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Adaptive radiation

In evolutionary biology, adaptive radiation is a process in which organisms diversify rapidly from an ancestral species into a multitude of new forms, particularly when a change in the environment makes new resources available, alters biotic interactions or opens new environmental niches. Starting with a single ancestor, this process results in the speciation and phenotypic adaptation of an array of species exhibiting different morphological and physiological traits. The prototypical example of adaptive radiation is finch speciation on the Galapagos ("Darwin's finches"), but examples are known from around the world.

Characteristics
Four features can be used to identify an adaptive radiation:

 * 1) A common ancestry of component species: specifically a recent ancestry. Note that this is not the same as a monophyly in which all descendants of a common ancestor are included.
 * 2) A phenotype-environment correlation: a significant association between environments and the morphological and physiological traits used to exploit those environments.
 * 3) Trait utility: the performance or fitness advantages of trait values in their corresponding environments.
 * 4) Rapid speciation: presence of one or more bursts in the emergence of new species around the time that ecological and phenotypic divergence is underway.

Conditions
Adaptive radiations are thought to be triggered by an ecological opportunity or a new adaptive zone. Sources of ecological opportunity can be the loss of antagonists (competitors or predators), the evolution of a key innovation, or dispersal to a new environment. Any one of these ecological opportunities has the potential to result in an increase in population size and relaxed stabilizing (constraining) selection. As genetic diversity is positively correlated with population size the expanded population will have more genetic diversity compared to the ancestral population. With reduced stabilizing selection phenotypic diversity can also increase. In addition, intraspecific competition will increase, promoting divergent selection to use a wider range of resources. This ecological release provides the potential for ecological speciation and thus adaptive radiation.

Occupying a new environment might take place under the following conditions:

 * 1) A new habitat has opened up: a volcano, for example, can create new ground in the middle of the ocean. This is the case in places like Hawaii and the Galapagos. For aquatic species, the formation of a large new lake habitat could serve the same purpose; the tectonic movement that formed the East African Rift, ultimately leading to the creation of the Rift Valley Lakes, is an example of this. An extinction event could effectively achieve this same result, opening up niches that were previously occupied by species that no longer exist.
 * 2) This new habitat is relatively isolated. When a volcano erupts on the mainland and destroys an adjacent forest, it is likely that the terrestrial plant and animal species that used to live in the destroyed region will recolonize without evolving greatly. However, if a newly formed habitat is isolated, the species that colonize it will likely be somewhat random and uncommon arrivals.
 * 3) The new habitat has a wide availability of niche space. The rare colonist can only adaptively radiate into as many forms as there are niches.

Relationship between mass-extinctions and mass adaptive radiations
A 2020 study found there to be no direct causal relationship between the proportionally most comparable mass radiations and extinctions in terms of "co-occurrence of species", substantially challenging the hypothesis of "creative mass extinctions".

Darwin's finches
Darwin's finches are an often-used textbook example of adaptive radiation. Today represented by approximately 15 species, Darwin's finches are Galapagos endemics famously adapted for a specialized feeding behavior (although one species, the Cocos finch (Pinaroloxias inornata), is not found in the Galapagos but on the island of Cocos south of Costa Rica). Darwin's finches are not actually finches in the true sense, but are members of the tanager family Thraupidae, and are derived from a single ancestor that arrived in the Galapagos from mainland South America perhaps just 3 million years ago. Excluding the Cocos finch, each species of Darwin's finch is generally widely distributed in the Galapagos and fills the same niche on each island. For the ground finches, this niche is a diet of seeds, and they have thick bills to facilitate the consumption of these hard materials. The ground finches are further specialized to eat seeds of a particular size: the large ground finch (Geospiza magnirostris) is the largest species of Darwin's finch and has the thickest beak for breaking open the toughest seeds, the small ground finch (Geospiza fuliginosa) has a smaller beak for eating smaller seeds, and the medium ground finch (Geospiza fortis) has a beak of intermediate size for optimal consumption of intermediately sized seeds (relative to G. magnirostris and G. fuliginosa). There is some overlap: for example, the most robust medium ground finches could have beaks larger than those of the smallest large ground finches. Because of this overlap, it can be difficult to tell the species apart by eye, though their songs differ. These three species often occur sympatrically, and during the rainy season in the Galapagos when food is plentiful, they specialize little and eat the same, easily accessible foods. It was not well-understood why their beaks were so adapted until Peter and Rosemary Grant studied their feeding behavior in the long dry season, and discovered that when food is scarce, the ground finches use their specialized beaks to eat the seeds that they are best suited to eat and thus avoid starvation.

The other finches in the Galapagos are similarly uniquely adapted for their particular niche. The cactus finches (Geospiza sp.) have somewhat longer beaks than the ground finches that serve the dual purpose of allowing them to feed on Opuntia cactus nectar and pollen while these plants are flowering, but on seeds during the rest of the year. The warbler-finches (Certhidea sp.) have short, pointed beaks for eating insects. The woodpecker finch (Camarhynchus pallidus) has a slender beak which it uses to pick at wood in search of insects; it also uses small sticks to reach insect prey inside the wood, making it one of the few animals that use tools.

The mechanism by which the finches initially diversified is still an area of active research. One proposition is that the finches were able to have a non-adaptive, allopatric speciation event on separate islands in the archipelago, such that when they reconverged on some islands, they were able to maintain reproductive isolation. Once they occurred in sympatry, niche specialization was favored so that the different species competed less directly for resources. This second, sympatric event was adaptive radiation.

Cichlids of the African Great Lakes
The haplochromine cichlid fishes in the Great Lakes of the East African Rift (particularly in Lake Tanganyika, Lake Malawi, and Lake Victoria) form the most speciose modern example of adaptive radiation. These lakes are believed to be home to about 2,000 different species of cichlid, spanning a wide range of ecological roles and morphological characteristics. Cichlids in these lakes fill nearly all of the roles typically filled by many fish families, including those of predators, scavengers, and herbivores, with varying dentitions and head shapes to match their dietary habits. In each case, the radiation events are only a few million years old, making the high level of speciation particularly remarkable. Several factors could be responsible for this diversity: the availability of a multitude of niches probably favored specialization, as few other fish taxa are present in the lakes (meaning that sympatric speciation was the most probable mechanism for initial specialization). Also, continual changes in the water level of the lakes during the Pleistocene (which often turned the largest lakes into several smaller ones) could have created the conditions for secondary allopatric speciation.

