Insect antifreeze protein, Tenebrio-type | |||||||||
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Identifiers | |||||||||
Symbol | AFP | ||||||||
Pfam | PF02420 | ||||||||
InterPro | IPR003460 | ||||||||
SCOP2 | 1ezg / SCOPe / SUPFAM | ||||||||
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Insect antifreeze protein (CfAFP) | |||||||||
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Identifiers | |||||||||
Symbol | CfAFP | ||||||||
Pfam | PF05264 | ||||||||
InterPro | IPR007928 | ||||||||
SCOP2 | 1m8n / SCOPe / SUPFAM | ||||||||
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Fish antifreeze protein, type I | |
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Identifiers | |
Symbol | ? |
InterPro | IPR000104 |
SCOP2 | 1wfb / SCOPe / SUPFAM |
Fish antifreeze protein, type II | |
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Identifiers | |
Symbol | ? |
InterPro | IPR002353 |
CATH | 2py2 |
SCOP2 | 2afp / SCOPe / SUPFAM |
Fish antifreeze protein, type III | |
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Identifiers | |
Symbol | ? |
InterPro | IPR006013 |
SCOP2 | 1hg7 / SCOPe / SUPFAM |
See also the SAF domain (InterPro: IPR013974 ). |
Ice-binding protein-like (sea ice organism) | |||||||||
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Identifiers | |||||||||
Symbol | DUF3494 | ||||||||
Pfam | PF11999 | ||||||||
InterPro | IPR021884 | ||||||||
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Antifreeze proteins (AFPs) or ice structuring proteins refer to a class of polypeptides produced by certain animals, plants, fungi and bacteria that permit their survival in temperatures below the freezing point of water. AFPs bind to small ice crystals to inhibit the growth and recrystallization of ice that would otherwise be fatal. [3] There is also increasing evidence that AFPs interact with mammalian cell membranes to protect them from cold damage. This work suggests the involvement of AFPs in cold acclimatization. [4]
Unlike the widely used automotive antifreeze, ethylene glycol, AFPs do not lower freezing point in proportion to concentration.[ citation needed ] Rather, they work in a noncolligative manner. This phenomenon allows them to act as an antifreeze at concentrations 1/300th to 1/500th of those of other dissolved solutes. Their low concentration minimizes their effect on osmotic pressure. [4] The unusual properties of AFPs are attributed to their selective affinity for specific crystalline ice forms and the resulting blockade of the ice-nucleation process. [5]
AFPs create a difference between the melting point and freezing point (busting temperature of AFP bound ice crystal) known as thermal hysteresis. The addition of AFPs at the interface between solid ice and liquid water inhibits the thermodynamically favored growth of the ice crystal. Ice growth is kinetically inhibited by the AFPs covering the water-accessible surfaces of ice. [5]
Thermal hysteresis is easily measured in the lab with a nanolitre osmometer. Organisms differ in their values of thermal hysteresis. The maximum level of thermal hysteresis shown by fish AFP is approximately −3.5 °C (Sheikh Mahatabuddin et al., SciRep)(29.3 °F). In contrast, aquatic organisms are exposed only to −1 to −2 °C below freezing. During the extreme winter months, the spruce budworm resists freezing at temperatures approaching −30 °C. [4]
The rate of cooling can influence the thermal hysteresis value of AFPs. Rapid cooling can substantially decrease the nonequilibrium freezing point, and hence the thermal hysteresis value. Consequently, organisms cannot necessarily adapt to their subzero environment if the temperature drops abruptly. [4]
Species containing AFPs may be classified as
Freeze avoidant: These species are able to prevent their body fluids from freezing altogether. Generally, the AFP function may be overcome at extremely cold temperatures, leading to rapid ice growth and death.
Freeze tolerant: These species are able to survive body fluid freezing. Some freeze tolerant species are thought to use AFPs as cryoprotectants to prevent the damage of freezing, but not freezing altogether. The exact mechanism is still unknown. However, it is thought AFPs may inhibit recrystallization and stabilize cell membranes to prevent damage by ice. [6] They may work in conjunction with ice nucleating proteins (INPs) to control the rate of ice propagation following freezing. [6]
There are many known nonhomologous types of AFPs.
