statistical and inductive inference 1970 – Valerii Denisovich Goppa introduces Goppa codes 1972 – Jørn Justesen proposes Justesen codes, an improvement of Reed–Solomon codes 1972 – Nasir Ahmed proposes the discrete cosine transform (DCT), which he develops with T. Natarajan and K. R. Rao in 1973; the DCT later became the most widely used lossy compression algorithm, the basis for multimedia formats such as JPEG, MPEG and MP3
|
{
"page_id": 3475938,
"source": null,
"title": "Timeline of information theory"
}
|
1973 – David Slepian and Jack Wolf discover and prove the Slepian–Wolf coding limits for distributed source coding 1976 – Gottfried Ungerboeck gives the first paper on trellis modulation; a more detailed exposition in 1982 leads to a raising of analogue modem POTS speeds from 9.6 kbit/s to 33.6 kbit/s 1976 – Richard Pasco and Jorma J. Rissanen develop effective arithmetic coding techniques 1977 – Abraham Lempel and Jacob Ziv develop Lempel–Ziv compression (LZ77) 1982 – Valerii Denisovich Goppa introduces algebraic geometry codes 1989 – Phil Katz publishes the .zip format including DEFLATE (LZ77 + Huffman coding); later to become the most widely used archive container 1993 – Claude Berrou, Alain Glavieux and Punya Thitimajshima introduce Turbo codes 1994 – Michael Burrows and David Wheeler publish the Burrows–Wheeler transform, later to find use in bzip2 1995 – Benjamin Schumacher coins the term qubit and proves the quantum noiseless coding theorem 2003 – David J. C. MacKay shows the connection between information theory, inference and machine learning in his book. 2006 – Jarosław Duda introduces first Asymmetric numeral systems entropy coding: since 2014 popular replacement of Huffman and arithmetic coding in compressors like Facebook Zstandard, Apple LZFSE, CRAM or JPEG XL 2008 – Erdal Arıkan introduces polar codes, the first practical construction of codes that achieves capacity for a wide array of channels == References ==
|
{
"page_id": 3475938,
"source": null,
"title": "Timeline of information theory"
}
|
Substrate is a term used in materials science and engineering to describe the base material on which processing is conducted. Surfaces have different uses, including producing new film or layers of material and being a base to which another substance is bonded. == Description == In materials science and engineering, a substrate refers to a base material on which processing is conducted. This surface could be used to produce new film or layers of material such as deposited coatings. It could be the base to which paint, adhesives, or adhesive tape is bonded. A typical substrate might be rigid such as metal, concrete, or glass, onto which a coating might be deposited. Flexible substrates are also used. Some substrates are anisotropic with surface properties being different depending on the direction: examples include wood and paper products. == Coatings == With all coating processes, the condition of the surface of the substrate can strongly affect the bond of subsequent layers. This can include cleanliness, smoothness, surface energy, moisture, etc. Coating can be by a variety of processes, including: Adhesives and adhesive tapes Coating and printing processes Chemical vapor deposition and physical vapor deposition Conversion coating Anodizing Chromate conversion coating Plasma electrolytic oxidation Phosphate coating Paint Enamel paint Powder coating Industrial coating Silicate mineral paint Fusion bonded epoxy coating (FBE coating) Pickled and oiled, a type of plate steel coating. Plating Electroless plating Electrochemical plating Polymer coatings, such as Teflon Sputtered or vacuum deposited materials Vitreous enamel In optics, glass may be used as a substrate for an optical coating—either an antireflection coating to reduce reflection, or a mirror coating to enhance it. Ceramic substrates are also used in the renewable energy sector to produce inverters for photovoltaic solar systems and concentrators for concentrated photovoltaic systems. A substrate may be also an
|
{
"page_id": 10160612,
"source": null,
"title": "Substrate (materials science)"
}
|
engineered surface where an unintended or natural process occurs, like in: Fouling Corrosion Biofouling Heterogeneous catalysis Adsorption == See also == List of coating techniques Thin film Wetting == References ==
|
{
"page_id": 10160612,
"source": null,
"title": "Substrate (materials science)"
}
|
Strategic pluralism (also known as the dual-mating strategy) is a theory in evolutionary psychology regarding human mating strategies that suggests women have evolved to evaluate men in two categories: whether they are reliable long term providers, and whether they contain high quality genes. The theory of strategic pluralism was proposed by Steven Gangestad and Jeffry Simpson, two professors of psychology at the University of New Mexico and Texas A&M University, respectively. == Experiments and studies == Although strategic pluralism is believed to occur for both animals and humans, the majority of experiments have been performed with humans. One experiment concluded that between short term and long-term relationships, males and females prioritized different things. It was shown that both preferred physical attractiveness for short term mates. However, for long term, females preferred males with traits that indicated that they could be better caretakers, whereas the males did not change their priorities. The experimenters used the following setup: subjects were given an overall 'budget' and asked to assign points to different traits. For long-term mates, women gave more points to social and kindness traits, agreeing with results found in other studies suggesting that females prefer long-term mates who would provide resources and emotional security for them, as opposed to physically attractive mates. The females also prefer males who can offer them more financial security as this would help them raise their offspring. Females have also chosen males who have more feminine appearances because of a (hypothesized) inverse relationship between a male's facial attractiveness and effort willing to spend in raising offspring. That is, in theory, a more attractive male would put in less work as a caretaker while a less attractive male would put in more work. On average, there is a wider amount of variability in male characteristics than in females.
|
{
"page_id": 44960229,
"source": null,
"title": "Strategic pluralism"
}
|
This suggests there are enough of both males more suited for short-term relationships and those more suited for longer relationships. == Criticism == Bellis and Baker calculated that if double-mating strategy does occur, the rate of paternal discrepancy would be between 6.9 and 13.8%. When taking kin selection into account, Gaulin, McBurney, and Brakeman-Wartell hypothesised that mother’s side of family is more certain that the child is their kin and therefore invest more. Based on this matrilateral bias they calculated the rate of cuckoldry to be roughly 13% to 20%. These estimates were refuted by Y-chromosome tracking and HLA tracking that put the estimates between 1-2%. David Buss, prominent evolutionary psychologist, cited this evidence as a reason to be sceptical of dual-mating strategy hypothesis. == See also == Ovulatory shift hypothesis Human mating strategies Extra-pair copulation Sexual selection in humans == References ==
|
{
"page_id": 44960229,
"source": null,
"title": "Strategic pluralism"
}
|
CAESAR (Comet Astrobiology Exploration Sample Return) is a sample-return mission concept to comet 67P/Churyumov–Gerasimenko. The mission was proposed in 2017 to NASA's New Frontiers program mission 4, and on 20 December 2017 it was one of two finalists selected for further concept development. On 27 June 2019, the other finalist, the Dragonfly mission, was chosen instead. Had it been selected in June 2019, it would have launched between 2024 and 2025, with a capsule delivering a sample back to Earth in 2038. The Principal Investigator is Alexander Hayes of Cornell University in Ithaca, New York. CAESAR would be managed by NASA's Goddard Space Flight Center in Greenbelt, Maryland. Curation of the returned sample would take place at NASA's Astromaterials Research and Exploration Science Directorate, based at Johnson Space Center in Houston, Texas. The CAESAR team chose comet 67P over other cometary targets in part because the data collected by the Rosetta mission, which studied the comet from 2014 to 2016, allows the spacecraft to be designed to the conditions there, increasing the mission's chance of success. The Rosetta mission also provides a vast geologic context for this mission's sample-return analysis. == Overview == The two New Frontiers program Mission 4 finalists, announced on 20 December 2017, were Dragonfly to Titan, and CAESAR. Comet 67P was previously explored by the European Space Agency's Rosetta probe and its lander Philae during 2014-2016 to determine its origin and history. Squyres explained that knowing the existing conditions at the comet allows them to design systems that would dramatically improve the chances for success. The CAESAR and Dragonfly missions received US$4 million funding each through the end of 2018 to further develop and mature their concepts. NASA selected the Dragonfly mission on 27 June 2019 to build and launch in 2026. === Background === A
|
{
"page_id": 56101350,
"source": null,
"title": "CAESAR (spacecraft)"
}
|
comet sample-return mission was one of the goals in a list of options for a New Frontiers mission in both the 2003 and the 2011 Planetary Science Decadal Survey, which were guiding surveys among those in the scientific community of what and where NASA should prioritize. Another comet mission proposal, Comet Hopper, was one of three Discovery Program finalists that received US$3 million in May 2011 to develop a detailed concept study; however, it was not selected. NASA has launched several missions to comets in the late 1990s and 2000s; these missions include Deep Space 1 (launched 1998), Stardust (launched 1999), CONTOUR (launched 2002 but failed after launch), and Deep Impact (launched 2005), as well as some participation on the Rosetta mission. === Astrobiology === CAESAR's objectives were to understand the formation of the Solar System and how these components came together to form planets and give rise to life. Some researchers have hypothesized that Earth may have been seeded with organic compounds early in its development by tholin-rich comets, providing the raw material necessary for life to emerge. Tholins were detected by the Rosetta mission to comet 67P/Churyumov–Gerasimenko. == Spacecraft == The spacecraft would be built by Northrop Grumman Innovation Systems and it would inherit technology used by the successful Dawn mission. Navigation, sample site selection, and sample documentation are enabled by the camera suite, provided by Malin Space Science Systems. This camera suite consists of six cameras of varying fields of view and focal ranges: narrow angle camera (NAC), medium angle camera (MAC), touch-and-go camera (TAGCAM), two navigation cameras (NAVCAMs), and a sample container camera (CANCAM). The robotic arm (TAG) and the Sample Acquisition System would be provided by Honeybee Robotics. The sample return capsule and heatshield are provided by the Japanese space agency JAXA. === Propulsion ===
|
{
"page_id": 56101350,
"source": null,
"title": "CAESAR (spacecraft)"
}
|
The propulsion system on CAESAR would be NASA's Evolutionary Xenon Thruster (NEXT), a type of solar electric propulsion. It would employ three NEXT thrusters, with one used as a spare. The propellant is xenon. == Sample return == The spacecraft would not land on the comet, but would momentarily contact the surface with its TAG (Touch-And-Go) robotic arm, as done by OSIRIS-REx on an asteroid, including raising the solar arrays into a Y-shaped configuration to minimize the chance of dust accumulation during contact and provide more ground clearance. The sampler mechanism on the arm would produce a burst of nitrogen gas to blow regolith particles into the sampler head located at the end of the arm. CAESAR would collect between 80 and 800 g (2.8 and 28.2 oz) of regolith from the comet. The maximum pebble size would be 4.5 cm (1.8 in). The system has enough compressed nitrogen gas for three samplings. The system would separate the volatiles from the solid substances into separate containers and preserve the samples cold for the return trip. The spacecraft would head back to Earth and drop off the sample in a capsule, which would re-enter Earth's atmosphere and parachute down to the surface in 2038. The sample-return capsule (SRC) would be provided by JAXA and its design is based upon the SRC flown on the Hayabusa and Hayabusa2 spacecraft. The capsule would parachute down at the Utah Test and Training Range (UTTR), and it would be transported to NASA's Johnson Space Center for curation and analyses at the laboratory called Astromaterials Research and Exploration Science Directorate (ARES). A small portion of the sample will also be curated at Japan's Extraterrestrial Sample Curation Center. Most of the sample (≥75% of the total) would be preserved for analysis by future generations of scientists. ==
|
{
"page_id": 56101350,
"source": null,
"title": "CAESAR (spacecraft)"
}
|
See also == List of missions to comets TAGSAM – Regolith scoop used on asteroid Bennu by the NASA probe OSIRIS-REx == References ==
|
{
"page_id": 56101350,
"source": null,
"title": "CAESAR (spacecraft)"
}
|
Anthranilic hydroxylase may refer to: Anthranilate 3-monooxygenase Anthranilate 1,2-dioxygenase (deaminating, decarboxylating)
|
{
"page_id": 38406629,
"source": null,
"title": "Anthranilic hydroxylase"
}
|
In computer science, SimHash is a technique for quickly estimating how similar two sets are. The algorithm is used by the Google Crawler to find near duplicate pages. It was created by Moses Charikar. In 2021 Google announced its intent to also use the algorithm in their newly created FLoC (Federated Learning of Cohorts) system. == Evaluation and benchmarks == A large scale evaluation has been conducted by Google in 2006 to compare the performance of Minhash and Simhash algorithms. In 2007 Google reported using Simhash for duplicate detection for web crawling and using Minhash and LSH for Google News personalization. == See also == MinHash w-shingling Count–min sketch Locality-sensitive hashing == References == == External links == Simhash Princeton Paper Simhash explained Comparison of MinHash vs. Simhash
|
{
"page_id": 53021161,
"source": null,
"title": "SimHash"
}
|
Vida Mary Stout (20 February 1930 – 21 July 2012) was a New Zealand limnographer and academic administrator. She was the first woman to be Dean of Science at a New Zealand university. == Biography == Stout was the daughter of Thomas Duncan MacGregor Stout and granddaughter of Robert Stout. Born and raised in Wellington, Stout was educated at Woodford House in Hawke's Bay, where she was Dux. She then studied at Victoria University College, where she completed a Bachelor of Science and Masters of Science in zoology. Her Masters thesis was on "Hydracarina from the Wellington province". Stout then completed a PhD at Bedford College, University of London, where she studied Daphnia. She returned to New Zealand after post-doctoral work in Sweden and in 1968 she and Ann Chapman founded the New Zealand Limnological Society (now the New Zealand Freshwater Sciences Society). Stout was the first president of the society and later was made an honorary life member. She was also a long-term member of the Canterbury branch of the Royal Society of New Zealand, and was the branch president in 1983. Stout was appointed to the Zoology Department at the University of Canterbury in 1958, where she remained until her retirement in 1996. During her tenure she held the positions of dean of science from 1984 to 1998, deputy chair of the university's Academic Administration Committee from 1992 to 1995 and played a role in establishing the Masters in Environmental Science Course. Her research focused on the biology and chemistry of South Island lakes, including the nature and changes in zooplankton communities over time. She undertook long-term studies on lakes Pearson and Grassmere, near the university's Cass field station. The University of Canterbury also holds her archives. After retiring in 1996, Stout continued to go to her office
