It is important to note that the word  phenotype  was originally used to refer to both the trait/character itself (e.g. the blue eyes phenotype) and the set of traits/characteristics possessed by the organism (clair's eye-colour phenotype is blue). While this definition is still used in many places, the lack of distinction can make in-depth explanations confusing and thus use of the term Phene becomes necessary. Indeed, it is extremely difficult to determine precisely what the fundamental building blocks of a phenome are. Since the term "phenotype" has been used to describe traits and syndromes and population characteristics  [ 3 ]  it is not helpful in the collective search for specific traits that could be a consequence of a single gene or gene–environmental interaction. Phene has emerged as a candidate building block for the phenome.


Genes  give rise to phenes. Genes are the biochemical instructions encoding what an organism  can  be, while phenes are what the organism  is . In general it takes a combination of particular genes, environmental influences and random variation to give rise to any one phene in an organism. Both phenes and genes are subject to evolution. However, if one defines "genes" as "DNA sequences encoding  polypeptides ", they are not directly accessible to  natural selection ; the associated phenes are. Note that some, e.g.  Richard Dawkins , have used a wider definition of "gene" than the one used in  genetics  on occasion, extending it to any  DNA sequence with a function .


Due to the distinct chemical and physical properties of the  nucleotides  in the DNA and some  mutations  being " silent " (that is, not altering  gene expression ), the DNA  primary sequence  may also be a phene. For example, A-T and C-G base pairs are differently resistant to heat (see also  DNA-DNA hybridization ). In a  thermophilic  microorganism, "silent" mutations may have an effect on DNA stability and thus survival. While being subject to  evolution ,  natural selection  affects the primary sequence directly in this case, with or without it being expressed.


Consider, for example, a mutation that makes a  zygote  abort development as a young  embryo . This mutation, obviously, will not spread, as it is quickly fatal. It is not the mutated nucleotide that is selected against, but the fact that  due to  this mutation, the phene (a key enzyme or  developmental factor  for example) does not get expressed.


Compare a (fictional) kind of mutation that breaks the DNA strand in a crucial position and defies all attempts to repair it, leading to  cell death . Here, the mutated and unmutated DNA sequences would be phenes themselves; it is the changed primary sequence itself which by failing would cause death, not the corresponding polypeptide.


See also Dawkin's concept of  extended phenotype .


The term has been widely adopted by the academic community and appears in scientific literature. A quick keyword search of titles and abstracts containing "phene" at PubMed returns many articles. [ 4 ]
It is a valuable concept in the genomic era where "phenes" or "traits" (symptoms) are used to distinguish groups with genetic disorders.


"Phene" is used as to refer to relevant phenotypic traits in the OMIA ( Online Mendelian Inheritance in Animals ) database. One of the objectives of the OMIA is to match genotypes to phenotypes. Lenffer et al. (2006) describe the OMIA as a "comparative biology resource"  "(The) OMIA is a comprehensive resource of phenotypic information on heritable animal traits and genes in a strongly comparative context, relating traits to genes where possible. OMIA is modelled on and is complementary to Online Mendelian Inheritance in Man (OMIM)." [ 5 ]  The term "phene" is equated with "trait".


In  phenomics , a  phenocopy  is a variation in  phenotype  (generally referring to a single  trait ) which is caused by environmental conditions (often, but not necessarily, during the organism's  development ), such that the organism's phenotype matches a phenotype which is determined by  genetic  factors. It is not a type of  mutation , as it is non- hereditary .


The term was coined by German geneticist  Richard Goldschmidt  in 1935. [ 1 ]  He used it to refer to forms, produced by some experimental procedure, whose appearance duplicates or copies the phenotype of some  mutant  or combination of mutants.


The butterfly genus  Vanessa  can change phenotype based on the local temperature. If introduced to  Lapland  they mimic butterflies localised to this area; and if localised to  Syria  they mimic butterflies of this area.


The larvae of  Drosophila melanogaster  have been found to be particularly vulnerable to environmental factors which produce phenocopies of known mutations; these factors include temperature, shock, radiation, and various chemical compounds. In fruit fly,  Drosophila melanogaster , the normal body colour is brownish gray with black margins. A hereditary mutant for this was discovered by  T.H. Morgan  in 1910 where the body colour is yellow. This was a genotypic character which was constant in both the flies in all environments. However, in 1939, Rapoport discovered that if larvae of normal flies were fed with silver salts, they develop into yellow bodied flies irrespective of their genotype. [ 2 ]  The yellow bodied flies which are genetically brown is a variant of the original yellow bodied fly.


Phenocopy can also be observed in  Himalayan rabbits . When raised in moderate temperatures, Himalayan rabbits are white in colour with black tail, nose, and ears, making them phenotypically distinguishable from genetically black rabbits. However, when raised in cold temperatures, Himalayan rabbits show black colouration of their coats, resembling the genetically black rabbits. Hence this Himalayan rabbit is a phenocopy of the genetically black rabbit. [ 3 ]


Reversible and/or cosmetic modifications such as the use of  hair bleach  are not considered to be phenocopy, as they are not inherent traits.


Phenotypic integration  is a metric for measuring the correlation of multiple functionally-related traits to each other. [ 1 ]   Complex  phenotypes  often require multiple traits working together in order to function properly. Phenotypic integration is significant because it provides an explanation as to how phenotypes are sustained by relationships between traits. Every organism's phenotype is integrated, organized, and a functional whole.  Integration is also associated with functional modules.  Modules are complex character units that are tightly associated, such as a flower. [ 2 ]  It is hypothesized that organisms with high correlations between traits in a module have the most efficient functions. [ 3 ]  The fitness of a particular value for one phenotypic trait frequently depends on the value of the other phenotypic traits, making it important for those traits evolve together. One trait can have a direct effect on fitness, and it has been shown that the correlations among traits can also change fitness, causing these correlations to be adaptive, rather than solely genetic. [ 4 ]  Integration can be involved in multiple aspects of life, not just at the genetic level, but during development, or simply at a functional level.


Integration can be caused by  genetic , developmental, environmental, or physiological relationships among characters. [ 5 ]  Environmental conditions can alter or cause integration, i.e. they may be  plastic . [ 6 ]  Correlational selection, a form of natural selection can also produce integration. At the genetic level, integration can be caused by  pleiotropy , close  linkage , or  linkage disequilibrium  among unlinked genes. [ 7 ]  At the developmental level it can be due to cell-cell signaling such as in the development of the ectopic eyes in Drosophila.   It is believed that the patterns of genetic covariance helped distinguish certain species. [ 8 ]   It can create variation among certain phenotypes, and can facilitate efficiency. This is significant because integration may play a huge role in phenotypic evolution.  Phenotypic integration and its evolution can not only create large amounts of variety among phenotypes which can cause variation among species.  For example, the color patterns on  Garter snakes  range widely and are caused by the covariance among multiple phenotypes.


Shortly after the structure of DNA was uncovered,  Everett C. Olson  and Robert L. Miller (1958) wrote the first book regarding the topic of phenotypic integration. [ 9 ]  The term  integration  was first used in reference to genetics by Olson and Miller, referring to correlations among characters that are influenced by selection. [ 10 ]  Following Olson and Miller, botanical studies on coherence between characters were done spanning over many years. [ 11 ]  Its first expansion was in the construction of a morphological integration genetic model constructed by  Russell Lande  (1980). However, the term "Phenotypic Integration" was first coined by  Massimo Pigliucci  and Katherine Preston, in their book,  Phenotypic Integration , which helped elucidate the observed laws of correlation and some theoretical issues regarding the topic. [ 12 ]


Phenotypic Integration can be favorable or unfavorable with respect to natural selection. It has been shown that certain combinations of correlated traits can be unfavorable to an organism.  In an  ontogenetic  study of laboratory rats, certain covariances among developmental characters which produced differing functions in the skull and limb were less favorable than another set that contributed to skull and limb structure. [ 13 ]  The most common form of selection on phenotypic integration is correlational selection.  Correlational selection is a form of natural selection that favors certain combinations of traits (phenotypic integration). It can promote both genetic correlations and high levels of genetic variation. It has even been found that correlational selection may be the most common form of natural selection. [ 14 ]  Occasionally, this form of selection will favor a group of traits at the expense of others and if it does favor a particular set of traits it will include the most used traits whose functional effectiveness is essential for their ability to work together, and whose successful interaction is needed for the fitness of the individual. [ 15 ] [ 16 ]  Phenotypic integration may be the adaptive product of correlational selection. An example of natural selection favoring integration is in the color patterns and escape mechanisms of the Garter snake,  Thamnophis Ordinoides . [ 17 ]  Another example is in plants that have highly-specific pollinators, natural selection favors plants that have highly specialized flowering to pair with the specific pollinators, and therefore high floral integration. [ 18 ]


Integration can be found at the genetic level due to genetic linkage. Genetic linkage involves multiple genes being inherited together during meiosis because they are close to each other on the same chromosome.  Alleles at different loci can be inherited together if they are tightly linked. Large genetic correlations can only be upheld if the loci that influence different characters are tightly linked, or if high levels of inbreeding in the population occur.  Even if selection favors the correlations, it will not be maintained unless those conditions are met.  Selection will favor tight linkage because it is maintained better. Poorly linked genetic correlations will not last. [ 19 ]   Transposition allows the loci at different locations on the chromosome to move so that they can become close to each other and be inherited together.  This is significant to understanding the relationship between phenotypic integration and evolution because it is one of the mechanisms of how multiple traits that are connected to each other to evolve and change together.  For instance, the  Papilio dardanus  butterflies come in three different forms, each mimicking a different distasteful butterfly species. [ 20 ]   Multiple loci contribute to these different forms, and a butterfly with alleles for form A at one locus and B at another locus would have poor fitness.  However, the multiple loci are tightly linked, so they are inherited together as a single allele.  Through transposition, these multiple loci ended up close to each other. [ 21 ]


Mutations among these linked genes are the nonadaptive fuel which can create evolution.  Evolution may also occur because the integration may have an adaptive advantage in a particular environment for an organism.  It is also important to recognize that not only can the traits be inherited together, but inherited separately and selected together.  Another important example of phenotypic integration evolving over time is the relationship between the  neurocranium  and the brain.  Over the last 150 million years the number of bones in the brain has decreased while the size of the brain in mammals has changed.  Integration between the brain and the skull has evolved over this time period to reduce the number of bones in the cranium, while increasing the size of the brain.  This relationship between correlated traits has played an important role in the evolution of mammalian cranium structure and brain size. [ 22 ]  Finally, development is another crucial cause of phenotypic integration that has evolved over time.  Cell-signaling pathways which utilize integration in the form of complex interactions among specific cells in the pathway are crucial to proper development in many organisms.  The interactions among the cells in the pathway, and the interaction of the pathways with other pathways have evolved over time to create complex structures. [ 23 ]


