Mallomonas

Mallomonas is a genus comprising unicellular algal eukaryotes and characterized by their intricate cell coverings made of silica scales and bristles. The group was first named and classified by Dr. Maximilian Perty in 1852. These organisms live in freshwater and are widely distributed around the world. Some well known species include "Mallomonas caudata" and "Mallomonas splendens".
"Mallomonas" is a genus of many from the phylum Ochrophyta, which describes organisms as having heterokont flagella in some part of their life history. At first, the family Mallomonadaceae was placed under class Chrysophyceae. However, after finding key biochemical and ultrastructural differences, the family was then placed under the class Synurophyceae. In a broader context, both Chrysophyceae and Synurophyceae are referred to as “chrysophytes”, meaning “golden algae”, because of their close similarities. Despite being quite similar, there are various, noticeable differences.
History of knowledge.
The genus "Mallomonas" was first named and classified by Dr. Maximilian Perty in 1852. It was assigned its own genus because "Mallomonas" consisted of individually living cells, while its sister group "Synura" is composed of colonial cells that are connected to one another through stalks.
Other distinguishing features that differentiate "Mallomonas" cells from "Synura" cells are the presence of bristles and V-shaped ridges on their scales. Pore-collar complexes on stomatocysts are species differentiating features.
Habitat and ecology.
"Mallomonas" is composed of planktonic, freshwater organisms.
Cells range in many ecological factors. Many species can tolerate pH levels ranging from 4 to 8, and can live in slightly acidic waters. Some species prefer low phosphorus gradients. Temperature tolerance ranges from 1.5 to 25.5 °C.
According to the temperature-size rule, as the temperature increases, the size of protists decreases. As with all Synurophytes, the inorganic scales produced by organisms in the genus "Mallomonas" also decrease in size as a response to increasing temperature, the same way as the cells themselves decrease. The shape of the scales became less round and more elongated or oval-shaped. Also, higher temperatures negatively affect scale biogenesis, interfering with the cellular processes that produce the scales.
Description of organism.
General characteristics.
The organisms in this genus have streamlined morphology in spherical, oval, or elliptical forms, and they have a wide range of sizes that vary from the smallest being 10 µm to the largest being 100 µm. Two flagella emerge from the anterior apical flagellar pocket; one can be easily seen in the light microscope as it is longer and covered in hairs (called mastigonemes) while the other is much shorter, with no hairs, and is not as easily seen.
Pigments such as chlorophyll c1 and fucoxanthin within the chloroplasts cause the cells to have a distinct, golden or yellow-brown colour. The chloroplasts themselves are bi-lobed, but some cells have two single-lobed chloroplasts. Cells have a girdle lamella, grouped thylakoids stacked in three, and additional membranes around the chloroplast called the chloroplast endoplasmic reticulum (CER).
The large nucleus is located between the chloroplast and the Golgi complex. Vacuoles full of the storage product known as chrysolaminarin are found near the posterior end of the cell.
Flagella.
Flagella are microtubule-based structures that allow cells to have controlled movement to a certain degree. The root of the microtubule arrangement that is associated with the flagellar basal bodies, R1, which is also the site of cytoskeletal microtubules, is positioned uniquely in the genus "Mallomonas". Instead of pulling away from the basal bodies, R1 actually loops around them in a clockwise fashion. There is also a second root of microtubules extending from the point of origin towards the cell’s centre. Both basal bodies, each assigned one of the two flagella, are enclosed in a thick, fibrous capsule.
Morphometry.
Scales.
The genus "Mallomonas" is based on the organization of its scales, which are silica plates that are intricately designed, species-specific, and cover the cell. There are many parts to the entire structure; it’s made up of anterior spine scales, posterior spine scales, body scales, and some specialized scales. An example of a specialized scale is one that can fit around a flagellar pocket. The scales are accompanied by bristles, which are long, elongated structures that are tucked under the scales with the use of a small bend in the end, which is called a ‘foot’.
Scale size varies from 1 µm to 10 µm with surface area also varying from 1 µm2 to 50 µm2. Scale shapes are circular, elliptical, or ovate, generally rhombic in nature, but they are wider than the scales of their sister genus "Synura". Scales without domes exhibit bilateral symmetry, except for the collar scales, which are different in terms of shape altogether. Scales with domes exhibit slight asymmetry due to the dome shape in regards to the poster rim and the V-rib. Instead of being flat, scales are curved so they can conform to the cell shape. Curvature increases with scale size and thickness. More information about specific structures mentioned follow.
Each scale and bristle is produced intracellularly in a vesicle known as the silica deposition vesicle (SDV), which is connected to the chloroplast endoplasmic reticulum. Their production is also associated with the Golgi body, the nucleus, the chloroplast, and how the complex of these organelles is arranged in relation to the SDV within the cell. Formation of the scales and bristles occurs along the chloroplast’s outer surface because of SDV’s close placement to the CER. Directional placement could be parallel to cell length or at an angle away from either the posterior or anterior ends of the cell.
Patterns of perforation and ridge detail vary among species, but all have a general shape consisting of a wide, rough oblong with a dome and posterior rim. The base plate is perforated with pores, and in some species, they are either present or lacking. Usually, they are spaced evenly over the base plate, but the posterior rim, flanges, and domes are not usually perforated. The upturned posterior rim bends forward and encircles about half the scale’s perimeter. The rim can be narrow or broad, equal in length on both sides of the scale or asymmetric, depending upon the species, but the location is consistent throughout the genus and is known as the proximal end.
Majority of species have a V-shaped ridge (V-rib) positioned just ahead of the posterior rim on their scales. Also made of silica, the V-rib extends further towards the distal end and stops close to the dome (if present) or at the perimeter of the scale. Near the distal ends of the V-rib, some species have two additional ridges called anterior submarginal ribs, but they’re quite small and terminate at the distal end. Species with V-ribs also have the two anterior submarginal ribs, and the junction between the two is of taxonomic significance, defining some of the many species within this genus.
Scales that have a dome are associated with bristle attachment. A dome is a raised portion of the base plate at the distal end where the foot of a bristle is tucked underneath. The bristle locks into place under the dome and emerges through an inverted U-shaped opening that is located slightly away from the center of the dome, which causes an asymmetric balance between the bristle and the scale. However, this allows the bristle to rotate with the longitudinal axis of the cell through a wider angle than if it extended straight through the center of the dome. The lip, or rim of the inverted U-shaped opening, could protrude forward in some cases, however, in most, it is slightly off to the right.
The anterior submarginal ribs and the V-rib divide the scale into regions that are in turn ornamented differently for each species. The section of the base plate that is between the submarginal rib and the V-rib is referred to as the shield while the section that is outside both the V-rib and the anterior submarginal ribs is referred to as the posterior flange and the anterior flange, respectively.
The anterior submarginal ribs, V-rib, and posterior rim are considered to be secondary structures in regards to the perforated base plate; however, some species also have other secondary structures such as additional ribs or papillae. Rib placement is dependent upon pore placement, as ribs protrude from between pores. Irregular pore patterns lead to irregular rib placement. Papillae consist of small protrusions sticking out of the dome, shield, or anterior flanges that are regularly spaced, vary in density, and can be solid or hollow.
Bristles.
Bristles are composed of two parts, the foot and the shaft. The foot is at the proximal end, in regards to the bristle, and it is the part of the structure that is tucked under the distal end of the scale, under the dome. The foot is flat and bends at a 30° to 90° angle relative to the shaft. The shaft could be smooth, curved, ribbed, or serrated, and in some species, instead of being a solid bar, it appears rolled up so that the slit running along the shaft length is the point of convergence where both sides meet.
Many variations arise at the distal tip of the bristle, the end that is exposed to the environment. The tips can be sharp, blunt, forked, bifurcated, pseudobifurcated, swollen, expanded, C-shaped, cleft-like (to form helmet bristles), hooked, folded (to form lance bristles), plumed, and serrated - and possibly more. Even within these variations, there are variations, and this diversity gives rise to many different species within this genus.
Each region of the bristle (whether it is the proximal end, the middle, or the distal end) has varying degrees of differences and flexibility in morphology. This variation in characteristics differentiates species.
Stomatocyst.
The resting stage is called a stomatocyst, and it is also composed of silica. It ranges in diameter from 4 µm to 30 µm, can be spherical or oval in shape, and varies considerably in structure and ornamentation between species. Overall texture can vary; some cysts are smooth, some have reticulate designs, while others can have spines, or ridges, or depressions. The pore-collar complex, which is the presence and shape of a silica collar around the pore (or entrance) of the stomatocyst, is taxonomically significant. The cyst wall is also produced in the silica deposition vesicle (SDV), where parts of the wall are produced intracellularly and then excreted into the extracellular complex, where the wall is then formed and stabilized. The standard size and shape is retained throughout the number of species, but the variations between species of ornamentation may be due to physiological influences from the environment.
Development occurs in two phases within the continuous process. The first phase involves the primary inner wall of the cyst being formed before the collar and surface, which is thin and occurs rapidly from a proximal to distal manner. The second phase is more controlled and occurs more slowly while the wall is being thickened, and the collar and surface ornamentation are being produced. Because of this process of making a stomatocyst, cysts can be found at any stage of development. After development has been completed, the cyst sinks down to the sediment, and remains in its resting stage until certain conditions trigger its germination. After germination, a flagellated cell emerges from the cyst through pore-collar complex and produces new siliceous armour of scales and bristles. It is currently unclear if germination occurs in the water column after redistribution or if it occurs while the cyst is sitting in the sediment.
Cell division.
Very little is known about reproduction in "Mallomonas." All that is known is that two vegetative cells fuse to produce a zygote, which then encysts and remains in sediment until germination. Vegetative cell division occurs after excystment. In only minutes cytokinesis occurs, beginning from the anterior end and proceeding down the longitudinal axis of the cell. Sexual reproduction is also noted to occur within this genus, although it is rare.
Fossil history.
Stomatocyst microfossils are used in the study of lake paleontology.
When comparing bristle formation of species "Mallomonas muskokana" with the Eocene fossil taxon "Mallomonas dispar", it was found that the asymmetrical pattern observed was identical to the extant species. The Eocene Epoch is a part of the Paleogene Period, occurring about 56 to 33.9 million years ago. Studies with this fossil taxon would suggest that parts of its morphology have been retained up to the present.
List of species.
To date, the genus "Mallomonas" has 223 species. A list of well-known species is provided in the table below.


