Suillus luteus

Suillus luteus is a bolete fungus, and the type species of the genus "Suillus". A common fungus native to Eurasia, from the British Isles to Korea, it has been introduced widely elsewhere, including North and South America, southern Africa, Australia and New Zealand. Commonly referred to as slippery jack or sticky bun in English-speaking countries, its names refer to the brown cap, which is characteristically slimy in wet conditions. The fungus, initially described as "Boletus luteus" by Carl Linnaeus in 1753, is now classified in a different family as well as genus. "Suillus luteus" is edible, though not as highly regarded as other bolete mushrooms, and is commonly prepared and eaten in soups, stews or fried dishes. The slime coating, however, may cause indigestion if not removed before eating.
The fungus grows in coniferous forests in its native range, and pine plantations in countries where it has become naturalized. It forms symbiotic ectomycorrhizal associations with living trees by enveloping the tree's underground roots with sheaths of fungal tissue. The fungus produces spore-bearing fruit bodies, often in large numbers, above ground in summer and autumn. The fruit body cap often has a distinctive conical shape before flattening with age, reaching up to in diameter. Like other boletes, it has tubes extending downward from the underside of the cap, rather than gills; spores escape at maturity through the tube openings, or pores. The pore surface is yellow, and covered by a membranous partial veil when young. The pale stipe, or stem, measures up to 10 cm (4 in) tall and thick and bears small dots near the top. Unlike most other boletes, it bears a distinctive membranous ring that is tinged brown to violet on the underside.
Taxonomy and naming.
The slippery jack was one of the many species first described in 1753 by the "father of taxonomy" Carl Linnaeus, who, in the second volume of his "Species Plantarum", gave it the name "Boletus luteus". The specific epithet is the Latin adjective "lūtěus", meaning "yellow". The fungus was reclassified as (and became the type species of) the genus "Suillus" by French naturalist Henri François Anne de Roussel in 1796. "Suillus" is an ancient term for fungi, and is derived from "swine". In addition to the British Mycological Society approved name "slippery jack", other common names for this bolete include "pine boletus" and "sticky bun"—the latter referring to its resemblance to the pastry.
German naturalist August Batsch described "Boletus volvatus" (the specific epithet derived from the Latin "volva", meaning "sheath", "covering" or "womb") alongside "B. luteus" in his 1783 work "Elenchus Fungorum". Batsch placed both of these species, along with "B. bovinus" and the now obsolete names "Boletus mutabilis" and "B. canus", in a grouping of similar boletes he called "subordo Suilli". "Boletus volvatus" is now considered a synonym of "Suillus luteus". Several authors have placed the slippery jack in other genera: Finnish mycologist Petter Karsten classified it as "Cricunopus luteus" in 1881—the genus "Cricinopus" defined by yellow adnate tubes; Lucien Quélet classified it as "Viscipellis luteus" in 1886, and "Ixocomus luteus" in 1888; and Paul Christoph Hennings placed it in the section "Cricinopus" of the genus "Boletopsis" in 1900.
In works published before 1987, the slippery jack was written fully as , as the description by Linnaeus had been name sanctioned in 1821 by the "father of mycology", Swedish naturalist Elias Magnus Fries. The starting date for all the mycota had been set by general agreement as 1 January 1821, the date of Fries's work. Furthermore, as Roussel's description of "Suillus" predated this as well, the authority for the genus was assigned to British botanist Samuel Frederick Gray in the first volume of his 1821 work "A Natural Arrangement of British Plants". The 1987 edition of the International Code of Botanical Nomenclature changed the rules on the starting date and primary work for names of fungi, and names can now be considered valid as far back as 1 May 1753, the date of publication of Linnaeus's work. In 1986, a collection of fruit bodies from Sweden was designated as the neotype of "Suillus luteus".
In their 1964 monograph on North American "Suillus" species, Alexander H. Smith and Harry Delbert Thiers classified "S. luteus" in the series "Suilli" of the section "Suillus" in genus "Suillus". This group is characterized by the presence of either a ring on the stipe, a partial veil adhering to the cap margin, or a "false veil" not attached to the stipe but initially covering the tube cavity. Species closely related to "Suillus luteus" include "S. pseudobrevipes" (a sister species), "S. brevipes" and "S. weaverae" (formerly "Fuscoboletinus weaverae"). A genetic study of nucleotide DNA reinforced the species' monophyly and low genetic divergence, with material of "S. luteus" from the United Kingdom, Austria, Germany and North America forming a clade, in contrast with some other species, such as "S. granulatus", which were shown to be polyphyletic.