Aposematism  in  poison dart frogs  has also shown that phenotypic integration may be involved.  Aposematism is the use of warning colors to deter predators because it often conveys the organism being poisonous, and this study found that diet specialization, and chemical defense are integrated and help affect aposematism. [ 24 ]


In another study regarding the relationship of sexual ornaments and phenotypic integration, there seems to be a paradox where sexual traits are expected to be both less integrated for greater expression, and more integrated to better indicate physiological quality. However, in the case of the  house finch , the female house finches select for males based on their likelihood to be a good parent. The females base their choice of male parental behaviors on the elaboration of the male's sexual ornamentation. Thus, female choice favors hormonally controlled integration of male sexual behaviors and male sexual ornamentation. [ 25 ]


Phylogenetically consistent patterns of phenotypic integration have also been recently reported in leaves, floral morphology, and dry fruits as well as in the morphology of some animal organs. [ 26 ] [ 27 ]


Understanding phenotypic integration will continue as more research and understanding is done with regards to genetic, developmental, and physiological mechanisms, and learn more about the relationship of selection and complex phenotypes. [ 28 ]   Research of this topic can even be beneficial to modern biomedicine. [ 29 ]


Phenotypic plasticity  refers to some of the changes in an  organism 's behavior, morphology and physiology in response to a unique environment. [ 1 ] [ 2 ]  Fundamental to the way in which organisms cope with environmental variation, phenotypic plasticity encompasses all types of environmentally induced changes (e.g.  morphological ,  physiological ,  behavioural ,  phenological ) that may or may not be permanent throughout an individual's lifespan. [ 3 ]


The term was originally used to describe developmental effects on morphological characters, but is now more broadly used to describe all phenotypic responses to environmental change, such as  acclimation  ( acclimatization ), as well as  learning . [ 3 ]  The special case when differences in environment induce discrete phenotypes is termed  polyphenism .


Generally, phenotypic plasticity is more important for immobile organisms (e.g.  plants ) than mobile organisms (e.g. most  animals ), as mobile organisms can often move away from unfavourable environments. [ 4 ]  Nevertheless, mobile organisms also have at least some degree of plasticity in at least some aspects of the  phenotype . [ 2 ]
One mobile organism with substantial phenotypic plasticity is  Acyrthosiphon pisum  of the  aphid  family, which exhibits the ability to interchange between asexual and sexual reproduction, as well as growing wings between generations when plants become too populated. [ 5 ]
Water fleas ( Daphnia magna ) have shown both phenotypic plasticity and the ability to genetically evolve to deal with the heat stress of warmer, urban pond waters. [ 2 ]


Phenotypic plasticity in plants includes the timing of transition from vegetative to reproductive growth stage, the allocation of more resources to the  roots  in soils that contain low concentrations of  nutrients , the size of the seeds an individual produces depending on the environment, [ 7 ]  and the alteration of  leaf  shape, size, and thickness. [ 8 ]  Leaves are particularly plastic, and their growth may be altered by light levels. Leaves grown in the light tend to be thicker, which maximizes photosynthesis in direct light; and have a smaller area, which cools the leaf more rapidly (due to a thinner  boundary layer ). Conversely, leaves grown in the shade tend to be thinner, with a greater surface area to capture more of the limited light. [ 9 ] [ 10 ]   Dandelion  are well known for exhibiting considerable plasticity in form when growing in sunny versus shaded environments. The  transport proteins  present in roots also change depending on the concentration of the nutrient and the salinity of the soil. [ 11 ]   Some plants,  Mesembryanthemum crystallinum  for example, are able to alter their photosynthetic pathways to use less water when they become water- or salt-stressed. [ 12 ]


Because of phenotypic plasticity, it is hard to explain and predict the traits when plants are grown in natural conditions unless an explicit environment index can be obtained to quantify environments. Identification of such explicit environment indices from critical growth periods being highly correlated with sorghum and rice flowering time enables such predictions. [ 6 ] [ 13 ]   Additional work is being done to support the agricultural industry, which faces severe challenges in prediction of crop phenotypic expression in changing environments. Since many crops supporting the global food supply are grown in a wide variety of environments, understanding and ability to predict crop genotype by environment interaction will be essential for future food stability. [ 14 ]


Leaves are very important to a plant in that they create an avenue where photosynthesis and thermoregulation can occur.  Evolutionarily, the environmental contribution to leaf shape allowed for a myriad of different types of leaves to be created. [ 15 ]  Leaf shape can be determined by both genetics and the environment. [ 16 ]  Environmental factors, such as light and humidity, have been shown to affect leaf morphology, [ 17 ]  giving rise to the question of how this shape change is controlled at the molecular level. This means that different leaves could have the same gene but present a different form based on environmental factors. Plants are sessile, so this phenotypic plasticity allows the plant to take in information from its environment and respond without changing its location.


In order to understand how leaf morphology works, the anatomy of a leaf must be understood. The main part of the leaf, the blade or lamina, consists of the epidermis, mesophyll, and vascular tissue. The epidermis contains  stomata  which allows for gas exchange and controls perspiration of the plant. The mesophyll contains most of the  chloroplast  where  photosynthesis  can occur. Developing a wide blade/lamina can maximize the amount of light hitting the leaf, thereby increasing photosynthesis, however too much sunlight can damage the plant. Wide lamina can also catch wind easily which can cause stress to the plant, so finding a happy medium is imperative to the plants’ fitness. The Genetic Regulatory Network is responsible for creating this phenotypic plasticity and involves a variety of genes and proteins regulating leaf morphology.
Phytohormones have been shown to play a key role in signaling throughout the plant, and changes in concentration of the phytohormones can cause a change in development. [ 18 ]


Studies on the aquatic plant species  Ludwigia arcuata  have been done to look at the role of  abscisic acid  (ABA), as  L. arcuata  is known to exhibit phenotypic plasticity and has two different types of leaves, the aerial type (leaves that touch the air) and the submerged type (leaves that are underwater). [ 19 ]  When adding ABA to the underwater shoots of  L. arcuata , the plant was able to produce aerial type leaves underwater, suggesting that increased concentrations of ABA in the shoots, likely caused by air contact or a lack of water, triggers the change from the submerged type of leaf to the aerial type. This suggests ABA's role in leaf phenotypic change and its importance in regulating stress through environmental change (such as adapting from being underwater to above water). In the same study, another phytohormone, ethylene, was shown to induce the submerged leaf phenotype unlike ABA, which induced aerial leaf phenotype. Because ethylene is a gas, it tends to stay endogenously within the plant when underwater – this growth in concentration of ethylene induces a change from aerial to submerged leaves and has also been shown to inhibit ABA production, further increasing the growth of submerged type leaves.
These factors (temperature, water availability, and phytohormones) contribute to changes in leaf morphology throughout a plants lifetime and are vital to maximize plant fitness.


The developmental effects of nutrition and temperature have been demonstrated. [ 20 ]  The  gray wolf  ( Canis lupus ) has wide phenotypic plasticity. [ 21 ] [ 22 ]  Additionally, male  speckled wood  butterflies have two morphs: one with three dots on its hindwing, and one with four dots on its hindwings. The development of the fourth dot is dependent on environmental conditions – more specifically, location and the time of year. [ 23 ]  In  amphibians ,  Pristimantis mutabilis  has remarkable phenotypic plasticity, [ 24 ]  as well as  Agalychnis callidryas  whose embryos exhibit phenotypic plasticity, hatching early in response to disturbance to protect themselves. Another example is the  southern rockhopper penguin . [ 25 ]  Rockhopper penguins are present at a variety of climates and locations; Amsterdam Island's subtropical waters,  Kerguelen Archipelago  and  Crozet Archipelago 's subantarctic coastal waters. [ 25 ]  Due to the species plasticity they are able to express different strategies and foraging behaviors depending on the climate and environment. [ 25 ]  A main factor that has influenced the species' behavior is where food is located. [ 25 ]


Plastic responses to  temperature  are essential among  ectothermic organisms , as all aspects of their physiology are directly dependent on their thermal environment. As such, thermal acclimation entails phenotypic adjustments that are found commonly across  taxa , such as changes in the  lipid  composition of  cell membranes . Temperature change influences the fluidity of cell membranes by affecting the motion of the  fatty acyl  chains of  glycerophospholipids . Because maintaining membrane fluidity is critical for cell function, ectotherms adjust the phospholipid composition of their cell membranes such that the strength of  van der Waals forces  within the membrane is changed, thereby maintaining fluidity across temperatures. [ 26 ]


Phenotypic plasticity  of the  digestive system  allows some animals to respond to changes in dietary nutrient composition, [ 27 ] [ 28 ]  diet quality, [ 29 ] [ 30 ]  and energy requirements. [ 31 ] [ 32 ] [ 33 ]


Changes in the  nutrient  composition of the diet (the proportion of lipids, proteins and carbohydrates) may occur during development (e.g. weaning) or with seasonal changes in the abundance of different food types. These diet changes can elicit plasticity in the  activity  of particular digestive enzymes on the  brush border  of the  small intestine . For example, in the first few days after hatching, nestling  house sparrows  ( Passer domesticus ) transition from an insect diet, high in protein and lipids, to a seed based diet that contains mostly carbohydrates; this diet change is accompanied by two-fold increase in the activity of the enzyme  maltase , which digests carbohydrates. [ 27 ]  Acclimatizing animals to high protein diets can increase the activity of  aminopeptidase -N, which digests proteins. [ 28 ] [ 34 ]


Poor quality diets (those that contain a large amount of non-digestible material) have lower concentrations of nutrients, so animals must process a greater total volume of poor-quality food to extract the same amount of energy as they would from a high-quality diet. Many species respond to poor quality diets by increasing their food intake, enlarging digestive organs, and increasing the capacity of the digestive tract (e.g.  prairie voles , [ 33 ]   Mongolian gerbils , [ 30 ]   Japanese quail , [ 29 ]   wood ducks , [ 35 ]   mallards [ 36 ] ). Poor quality diets also result in lower concentrations of nutrients in the lumen of the intestine, which can cause a decrease in the activity of several digestive enzymes. [ 30 ]


Animals often consume more food during periods of high energy demand (e.g. lactation or cold exposure in  endotherms ), this is facilitated by an increase in digestive organ size and capacity, which is similar to the phenotype produced by poor quality diets. During lactation,  common degus  ( Octodon degus ) increase the mass of their liver, small intestine, large intestine and cecum by 15–35%. [ 31 ]  Increases in food intake do not cause changes in the activity of digestive enzymes because nutrient concentrations in the intestinal  lumen  are determined by food quality and remain unaffected. [ 31 ]  Intermittent feeding also represents a temporal increase in food intake and can  induce dramatic changes in the size of the gut; the  Burmese python  ( Python molurus bivittatus ) can triple the size of its small intestine just a few days after feeding. [ 37 ]