Phoenix (novel)

Phoenix is a fantasy novel by American writer Steven Brust, the fifth book in his Vlad Taltos series, set in the fantasy world of Dragaera. Originally published in 1990 by Ace Books, it was reprinted in 2002 along with "Taltos" in the omnibus "The Book of Taltos". Following the trend of the Vlad Taltos books, it is named after one of the Great Houses and features that house as an important element to its plot.
Plot summary.
During an unusual attempt on his life, Vlad prays to his goddess Verra for aid and surprisingly receives it. As payment, Verra requests that Vlad kill the King of Greenaere, an island kingdom off the coast of the Empire, where magic does not work. Vlad agrees and sails to Greenaere, where he completes the assassination without difficulty. Fleeing the island, however, proves more difficult. After fighting off some guards, an injured Vlad stumbles upon a drummer in the forest named Aibynn who tends his wounds and tries to cover for him when more guards arrive. Vlad faints from Aibynn's dreamgrass and reveals his hidden location, causing the guards to arrest both of them.
In prison, Vlad talks with Aibynn, who thinks of nothing but drumming, and waits for an opportunity to escape. Eventually he learns that Loiosh had flown across the ocean to warn their friends. Aliera and Cawti arrive at the prison and free Vlad using elder sorcery, which does not require a link to the Orb. Vlad brings Aibynn along, though he suspects that he might be a spy. Morrolan provides a boat and the group sails away.
Back in Adrilankha, Vlad is still stuck between the Jhereg Organization and his wife's group of Easterner and Teckla revolutionists. Vlad's superior warns him that members of the Council are displeased with the situation. Matters worsen when Greenaere declares war on the Empire and press gangs begin forcibly recruiting Easterners. A watchtower in South Adrilankha is destroyed, and most of the high-ranking revolutionists are arrested, including Cawti.
Vlad suspects that the Jhereg are involved in the arrest. After threatening the Jhereg representative at the Capital, Vlad pursues Boralinoi, the Council member whose territory includes Vlad's and South Adrilankha. Boralinoi confirms that he framed the revolutionists and a fight breaks out in his office. Vlad escapes, but knows that the council will be targeting him for assassination. He is summoned before the Empress and convinces her to have Cawti released.
Vlad goes to South Adrilankha to visit his grandfather, whom he calls Noish-pa, at his shop. After a heartfelt conversation about Vlad's growing self-doubt, Noish-pa warns Vlad of an assassin waiting outside the shop. Vlad exits the shop and kills the assassin with the help of Loiosh. As he flees the murder scene, Vlad becomes aware of a menacing charge in the South Adrilankha residents. After Vlad stumbles upon a slain Phoenix Guard, a riot breaks out. Vlad remembers only short flashes of the violence, but mostly avoids taking part in it. He makes his way back to Noish-pa, who has killed several Phoenix Guards but allowed a female soldier to escape. Vlad convinces Noish-pa to teleport with him to safety at Castle Black.
At Castle Black, Morrolan tells Vlad that the riot turned into a revolt, including a short siege on the Imperial Palace. Cawti has been arrested again, this time for treason. While angered by the Empire's brutal suppression of the revolt, Vlad is agonized by the inevitable execution Cawti faces. He visits the Empress again and strikes a deal: he will testify to Boralinoi's framing of Cawti before the Orb and single-handedly end the war with Greenaere in exchange for the pardon of Cawti and her the revolutionists. By testifying, Vlad commits the ultimate sin in the Organization, ending his career and branding him for death. Testifying in public, "under the orb," (which can detect falsehoods) is what ultimately sets the Jhereg Council against him. His previous acts of threatening the lives of his immediate superior in the Jhereg, Toronnan, and his boss' boss, Lord Boralinoi, as well as the Jhereg representative at court, Count Soffta, got the Jhereg to put out a (non-Morganti) contract on him but, given the nature of the organization, Vlad would have been "forgiven" had he "won" his war. But nobody gives open evidence about the Jhereg in public, much less in testimony before the Empress, and lives (except, it seems, Vlad). After his testimony, the contract is revised to be executed with a Morganti weapon, which would destroy Vlad's soul forever.
Vlad executes his second obligation with the help of his Dragaeran friends. Together they penetrate Greenaere's magic barrier and teleport outside the Greenaere throne room. Vlad negotiates a peace treaty during a tense stand-off, but the new King wants vengeance on the one responsible for ordering his father killed. Vlad knows that this last stipulation is impossible, but sends the treaty to the Empress. Vlad offers himself to the King, but before he can be executed, the Empress has Boralinoi sent back, claiming him to be the mastermind of the assassination. Vlad kills him for the King, satisfying the terms of the peace treaty. The King still orders Vlad to be killed, but he escapes with the help of his friends. Aibynn begins drumming and inadvertently contacts Verra, who rescues the group.
The Empress frees all the revolutionists and honors Vlad with the title of Count Szurke. He gives his primary businesses to his loyal lieutenant, Kragar. Following Cawti's second release, Vlad and Cawti acknowledge that Cawti has changed and they no longer love each other as they first did. He lets her know that he gives her all his South Adrilankha interests, and leaves her for Castle Black, where he convinces Noish-pa to live in his new county. After these arrangements, Vlad flees Adrilankha to avoid Jhereg vengeance. As he sets out, he wonders what his new life will have in store for him.
The House of the Phoenix.
House Phoenix is the smallest noble house in the Empire because a Dragaeran is not considered a Phoenix unless an actual phoenix passes overhead at the time of birth. Members of Phoenix are the most noble of all Dragaerans and tend to have an air of majesty. Their house color is gold, and they usually have gold hair and eyes. Phoenix is the first house in the Cycle, and thus each Phoenix Emperor is responsible for beginning the cycle anew. Most become decadent at the end of their reigns, but every seventeenth cycle the decadent Phoenix is followed by a "reborn" Phoenix who never sinks to decadence.
Like the mythological beast, Dragaeran phoenixes are flying creatures that die in flames and resurrect from the ashes, representing the house's role of rebirth, rejuvenation, and decay in the cycle. Phoenix appears twice in the Cycle Poem: at the beginning, "Phoenix sinks into decay", and at the end, "Phoenix rise from ashes gray".


Mycoparasitism

A mycoparasite is an organism with the ability to be a parasite to fungi. A variety of fungicolous fungi have been found in nature, either as parasites, commensals or saprobes. Biotrophic mycoparasites get nutrients from living host cells. Necrotrophic mycoparasites rely on decayed matter (saprophytic growth).
Types of mycoparasitism.
Biotrophic mycoparasites and nectrophic mycoparasites are two main groups of mycoparasite.
Biotrophic and necrotrophic mycoparasites.
Biotrophic mycoparasites get nutrients from living host cells and their growth of these parasites is greatly influenced by the metabolism of the host. Biotrophic mycoparasites tend to have a high host specificity, and often form specialized infection structures or a host parasite transition. Necrotrophic mycoparasites could only rely on saprophytic growth. On the other hand, the antagonistic action is strongly aggressive in necrotrophic relationships which is dominated by necrotrophic mycoparasites. Necrotrophic parasites tend to have a low host specificity, and are relatively unspecialized in their mechanism of parasitism.
Balanced and destructive mycoparasites.
Balanced mycoparsites have little or no destructive effect on the host, whereas destructive mycoparasites have the opposite effect. Biotrophic mycoparasites are generally considered as balanced mycoparasites; Necrotrophic mycoparasites usually have low host specificity and could use toxic and related enzyme to kill host, therefore necrotrophic mycoparasites are usually considered as destructive mycoparasites. However, in some combinations, the parasite may live during its early development as a biotrophic parasite, then kill their host and change into destructive mycoparasites in their late stage of parasitization.
Myco-heterotrophy.
"Monotropa uniflora" (or other angiosperm species), which are parasitic on fungus and do not photosynthesize, are sometimes classified as mycoparasites, however they should be referred to as myco-heterotrophs.
Mechanism.
There are normally four continuous steps of mycoparasitism: target location; recognition; contact and penetration; nutrient acquisition.
Target location.
Many research indicate that the growth direction of mycelium, spore germination, and bud tube elongation of mycoparasites have tropic reaction or tropism before attaching the host fungi. This tropic reaction is resulted from chemical stimulants secreted from mycohost and the direction of concentration gradient determines the growth direction of the parasite. As the mycoparasitic interaction is host-specific and not merely a contact response, it is likely that signals from the host fungus are recognized by mycoparasites such as "Trichoderma" and provoke transcription of mycoparasitism-related genes.
Recognition.
When mycoparasites get attachment of mycohost, they will recognize each other. It is indicated that the recognition between mycoparasites and their host fungi is related to the agglutinin on the cell surface of the mycohost. The carbohydrate residues on the cell wall of mycoparasites could specifically bind to the lectins on the surface of the host fungi to achieve mutual recognition.
Contact and penetration.
Once mycoparasites and mycohost recognize each other, both of them would have some changes in external form and internal structure to some extents. The manifestations of the mycoparasitic fungi are usually as follows: (1) the hypha grows rapidly on the host fungi and coils around the hypha of the host fungi; (2) the hypha penetrates and elongates the hypha of the host fungi (3) the infection filament is produced and penetrates the cells of host fungi to build parasitic relationship. In terms of necrotrophic/destructive mycoparasites, on the other hand, the hyphae of host fungi, due to the role of mycoparasites, will stop the growth, deform, shrivel and even dissolve.
Application.
Recently, it is popular to use integrated pest management (IPM) as an approach to reduce the amount of pesticides used, through preventive cultural practices, the use of disease resistant plant cultivars, and the use of mechanical and biological control of pathogen populations. Biocontrol of plant pathogens by microbial antagonists is one promising component in future disease control strategies that is compatible with both organic agriculture and IPM. As some mycoparasitic fungi have the ability to parasite and kill other fungi, these fungi could be used to antagonize plant pathogenic fungi directly as biocontrol agent. Mycoparasitism of plant pathogenic fungi by "Trichoderma" isolates has been well researched and is widely considered to be a major contributing factor to the biocontrol of a range of commercially important diseases. In, among others, the United States, India, Israel, New Zealand, and Sweden have applied "Trichoderma" species commercially such as "Rhizoctonia solani", "Botrytis cinerea", "Sclerotium rolfsii", "Sclerotinia sclerotiorum", "Pythium" spp., and "Fusarium" spp. as a promising alternative to chemical pesticides. Moreover, with the better understanding of mycoparasitism, more bioactive compounds including biopesticides and biofertilizers would be introduced as beneficial products.