Antifreeze glycoproteins or AFGPs are found in Antarctic notothenioids and northern cod. They are 2.6-3.3 kD. [7] AFGPs evolved separately in notothenioids and northern cod. In notothenioids, the AFGP gene arose from an ancestral trypsinogen-like serine protease gene. [8]
The classification of AFPs became more complicated when antifreeze proteins from plants were discovered. [17] Plant AFPs are rather different from the other AFPs in the following aspects:
There are a number of AFPs found in insects, including those from Dendroides, Tenebrio and Rhagium beetles, spruce budworm and pale beauty moths, and midges (same order as flies). Insect AFPs share certain similarities, with most having higher activity (i.e. greater thermal hysteresis value, termed hyperactive) and a repetitive structure with a flat ice-binding surface. Those from the closely related Tenebrio and Dendroides beetles are homologous and each 12–13 amino-acid repeat is stabilized by an internal disulfide bond. Isoforms have between 6 and 10 of these repeats that form a coil, or beta-solenoid. One side of the solenoid has a flat ice-binding surface that consists of a double row of threonine residues. [6] [19] Other beetles (genus Rhagium) have longer repeats without internal disulfide bonds that form a compressed beta-solenoid (beta sandwich) with four rows of threonine residus, [20] and this AFP is structurally similar to that modelled for the non-homologous AFP from the pale beauty moth. [21] In contrast, the AFP from the spruce budworm moth is a solenoid that superficially resembles the Tenebrio protein, with a similar ice-binding surface, but it has a triangular cross-section, with longer repeats that lack the internal disulfide bonds. The AFP from midges is structurally similar to those from Tenebrio and Dendroides, but the disulfide-braced beta-solenoid is formed from shorter 10 amino-acids repeats, and instead of threonine, the ice-binding surface consists of a single row of tyrosine residues. [22] Springtails (Collembola) are not insects, but like insects, they are arthropods with six legs. A species found in Canada, which is often called a "snow flea", produces hyperactive AFPs. [23] Although they are also repetitive and have a flat ice-binding surface, the similarity ends there. Around 50% of the residues are glycine (Gly), with repeats of Gly-Gly- X or Gly-X-X, where X is any amino acid. Each 3-amino-acid repeat forms one turn of a polyproline type II helix. The helices then fold together, to form a bundle that is two helices thick, with an ice-binding face dominated by small hydrophobic residues like alanine, rather than threonine. [24] Other insects, such as an Alaskan beetle, produce hyperactive antifreezes that are even less similar, as they are polymers of sugars (xylomannan) rather than polymers of amino acids (proteins). [25] Taken together, this suggests that most of the AFPs and antifreezes arose after the lineages that gave rise to these various insects diverged. The similarities they do share are the result of convergent evolution.
Many microorganisms living in sea ice possess AFPs that belong to a single family. The diatoms Fragilariopsis cylindrus and F. curta play a key role in polar sea ice communities, dominating the assemblages of both platelet layer and within pack ice. AFPs are widespread in these species, and the presence of AFP genes as a multigene family indicates the importance of this group for the genus Fragilariopsis. [26] AFPs identified in F. cylindrus belong to an AFP family which is represented in different taxa and can be found in other organisms related to sea ice ( Colwellia spp., Navicula glaciei, Chaetoceros neogracile and Stephos longipes and Leucosporidium antarcticum) [27] [28] and Antarctic inland ice bacteria (Flavobacteriaceae), [29] [30] as well as in cold-tolerant fungi ( Typhula ishikariensis , Lentinula edodes and Flammulina populicola ). [31] [32]
Several structures for sea ice AFPs have been solved. This family of proteins fold into a beta helix that form a flat ice-binding surface. [33] Unlike the other AFPs, there is not a singular sequence motif for the ice-binding site. [34]