AMY2B  (Alpha-Amylase 2B) is a gene that codes a protein that assists with the first step in the digestion of dietary  starch  and  glycogen . An expansion of this gene in dogs would enable early dogs to exploit a starch-rich diet as they fed on refuse from agriculture. Data indicated that the wolves and dingo had just two copies of the gene and the Siberian Husky that is associated with hunter-gatherers had just three or four copies, whereas the  Saluki  that is associated with the  Fertile Crescent  where agriculture originated had 29 copies. The results show that on average, modern dogs have a high copy number of the gene, whereas wolves and dingoes do not. The high copy number of AMY2B variants likely already existed as a standing variation in early domestic dogs, but expanded more recently with the development of large agriculturally based civilizations. [ 38 ]


Infection with  parasites  can induce phenotypic plasticity as a means to compensate for the detrimental effects caused by parasitism. Commonly,  invertebrates  respond to  parasitic castration  or increased parasite  virulence  with  fecundity  compensation in order to increase their reproductive output, or  fitness . For example,  water fleas  ( Daphnia magna ), exposed to  microsporidian  parasites produce more offspring in the early stages of exposure to compensate for future loss of reproductive success. [ 39 ]  A reduction in fecundity may also occur as a means of re-directing nutrients to an immune response, [ 40 ]  or to increase   longevity  of the host. [ 41 ]  This particular form of plasticity has been shown in certain cases to be mediated by host-derived molecules (e.g. schistosomin in snails  Lymnaea stagnalis  infected with  trematodes   Trichobilharzia ocellata ) that interfere with the action of reproductive hormones on their target organs. [ 42 ]  Changes in reproductive effort during infection is also thought to be a less costly alternative to mounting resistance or defence against invading parasites, although it can occur in concert with a defence response. [ 43 ]


Hosts can also respond to parasitism through plasticity in physiology aside from reproduction. House mice infected with intestinal  nematodes  experience decreased rates of   glucose  transport in the intestine. To compensate for this, mice increase the total mass of mucosal cells, cells responsible for glucose transport, in the intestine. This allows infected mice to maintain the same capacity for  glucose uptake  and body size as uninfected mice. [ 44 ]


Phenotypic plasticity can also be observed as changes in behaviour. In response to infection, both vertebrates and invertebrates practice  self-medication , which can be considered a form of adaptive plasticity. [ 45 ]  Various species of non-human primates infected with intestinal worms engage in leaf-swallowing, in which they ingest rough, whole leaves that physically dislodge parasites from the intestine. Additionally, the leaves irritate the  gastric mucosa , which promotes the secretion of gastric acid and increases  gut motility , effectively flushing parasites from the system. [ 46 ]   The term "self-induced adaptive plasticity" has been used to describe situations in which a behavior under selection causes changes in subordinate traits that in turn enhance the ability of the organism to perform the behavior. [ 47 ]  For example, birds that engage in  altitudinal migration  might make "trial runs" lasting a few hours that would induce physiological changes that would improve their ability to function at high altitude. [ 47 ]


Woolly bear caterpillars ( Grammia incorrupta ) infected with  tachinid flies  increase their survival by ingesting plants containing toxins known as  pyrrolizidine alkaloids . The physiological basis for this change in behaviour is unknown; however, it is possible that, when activated, the immune system sends signals to the taste system that trigger plasticity in feeding responses during infection. [ 45 ]


Reproduction


The red-eyed tree frog,  Agalychnis callidryas , is an arboreal frog (hylid) that resides in the tropics of Central America.  Unlike many frogs, the red-eyed tree frog has arboreal eggs which are laid on leaves hanging over ponds or large puddles and, upon hatching, the tadpoles fall into the water below. One of the most common predators encountered by these arboreal eggs is the cat-eyed snake,  Leptodeira septentrionalis .  In order to escape predation, the red-eyed tree frogs have developed a form of adaptive plasticity, which can also be considered phenotypic plasticity, when it comes to hatching age; the clutch is able to hatch prematurely and survive outside of the egg five days after oviposition when faced with an immediate threat of predation.  The egg clutches take in important information from the vibrations felt around them and use it to determine whether or not they are at risk of predation. In the event of a snake attack, the clutch identifies the threat by the vibrations given off which, in turn, stimulates hatching almost instantaneously.  In a controlled experiment conducted by Karen Warkentin, hatching rate and ages of red-eyed tree frogs were observed in clutches that were and were not attacked by the cat-eyed snake.  When a clutch was attacked at six days of age, the entire clutch hatched at the same time, almost instantaneously. However, when a clutch is not presented with the threat of predation, the eggs hatch gradually over time with the first few hatching around seven days after oviposition, and the last of the clutch hatching around day ten. Karen Warkentin's study further explores the benefits and trade-offs of hatching plasticity in the red-eyed tree frog. [ 48 ]


Plasticity is usually thought to be an  evolutionary adaptation  to environmental variations that is reasonably predictable and occurs within the lifespan of an individual organism, as it allows individuals to 'fit' their phenotype to different environments. [ 49 ] [ 50 ]  If the optimal phenotype in a given environment changes with environmental conditions, then the ability of individuals to express different traits should be advantageous and thus  selected for . Hence, phenotypic plasticity can evolve if Darwinian fitness is increased by changing phenotype. [ 51 ] [ 52 ]  A similar logic should apply in  artificial evolution  attempting to introduce phenotypic plasticity to artificial agents. [ 53 ]  However, the fitness benefits of plasticity can be limited by the energetic costs of plastic responses (e.g. synthesizing new proteins, adjusting expression ratio of  isozyme  variants, maintaining sensory machinery to detect changes) as well as the predictability and reliability of environmental cues [ 54 ]  (see  Beneficial acclimation hypothesis ).


Freshwater snails  ( Physa virgata ), provide an example of when phenotypic plasticity can be either adaptive or  maladaptive .  In the presence of a predator,  bluegill sunfish , these snails make their shell shape more rotund and reduce growth.  This makes them more crush-resistant and better protected from predation.  However, these snails cannot tell the difference in chemical cues between the predatory and non-predatory sunfish.  Thus, the snails respond inappropriately to non-predatory sunfish by producing an altered shell shape and reducing growth.  These changes, in the absence of a predator, make the snails susceptible to other predators and limit  fecundity .  Therefore, these freshwater snails produce either an adaptive or maladaptive response to the environmental cue depending on whether predatory sunfish are present or not. [ 55 ] [ 56 ]


Given the profound ecological importance of temperature and its predictable variability over large spatial and temporal scales, adaptation to thermal variation has been hypothesized to be a key mechanism dictating the capacity of organisms for phenotypic plasticity. [ 57 ]  The magnitude of thermal variation is thought to be directly proportional to plastic capacity, such that species that have evolved in the warm, constant  climate  of the  tropics  have a lower capacity for plasticity compared to those living in variable  temperate  habitats. Termed the "climatic variability hypothesis", this idea has been supported by several studies of plastic capacity across  latitude  in both plants and animals. [ 58 ] [ 59 ]  However, recent studies of  Drosophila  species have failed to detect a clear pattern of plasticity over latitudinal gradients, suggesting this hypothesis may not hold true across all taxa or for all traits. [ 60 ]  Some researchers propose that direct measures of environmental variability, using factors such as precipitation, are better predictors of phenotypic plasticity than latitude alone. [ 61 ]


Selection experiments  and  experimental evolution  approaches have shown that plasticity is a trait that can evolve when under direct selection and also as a correlated response to selection on the average values of particular traits. [ 62 ]


Temporal plasticity , also known as fine-grained environmental adaptation, [ 63 ]  is a type of phenotypic plasticity that involves the  phenotypic  change of organisms in response to changes in the environment over time. Animals can respond to short-term environmental changes with  physiological  (reversible) and  behavioral  changes; plants, which are sedentary, respond to short-term environmental changes with both physiological and  developmental  (non-reversible) changes. [ 64 ]


Unprecedented rates of  climate change  are predicted to occur over the next 100 years as a result of human activity. [ 67 ]  Phenotypic plasticity is a key mechanism with which organisms can cope with a changing climate, as it allows individuals to respond to change within their lifetime. [ 68 ]  This is thought to be particularly important for species with long generation times, as evolutionary responses via  natural selection  may not produce change fast enough to mitigate the effects of a warmer climate.


The  North American red squirrel  ( Tamiasciurus hudsonicus ) has experienced an increase in average temperature over this last decade of almost 2 °C.  This increase in temperature has caused an increase in abundance of white spruce cones, the main food source for winter and spring reproduction. In response, the mean lifetime  parturition  date of this species has advanced by 18 days.  Food abundance showed a significant effect on the breeding date with individual females, indicating a high amount of phenotypic plasticity in this trait. [ 69 ]


Plant genetic resources  describe the variability within plants that comes from human and natural selection over millennia. Their intrinsic value mainly concerns agricultural crops ( crop biodiversity ).


According to the 1983 revised International Undertaking on Plant Genetic Resources for Food and Agriculture of the  Food and Agriculture Organization  (FAO), plant genetic resources are defined as  the entire generative and vegetative reproductive material of species with economical and/or social value, especially for the agriculture of the present and the future, with special emphasis on nutritional plants . [ 1 ]


In the State of the World’s Plant Genetic Resources for Food and Agriculture (1998) the FAO defined Plant Genetic Resources for Food and Agriculture (PGRFA) as  the diversity of genetic material contained in traditional varieties and modern cultivars as well as  crop wild relatives  and other wild plant species that can be used now or in the future for food and agriculture . [ 2 ]


The first use of plant genetic resources dates to more than 10,000 years ago, when farmers selected from the  genetic variation  they found in wild plants to develop their crops. As human populations moved to different climates and ecosystems, taking the crops with them, the crops adapted to the new environments, developing, for example, genetic traits providing tolerance to conditions such as drought, water logging, frost and extreme heat. These traits - and the plasticity inherent in having wide genetic variability - are important properties of plant genetic resources. [ citation needed ]


In recent centuries, although humans had been prolific in collecting exotic flora from all corners of the globe to fill their gardens, it wasn’t until the early 20th century that the widespread and organized collection of plant genetic resources for agricultural use began in earnest. Russian geneticist  Nikolai Vavilov , considered by some as the father of plant genetic resources, realized the value of genetic variability for breeding and collected thousands of seeds during his extensive travels to establish one of the first  gene banks . [ 3 ]  Vavilov inspired the American  Jack Harlan  to collect seeds from across the globe for the  United States Department of Agriculture  (USDA). [ 4 ]   David Fairchild , another botanist at USDA, successfully introduced many important crops (e.g. cherries, soybeans, pistachios) into the United States. [ 5 ]


It was not until 1967 that the term  genetic resources  was coined by  Otto Frankel  and  Erna Bennett  at the historic International Conference on Crop Plant Exploration and Conservation, organized by the FAO and the  International Biological Program  (IBP) [ 6 ] [ 7 ]  “The effective utilization of genetic resources requires that they are adequately classified and evaluated” was a key message from the conference. [ 8 ]


Plant genetic resource conservation has become increasingly important as more plants have become threatened or rare. At the same time, an exploding world population and rapid  climate change  have led humans to seek new resilient and nutritious crops. Plant conservation strategies generally combine elements of conservation on farm (as part of the crop production cycle, where it continues to evolve and support farmer needs),  ex situ  (for example in gene banks or field collections as seed or tissue samples) or  in situ  (where they grow in the wild or protected areas). Most  in situ  conservation concerns  crop wild relatives , an important source of genetic variation to crop breeding programs. [ 9 ]


Plant genetic resources that are conserved by any of these methods are often referred to as  germplasm , which is a shorthand term meaning "any genetic materials". The term originates from  germ plasm ,  August Weismann 's theory that heritable information is transmitted only by germ cells, and which has been superseded by modern insights on inheritance, including  epigenetics  and non-nuclear  DNA .