Cortactin

Cortactin (from ""cortical actin" binding protein") is a monomeric protein located in the cytoplasm of cells that can be activated by external stimuli to promote polymerization and rearrangement of the actin cytoskeleton, especially the actin cortex around the cellular periphery. It is present in all cell types. When activated, it will recruit Arp2/3 complex proteins to existing actin microfilaments, facilitating and stabilizing nucleation sites for actin branching. Cortactin is important in promoting lamellipodia formation, invadopodia formation, cell migration, and endocytosis.
Gene.
In humans, cortactin is encoded by the "CTTN" gene on chromosome 11.
Structure.
Cortactin is a thin, elongated monomer that consists of an amino-terminal acidic (NTA) region; 37-residue-long segments that are highly conserved among cortactin proteins of all species and repeated up to 6.5 times in tandem (“cortactin repeats”); a proline-rich region; and an SH3 domain. This basic structure is highly conserved among all species that express cortactin.
Activation and binding.
Cortactin is activated via phosphorylation, by tyrosine kinases or serine/threonine kinases, in response to extracellular signals like growth factors, adhesion sites, or pathogenic invasion of the epithelial layer.
The SH3 domain of certain tyrosine kinases, such as the oncogene Src kinase, binds to cortactin's proline-rich region and phosphorylates it on Tyr421, Tyr466, and Tyr482. Once activated in this way, it can bind to filamentous actin (F-actin) with the fourth of its cortactin repeats. As the concentration of phosphorylated cortactin increases in specific regions within the cell, the monomers each begin to recruit an Arp2/3 complex to F-actin. It binds to Arp2/3 with an aspartic acid-aspartic acid-tryptophan (DDW) sequence in its NTA region, a motif that is often seen in other actin nucleation-promoting factors (NPFs).
Certain serine/threonine kinases, such as ERK, can phosphorylate cortactin on Ser405 and Ser418 in the SH3 domain. Activated like this, it still associates with Arp2/3 and F-actin, but will also allow other actin NPFs, most importantly N-WASp (Neuronal Wiskott-Aldrich syndrome protein), to bind to the complex as well; when phosphorylated by tyrosine kinases, other NPFs are excluded. The ability of these other NPFs to bind the Arp2/3 complex while cortactin is also bound could come from new interactions with cortactin's SH3 domain, which is in a different conformation when phosphorylated by Ser/Thr kinases and thus may be more open to interactions with other NPFs. Having other NPFs bind to the Arp2/3 complex at the same time as cortactin may enhance nucleation site stability.
Location and function in the cell.
Inactive cortactin diffuses throughout the cytoplasm, but upon phosphorylation, the protein begins to target certain areas in the cell. Cortactin-assisted Arp2/3-nucleated actin branches are most prominent in the actin cortex, around the periphery of the cell. A phosphorylated cortactin monomer binds to, activates, and stabilizes an Arp2/3 complex on preexisting F-actin, which provides a nucleation site for a new actin branch to form from the “mother” filament. Branches formed from cortactin-assisted nucleation sites are very stable; cortactin has been shown to inhibit debranching. Thus, polymerization and branching of actin is promoted in areas of the cell where cortactin is localized.
Cortactin is very active in lamellipodia, protrusions of the cell membrane formed by actin polymerization and treadmilling that propel the cell along a surface as it migrates towards some target.
Cortactin acts as a link between extracellular signals and lamellipodial “steering.” When a receptor tyrosine kinase on the cell membrane binds to an adhesion site, for example, cortactin will be phosphorylated locally to the area of binding, activate and recruit Arp2/3 to the actin cortex in that region, and thus stimulate cortical actin polymerization and movement of the cell in that direction. Macrophages, highly motile immune cells that engulf cellular debris and pathogens, are propelled by lamellipodia and identify/migrate toward a target via chemotaxis; thus, cortactin must also be activated by receptor kinases that pick up a large variety of chemical signals.
Studies have implicated cortactin in both clathrin-mediated endocytosis and clathrin-independent endocytosis. In both kinds of endocytosis, it has long been known that actin localizes to sites of vesicle invagination and is a vital part of the endocytic pathway, but the actual mechanisms by which actin facilitates endocytosis are still unclear. Recently, however, it has been found that dynamin, the protein responsible for breaking the newly formed vesicular bud off the inside of the plasma membrane, can associate with the SH3 domain of cortactin. Since cortactin recruits the Arp2/3 complexes that lead to actin polymerization, this suggests that it may play an important part in linking vesicle formation to the as yet unknown functions actin has in endocytosis.
Clinical significance.
Amplification of the genes encoding cortactin—in humans, EMS1—has been found to occur in certain tumors. Overexpression of cortactin can lead to highly-active lamellipodia in tumor cells, dubbed “invadopodia.” These cells are especially invasive and migratory, making them very dangerous, for they can easily spread cancer across the body into other tissues.
Interactions.
Cortactin has been shown to interact with:


Variecolin

Variecolin is a bio-active ascomycete isolate.


Script lichen

A script lichen, or graphid lichen, is a member of a group of lichens which have spore producing structures that look like writing on the lichen body. The structures are elongated and narrow apothecia called lirellae, which look like short scribbles on the thallus. "Graphid" is derived from Greek for "writing". An example is "Graphis mucronata".


Hyaloraphidium

Hyaloraphidium is a genus of fungi belonging to the class Chytridiomycetes, unknown order and family.
The genus has almost cosmopolitan distribution.
Species:


Professor of Physiology (Cambridge)

The Professorship of Physiology, also known as the Chair of Physiology (1883), is a chair at the University of Cambridge. In 2006, the Department of Physiology was merged with the Department of Anatomy to form the Department of Physiology, Development and Neuroscience where the chair is now based.


Basidiobolales


Phycicoccus

Phycicoccus is a genus of Gram positive, aerobic, non-endosporeforming bacteria. Species in this genus are mesophilic and have cells that are short rods or coccoid.
The genus was first proposed in 2006. The type species "P. jejuensis" was first isolated from dried seaweed from a beach in South Korea. The genus name is derived from Latin "phycos" (seaweed) and coccus, referring to the source of the original isolate and the shape of the cells. However, subsequently discovered species were found to be either short rods or cocci. Other members of this genus have been initially isolated from air, soil, bark, and scoria.
Species from this genus produce yellow, white, or cream-colored colonies on R2A agar. All species are mesophilic; most species cannot grow at temperatures above 35-37 °C, with the exception of "P. ginsenosidimutans", which can grow at 45 °C. "P. jejuensis" and "P. aerophilus" are the only psychrotrophs.


Lachnea

Lachnea is a genus of fungi belonging to the family Pyronemataceae. The genus was first described in 1822 as "Peziza" ser. "Lachnea" by Elias Magnus Fries. This was elevated to genus status by Claude Casimir Gillet in 1880.
The species of this genus are found in Eurasia.
Species.
Species:


Rhodactina

Rhodactina is a genus of secotioid fungi in the family Boletaceae. The genus was circumscribed in 1989 based on the type species "Rhodactina himalayensis", found in India and northern Thailand. The genus was originally classified in the family Gauteriaceae because of similarities in spore ornamentation to the genera "Gautieria" and "Austrogautieria". A second species, "Rhodactina incarnata", was added to the genus in 2006. It is found in Dipterocarpaceae-dominated forests in Chiang Mai (northern Thailand). Molecular phylogenetics analysis shows that "Rhodactina" is aligned with the Boletaceae.


Neisseriales


Mycobacterium frederiksbergense

Mycobacterium frederiksbergense is a species of the phylum Actinobacteria (Gram-positive bacteria with high guanine and cytosine content, one of the dominant phyla of all bacteria), belonging to the genus "Mycobacterium".
Etymology: frederiksbergense, of Frederiksberg, Denmark, referring to the place of isolation.
Type strain.
First isolated in Frederiksberg, Denmark.
Strain FAn9 = CIP 107205 = DSM 44346 = NRRL B-24126.


Peanut stunt virus

Peanut stunt virus (PSV) is a plant pathogenic virus in the family "Bromoviridae". It is a member of the genus " Cucumovirus ". The members of this genus are positive-stranded RNA viruses with a multipartite genome (3-4 parts). The virus particles have an isometric or spherical shape.
Distribution and host range.
PSV was first named as a new disease of groundnuts or peanuts (" Arachis hypogaea ") in 1966. Disease symptoms on the above ground parts of the peanut plants were described as severe dwarfing or stunting – hence the name "Peanut stunt virus". Fruit production was also severely reduced. Virginia peanut fields, where this disease was first observed in 1964, had yield reductions of 10-50%.
Severe stunting of peanuts had also been observed in North Carolina in 1964. The peanut disease in N. Carolina was reported to be caused by the PSV in 1967. The later report also stated that this virus caused disease in bean ("Phaseolus vulgaris") and in white clover ("Trifolium repens").
After its first description, PSV was quickly diagnosed in beans in Washington State, white clover in South Carolina, peanuts, beans and white clover in Georgia, peanuts in Alabama, and white clover in Florida. Strains of PSV have now been identified in Africa (Morocco), Europe (France, Poland, Russia, and Spain) and Asia (India, Japan, Korea and China ) as well as in the United States.
PSV is an economically important pathogen of plants in the family Leguminosae. In addition to beans, peanuts, and clover (7 different species of "Trifolium" ), PSV has been reported to naturally infect peas ("Pisum sativum"), soybeans ("Glycine max"), alfalfa ("Medicago sativa") and lupine ("Lupinus luteus"). In 2002, PSV was reported to infect rhizoma or perennial peanut ("Arachis glabrata") in N. Florida and S. Georgia.
Host range studies have shown that fourteen other plant families can be infected with this virus including agriculturally important crops in the plant families Cucurbitaceae (squash, cucumber, watermelon) and Solanceae (tomatoes, peppers, tobacco). Cultivated Tobacco ("Nicotiana tabacum") and celery ("Apium graveolens") have also been reported to be naturally infected.
Transmission.
PSV is transmitted from plant to plant by several species of aphids ("Aphis craccivora", "A. spiraecola" and "Myzus persicae") in a stylet-borne manner. It can also be transmitted by mechanical inoculation. It has been shown to be transmitted by seeds in peanuts at a very low level but this is not considered to be very important to the spread of this virus.
The virus can be introduced into a susceptible field crop by aphids from a nearby reservoir (infected perennial hosts like clover, alfalfa or perennial peanuts) and then is spread further into the field by aphids. It can be spread in perennial crops by harvesting (mechanical transmission) and possibly by root grafts.
Diagnosis.
Correct diagnosis of any plant disease requires some expertise. Plants suspected of a viral infection should be sent to a plant diagnostic laboratory where the presence or absence of the virus can be confirmed by serological ( ELISA ), genetic (PCR), or host range tests. Antiserum and sequence data are available for this virus.