Tanganyika cichlids
Lake Tanganyika is the site from which nearly all the cichlid lineages of East Africa (including both riverine and lake species) originated. Thus, the species in the lake constitute a single adaptive radiation event but do not form a single monophyletic clade. Lake Tanganyika is also the least speciose of the three largest African Great Lakes, with only around 200 species of cichlid; however, these cichlids are more morphologically divergent and ecologically distinct than their counterparts in lakes Malawi and Victoria, an artifact of Lake Tanganyika's older cichlid fauna. Lake Tanganyika itself is believed to have formed 9–12 million years ago, putting a recent cap on the age of the lake's cichlid fauna. Many of Tanganyika's cichlids live very specialized lifestyles. The giant or emperor cichlid (Boulengerochromis microlepis) is a piscivore often ranked the largest of all cichlids (though it competes for this title with South America's Cichla temensis, the speckled peacock bass). It is thought that giant cichlids spawn only a single time, breeding in their third year and defending their young until they reach a large size, before dying of starvation some time thereafter. The three species of Altolamprologus are also piscivores, but with laterally compressed bodies and thick scales enabling them to chase prey into thin cracks in rocks without damaging their skin. Plecodus straeleni has evolved large, strangely curved teeth that are designed to scrape scales off of the sides of other fish, scales being its main source of food. Gnathochromis permaxillaris possesses a large mouth with a protruding upper lip, and feeds by opening this mouth downward onto the sandy lake bottom, sucking in small invertebrates. A number of Tanganyika's cichlids are shell-brooders, meaning that mating pairs lay and fertilize their eggs inside of empty shells on the lake bottom. Lamprologus callipterus is a unique egg-brooding species, with 15 cm-long males amassing collections of shells and guarding them in the hopes of attracting females (about 6 cm in length) to lay eggs in these shells. These dominant males must defend their territories from three types of rival: (1) other dominant males looking to steal shells; (2) younger, "sneaker" males looking to fertilize eggs in a dominant male's territory; and (3) tiny, 2–4 cm "parasitic dwarf" males that also attempt to rush in and fertilize eggs in the dominant male's territory. These parasitic dwarf males never grow to the size of dominant males, and the male offspring of dominant and parasitic dwarf males grow with 100% fidelity into the form of their fathers. A number of other highly specialized Tanganyika cichlids exist aside from these examples, including those adapted for life in open lake water up to 200m deep.

Malawi cichlids
The cichlids of Lake Malawi constitute a "species flock" of up to 1000 endemic species. Only seven cichlid species in Lake Malawi are not a part of the species flock: the Eastern happy (Astatotilapia calliptera), the sungwa (Serranochromis robustus), and five tilapia species (genera Oreochromis and Coptodon). All of the other cichlid species in the lake are descendants of a single original colonist species, which itself was descended from Tanganyikan ancestors. The common ancestor of Malawi's species flock is believed to have reached the lake 3.4 million years ago at the earliest, making Malawi cichlids' diversification into their present numbers particularly rapid. Malawi's cichlids span a similarly range of feeding behaviors to those of Tanganyika, but also show signs of a much more recent origin. For example, all members of the Malawi species flock are mouth-brooders, meaning the female keeps her eggs in her mouth until they hatch; in almost all species, the eggs are also fertilized in the female's mouth, and in a few species, the females continue to guard their fry in their mouth after they hatch. Males of most species display predominantly blue coloration when mating. However, a number of particularly divergent species are known from Malawi, including the piscivorous Nimbochromis livingtonii, which lies on its side in the substrate until small cichlids, perhaps drawn to its broken white patterning, come to inspect the predator - at which point they are swiftly eaten.

Victoria's cichlids
Lake Victoria's cichlids are also a species flock, once composed of some 500 or more species. The deliberate introduction of the Nile Perch (Lates niloticus) in the 1950s proved disastrous for Victoria cichlids, and the collective biomass of the Victoria cichlid species flock has decreased substantially and an unknown number of species have become extinct. However, the original range of morphological and behavioral diversity seen in the lake's cichlid fauna is still mostly present today, if endangered. These again include cichlids specialized for niches across the trophic spectrum, as in Tanganyika and Malawi, but again, there are standouts. Victoria is famously home to many piscivorous cichlid species, some of which feed by sucking the contents out of mouthbrooding females' mouths. Victoria's cichlids constitute a far younger radiation than even that of Lake Malawi, with estimates of the age of the flock ranging from 200,000 years to as little as 14,000.

Adaptive radiation in Hawaii
Hawaii has served as the site of a number of adaptive radiation events, owing to its isolation, recent origin, and large land area. The three most famous examples of these radiations are presented below, though insects like the Hawaiian drosophilid flies and Hyposmocoma moths have also undergone adaptive radiation.

Hawaiian honeycreepers
The Hawaiian honeycreepers form a large, highly morphologically diverse species group of birds that began radiating in the early days of the Hawaiian archipelago. While today only 17 species are known to persist in Hawaii (3 more may or may not be extinct), there were more than 50 species prior to Polynesian colonization of the archipelago (between 18 and 21 species have gone extinct since the discovery of the islands by westerners). The Hawaiian honeycreepers are known for their beaks, which are specialized to satisfy a wide range of dietary needs: for example, the beak of the ʻakiapōlāʻau (Hemignathus wilsoni) is characterized by a short, sharp lower mandible for scraping bark off of trees, and the much longer, curved upper mandible is used to probe the wood underneath for insects. Meanwhile, the ʻiʻiwi (Drepanis coccinea) has a very long curved beak for reaching nectar deep in Lobelia flowers. An entire clade of Hawaiian honeycreepers, the tribe Psittirostrini, is composed of thick-billed, mostly seed-eating birds, like the Laysan finch (Telespiza cantans). In at least some cases, similar morphologies and behaviors appear to have evolved convergently among the Hawaiian honeycreepers; for example, the short, pointed beaks of Loxops and Oreomystis evolved separately despite once forming the justification for lumping the two genera together. The Hawaiian honeycreepers are believed to have descended from a single common ancestor some 15 to 20 million years ago, though estimates range as low as 3.5 million years.