After the  Second World War , efforts to conserve plant genetic resources came mainly from breeders’ organizations in the USA and Europe, which led to crop-specific collections primarily located in developed countries (e.g.  IRRI ,  CIMMYT ). In the 1960s and 1970s, more focus was put on the collection and conservation of plant genetic resources in face of genetic erosion by organizations such as the  Rockefeller Foundation  and the  European Society of Breeding Research  (EUCARPIA). [ 8 ]


A key event in the conservation of plant genetic resources was the establishment of the International Board for Plant Genetic Resources (IBPGR) (now  Bioversity International ) in 1974, whose mandate was  to promote and assist in the worldwide effort to collect and conserve the plant germplasm needed for future research and production . IBPGR mobilized scientists to create a global network of gene banks, thus marking the international recognition of the importance of plant genetic resources. [ 8 ]


In 2002, the  Global Crop Diversity Trust  was established by Bioversity International on behalf of the  CGIAR  and the FAO through a Crop Diversity Endowment Fund. The goal of the Trust is to provide a secure and sustainable source of funding for the world's most important  ex situ  crop collections.


In response to the growing awareness of the global value of and threat to biological diversity, the United Nations drafted the 1992  Convention on Biological Diversity  (CBD), [ 10 ]  the first global multilateral treaty focused on the conservation and sustainable use of  biodiversity . Article 15 of the CBD specified that countries have national sovereignty over their genetic resources, but that there should be facilitated access and benefit sharing  (ABS)  under mutually agreed terms and with prior informed consent.


Going further to protect national sovereignty of plant genetic resources, an instrumental piece of legislation, The  International Treaty on Plant Genetic Resources for Food and Agriculture  (ITPGRFA), was adopted by the FAO in November 2001 and came into force in 2004. [ 11 ]


The ITPGRFA established several mechanisms under the Multilateral System, which grants free access and equitable use of 64 of the world’s most important crops ( Annex 1 crops ) for some uses (research, breeding and training for food and agriculture). The treaty prevents the recipients of genetic resources from claiming intellectual property rights over those resources in the form in which they received them, and ensures that access to genetic resources is consistent with international and national laws. This is facilitated by the  Standard Material Transfer Agreement , a mandatory contract between providers and recipients for the exchange of germplasm under the Multilateral System. The Governing Body of the treaty, through FAO as the Third Party Beneficiary, has an interest in the agreements. [ 11 ]


The  Nagoya Protocol  on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization is a supplementary agreement to the Convention on Biological Diversity that was adopted in 2010 and enforced in 2014. It provides greater legal transparency to policies governing fair and equitable sharing of benefits arising from the utilization of genetic resources. [ 12 ]


Due to the high value and complexity of plant genetic resources and the number of parties involved globally, some issues have arisen over their conservation and use.


Much of the material for breeding programs was collected from the Southern hemisphere and sent to gene banks in the Northern hemisphere, a concern that led to more emphasis on the national sovereignty of plant genetic resources and instigated policies that addressed the imbalance. [ 13 ]


The increased use of  plant genetic information  for research, for example to find genes of interest for drought tolerance, has led to controversy on whether and to what extent the genetic data (separate from the organism) are subject to the international ABS regulations described above. [ 13 ]


Forest genetic resources  represent a specific case of plant genetic resources.


Plant–fungus horizontal gene transfer  is the movement of  genetic material  between individuals in the  plant  and  fungus   kingdoms .  Horizontal gene transfer  is universal in  fungi ,  viruses ,  bacteria , and other  eukaryotes . [ 1 ]  Horizontal gene transfer research often focuses on  prokaryotes  because of the abundant sequence data from diverse lineages, and because it is assumed not to play a significant role in eukaryotes. [ 2 ]


Most plant–fungus horizontal gene transfer events are ancient and rare, but they may have provided important gene functions leading to wider substrate use and habitat spread for plants and fungi. [ 3 ]  Since these events are rare and ancient, they have been difficult to detect and remain relatively unknown. [ 4 ]  Plant–fungus interactions could play a part in a multi-horizontal gene transfer pathway among many other organisms. [ 5 ]


Fungus–plant-mediated horizontal gene transfer can occur via  phagotrophic  mechanisms (mediated by phagotrophic eukaryotes) and nonphagotropic mechanisms. Nonphagotrophic mechanisms have been seen in the transmission of  transposable elements ,  plastid -derived  endosymbiotic  gene transfer, prokaryote-derived gene transfer,  Agrobacterium tumefaciens -mediated  DNA  transfer, cross-species  hybridization  events, and gene transfer between  mitochondrial  genes. [ 3 ]  Horizontal gene transfer could bypass eukaryotic barrier features like linear  chromatin -based  chromosomes ,  intron – exon  gene structures, and the  nuclear envelope . [ 6 ]


Horizontal gene transfer occurs between microorganisms sharing overlapping ecological niches and associations like  parasitism  or  symbiosis . Ecological association can facilitate horizontal gene transfer in plants and fungi and is an unstudied factor in shared evolutionary histories.


Most horizontal gene transfers from fungi into plants predate the rise of land plants. A greater genomic inventory of gene family and taxon sampling has been identified as a desirable prerequisite for identifying further plant–fungus events. [ 4 ]


Evidence for gene transfer between fungi and eukaryotes is discovered indirectly. Evidence is found in the unusual features of genetic elements. These features include: inconsistency between  phylogeny  across genetic elements, high  DNA  or  amino acid  similarity from phylogenetically distant organisms, irregular distribution of genetic elements in a variety of species, similar genes shared among species within a specific habitat or geography independent of their phylogenetic relationship, and gene characteristics inconsistent with the resident genome such as high  guanine  and  cytosine  content,  codon  usage, and introns. [ 4 ]


Alternative hypotheses and explanations for such findings include erroneous species phylogenies, inappropriate comparison of  paralogous  sequences, sporadic retention of shared ancestral characteristics, uneven rates of character change in other lineages, and  introgressive hybridization . [ 4 ]


The "complexity hypothesis" is a different approach to understanding why informational genes have less success in being transferred than operational genes. It has been proposed that informational genes are part of larger, more conglomerate systems, while operational genes are less complex, allowing them to be horizontally transferred at higher frequencies. The hypothesis incorporates the "continual hypothesis", which states that horizontal gene transfer is constantly occurring in operational genes. [ 7 ]


Plant–fungus horizontal gene transfer could take place during plant infection. There are many possible vectors, such as plant–fungus–insect interactions. The ability for fungi to infect other organisms provides this possible pathway. [ 5 ]


A fungus–plant pathway has been demonstrated in rice ( Oryza sativa ) through ancestral lineages. A phylogeny was constructed from 1689 identified genes and all  homologs  available from the rice genome (3177 gene families). Fourteen candidate plant–fungus horizontal gene transfer events were identified, nine of which showed infrequent patterns of transfer between plants and fungi. From the phylogenetic analysis, horizontal gene transfer events could have contributed to the L-fucose permease sugar transporter, zinc binding  alcohol dehydrogenase ,  membrane transporter ,  phospholipase / carboxylesterase ,  iucA / iucC  family protein in  siderophore  biosynthesis,  DUF239  domain protein, phosphate-response 1 family protein, a hypothetical protein similar to  zinc finger  (C2H2-type) protein, and another conserver hypothetical protein. [ 3 ]


Some plants may have obtained the  shikimate pathway  from symbiotic fungi. Plant shikimate pathway enzymes share similarities to prokaryote homologs and could have ancestry from a  plastid  progenitor genome. It is possible that the shikimate pathway and the pentafunctional  arom  have their ancient origins in eukaryotes or were conveyed by eukaryote–eukaryote horizontal gene transfer. The evolutionary history of the pathway could have been influenced by a prokaryote-to-eukaryote gene transfer event.  Ascomycete  fungi along with  zygomycetes ,  basidiomycetes ,  apicomplexa ,  ciliates , and  oomycetes  retained elements of an ancestral pathway given through the bikont/unikont eukaryote root. [ 8 ]


Fungi and bacteria could have contributed to the phenylpropanoid pathway in ancestral land plants for the synthesis of  flavonoids  and  lignin  through horizontal gene transfer.  Phenylalanine ammonia lyase  (PAL) is known to be present in fungi, such as  Basidiomycota  yeast like  Rhodotorula  and  Ascomycota  such as  Aspergillus  and  Neurospora . These fungi participate in the  catabolism  of  phenylalanine  for carbon and nitrogen. PAL in some plants and fungi also has a  tyrosine ammonia lyase  (TAL) for the synthesis of  p-coumaric acid  into  p-coumaroyl-CoA . PAL likely emerged from bacteria in an antimicrobial role. Horizontal gene transfer took place through a pre- Dikarya  divergent fungal lineage and a  Nostocale  or soil-sediment bacterium through symbiosis. The fungal PAL was then transferred to an ancestor of a land plant by an ancient  arbuscular mycorrhizal  symbiosis that later developed in the phenylpropanoid pathway and land plant colonization. PAL enzymes in early bacteria and fungi could have contributed to protection against  ultraviolet radiation , acted as a light capturing pigment, or assisted in antimicrobial defense. [ 9 ]


Sterigmatocystin  gene transfer has been observed with  Podospora anserina  and  Aspergillus . Horizontal gene transfer in  Aspergillus  and  Podospora  contributed to fungal metabolic diversity in secondary metabolism.  Aspergillus nidulans  produces  sterigmatocystin  – a precursor to  aflatoxins .  Aspergillus  was found to have horizontally transferred genes to  Podospora anserina .  Podospora  and  Aspergillus  show high conservation and microsynteny sterigmatocystin/aflatoxin clusters along with intergenic regions containing 14 binding sites for  AfIR , a transcription factor for the activation of sterigmatocystin/aflatoxin biosynthetic genes.  Aspergillus  to  Podospora  represents a large metabolic gene transfer which could have contributed to fungal metabolic diversity. Transposable elements and other mobile genetic elements like plasmids and viruses could allow for chromosomal rearrangement and integration of foreign genetic material. Horizontal gene transfer could have significantly contributed to fungal genome remodeling and metabolic diversity. [ 10 ]


In  Stagonospora  and  Pyrenophora , as well as in  Fusarium  and  Alternaria , horizontal gene transfer provides a powerful mechanism for fungi to acquire  pathogenic  capabilities to infect a new host plant. Horizontal gene transfer and interspecific hybridization between pathogenic species allow for hybrid offspring with an expanded host range. This can cause disease outbreaks on new crops when an encoded protein is able to cause pathogenicity. [ 11 ]


The interspecific transfer of virulence factors in fungal pathogens has been shown between  Stagonospora modorum  and  Pyrenophora tritici-repentis , where a host-selective toxin from  S. nodorum  conferred virulence to  P. tritici-repentis  on wheat. [ 12 ]


In  Fusarium , a nonpathogenic strain was experimentally converted into a pathogen and could have contributed to pathogen adaption in large genome portions.  Fusarium graminearum ,  Fusarium verticilliodes , and  Fusarium oxysprorum  are maize and tomato pathogens that produce  fumonisin   mycotoxins  that contaminate grain. These examples highlight the apparent polyphyletic origins of host specialization and the emergence of new pathogenic lineages distinct from genetic backgrounds. [ 13 ]  The ability to transfer genetic material could increase disease in susceptible plant populations.