|
{
"page_id": 37095913,
"source": null,
"title": "Vida Stout"
}
|
almost every day until the university forbid her access, citing fears for her safety due to her progressive Parkinson's disease, which caused her death in 2012. In 2017, Stout was selected as one of the Royal Society Te Apārangi's "150 women in 150 words", celebrating the contributions of women to knowledge in New Zealand. == References ==
|
{
"page_id": 37095913,
"source": null,
"title": "Vida Stout"
}
|
Kalanchoe ( KAL-əng-KOH-ee), (also called "kalanchöe" or "kalanchoë"), is a genus of about 125 species of tropical, succulent plants in the stonecrop family Crassulaceae, mainly native to Madagascar and tropical Africa. A Kalanchoe species was one of the first plants to be sent into space, sent on a resupply to the Soviet Salyut 1 space station in 1979. The majority of kalanchoes require around 6–8 hours of sunlight a day; a few cannot tolerate this, and survive with bright, indirect sunlight to bright shade. == Description == Most are shrubs or perennial herbaceous plants, but a few are annual or biennial. The largest, Kalanchoe beharensis from Madagascar, can reach 6 m (20 ft) tall, but most species are less than 1 m (3 ft) tall. Kalanchoes open their flowers by growing new cells on the inner surface of the petals to force them outwards, and on the outside of the petals to close them. Kalanchoe flowers are divided into 4 sections with 8 stamens. The petals are fused into a tube, in a similar way to some related genera such as Cotyledon. == Taxonomy == The genus Kalanchoe was first described by the French botanist Michel Adanson in 1763. The genus Bryophyllum was described by Salisbury in 1806 and the genus Kitchingia was created by Baker in 1881. Kitchingia is now regarded as a synonym for Kalanchoe, while Bryophyllum has also been treated as a separate genus, since species of Bryophyllum appear to be nested within Kalanchoe on molecular phylogenetic analysis, Bryophyllum is considered as a section of the former, dividing the genus into three sections, Kitchingia, Bryophyllum, and Eukalanchoe. these were formalised as subgenera by Smith and Figueiredo (2018). === Etymology === Adanson cited Georg Joseph Kamel (Camellus) as his source for the name. The name came from the
|
{
"page_id": 526827,
"source": null,
"title": "Kalanchoe"
}
|
Cantonese name 伽藍菜 (Jyutping: gaa1 laam4 coi3). Kalanchoe ceratophylla and Kalanchoe laciniata are both called 伽蓝菜 (apparently "Buddhist monastery [samghārāma] herb") in China. In Mandarin Chinese, it does not seem very close in pronunciation (qiélán cài, but possibly jiālán cài or gālán cài as the character 伽 has multiple pronunciations), but the Cantonese gālàahm choi is closer. == List of selected species == === List of hybrids === Several hybrids within Kalanchoe are known: K. houghtonii = K. daigremontiana × K. delagoensis K. lokarana K. poincarei K. rechingeri K. richaudii = K. delagoensis × K. rosei == Distribution and ecology == The genus is predominantly native to the Old World. Only one species originates from the Americas. Fifty-six are from southern and eastern Africa and 60 species on the island of Madagascar. It is also found in south-eastern Asia and China. These plants are food plants for caterpillars of the Red Pierrot butterfly. The butterfly lays its eggs on leaves, and after hatching, caterpillars burrow into the leaves and eat their inside cells. == Cultivation and uses == These plants are cultivated as ornamental houseplants and rock or succulent garden plants. They are popular because of their ease of propagation, low water requirements, and wide variety of flower colors typically borne in clusters well above the leaves. The section Bryophyllum—formerly an independent genus—contains species such as the "air-plant" Kalanchoe pinnata. In these plants, new individuals develop vegetatively as plantlets, also known as bulbils or gemmae, at indentations in leaf margins. These young plants eventually drop off and take root. No males have been found of one species of this genus which does flower and produce seeds, and it is commonly called the mother of thousands: Kalanchoe daigremontiana is thus an example of asexual reproduction. The cultivars 'Tessa' and 'Wendy' have
|
{
"page_id": 526827,
"source": null,
"title": "Kalanchoe"
}
|
gained the Royal Horticultural Society's Award of Garden Merit. == Diseases == == Traditional medicine == In traditional medicine, Kalanchoe species have been used to treat ailments such as infections, rheumatism and inflammation. Kalanchoe extracts also have immunosuppressive effects. Kalanchoe pinnata has been recorded in Trinidad and Tobago as being used as a traditional treatment for hypertension. A variety of bufadienolide compounds have been isolated from various Kalanchoe species. Five different bufadienolides have been isolated from Kalanchoe daigremontiana. Two of these, daigremontianin and bersaldegenin 1,3,5-orthoacetate, have been shown to have a pronounced sedative effect. They also have the strong positive inotropic effect associated with cardiac glycosides, and with greater doses an increasing effect on the central nervous system. Bufadienolide compounds isolated from Kalanchoe pinnata include bryophillin A which showed strong anti-tumor promoting activity, and bersaldegenin-3-acetate and bryophillin C which were less active. Bryophillin C also showed insecticidal properties. == References == == Bibliography == == External links == Media related to Kalanchoe at Wikimedia Commons Data related to Kalanchoe at Wikispecies
|
{
"page_id": 526827,
"source": null,
"title": "Kalanchoe"
}
|
The American Species Survival Plan or SSP program was developed in 1981 by the (American) Association of Zoos and Aquariums to help ensure the survival of selected species in zoos and aquariums, most of which are threatened or endangered in the wild. == SSP program == SSP programs focus on animals that are near threatened, threatened, endangered, or otherwise in danger of extinction in the wild, when zoo and zoology conservationists believe captive breeding programs will aid in their chances of survival. These programs help maintain healthy and genetically diverse animal populations within the Association of Zoos and Aquariums-accredited zoo community. AZA accredited zoos and AZA conservation partners that are involved in SSP programs engage in cooperative population management and conservation efforts that include research, conservation genetics, public education, reintroduction, and in situ or field conservation projects. The process for selecting recommended species is guided by Taxon Advisory Groups, whose sole objective is to curate Regional Collection Plans for the conservation needs of a species and how AZA institutions will cooperate to reach those needs. Today, there are almost 300 existing SSP programs. The SSP has been met with widespread success in ensuring that, should a species population become functionally extinct in its natural habitat, a viable population still exists within a zoological setting. This has also led to AZA species reintroduction programs, examples of which include the black-footed ferret, the California condor, the northern riffleshell, the golden lion tamarin, the Karner blue butterfly, the Oregon spotted frog, the palila finch, the red wolf, and the Wyoming toad. == SSP master plan == An SSP master plan is a document produced by the SSP coordinator (generally a zoo professional under the guidance of an elected management committee) for a certain species. This document sets ex situ population goals and other
|
{
"page_id": 7211500,
"source": null,
"title": "Species Survival Plan"
}
|
management recommendations to achieve the maximum genetic diversity and demographic stability for a species, given transfer and space constraints. == See also == European Endangered Species Programme == List of SSP programs == As of 2025, there are 295 species that are a part of the Species Survival Plan program. == Notes == == References == == External links == AZA website
|
{
"page_id": 7211500,
"source": null,
"title": "Species Survival Plan"
}
|
Isopeptag is a 16-amino acid peptide tag (TDKDMTITFTNKKDAE) that can be genetically linked to proteins without interfering with protein folding. What makes the isopeptag different from other peptide tags is that it can bind its binding protein through a permanent and irreversible covalent bond. Other peptide tags generally bind their targets through weak non-covalent interactions, thus limiting their use in applications where molecules experience extreme forces. The isopeptag's covalent binding to its target overcomes these barriers and allows target proteins to be studied in harsher molecular environments. == Development == The isopeptag was developed by dissecting the pilin protein (Spy0128) from Streptococcus pyogenes. Spy0128 contains two intramolecular isopeptide bonds, and to generate the isopeptag one of these bonds was split by removing the last β-strand in the protein. == Mode of action == When the isopeptag is bound to a target protein, it spontaneously binds its binding partner through an isopeptide bond, an amide bond formed autocatalytically. The reaction is robust and occurs at various temperatures from 4-37 °C, a pH range of 5–8, and in the presence of commonly used detergents. Also, the reaction is independent of the redox state of the environment and can occur equally well in both reducing and oxidizing conditions. == Applications == The covalent binding of the isopeptag to its binding partner can be used to permanently link proteins together in the complex environment of a bacterial cell, to target proteins of interest for cellular imaging, and to develop new protein structures. == References ==
|
{
"page_id": 28117484,
"source": null,
"title": "Isopeptag"
}
|
Miguel Andonie Fernández (30 October 1921 in Gualala, Santa Bárbara – 30 November 2013) was a Honduran chemist, pharmacologist, academic, politician and businessman of paternal Palestinian origin. He was associated with the Colegio de Químicos y Farmacéuticos. He was the chairman of Multimedia, SA and a real estate investor, and invested much in a chain of pharmacies in Honduras. He owned one of Honduras's most notable radio stations, Radio America. The National Congress of Honduras awarded him the Honor of Merit for his contributions to politics and science. == References ==
|
{
"page_id": 46795242,
"source": null,
"title": "Miguel Andonie Fernández"
}
|
== See also == Freezing-point depression Boiling-point elevation List of cooling baths == References ==
|
{
"page_id": 4655598,
"source": null,
"title": "List of boiling and freezing information of solvents"
}
|
In chemistry, efflorescence (Derived from the Latin verb 'efflorescere' roughly meaning 'to flower') is the migration of a salt to the surface of a porous material, where it forms a coating. The essential process involves the dissolving of an internally held salt in water or occasionally, in another solvent. The water, with the salt now held in solution, migrates to the surface, then evaporates, leaving a coating of the salt. In what has been described as "primary efflorescence", the water is the invader and the salt was already present internally, and a reverse process, where the salt is originally present externally and is then carried inside in solution, is referred to as "secondary efflorescence". Efflorescences can occur in natural and built environments. On porous construction materials it may present a cosmetic outer problem only (primary efflorescence causing staining), but can sometimes indicate internal structural weakness (migration/degradation of component materials). Efflorescence may clog the pores of porous materials, resulting in the destruction of those materials by internal water pressure, as seen in the spalling of brick. == Examples == A 5 molar concentration aqueous droplet of NaCl will spontaneously crystallize at 45% relative humidity (298 K) to form an NaCl cube by the mechanism of homogeneous nucleation. The original water is released to the gas phase. Gypsum (CaSO4.2H2O) is a hydrate solid that, in a sufficiently dry environment, will give up its water to the gas phase and form anhydrite (CaSO4). Copper(II) sulfate (bluestone) (CuSO4.5H2O) is a blue crystalline solid that when exposed to air, slowly loses water of crystallization from its surface to form a white layer of anhydrous copper(II) sulfate. Sodium carbonate decahydrate (Na2CO3.10H2O) will lose water when exposed to air. == Masonry == === Primary efflorescence === Primary efflorescence is named such, as it typically occurs during the
|
{
"page_id": 1378800,
"source": null,
"title": "Efflorescence"
}
|
initial cure of a cementitious product. It often occurs on masonry construction, particularly brick, as well as some firestop mortars, when water moving through a wall or other structure, or water being driven out as a result of the heat of hydration as cement stone is being formed, brings salts to the surface that are not commonly bound as part of the cement stone. As the water evaporates, it leaves the salt behind, which forms a white, fluffy deposit, that can normally be brushed off. The resulting white deposits are referred to as "efflorescence" in this instance. In this context efflorescence is sometimes referred to as "saltpetering." Since primary efflorescence brings out salts that are not ordinarily part of the cement stone, it is not a structural, but, rather, an aesthetic concern. For controlling primary efflorescence, formulations containing liquid fatty acid mixtures (e.g., oleic acid and linoleic acid) have commonly been used. The oily liquid admixture is introduced into the batch mix at an early stage by coating onto the sand particles prior to the introduction of any mix water, so that the oily admixture is distributed uniformly throughout the concrete batch mix. === Secondary efflorescence === Secondary efflorescence is named such as it does not occur as a result of the forming of the cement stone or its accompanying hydration products. Rather, it is usually due to the external influence of concrete poisons, such as chlorides. A very common example of where secondary efflorescence occurs is steel-reinforced concrete bridges as well as parking garages. Saline solutions are formed due to the presence of road salt in the winter. This saline solution is absorbed into the concrete, where it can begin to dissolve cement stone, which is of primary structural importance. Virtual stalactites can be formed in some cases as
|
{
"page_id": 1378800,
"source": null,
"title": "Efflorescence"
}
|