Chemical analysis of pigments and chromogens showed that "Suillus" was more closely related to "Gomphidius" and "Rhizopogon" than to other boletes, and hence "Suillus luteus" and its allies were transferred from the Boletaceae to the newly circumscribed family Suillaceae in 1997. Molecular studies have reinforced how distantly related these fungi are from "Boletus edulis" and its allies.
Description.
The cap is chestnut, rusty, olive brown, or dark brown in color and generally 4–10 cm (rarely to 20 cm) in diameter at maturity. The cap has a distinctive conical shape, later flattening out. It is slimy to the touch, bare, smooth, and glossy even when dry, and the cuticle is easily peeled off. The tiny, circular pores of the tubes are initially yellow but turn olive to dark yellow with maturity. Like the skin of the cap, they can be readily peeled away from the flesh.
Tubes comprising the hymenophore on the underside of the cap are deep, with an attachment to the stipe ranging from adnate to somewhat decurrent. The pores are tiny, numbering 3 per mm in young specimens and 1–2 per mm in maturity. The stipe is tall and wide. It is pale yellow and more or less cylindrical but may bear a swollen base. A membranous partial veil initially links the stipe with the edge of the cap. When it ruptures, it forms a membranous, hanging ring. The top side of the ring is whitish, while the underside is characteristically dark brown to violet. This species is one of the few members of the genus "Suillus" that have such a ring. Above the ring, the stipe features glandular dots—minute clumps of pigmented cells. Below the ring, the stipe is dingy white, sometimes streaked with brownish slime. In humid conditions, the ring has a gelatinous texture. The white flesh of the entire fungus does not discolour when damaged, and is soft—particularly in mature specimens. It has a "pleasant" taste and lacks any distinctive odour.
The spore print is ochre or clay coloured, the elongated elliptical spores measuring 7–10 by 3–3.5 μm. Basidia (spore-producing cells) are four spored, with dimensions of 14–18 by 4–5 μm. Cystidia are present on both the tube faces (pleurocystidia) and edges (cheilocystidia), either scattered or, more rarely, as bundles. They measure 20–35 by 5–7 μm and have a narrow club shape. Clamp connections are not present in the hyphae of "S. luteus".
Similar species.
Good field characteristics for "Suillus luteus" include the slimy brown cap, glandular dots on the upper stipe, and prominent purplish ring. A frequent lookalike is "Suillus granulatus", which is another common, widely distributed and edible species occurring in the same habitat. "Suillus granulatus" is yellow fleshed and exudes latex droplets when young, but most conspicuously bears neither a partial veil nor a ring. Other than that, "Suillus luteus" is unlikely to be confused with other mushrooms, especially if its preferred habitat under pine trees and the whitish partial veil are considered. In Europe, the related "Suillus grevillei" is found under larch and has a yellow cap, while immature fruit bodies of "Gomphidius glutinosus" may look comparable from above but have gills rather than pores underneath. In North America, "Suillus borealis" and "S. pseudobrevipes" also have partial veils, but lack the distinctive ring of "S. luteus". "S. cothurnatus" forms a band-like ring on the stipe that tends to be brownish rather than purplish.
In some specimens of "S. luteus", the partial veil separates from the stipe (rather than the cap margin), leaving cottony patches of veil hanging from the cap margin. In this state, fruit bodies can be confused with those of "S. albidipes". Unlike "S. luteus", however, "S. albidipes" does not have glandular dots on its stipe.
Distribution and habitat.