Hawaiian silverswords

Adaptive radiation is not a strictly vertebrate phenomenon, and examples are also known from among plants. The most famous example of adaptive radiation in plants is quite possibly the Hawaiian silverswords, named for alpine desert-dwelling Argyroxiphium species with long, silvery leaves that live for up to 20 years before growing a single flowering stalk and then dying. The Hawaiian silversword alliance consists of twenty-eight species of Hawaiian plants which, aside from the namesake silverswords, includes trees, shrubs, vines, cushion plants, and more. The silversword alliance is believed to have originated in Hawaii no more than 6 million years ago, making this one of Hawaii's youngest adaptive radiation events. This means that the silverswords evolved on Hawaii's modern high islands, and descended from a single common ancestor that arrived on Kauai from western North America. The closest modern relatives of the silverswords today are California tarweeds of the family Asteraceae.

Hawaiian lobelioids
Hawaii is also the site of a separate major floral adaptive radiation event: the Hawaiian lobelioids. The Hawaiian lobelioids are significantly more speciose than the silverswords, perhaps because they have been present in Hawaii for so much longer: they descended from a single common ancestor who arrived in the archipelago up to 15 million years ago. Today the Hawaiian lobelioids form a clade of over 125 species, including succulents, trees, shrubs, epiphytes, etc. Many species have been lost to extinction and many of the surviving species endangered.

Caribbean anoles
Anole lizards are distributed broadly in the New World, from the Southeastern US to South America. With over 400 species currently recognized, often placed in a single genus (Anolis), they constitute one of the largest radiation events among all lizards. Anole radiation on the mainland has largely been a process of speciation, and is not adaptive to any great degree, but anoles on each of the Greater Antilles (Cuba, Hispaniola, Puerto Rico, and Jamaica) have adaptively radiated in separate, convergent ways. On each of these islands, anoles have evolved with such a consistent set of morphological adaptations that each species can be assigned to one of six "ecomorphs": trunk–ground, trunk–crown, grass–bush, crown–giant, twig, and trunk. Take, for example, crown–giants from each of these islands: the Cuban Anolis luteogularis, Hispaniola's Anolis ricordii, Puerto Rico's Anolis cuvieri, and Jamaica's Anolis garmani (Cuba and Hispaniola are both home to more than one species of crown–giant). These anoles are all large, canopy-dwelling species with large heads and large lamellae (scales on the undersides of the fingers and toes that are important for traction in climbing), and yet none of these species are particularly closely related and appear to have evolved these similar traits independently. The same can be said of the other five ecomorphs across the Caribbean's four largest islands. Much like in the case of the cichlids of the three largest African Great Lakes, each of these islands is home to its own convergent Anolis adaptive radiation event.

Other examples
Presented above are the most well-documented examples of modern adaptive radiation, but other examples are known. Populations of three-spined sticklebacks have repeatedly diverged and evolved into distinct ecotypes. On Madagascar, birds of the family Vangidae are marked by very distinct beak shapes to suit their ecological roles. Madagascan mantellid frogs have radiated into forms that mirror other tropical frog faunas, with the brightly colored mantellas (Mantella) having evolved convergently with the Neotropical poison dart frogs of Dendrobatidae, while the arboreal Boophis species are the Madagascan equivalent of tree frogs and glass frogs. The pseudoxyrhophiine snakes of Madagascar have evolved into fossorial, arboreal, terrestrial, and semi-aquatic forms that converge with the colubroid faunas in the rest of the world. These Madagascan examples are significantly older than most of the other examples presented here: Madagascar's fauna has been evolving in isolation since the island split from India some 88 million years ago, and the Mantellidae originated around 50 mya. Older examples are known: the K-Pg extinction event, which caused the disappearance of the dinosaurs and most other reptilian megafauna 65 million years ago, is seen as having triggered a global adaptive radiation event that created the mammal diversity that exists today. Also the Cambrian Explosion, where vacant niches left by the extinction of Ediacaran biota during End-Ediacaran mass extinction were filled up by the emergence of new phyla.

title: Adaptive radiation


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Agarose gel electrophoresis

Agarose gel electrophoresis is a method of gel electrophoresis used in biochemistry, molecular biology, genetics, and clinical chemistry to separate a mixed population of macromolecules such as DNA or proteins in a matrix of agarose, one of the two main components of agar. The proteins may be separated by charge and/or size (isoelectric focusing agarose electrophoresis is essentially size independent), and the DNA and RNA fragments by length. Biomolecules are separated by applying an electric field to move the charged molecules through an agarose matrix, and the biomolecules are separated by size in the agarose gel matrix.

Agarose gel is easy to cast, has relatively fewer charged groups, and is particularly suitable for separating DNA of size range most often encountered in laboratories, which accounts for the popularity of its use. The separated DNA may be viewed with stain, most commonly under UV light, and the DNA fragments can be extracted from the gel with relative ease. Most agarose gels used are between 0.7–2% dissolved in a suitable electrophoresis buffer.

Properties of agarose gel

Agarose gel is a three-dimensional matrix formed of helical agarose molecules in supercoiled bundles that are aggregated into three-dimensional structures with channels and pores through which biomolecules can pass. The 3-D structure is held together with hydrogen bonds and can therefore be disrupted by heating back to a liquid state. The melting temperature is different from the gelling temperature, depending on the sources, agarose gel has a gelling temperature of 35–42 °C and a melting temperature of 85–95 °C. Low-melting and low-gelling agaroses made through chemical modifications are also available.

Agarose gel has large pore size and good gel strength, making it suitable as an anticonvection medium for the electrophoresis of DNA and large protein molecules. The pore size of a 1% gel has been estimated from 100 nm to 200–500 nm, and its gel strength allows gels as dilute as 0.15% to form a slab for gel electrophoresis. Low-concentration gels (0.1–0.2%) however are fragile and therefore hard to handle. Agarose gel has lower resolving power than polyacrylamide gel for DNA but has a greater range of separation, and is therefore used for DNA fragments of usually 50–20,000 bp in size. The limit of resolution for standard agarose gel electrophoresis is around 750 kb, but resolution of over 6 Mb is possible with pulsed field gel electrophoresis (PFGE). It can also be used to separate large proteins, and it is the preferred matrix for the gel electrophoresis of particles with effective radii larger than 5–10 nm. A 0.9% agarose gel has pores large enough for the entry of bacteriophage T4.