a result of dissolved cement stone, hanging off cracks in concrete structures. Where this process has taken hold, the structural integrity of a concrete element is at risk. This is a common traffic infrastructure and building maintenance concern. Secondary efflorescence is akin to osteoporosis of the concrete. For controlling secondary efflorescence, admixtures containing aqueous-based calcium stearate dispersion (CSD) are often added at a later stage of the batching process with the mix water. In a typical batching process, sand is first charged into the mixer, then the oil-based primary anti-efflorescence admixture is added with constant mixing to allow the oil to coat the sand. Then coarse aggregates, colorants, and cement are added, followed by water. If CSD is used, it is then introduced usually at this point during or after the addition of the mix water. CSD is an aqueous dispersion wherein fine solid particles of calcium stearate are suspended in the water uniformly. Commercially available CSD has an average particle size of about 1 to 10 micrometres. The uniform distribution of CSD in the mix may render the resulting concrete masonry unit water repellent, as CSD particles are well distributed in the pores of the unit to interfere with the capillary movement of water. Calthemite is also a secondary deposit derived from concrete, mortar or lime, which can be mistakenly assumed to be efflorescence. Calthemites are usually deposited as calcite which is the most stable polymorph of calcium carbonate (CaCO3). === Protecting against efflorescence === The only way to completely and permanently prevent (both primary and secondary) efflorescence in cementitious materials is by using special admixtures that chemically react with and bind the salt-based impurities in the concrete when hydrogen (H) is present. The chemical reaction in these special additives fuses the sodium chloride on a nanomolecular level, converting
|
{
"page_id": 1378800,
"source": null,
"title": "Efflorescence"
}
|
it into non-sodium chemicals and other harmless matter that will not leach out or migrate to the surface. In fact, the nanotechnology in these additives can be up to 100,000 times smaller than even the smallest cement particles, allowing their molecules to literally pass through cement minerals or sand particles and ultimately become part of the cement or sand with which they react. And since they require the presence of hydrogen they stop reacting as the concrete dries out and begin reacting again when the concrete is exposed to moisture. It is also possible to protect porous building materials such as brick, tiles, and concrete against efflorescence by treating the material with an impregnating, hydro-phobic sealer. This is a sealer that repels water and will penetrate deeply enough into the material to keep water and dissolved salts well away from the surface. However, in climates where freezing is a concern, such a sealer may lead to damage from freeze/thaw cycles. And while it will help to protect against efflorescence, it cannot permanently prevent the problem. Efflorescence can often be removed from concrete using phosphoric acid. After application the acid dilution is neutralised with mild diluted detergent, and then well rinsed with water. However, if the source of the water penetration is not addressed efflorescence may reappear. Common rebar protective measures include the use of epoxy coating as well as the use of a slight electrical charge, both of which prevent rusting. One may also use stainless steel rebar. Certain cement types are less resistant to chlorides than others. The choice of cement, therefore, can have a large effect upon the concrete's reaction to chlorides. Today's water repellents help create a vapor permeable barrier; liquid water, especially from wind driven rains, will stay out of the brick and masonry. Water vapor
|
{
"page_id": 1378800,
"source": null,
"title": "Efflorescence"
}
|
from the interior of the building, or from the underside of pavers can escape. This will reduce efflorescence, spalling and scaling that can occur from water being trapped inside the brick substrate and freezing during cold weather. Years ago, the water repellents trapped moisture in the masonry wall creating more problems than they solved. Condensation in areas that experienced the four seasons were much more problematic than their counterparts. === Image gallery === == See also == Calthemite Hydrate Hygroscopy Our Lady of the Underpass == References ==
|
{
"page_id": 1378800,
"source": null,
"title": "Efflorescence"
}
|
A field-theoretic simulation is a numerical strategy to calculate structure and physical properties of a many-particle system within the framework of a statistical field theory, like e.g. a polymer field theory. A convenient possibility is to use Monte Carlo (MC) algorithms, to sample the full partition function integral expressed in field-theoretic representation. The procedure is then called the auxiliary field Monte Carlo method. However, it is well known that MC sampling in conjunction with the basic field-theoretic representation of the partition function integral, directly obtained via the Hubbard-Stratonovich transformation, is impracticable, due to the so-called numerical sign problem (Baeurle 2002, Fredrickson 2002). The difficulty is related to the complex and oscillatory nature of the resulting distribution function, which causes a bad statistical convergence of the ensemble averages of the desired structural and thermodynamic quantities. In such cases special analytical and numerical techniques are required to accelerate the statistical convergence of the field-theoretic simulation (Baeurle 2003, Baeurle 2003a, Baeurle 2004). == Shifted-contour Monte Carlo technique == === Mean field representation === To make the field-theoretic methodology amenable for computation, Baeurle proposed to shift the contour of integration of the partition function integral through the homogeneous mean field (MF) solution using Cauchy's integral theorem, which provides its so-called mean-field representation. This strategy was previously successfully employed in field-theoretic electronic structure calculations (Rom 1997, Baer 1998). Baeurle could demonstrate that this technique provides a significant acceleration of the statistical convergence of the ensemble averages in the MC sampling procedure (Baeurle 2002). === Gaussian equivalent representation === In subsequent works Baeurle et al. (Baeurle 2002, Baeurle 2002a) applied the concept of tadpole renormalization, which originates from quantum field theory and leads to the Gaussian equivalent representation of the partition function integral, in conjunction with advanced MC techniques in the grand canonical ensemble. They could
|
{
"page_id": 19728890,
"source": null,
"title": "Field-theoretic simulation"
}
|
convincingly demonstrate that this strategy provides an additional boost in the statistical convergence of the desired ensemble averages (Baeurle 2002). == Alternative techniques == Other promising field-theoretic simulation techniques have been developed recently, but they either still lack the proof of correct statistical convergence, like e.g. the Complex Langevin method (Ganesan 2001), and/or still need to prove their effectiveness on systems, where multiple saddle points are important (Moreira 2003). == References == Baeurle, S.A. (2002). "Method of Gaussian Equivalent Representation: A New Technique for Reducing the Sign Problem of Functional Integral Methods". Physical Review Letters. 89 (8): 080602. Bibcode:2002PhRvL..89h0602B. doi:10.1103/PhysRevLett.89.080602. PMID 12190451. Fredrickson, G.H.; Ganesan, V.; Drolet, F. (2002). "Field-Theoretic Computer Simulation Methods for Polymers and Complex Fluids" (PDF). Macromolecules. 35 (1): 16. Bibcode:2002MaMol..35...16F. doi:10.1021/ma011515t. Archived from the original (PDF) on 2005-09-02. Baeurle, S.A. (2003). "Computation within the auxiliary field approach". Journal of Computational Physics. 184 (2): 540–558. Bibcode:2003JCoPh.184..540B. doi:10.1016/S0021-9991(02)00036-0. Baeurle, S.A. (2003a). "The stationary phase auxiliary field Monte Carlo method: a new strategy for reducing the sign problem of auxiliary field methodologies". Computer Physics Communications. 154 (2): 111–120. Bibcode:2003CoPhC.154..111B. doi:10.1016/S0010-4655(03)00284-4. Baeurle, S.A. (2004). "Grand canonical auxiliary field Monte Carlo: a new technique for simulating open systems at high density". Computer Physics Communications. 157 (3): 201–206. Bibcode:2004CoPhC.157..201B. doi:10.1016/j.comphy.2003.11.001. Rom, N.; Charutz, D.M.; Neuhauser, D. (1997). "Shifted-contour auxiliary-field Monte Carlo: circumventing the sign difficulty for electronic-structure calculations". Chemical Physics Letters. 270 (3–4): 382. Bibcode:1997CPL...270..382R. doi:10.1016/S0009-2614(97)00370-9. Baer, R.; Head-Gordon, M.; Neuhauser, D. (1998). "Shifted-contour auxiliary field Monte Carlo for ab initio electronic structure: Straddling the sign problem". Journal of Chemical Physics. 109 (15): 6219. Bibcode:1998JChPh.109.6219B. doi:10.1063/1.477300. Baeurle, S.A.; Martonak, R.; Parrinello, M. (2002a). "A field-theoretical approach to simulation in the classical canonical and grand canonical ensemble". Journal of Chemical Physics. 117 (7): 3027. Bibcode:2002JChPh.117.3027B. doi:10.1063/1.1488587. Ganesan, V.; Fredrickson, G.H. (2001). "Field-theoretic polymer
|
{
"page_id": 19728890,
"source": null,
"title": "Field-theoretic simulation"
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|
simulations". Europhysics Letters. 55 (6): 814. Bibcode:2001EL.....55..814G. doi:10.1209/epl/i2001-00353-8. S2CID 250821375. Moreira, A.G.; Baeurle, S.A.; Fredrickson, G.H. (2003). "Global Stationary Phase and the Sign Problem". Physical Review Letters. 91 (15): 150201. arXiv:physics/0304086. Bibcode:2003PhRvL..91o0201M. doi:10.1103/PhysRevLett.91.150201. PMID 14611450. S2CID 38324821. == External links == Theory and Computation of Advanced Materials and Sensors Group
|
{
"page_id": 19728890,
"source": null,
"title": "Field-theoretic simulation"
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Supersonic fractures are fractures where the fracture propagation velocity is higher than the speed of sound in the material. This phenomenon was first discovered by scientists from the Max Planck Institute for Metals Research in Stuttgart (Markus J. Buehler and Huajian Gao) and IBM Almaden Research Center in San Jose, California (Farid F. Abraham). The issues of intersonic and supersonic fracture become the frontier of dynamic fracture mechanics. The work of Burridge initiated the exploration for intersonic crack growth (when the crack tip velocity V is between the shear in wave speed C^8 and the longitudinal wave speed C^1. Supersonic fracture was a phenomenon totally unexplained by the classical theories of fracture. Molecular dynamics simulations by the group around Abraham and Gao have shown the existence of intersonic mode I and supersonic mode II cracks. This motivated a continuum mechanics analysis of supersonic mode III cracks by Yang. Recent progress in the theoretical understanding of hyperelasticity in dynamic fracture has shown that supersonic crack propagation can only be understood by introducing a new length scale, called χ; which governs the process of energy transport near a crack tip. The crack dynamics is completely dominated by material properties inside a zone surrounding the crack tip with characteristic size equal to χ. When the material inside this characteristic zone is stiffened due to hyperelastic properties, cracks propagate faster than the longitudinal wave speed. The research group of Gao has used this concept to simulate the Broberg problem of crack propagation inside a stiff strip embedded in a soft elastic matrix. These simulations confirmed the existence of an energy characteristic length. This study also had implications for dynamic crack propagation in composite materials. If the characteristic size of the composite microstructure is larger than the energy characteristic length, χ; models that homogenize the
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{
"page_id": 2230778,
"source": null,
"title": "Supersonic fracture"
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|
materials into an effective continuum would be in significant error. The challenge arises of designing experiments and interpretative simulations to verify the energy characteristic length. Confirmation of the concept must be sought in the comparison of experiments on supersonic cracks and the predictions of the simulations and analysis. While much excitement rightly centres on the relatively new activity related to intersonic cracking, an old but interesting possibility remains to be incorporated in the modern work: for an interface between elastically dissimilar materials, crack propagation that is subsonic but exceeds the Rayleigh wave speed has been predicted for at least some combinations of the elastic properties of the two materials. == See also == Characteristic energy length scale == References ==
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{
"page_id": 2230778,
"source": null,
"title": "Supersonic fracture"
}
|
Cultured dextrose is a food additive used to inhibit the growth of undesirable bacteria and mold in food. Often used in place of benzoates and sorbates, it is considered by some consumers to be a more "natural" ingredient, because it is prepared by the fermentation of milk or sugar powders by the probiotic bacteria Propionibacterium freudenreichii and Lactococcus lactis, both of which are extensively used in the production of cheese and other dairy products. Cultured dextrose consists of a mixture of fermentation metabolites, including butyric, propionic and lactic acids and small peptides. As sold, it is an off-white powder. Cultured dextrose is marketed under several trade names including bioVONTAGE from Third Wave Bioactives and MicroGARD by Danisco, a unit of DuPont. These ingredients are used in a range of foods including dairy products, salad dressings, and baked goods. == References ==
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{
"page_id": 36571648,
"source": null,
"title": "Cultured dextrose"
}
|
The following is a list of terms used to describe biological disorders of development, arranged by root word and shared prefix: == References == == Bibliography == Reece JB, Urry LA, Cain ML, Wasserman SA, Minorsky PV, Jackson RB. Campbell Biology (10th ed.). Addison Wesley Longman; 2014. ISBN 978-0321834959
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{
"page_id": 50727426,
"source": null,
"title": "List of biological development disorders"
}
|
Strange matter (or strange quark matter) is quark matter containing strange quarks. In extreme environments, strange matter is hypothesized to occur in the core of neutron stars, or, more speculatively, as isolated droplets that may vary in size from femtometers (strangelets) to kilometers, as in the hypothetical strange stars. At high enough density, strange matter is expected to be color superconducting. Ordinary matter, also referred to as atomic matter, is composed of atoms, with nearly all matter concentrated in the atomic nuclei. Nuclear matter is a liquid composed of neutrons and protons, and they are themselves composed of up and down quarks. Quark matter is a condensed form of matter composed entirely of quarks. When quark matter does not contain strange quarks, it is sometimes referred to as non-strange quark matter. == Context == In particle physics and astrophysics, the term 'strange matter' is used in two different contexts, one broader and the other more specific and hypothetical: In the broader context, our current understanding of the laws of nature predicts that strange matter could be created when nuclear matter (made of protons and neutrons) is compressed beyond a critical density. At this critical pressure and density, the protons and neutrons dissociate into quarks, yielding quark matter and potentially strange matter. A more specific hypothesis is that quark matter is the true ground state of all matter, and thus more stable than ordinary nuclear matter. This idea is known as the "strange matter hypothesis", or the Bodmer–Witten assumption. Under this hypothesis, the nuclei of the atoms we see around us are only metastable, even when the external critical pressure is zero, and given enough time (or the right stimulus) the nuclei would decay into stable droplets of strange matter. Droplets of strange matter are also referred to as strangelets. ==