AFP found from the metagenome of the ciliate Euplotes focardii and psychrophilic bacteria has an efficient ice re-crystallization inhibition ability. [35] 1 μM of Euplotes focardii consortium ice-binding protein (EfcIBP) is enough for the total inhibition of ice re-crystallization in –7.4 °C temperature. This ice-recrystallization inhibition ability helps bacteria to tolerate ice rather than preventing the formation of ice. EfcIBP produces also thermal hysteresis gap, but this ability is not as efficient as the ice-recrystallization inhibition ability. EfcIBP helps to protect both purified proteins and whole bacterial cells in freezing temperatures. Green fluorescent protein is functional after several cycles of freezing and melting when incubated with EfcIBP. Escherichia coli survives longer periods in 0 °C temperature when the efcIBP gene was inserted to E. coli genome. [35] EfcIBP has a typical AFP structure consisting of multiple beta-sheets and an alpha-helix. Also, all the ice-binding polar residues are at the same site of the protein. [35]
The remarkable diversity and distribution of AFPs suggest the different types evolved recently in response to sea level glaciation occurring 1–2 million years ago in the Northern hemisphere and 10-30 million years ago in Antarctica. Data collected from deep sea ocean drilling has revealed that the development of the Antarctic Circumpolar Current was formed over 30 million years ago. [36] The cooling of Antarctic imposed from this current caused a mass extinction of teleost species that were unable to withstand freezing temperatures. [37] Notothenioids species with the antifreeze gylcoprotein were able to survive the glaciation event and diversify into new niches. [37] [8]
This independent development of similar adaptations is referred to as convergent evolution. [4] Evidence for convergent evolution in Northern cod (Gadidae) and Notothenioids is supported by the findings of different spacer sequences and different organization of introns and exons as well as unmatching AFGP tripeptide sequences, which emerged from duplications of short ancestral sequences which were differently permuted (for the same tripeptide) by each group. These groups diverged approximately 7-15 million years ago. Shortly after (5-15 mya), the AFGP gene evolved from an ancestral pancreatic trypsinogen gene in Notothenioids. AFGP and trypsinogen genes split via a sequence divergence - an adaptation which occurred alongside the cooling and eventual freezing of the Antarctic Ocean. The evolution of the AFGP gene in Northern cod occurred more recently (~3.2 mya) and emerged from a noncoding sequence via tandem duplications in a Thr-Ala-Ala unit. Antarctic notothenioid fish and arctic cod, Boreogadus saida, are part of two distinct orders and have very similar antifreeze glycoproteins. [38] Although the two fish orders have similar antifreeze proteins, cod species contain arginine in AFG, while Antarctic notothenioid do not. [38] The role of arginine as an enhancer has been investigated in Dendroides canadensis antifreeze protein (DAFP-1) by observing the effect of a chemical modification using 1-2 cyclohexanedione. [39] Previous research has found various enhancers of this bettles' antifreeze protein including a thaumatin-like protein and polycarboxylates. [40] [41] Modifications of DAFP-1 with the arginine specific reagent resulted in the partial and complete loss of thermal hysteresis in DAFP-1, indicating that arginine plays a crucial role in enhancing its ability. [39] Different enhancer molecules of DAFP-1 have distinct thermal hysteresis activity. [41] Amornwittawat et al. 2008 found that the number of carboxylate groups in a molecules influence the enhancing ability of DAFP-1. [41] Optimum activity in TH is correlated with high concentration of enhancer molecules. [41] Li et al. 1998 investigated the effects of pH and solute on thermal hysteresis in Antifreeze proteins from Dendrioides canadensis. [42] TH activity of DAFP-4 was not affected by pH unless the there was a low solute concentration (pH 1) in which TH decreased. [42] The effect of five solutes; succinate, citrate, malate, malonate, and acetate, on TH activity was reported. [42] Among the five solutes, citrate was shown to have the greatest enhancing effect. [42]
This is an example of a proto-ORF model, a rare occurrence where new genes pre exist as a formed open reading frame before the existence of the regulatory element needed to activate them.