Involution (medicine)

Involution is the shrinking or return of an organ to a former size. At a cellular level, involution is characterized by the process of proteolysis of the basement membrane (basal lamina), leading to epithelial regression and apoptosis, with accompanying stromal fibrosis. The consequent reduction in cell number and reorganization of stromal tissue leads to the reduction in the size of the organ.
Examples.
Thymus.
The thymus continues to grow between birth and puberty and then begins to atrophy, a process directed by the high levels of circulating sex hormones. Proportional to thymic size, thymic activity (T cell output) is most active before puberty. Upon atrophy, the size and activity are dramatically reduced, and the organ is primarily replaced with fat. The atrophy is due to the increased circulating level of sex hormones, and chemical or physical castration of an adult results in the thymus increasing in size and activity.
Uterus.
Involution is the process by which the uterus is transformed from pregnant to non-pregnant state. This period is characterized by the restoration of ovarian function in order to prepare the body for a new pregnancy. It is a physiological process occurring after parturition; the hypertrophy of the uterus has to be undone since it does not need to house the fetus anymore. This process is primarily due to the hormone oxytocin. The completion of this period is defined as when the diameter of the uterus returns to the size it is normally during a woman's menstrual cycle.
Mammary gland.
During pregnancy until after birth, mammary glands grow steadily to a size required for optimal milk production. At the end of breastfeeding, the number of cells in the mammary gland becomes reduced until approximately the same number is reached as before the start of pregnancy.


Acaulospora alpina

Acaulospora alpina is a species of fungus in the family Acaulosporaceae. It forms arbuscular mycorrhiza and vesicles in roots. The fungus was discovered in Switzerland, in the rhizosphere of an alpine grassland at altitudes between .


Candidatus Caballeronia nigropunctata

""Candidatus" Caballeronia nigropunctata" is a "Candidatus" species of bacteria from the genus "Caballeronia" and the family Burkholderiaceae. ""Candidatus" Caballeronia nigropunctata" is an endosymbiont of the plant "Psychotria nigropunctata".


Ana Colovic Lesoska

Ana Colovic Lesoska (born c.1979) is a Macedonian biologist who since 2011 has campaigned against the construction of dams for hydroelectric power production in the Mavrovo National Park in order to safeguard threatened species, including the Balkan lynx. This led to the withdrawal of loans from the World Bank and the European Bank for Reconstruction and Development (EBRD), convincing the Government of North Macedonia to suspend further work on dams in the national park. In recognition of her efforts, in April 2019 she was one of six environmentalists to be awarded the Goldman Environmental Prize.
Colovic Lesoska, a biologist, heard about plans to create hydroelectric power facilities in Mavrovo in 2010. They included the 33m-high Boškov Most dam and the 70m-high Lukovo Pole dam. As executive director of Eko-svest, a Macedonian environmental research centre, in collaboration with other NGOs and activists, she launched the "Save Mavrovo" campaign. In November 2011, she filed a complaint with the ERBD, explaining that they had approved a loan for the Boškov Most project without conducting the required biodiversity assessment. She encouraged the ambassadors of countries with representatives on the EBRD board to push for an end to the funding. A petition she launched urging the government, the ERBD and the World Bank to bring the projects to a close was supported by almost 100,000 signatures.
In 2013, she filed a complaint with the Berne Convention on the Conservation of European Wildlife and Natural Habitats, explaining that the Boškov Most hydropower project "could have a decisive negative impact on the lynx". In December 2015, the Berne Convention ordered the ERBD and the World Bank to suspend financing as the project could have "a decisive negative impact on the lynx". The World Bank immediately withdrew funding and the following May, a court decision to annul the environmental permit for the Boškov Most project. In January 2017, the EBRD cancelled financing.
In recognition of these achievements, in April 2019 Ana Colovic Lesoska was awarded the Goldman Environmental Prize. It was the first time the prize had been awarded to North Macedonia.


Bolidophyceae

Bolidophyceae is a class of photosynthetic heterokont picophytoplankton, and consist of less than 20 known species. They are distinguished by the angle of flagellar insertion and swimming patterns as well as recent molecular analyses. Bolidophyceaes are sister taxa to the diatoms (Bacillariophyceae) but lack characteristic theca, and have been proposed as an intermediate group between the diatoms and all other heterokonts.
Gallery.
In the gallery, all scale bar represent 1 μm.


Tetrahymena

Tetrahymena, a unicellular eukaryote, is a genus of free-living ciliates that can also switch from commensalistic to pathogenic modes of survival. They are common in freshwater ponds. "Tetrahymena" species used as model organisms in biomedical research are "T. thermophila" and "T. pyriformis".
"T. thermophila": a model organism in experimental biology.
As a ciliated protozoan, Tetrahymena thermophila exhibits nuclear dimorphism: two types of cell nuclei. They have a bigger, non-germline macronucleus and a small, germline micronucleus in each cell at the same time and these two carry out different functions with distinct cytological and biological properties. This unique versatility allows scientists to use "Tetrahymena" to identify several key factors regarding gene expression and genome integrity. In addition, "Tetrahymena" possess hundreds of cilia and has complicated microtubule structures, making it an optimal model to illustrate the diversity and functions of microtubule arrays.
Because "Tetrahymena" can be grown in a large quantity in the laboratory with ease, it has been a great source for biochemical analysis for years, specifically for enzymatic activities and purification of sub-cellular components. In addition, with the advancement of genetic techniques it has become an excellent model to study the gene function "in vivo". The recent sequencing of the macronucleus genome should ensure that "Tetrahymena" will be continuously used as a model system.
"Tetrahymena thermophila" exists in 7 different sexes (mating types) that can reproduce in 21 different combinations, and a single tetrahymena cannot reproduce sexually with itself. Each organism "decides" which sex it will become during mating, through a stochastic process.
Studies on "Tetrahymena" have contributed to several scientific milestones including:
Life cycle.
The life cycle of "T. thermophila" consists of an alternation between asexual and sexual stages. In nutrient rich media during vegetative growth cells reproduce asexually by binary fission. This type of cell division occurs by a sequence of morphogenetic events that results in the development of duplicate sets of cell structures, one for each daughter cell. Only during starvation conditions will cells commit to sexual conjugation, pairing and fusing with a cell of opposite mating type. Tetrahymena has seven mating types; each of which can mate with any of the other six without preference, but not its own.
Typical of ciliates, "T. thermophila" differentiates its genome into two functionally distinct types of nuclei, each specifically used during the two different stages of the life cycle. The diploid germline micronucleus is transcriptionally silent and only plays a role during sexual life stages. The germline nucleus contains 5 pairs of chromosomes which encode the heritable information passed down from one sexual generation to the next. During sexual conjugation, haploid micronuclear meiotic products from both parental cells fuse, leading to the creation of a new micro- and macronucleus in progeny cells. Sexual conjugation occurs when cells starved for at least 2hrs in a nutrient-depleted media encounter a cell of complementary mating type. After a brief period of co-stimulation (~1hr), starved cells begin to pair at their anterior ends to form a specialized region of membrane called the conjugation junction.
It is at this junctional zone that several hundred fusion pores form, allowing for the mutual exchange of protein, RNA and eventually a meiotic product of their micronucleus. This whole process takes about 12 hours at 30 °C, but even longer than this at cooler temperatures. The sequence of events during conjugation is outlined in the accompanying figure.
The larger polyploid macronucleus is transcriptionally active, meaning its genes are actively expressed, and so it controls somatic cell functions during vegetative growth. The polyploid nature of the macronucleus refers to the fact that it contains approximately 200–300 autonomously replicating linear DNA mini-chromosomes. These minichromosomes have their own telomeres and are derived via site-specific fragmentation of the five original micronuclear chromosomes during sexual development. In T. thermophila each of these minichromosomes encodes multiple genes and exists at a copy number of approximately 45-50 within the macronucleus. The exception to this is the minichromosome encoding the rDNA, which is massively upregulated, existing at a copy number of approximately 10,000 within the macronucleus. Because the macronucleus divides amitotically during binary fission, these minichromosomes are un-equally divided between the clonal daughter cells. Through natural or artificial selection, this method of DNA partitioning in the somatic genome can lead to clonal cell lines with different macronuclear phenotypes fixed for a particular trait, in a process called phenotypic assortment. In this way, the polyploid genome can fine-tune its adaptation to environmental conditions through gain of beneficial mutations on any given mini-chromosome whose replication is then selected for, or conversely, loss of a minichromosome which accrues a negative mutation. However, the macronucleus is only propagated from one cell to the next during the asexual, vegetative stage of the life cycle, and so it is never directly inherited by sexual progeny. Only beneficial mutations that occur in the germline micronucleus of "T. thermophila" are passed down between generations, but these mutations would never be selected for environmentally in the parental cells because they are not expressed.
Behavior.
Free swimming cells of "Tetrahymena" are attracted to certain chemicals by chemokinesis. The major chemo-attractants are peptides and/or proteins.
A 2016 study found that cultured "Tetrahymena" have the capacity to 'learn' the shape and size of their swimming space. Cells confined in a droplet of a water for a short time were, upon release, found to repeat the circular swimming trajectories 'learned' in the droplet. The diameter and duration of these swimming paths reflected the size of the droplet and time allowed to adapt.
DNA repair.
It is common among protists that the sexual cycle is inducible by stressful conditions such as starvation. Such conditions often cause DNA damage. A central feature of meiosis is homologous recombination between non-sister chromosomes. In "T. thermophila" this process of meiotic recombination may be beneficial for repairing DNA damages caused by starvation.
Exposure of "T. thermophila" to UV light resulted in a greater than 100-fold increase in "Rad51" gene expression. Treatment with the DNA alkylating agent methyl methane sulfonate also resulted in substantially elevated Rad 51 protein levels. These findings suggest that ciliates such as "T. thermophila" utilize a Rad51-dependent recombinational pathway to repair damaged DNA.
The Rad51 recombinase of "T. thermophila" is a homolog of the "Escherichia coli" RecA recombinase. In "T. thermophila", Rad51 participates in homologous recombination during mitosis, meiosis and in the repair of double-strand breaks. During conjugation, Rad51 is necessary for completion of meiosis. Meiosis in "T. thermophila" appears to employ a Mus81-dependent pathway that does not use a synaptonemal complex and is considered secondary in most other model eukaryotes. This pathway includes the Mus81 resolvase and the Sgs1 helicase. The Sgs1 helicase appears to promote the non-crossover outcome of meiotic recombinational repair of DNA, a pathway that generates little genetic variation.
Uses in education.
The ASSET program seeks to use this organism to help teach biological concepts and methods to secondary students. An outreach program, Advancing Secondary Science Education thru Tetrahymena, has been established at Cornell University.


Cochlonemataceae

The family Cochlonemataceae is a fungus classified in the order Zoopagales. Fungi found in this family are predominantly parasitic and can be found in any substrate that contains an ample amount of host or prey organisms.
The family contains six genera.