|
{
"page_id": 20646400,
"source": null,
"title": "Strange matter"
}
|
Stability of strange matter only at high pressure == In the general context, strange matter might occur inside neutron stars, if the pressure at their core is high enough to provide a sufficient gravitational force (i.e. above the critical pressure). At the sort of densities and high pressures we expect in the center of a neutron star, the quark matter would probably be strange matter. It could conceivably be non-strange quark matter, if the effective mass of the strange quark were too high. Charm quarks and heavier quarks would only occur at much higher densities. Strange matter comes about as a way to relieve degeneracy pressure. The Pauli exclusion principle forbids fermions such as quarks from occupying the same position and energy level. When the particle density is high enough that all energy levels below the available thermal energy are already occupied, increasing the density further requires raising some to higher, unoccupied energy levels. This need for energy to cause compression manifests as a pressure. Neutrons consist of twice as many down quarks (charge −1/3 e) as up quarks (charge +2/3 e), so the degeneracy pressure of down quarks usually dominates electrically neutral quark matter. However, when the required energy level is high enough, an alternative becomes available: half of the down quarks can be transmuted to strange quarks (charge −1/3 e). The higher rest mass of the strange quark costs some energy, but by opening up an additional set of energy levels, the average energy per particle can be lower,: 5 making strange matter more stable than non-strange quark matter. A neutron star with a quark matter core is often called a hybrid star. However, it is difficult to know whether hybrid stars really exist in nature because physicists currently have little idea of the likely value of the
|
{
"page_id": 20646400,
"source": null,
"title": "Strange matter"
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|
critical pressure or density. It seems plausible that the transition to quark matter will already have occurred when the separation between the nucleons becomes much smaller than their size, so the critical density must be less than about 100 times nuclear saturation density. But a more precise estimate is not yet available, because the strong interaction that governs the behavior of quarks is mathematically intractable, and numerical calculations using lattice QCD are currently blocked by the fermion sign problem. One major area of activity in neutron star physics is the attempt to find observable signatures by which we could tell whether neutron stars have quark matter (probably strange matter) in their core. During the merger of two neutron stars, strange matter may be ejected out into the space around the stars, which may allow for the studying of strange matter. However, the rate at which strange matter decays is unknown, and there are very few binary pairs of neutron stars nearby to the Solar System, which could make the official discovery of strange matter very difficult. == Stability of strange matter at zero pressure == If the "strange matter hypothesis" is true, then nuclear matter is metastable against decaying into strange matter. The lifetime for spontaneous decay is very long, so we do not see this decay process happening around us. However, under this hypothesis there should be strange matter in the universe: Quark stars (often called "strange stars") consist of quark matter from their core to their surface. They would be several kilometers across, and may have a very thin crust of nuclear matter. Strangelets are small pieces of strange matter, perhaps as small as nuclei. They would be produced when strange stars are formed or collide, or when a nucleus decays. == See also == Exotic matter –
|
{
"page_id": 20646400,
"source": null,
"title": "Strange matter"
}
|
Physics term for multiple concepts Quark star – Compact exotic star which forms matter consisting mostly of quarks Strangeness and quark–gluon plasma – subatomic signature Strangelet – Type of hypothetical particle Quark – Elementary particle, main constituent of matter QCD matter – Hypothetical phases of matter == References ==
|
{
"page_id": 20646400,
"source": null,
"title": "Strange matter"
}
|
The chaperone code refers to post-translational modifications of molecular chaperones that control protein folding. Whilst the genetic code specifies how DNA makes proteins, and the histone code regulates histone-DNA interactions, the chaperone code controls how proteins are folded to produce a functional proteome. The chaperone code refers to the combinatorial array of post-translational modifications (enzymes add chemical modifications to amino acids that change their properties) —i.e. phosphorylation, acetylation, ubiquitination, methylation, etc.—that are added to molecular chaperones to modulate their activity. Molecular chaperones are proteins specialized in folding and unfolding of the other cellular proteins, and the assembly and dismantling of protein complexes. This is critical in the regulation of protein-protein interactions and many cellular functions. Because post-translational modifications are marks that can be added and removed rapidly, they provide an efficient mechanism to explain the plasticity observed in proteome organization during cell growth and development. The chaperone code concept posits that combinations of post-translational modifications at the surface of chaperones, including phosphorylation, acetylation, methylation, ubiquitination, control protein folding/unfolding and protein complex assembly/disassembly by modulating: 1) chaperone-substrate affinity and specificity 2) chaperone ATPase and therefore its refolding activity 3) chaperone localization 4) chaperone-co-chaperone interaction. == Levels of the Chaperone Code == The Chaperone code is incredibly complex with multiple layers of potential regulation. Studies of the chaperone code may include: Level 1: Understanding the role and regulation of single PTMs on a single chaperone Level 2: Cross-talk of different PTMs on a single amino acid or between PTMs on different amino acids (on a single chaperone) Level 3: Understanding of why chaperone paralogs have different PTMs Level 4: Cross-talk of PTMs between different chaperones i.e. between Hsp90 and Hsp70 Level 5: Understanding the role and regulation of single PTMs on a single co-chaperone molecule Level 6: Understanding the entire chaperone code-all
|
{
"page_id": 38734340,
"source": null,
"title": "Chaperone code"
}
|
the PTMs on all major chaperones, co-chaperones that control all aspects of life. == Phosphorylation == Site-specific phosphorylation of chaperone proteins can affect their activity. In some cases phosphorylation may disrupt the interaction with a co-chaperone protein thus negatively affecting its activity. In other instances it may promote the activation of particular chaperone targets (referred to as clients). Enzymes such as protein kinase A, casein kinase 1 and 2 (CK1 and CK2), and glycogen synthase kinase B serve as kinases for chaperone proteins. HSP70, a major chaperone protein, was identified in 2012 as a hotspot of phospho-regulation. Subsequently, phosphorylation of chaperone protein HSP70 by a cyclin dependent kinase was shown to delay cell cycle progression in yeast and mammals by altering cyclin D1 stability (a key regulator of the cell cycle). Phosphorylation of HSP90 (another major chaperone) at threonine 22, was shown to disrupt its interaction with co-chaperone proteins Aha1 and CD37 (interacting proteins required for function) and decrease its activity. Certain pathogenic bacteria may manipulate host chaperone phosphorylation through bacterial effectors to promote their survival. HoPBF1, a family of bacterial effector protein kinases, phosphorylates HSP90 at Serine 99 to dampen immunity. == Methylation == Chaperone proteins are also regulated by methylation. This can occur through a conformational change (or a change in the structure of the protein), such that the interactions and activity of the protein are changed. For instance, the monomethylation of HSP90 lysine 616 by Smyd2, and its reversal by LSD1, regulate enzymatic activity of HSP90. == References ==
|
{
"page_id": 38734340,
"source": null,
"title": "Chaperone code"
}
|
The Russo–Susskind–Thorlacius model or RST model in short is a modification of the CGHS model to take care of conformal anomalies and render it analytically soluble. In the CGHS model, if we include Faddeev–Popov ghosts to gauge-fix diffeomorphisms in the conformal gauge, they contribute an anomaly of -24. Each matter field contributes an anomaly of 1. So, unless N=24, we will have gravitational anomalies. To the CGHS action S CGHS = 1 2 π ∫ d 2 x − g { e − 2 ϕ [ R + 4 ( ∇ ϕ ) 2 + 4 λ 2 ] − ∑ i = 1 N 1 2 ( ∇ f i ) 2 } {\displaystyle S_{\text{CGHS}}={\frac {1}{2\pi }}\int d^{2}x\,{\sqrt {-g}}\left\{e^{-2\phi }\left[R+4\left(\nabla \phi \right)^{2}+4\lambda ^{2}\right]-\sum _{i=1}^{N}{\frac {1}{2}}\left(\nabla f_{i}\right)^{2}\right\}} , the following term S RST = − κ 8 π ∫ d 2 x − g [ R 1 ∇ 2 R − 2 ϕ R ] {\displaystyle S_{\text{RST}}=-{\frac {\kappa }{8\pi }}\int d^{2}x\,{\sqrt {-g}}\left[R{\frac {1}{\nabla ^{2}}}R-2\phi R\right]} is added, where κ is either ( N − 24 ) / 12 {\displaystyle (N-24)/12} or N / 12 {\displaystyle N/12} depending upon whether ghosts are considered. The nonlocal term leads to nonlocality. In the conformal gauge, S RST = − κ π ∫ d x + d x − [ ∂ + ρ ∂ − ρ + ϕ ∂ + ∂ − ρ ] {\displaystyle S_{\text{RST}}=-{\frac {\kappa }{\pi }}\int dx^{+}\,dx^{-}\left[\partial _{+}\rho \partial _{-}\rho +\phi \partial _{+}\partial _{-}\rho \right]} . It might appear as if the theory is local in the conformal gauge, but this overlooks the fact that the Raychaudhuri equations are still nonlocal. == References ==
|
{
"page_id": 30542341,
"source": null,
"title": "RST model"
}
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Jordan's rule (sense 1) is an ecogeographical rule that describes the inverse relationship between water temperature and meristic characteristics in various species of fish. The most commonly observed relationship is that fin ray, vertebrae, or scale numbers increase with decreasing temperature. The rule is named after David Starr Jordan (1851–1931), the father of American ichthyology. Jordan's law (or rule) (sense 2) is also an ecogeographical rule (named after the same scientist) that states: "‘[g]iven any species in any region, the nearest related species is not likely to be found in the same region nor in a remote region, but in a neighbouring district separated from the first by a barrier of some sort’ This "rule" is frequently violated (see discussion in Fitzpatrick & Turelli 2007), but when patterns are consistent with Jordan's rule (sense 2), this suggests an important role for allopatric speciation in the diversification of the clade in question. Jordan himself wrote: "To this generalization Dr. Allen, in a late number of Science, gives the name of 'Jordan's Law.' The present writer makes no claim to the discovery of this law. The language above quoted is his, but the idea is familiar to all students of geographical distribution and goes back to the master in that field, Moritz Wagner." Thus, Jordan's law is an example of Stigler's law. == See also == Allen's rule Allopatric speciation Bergman's rule Jordan's Principle == References ==
|
{
"page_id": 13961741,
"source": null,
"title": "Jordan's rule"
}
|
In polymer chemistry, gelation (gel transition) is the formation of a gel from a system with polymers. Branched polymers can form links between the chains, which lead to progressively larger polymers. As the linking continues, larger branched polymers are obtained and at a certain extent of the reaction, links between the polymer result in the formation of a single macroscopic molecule. At that point in the reaction, which is defined as gel point, the system loses fluidity and viscosity becomes very large. The onset of gelation, or gel point, is accompanied by a sudden increase in viscosity. This "infinite" sized polymer is called the gel or network, which does not dissolve in the solvent, but can swell in it. == Background == Gelation is promoted by gelling agents. Gelation can occur either by physical linking or by chemical crosslinking. While the physical gels involve physical bonds, chemical gelation involves covalent bonds. The first quantitative theories of chemical gelation were formulated in the 1940s by Flory and Stockmayer. Critical percolation theory was successfully applied to gelation in 1970s. A number of growth models (diffusion limited aggregation, cluster-cluster aggregation, kinetic gelation) were developed in the 1980s to describe the kinetic aspects of aggregation and gelation. == Quantitative approaches to determine gelation == It is important to be able to predict the onset of gelation, since it is an irreversible process that dramatically changes the properties of the system. === Average functionality approach === According to the Carothers equation number-average degree of polymerization D P n {\displaystyle DP_{n}} is given by D P n = 2 2 − p . f a v {\displaystyle DP_{n}={\frac {2}{2-p.f_{av}}}} where p {\displaystyle p} is the extent of the reaction and f a v {\displaystyle f_{av}} is the average functionality of reaction mixture. For the gel D
|
{
"page_id": 21301778,
"source": null,
"title": "Gelation"
}
|
P n {\displaystyle DP_{n}} can be considered to be infinite, thus the critical extent of the reaction at the gel point is found as p c = 2 f a v {\displaystyle p_{c}={\frac {2}{f_{av}}}} If p {\displaystyle p} is greater or equal to p c {\displaystyle p_{c}} , gelation occurs. === Flory Stockmayer approach === Flory and Stockmayer used a statistical approach to derive an expression to predict the gel point by calculating when D P n {\displaystyle DP_{n}} approaches infinite size. The statistical approach assumes that (1) the reactivity of the functional groups of the same type is the same and independent of the molecular size and (2) there are no intramolecular reactions between the functional groups on the same molecule. Consider the polymerization of bifunctional molecules A − A {\displaystyle A-A} , B − B {\displaystyle B-B} and multifunctional A f {\displaystyle A_{f}} , where f {\displaystyle f} is the functionality. The extends of the functional groups are p A {\displaystyle p_{A}} and p B {\displaystyle p_{B}} , respectively. The ratio of all A groups, both reacted and unreacted, that are part of branched units, to the total number of A groups in the mixture is defined as ρ {\displaystyle \rho } . This will lead to the following reaction A − A + B − B + A f → A f − 1 − ( B − B A − A ) n B − B A − A f − 1 {\displaystyle A-A+B-B+A_{f}\rightarrow A_{f-1}-(B-BA-A)_{n}B-BA-A_{f-1}} The probability of obtaining the product of the reaction above is given by p A [ p B ( 1 − ρ ) p A ] n p B ρ {\displaystyle p_{A}[p_{B}(1-\rho )p_{A}]^{n}p_{B}\rho } , since the probability that a B group reach with a branched unit is p B ρ
|
{
"page_id": 21301778,
"source": null,
"title": "Gelation"
}
|