In fishes, horizontal gene transfer is responsible for the presence of Type II AFP proteins in some groups without a recently shared phylogeny. In Herring and smelt, up to 98% of introns for this gene are shared; the method of transfer is assumed to occur during mating via sperm cells exposed to foreign DNA. [43] The direction of transfer is known to be from herring to smelt as herring have 8 times the copies of AFP gene as smelt (1) and the segments of the gene in smelt house transposable elements which are otherwise characteristic of and common in herring but not found in other fishes. [43]
There are two reasons why many types of AFPs are able to carry out the same function despite their diversity:
Antifreeze glycoprotein activity has been observed across several ray-finned species including eelpouts, sculpins, and cod species. [45] [46] Fish species that possess the antifreeze glycoprotein express different levels of protein activity. [47] Polar cod (Boreogadus saida) exhibit similar protein activity and properties to the Antarctic species, T. borchgrevinki. [47] Both species have higher protein activity than saffron cod (Eleginus gracilis). [47] Ice antifreeze proteins have been reported in diatom species to help decrease the freezing point of organism's proteins. [26] Bayer-Giraldi et al. 2010 found 30 species from distinct taxa with homologues of ice antifreeze proteins. [26] The diversity is consistent with previous research that has observed the presence of these genes in crustaceans, insects, bacteria, and fungi. [8] [48] [49] Horizontal gene transfer is responsible for the presence of ice antifreeze proteins in two sea diatom species, F. cylindrus and F. curta. [26]
AFPs are thought to inhibit ice growth by an adsorption–inhibition mechanism. [50] They adsorb to nonbasal planes of ice, inhibiting thermodynamically-favored ice growth. [51] The presence of a flat, rigid surface in some AFPs seems to facilitate its interaction with ice via Van der Waals force surface complementarity. [52]
Normally, ice crystals grown in solution only exhibit the basal (0001) and prism faces (1010), and appear as round and flat discs. [5] However, it appears the presence of AFPs exposes other faces. It now appears the ice surface 2021 is the preferred binding surface, at least for AFP type I. [53] Through studies on type I AFP, ice and AFP were initially thought to interact through hydrogen bonding (Raymond and DeVries, 1977). However, when parts of the protein thought to facilitate this hydrogen bonding were mutated, the hypothesized decrease in antifreeze activity was not observed. Recent data suggest hydrophobic interactions could be the main contributor. [54] It is difficult to discern the exact mechanism of binding because of the complex water-ice interface. Currently, attempts to uncover the precise mechanism are being made through use of molecular modelling programs (molecular dynamics or the Monte Carlo method). [3] [5]
According to the structure and function study on the antifreeze protein from Pseudopleuronectes americanus , [55] the antifreeze mechanism of the type-I AFP molecule was shown to be due to the binding to an ice nucleation structure in a zipper-like fashion through hydrogen bonding of the hydroxyl groups of its four Thr residues to the oxygens along the direction in ice lattice, subsequently stopping or retarding the growth of ice pyramidal planes so as to depress the freeze point. [55]
The above mechanism can be used to elucidate the structure-function relationship of other antifreeze proteins with the following two common features:
In the 1950s, Norwegian scientist Scholander set out to explain how Arctic fish can survive in water colder than the freezing point of their blood. His experiments led him to believe there was “antifreeze” in the blood of Arctic fish. [3] Then in the late 1960s, animal biologist Arthur DeVries was able to isolate the antifreeze protein through his investigation of Antarctic fish. [56] These proteins were later called antifreeze glycoproteins (AFGPs) or antifreeze glycopeptides to distinguish them from newly discovered nonglycoprotein biological antifreeze agents (AFPs). DeVries worked with Robert Feeney (1970) to characterize the chemical and physical properties of antifreeze proteins. [57] In 1992, Griffith et al. documented their discovery of AFP in winter rye leaves. [17] Around the same time, Urrutia, Duman and Knight (1992) documented thermal hysteresis protein in angiosperms. [58] The next year, Duman and Olsen noted AFPs had also been discovered in over 23 species of angiosperms, including ones eaten by humans. [59] They reported their presence in fungi and bacteria as well.
Recent attempts have been made to relabel antifreeze proteins as ice structuring proteins to more accurately represent their function and to dispose of any assumed negative relation between AFPs and automotive antifreeze, ethylene glycol. These two things are completely separate entities, and show loose similarity only in their function. [60]
Numerous fields would be able to benefit from the protection of tissue damage by freezing. Businesses are currently investigating the use of these proteins in:[ citation needed ]
Unilever has obtained UK, US, EU, Mexico, China, Philippines, Australia and New Zealand approval to use a genetically modified yeast to produce antifreeze proteins from fish for use in ice cream production. [61] [62] They are labeled "ISP" or ice structuring protein on the label, instead of AFP or antifreeze protein.