The agarose polymer contains charged groups, in particular pyruvate and sulphate. These negatively charged groups create a flow of water in the opposite direction to the movement of DNA in a process called electroendosmosis (EEO), and can therefore retard the movement of DNA and cause blurring of bands. Higher concentration gels would have higher electroendosmotic flow. Low EEO agarose is therefore generally preferred for use in agarose gel electrophoresis of nucleic acids, but high EEO agarose may be used for other purposes. The lower sulphate content of low EEO agarose, particularly low-melting point (LMP) agarose, is also beneficial in cases where the DNA extracted from gel is to be used for further manipulation as the presence of contaminating sulphates may affect some subsequent procedures, such as ligation and PCR. Zero EEO agaroses however are undesirable for some applications as they may be made by adding positively charged groups and such groups can affect subsequent enzyme reactions. Electroendosmosis is a reason agarose is used in preference to agar as the agaropectin component in agar contains a significant amount of negatively charged sulphate and carboxyl groups. The removal of agaropectin in agarose substantially reduces the EEO, as well as reducing the non-specific adsorption of biomolecules to the gel matrix. However, for some applications such as the electrophoresis of serum proteins, a high EEO may be desirable, and agaropectin may be added in the gel used.

Factors affecting migration of nucleic acid in gel

A number of factors can affect the migration of nucleic acids: the dimension of the gel pores (gel concentration), size of DNA being electrophoresed, the voltage used, the ionic strength of the buffer, and the concentration of intercalating dye such as ethidium bromide if used during electrophoresis.

Smaller molecules travel faster than larger molecules in gel, and double-stranded DNA moves at a rate that is inversely proportional to the logarithm of the number of base pairs. This relationship however breaks down with very large DNA fragments, and separation of very large DNA fragments requires the use of pulsed field gel electrophoresis (PFGE), which applies alternating current from different directions and the large DNA fragments are separated as they reorient themselves with the changing field.

For standard agarose gel electrophoresis, larger molecules are resolved better using a low concentration gel while smaller molecules separate better at high concentration gel. Higher concentration gels, however, require longer run times (sometimes days).

The movement of the DNA may be affected by the conformation of the DNA molecule, for example, supercoiled DNA usually moves faster than relaxed DNA because it is tightly coiled and hence more compact. In a normal plasmid DNA preparation, multiple forms of DNA may be present. Gel electrophoresis of the plasmids would normally show the negatively supercoiled form as the main band, while nicked DNA (open circular form) and the relaxed closed circular form appears as minor bands. The rate at which the various forms move however can change using different electrophoresis conditions, and the mobility of larger circular DNA may be more strongly affected than linear DNA by the pore size of the gel.

Ethidium bromide which intercalates into circular DNA can change the charge, length, as well as the superhelicity of the DNA molecule, therefore its presence in gel during electrophoresis can affect its movement. For example, the positive charge of ethidium bromide can reduce the DNA movement by 15%. Agarose gel electrophoresis can be used to resolve circular DNA with different supercoiling topology.

DNA damage due to increased cross-linking will also reduce electrophoretic DNA migration in a dose-dependent way.

The rate of migration of the DNA is proportional to the voltage applied, i.e. the higher the voltage, the faster the DNA moves. The resolution of large DNA fragments however is lower at high voltage. The mobility of DNA may also change in an unsteady field – in a field that is periodically reversed, the mobility of DNA of a particular size may drop significantly at a particular cycling frequency. This phenomenon can result in band inversion in field inversion gel electrophoresis (FIGE), whereby larger DNA fragments move faster than smaller ones.

Migration anomalies

 * "Smiley" gels - this edge effect is caused when the voltage applied is too high for the gel concentration used.
 * Overloading of DNA - overloading of DNA slows down the migration of DNA fragments.
 * Contamination - presence of impurities, such as salts or proteins can affect the movement of the DNA.

Mechanism of migration and separation
The negative charge of its phosphate backbone moves the DNA towards the positively charged anode during electrophoresis. However, the migration of DNA molecules in solution, in the absence of a gel matrix, is independent of molecular weight during electrophoresis. The gel matrix is therefore responsible for the separation of DNA by size during electrophoresis, and a number of models exist to explain the mechanism of separation of biomolecules in gel matrix. A widely accepted one is the Ogston model which treats the polymer matrix as a sieve. A globular protein or a random coil DNA moves through the interconnected pores, and the movement of larger molecules is more likely to be impeded and slowed down by collisions with the gel matrix, and the molecules of different sizes can therefore be separated in this sieving process.

The Ogston model however breaks down for large molecules whereby the pores are significantly smaller than size of the molecule. For DNA molecules of size greater than 1 kb, a reptation model (or its variants) is most commonly used. This model assumes that the DNA can crawl in a "snake-like" fashion (hence "reptation") through the pores as an elongated molecule. A biased reptation model applies at higher electric field strength, whereby the leading end of the molecule become strongly biased in the forward direction and pulls the rest of the molecule along. Real-time fluorescence microscopy of stained molecules, however, showed more subtle dynamics during electrophoresis, with the DNA showing considerable elasticity as it alternately stretching in the direction of the applied field and then contracting into a ball, or becoming hooked into a U-shape when it gets caught on the polymer fibres.

General procedure
The details of an agarose gel electrophoresis experiment may vary depending on methods, but most follow a general procedure.

Casting of gel

The gel is prepared by dissolving the agarose powder in an appropriate buffer, such as TAE or TBE, to be used in electrophoresis. The agarose is dispersed in the buffer before heating it to near-boiling point, but avoid boiling. The melted agarose is allowed to cool sufficiently before pouring the solution into a cast as the cast may warp or crack if the agarose solution is too hot. A comb is placed in the cast to create wells for loading sample, and the gel should be completely set before use.