{\displaystyle p_{B}\rho } and the probability that a B group react with non-branched A is p B ( 1 − ρ ) {\displaystyle p_{B}(1-\rho )} . This relation yields to an expression for the extent of reaction of A functional groups at the gel point p c = 1 { r [ 1 + ρ ( f − 2 ) ] } 1 / 2 {\displaystyle p_{c}={\frac {1}{\{r[1+\rho (f-2)]\}^{1/2}}}} where r is the ratio of all A groups to all B groups. If more than one type of multifunctional branch unit is present and average f {\displaystyle f} value is used for all monomer molecules with functionality greater than 2. Note that the relation does not apply for reaction systems containing monofunctional reactants and/or both A and B type of branch units. === Erdős–Rényi model === Gelation of polymers can be described in the framework of the Erdős–Rényi model or the Lushnikov model, which answers the question when a giant component arises. === Random graph === The structure of a gel network can be conceptualised as a random graph. This analogy is exploited to calculate the gel point and gel fraction for monomer precursors with arbitrary types of functional groups. Random graphs can be used to derive analytical expressions for simple polymerisation mechanisms, such as step-growth polymerisation, or alternatively, they can be combined with a system of rate equations that are integrated numerically. == See also == Mechanics of gelation == References ==
|
{
"page_id": 21301778,
"source": null,
"title": "Gelation"
}
|
Group Aβ of the type II sensory fiber is a type of sensory fiber, the second of the two main groups of touch receptors. The responses of different type Aβ fibers to these stimuli can be subdivided based on their adaptation properties, traditionally into rapidly adapting (RA) or slowly adapting (SA) neurons. Type II sensory fibers are slowly-adapting (SA), meaning that even when there is no change in touch, they keep respond to stimuli and fire action potentials. In the body, Type II sensory fibers belong to pseudounipolar neurons. The most notable example are neurons with Merkel cell-neurite complexes on their dendrites (sense static touch) and Ruffini endings (sense stretch on the skin and over-extension inside joints). Under pathological conditions they may become hyper-excitable leading to stimuli that would usually elicit sensations of tactile touch causing pain. These changes are in part induced by PGE2 which is produced by COX1, and type II fibers with free nerve endings are likely to be the subdivision of fibers that carry out this function. Group Aα of the type II sensory fiber is another type of sensory fiber, which participate in the sensation of body position (proprioception). In each muscle, we have 10-100 tiny muscle-like pockets called muscle spindles. The type II fibers (aka secondary fibers) connect to nuclear chain fibers and static nuclear bag fibers in muscle spindles, but not to dynamic nuclear bag fibers. The typical innervation to muscle spindles consists of one type Ia fiber and 2 type II fibers. The type Ia fiber has "annulospiral" endings around the middle parts of the intrafusal fibers compared to type II fibers that have "flower spray" endings which may be spray shaped or annular, spreading in narrow bands on both sides of the chain or bag fiber. It is thought that the
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{
"page_id": 11078164,
"source": null,
"title": "Type II sensory fiber"
}
|
Ia fibers signal the degree of change in muscle movement, and the type II fibers signal the length of the muscle (which is later used for forming the perception of the body in space). == References ==
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{
"page_id": 11078164,
"source": null,
"title": "Type II sensory fiber"
}
|
In mechanical engineering, the Beale number is a parameter that characterizes the performance of Stirling engines. It is often used to estimate the power output of a Stirling engine design. For engines operating with a high temperature differential, typical values for the Beale number are in the range 0.11−0.15; where a larger number indicates higher performance. == Definition == The Beale number can be defined in terms of a Stirling engine's operating parameters: B n = W o P V F {\displaystyle B_{n}={\frac {Wo}{PVF}}} where: Bn is the Beale number Wo is the power output of the engine (watts) P is the mean average gas pressure (Pa) or (MPa, if volume is in cm3) V is swept volume of the power piston (m3, or cm3, if pressure is in MPa) F is the engine cycle frequency (Hz) == Estimating Stirling power == To estimate the power output of an engine, nominal values are assumed for the Beale number, pressure, swept volume and frequency, then the power is calculated as the product of these parameters, as follows: W o = B n P V F {\displaystyle Wo=B_{n}PVF} == See also == West number == References == == External links == Stirling Engine Performance Calculator Beale number calculator
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{
"page_id": 7604764,
"source": null,
"title": "Beale number"
}
|
In chronobiology, an infradian rhythm is a rhythm with a period longer than the period of a circadian rhythm, i.e., one cycle is longer than 24 hours. Some examples of infradian rhythms in mammals include menstruation, breeding, migration, hibernation, molting and fur or hair growth, and tidal or seasonal rhythms. In contrast, ultradian rhythms have periods shorter (<24 hours) than the period of a circadian rhythm. Several infradian rhythms are known to be caused by hormone or neurotransmitter stimulation or by environmental factors such as the lunar cycles. For example, seasonal depression, an example of an infradian rhythm occurring once a year, can be caused by the systematic lowering of light levels during the winter. The seasonal affective disorder can be classified as infradian, or as circannual, which means occurring on a yearly basis. The most well-known infradian rhythm in humans is the fluctuation of estrogens and progesterone across the menstrual cycle. Another example in humans is the ~10-day rhythms of enamel growth. Other infradian rhythms have been documented in organisms such as dormice, lemmings, voles, lynx, mice, etc. Other writers more narrowly define infradian rhythms as rhythms longer than 24 hour but shorter than one year; categorizing rhythms of about a year as circannual rhythms (circannual cycle). Some studies observe an infradian rhythm with a period of approximately 7 days (circaseptan rhythm). However, these rhythms appear to be an artifact of the statistics applied to the raw data. == See also == Photoperiodicity == References ==
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{
"page_id": 3541535,
"source": null,
"title": "Infradian rhythm"
}
|
Ants are eusocial insects of the family Formicidae and, along with the related wasps and bees, belong to the order Hymenoptera. Ants evolved from vespoid wasp ancestors in the Cretaceous period. More than 13,800 of an estimated total of 22,000 species have been classified. They are easily identified by their geniculate (elbowed) antennae and the distinctive node-like structure that forms their slender waists. Ants form colonies that range in size from a few dozen individuals often living in small natural cavities to highly organised colonies that may occupy large territories with sizeable nest that consist of millions of individuals or into the hundreds of millions in super colonies. Typical colonies consist of various castes of sterile, wingless females, most of which are workers (ergates), as well as soldiers (dinergates) and other specialised groups. Nearly all ant colonies also have some fertile males called "drones" and one or more fertile females called "queens" (gynes). The colonies are described as superorganisms because the ants appear to operate as a unified entity, collectively working together to support the colony. Ants have colonised almost every landmass on Earth. The only places lacking indigenous ants are Antarctica and a few remote or inhospitable islands. Ants thrive in moist tropical ecosystems and may exceed the combined biomass of wild birds and mammals. Their success in so many environments has been attributed to their social organisation and their ability to modify habitats, tap resources, and defend themselves. Their long co-evolution with other species has led to mimetic, commensal, parasitic, and mutualistic relationships. Ant societies have division of labour, communication between individuals, and an ability to solve complex problems. These parallels with human societies have long been an inspiration and subject of study. Many human cultures make use of ants in cuisine, medication, and rites. Some species are
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{
"page_id": 2594,
"source": null,
"title": "Ant"
}
|
valued in their role as biological pest control agents. Their ability to exploit resources may bring ants into conflict with humans, however, as they can damage crops and invade buildings. Some species, such as the red imported fire ant (Solenopsis invicta) of South America, are regarded as invasive species in other parts of the world, establishing themselves in areas where they have been introduced accidentally. == Etymology == The word ant and the archaic word emmet are derived from ante, emete of Middle English, which come from ǣmette of Old English; these are all related to Low Saxon e(e)mt, empe and varieties (Old Saxon emeta) and to German Ameise (Old High German āmeiza). All of these words come from West Germanic *ǣmaitjōn, and the original meaning of the word was "the biter" (from Proto-Germanic *ai-, "off, away" + *mait- "cut"). The family name Formicidae is derived from the Latin formīca ("ant") from which the words in other Romance languages, such as the Portuguese formiga, Italian formica, Spanish hormiga, Romanian furnică, and French fourmi are derived. The study of ants is called myrmecology, from Ancient Greek μύρμηξ mýrmēx ("ant"). It has been hypothesised that a Proto-Indo-European word *morwi- was the root for Sanskrit vamrah, Greek μύρμηξ mýrmēx, Latin formīca, Old Church Slavonic mraviji, Old Irish moirb, Old Norse maurr, Dutch mier, Swedish myra, Danish myre, Middle Dutch miere, and Crimean Gothic miera. == Taxonomy and evolution == The family Formicidae belongs to the order Hymenoptera, which also includes sawflies, bees, and wasps. Ants evolved from a lineage within the stinging wasps, and a 2013 study suggests that they are a sister group of the Apoidea. However, since Apoidea is a superfamily, ants must be upgraded to the same rank. A more detailed basic taxonomy was proposed in 2020. Three species of
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{
"page_id": 2594,
"source": null,
"title": "Ant"
}
|
the extinct mid-Cretaceous genera Camelomecia and Camelosphecia were placed outside of the Formicidae, in a separate clade within the general superfamily Formicoidea, which, together with Apoidea, forms the higher-ranking group Formicapoidina. Fernández et al. (2021) suggest that the common ancestors of ants and apoids within the Formicapoidina probably existed as early as in the end of the Jurassic period, before divergence in the Cretaceous. In 1966, E. O. Wilson and his colleagues identified the fossil remains of an ant (Sphecomyrma) that lived in the Cretaceous period. The specimen, trapped in amber dating back to around 92 million years ago, has features found in some wasps, but not found in modern ants. The oldest fossils of ants date to the mid-Cretaceous, around 113-100 million years ago, which belong to extinct stem-groups such as the Haidomyrmecinae, Sphecomyrminae and Zigrasimeciinae, with modern ant subfamilies appearing towards the end of the Cretaceous around 80–70 million years ago. Ants diversified extensively during the Angiosperm Terrestrial Revolution and assumed ecological dominance around 60 million years ago. Some groups, such as the Leptanillinae and Martialinae, are suggested to have diversified from early primitive ants that were likely to have been predators underneath the surface of the soil. During the Cretaceous period, a few species of primitive ants ranged widely on the Laurasian supercontinent (the Northern Hemisphere). Their representation in the fossil record is poor, in comparison to the populations of other insects, representing only about 1% of fossil evidence of insects in the era. Ants became dominant after adaptive radiation at the beginning of the Paleogene period. By the Oligocene and Miocene, ants had come to represent 20–40% of all insects found in major fossil deposits. Of the species that lived in the Eocene epoch, around one in 10 genera survive to the present. Genera surviving today
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{
"page_id": 2594,
"source": null,
"title": "Ant"
}
|
comprise 56% of the genera in Baltic amber fossils (early Oligocene), and 92% of the genera in Dominican amber fossils (apparently early Miocene). Termites live in colonies and are sometimes called "white ants", but termites are only distantly related to ants. They are the sub-order Isoptera, and together with cockroaches, they form the order Blattodea. Blattodeans are related to mantids, crickets, and other winged insects that do not undergo complete metamorphosis. Like ants, termites are eusocial, with sterile workers, but they differ greatly in the genetics of reproduction. The similarity of their social structure to that of ants is attributed to convergent evolution. Velvet ants look like large ants, but are wingless female wasps. == Distribution and diversity == Ants have a cosmopolitan distribution. They are found on all continents except Antarctica, and only a few large islands, such as Greenland, Iceland, parts of Polynesia and the Hawaiian Islands lack native ant species. Ants occupy a wide range of ecological niches and exploit many different food resources as direct or indirect herbivores, predators and scavengers. Most ant species are omnivorous generalists, but a few are specialist feeders. There is considerable variation in ant abundance across habitats, peaking in the moist tropics to nearly six times that found in less suitable habitats. Their ecological dominance has been examined primarily using estimates of their biomass: myrmecologist E. O. Wilson had estimated in 2009 that at any one time the total number of ants was between one and ten quadrillion (short scale) (i.e., between 1015 and 1016) and using this estimate he had suggested that the total biomass of all the ants in the world was approximately equal to the total biomass of the entire human race. More careful estimates made in 2022 which take into account regional variations puts the global ant
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{
"page_id": 2594,
"source": null,
"title": "Ant"
}
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contribution at 12 megatons of dry carbon, which is about 20% of the total human contribution, but greater than that of the wild birds and mammals combined. This study also puts a conservative estimate of the ants at about 20 × 1015 (20 quadrillion). Ants range in size from 0.75 to 52 millimetres (0.030–2.0 in), the largest species being the fossil Titanomyrma giganteum, the queen of which was 6 cm (2+1⁄2 in) long with a wingspan of 15 cm (6 in). Ants vary in colour; most ants are yellow to red or brown to black, but a few species are green and some tropical species have a metallic lustre. More than 13,800 species are currently known (with upper estimates of the potential existence of about 22,000; see the article List of ant genera), with the greatest diversity in the tropics. Taxonomic studies continue to resolve the classification and systematics of ants. Online databases of ant species, including AntWeb and the Hymenoptera Name Server, help to keep track of the known and newly described species. The relative ease with which ants may be sampled and studied in ecosystems has made them useful as indicator species in biodiversity studies. == Morphology == Ants are distinct in their morphology from other insects in having geniculate (elbowed) antennae, metapleural glands, and a strong constriction of their second abdominal segment into a node-like petiole. The body is divided into three distinct sections (formally known as tagmata): the head, mesosoma, and metasoma. The petiole forms a narrow waist between their mesosoma (thorax plus the first abdominal segment, which is fused to it) and gaster (abdomen less the abdominal segments in the petiole). The petiole may be formed by one or two nodes (the second alone, or the second and third abdominal segments). Tergosternal fusion, when the