Poison exons  (PEs); also called  premature termination codon (PTC)  exons or  nonsense-mediated decay (NMD)  exons] are a class of  cassette exons  that contain PTCs. Inclusion of a PE in a  transcript  targets the transcript for degradation via NMD. PEs are generally highly conserved elements of the genome and are thought to have important regulatory roles in biology. [ 1 ] [ 2 ]  Targeting PE inclusion or exclusion in certain transcripts is being evaluated as a therapeutic strategy.


In 2002, a model termed regulated unproductive splicing and translation (RUST) was proposed based on the finding that many (~one-third) alternatively spliced transcripts contain PEs. In this model, coupling alternative splicing to NMD (AS-NMD) is thought to tune transcript levels to regulate protein expression. [ 3 ]  Alternative splicing may also lead to NMD via other pathways besides PE inclusion, e.g., intron retention. [ 4 ] [ 5 ]


PEs were initially characterized in  RNA-binding proteins  from the  SR protein family . [ 1 ] [ 2 ]  Genes for other  RNA-binding proteins (RBPs)  such as those for  heterogenous nuclear ribonucleoprotein (hnRNP)  also contain PEs. [ 2 ]  Numerous  chromatin  regulators also contain PEs, though these are less conserved than PEs within RBPs such as the SR proteins. [ 6 ]  Multiple  spliceosomal  components contain PEs. [ 7 ]  Certain PEs may occur only in specific tissues. [ 8 ]


PE-containing transcripts generally represent a minority of the overall transcript population, in part due to their active degradation via NMD, though this relative abundance can be elevated upon inhibition of NMD or certain biological states. [ 2 ] [ 7 ] [ 9 ] [ 10 ] [ 11 ]  Certain PE-containing transcripts are resistant to NMD and may be translated into truncated proteins. [ 12 ]


Cis -regulatory elements neighboring PEs have been found to affect PE inclusion. [ 13 ]


Many proteins whose corresponding genes contain PEs autoregulate PE inclusion in their respective transcripts and thereby control their own levels via a feedback loop. [ 12 ] [ 14 ] [ 15 ] [ 16 ] [ 17 ] [ 18 ] [ 19 ]  Cross-regulation of PE inclusion has also been observed. [ 20 ] [ 21 ] [ 22 ]


Differential splicing of PEs is implicated in biological processes such as  differentiation , [ 23 ] [ 24 ]   neurodevelopment , [ 25 ]  dispersal of  nuclear speckles  during  hypoxia , [ 26 ]   tumorigenesis , [ 24 ] [ 27 ]  organism growth, [ 15 ]  and  T cell  expansion. [ 28 ]


Protein kinases  that regulate phosphorylation of splicing factors can affect splicing processes, thus kinase inhibitors may affect inclusion of PEs. For example, CMGC kinase inhibitors and  CDK9  inhibitors have been found to induce PE inclusion in  RBM39 . [ 29 ]


Small molecules that modulate chromatin accessibility can affect PE inclusion. [ 30 ]


Mutations in splicing factors can lead to inclusion of PEs in certain transcripts. [ 31 ]


PE inclusion can be regulated by external variables such as temperature and electrical activity. For example, PE inclusion in  RBM3  transcript is lowered during  hypothermia . This is mediated by temperature-dependent binding of the splicing factor  HNRNPH1  to the  RBM3  transcript. [ 9 ]  The neuronal RBPs  NOVA1/2  are translocated from the nucleus to the cytoplasm during  pilocarpine -induced seizure in mice, and it was found that NOVA1/2 regulates the expression of cryptic PEs. [ 32 ]  The glycosyltransferase  O-GlcNAc transferase  is responsible for installing the  O-GlcNAc   post-translational modification  and contains a PE. [ 33 ]  It has been frequently observed that pharmacological or genetic perturbations that elevate cellular O-GlcNAc levels increase PE inclusion in the  OGT  transcript. [ 34 ]


Proper regulation of PE inclusion and exclusion is important for health. Genetic mutations can affect inclusion of PEs and cause disease. For example, loss of  CCAR1  leads to PE inclusion in the  FANCA  transcript, resulting in a  Fanconi anemia  phenotype. [ 35 ]


Dysregulation of components of the splicing machinery can also cause dysregulation of PE inclusion. Mutations in the splicing factor  SF3B1  have been found to promote PE inclusion in  BRD9 , reducing BRD9 mRNA and protein levels and leading to  melanomagenesis . [ 36 ]  Mutations in  U2AF1  promote PE inclusion in  EIF4A2 , leading to impaired global mRNA translation and  acute myeloid leukemia (AML)  chemoresistance through the  integrated stress response  pathway. [ 37 ]  The splicing factor  SRSF6  contains a PE whose skipping is connected to T cell acute lymphoblastic leukemia (T-ALL), [ 38 ]  and PE inclusion in  SRSF10  is linked to  acute lymphoblastic leukemia (ALL) . [ 39 ]


Intronic mutations can lead to PE inclusion, such as in the case of  SCN1A , where mutations within intron 20 promote inclusion of the nearby PE 20N, leading to  Dravet syndrome -like phenotypes in mouse models. [ 40 ] [ 41 ]  An intronic mutation in  FLNA  has been found to impair binding of the splicing regulator  PTBP1 , leading to inclusion of a poison exon in  FLNA  transcripts that causes a brain-specific malformation. [ 25 ]  In  RAD50 , TGAGT deletion is associated with a cryptic poison exon that occurs 30 nucleotides downstream within intron 21 mediated by altered U2AF recognition. [ 42 ]


Differential inclusion of PEs in various splicing factor and hnRNP genes has been reported in  type 1 diabetes . [ 43 ]   SRSF2  mutations have been found to promote PE inclusion in the epigenetic regulator  EZH2 , resulting in impaired hematopoietic differentiation. [ 31 ]


The  TRA2B  PE is essential for male fertility and meiotic cell division in mouse models. Deletion of this PE leads to an  azoospermia  phenotype. [ 44 ]


With the advent of  next-generation sequencing  technologies, [ 45 ]   diagnostic genetic testing  has emerged as a powerful tool to diagnose afflictions associated with specific genetic variants. Many diagnostic genetic testing efforts have focused on  exome sequencing . [ 46 ]  PE annotations may improve the diagnostic yield of these tests for certain diseases. For example, variants that affect PE inclusion in sodium channel genes ( SCN1A ,  SCN2A , and  SCN8A ) have been found to be associated with epilepsies, and analogous variants in  SNRPB  have been found to be associated with  cerebrocostomandibular syndrome . [ 47 ] [ 48 ]


As PE inclusion results in transcript degradation, targeted PE inclusion or exclusion is being evaluated as a therapeutic strategy. [ 49 ]  This strategy may prove especially applicable towards targets whose gene products are not easily ligandable such as  "undruggable" proteins . Targeting PE inclusion/exlusion has been demonstrated with both  small molecules [ 50 ] [ 51 ]  and  antisense oligonucleotides (ASOs) . [ 24 ] [ 52 ]  Small molecules may modulate splicing by stabilizing alternative splice sites. [ 50 ] [ 53 ]  ASOs may block specific splice sites or target certain  cis -regulatory elements to promote splicing at other sites. [ 54 ] [ 55 ]  These ASOs may also be referred to as splice-switching oligonucleotides (SSOs). [ 24 ] [ 55 ]  ASO walks tiling different ASOs across a gene sequence may be necessary to identify ASOs that have the desired effect on PE inclusion. [ 52 ]


Stoke Therapeutics is evaluating a strategy termed  T argeted  A ugmentation of  N uclear  G ene  O utput (TANGO). [ 52 ]  Targeting exon 20N in  SCN1A  mRNA with the antisense oligonucleotide zorevunersen (STK-001) blocks inclusion of this PE, leading to elevated levels of the productive  SCN1A  transcript and the gene product sodium channel protein 1 subunit alpha (Na V 1.1). In mouse models of Dravet syndrome, which is driven by mutations in  SCN1A , [ 40 ] [ 41 ] [ 56 ]  zorevunersen was able to reduce incidence of electrographic seizures and sudden unexpected death in epilepsy and prolong survival. [ 57 ] [ 58 ]  As of October 2024, zorevunersen is being evaluated in phase 2 clinical trials (NCT04740476). [ 59 ]  Zorevunersen received FDA Breakthrough Therapy Designation in December 2024. [ 60 ]  Also in December 2024, Stoke Therapeutics disclosed that zorevunersen is generally well tolerated and shows substantial and sustained reductions in convulsive seizure frequency. [ 61 ]  Stoke Therapeutics expects to launch a phase 3 clinical trial in 2025 evaluating zorevunersen for reduction in seizure frequency as the primary endpoint and cognition and behavioral changes as secondary endpoints. [ 62 ]


Stoke Therapeutics is also evaluating the ASO STK-002 for treatment of  autosomal dominant optic atrophy (ADOA) . STK-002 promotes removal of a PE in the transcript of  OPA1 , leading to elevated OPA1 protein levels. [ 63 ]


Remix Therapeutics developed REM-422, which is an oral small molecule that promotes PE inclusion in the oncogene  MYB . REM-422 was discovered through a screening campaign for molecules that promote PE inclusion in  MYB . Subsequent  in vitro  experiments showed that REM-422 selectively facilitates binding of the U1 snRNP complex to oligonucleotides containing the  MYB  5' splice site sequence. In various AML cell lines, REM-422 leads to degradation of  MYB  mRNA and lower MYB protein levels. REM-422 demonstrated antitumor activity in mouse xenograft models of acute myeloid leukemia. [ 50 ] [ 64 ]  As of October 2024, REM-422 is being evaluated in phase 1 clinical trials (NCT06118086, NCT06297941). [ 65 ] [ 66 ]  The splicing modulator small molecule  risdiplam , originally developed to promote exon 7 inclusion in the  SMN2  transcript for treatment of spinal muscular atrophy, [ 67 ] [ 68 ]  dose-dependently promotes PE inclusion in the  MYB  transcript as well. [ 69 ]