"Suillus luteus" can be found all over the Northern Hemisphere. Native to Eurasia, it is widespread across the British Isles. To the east it has been recorded from Pakistan, where it was found along canals in Dashkin in the district of Astore, and as far east as South Korea. It has also been widely introduced elsewhere by way of pine plantations around the globe. It is very commonly found in Monterey pine ("Pinus radiata") plantations, despite the tree being native to California and hence not in the fungus' native range. In North America it is found in the northeast, the Pacific Northwest and the southwestern United States. According to Ernst Both, it was Charles Horton Peck who first suggested in 1887 that the fungus was introduced to New York State on "Pinus sylvestris". DNA studies show that the North American populations differ little genetically from European populations, supporting the idea that the fungus arrived to North America relatively recently as a result of human activity. "Suillus luteus" is found in coastal and mountainous pine forests and exhibits a tolerance of the northern latitudes. Southern Hemisphere locales where the slippery jack grow with plantation pines include South America, Africa, Australia, and New Zealand. In southwestern Australia, the bolete is limited to areas of greater than 1000 mm (40 in) annual rainfall. It has been recorded as far north as the Darling Downs and southern Queensland, and occasionally in Tasmania. The fungus fruits in spring, summer and fairly prolifically in autumn, following periods of wet weather. Mushrooms can appear in large troops or fairy rings.
In Ecuador, "Pinus radiata" plantations were planted extensively around Cotopaxi National Park, and "Suillus luteus" boletes appear in abundance year-round. A 1985 field study estimated production to be 3000–6000 mushrooms per hectare—up to (dry weight) of mushrooms hectare per year. This continuous production contrasts with the bolete's seasonal appearance elsewhere. The fungus is not found in adjacent areas of native vegetation. The fruiting is so bountiful that the harvest of slippery jacks has become the main reason that pine plantations are established or maintained in parts of Ecuador. In southern Brazil, it has been recorded in plantations of slash pine ("P. elliottii") in the municipalities of Pelotas, Nova Petrópolis and Canela in Rio Grande do Sul, and Colombo in Paraná. It is particularly common in plantations in Patagonia. "Suillus luteus" is the commonest bolete encountered in the Falkland Islands, where it is found in windbreaks and gardens.
In South Africa, "Suillus luteus" has been occasionally recorded under pines in Bloemfontein, Johannesburg and Royal Natal National Park.
Ecology.
"Suillus luteus" is a pioneer species that typically establishes itself in the early stages of forest succession. The fungus forms mycorrhizal associations with various species of pine, including Scots pine ("P. sylvestris"), black pine ("P. nigra"), and Macedonian pine ("P. peuce") in Europe, and red pine ("P. resinosa") and white pine ("P. strobus") in North America. An "in vitro" experiment demonstrated that the species could form an ectomycorrhizal association with Aleppo pine ("P. halepensis"), a key species used in reforestation in the Mediterranean. A study of the ectomycorrhizal fungi associated with a lodgepole pine ("P. contorta") invasion front near Coyhaique, Chile, showed that many invasive trees were supported by "S. luteus" as the sole mycorrhizal partner.
The ectomycorrhizae formed between the fungus and host plant can be influenced by soil microorganisms present in the mycorrhizosphere. For example, soil bacteria from the genera "Paenibacillus" and "Burkholderia" alter the branching structure of the root, whereas "Bacillus" species increase root growth and mycorrhizal colonization. The fungus does not require a specific soil but seems to prefer acidic and nutrient-deficient soil. "Suillus luteus" produces hydroxamic acid-based siderophores, which are compounds that can chelate iron and extract it from the soil in nutrient-poor conditions. Ignacio Chapela and colleagues analysed the carbon uptake of "S. luteus" in Ecuador, concluding pine plantations accompanied by "S. luteus" deplete carbon stored in the soil and raising concerns that these might not be a remedy for rising carbon dioxide levels in the atmosphere.
The fungus has been shown to provide a protective effect against heavy metal toxicity when associated with the host "Pinus sylvestris", preventing copper accumulation in the needles, and protecting seedlings against cadmium toxicity. Owing to its frequent rate of sexual reproduction and the resulting extensive gene flow within populations, the fungus can rapidly evolve a trait to tolerate otherwise toxic levels of heavy metals in the environment. The genetic basis of this adaptation—intriguing to researchers investigating the bioremediation potential of metal-adapted plants and their fungal associates—are contained in the genome sequence of "S. luteus", published in 2015.
"Suillus luteus" fruit bodies are sometimes infested with larvae, though not nearly as often as "S. granulatus" or "B. edulis". Damage from maggots is much more common in warmer months, and rare late in the season with cooler weather. In a Finnish study, researchers found that 70–95% of fruit bodies collected from typical forest habitats were infested with larvae; the most common species were the flies "Mycetophila fungorum", "Pegomya deprimata", and "Pegohylemyia silvatica". In contrast, other studies have shown that fruit bodies collected from pine plantations are relatively free of larvae. The fungus produces microscopic crystals of oxalic acid at the surface of its hyphae, a feature that is thought to help deter grazing by the springtail species "Folsomia candida".