Nitrosopumilales

The Nitrosopumilales are an order of the Archaea class Thermoprotei.


Loma salmonae

Loma salmonae is a species of microsporidian parasite, infecting Pacific salmon ("Oncorhynchus" spp.). "L. salmonae" is the causative agent of microsporidial gill disease of salmon. It is an intracellular parasite which induces respiratory distress, secondary infection, and increased mortality rates.
Life Cycle.
"Loma salmonae" enters the "Oncorhynchus" host's gut via an infective spores. Once in the gut, the spore injects its sporoplasm into an epithelial cell. From there, it migrates to the heart for a two-week merogony-like phase. In the heart, the host's immune system phagocytizes the parasite. Following macrophage mediated transportation, "L. salmonae" enters into the host's gills where it enters a final developmental stage. At this stage, it becomes a spore laden xenoma. This xenoma ruptures and causes inflammation and severe gill damage. This also opens up the possibility of secondary infection. The released spores can then be consumed by another "Oncorynchus spp." completing the life cycle.


Gomphidius pseudoflavipes

Gomphidius pseudoflavipes is a mushroom in the family Gomphidiaceae that is found in California in North America.


Pelosinus

Pelosinus is a genus of Firmicutes bacteria classified within the class Negativicutes.
Phylogeny.
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI)
and the phylogeny is based on 16S rRNA-based LTP release 111 by The All-Species Living Tree Project


Chthonomonas calidirosea

Chthonomonas calidirosea is a Gram-negative bacterium and also the first representative of the new class Chthonomonadetes within the phylum Armatimonadetes. The Armatimonadetes were previously known as candidate phylum OP10. OP10 was composed solely of environmental 16S rRNA gene clone sequences prior to "C. calidirosea's" relative, "Armatimonas rosea's" discovery. It is now known that bacterial communities from geothermal environments, are generally constituted by, at least 5–10% of bacteria belonging to Armatimonadetes.
Discovery.
"Chthonomonas calidirosea" was originally isolated from geothermally heated soil at Hell's Gate, Tikitere, New Zealand. The soil was aseptically sampled at an approximate depth of 15 cm below the surface. The sampled soil had a pH of 4.3 and an "in situ" temperature of 55 °C.
Relatives.
The environmental 16S rRNA gene sequences, belonging to the phylum "Armatimonadetes" are currently sorted into six groups. Groups 2, 5, and 6 consist solely of sequences. Group 1 contains "Armatimonadetes rosea", Group 3 contains "Chthonomonadetes calidirosea", and Group 4 contains "Fimbriimonas ginsengisoli".
"Armatimonas rosea", an aerobic, Gram-negative, pink pigmented, nonmotile, ovoid/rod shaped bacterium, was isolated from the rhizoplane of an aquatic plant "Phragmites australis" in Japan. It is the first representative of the phylum Armatimonadetes.
"Fimbriimonas ginsengisoli", an aerobic, non-motile, mesophilic, rod-shaped bacterium, was isolated from a ginseng field soil sample. It represents the first cultured representative of the Fimbriimonadia class, corresponding with Group 4 of the phylum Armatimonadetes.
Characteristics.
When grown on solid medium AOM1, colonies were light-pink pigmented, circular, convex, relatively small (2–4 mm) in size after one week of incubation at 60 °C. "Chthonomonas calidirosea" has an optimum temperature at 68 °C with a range of 50–73 °C. The optimum pH for growth was 5.3 with a range of 4.5–5.8. Optimum growth was observed in NaCl free medium, although growth was observed in NaCl amended FSV1 medium up to 2% NaCl.
When examined by phase-contrast and transmission electron microscopy a limited number of cells were observed to exhibit a tumbling motility that was highly dependent on growth phase, medium pH and substrate. An irregular, corrugated outer membrane was consistently observed. Cells were rod shaped, with sizes ranging from 0.5–0.7 µm in diameter and 2.5–3.0 µm in length. Neither spores nor flagella were observed.
Cultures of "C. calidirosea" were observed to be aerobic, saccharolytic, obligately thermophilic, motile, non-spore-forming bacterium with no evidence of growth under anaerobic conditions.


Neocallimastigomycetes


Obligate anaerobe

Obligate anaerobes are microorganisms killed by normal atmospheric concentrations of oxygen (20.95% O2). Oxygen tolerance varies between species, with some species capable of surviving in up to 8% oxygen, while others lose viability in environments with an oxygen concentration greater than 0.5%.
Oxygen sensitivity.
The oxygen sensitivity of obligate anaerobes has been attributed to a combination of factors including oxidative stress and enzyme production. Oxygen can also damage obligate anaerobes in ways not involving oxidative stress.
Because molecular oxygen contains two unpaired electrons in the highest occupied molecular orbital, it is readily reduced to superoxide () and hydrogen peroxide () within cells. A reaction between these two products results in the formation of a free hydroxyl radical (OH.). Superoxide, hydrogen peroxide, and hydroxyl radicals are a class of compounds known as reactive oxygen species (ROS), highly reactant products that are damaging to microbes, including obligate anaerobes. Aerobic organisms produce superoxide dismutase and catalase to detoxify these products, but obligate anaerobes produce these enzymes in very small quantities, or not at all. (The variability in oxygen tolerance of obligate anaerobes (<0.5 to 8% O2) is thought to reflect the quantity of superoxide dismutase and catalase being produced.).
Carlioz and Touati (1986) performed experiments which support the idea that reactive oxygen species may be toxic to anaerobes. "E. coli," a facultative anaerobe, was mutated by a deletion of superoxide dismutase genes. In the presence of oxygen, this mutation resulted in the inability to properly synthesize certain amino acids or use common carbon sources as substrates during metabolism. In the absence of oxygen, the mutated samples grew normally. In 2018, Lu et al. found that in "Bacteroides thetaiotaomicron," an obligate anaerobe found in the mammalian digestive tract, exposure to oxygen results in increased levels of superoxide which inactivated important metabolic enzymes.
Dissolved oxygen increases the redox potential of a solution, and high redox potential inhibits the growth of some obligate anaerobes. For example, methanogens grow at a redox potential lower than -0.3 V. Sulfide is an essential component of some enzymes, and molecular oxygen oxidizes this to form disulfide, thus inactivating certain enzymes (e.g. nitrogenase). Organisms may not be able to grow with these essential enzymes deactivated. Growth may also be inhibited due to a lack of reducing equivalents for biosynthesis because electrons are exhausted in reducing oxygen.
Energy metabolism.
Obligate anaerobes convert nutrients into energy through anaerobic respiration or fermentation. In aerobic respiration, the pyruvate generated from glycolysis is converted to acetyl-CoA. This is then broken down via the TCA cycle and electron transport chain. Anaerobic respiration differs from aerobic respiration in that it uses an electron acceptor other than oxygen in the electron transport chain. Examples of alternative electron acceptors include sulfate, nitrate, iron, manganese, mercury, and carbon monoxide.
Fermentation differs from anaerobic respiration in that the pyruvate generated from glycolysis is broken down without the involvement of an electron transport chain (i.e. there is no oxidative phosphorylation). Numerous fermentation pathways exist such as lactic acid fermentation, mixed acid fermentation, 2-3 butanediol fermentation where organic compounds are reduced to organic acids and alcohol.
The energy yield of anaerobic respiration and fermentation (i.e. the number of ATP molecules generated) is less than in aerobic respiration. This is why facultative anaerobes, which can metabolise energy both aerobically and anaerobically, preferentially metabolise energy aerobically. This is observable when facultative anaerobes are cultured in thioglycolate broth.
Ecology and Examples.
Obligate anaerobes are found in oxygen-free environments such as the intestinal tracts of animals, the deep ocean, still waters, landfills, in deep sediments of soil. Examples of obligately anaerobic bacterial genera include "Actinomyces","Bacteroides", "Clostridium", "Fusobacterium", "Peptostreptococcus", "Porphyromonas", "Prevotella", "Propionibacterium", and "Veillonella". "Clostridium" species are endospore-forming bacteria, and can survive in atmospheric concentrations of oxygen in this dormant form. The remaining bacteria listed do not form endospores.
Several species of the "Mycobacterium, Streptomyces, and Rhodococcus" generas are examples of obligate anaerobe found in soil. Obligate anaerobes are also found in the digestive tracts of humans and other animals as well as in the first stomach of ruminants.
Examples of obligately anaerobic fungal genera include the rumen fungi "Neocallimastix", "Piromonas", and "Sphaeromonas".