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{
"page_id": 2594,
"source": null,
"title": "Ant"
}
|
tergite and sternite of a segment fuse together, can occur partly or fully on the second, third and fourth abdominal segment and is used in identification. Fourth abdominal tergosternal fusion was formerly used as character that defined the poneromorph subfamilies, Ponerinae and relatives within their clade, but this is no longer considered a synapomorphic character. Like other arthropods, ants have an exoskeleton, an external covering that provides a protective casing around the body and a point of attachment for muscles, in contrast to the internal skeletons of humans and other vertebrates. Insects do not have lungs; oxygen and other gases, such as carbon dioxide, pass through their exoskeleton via tiny valves called spiracles. Insects also lack closed blood vessels; instead, they have a long, thin, perforated tube along the top of the body (called the "dorsal aorta") that functions like a heart, and pumps haemolymph toward the head, thus driving the circulation of the internal fluids. The nervous system consists of a ventral nerve cord that runs the length of the body, with several ganglia and branches along the way reaching into the extremities of the appendages. === Head === An ant's head contains many sensory organs. Like most insects, ants have compound eyes made from numerous tiny lenses attached together. Ant eyes are good for acute movement detection, but do not offer a high resolution image. They also have three small ocelli (simple eyes) on the top of the head that detect light levels and polarization. Compared to vertebrates, ants tend to have blurrier eyesight, particularly in smaller species, and a few subterranean taxa are completely blind. However, some ants, such as Australia's bulldog ant, have excellent vision and are capable of discriminating the distance and size of objects moving nearly a meter away. Based on experiments conducted to
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{
"page_id": 2594,
"source": null,
"title": "Ant"
}
|
test their ability to differentiate between selected wavelengths of light, some ant species such as Camponotus blandus, Solenopsis invicta, and Formica cunicularia are thought to possess a degree of colour vision. Two antennae ("feelers") are attached to the head; these organs detect chemicals, air currents, and vibrations; they also are used to transmit and receive signals through touch. The head has two strong jaws, the mandibles, used to carry food, manipulate objects, construct nests, and for defence. In some species, a small pocket (infrabuccal chamber) inside the mouth stores food, so it may be passed to other ants or their larvae. === Mesosoma === Both the legs and wings of the ant are attached to the mesosoma ("thorax"). The legs terminate in a hooked claw which allows them to hook on and climb surfaces. Only reproductive ants (queens and males) have wings. Queens shed their wings after the nuptial flight, leaving visible stubs, a distinguishing feature of queens. In a few species, wingless queens (ergatoids) and males occur. === Metasoma === The metasoma (the "abdomen") of the ant houses important internal organs, including those of the reproductive, respiratory (tracheae), and excretory systems. Workers of many species have their egg-laying structures modified into stings that are used for subduing prey and defending their nests. === Polymorphism === In the colonies of a few ant species, there are physical castes—workers in distinct size-classes, called minor (micrergates), median, and major ergates (macrergates). Often, the larger ants have disproportionately larger heads, and correspondingly stronger mandibles. Although formally known as dinergates, such individuals are sometimes called "soldier" ants because their stronger mandibles make them more effective in fighting, although they still are workers and their "duties" typically do not vary greatly from the minor or median workers. In a few species, the median workers are
|
{
"page_id": 2594,
"source": null,
"title": "Ant"
}
|
absent, creating a sharp divide between the minors and majors. Weaver ants, for example, have a distinct bimodal size distribution. Some other species show continuous variation in the size of workers. The smallest and largest workers in Carebara diversa show nearly a 500-fold difference in their dry weights. Workers cannot mate; however, because of the haplodiploid sex-determination system in ants, workers of a number of species can lay unfertilised eggs that become fully fertile, haploid males. The role of workers may change with their age and in some species, such as honeypot ants, young workers are fed until their gasters are distended, and act as living food storage vessels. These food storage workers are called repletes. For instance, these replete workers develop in the North American honeypot ant Myrmecocystus mexicanus. Usually the largest workers in the colony develop into repletes; and, if repletes are removed from the colony, other workers become repletes, demonstrating the flexibility of this particular polymorphism. This polymorphism in morphology and behaviour of workers initially was thought to be determined by environmental factors such as nutrition and hormones that led to different developmental paths; however, genetic differences between worker castes have been noted in Acromyrmex sp. These polymorphisms are caused by relatively small genetic changes; differences in a single gene of Solenopsis invicta can decide whether the colony will have single or multiple queens. The Australian jack jumper ant (Myrmecia pilosula) has only a single pair of chromosomes (with the males having just one chromosome as they are haploid), the lowest number known for any animal, making it an interesting subject for studies in the genetics and developmental biology of social insects. === Genome size === Genome size is a fundamental characteristic of an organism. Ants have been found to have tiny genomes, with the evolution of
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{
"page_id": 2594,
"source": null,
"title": "Ant"
}
|
genome size suggested to occur through loss and accumulation of non-coding regions, mainly transposable elements, and occasionally by whole genome duplication. This may be related to colonisation processes, but further studies are needed to verify this. == Life cycle == The life of an ant starts from an egg; if the egg is fertilised, the progeny will be female diploid, if not, it will be male haploid. Ants develop by complete metamorphosis with the larva stages passing through a pupal stage before emerging as an adult. The larva is largely immobile and is fed and cared for by workers. Food is given to the larvae by trophallaxis, a process in which an ant regurgitates liquid food held in its crop. This is also how adults share food, stored in the "social stomach". Larvae, especially in the later stages, may also be provided solid food, such as trophic eggs, pieces of prey, and seeds brought by workers. The larvae grow through a series of four or five moults and enter the pupal stage. The pupa has the appendages free and not fused to the body as in a butterfly pupa. The differentiation into queens and workers (which are both female), and different castes of workers, is influenced in some species by the nutrition the larvae obtain. Genetic influences and the control of gene expression by the developmental environment are complex and the determination of caste continues to be a subject of research. Winged male ants, called drones (termed "aner" in old literature), emerge from pupae along with the usually winged breeding females. Some species, such as army ants, have wingless queens. Larvae and pupae need to be kept at fairly constant temperatures to ensure proper development, and so often are moved around among the various brood chambers within the colony. A
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{
"page_id": 2594,
"source": null,
"title": "Ant"
}
|
new ergate spends the first few days of its adult life caring for the queen and young. She then graduates to digging and other nest work, and later to defending the nest and foraging. These changes are sometimes fairly sudden, and define what are called temporal castes. Such age-based task-specialization or polyethism has been suggested as having evolved due to the high casualties involved in foraging and defence, making it an acceptable risk only for ants who are older and likely to die sooner from natural causes. In the Brazilian ant Forelius pusillus, the nest entrance is closed from the outside to protect the colony from predatory ant species at sunset each day. About one to eight workers seal the nest entrance from the outside and they have no chance of returning to the nest and are in effect sacrificed. Whether these seemingly suicidal workers are older workers has not been determined. Ant colonies can be long-lived. The queens can live for up to 30 years, and workers live from 1 to 3 years. Males, however, are more transitory, being quite short-lived and surviving for only a few weeks. Ant queens are estimated to live 100 times as long as solitary insects of a similar size. Ants are active all year long in the tropics; however, in cooler regions, they survive the winter in a state of dormancy known as hibernation. The forms of inactivity are varied and some temperate species have larvae going into the inactive state (diapause), while in others, the adults alone pass the winter in a state of reduced activity. === Reproduction === A wide range of reproductive strategies have been noted in ant species. Females of many species are known to be capable of reproducing asexually through thelytokous parthenogenesis. Secretions from the male accessory glands
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{
"page_id": 2594,
"source": null,
"title": "Ant"
}
|
in some species can plug the female genital opening and prevent females from re-mating. Most ant species have a system in which only the queen and breeding females have the ability to mate. Contrary to popular belief, some ant nests have multiple queens, while others may exist without queens. Workers with the ability to reproduce are called "gamergates" and colonies that lack queens are then called gamergate colonies; colonies with queens are said to be queen-right. Drones can also mate with existing queens by entering a foreign colony, such as in army ants. When the drone is initially attacked by the workers, it releases a mating pheromone. If recognized as a mate, it will be carried to the queen to mate. Males may also patrol the nest and fight others by grabbing them with their mandibles, piercing their exoskeleton and then marking them with a pheromone. The marked male is interpreted as an invader by worker ants and is killed. Most ants are univoltine, producing a new generation each year. During the species-specific breeding period, winged females and winged males, known to entomologists as alates, leave the colony in what is called a nuptial flight. The nuptial flight usually takes place in the late spring or early summer when the weather is hot and humid. Heat makes flying easier and freshly fallen rain makes the ground softer for mated queens to dig nests. Males typically take flight before the females. Males then use visual cues to find a common mating ground, for example, a landmark such as a pine tree to which other males in the area converge. Males secrete a mating pheromone that females follow. Males will mount females in the air, but the actual mating process usually takes place on the ground. Females of some species mate with
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{
"page_id": 2594,
"source": null,
"title": "Ant"
}
|
just one male but in others they may mate with as many as ten or more different males, storing the sperm in their spermathecae. The genus Cardiocondyla have species with both winged and wingless males, where the latter will only mate with females living in the same nest. Some species in the genus have lost winged males completely, and only produce wingless males. In C. elegans, workers may transport newly emerged queens to other conspecific nests where the wingless males from unrelated colonies can mate with them, a behavioural adaptation that may reduce the chances of inbreeding. Mated females then seek a suitable place to begin a colony. There, they break off their wings using their tibial spurs and begin to lay and care for eggs. The females can selectively fertilise future eggs with the sperm stored to produce diploid workers or lay unfertilized haploid eggs to produce drones. The first workers to hatch, known as nanitics, are weaker and smaller than later workers but they begin to serve the colony immediately. They enlarge the nest, forage for food, and care for the other eggs. Species that have multiple queens may have a queen leaving the nest along with some workers to found a colony at a new site, a process akin to swarming in honeybees. === Nests, colonies, and supercolonies === The typical ant species has a colony occupying a single nest, housing one or more queens, where the brood is raised. There are however more than 150 species of ants in 49 genera that are known to have colonies consisting of multiple spatially separated nests. These polydomous (as opposed to monodomous) colonies have food and workers moving between the nests. Membership to a colony is identified by the response of worker ants which identify whether another individual belongs
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{
"page_id": 2594,
"source": null,
"title": "Ant"
}
|
to their own colony or not. A signature cocktail of body surface chemicals (also known as cuticular hydrocarbons or CHCs) forms the so-called colony odor which other members can recognize. Some ant species appear to be less discriminating and in the Argentine ant Linepithema humile, workers carried from a colony anywhere in the southern US and Mexico are acceptable within other colonies in the same region. Similarly workers from colonies that have established in Europe are accepted by any other colonies within Europe but not by the colonies in the Americas. The interpretation of these observations has been debated and some have been termed these large populations as supercolonies while others have termed the populations as unicolonial. == Behaviour and ecology == === Communication === Ants communicate with each other using pheromones, sounds, and touch. Since most ants live on the ground, they use the soil surface to leave pheromone trails that may be followed by other ants. In species that forage in groups, a forager that finds food marks a trail on the way back to the colony; this trail is followed by other ants, these ants then reinforce the trail when they head back with food to the colony. When the food source is exhausted, no new trails are marked by returning ants and the scent slowly dissipates. This behaviour helps ants deal with changes in their environment. For instance, when an established path to a food source is blocked by an obstacle, the foragers leave the path to explore new routes. If an ant is successful, it leaves a new trail marking the shortest route on its return. Successful trails are followed by more ants, reinforcing better routes and gradually identifying the best path. Ants use pheromones for more than just making trails. A crushed ant emits