Rgenta Therapeutics has also developed RGT-61159, an oral small molecule that promotes PE inclusion in  MYB , as a potential treatment for  adenoid cystic carcinoma (ACC) . [ 70 ]  RGT-61159 is being evaluated in phase 1 clinical trials (NCT06462183). [ 71 ]


PTC Therapeutics  is evaluating the oral small molecule PTC518 as a treatment for  Huntington's disease . [ 51 ]  PTC518 was well-tolerated and showed dose-dependent decreases in  HTT  mRNA and HTT protein levels in a phase 1 clinical trial. [ 72 ]  As of October 2024, PTC518 is being evaluated in phase 2 clinical trials (NCT05358717). [ 73 ]  In December 2024,  Novartis  entered a global license and collaboration agreement with PTC Therapeutics for PTC518 with an upfront payment of $1.0 billion and up to $1.9 billion in development, regulatory, and sales milestones. [ 74 ]


Therapeutic targeting of poison exon inclusion/exclusion has also been proposed for oncogenic splicing factors, [ 24 ] [ 27 ]  BRD9 (for treatment of cancer), [ 36 ]   SYNGAP1 , [ 75 ]  RBM3 (for treatment of neurodegeneration), [ 54 ]  and  CFTR  (for treatment of  cystic fibrosis ). [ 76 ]


Polar overdominance  is a unique form of inheritance originally described in livestock, with relevant examples in humans [ 1 ]  and mice being discovered shortly after. The term polar is used to describe this type of  overdominance  because the  phenotype  of the  heterozygote  is more prevalent than the other  genotypes . This polarity is shown as differential phenotype is only present in one of the heterozygote configurations when the recessive  allele  is inherited in a parent of origin type fashion. [ 2 ]  Polar overdominance differs from regular overdominance (also known as  heterozygote advantage ) where both heterozygote genotypes display a phenotype that has increased fitness regardless of the parent of origin. Studying this type of inheritance could have practical applications in preventative medicine for humans as well as a variety of other agricultural applications.


The first described occurrence of polar overdominance in sheep was shown after finding that a  mutant  allele, called  callipyge  (after  Venus Callipyge ), must be inherited from the father to cause a condition called  muscle   hypertrophy . Muscle hypertrophy in the offspring is caused by an increase in the size and proportion of  muscle fibers , namely the  fast-twitch  muscle fibers. [ 3 ]  This increase is generally located in the hind quarters and torso. Muscle hypertrophy only manifests itself in the offspring approximately one month after birth. [ 4 ]  Polar overdominance shows evidence of an imprinted  locus  displayed as the difference between the expression of heterozygote phenotypes in a parent-of-origin type fashion. It was discovered that a  single-nucleotide polymorphism  in the  DLK1 – DIO3  imprinted  gene cluster  affects the gene expression of paternal allele-specific genes and several maternal allele-specific  long non-coding RNA  and  microRNA . [ 5 ]   Ectopic expression  of the  Delta-like 1 homologue (DLK1)  and the  Retrotransposon-like 1 (RTL1/PEG11)  genes which are paternally expressed proteins in skeletal muscle are a hallmark of these mutant individuals. [ 6 ]


More and more studies have identified  quantitative trait loci (QTL)  that show evidence of  genomic imprinting  in farm animals other than sheep. [ 7 ]  After polar overdominant inheritance was discovered to be the cause of muscular hypertrophy in sheep, the  ortholog  for the human DLK1 gene (DLK1-GTL2  intergenic region ) was studied in pigs to try to determine the effects of inheritance on ham weight. The original purpose of this study was to find the connection between genetics and ham weight to try to produce pigs that were abnormally large compared to the average. Before conducting this research, it was also hypothesized that the locus for ham weight was related to the  ovine  callipyge locus in sheep. After researching it was discovered that the two regions were likely unrelated due to different forms of parental inheritance exhibited in both cases and a relatively large physical distance between the loci on the chromosome. Unlike the form of paternal polar overdominance that occurs in the ovine callipyge locus, the locus that controls ham weight operates in a maternal polar overdominant fashion. [ 8 ]


The term polar is used to describe this type of inheritance because the phenotype of one heterozygote is expressed at a level higher than other genotypes for the same locus including those displaying either homozygous geneotype. [ 2 ]  This unique form of inheritance has largely been studied in non-human mammals since 1996 [ 4 ]  until it was first described in humans in 2008. In humans, the inheritance of the alleles for the  DLK1  gene (imprinted in  eutherian mammals ) is linked to a higher rate of obesity in the  F1 generation . [ 1 ]  The imprinted DLK1-GTL2 in sheep is homologous to the DLK1 gene in humans, and includes the callipyge locus. [ 9 ]  There has been evidence to show that by screening potential fathers for a mutation at the DLK1 locus one could potentially see if their child is at a higher risk for obesity. [ 10 ]  Individuals who inherit this mutant allele from their father are more likely to show signs of obesity because the DLK1 gene is key in  adipogenesis , or more simply the formation of fat cells. [ 11 ]


Polydactyly-myopia syndrome , also known as  Czeizel-Brooser syndrome , is a very rare genetic disorder which is characterized by post-axial  polydactyly  on all 4 limbs and progressive  myopia . [ 1 ]  Additional symptoms include bilateral congenital  inguinal hernia  and undescended testes. [ 2 ]  It has only been described in nine members of a 4-generation  Hungarian  family in the year 1986. [ 3 ] [ 4 ] [ 5 ] [ 6 ]  This disorder is inherited in an autosomal dominant manner. [ 7 ] [ 8 ]


Polygenic adaptation  describes a process in which a  population  adapts through small changes in  allele frequencies  at hundreds or thousands of  loci . [ 1 ]


Many traits in humans and other species are highly  polygenic , i.e., affected by standing genetic variation at hundreds or thousands of loci. Under normal conditions, the genetic variation underlying such traits is governed by  stabilizing selection , in which natural selection acts to hold the population close to an optimal  phenotype . However, if the phenotypic optimum changes, then the population can adapt by small directional shifts in allele frequencies spread across all the variants that affect the  trait . Polygenic adaptation can occur relatively quickly (as described in the  breeder's equation ), however it is difficult to detect from genomic data because the changes in allele frequencies at individual loci are very small.


Polygenic adaptation represents an alternative to adaptation by  selective sweeps .  In classic selective sweep models, a single new mutation sweeps through a population to  fixation , purging variation from a region of linkage around the selected site. [ 2 ]   More recent models have focused on partial sweeps, and on soft sweeps [ 3 ]  - i.e., sweeps that start from standing variation or comprise multiple sweeping variants at the same locus. All of these models focus on adaptation through genetic changes at a single locus and they generally assume large changes in allele frequencies.


The concept of polygenic adaptation is related to classical models from  quantitative genetics .  However, traditional models in quantitative genetics usually abstract away the contributions of individual loci by focusing instead on means and variances of genetic scores.  In contrast, population genetics models and data analysis have generally emphasized models of adaptation through  sweeps  at individual loci. The modern formulation of polygenic adaptation in population genetics was developed in a pair of 2010 review articles. [ 1 ] [ 4 ]


Polygenic adaptation is presumed to be the dominant mode of adaptation in  artificial selection , when plants or animals undergo rapid responses to selective pressures.  However, in most cases the actual genetic loci involved are not yet known (but see e.g., [ 5 ] ).


At present the best-understood examples of polygenic adaptation are in humans, and particularly for height, a trait that can be interpreted using data from  genome-wide association studies .  In a 2012 paper, Joel Hirschhorn and colleagues showed that there was a consistent tendency for the "tall" alleles at genome-wide significant loci to be at higher frequencies in northern Europeans than in southern Europeans. [ 6 ]  They interpreted this observation to indicate that the difference in average height between northern and southern Europeans is at least partly genetic (as opposed to environmental) and that it was driven by selection.  This result has been replicated by subsequent studies, [ 7 ] [ 8 ] [ 9 ] [ 10 ]  however the environmental factor driving the selection remains unclear.  A study of recent polygenic adaptation in the English has shown that selection on height has had small effects on allele frequencies (<1%) across most of the genome, and found evidence for polygenic adaptation in a wide variety of other traits as well including selection for increased infant birth size and increased female hip and waist size. [ 10 ]


Polymerase stuttering  is the process by which a  polymerase   transcribes  a nucleotide several times without progressing further on the  mRNA  chain.  It is often used in addition of  poly A tails  or  capping  mRNA chains by less complex  organisms  such as viruses.


A  polymerase  may undergo stuttering as a  probability  controlled event, hence it is not explicitly controlled by any mechanisms in the translation process.  Generally, it is a result of many short repeated  frameshifts  on a slippery sequence of  nucleotides  on the mRNA strand. [ 1 ]   However, the frameshift is restricted to one (in some cases two [ 2 ] ) nucleotides with a  pseudoknot  or  choke points  on both sides of the sequence.


A polymerase that exhibits this behavior is  RNA-dependent RNA polymerase , present in many  RNA viruses .   Reverse transcriptase  has also been observed to undergo this polymerase stuttering. [ 3 ]


A  polyploid complex , also called a  diploid-polyploid complex , is a group of interrelated and interbreeding species that also have differing levels of  ploidy  that can allow  interbreeding .


A  polyploid  complex was described by  E. B. Babcock  and  G. Ledyard Stebbins  in their 1938 monograph  The American Species of  Crepis : their interrelationships and distribution as affected by polyploidy and apomixis . In  Crepis  and some other perennial plant species, a polyploid complex may arise where there are at least two genetically isolated diploid populations, in addition to auto- and allopolyploid derivatives that coexist and interbreed. Thus a complex network of interrelated forms may exist where the polyploid forms allow for intermediate forms between the diploid species that are otherwise unable to interbreed. [ 1 ]


This complex situation does not fit well within the  biological species concept  of  Ernst Mayr  which defines a species as "groups of actually or potentially interbreeding natural populations which are reproductively isolated from other such groups".