Chlorogloeopsidaceae


Common cuckoo

The common cuckoo ("Cuculus canorus") is a member of the cuckoo order of birds, Cuculiformes, which includes the roadrunners, the anis and the coucals.
This species is a widespread summer migrant to Europe and Asia, and winters in Africa. It is a brood parasite, which means it lays eggs in the nests of other bird species, particularly of dunnocks, meadow pipits, and reed warblers. Although its eggs are larger than those of its hosts, the eggs in each type of host nest resemble the host's eggs. The adult too is a mimic, in its case of the sparrowhawk; since that species is a predator, the mimicry gives the female time to lay her eggs without being attacked.
Taxonomy.
The species' binomial name is derived from the Latin "cuculus" (the cuckoo) and "canorus" (melodious; from "canere", meaning to sing). The cuckoo family gets its common name and genus name by onomatopoeia for the call of the male common cuckoo. The English word "cuckoo" comes from the Old French "cucu", and its earliest recorded usage in English is from around 1240, in the song "Sumer Is Icumen In". The song is written in Middle English, and the first two lines are: "Svmer is icumen in / Lhude sing cuccu." In modern English, this translates to "Summer has come in / Loudly sing, Cuckoo!".
There are four subspecies worldwide:
Lifespan and demography.
Although the common cuckoo's global population appears to be declining, it is classified of being of least concern by the International Union for Conservation of Nature. It is estimated that the species numbers between 25 million and 100 million individuals worldwide, with around 12.6 million to 25.8 million of those birds breeding in Europe. The maximum recorded lifespan of a common cuckoo in the United Kingdom is 6 years, 11 months and 2 days.
Description.
The common cuckoo is long from bill to tail (with a tail of and a wingspan of . The legs are short. It has a greyish, slender body and long tail, similar to a sparrowhawk in flight, where the wingbeats are regular. During the breeding season, common cuckoos often settle on an open perch with drooped wings and raised tail. There is a rufous colour morph, which occurs occasionally in adult females but more often in juveniles.
All adult males are slate-grey; the grey throat extends well down the bird's breast with a sharp demarcation to the barred underparts. The iris, orbital ring, the base of the bill and feet are yellow. Grey adult females have a pinkish-buff or buff background to the barring and neck sides, and sometimes small rufous spots on the median and greater coverts and the outer webs of the secondary feathers.
Rufous morph adult females have reddish-brown upperparts with dark grey or black bars. The black upperpart bars are narrower than the rufous bars, as opposed to rufous juvenile birds, where the black bars are broader.
Common cuckoos in their first autumn have variable plumage. Some have strongly-barred chestnut-brown upperparts, while others are plain grey. Rufous-brown birds have heavily barred upperparts with some feathers edged with creamy-white. All have whitish edges to the upper wing-coverts and primaries. The secondaries and greater coverts have chestnut bars or spots. In spring, birds hatched in the previous year may retain some barred secondaries and wing-coverts. The most obvious identification features of juvenile common cuckoos are the white nape patch and white feather fringes.
Common cuckoos moult twice a year: a partial moult in summer and a complete moult in winter. Males weigh around and females . The common cuckoo looks very similar to the Oriental cuckoo, which is slightly shorter-winged on average.
Mimicry in adult.
The barred underparts of the common cuckoo resemble those of the Eurasian sparrowhawk, a predator of adult birds. A study comparing the responses of Eurasian reed warblers, a host of cuckoo chicks, to manipulated taxidermy model cuckoos and sparrowhawks found that reed warblers were more aggressive to cuckoos with obscured underparts, suggesting that the resemblance to sparrowhawks is likely to help the cuckoo access the nests of potential hosts. Other small birds, great tits and blue tits, showed alarm and avoided attending feeders on seeing either (mounted) sparrowhawks or cuckoos; this implies that the cuckoo's hawklike appearance functions as protective mimicry, whether to reduce attacks by hawks or to make brood parasitism easier.
Hosts attack cuckoos more when they see neighbors mobbing cuckoos. The existence of the two plumage morphs in females may be due to frequency-dependent selection if this learning applies only to the morph that hosts see neighbors mob. In an experiment with dummy cuckoos of each morph and a sparrowhawk, reed warblers were more likely to attack both cuckoo morphs than the sparrowhawk, and even more likely to mob a certain cuckoo morph when they saw neighbors mobbing that morph, decreasing the reproductive success of that morph and selecting for the less common morph.
Voice.
The male's song, "goo-ko", is usually given from an open perch. During the breeding season the male typically gives this vocalisation with intervals of 1–1.5 seconds, in groups of 10–20 with a rest of a few seconds between groups. The female has a loud bubbling call. The song starts as a descending minor third early in the year in April, and the interval gets wider, through a major third to a fourth as the season progresses, and in June the cuckoo "forgets its tune" and may make other calls such as ascending intervals. The wings are drooped when calling intensely and when in the vicinity of a potential female, the male often wags its tail from side to side or the body may pivot from side to side.
Distribution and habitat.
Essentially a bird of open land, the common cuckoo is a widespread summer migrant to Europe and Asia, and winters in Africa. Birds arrive in Europe in April and leave in September. The common cuckoo has also occurred as a vagrant in countries including Barbados, the United States, Greenland, the Faroe Islands, Iceland, Indonesia, Palau, Seychelles, Taiwan and China. Between 1995 and 2015, the distribution of cuckoos within the UK has shifted towards the north, with a decline by 69% in England but an increase by 33% in Scotland.
Behaviour.
Food and feeding.
The common cuckoo's diet consists of insects, with hairy caterpillars, which are distasteful to many birds, being a specialty of preference. It also occasionally eats eggs and chicks.
Breeding.
The common cuckoo is an obligate brood parasite; it lays its eggs in the nests of other birds. Hatched cuckoo chicks may push out host eggs out of the nest or be raised alongside the host's chicks. A female may visit up to 50 nests during a breeding season. Common cuckoos first breed at the age of two years.
Egg mimicry.
More than 100 host species have been recorded: meadow pipit, dunnock and Eurasian reed warbler are the most common hosts in northern Europe; garden warbler, meadow pipit, pied wagtail and European robin in central Europe; brambling and common redstart in Finland; and great reed warbler in Hungary.
Female common cuckoos are divided into gentes – groups of females favouring a particular host species' nest and laying eggs that match those of that species in color and pattern. Evidence from mitochondrial DNA analyses suggest that each gente may have multiple independent origins due to parasitism of specific hosts by different ancestors. One hypothesis for the inheritance of egg appearance mimicry is that this trait is inherited from the female only, suggesting that it is carried on the sex-determining W chromosome (females are WZ, males ZZ). A genetic analysis of gentes supports this proposal by finding significant differentiation in mitochondrial DNA, but not in microsatellite DNA. A second proposal for the inheritance of this trait is that the genes controlling egg characteristics are carried on autosomes rather than just the W chromosome. Another genetic analysis of sympatric gentes supports this second proposal by finding significant genetic differentiation in both microsatellite DNA and mitochondrial DNA. Considering the tendency for common cuckoo males to mate with multiple females and produce offspring raised by more than one host species, it appears as though males do not contribute to the maintenance of common cuckoo gentes. However, it was found that only nine percent of offspring were raised outside of their father's presumed host species. Therefore, both males and females may contribute to the maintenance of common cuckoo egg mimicry polymorphism. It is notable that most non-parasitic cuckoo species lay white eggs, like most non-passerines other than ground-nesters.
As the common cuckoo evolves to lay eggs that better imitate the host's eggs, the host species adapts and is more able to distinguish the cuckoo egg. A study of 248 common cuckoo and host eggs demonstrated that female cuckoos that parasitised common redstart nests laid eggs that matched better than those that targeted dunnocks. Spectroscopy was used to model how the host species saw the cuckoo eggs. Cuckoos that target dunnock nests lay white, brown-speckled eggs, in contrast to the dunnock's own blue eggs. The theory suggests that common redstarts have been parasitised by common cuckoos for longer, and so have evolved to be better than the dunnocks at noticing the cuckoo eggs. The cuckoo, over time, has needed to evolve more accurate mimicking eggs to successfully parasitise the redstart. In contrast, cuckoos do not seem to have experienced evolutionary pressure to develop eggs which closely mimic the dunnock's, as dunnocks do not seem to be able to distinguish between the two species' eggs, despite the significant colour differences. The dunnock's inability to distinguish the eggs suggests that they have not been parasitised for very long, and have not yet evolved defences against it, unlike the redstart.
Studies performed on great reed warbler nests in central Hungary, showed an "unusually high" frequency of common cuckoo parasitism, with 64% of the nests parasitised. Of the nests targeted by cuckoos, 64% contained one cuckoo egg, 23% had two, 10% had three and 3% had four common cuckoo eggs. In total, 58% of the common cuckoo eggs were laid in nests that were multiply parasitised. When laying eggs in nests already parasitised, the female cuckoos removed one egg at random, showing no discrimination between the great reed warbler eggs and those of other cuckoos.
It was found that nests close to cuckoo perches were most vulnerable: multiple parasitised nests were closest to the vantage points, and unparasitised nests were farthest away. Nearly all the nests "in close vicinity" to the vantage points were parasitised. More visible nests were more likely to be selected by the common cuckoos. Female cuckoos use their vantage points to watch for potential hosts and find it easier to locate the more visible nests while they are egg-laying, however, novel studies highlight that host alarm calls might also play an important role during nest searching. In addition, cuckoos tend to lay the eggs on the host clutch initiation day or one day before.
The great reed warblers' responses to the common cuckoo eggs varied: 66% accepted the egg(s); 12% ejected them; 20% abandoned the nests entirely; 2% buried the eggs. 28% of the cuckoo eggs were described as "almost perfect" in their mimesis of the host eggs, and the warblers rejected "poorly mimetic" cuckoo eggs more often. The degree of mimicry made it difficult for both the great reed warblers and the observers to tell the eggs apart.
The egg measures and weighs , of which 7% is shell. Research has shown that the female common cuckoo is able to keep its egg inside its body for an extra 24 hours before laying it in a host's nest. This means the cuckoo chick can hatch before the host's chicks do, and it can eject the unhatched eggs from the nest. Scientists incubated common cuckoo eggs for 24 hours at the bird's body temperature of , and examined the embryos, which were found "much more advanced" than those of other species studied. The idea of 'internal incubation' was first put forward in 1802 and 18th- and 19th-century egg collectors had reported finding that cuckoo embryos were more advanced than those of the host species.
Complete list of common cuckoo's nest-host by Aleksander D. Numerov (2003); names of birds in whose nests cuckoo's eggs and chicks were found more than 10 times (in bold):
Chicks.
The naked, altricial chick hatches after 11–13 days. It methodically evicts all host progeny from host nests. It is a much larger bird than its hosts, and needs to monopolize the food supplied by the parents. The chick will roll the other eggs out of the nest by pushing them with its back over the edge. If the host's eggs hatch before the cuckoo's, the cuckoo chick will push the other chicks out of the nest in a similar way. At 14 days old, the common cuckoo chick is about three times the size of an adult Eurasian reed warbler.
The necessity of eviction behavior is unclear. One hypothesis is that competing with host chicks leads to decreased cuckoo chick weight, which is selective pressure for eviction behavior. An analysis of the amount of food provided to common cuckoo chicks by host parents in the presence and absence of host siblings showed that when competing against host siblings, cuckoo chicks did not receive enough food, showing an inability to compete. Selection pressure for eviction behavior may come from cuckoo chicks lacking the correct visual begging signals, hosts distributing food to all nestlings equally, or host recognition of the parasite. Another hypothesis is that decreased cuckoo chick weight is not selective pressure for eviction behavior. An analysis of resources provided to cuckoo chick in the presence and absence of host siblings also showed that the weights of cuckoos raised with host chicks were much smaller upon fledging than cuckoos raised alone, but within 12 days cuckoos raised with siblings grew faster than cuckoos raised alone and made up for developmental differences, showing a flexibility that would not necessarily select for eviction behavior.
Species whose broods are parasitised by the common cuckoo have evolved to discriminate against cuckoo eggs but not chicks. Experiments have shown that common cuckoo chicks persuade their host parents to feed them by making a rapid begging call that sounds "remarkably like a whole brood of host chicks." The researchers suggested that "the cuckoo needs vocal trickery to stimulate adequate care to compensate for the fact that it presents a visual stimulus of just one gape." However, a cuckoo chick needs the amount of food of a whole brood of host nestlings, and it struggles to elicit that much from the host parents with only the vocal stimulus. This may reflect a tradeoff—the cuckoo chick benefits from eviction by receiving all the food provided, but faces a cost in being the only one influencing feeding rate. For this reason, cuckoo chicks exploit host parental care by remaining with the host parent longer than host chicks do, both before and after fledging.
Common cuckoo chicks fledge about 17–21 days after hatching, compared to 12–13 days for Eurasian reed warblers. If the hen cuckoo is out-of-phase with a clutch of Eurasian reed warbler eggs, she will eat them all so that the hosts are forced to start another brood.
The common cuckoo's behaviour was firstly observed and described by Aristotle and the combination of behaviour and anatomical adaptation by Edward Jenner, who was elected as Fellow of the Royal Society in 1788 for this work rather than for his development of the smallpox vaccine. It was first documented on film in 1922 by Edgar Chance and Oliver G Pike, in their film "The Cuckoo's Secret".
A study in Japan found that young common cuckoos probably acquire species-specific feather lice from body-to-body contact with other cuckoos between the time of leaving the nest and returning to the breeding area in spring. A total of 21 nestlings were examined shortly before they left their hosts' nests and none carried feather lice. However, young birds returning to Japan for the first time were found just as likely as older individuals to be lousy.
As a biodiversity indicator.
The occurrence of common cuckoo in Europe is a good surrogate for biodiversity facets including taxonomic diversity and functional diversity in bird communities, and better than the traditional use of top predators as bioindicators. The reason for this is the strong correlation between the cuckoo's host species richness and overall bird species richness, due to co-evolutionary relationships. This may be useful for citizen science.
In culture.
Aristotle was aware of the old tale that cuckoos turned into hawks in winter. The tale was an explanation for their absence outside the summer season, later accepted by Pliny the Elder in his "Natural History". Aristotle rejected the claim, observing in his "History of Animals" that cuckoos do not have the predators' talons or hooked bills. These Classical era accounts were known to the Early Modern English naturalist, William Turner.
The 13th-century medieval English round, "Sumer Is Icumen In", celebrates the cuckoo as a sign of spring, the beginning of summer, in the first stanza, and in the chorus:
<poem>
Svmer is icumen in
Lhude sing cuccu
Groweþ sed
and bloweþ med
and springþ þe wde nu
Sing cuccu
</poem>
<poem>
Summer has arrived,
Sing loudly, cuckoo!
The seed is growing
And the meadow is blooming,
And the wood is coming into leaf now,
Sing, cuckoo!
</poem>
In England, William Shakespeare alludes to the common cuckoo's association with spring, and with cuckoldry, in the courtly springtime song in his play "Love's Labours Lost":
In Europe, hearing the call of the common cuckoo is regarded as the first harbinger of spring. Many local legends and traditions are based on this. In Scotland, gowk stanes (cuckoo stones) sometimes associated with the arrival of the first cuckoo of spring. "Gowk" is an old name for the common cuckoo in northern England, derived from the harsh repeated "gowk" call the bird makes when excited. The well-known cuckoo clock features a mechanical bird and is fitted with bellows and pipes that imitate the call of the common cuckoo. Cuckoos feature in traditional rhymes, such as '"In April the cuckoo comes, In May she'll stay, In June she changes her tune, In July she prepares to fly, Come August, go she must,"' quoted Peggy. 'But you haven't said it all,' put in Bobby. '"And if the cuckoo stays till September, It's as much as the oldest man can remember."'
"On Hearing the First Cuckoo in Spring" is a symphonic poem from Norway composed for orchestra by Frederick Delius.
Two English folk songs feature cuckoos. One usually called "The Cuckoo" starts:
The cuckoo is a fine bird and she sings as she flies,
She brings us good tidings, she tells us no lies.
She sucks little birds' eggs to make her voice clear,
And never sings cuckoo till the summer draws near
The second, "The Cuckoo's Nest" is a song about a courtship, with the eponymous (and of course, non-existent) nest serving as a metaphor for the vulva and its tangled "nest" of pubic hair.
Some like a girl who is pretty in the face
and some like a girl who is slender in the waist
But give me a girl who will wriggle and will twist
At the bottom of the belly lies the cuckoo's nest...
...Me darling, says she, I can do no such thing
For me mother often told me it was committing sin
Me maidenhead to lose and me sex to be abused
So have no more to do with me cuckoo's nest
One of the tales of the Wise Men of Gotham tells how they built a hedge round a tree in order to trap a cuckoo so that it would always be summer.
The theme music for film comedians Laurel and Hardy, titled "Dance of The Cuckoos" and composed by Marvin Hatley, was based on the call of the common cuckoo.