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{
"page_id": 2594,
"source": null,
"title": "Ant"
}
|
an alarm pheromone that sends nearby ants into an attack frenzy and attracts more ants from farther away. Several ant species even use "propaganda pheromones" to confuse enemy ants and make them fight among themselves. Pheromones are produced by a wide range of structures including Dufour's glands, poison glands and glands on the hindgut, pygidium, rectum, sternum, and hind tibia. Pheromones also are exchanged, mixed with food, and passed by trophallaxis, transferring information within the colony. This allows other ants to detect what task group (e.g., foraging or nest maintenance) other colony members belong to. In ant species with queen castes, when the dominant queen stops producing a specific pheromone, workers begin to raise new queens in the colony. Some ants produce sounds by stridulation, using the gaster segments and their mandibles. Sounds may be used to communicate with colony members or with other species. === Defence === Ants attack and defend themselves by biting and, in many species, by stinging often injecting or spraying chemicals. Bullet ants (Paraponera), located in Central and South America, are considered to have the most painful sting of any insect, although it is usually not fatal to humans. This sting is given the highest rating on the Schmidt sting pain index. The sting of jack jumper ants can be lethal for humans, and an antivenom has been developed for it. Fire ants, Solenopsis spp., are unique in having a venom sac containing piperidine alkaloids. Their stings are painful and can be dangerous to hypersensitive people. Formicine ants secrete a poison from their glands, made mainly of formic acid. Trap-jaw ants of the genus Odontomachus are equipped with mandibles called trap-jaws, which snap shut faster than any other predatory appendages within the animal kingdom. One study of Odontomachus bauri recorded peak speeds of between 126
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{
"page_id": 2594,
"source": null,
"title": "Ant"
}
|
and 230 km/h (78 and 143 mph), with the jaws closing within 130 microseconds on average. The ants were also observed to use their jaws as a catapult to eject intruders or fling themselves backward to escape a threat. Before striking, the ant opens its mandibles extremely widely and locks them in this position by an internal mechanism. Energy is stored in a thick band of muscle and explosively released when triggered by the stimulation of sensory organs resembling hairs on the inside of the mandibles. The mandibles also permit slow and fine movements for other tasks. Trap-jaws also are seen in other ponerines such as Anochetus, as well as some genera in the tribe Attini, such as Daceton, Orectognathus, and Strumigenys, which are viewed as examples of convergent evolution. A Malaysian species of ant in the Camponotus cylindricus group has enlarged mandibular glands that extend into their gaster. If combat takes a turn for the worse, a worker may perform a final act of suicidal altruism by rupturing the membrane of its gaster, causing the content of its mandibular glands to burst from the anterior region of its head, spraying a poisonous, corrosive secretion containing acetophenones and other chemicals that immobilise small insect attackers. The worker subsequently dies. In addition to defence against predators, ants need to protect their colonies from pathogens. Secretions from the metapleural gland, unique to the ants, produce a complex range of chemicals including several with antibiotic properties. Some worker ants maintain the hygiene of the colony and their activities include undertaking or necrophoresis, the disposal of dead nest-mates. Oleic acid has been identified as the compound released from dead ants that triggers necrophoric behaviour in Atta mexicana while workers of Linepithema humile react to the absence of characteristic chemicals (dolichodial and iridomyrmecin) present on
|
{
"page_id": 2594,
"source": null,
"title": "Ant"
}
|
the cuticle of their living nestmates to trigger similar behaviour. In Megaponera analis, injured ants are treated by nestmastes with secretions from their metapleural glands which protect them from infection. Camponotus ants do not have a metapleural gland and Camponotus maculatus as well as C. floridanus workers have been found to amputate the affected legs of nestmates when the femur is injured. A femur injury carries a greater risk of infection unlike a tibia injury. Nests may be protected from physical threats such as flooding and overheating by elaborate nest architecture. Workers of Cataulacus muticus, an arboreal species that lives in plant hollows, respond to flooding by drinking water inside the nest, and excreting it outside. Camponotus anderseni, which nests in the cavities of wood in mangrove habitats, deals with submergence under water by switching to anaerobic respiration. === Learning === Many animals can learn behaviours by imitation, but ants may be the only group apart from mammals where interactive teaching has been observed. A knowledgeable forager of Temnothorax albipennis can lead a naïve nest-mate to newly discovered food by the process of tandem running. The follower obtains knowledge through its leading tutor. The leader is acutely sensitive to the progress of the follower and slows down when the follower lags and speeds up when the follower gets too close. Controlled experiments with colonies of Cerapachys biroi suggest that an individual may choose nest roles based on her previous experience. An entire generation of identical workers was divided into two groups whose outcome in food foraging was controlled. One group was continually rewarded with prey, while it was made certain that the other failed. As a result, members of the successful group intensified their foraging attempts while the unsuccessful group ventured out fewer and fewer times. A month later, the
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{
"page_id": 2594,
"source": null,
"title": "Ant"
}
|
successful foragers continued in their role while the others had moved to specialise in brood care. === Nest construction === Complex nests are built by many ant species, but other species are nomadic and do not build permanent structures. Ants may form subterranean nests or build them on trees. These nests may be found in the ground, under stones or logs, inside logs, hollow stems, or even acorns. The materials used for construction include soil and plant matter, and ants carefully select their nest sites; Temnothorax albipennis will avoid sites with dead ants, as these may indicate the presence of pests or disease. They are quick to abandon established nests at the first sign of threats. The army ants of South America, such as the Eciton burchellii species, and the driver ants of Africa do not build permanent nests, but instead, alternate between nomadism and stages where the workers form a temporary nest (bivouac) from their own bodies, by holding each other together. Weaver ant (Oecophylla spp.) workers build nests in trees by attaching leaves together, first pulling them together with bridges of workers and then inducing their larvae to produce silk as they are moved along the leaf edges. Similar forms of nest construction are seen in some species of Polyrhachis. Formica polyctena, among other ant species, constructs nests that maintain a relatively constant interior temperature that aids in the development of larvae. The ants maintain the nest temperature by choosing the location, nest materials, controlling ventilation and maintaining the heat from solar radiation, worker activity and metabolism, and in some moist nests, microbial activity in the nest materials. Some ant species, such as those that use natural cavities, can be opportunistic and make use of the controlled micro-climate provided inside human dwellings and other artificial structures to house
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{
"page_id": 2594,
"source": null,
"title": "Ant"
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|
their colonies and nest structures. === Cultivation of food === Most ants are generalist predators, scavengers, and indirect herbivores, but a few have evolved specialised ways of obtaining nutrition. It is believed that many ant species that engage in indirect herbivory rely on specialized symbiosis with their gut microbes to upgrade the nutritional value of the food they collect and allow them to survive in nitrogen poor regions, such as rainforest canopies. Leafcutter ants (Atta and Acromyrmex) feed exclusively on a fungus that grows only within their colonies. They continually collect leaves which are taken to the colony, cut into tiny pieces and placed in fungal gardens. Ergates specialise in related tasks according to their sizes. The largest ants cut stalks, smaller workers chew the leaves and the smallest tend the fungus. Leafcutter ants are sensitive enough to recognise the reaction of the fungus to different plant material, apparently detecting chemical signals from the fungus. If a particular type of leaf is found to be toxic to the fungus, the colony will no longer collect it. The ants feed on structures produced by the fungi called gongylidia. Symbiotic bacteria on the exterior surface of the ants produce antibiotics that kill bacteria introduced into the nest that may harm the fungi. === Navigation === Foraging ants travel distances of up to 200 metres (700 ft) from their nest and scent trails allow them to find their way back even in the dark. In hot and arid regions, day-foraging ants face death by desiccation, so the ability to find the shortest route back to the nest reduces that risk. Diurnal desert ants of the genus Cataglyphis such as the Sahara desert ant navigate by keeping track of direction as well as distance travelled. Distances travelled are measured using an internal pedometer that
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{
"page_id": 2594,
"source": null,
"title": "Ant"
}
|
keeps count of the steps taken and also by evaluating the movement of objects in their visual field (optical flow). Directions are measured using the position of the sun. They integrate this information to find the shortest route back to their nest. Like all ants, they can also make use of visual landmarks when available as well as olfactory and tactile cues to navigate. Some species of ant are able to use the Earth's magnetic field for navigation. The compound eyes of ants have specialised cells that detect polarised light from the Sun, which is used to determine direction. These polarization detectors are sensitive in the ultraviolet region of the light spectrum. In some army ant species, a group of foragers who become separated from the main column may sometimes turn back on themselves and form a circular ant mill. The workers may then run around continuously until they die of exhaustion. === Locomotion === The female worker ants do not have wings and reproductive females lose their wings after their mating flights in order to begin their colonies. Therefore, unlike their wasp ancestors, most ants travel by walking. Some species are capable of leaping. For example, Jerdon's jumping ant (Harpegnathos saltator) is able to jump by synchronising the action of its mid and hind pairs of legs. There are several species of gliding ant including Cephalotes atratus; this may be a common trait among arboreal ants with small colonies. Ants with this ability are able to control their horizontal movement so as to catch tree trunks when they fall from atop the forest canopy. Other species of ants can form chains to bridge gaps over water, underground, or through spaces in vegetation. Some species also form floating rafts that help them survive floods. These rafts may also have a
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{
"page_id": 2594,
"source": null,
"title": "Ant"
}
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role in allowing ants to colonise islands. Polyrhachis sokolova, a species of ant found in Australian mangrove swamps, can swim and live in underwater nests. Since they lack gills, they go to trapped pockets of air in the submerged nests to breathe. === Cooperation and competition === Not all ants have the same kind of societies. The Australian bulldog ants are among the biggest and most basal of ants. Like virtually all ants, they are eusocial, but their social behaviour is poorly developed compared to other species. Each individual hunts alone, using her large eyes instead of chemical senses to find prey. Some species attack and take over neighbouring ant colonies. Extreme specialists among these slave-raiding ants, such as the Amazon ants, are incapable of feeding themselves and need captured workers to survive. Captured workers of enslaved Temnothorax species have evolved a counter-strategy, destroying just the female pupae of the slave-making Temnothorax americanus, but sparing the males (who do not take part in slave-raiding as adults). Ants identify kin and nestmates through their scent, which comes from hydrocarbon-laced secretions that coat their exoskeletons. If an ant is separated from its original colony, it will eventually lose the colony scent. Any ant that enters a colony without a matching scent will be attacked. Parasitic ant species enter the colonies of host ants and establish themselves as social parasites; species such as Strumigenys xenos are entirely parasitic and do not have workers, but instead, rely on the food gathered by their Strumigenys perplexa hosts. This form of parasitism is seen across many ant genera, but the parasitic ant is usually a species that is closely related to its host. A variety of methods are employed to enter the nest of the host ant. A parasitic queen may enter the host nest before
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{
"page_id": 2594,
"source": null,
"title": "Ant"
}
|
the first brood has hatched, establishing herself prior to development of a colony scent. Other species use pheromones to confuse the host ants or to trick them into carrying the parasitic queen into the nest. Some simply fight their way into the nest. A conflict between the sexes of a species is seen in some species of ants with these reproducers apparently competing to produce offspring that are as closely related to them as possible. The most extreme form involves the production of clonal offspring. An extreme of sexual conflict is seen in Wasmannia auropunctata, where the queens produce diploid daughters by thelytokous parthenogenesis and males produce clones by a process whereby a diploid egg loses its maternal contribution to produce haploid males who are clones of the father. === Relationships with other organisms === Ants form symbiotic associations with a range of species, including other ant species, other insects, plants, and fungi. They also are preyed on by many animals and even certain fungi. Some arthropod species spend part of their lives within ant nests, either preying on ants, their larvae, and eggs, consuming the food stores of the ants, or avoiding predators. These inquilines may bear a close resemblance to ants. The nature of this ant mimicry (myrmecomorphy) varies, with some cases involving Batesian mimicry, where the mimic reduces the risk of predation. Others show Wasmannian mimicry, a form of mimicry seen only in inquilines. Aphids and other hemipteran insects secrete a sweet liquid called honeydew, when they feed on plant sap. The sugars in honeydew are a high-energy food source, which many ant species collect. In some cases, the aphids secrete the honeydew in response to ants tapping them with their antennae. The ants in turn keep predators away from the aphids and will move them from
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{