The concentration of gel affects the resolution of DNA separation. The agarose gel is composed of microscopic pores through which the molecules travel, and there is an inverse relationship between the pore size of the agarose gel and the concentration – pore size decreases as the density of agarose fibers increases. High gel concentration improves separation of smaller DNA molecules, while lowering gel concentration permits large DNA molecules to be separated. The process allows fragments ranging from 50 base pairs to several mega bases to be separated depending on the gel concentration used. The concentration is measured in weight of agarose over volume of buffer used (g/ml). For a standard agarose gel electrophoresis, a 0.8% gel gives good separation or resolution of large 5–10kb DNA fragments, while 2% gel gives good resolution for small 0.2–1kb fragments. 1% gels is often used for a standard electrophoresis. High percentage gels are often brittle and may not set evenly, while low percentage gels (0.1-0.2%) are fragile and not easy to handle. Low-melting-point (LMP) agarose gels are also more fragile than normal agarose gel. Low-melting point agarose may be used on its own or simultaneously with standard agarose for the separation and isolation of DNA. PFGE and FIGE are often done with high percentage agarose gels.

Loading of samples
Once the gel has set, the comb is removed, leaving wells where DNA samples can be loaded. Loading buffer is mixed with the DNA sample before the mixture is loaded into the wells. The loading buffer contains a dense compound, which may be glycerol, sucrose, or Ficoll, that raises the density of the sample so that the DNA sample may sink to the bottom of the well. If the DNA sample contains residual ethanol after its preparation, it may float out of the well. The loading buffer also includes colored dyes such as xylene cyanol and bromophenol blue used to monitor the progress of the electrophoresis. The DNA samples are loaded using a pipette.

Electrophoresis
Agarose gel electrophoresis is most commonly done horizontally in a subaquaeous mode whereby the slab gel is completely submerged in buffer during electrophoresis. It is also possible, but less common, to perform the electrophoresis vertically, as well as horizontally with the gel raised on agarose legs using an appropriate apparatus. The buffer used in the gel is the same as the running buffer in the electrophoresis tank, which is why electrophoresis in the subaquaeous mode is possible with agarose gel.

For optimal resolution of DNA greater than 2   kb in size in standard gel electrophoresis, 5 to 8 V/cm is recommended (the distance in cm refers to the distance between electrodes, therefore this recommended voltage would be 5 to 8 multiplied by the distance between the electrodes in cm). Voltage may also be limited by the fact that it heats the gel and may cause the gel to melt if it is run at high voltage for a prolonged period, especially if the gel used is LMP agarose gel. Too high a voltage may also reduce resolution, as well as causing band streaking for large DNA molecules. Too low a voltage may lead to broadening of band for small DNA fragments due to dispersion and diffusion.

Since DNA is not visible in natural light, the progress of the electrophoresis is monitored using colored dyes. Xylene cyanol (light blue color) comigrates large DNA fragments, while Bromophenol blue (dark blue) comigrates with the smaller fragments. Less commonly used dyes include Cresol Red and Orange G which migrate ahead of bromophenol blue. A DNA marker is also run together for the estimation of the molecular weight of the DNA fragments. Note however that the size of a circular DNA like plasmids cannot be accurately gauged using standard markers unless it has been linearized by restriction digest, alternatively a supercoiled DNA marker may be used.

Staining and visualization

DNA as well as RNA are normally visualized by staining with ethidium bromide, which intercalates into the major grooves of the DNA and fluoresces under UV light. The intercalation depends on the concentration of DNA and thus, a band with high intensity will indicate a higher amount of DNA compared to a band of less intensity. The ethidium bromide may be added to the agarose solution before it gels, or the DNA gel may be stained later after electrophoresis. Destaining of the gel is not necessary but may produce better images. Other methods of staining are available; examples are MIDORI Green, SYBR Green, GelRed, methylene blue, brilliant cresyl blue, Nile blue sulphate, and crystal violet. SYBR Green, GelRed and other similar commercial products are sold as safer alternatives to ethidium bromide as it has been shown to be mutagenic in Ames test, although the carcinogenicity of ethidium bromide has not actually been established. SYBR Green requires the use of a blue-light transilluminator. DNA stained with crystal violet can be viewed under natural light without the use of a UV transilluminator which is an advantage, however it may not produce a strong band.

When stained with ethidium bromide, the gel is viewed with an ultraviolet (UV) transilluminator. The UV light excites the electrons within the aromatic ring of ethidium bromide, and once they return to the ground state, light is released, making the DNA and ethidium bromide complex fluoresce. Standard transilluminators use wavelengths of 302/312-nm (UV-B), however exposure of DNA to UV radiation for as little as 45 seconds can produce damage to DNA and affect subsequent procedures, for example reducing the efficiency of transformation, in vitro transcription, and PCR. Exposure of DNA to UV radiation therefore should be limited. Using a higher wavelength of 365 nm (UV-A range) causes less damage to the DNA but also produces much weaker fluorescence with ethidium bromide. Where multiple wavelengths can be selected in the transilluminator, shorter wavelength can be used to capture images, while longer wavelength should be used if it is necessary to work on the gel for any extended period of time.

The transilluminator apparatus may also contain image capture devices, such as a digital or polaroid camera, that allow an image of the gel to be taken or printed.

For gel electrophoresis of protein, the bands may be visualised with Coomassie or silver stains.

Downstream procedures
The separated DNA bands are often used for further procedures, and a DNA band may be cut out of the gel as a slice, dissolved and purified. Contaminants however may affect some downstream procedures such as PCR, and low melting point agarose may be preferred in some cases as it contains fewer of the sulphates that can affect some enzymatic reactions. The gels may also be used for blotting techniques.

Buffers
In general, the ideal buffer should have good conductivity, produce less heat and have a long life. There are a number of buffers used for agarose electrophoresis; common ones for nucleic acids include Tris/Acetate/EDTA (TAE) and Tris/Borate/EDTA (TBE). The buffers used contain EDTA to inactivate many nucleases which require divalent cation for their function. The borate in TBE buffer can be problematic as borate can polymerize, and/or interact with cis diols such as those found in RNA. TAE has the lowest buffering capacity, but it provides the best resolution for larger DNA. This means a lower voltage and more time, but a better product.