Senostoma

Senostoma is a genus of parasitoid tachinid flies in the family Tachinidae. Endemic to Australasia, the flies are medium-sized, bristly, and long-legged.
Taxonomy.
French entomologist Pierre-Justin-Marie Macquart first described the genus in 1847 in the work "Diptères Exotiques, Nouveaux Ou Peu Connus, Supplément I", published in "Memoires de la Societe royale des sciences, de l'agriculture et des arts, de Lille". Macquart stated that "Senostoma" signifies "narrow mouth".
At various times the name has been used generically, and misapplied to "Prodiaphania" and "Microrutilia". "Senostoma" is classified in the subfamily Dexiinae; some older texts use the synonym Proseninae.
The genus comprises four species-groups, "punctipenne", "rubricarinaturn", "longipes", and "hirsutilunula".
There are approximately 10,000 species described within Tachinidae, and the geographic range and diversity of the species and difficulties encountered in classification means the count is probably thousands more. The monophyletic features that support Tachinidae classification are subtle, and detailed information on most genera and species is sparse. "Senostoma" is one such genus that lacks extensive research, with most studies having focussed only on a few of its 29 identified species.
Distribution and habitat.
As a member of the subfamily Dexiinae, "Senostoma" flies are endemic to the Australasian region. More specifically, the flies inhabit the Australian mainland and Tasmania, with two species present in New Caledonia and none in New Zealand. In Australia, members of the genus are non-existent in Cape York Peninsula and the Northern Territory. Some species are particularly narrow in distribution; "S. basale" inhabits only the Gondwana Rainforests, while "S. hirticauda" and "S. simulcercus" are limited to Barrington Tops and Tamborine Mountain, respectively.
"Senostoma" can be found in a variety of habitats in the Australian region, but most species appear to prefer dry eucalypt forest at elevations above 600 metres. Adults are attracted to flowers and feed on their nectar, contributing to pollination, with "Leptospermum" being favoured by some species. As well as resting on "Eucalyptus" tree trunks and the surrounding substrate at hill-topping sites, the flies are observable elsewhere feeding on flowers and resting on rocks and vegetation.
Parasitism.
As with all known Tachinidae, "Senostoma" are parasitoids. The larvae develop inside a host, as intercellular endoparasites, consuming and killing the host in the process. For "Senostoma", these hosts are exclusively beetles, most usually Scarabaeidae in the larval stage. In some cases, the host may survive the attack.
The eggs are laid containing mature first instars, the female having incubated the eggs within her reproductive system until ready to hatch, a mode of reproduction known as ovolarviparity, more generally known as ovoviviparity. Deposition usually occurs on the ground and the eggs may hatch within seconds or a few minutes of being laid, whereupon the larvae hunt for a host beetle by burrowing into the soil. Other tachinids lay eggs directly onto potential hosts or food plants and therefore enjoy a higher success rate of infection; the number of eggs produced by "Senostoma" females is consequently higher than for some other genera, numbering somewhere between 1000 and 3000.
The labrum of the larval mouthparts is sharp and functions as a cutting device, with which they penetrate the integument of the selected host, possibly helped by enzymes in their saliva. Once established inside the hosts, the larvae feed on them, passing through second and third instars before pupation occurs. Larval development for tachinids may take between one and three weeks to complete, and the death of the host does not usually occur until the final stage, when the fly is ready to emerge for pupation. As such, "Senostoma" are considered koinobiont parasitoids, as they co-exist with a living, functional host during development and avoid feeding on vital organs or other critical tissues until it is necessary for their continued growth.
Morphology.
Adult members of the genus have bristly bodies and long, thin legs. Their size is generally in the range of 10 to 12 mm, making them medium-sized within the family, as measurements for tachinids span from 2 mm to 20 mm. Mouthparts are distinctively elongated and narrow. Limited information suggests that "Senostoma" colourings are usually at the nondescript end of tachinid fly variation, with at least a few species being light grey and brown.
Along with other genera, "Senostoma" flies possess two morphological features that support their inclusion in the family Tachinidiae. As larvae in the first instar, the labrum is attached to the cephalopharyngeal sclerites (the skeleton of the larval anterior digestive system), and as adults, the postscutellum is well-developed.
Behaviour.
A few species, "S. longipes", "S. pallidihirturn", and "S. tessellaturn", have been noted to exhibit behaviour strongly suggestive of hill-topping, with males maintaining downward-facing positions on trunks of "Eucalyptus" trees, at elevations above 900 metres. This behaviour is likely to be applicable to other species within the genus. Each species studied appeared to prefer certain times of day for hill-topping and selected their positions on tree trunks based on bark smoothness or roughness, degree of illumination by sunlight, and distance from the ground. Males are competitive for these positions and can be observed engaging with each other aggressively, approaching each other for face-offs, spiral flights, and simulated copulation. While males congregating at altitude were in abundance, females were infrequently spotted at hill-topping sites, and when present, did not exhibit any territorial behaviour and preferred locations near the substrate. Female absence may be due to females only visiting the congregation sites when ready to mate. Although the behaviour of males and females at elevation are considered to be for mating purposes, direct evidence of this is lacking and little is known of their courtship and mating rituals.


Potato yellow vein virus

The Potato yellow vein virus (PYVV) is a plant pathogen of the "Closteroviridae" family. It is a whitefly-transmitted closterovirus vectored by "Trialeurodes vaporariorum", which is known to cause a yellowing disease in potato crops in South America.
PYVV RNA have a conserved 3'-terminal secondary structure, which includes a pseudoknot.