In many diploid-polyploid complexes the polyploid hybrid members reproduce  asexually  while diploids reproduce sexually. [ 2 ]  Thus polyploidy is related to the phenomenon called "geographic parthenogenesis" by zoologist  Albert Vandel , [ 3 ]  that asexual organisms often have greater geographic ranges than their sexual relatives. It is not known which of the associated factors is the major determiner of geographic parthenogenesis,  hybridization , polyploidy, or asexual reproduction. [ 2 ]


Position-effect variegation  ( PEV ) is a  variegation  caused by the silencing of a  gene  in some cells through its abnormal juxtaposition with  heterochromatin  via rearrangement or  transposition . [ 1 ]  It is also associated with changes in  chromatin conformation . [ 2 ]


The classical example is the  Drosophila  w m4  (speak white-mottled-4)  translocation . In this  mutation , an  inversion  on the  X chromosome  placed the  white  gene next to pericentric heterochromatin, or a sequence of repeats that becomes heterochromatic. [ 3 ]  Normally, the  white  gene is expressed in every cell of the adult  Drosophila  eye resulting in a red-eye  phenotype . In the w[m4] mutant, the eye color was variegated (red-white mosaic colored) where the  white  gene was expressed in some cells in the eyes and not in others. The mutation was described first by  Hermann Muller  in 1930. [ 4 ]  PEV is a  heterochromatin-induced gene inactivation . [ 5 ]  Gene silencing phenomena similar to this have also been observed in  S. cerevisiae  and  S. pombe . [ 5 ]


Typically, the barrier DNA sequences prevent the heterochromatic region from spreading into the euchromatin but they are no longer present in the flies that inherit certain chromosomal rearrangements. [ 6 ]


PEV is a  position effect  because   the change in  position  of a gene from its original position to somewhere near a heterochromatic region has an  effect  on its  expression . [ 7 ]  The effect is the  variegation  in a particular phenotype i.e., the appearance of irregular patches of different colour(s), due to the expression of the original wild-type gene in some cells of the tissue but not in others, [ 8 ]  as seen in the eye of  mutated   Drosophila melanogaster .


However, it is possible that the effect of the silenced gene is not phenotypically visible in some cases. PEV was observed first in  Drosophila  because it was one of the first organisms on which X-ray irradiation was used as a mutation inducer. [ 1 ]  X-rays can cause chromosomal rearrangements that can result in PEV. [ 1 ]


Among a number of models, two  epigenetic  models are popular. One is the  cis -spreading  of the heterochromatin past the rearrangement breakpoint. The  trans -interactions  come in when the  cis- spreading model is unable to explain certain phenomena. [ 5 ]


According to this model, the heterochromatin forces an altered chromatin conformation on the euchromatic region. Due to this, the transcriptional machinery cannot access the gene which leads to the inhibition of transcription. [ 5 ]  In other words, the heterochromatin spreads and causes gene silencing by packaging the normally euchromatic region. [ 2 ]  But this model fails to explain some aspects of PEV. For example, variegation can be induced in a gene located several megabases from the heterochromatin-euchromatin breakpoint due to rearrangements in that breakpoint. Also, the austerity of the variegated phenotype can be altered by the distance of the heterochromatic region from the breakpoint. [ 5 ]


This suggests that  trans -interactions are crucial for PEV.


These are interactions between the different heterochromatic regions and the global chromosomal organisation in the interphase nucleus. [ 5 ]  The rearrangements due to PEV places the  reporter gene  in a new compartment of the nucleus where the transcriptional machinery required is not available, thus silencing the gene and modifying the chromatin structure. [ 2 ]


These two mechanisms affect each other as well. Which mechanism dominates to influence the phenotype depends upon the type of heterochromatin and the intricacy of the rearrangement. [ 5 ]


The mutations in  mus  genes are the candidates as PEV modifiers, as these genes are involved in chromosome maintenance and repair. Chromosome structure in the vicinity of the breakpoint appears to be an important determinant of the gene inactivation process. Six second chromosomal  mus  mutations were isolated with w m4 . A copy of wild-type white gene was placed adjacent to heterochromatin. The different  mus  mutants that were taken were:  mus 201 D1 ,  mus 205 B1 ,  mus 208 B1 ,  mus 209 B1 ,  mus 210 B1 ,  mus 211 B1 . A stock was constructed with the replacement of standard X-chromosome with w m4 . It was observed that the suppression of PEV is not a characteristic of  mus  mutations in general. Only for homozygous  mus 209 B1 , the variegation was significantly suppressed. Also, when homozygous, 2735 and D-1368 and all heteroallelic combinations of its Pcna mutations strongly suppress PEV. [ 9 ]


In mouse, variegating coat colour has been observed. When an  autosomal  region carrying a fur color gene is inserted onto the X chromosome, variable silencing of the  allele  is seen. Variegation is, however, observed only in the female having this insertion along with a  homozygous  mutation in the original coat color gene. [ 1 ]  The  wild-type  allele gets inactivated due to heterochromatinization. [ 1 ]


In plants, PEV has been observed in  Oenothera blandina . The silencing of euchromatic genes occurs when the genes get placed into a new heterochromatic neighborhood. [ 1 ]


Positional sequencing  is a method of  sequencing DNA  that simultaneously generates information about both identity and location of  nucleotide sequences . [ 1 ]  The method involves detecting the location of sequence specific recognition events (e.g., such as  hybridization of probes  of known sequence) on single DNA molecules in each read, and generating  maps  of the location of such events. Multiple reads can be  assembled  into a consensus map that identifies the multiple locations of a specific sub-sequence. The assembly process is greatly facilitated by knowledge of the location of each sub-sequence, as well as the fact that individual reads produce  non-contiguous  sequence data over length scales that can be  orders of magnitude  greater than what can be achieved with  Sanger sequencing  or nextgen  sequencing by synthesis .


A collection of maps may be used to reconstruct single-base resolved sequence in a process analogous to sequence reconstruction in  sequencing by hybridization . Ambiguities in the reconstruction of sequences are resolved through the knowledge of the relative position of overlapping sequence specific recognition events. By varying the parameters (e.g., length of read, density of recognition events, resolution of the detector) governing a specific implementation of the method, it is possible to query all size scales of DNA variation, from single nucleotide sequence all the way to large  structural variants  and  chromosomal aneuploidies . [ 1 ] [ 2 ]


In molecular biology, a  primosome  is a  protein  complex responsible for creating  RNA   primers  on single stranded  DNA  during  DNA replication .


The primosome consists of seven proteins:  DnaG   primase ,  DnaB helicase ,  DnaC  helicase assistant,  DnaT ,  PriA ,  Pri B , and  PriC .  At each  replication fork , the primosome is utilized once on the leading strand of  DNA  and repeatedly, initiating each  Okazaki fragment , on the lagging  DNA  strand. Initially the complex formed by PriA, PriB, and PriC binds to DNA. Then the DnaB-DnaC helicase complex attaches along with DnaT.  This structure is referred to as the pre-primosome.  Finally,  DnaG  will bind to the pre-primosome forming a complete primosome.  The primosome attaches 1-10 RNA nucleotides to the single stranded DNA creating a DNA-RNA hybrid. This sequence of RNA is used as a primer to initiate  DNA polymerase III .  The RNA bases are ultimately replaced with DNA bases by  RNase H  nuclease (eukaryotes) or  DNA polymerase I  nuclease (prokaryotes).  DNA Ligase  then acts to join the two ends together.


Assembly of the  Escherichia coli  primosome requires six proteins, PriA, PriB, PriC, DnaB, DnaC, and DnaT, acting at a primosome assembly site (pas) on an SSBcoated single-stranded (8s) DNA. Assembly is initiated by interactions of PriA and PriB with ssDNA and the pas. PriC, DnaB, DnaC, and DnaT then act on the PriAPriB- DNA complex to yield the primosome. [ 1 ]


Primosomes are nucleoproteins assemblies that activate DNA replication forks. Their primary role is to recruit the replicative helicase onto single-stranded DNA. The "replication restart" primosome, defined in  Escherichia coli , is involved in the reactivation of arrested replication forks. Binding of the PriA protein to forked DNA triggers its assembly. PriA is conserved in bacteria, but its primosomal partners are not. In Bacillus subtilis, genetic analysis has revealed three primosomal proteins,  DnaB ,  DnaD , and  DnaI , that have no obvious homologues in  E. coli . They are involved in primosome function both at arrested replication forks and at the chromosomal origin. Our biochemical analysis of the DnaB and DnaD proteins unravels their role in primosome assembly. They are both multimeric and bind individually to DNA. Furthermore, DnaD stimulates DnaB binding activities. DnaD alone and the DnaD/DnaB pair interact specifically with PriA of B. subtilis on several DNA substrates. This suggests that the nucleoprotein assembly is sequential in the PriA, DnaD, DnaB order. The preferred DNA substrate mimics an arrested DNA replication fork with unreplicated lagging strand, structurally identical to a product of recombinational repair of a stalled replication fork.


A  prion   / ˈ p r iː ɒ n /   ⓘ  is a  misfolded protein  that induces misfolding in normal variants of the same protein, leading to  cellular death . Prions are responsible for prion diseases, known as  transmissible spongiform encephalopathy  (TSEs), which are fatal and transmissible  neurodegenerative diseases  affecting both humans and animals. [ 3 ] [ 4 ]  These proteins can misfold sporadically, due to genetic mutations, or by exposure to an already misfolded protein, leading to an abnormal  three-dimensional structure  that can propagate misfolding in other proteins. [ 5 ]


The term  prion  comes from "proteinaceous infectious particle". [ 6 ] [ 7 ]  Unlike other infectious agents such as viruses, bacteria, and fungi, prions do not contain  nucleic acids  ( DNA  or  RNA ). Prions are mainly twisted  isoforms  of the  major prion protein  (PrP), a naturally occurring protein with an uncertain function. They are the hypothesized cause of various  TSEs , including  scrapie  in sheep,  chronic wasting disease  (CWD) in deer,  bovine spongiform encephalopathy  (BSE) in cattle (mad cow disease), and  Creutzfeldt–Jakob disease  (CJD) in humans. [ 8 ]


All known prion diseases in  mammals  affect the structure of the  brain  or other  neural  tissues. These diseases are progressive, have no known effective treatment, and are invariably fatal. [ 9 ]  Most prion diseases were thought to be caused by PrP until 2015 when a prion form of  alpha-synuclein  was linked to  multiple system atrophy  (MSA). [ 10 ]  Prions are also linked to other neurodegenerative diseases like  Alzheimer's disease ,  Parkinson's disease , and  amyotrophic lateral sclerosis  (ALS), which are sometimes referred to as  prion-like diseases . [ 11 ] [ 12 ]


Prions are a type of  intrinsically disordered protein  that continuously changes conformation unless bound to a specific partner, such as another protein. Once a prion binds to another in the same conformation, it stabilizes and can form a  fibril , leading to abnormal protein aggregates called  amyloids . These amyloids accumulate in infected tissue, causing damage and cell death. [ 13 ]  The structural stability of prions makes them resistant to  denaturation  by chemical or physical agents, complicating disposal and containment, and raising concerns about  iatrogenic spread  through medical instruments.