Many other buffers have been proposed, e.g. lithium borate (LB), iso electric histidine, pK matched goods buffers, etc.; in most cases the purported rationale is lower current (less heat) and or matched ion mobilities, which leads to longer buffer life. Tris-phosphate buffer has high buffering capacity but cannot be used if DNA extracted is to be used in phosphate sensitive reaction. LB is relatively new and is ineffective in resolving fragments larger than 5 kbp; However, with its low conductivity, a much higher voltage could be used (up to 35 V/cm), which means a shorter analysis time for routine electrophoresis. As low as one base pair size difference could be resolved in 3% agarose gel with an extremely low conductivity medium (1 mM lithium borate).

Other buffering system may be used in specific applications, for example, barbituric acid-sodium barbiturate or Tris-barbiturate buffers may be used for in agarose gel electrophoresis of proteins, for example in the detection of abnormal distribution of proteins.

Applications

 * Estimation of the size of DNA molecules following digestion with restriction enzymes, e.g., in restriction mapping of cloned DNA.
 * Estimation of the DNA concentration by comparing the intensity of the nucleic acid band with the corresponding band of the size marker.
 * Analysis of products of a polymerase chain reaction (PCR), e.g., in molecular genetic diagnosis or genetic fingerprinting
 * Separation of DNA fragments for extraction and purification.
 * Separation of restricted genomic DNA prior to Southern transfer, or of RNA prior to Northern transfer.
 * Separation of proteins, for example, screening of protein abnormalities in clinical chemistry.

Agarose gels are easily cast and handled compared to other matrices and nucleic acids are not chemically altered during electrophoresis. Samples are also easily recovered. After the experiment is finished, the resulting gel can be stored in a plastic bag in a refrigerator.

Electrophoresis is performed in buffer solutions to reduce pH changes due to the electric field, which is important because the charge of DNA and RNA depends on pH, but running for too long can exhaust the buffering capacity of the solution. Further, different preparations of genetic material may not migrate consistently with each other, for morphological or other reasons.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

title: Agarose gel electrophoresis


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Allele

An allele, or allelomorph, is a variant of the sequence of nucleotides at a particular location, or locus, on a DNA molecule.

Alleles can differ at a single position through single nucleotide polymorphisms (SNP), but they can also have insertions and deletions of up to several thousand base pairs.

Most alleles observed result in little or no change in the function of the gene product it codes for. However, sometimes different alleles can result in different observable phenotypic traits, such as different pigmentation. A notable example of this is Gregor Mendel's discovery that the white and purple flower colors in pea plants were the result of a single gene with two alleles.

Nearly all multicellular organisms have two sets of chromosomes at some point in their biological life cycle; that is, they are diploid. In this case, the chromosomes can be paired. Each chromosome in the pair contains the same genes in the same order, and place, along the length of the chromosome. For a given gene, if the two chromosomes contain the same allele, they, and the organism, are homozygous with respect to that gene. If the alleles are different, they, and the organism, are heterozygous with respect to that gene.

Popular definitions of 'allele' typically refer only to different alleles within genes. For example, the ABO blood grouping is controlled by the ABO gene, which has six common alleles (variants). In population genetics, nearly every living human's phenotype for the ABO gene is some combination of just these six alleles.

Etymology
The word "allele" is a short form of "allelomorph" ("other form", a word coined by British geneticists William Bateson and Edith Rebecca Saunders) in the 1900s, which was used in the early days of genetics to describe variant forms of a gene detected as different phenotypes. It derives from the Greek prefix ἀλληλο-, allelo-, meaning "mutual", "reciprocal", or "each other", which itself is related to the Greek adjective ἄλλος, allos (cognate with Latin alius), meaning "other".

Alleles that lead to dominant or recessive phenotypes
In many cases, genotypic interactions between the two alleles at a locus can be described as dominant or recessive, according to which of the two homozygous phenotypes the heterozygote most resembles. Where the heterozygote is indistinguishable from one of the homozygotes, the allele expressed is the one that leads to the "dominant" phenotype, and the other allele is said to be "recessive". The degree and pattern of dominance varies among loci. This type of interaction was first formally-described by Gregor Mendel. However, many traits defy this simple categorization and the phenotypes are modelled by co-dominance and polygenic inheritance.

The term "wild type" allele is sometimes used to describe an allele that is thought to contribute to the typical phenotypic character as seen in "wild" populations of organisms, such as fruit flies (Drosophila melanogaster). Such a "wild type" allele was historically regarded as leading to a dominant (overpowering – always expressed), common, and normal phenotype, in contrast to "mutant" alleles that lead to recessive, rare, and frequently deleterious phenotypes. It was formerly thought that most individuals were homozygous for the "wild type" allele at most gene loci, and that any alternative "mutant" allele was found in homozygous form in a small minority of "affected" individuals, often as genetic diseases, and more frequently in heterozygous form in "carriers" for the mutant allele. It is now appreciated that most or all gene loci are highly polymorphic, with multiple alleles, whose frequencies vary from population to population, and that a great deal of genetic variation is hidden in the form of alleles that do not produce obvious phenotypic differences. Wild type alleles are often denoted by a superscript plus sign (i.e., p$+$ for an allele p).

Multiple alleles

A population or species of organisms typically includes multiple alleles at each locus among various individuals. Allelic variation at a locus is measurable as the number of alleles (polymorphism) present, or the proportion of heterozygotes in the population. A null allele is a gene variant that lacks the gene's normal function because it either is not expressed, or the expressed protein is inactive.

For example, at the gene locus for the ABO blood type carbohydrate antigens in humans, classical genetics recognizes three alleles, IA, IB, and i, which determine compatibility of blood transfusions. Any individual has one of six possible genotypes (IAIA, IAi, IBIB, IBi, IAIB, and ii) which produce one of four possible phenotypes: "Type A" (produced by IAIA homozygous and IAi heterozygous genotypes), "Type B" (produced by IBIB homozygous and IBi heterozygous genotypes), "Type AB" produced by IAIB heterozygous genotype, and "Type O" produced by ii homozygous genotype. (It is now known that each of the A, B, and O alleles is actually a class of multiple alleles with different DNA sequences that produce proteins with identical properties: more than 70 alleles are known at the ABO locus. Hence an individual with "Type A" blood may be an AO heterozygote, an AA homozygote, or an AA heterozygote with two different "A" alleles.)