Alphavirus

Alphavirus is a genus of RNA viruses, the sole genus in the "Togaviridae" family. Alphaviruses belong to group IV of the Baltimore classification of viruses, with a positive-sense, single-stranded RNA genome. There are 32 alphaviruses, which infect various vertebrates such as humans, rodents, fish, birds, and larger mammals such as horses, as well as invertebrates. Alphaviruses that could infect both vertebrates and arthropods are referred dual-host alphaviruses, while insect-specific alphaviruses such as Eilat virus and Yada yada virus are restricted to their competent arthropod vector. Transmission between species and individuals occurs mainly via mosquitoes, making the alphaviruses a member of the collection of arboviruses – or arthropod-borne viruses. Alphavirus particles are enveloped, have a 70 nm diameter, tend to be spherical (although slightly pleomorphic), and have a 40 nm isometric nucleocapsid.
Genome.
The alphaviruses are small, spherical, enveloped viruses with a genome of a single strand of positive-sense RNA. The total genome length ranges between 11,000 and 12,000 nucleotides, and has a 5’ cap and a 3’ poly-A tail. The four non-structural protein genes are encoded in the 5′ two-thirds of the genome, while the three structural proteins are translated from a subgenomic mRNA colinear with the 3′ one-third of the genome.
There are two open reading frames (ORFs) in the genome, nonstructural and structural. The first is non-structural and encodes proteins (nsP1–nsP4) necessary for transcription and replication of viral RNA. The second encodes three structural proteins: the core nucleocapsid protein C, and the envelope proteins P62 and E1, which associate as a heterodimer. The viral membrane-anchored surface glycoproteins are responsible for receptor recognition and entry into target cells through membrane fusion.
Structural proteins.
The proteolytic maturation of P62 into E2 and E3 causes a change in the viral surface. Together the E1, E2, and sometimes E3, glycoprotein "spikes" form an E1/E2 dimer or an E1/E2/E3 trimer, where E2 extends from the centre to the vertices, E1 fills the space between the vertices, and E3, if present, is at the distal end of the spike. Upon exposure of the virus to the acidity of the endosome, E1 dissociates from E2 to form an E1 homotrimer, which is necessary for the fusion step to drive the cellular and viral membranes together. The alphaviral glycoprotein E1 is a class II viral fusion protein, which is structurally different from the class I fusion proteins found in influenza virus and HIV. The structure of the Semliki Forest virus revealed a structure that is similar to that of flaviviral glycoprotein E, with three structural domains in the same primary sequence arrangement. The E2 glycoprotein functions to interact with the nucleocapsid through its cytoplasmic domain, while its ectodomain is responsible for binding a cellular receptor. Most alphaviruses lose the peripheral protein E3, but in Semliki viruses it remains associated with the viral surface.
Nonstructural proteins.
Four nonstructural proteins (nsP1–4) which are produced as a single polyprotein constitute the virus' replication machinery. The processing of the polyprotein occurs in a highly regulated manner, with cleavage at the P2/3 junction influencing RNA template use during genome replication. This site is located at the base of a narrow cleft and is not readily accessible. Once cleaved nsP3 creates a ring structure that encircles nsP2. These two proteins have an extensive interface.
Mutations in nsP2 that produce noncytopathic viruses or a temperature sensitive phenotypes cluster at the P2/P3 interface region. P3 mutations opposite the location of the nsP2 noncytopathic mutations prevent efficient cleavage of P2/3. This in turn affects RNA infectivity altering viral RNA production levels.
Virology.
The virus has a 60–70 nanometer diameter. It is enveloped, spherical and has a positive-strand RNA genome of ~12 kilobases. The genome encodes two polyproteins. The first polyprotein consists of four non-structural units: in order from the N terminal to the C terminal - nsP1, nsP2, nsP3, and nsP4. The second is a structural polyprotein composed of five expression units: from the N terminal to the C terminal - Capsid, E3, E2, 6K and E1. A sub genomic positive strand RNA - the 26S RNA - is replicated from a negative-stranded RNA intermediate. This serves as template for the synthesis of viral structural proteins. Most alphaviruses have conserved domains involved in regulation of viral RNA synthesis.
The nucleocapsid, 40 nanometers in diameter, contains 240 copies of the capsid protein and has a T = 4 icosahedral symmetry. The E1 and E2 viral glycoproteins are embedded in the lipid bilayer. Single E1 and E2 molecules associate to form heterodimers. The E1–E2 heterodimers form one-to-one contacts between the E2 protein and the nucleocapsid monomers. The E1 and E2 proteins mediate contact between the virus and the host cell.
Several receptors have been identified. These include prohibitin, phosphatidylserine, glycosaminoglycans and ATP synthase β subunit.
Replication occurs within the cytoplasm and virions mature by budding through the plasma membrane, where virus-encoded surface glycoproteins E2 and E1 are assimilated.
These two glycoproteins are the targets of numerous serologic reactions and tests including neutralization and hemagglutination inhibition. The alphaviruses show various degrees of antigenic cross-reactivity in these reactions and this forms the basis for the seven antigenic complexes, 32 species and many subtypes and varieties. The E2 protein is the site of most neutralizing epitopes, while the E1 protein contains more conserved, cross-reactive epitopes.
Evolution.
A study of this taxon suggests that this group of viruses had a marine origin—specifically the Southern Ocean—and that they have subsequently spread to both the Old and New World.
There are three subgroups in this genus: the Semliki Forest virus subgroup (Semliki Forest, O'nyong-nyong and Ross River viruses); the eastern equine encephalitis virus subgroup (eastern equine encephalitis and Venezuelan equine encephalitis viruses) and the Sindbis virus subgroup. Sindbis virus, geographically restricted to the Old World, is more closely related to the eastern equine encephalitis subgroup, which are New World viruses, than it is to the Semliki Forest virus subgroup which is also found in the Old World.
Taxonomy.
The following species are assigned to the genus:
The seven complexes are:
Notes.
Barmah Forest virus is related to the Semliki Forest virus. Middelburg virus, although classified as a separate complex, may be a member of the Semliki Forest virus group.
It seems likely that the genus evolved in the Old World from an insect-borne plant virus.
Sindbis virus may have originated in South America. The equine encephalitis viruses and the Sindbis virus are related.
The Old World and New World viruses appears to have diverged between 2000 and 3000 years ago. Divergence between the Venezuelan equine encephalitis virus and the eastern equine virus appears to have been ~1400 years ago.
The fish infecting clade appears to be basal to the other species.
The southern elephant seal virus appears to be related to the Sinbis clade.
Pathogenesis and immune response.
There are many alphaviruses distributed around the world with the ability to cause human disease. Infectious arthritis, encephalitis, rashes and fever are the most commonly observed symptoms. Larger mammals such as humans and horses are usually dead-end hosts or play a minor role in viral transmission; however, in the case of Venezuelan equine encephalitis the virus is mainly amplified in horses. In most other cases the virus is maintained in nature in mosquitoes, rodents and birds.
Terrestrial alphavirus infections are spread by insect vectors such as mosquitoes. Once a human is bitten by the infected mosquito, the virus can gain entry into the bloodstream, causing viremia. The alphavirus can also get into the CNS where it is able to grow and multiply within the neurones. This can lead to encephalitis, which can be fatal.
When an individual is infected with this particular virus, its immune system can play a role in clearing away the virus particles. Alphaviruses are able to cause the production of interferons. Antibodies and T cells are also involved. The neutralizing antibodies also play an important role to prevent further infection and spread.
Diagnosis, prevention, and control.
Diagnoses is based on clinical samples from which the virus can be easily isolated and identified. There are no alphavirus vaccines currently available. Vector control with repellents, protective clothing, breeding site destruction, and spraying are the preventive measures of choice.
Research.
Alphaviruses are of interest to gene therapy researchers, in particular the Ross River virus, Sindbis virus, Semliki Forest virus, and Venezuelan equine encephalitis virus have all been used to develop viral vectors for gene delivery. Of particular interest are the chimeric viruses that may be formed with alphaviral envelopes and retroviral capsids. Such chimeras are termed pseudotyped viruses. Alphaviral envelope pseudotypes of retroviruses or lentiviruses are able to integrate the genes that they carry into the expansive range of potential host cells that are recognized and infected by the alphaviral envelope proteins E2 and E1. The stable integration of viral genes is mediated by the retroviral interiors of these vectors. There are limitations to the use of alphaviruses in the field of gene therapy due to their lack of targeting, however, through the introduction of variable antibody domains in a non-conserved loop in the structure of E2, specific populations of cells have been targeted. Furthermore, the use of whole alphaviruses for gene therapy is of limited efficacy both because several internal alphaviral proteins are involved in the induction of apoptosis upon infection and also because the alphaviral capsid mediates only the transient introduction of mRNA into host cells. Neither of these limitations extend to alphaviral envelope pseudotypes of retroviruses or lentiviruses. However, the expression of Sindbis virus envelopes may lead to apoptosis, and their introduction into host cells upon infection by Sindbis virus envelope pseudotyped retroviruses may also lead to cell death. The toxicity of Sindbis viral envelopes may be the cause of the very low production titers realized from packaging cells constructed to produce Sindbis pseudotypes. Another branch of research involving alphaviruses is in vaccination. Alphaviruses are apt to be engineered to create replicon vectors which efficiently induce humoral and T-cell immune responses. They could therefore be used to vaccinate against viral, bacterial, protozoan, and tumor antigens.
History.
Initially, the "Togaviridae" family included what are now called the" Flaviviruses", within the "Alphavirus" genus. The flaviviruses were formed into their own family when sufficient differences with the alphaviruses were noted due to the development of sequencing. Rubella virus was formerly included in the family "Togaviridae" in its own genus "Rubivirus", but is now classified in its own family "Matonaviridae". Alphavirus is now the sole genus in the family.


Corynebacterium glutamicum

Corynebacterium glutamicum (previously known as Micrococcus glutamicus) is a Gram-positive, rod-shaped bacterium that is used industrially for large-scale production of amino acids. While originally identified in a screen for organisms secreting L-glutamate, mutants of "C. glutamicum" have also been identified that produce various other amino acids.
Due to its industrial importance, several clones of "C. glutamicum" have been sequenced by both industry and academic groups. Furthermore, small RNA data was obtained by RNA-Seq in "C. glutamicum ATCC 13032."
Synonyms.
"Corynebacterium glutamicum" ATCC 14067 was previously known as "".


Otroeda nerina

Otroeda nerina is a species of moth in the tussock-moth subfamily Lymantriinae. It was first described by Dru Drury in 1782 from Sierra Leone, and is also found in Cameroon, DR Congo, Gabon, Ghana and Nigeria.
Description.
Upperside. Antennae strongly pectinated and brown. Head brown, the front being white. Thorax brown, with two white streaks along it. Abdomen brown. Wings black, streaked with light brown from the shoulders along the tendons, and two light yellowish patches, almost crossing the wings from the anterior edges, with a row of white spots placed along the external edges. Posterior wings dark yellow, with a deep black border running along the external edges from the upper to the abdominal corners.
Underside. Palpi black. Mouth white. Neck and breast yellow. Legs brown, and yellow at top, and white beneath. Abdomen white, streaked longitudinally with brown. Anus yellow. Wings coloured as on the upperside, but brighter. Margins of all the wings entire. Wingspan inches (88 mm).


Acaulospora elegans

Acaulospora elegans is a species of fungi in the family Acaulosporaceae. It forms arbuscular mycorrhiza and vesicles in roots.