"page_id": 2594,
"source": null,
"title": "Ant"
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|
one feeding location to another. When migrating to a new area, many colonies will take the aphids with them, to ensure a continued supply of honeydew. Ants also tend mealybugs to harvest their honeydew. Mealybugs may become a serious pest of pineapples if ants are present to protect mealybugs from their natural enemies. Myrmecophilous (ant-loving) caterpillars of the butterfly family Lycaenidae (e.g., blues, coppers, or hairstreaks) are herded by the ants, led to feeding areas in the daytime, and brought inside the ants' nest at night. The caterpillars have a gland which secretes honeydew when the ants massage them. The chemicals in the secretions of Narathura japonica alter the behavior of attendant Pristomyrmex punctatus workers, making them less aggressive and stationary. The relationship, formerly characterized as "mutualistic", is now considered as possibly a case of the ants being parasitically manipulated by the caterpillars. Some caterpillars produce vibrations and sounds that are perceived by the ants. A similar adaptation can be seen in Grizzled skipper butterflies that emit vibrations by expanding their wings in order to communicate with ants, which are natural predators of these butterflies. Other caterpillars have evolved from ant-loving to ant-eating: these myrmecophagous caterpillars secrete a pheromone that makes the ants act as if the caterpillar is one of their own larvae. The caterpillar is then taken into the ant nest where it feeds on the ant larvae. A number of specialized bacteria have been found as endosymbionts in ant guts. Some of the dominant bacteria belong to the order Hyphomicrobiales whose members are known for being nitrogen-fixing symbionts in legumes but the species found in ant lack the ability to fix nitrogen. Fungus-growing ants that make up the tribe Attini, including leafcutter ants, cultivate certain species of fungus in the genera Leucoagaricus or Leucocoprinus of the family
|
{
"page_id": 2594,
"source": null,
"title": "Ant"
}
|
Agaricaceae. In this ant-fungus mutualism, both species depend on each other for survival. The ant Allomerus decemarticulatus has evolved a three-way association with the host plant, Hirtella physophora (Chrysobalanaceae), and a sticky fungus which is used to trap their insect prey. Lemon ants make devil's gardens by killing surrounding plants with their stings and leaving a pure patch of lemon ant trees, (Duroia hirsuta). This modification of the forest provides the ants with more nesting sites inside the stems of the Duroia trees. Although some ants obtain nectar from flowers, pollination by ants is somewhat rare, one example being of the pollination of the orchid Leporella fimbriata which induces male Myrmecia urens to pseudocopulate with the flowers, transferring pollen in the process. One theory that has been proposed for the rarity of pollination is that the secretions of the metapleural gland inactivate and reduce the viability of pollen. Some plants, mostly angiosperms but also some ferns, have special nectar exuding structures, extrafloral nectaries, that provide food for ants, which in turn protect the plant from more damaging herbivorous insects. Species such as the bullhorn acacia (Acacia cornigera) in Central America have hollow thorns that house colonies of stinging ants (Pseudomyrmex ferruginea) who defend the tree against insects, browsing mammals, and epiphytic vines. Isotopic labelling studies suggest that plants also obtain nitrogen from the ants. In return, the ants obtain food from protein- and lipid-rich Beltian bodies. In Fiji Philidris nagasau (Dolichoderinae) are known to selectively grow species of epiphytic Squamellaria (Rubiaceae) which produce large domatia inside which the ant colonies nest. The ants plant the seeds and the domatia of young seedling are immediately occupied and the ant faeces in them contribute to rapid growth. Similar dispersal associations are found with other dolichoderines in the region as well. Another example
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{
"page_id": 2594,
"source": null,
"title": "Ant"
}
|
of this type of ectosymbiosis comes from the Macaranga tree, which has stems adapted to house colonies of Crematogaster ants. Many plant species have seeds that are adapted for dispersal by ants. Seed dispersal by ants or myrmecochory is widespread, and new estimates suggest that nearly 9% of all plant species may have such ant associations. Often, seed-dispersing ants perform directed dispersal, depositing the seeds in locations that increase the likelihood of seed survival to reproduction. Some plants in arid, fire-prone systems are particularly dependent on ants for their survival and dispersal as the seeds are transported to safety below the ground. Many ant-dispersed seeds have special external structures, elaiosomes, that are sought after by ants as food. Ants can substantially alter rate of decomposition and nutrient cycling in their nest. By myrmecochory and modification of soil conditions they substantially alter vegetation and nutrient cycling in surrounding ecosystem. A convergence, possibly a form of mimicry, is seen in the eggs of stick insects. They have an edible elaiosome-like structure and are taken into the ant nest where the young hatch. Most ants are predatory and some prey on and obtain food from other social insects including other ants. Some species specialise in preying on termites (Megaponera and Termitopone) while a few Cerapachyinae prey on other ants. Some termites, including Nasutitermes corniger, form associations with certain ant species to keep away predatory ant species. The tropical wasp Mischocyttarus drewseni coats the pedicel of its nest with an ant-repellent chemical. It is suggested that many tropical wasps may build their nests in trees and cover them to protect themselves from ants. Other wasps, such as A. multipicta, defend against ants by blasting them off the nest with bursts of wing buzzing. Stingless bees (Trigona and Melipona) use chemical defences against ants. Flies
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{
"page_id": 2594,
"source": null,
"title": "Ant"
}
|
in the Old World genus Bengalia (Calliphoridae) prey on ants and are kleptoparasites, snatching prey or brood from the mandibles of adult ants. Wingless and legless females of the Malaysian phorid fly (Vestigipoda myrmolarvoidea) live in the nests of ants of the genus Aenictus and are cared for by the ants. Fungi in the genera Cordyceps and Ophiocordyceps infect ants. Ants react to their infection by climbing up plants and sinking their mandibles into plant tissue. The fungus kills the ants, grows on their remains, and produces a fruiting body. It appears that the fungus alters the behaviour of the ant to help disperse its spores in a microhabitat that best suits the fungus. Strepsipteran parasites also manipulate their ant host to climb grass stems, to help the parasite find mates. A nematode (Myrmeconema neotropicum) that infects canopy ants (Cephalotes atratus) causes the black-coloured gasters of workers to turn red. The parasite also alters the behaviour of the ant, causing them to carry their gasters high. The conspicuous red gasters are mistaken by birds for ripe fruits, such as Hyeronima alchorneoides, and eaten. The droppings of the bird are collected by other ants and fed to their young, leading to further spread of the nematode. A study of Temnothorax nylanderi colonies in Germany found that workers parasitized by the tapeworm Anomotaenia brevis (ants are intermediate hosts, the definitive hosts are woodpeckers) lived much longer than unparasitized workers and had a reduced mortality rate, comparable to that of the queens of the same species, which live for as long as two decades. South American poison dart frogs in the genus Dendrobates feed mainly on ants, and the toxins in the skin of some species come from the ants. Formicine ants in the genera Brachymyrmex and Paratrechina have been found to contain
|
{
"page_id": 2594,
"source": null,
"title": "Ant"
}
|
pumiliotoxin found in Dendrobates pumilio. The West African frog Phrynomantis microps is able to move within the nests of Paltothyreus tarsatus ants, producing peptides on its skin that prevent the ants from stinging them. Army ants which is the toxin found in forage in a wide roving column, attacking any animals in that path that are unable to escape. In Central and South America, Eciton burchellii is the swarming ant most commonly attended by "ant-following" birds such as antbirds and woodcreepers. This behaviour was once considered mutualistic, but later studies found the birds to be parasitic. Direct kleptoparasitism (birds stealing food from the ants' grasp) is rare and has been noted in Inca doves which pick seeds at nest entrances as they are being transported by species of Pogonomyrmex. Birds that follow ants eat many prey insects and thus decrease the foraging success of ants. Birds indulge in a peculiar behaviour called anting that, as yet, is not fully understood. Here birds rest on ant nests, or pick and drop ants onto their wings and feathers; this may be a means to remove ectoparasites from the birds. Anteaters, aardvarks, pangolins, echidnas and numbats have special adaptations for living on a diet of ants. These adaptations include long, sticky tongues to capture ants and strong claws to break into ant nests. Brown bears (Ursus arctos) have been found to feed on ants. About 12%, 16%, and 4% of their faecal volume in spring, summer and autumn, respectively, is composed of ants. == Relationship with humans == Ants perform many ecological roles that are beneficial to humans, including the suppression of pest populations and aeration of the soil. The use of weaver ants in citrus cultivation in southern China is considered one of the oldest known applications of biological control. On the
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{
"page_id": 2594,
"source": null,
"title": "Ant"
}
|
other hand, ants may become nuisances when they invade buildings or cause economic losses. In some parts of the world (mainly Africa and South America), large ants, especially army ants, are used as surgical sutures. The wound is pressed together and ants are applied along it. The ant seizes the edges of the wound in its mandibles and locks in place. The body is then cut off and the head and mandibles remain in place to close the wound. The large heads of the dinergates (soldiers) of the leafcutting ant Atta cephalotes are also used by native surgeons in closing wounds. Some ants have toxic venom and are of medical importance. The species include Paraponera clavata (tocandira) and Dinoponera spp. (false tocandiras) of South America and the Myrmecia ants of Australia. In South Africa, ants are used to help harvest the seeds of rooibos (Aspalathus linearis), a plant used to make a herbal tea. The plant disperses its seeds widely, making manual collection difficult. Black ants collect and store these and other seeds in their nest, where humans can gather them en masse. Up to half a pound (200 g) of seeds may be collected from one ant-heap. Although most ants survive attempts by humans to eradicate them, a few are highly endangered. These tend to be island species that have evolved specialized traits and risk being displaced by introduced ant species. Examples include the critically endangered Sri Lankan relict ant (Aneuretus simoni) and Adetomyrma venatrix of Madagascar. === As food === Ants and their larvae are eaten in different parts of the world. The eggs of two species of ants are used in Mexican escamoles. They are considered a form of insect caviar and can sell for as much as US$50 per kg going up to US$200 per kg
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{
"page_id": 2594,
"source": null,
"title": "Ant"
}
|
(as of 2006) because they are seasonal and hard to find. In the Colombian department of Santander, hormigas culonas (roughly interpreted as "large-bottomed ants") Atta laevigata are toasted alive and eaten. In areas of India, and throughout Burma and Thailand, a paste of the green weaver ant (Oecophylla smaragdina) is served as a condiment with curry. Weaver ant eggs and larvae, as well as the ants, may be used in a Thai salad, yam (Thai: ยำ), in a dish called yam khai mot daeng (Thai: ยำไข่มดแดง) or red ant egg salad, a dish that comes from the Issan or north-eastern region of Thailand. Saville-Kent, in the Naturalist in Australia wrote "Beauty, in the case of the green ant, is more than skin-deep. Their attractive, almost sweetmeat-like translucency possibly invited the first essays at their consumption by the human species". Mashed up in water, after the manner of lemon squash, "these ants form a pleasant acid drink which is held in high favor by the natives of North Queensland, and is even appreciated by many European palates". Ants or their pupae are used as starters for yogurt making in parts of Bulgaria and Turkey. In his First Summer in the Sierra, John Muir notes that the Digger Indians of California ate the tickling, acid gasters of the large jet-black carpenter ants. The Mexican Indians eat the repletes, or living honey-pots, of the honey ant (Myrmecocystus). === As pests === Some ant species are considered as pests, primarily those that occur in human habitations, where their presence is often problematic. For example, the presence of ants would be undesirable in sterile places such as hospitals or kitchens. Some species or genera commonly categorized as pests include the Argentine ant, immigrant pavement ant, yellow crazy ant, banded sugar ant, pharaoh ant, red wood
|
{
"page_id": 2594,
"source": null,
"title": "Ant"
}
|
ant, black carpenter ant, odorous house ant, red imported fire ant, and European fire ant. Some ants will raid stored food, some will seek water sources, others may damage indoor structures, some may damage agricultural crops directly or by aiding sucking pests. Some will sting or bite. The adaptive nature of ant colonies make it nearly impossible to eliminate entire colonies and most pest management practices aim to control local populations and tend to be temporary solutions. Ant populations are managed by a combination of approaches that make use of chemical, biological, and physical methods. Chemical methods include the use of insecticidal bait which is gathered by ants as food and brought back to the nest where the poison is inadvertently spread to other colony members through trophallaxis. Management is based on the species and techniques may vary according to the location and circumstance. === In science and technology === Observed by humans since the dawn of history, the behaviour of ants has been documented and the subject of early writings and fables passed from one century to another. Those using scientific methods, myrmecologists, study ants in the laboratory and in their natural conditions. Their complex and variable social structures have made ants ideal model organisms. Ultraviolet vision was first discovered in ants by Sir John Lubbock in 1881. Studies on ants have tested hypotheses in ecology and sociobiology, and have been particularly important in examining the predictions of theories of kin selection and evolutionarily stable strategies. Ant colonies may be studied by rearing or temporarily maintaining them in formicaria, specially constructed glass framed enclosures. Individuals may be tracked for study by marking them with dots of colours. The successful techniques used by ant colonies have been studied in computer science and robotics to produce distributed and fault-tolerant systems for
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{
"page_id": 2594,
"source": null,
"title": "Ant"
}
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