One recent, successful business endeavor has been the introduction of AFPs into ice cream and yogurt products. This ingredient, labelled ice-structuring protein, has been approved by the Food and Drug Administration. The proteins are isolated from fish and replicated, on a larger scale, in genetically modified yeast. [63]
There is concern from organizations opposed to genetically modified organisms (GMOs) who believe that antifreeze proteins may cause inflammation. [64] Intake of AFPs in diet is likely substantial in most northerly and temperate regions already. [7] Given the known historic consumption of AFPs, it is safe to conclude their functional properties do not impart any toxicologic or allergenic effects in humans. [7]
As well, the transgenic process of ice structuring proteins production is widely used in society. Insulin and rennet are produced using this technology. The process does not impact the product; it merely makes production more efficient and prevents the death of fish that would otherwise be killed to extract the protein.
Currently, Unilever incorporates AFPs into some of its American products, including some Popsicle ice pops and a new line of Breyers Light Double Churned ice cream bars. In ice cream, AFPs allow the production of very creamy, dense, reduced fat ice cream with fewer additives. [65] They control ice crystal growth brought on by thawing on the loading dock or kitchen table, which reduces texture quality. [66]
In November 2009, the Proceedings of the National Academy of Sciences published the discovery of a molecule in an Alaskan beetle that behaves like AFPs, but is composed of saccharides and fatty acids. [25]
A 2010 study demonstrated the stability of superheated water ice crystals in an AFP solution, showing that while the proteins can inhibit freezing, they can also inhibit melting. [67] In 2021, EPFL and Warwick scientists have found an artificial imitation of antifreeze proteins. [68]
Supercooling, also known as undercooling, is the process of lowering the temperature of a liquid below its freezing point without it becoming a solid. As per the established international definition, supercooling means ‘cooling a substance below the normal freezing point without solidification’ While it can be achieved by different physical means, the postponed solidification is most often due to the absence of seed crystals or nuclei around which a crystal structure can form. The supercooling of water can be achieved without any special techniques other than chemical demineralization, down to −48.3 °C (−54.9 °F). Supercooled water can occur naturally, for example in the atmosphere, animals or plants.
Boreogadus saida, known as the polar cod or as the Arctic cod, is a fish of the cod family Gadidae, related to the true cod. Another fish species for which both the common names Arctic cod and polar cod are used is Arctogadus glacialis.
Nototheniidae, the notothens or cod icefishes, is a family of ray-finned fishes, part of the suborder Notothenioidei which is traditionally placed within the order Perciformes. They are largely found in the Southern Ocean.
A cryoprotectant is a substance used to protect biological tissue from freezing damage. Arctic and Antarctic insects, fish and amphibians create cryoprotectants in their bodies to minimize freezing damage during cold winter periods. Cryoprotectants are also used to preserve living materials in the study of biology and to preserve food products.
Calnexin (CNX) is a 67kDa integral protein of the endoplasmic reticulum (ER). It consists of a large N-terminal calcium-binding lumenal domain, a single transmembrane helix and a short, acidic cytoplasmic tail. In humans, calnexin is encoded by the gene CANX.
Notothenioidei is one of 19 suborders of the order Perciformes. The group is found mainly in Antarctic and Subantarctic waters, with some species ranging north to southern Australia and southern South America. Notothenioids constitute approximately 90% of the fish biomass in the continental shelf waters surrounding Antarctica.
A beta helix is a tandem protein repeat structure formed by the association of parallel beta sheet in a helical pattern with either two or three faces. The beta helix is a type of solenoid protein domain. The structure is stabilized by inter-strand hydrogen bonds, protein-protein interactions, and sometimes bound metal ions. Both left- and right-handed beta helices have been identified. These structures are distinct from jelly-roll folds, a different protein structure sometimes known as a "double-stranded beta helix".
Insect winter ecology describes the overwinter survival strategies of insects, which are in many respects more similar to those of plants than to many other animals, such as mammals and birds. Unlike those animals, which can generate their own heat internally (endothermic), insects must rely on external sources to provide their heat (ectothermic). Thus, insects persisting in winter weather must tolerate freezing or rely on other mechanisms to avoid freezing. Loss of enzymatic function and eventual freezing due to low temperatures daily threatens the livelihood of these organisms during winter. Not surprisingly, insects have evolved a number of strategies to deal with the rigors of winter temperatures in places where they would otherwise not survive.
Pancreatic ribonuclease family is a superfamily of pyrimidine-specific endonucleases found in high quantity in the pancreas of certain mammals and of some reptiles.