Genotype frequencies
The frequency of alleles in a diploid population can be used to predict the frequencies of the corresponding genotypes (see Hardy–Weinberg principle). For a simple model, with two alleles;

 * $$p + q=1 \, $$

 * $$p^2 + 2pq + q^2=1 \,$$

where p is the frequency of one allele and q is the frequency of the alternative allele, which necessarily sum to unity. Then, p2 is the fraction of the population homozygous for the first allele, 2pq is the fraction of heterozygotes, and q2 is the fraction homozygous for the alternative allele. If the first allele is dominant to the second then the fraction of the population that will show the dominant phenotype is p2 + 2pq, and the fraction with the recessive phenotype is q2.

With three alleles:

 * $$p + q + r = 1 \, $$ and

 * $$p^2 + q^2 + r^2 + 2pq + 2pr + 2qr = 1. \,$$

In the case of multiple alleles at a diploid locus, the number of possible genotypes (G) with a number of alleles (a) is given by the expression:

 * $$G= \frac{a(a+1)}{2}. $$

Allelic dominance in genetic disorders
A number of genetic disorders are caused when an individual inherits two recessive alleles for a single-gene trait. Recessive genetic disorders include albinism, cystic fibrosis, galactosemia, phenylketonuria (PKU), and Tay–Sachs disease. Other disorders are also due to recessive alleles, but because the gene locus is located on the X chromosome, so that males have only one copy (that is, they are hemizygous), they are more frequent in males than in females. Examples include red–green color blindness and fragile X syndrome.

Other disorders, such as Huntington's disease, occur when an individual inherits only one dominant allele.

Epialleles
While heritable traits are typically studied in terms of genetic alleles, epigenetic marks such as DNA methylation can be inherited at specific genomic regions in certain species, a process termed transgenerational epigenetic inheritance. The term epiallele is used to distinguish these heritable marks from traditional alleles, which are defined by nucleotide sequence. A specific class of epiallele, the metastable epialleles, has been discovered in mice and in humans which is characterized by stochastic (probabilistic) establishment of epigenetic state that can be mitotically inherited.

Idiomorph
The term "idiomorph", from Greek 'morphos' (form) and 'idio' (singular, unique), was introduced in 1990 in place of "allele" to denote sequences at the same locus in different strains that have no sequence similarity and probably do not share a common phylogenetic relationship. It is used mainly in the genetic research of mycology.

title: Allele


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Ampicillin

Ampicillin is an antibiotic belonging to the aminopenicillin class of the penicillin family. The drug is used to prevent and treat a number of bacterial infections, such as respiratory tract infections, urinary tract infections, meningitis, salmonellosis, and endocarditis. It may also be used to prevent group B streptococcal infection in newborns. It is used by mouth, by injection into a muscle, or intravenously.

Common side effects include rash, nausea, and diarrhea. It should not be used in people who are allergic to penicillin. Serious side effects may include Clostridium difficile colitis or anaphylaxis. While usable in those with kidney problems, the dose may need to be decreased. Its use during pregnancy and breastfeeding appears to be generally safe.

Ampicillin was discovered in 1958 and came into commercial use in 1961. It is on the World Health Organization's List of Essential Medicines. The World Health Organization classifies ampicillin as critically important for human medicine. It is available as a generic medication.

Diseases

 * Bacterial meningitis; an aminoglycoside can be added to increase efficacy against gram-negative meningitis bacteria
 * Endocarditis by enterococcal strains (off-label use); often given with an aminoglycoside
 * Gastrointestinal infections caused by contaminated water or food (for example, by Salmonella)
 * Genito-urinary tract infections
 * Healthcare-associated infections that are related to infections from using urinary catheters and that are unresponsive to other medications
 * Otitis media (middle ear infection)
 * Prophylaxis (i.e. to prevent infection) in those who previously had rheumatic heart disease or are undergoing dental procedures, vaginal hysterectomies, or C-sections. It is also used in pregnant woman who are carriers of group B streptococci to prevent early-onset neonatal infections.
 * Respiratory infections, including bronchitis, pharyngitis
 * Sinusitis
 * Sepsis
 * Whooping cough, to prevent and treat secondary infections

Ampicillin used to also be used to treat gonorrhea, but there are now too many strains resistant to penicillins.

Bacteria
Ampicillin is used to treat infections by many gram-positive and gram-negative bacteria. It was the first "broad spectrum" penicillin with activity against gram-positive bacteria, including Streptococcus pneumoniae, Streptococcus pyogenes, some isolates of Staphylococcus aureus (but not penicillin-resistant or methicillin-resistant strains), Trueperella, and some Enterococcus. It is one of the few antibiotics that works against multidrug resistant Enterococcus faecalis and E. faecium. Activity against gram-negative bacteria includes Neisseria meningitidis, some Haemophilus influenzae, and some of the Enterobacteriaceae (though most Enterobacteriaceae and Pseudomonas are resistant). Its spectrum of activity is enhanced by co-administration of sulbactam, a drug that inhibits beta lactamase, an enzyme produced by bacteria to inactivate ampicillin and related antibiotics. It is sometimes used in combination with other antibiotics that have different mechanisms of action, like vancomycin, linezolid, daptomycin, and tigecycline.

Available forms
Ampicillin can be administered by mouth, an intramuscular injection (shot) or by intravenous infusion. The oral form, available as capsules or oral suspensions, is not given as an initial treatment for severe infections, but rather as a follow-up to an IM or IV injection. For IV and IM injections, ampicillin is kept as a powder that must be reconstituted.

IV injections must be given slowly, as rapid IV injections can lead to convulsive seizures.

Specific populations
Ampicillin is one of the most used drugs in pregnancy, and has been found to be generally harmless both by the Food and Drug Administration in the U.S. (which classified it as category B) and the Therapeutic Goods Administration in Australia (which classified it as category A). It is the drug of choice for treating Listeria monocytogenes in pregnant women, either alone or combined with an aminoglycoside. Pregnancy increases the clearance of ampicillin by up to 50%, and a higher dose is thus needed to reach therapeutic levels.