The word  prion , coined in 1982 by  Stanley B. Prusiner , is derived from  pr otein and infect ion , hence  prion , [ 14 ]  and is short for "proteinaceous infectious particle", [ 10 ]  in reference to its ability to self-propagate and transmit its conformation to other proteins. [ 15 ]  Its main pronunciation is  / ˈ p r iː ɒ n /   ⓘ , [ 16 ] [ 17 ] [ 18 ]  although  / ˈ p r aɪ ɒ n / , as the  homographic  name of  the bird  (prions or whalebirds) is pronounced, [ 18 ]  is also heard. [ 19 ]  In his 1982 paper introducing the term, Prusiner specified that it is "pronounced  pree-on ". [ 14 ]


Prions consist of a misfolded form of  major prion protein  (PrP), a protein that is a natural part of the bodies of humans and other animals. The PrP found in infectious prions has a different  structure  and is resistant to  proteases , the enzymes in the body that can normally break down proteins. The normal form of the protein is called PrP C , while the infectious form is called PrP Sc  – the  C  refers to 'cellular' PrP, while the  Sc  refers to ' scrapie ', the prototypic prion disease, occurring in sheep. [ 20 ]  PrP can also be induced to fold into other more-or-less well-defined isoforms in vitro; although their relationships to the form(s) that are pathogenic in vivo is often unclear, high-resolution structural analyses have begun to reveal structural features that correlate with prion infectivity. [ 21 ]


PrP C  is a normal protein found on the  membranes  of  cells , "including several blood components of which  platelets  constitute the largest reservoir in humans." [ 22 ]  It has 209  amino acids  (in humans), one  disulfide bond , a molecular mass of 35–36  kDa  and a mainly  alpha-helical  structure. [ 23 ] [ 24 ]  Several  topological  forms exist; one cell surface form anchored via  glycolipid  and two  transmembrane  forms. [ 25 ]  The normal protein is not sedimentable; meaning that it cannot be separated by  centrifuging techniques . [ 26 ]  It has a complex  function , which continues to be investigated. PrP C   binds   copper (II)  ions  (those in a +2  oxidation state ) with  high affinity . [ 27 ]  This property is supposed to play a role in PrP C ’s  anti-oxidative  properties via reversible  oxidation  of the  N-terminal’s   methionine  residues into  sulfoxide . [ 28 ]  Moreover, studies have suggested that,  in vivo , due to PrP C ’s low  selectivity  to metallic substrates, the protein’s anti oxidative function is impaired when in contact with metals other than  copper . [ 29 ]  PrP C  is readily  digested  by  proteinase K  and can be  liberated  from the cell surface by the enzyme  phosphoinositide phospholipase C  (PI-PLC), which  cleaves  the  glycophosphatidylinositol  (GPI) glycolipid anchor. [ 30 ]  PrP plays an important role in  cell-cell adhesion  and  intracellular signaling   in vivo , [ 31 ]  and may therefore be involved in cell-cell communication in the brain. [ 32 ]


The infectious  isoform  of PrP, known as PrP Sc , or simply the prion, is able to convert normal PrP C  proteins into the infectious isoform by changing their  conformation , or shape; this, in turn, alters the way the proteins  interconnect . PrP Sc  always causes prion disease. PrP Sc  has a higher proportion of  β-sheet  structure in place of the normal  α-helix  structure. [ 33 ] [ 34 ] [ 35 ]  Several highly infectious, brain-derived PrP Sc  structures have been discovered by  cryo-electron microscopy . [ 36 ] [ 37 ] [ 38 ]  Another brain-derived  fibril  structure isolated from humans with  Gerstmann-Straussler-Schienker syndrome  has also been determined. [ 39 ]  All of the structures described in high resolution so far are  amyloid  fibers in which individual PrP molecules are stacked via intermolecular beta sheets. However, 2-D  crystalline arrays  have also been reported at lower resolution in  ex vivo  preparations of prions. [ 40 ]  In the prion amyloids, the  glycolipid  anchors and  asparagine -linked glycans, when present, project outward from the lateral surfaces of the fiber cores. Often PrP Sc  is bound to cellular membranes, presumably via its array of glycolipid anchors, however, sometimes the fibers are dissociated from membranes and accumulate outside of cells in the form of plaques. The end of each fiber acts as a template onto which free protein molecules may attach, allowing the fiber to grow. This growth process requires complete refolding of PrP C . [ 36 ]  Different prion strains have distinct templates, or conformations, even when composed of PrP molecules of the same  amino acid sequence , as occurs in a particular host  genotype . [ 41 ] [ 42 ] [ 43 ] [ 44 ] [ 45 ]  Under most circumstances, only PrP molecules with an identical amino acid sequence to the infectious PrP Sc  are incorporated into the growing fiber. [ 26 ]  However,  cross-species transmission  also happens rarely. [ 46 ]


Protease-resistant PrP Sc -like protein (PrP res ) is the name given to any isoform of PrP c  which is structurally altered and converted into a misfolded  proteinase K -resistant form. [ 47 ]  To model conversion of PrP C  to PrP Sc   in vitro , Kocisko  et al . showed that PrP Sc  could cause PrP C  to convert to PrP res  under cell-free conditions  [ 48 ]  and Soto  et al . demonstrated sustained amplification of PrP res  and prion infectivity by a procedure involving  cyclic amplification of protein misfolding . [ 49 ]  The term "PrP res " may refer either to protease-resistant forms of PrP Sc , which is isolated from infectious tissue and associated with the transmissible spongiform encephalopathy agent, or to other protease-resistant forms of PrP that, for example, might be generated  in vitro . [ 50 ]  Accordingly, unlike PrP Sc , PrP res  may not necessarily be infectious.


The physiological function of the prion protein remains poorly understood. While data from in vitro experiments suggest many dissimilar roles, studies on PrP  knockout mice  have provided only limited information because these animals exhibit only minor abnormalities. In research done in mice, it was found that the cleavage of PrP in peripheral nerves causes the activation of  myelin  repair in  Schwann cells  and that the lack of PrP proteins caused demyelination in those cells. [ 51 ]


MAVS, RIP1, and RIP3 are prion-like proteins found in other parts of the body. They also polymerise into filamentous amyloid fibers which initiate regulated cell death in the case of a viral infection to prevent the spread of  virions  to other, surrounding cells. [ 52 ]


A review of evidence in 2005 suggested that PrP may have a normal function in the maintenance of  long-term memory . [ 53 ]  As well, a 2004 study found that mice lacking genes for normal cellular PrP protein show altered  hippocampal   long-term potentiation . [ 54 ] [ 55 ]  A recent study that also suggests why this might be the case, found that neuronal protein  CPEB  has a similar genetic sequence to yeast prion proteins. The prion-like formation of CPEB is essential for maintaining long-term synaptic changes associated with long-term memory formation. [ 56 ]


A 2006 article from the Whitehead Institute for Biomedical Research indicates that PrP expression on stem cells is necessary for an organism's self-renewal of  bone marrow . The study showed that all long-term  hematopoietic stem cells  express PrP on their cell membrane and that hematopoietic tissues with PrP-null stem cells exhibit increased sensitivity to cell depletion. [ 57 ]


There is some evidence that PrP may play a role in  innate immunity , as the expression of  PRNP , the PrP gene, is upregulated in many viral infections and PrP has antiviral properties against many viruses, including  HIV . [ 58 ]


The first hypothesis that tried to explain how prions replicate in a protein-only manner was the  heterodimer  model. [ 59 ]  This model assumed that a single PrP Sc  molecule binds to a single PrP C  molecule and  catalyzes  its conversion into PrP Sc . The two PrP Sc  molecules then come apart and can go on to convert more PrP C . However, a model of prion replication must explain both how prions propagate, and why their spontaneous appearance is so rare.  Manfred Eigen  showed that the heterodimer model requires PrP Sc  to be an extraordinarily effective catalyst, increasing the rate of the conversion reaction by a factor of around 10 15 . [ 60 ]  This problem does not arise if PrP Sc  exists only in aggregated forms such as  amyloid , where  cooperativity  may act as a barrier to spontaneous conversion. What is more, despite considerable effort, infectious monomeric PrP Sc  has never been isolated. [ 61 ]


An alternative model assumes that PrP Sc  exists only as  fibrils , and that fibril ends bind PrP C  and convert it into PrP Sc . If this were all, then the quantity of prions would increase  linearly , forming ever longer fibrils. But  exponential growth  of both PrP Sc  and of the  quantity of infectious particles  is observed during prion disease. [ 62 ] [ 63 ] [ 64 ]  This can be explained by taking into account fibril breakage. [ 65 ]  A mathematical solution for the exponential growth rate resulting from the combination of fibril growth and fibril breakage has been found. [ 66 ]  The exponential growth rate depends largely on the  square root  of the PrP C  concentration. [ 66 ]  The  incubation period  is determined by the exponential growth rate, and  in vivo  data on prion diseases in  transgenic mice  match this prediction. [ 66 ]  The same square root dependence is also seen  in vitro  in experiments with a variety of different  amyloid proteins . [ 67 ]


The mechanism of prion replication has implications for designing drugs. Since the incubation period of prion diseases is so long, an effective drug does not need to eliminate all prions, but simply needs to slow down the rate of exponential growth. Models predict that the most effective way to achieve this, using a drug with the lowest possible dose, is to find a drug that binds to fibril ends and blocks them from growing any further. [ 68 ]


Researchers at Dartmouth College discovered that endogenous host cofactor molecules such as the phospholipid molecule (e.g. phosphatidylethanolamine) and  polyanions  (e.g. single stranded RNA molecules) are necessary to form PrP Sc  molecules with high levels of specific infectivity  in vitro , whereas protein-only PrP Sc  molecules appear to lack significant levels of biological infectivity. [ 69 ] [ 70 ]


Prions cause neurodegenerative disease by aggregating extracellularly within the  central nervous system  to form plaques known as  amyloids , which disrupt the normal  tissue  structure. This disruption is characterized by "holes" in the tissue with resultant spongy architecture due to the  vacuole  formation in the neurons. [ 76 ]  Other histological changes include  astrogliosis  and the absence of an  inflammatory reaction . [ 77 ]  While the  incubation period  for prion diseases is relatively long (5 to 20 years), once symptoms appear the disease progresses rapidly, leading to brain damage and death. [ 78 ]  Neurodegenerative symptoms can include  convulsions ,  dementia ,  ataxia  (balance and coordination dysfunction), and behavioural or personality changes. [ 79 ] [ 80 ]


Many different mammalian species can be affected by prion diseases, as the prion protein (PrP) is very similar in all mammals. [ 81 ]  Due to small differences in PrP between different species it is unusual for a prion disease to transmit from one species to another. The human prion disease variant Creutzfeldt–Jakob disease, however, is thought to be caused by a prion that typically infects cattle, causing  bovine spongiform encephalopathy  and is transmitted through infected meat. [ 82 ]


All known prion diseases are untreatable and fatal. [ 9 ] [ 83 ] [ 84 ]