Notothenia is a genus of marine ray-finned fishes belonging to the family Nototheniidae, the notothens or cod icefishes with the species in this genus often having the common name of rockcod. They are native to the Southern Ocean and other waters around Antarctica.
Hemagglutinins are homotrimeric glycoproteins present on the protein capsids of viruses in the Paramyxoviridae and Orthomyxoviridae families. Hemagglutinins are responsible for binding to receptors, sialic acid residues, on host cell membranes to initiate virus docking and infection.
Xylomannan is an antifreeze molecule, found in the freeze-tolerant Alaskan beetle Upis ceramboides. Unlike antifreeze proteins, xylomannan is not a protein. Instead, it is a combination of a sugar (saccharide) and a fatty acid that is found in cell membranes. As such is expected to work in a different manner than AFPs. It is believed to work by incorporating itself directly into the cell membrane and preventing the freezing of water molecules within the cell.
Neofunctionalization, one of the possible outcomes of functional divergence, occurs when one gene copy, or paralog, takes on a totally new function after a gene duplication event. Neofunctionalization is an adaptive mutation process; meaning one of the gene copies must mutate to develop a function that was not present in the ancestral gene. In other words, one of the duplicates retains its original function, while the other accumulates molecular changes such that, in time, it can perform a different task.
RiAFP refers to an antifreeze protein (AFP) produced by the Rhagium inquisitor longhorned beetle. It is a type V antifreeze protein with a molecular weight of 12.8 kDa; this type of AFP is noted for its hyperactivity. R. inquisitor is a freeze-avoidant species, meaning that, due to its AFP, R. inquisitor prevents its body fluids from freezing altogether. This contrasts with freeze-tolerant species, whose AFPs simply depress levels of ice crystal formation in low temperatures. Whereas most insect antifreeze proteins contain cysteines at least every sixth residue, as well as varying numbers of 12- or 13-mer repeats of 8.3-12.5kDa, RiAFP is notable for containing only one disulfide bridge. This property of RiAFP makes it particularly attractive for recombinant expression and biotechnological applications.
The blackfin icefish, also known as the Scotia Sea icefish, is a species of crocodile icefish belonging to the family Channichthyidae. The blackfin icefish belongs to Notothenioidei, a suborder of fishes that accounts for 90% of the fish fauna on the Antarctic continental shelf. Icefishes, also called white-blooded fishes, are a unique family in that they are the only known vertebrates to lack haemoglobin, making their blood oxygen carrying capacity just 10% that of other teleosts. Icefishes have translucent blood and creamy white gills.
The emerald rockcod, also known as the emerald notothen is a species of marine ray-finned fish belonging to the family Nototheniidae, the notothens or cod icefishes. It is native to the Southern Ocean
Antarctic fish is a common name for a variety of fish that inhabit the Southern Ocean. There are relatively few families in this region, the most species-rich being the Liparidae (snailfishes), followed by Nototheniidae. The latter is one of eight different families that belong to the suborder Notothenioidei of the order Perciformes. They are also called notothenioids, but this name is also used to describe the other three, non-Antarctic families and some of the non-Antarctic genera in the mainly Antarctic families belonging to the suborder.
Cucujus clavipes is known as the flat bark beetle. It is found throughout North America. These are generally found near tree line under bark of dead poplar and ash trees. C. clavipes are described as phloem-feeding and often predators of other small insects, such as wood-boring beetles, and mites. These are usually seen during spring-summer seasons. Having a cold habitat, these beetles must go through several physiological mechanisms to survive; they are recognised for their ability to change their overwintering mechanisms.
Dendroides canadensis, the fire-colored beetle, is a species of fire-colored beetle in the family Pyrochroidae from southeastern Canada and the eastern and central United States. This beetle has both the adaptations of freezing tolerance and freezing susceptibility (supercooling).
Notothenia coriiceps, also known as the black rockcod, Antarctic yellowbelly rockcod, or Antarctic bullhead notothen, is a species of marine ray-finned fish, belonging to the family Nototheniidae, the notothens or cod icefishes. It is widely spread around the Antarctic continent. Like other Antarctic notothenioid fishes, N. coriiceps evolved in the stable, ice-cold environment of the Southern Ocean. It is not currently targeted by commercial fisheries.