Ampicillin crosses the placenta and remains in the amniotic fluid at 50–100% of the concentration in maternal plasma; this can lead to high concentrations of ampicillin in the newborn.

While lactating mothers secrete some ampicillin into their breast milk, the amount is minimal.

In newborns, ampicillin has a longer half-life and lower plasma protein binding. The clearance by the kidneys is lower, as kidney function has not fully developed.

Contraindications
Ampicillin is contraindicated in those with a hypersensitivity to penicillins, as they can cause fatal anaphylactic reactions. Hypersensitivity reactions can include frequent skin rashes and hives, exfoliative dermatitis, erythema multiforme, and a temporary decrease in both red and white blood cells.

Ampicillin is not recommended in people with concurrent mononucleosis, as over 40% of patients develop a skin rash.

Side effects
Ampicillin is comparatively less toxic than other antibiotics, and side effects are more likely in those who are sensitive to penicillins and those with a history of asthma or allergies. In very rare cases, it causes severe side effects such as angioedema, anaphylaxis, and C. difficile infection (that can range from mild diarrhea to serious pseudomembranous colitis). Some develop black "furry" tongue. Serious adverse effects also include seizures and serum sickness. The most common side effects, experienced by about 10% of users are diarrhea and rash. Less common side effects can be nausea, vomiting, itching, and blood dyscrasias. The gastrointestinal effects, such as hairy tongue, nausea, vomiting, diarrhea, and colitis, are more common with the oral form of penicillin. Other conditions may develop up several weeks after treatment.

Overdose
Ampicillin overdose can cause behavioral changes, confusion, blackouts, and convulsions, as well as neuromuscular hypersensitivity, electrolyte imbalance, and kidney failure.

Interactions
Ampicillin reacts with probenecid and methotrexate to decrease renal excretion. Large doses of ampicillin can increase the risk of bleeding with concurrent use of warfarin and other oral anticoagulants, possibly by inhibiting platelet aggregation. Ampicillin has been said to make oral contraceptives less effective, but this has been disputed. It can be made less effective by other antibiotic, such as chloramphenicol, erythromycin, cephalosporins, and tetracyclines. For example, tetracyclines inhibit protein synthesis in bacteria, reducing the target against which ampicillin acts. If given at the same time as aminoglycosides, it can bind to it and inactivate it. When administered separately, aminoglycosides and ampicillin can potentiate each other instead.

Ampicillin causes skin rashes more often when given with allopurinol.

Both the live cholera vaccine and live typhoid vaccine can be made ineffective if given with ampicillin. Ampicillin is normally used to treat cholera and typhoid fever, lowering the immunological response that the body has to mount.

Mechanism of action
Ampicillin is in the penicillin group of beta-lactam antibiotics and is part of the aminopenicillin family. It is roughly equivalent to amoxicillin in terms of activity. Ampicillin is able to penetrate gram-positive and some gram-negative bacteria. It differs from penicillin G, or benzylpenicillin, only by the presence of an amino group. This amino group, present on both ampicillin and amoxicillin, helps these antibiotics pass through the pores of the outer membrane of gram-negative bacteria, such as Escherichia coli, Proteus mirabilis, Salmonella enterica, and Shigella.

Ampicillin acts as an irreversible inhibitor of the enzyme transpeptidase, which is needed by bacteria to make the cell wall. It inhibits the third and final stage of bacterial cell wall synthesis in binary fission, which ultimately leads to cell lysis; therefore, ampicillin is usually bacteriolytic.

Pharmacokinetics
Ampicillin is well-absorbed from the GI tract (though food reduces its absorption), and reaches peak concentrations in one to two hours. The bioavailability is around 62% for parenteral routes. Unlike other penicillins, which usually bind 60–90% to plasma proteins, ampicillin binds to only 15–20%.

Ampicillin is distributed through most tissues, though it is concentrated in the liver and kidneys. It can also be found in the cerebrospinal fluid when the meninges become inflamed (such as, for example, meningitis). Some ampicillin is metabolized by hydrolyzing the beta-lactam ring to penicilloic acid, though most of it is excreted unchanged. In the kidneys, it is filtered out mostly by tubular secretion; some also undergoes glomerular filtration, and the rest is excreted in the feces and bile.

Hetacillin and pivampicillin are ampicillin esters that have been developed to increase bioavailability.

History
Ampicillin has been used extensively to treat bacterial infections since 1961. Until the introduction of ampicillin by the British company Beecham, penicillin therapies had only been effective against gram-positive organisms such as staphylococci and streptococci. Ampicillin (originally branded as "Penbritin") also demonstrated activity against gram-negative organisms such as H. influenzae, coliforms, and Proteus spp.

Economics
Ampicillin is relatively inexpensive. In the United States, it is available as a generic medication.

Veterinary use
In veterinary medicine, ampicillin is used in cats, dogs, and farm animals to treat: Horses are generally not treated with oral ampicillin, as they have low bioavailability of beta-lactams.
 * Anal gland infections
 * Cutaneous infections, such as abscesses, cellulitis, and pustular dermatitis
 * E. coli and Salmonella infections in cattle, sheep, and goats (oral form). Ampicillin use for this purpose had declined as bacterial resistance has increased.
 * Mastitis in sows
 * Mixed aerobic–anaerobic infections, such as from cat bites
 * Multidrug-resistant Enterococcus faecalis and E. faecium
 * Prophylactic use in poultry against Salmonella and sepsis from E. coli or Staphylococcus aureus
 * Respiratory tract infections, including tonsilitis, bovine respiratory disease, shipping fever, bronchopneumonia, and calf and bovine pneumonia
 * Urinary tract infections in dogs

The half-life in animals is around that same of that in humans (just over an hour). Oral absorption is less than 50% in cats and dogs, and less than 4% in horses.

title: Ampicillin


text:
Annealing

Annealing may refer to:

 * Annealing (biology), in genetics
 * Annealing (glass), heating a piece of glass to remove stress
 * Annealing (materials science), a heat treatment that alters the microstructure of a material
 * Quantum annealing, a method for solving combinatorial optimisation problems and ground states of glassy systems
 * Simulated annealing, a numerical optimization technique

title: Annealing