Edibility.
"Suillus luteus" is an edible mushroom, but the slime/pileipellis must be removed. Although some authors regard it as one of low quality, and generally inferior to co-occurring species such as "Boletus pinophilus", the species is considered a delicacy in Slavic cultures (known as "maslyata" in Russian or "maślaki" in Polish, deriving from words meaning "buttery"). It was highly regarded in Calabria, even more than "Boletus edulis", until the 1940s when increased interest in the latter species eclipsed the former. Mushrooms conforming to "Suillus luteus" are exported from Chile to Italy, and, since the 1970s, the United States. As of 2002, harvesters in Chile were paid on average US$0.5 per kilogram of fruit bodies.
In Burundi, "Suillus luteus" mushrooms are sold to Europeans as "cepes" in Bujumbura but not generally eaten by the Barundi. Based on samples collected from Chile, the boletes contain (as a percentage of dry weight) 20% protein, 57% carbohydrates, 6% fat, and 6% ash. "Pinus radiata" plantations in southeastern Australia have become tourist attractions as people flock to them in autumn to pick slippery jacks and saffron milk-caps ("Lactarius deliciosus"); Belanglo State Forest in particular has attracted large numbers of Polish foragers.
Slippery jacks do not keep for long after picking, nor are they suitable for drying, as their water content is too high. They are suited for frying, or cooking in stews and soups, either alone or with other mushroom species. Puréeing the mushroom is not recommended, however: "We once made the mistake of running it through a blender to make a soup. The result was a substance recommending itself for use when hanging wallpaper." "S. luteus" and other "Suillus" species may cause allergic reactions in some people or digestive problems that appear to result from consuming the slimy skin. The fungus is better cooked before eating, and some authors recommend discarding the glutinous cuticle and tubes before cooking. Moreover, the skin can spoil other fungi with which slippery jacks are collected.
Inexpensive powdered "S. luteus" fruit bodies are sometimes added to the more expensive "B. edulis" mushroom soup powder, a fraudulent practice that is difficult to detect with microscopy because the tissues are no longer intact. This adulteration can be determined chemically, however, by testing for increased levels of the sugar alcohols arabitol and mannitol. The practice can also be determined with a DNA-based method that is sensitive enough to detect the addition of 1–2% of "S. luteus" to "B. edulis" powder.


Kimberly (Catscratch)


Secretion

Secretion is the movement of material from one point to another, such as a secreted chemical substance from a cell or gland. In contrast, excretion, is the removal of certain substances or waste products from a cell or organism. The classical mechanism of cell secretion is via secretory portals at the cell plasma membrane called porosomes. Porosomes are permanent cup-shaped lipoprotein structure at the cell plasma membrane, where secretory vesicles transiently dock and fuse to release intra-vesicular contents from the cell.
Secretion in bacterial species means the transport or translocation of effector molecules for example: proteins, enzymes or toxins (such as cholera toxin in pathogenic bacteria for example "Vibrio cholerae") from across the interior (cytoplasm or cytosol) of a bacterial cell to its exterior. Secretion is a very important mechanism in bacterial functioning and operation in their natural surrounding environment for adaptation and survival.
In eukaryotic cells.
Mechanism.
Eukaryotic cells, including human cells, have a highly evolved process of secretion. Proteins targeted for the outside are synthesized by ribosomes docked to the rough endoplasmic reticulum (ER). As they are synthesized, these proteins translocate into the ER lumen, where they are glycosylated and where molecular chaperones aid protein folding. Misfolded proteins are usually identified here and retrotranslocated by ER-associated degradation to the cytosol, where they are degraded by a proteasome. The vesicles containing the properly folded proteins then enter the Golgi apparatus.
In the Golgi apparatus, the glycosylation of the proteins is modified and further posttranslational modifications, including cleavage and functionalization, may occur. The proteins are then moved into secretory vesicles which travel along the cytoskeleton to the edge of the cell. More modification can occur in the secretory vesicles (for example insulin is cleaved from proinsulin in the secretory vesicles).
Eventually, there is vesicle fusion with the cell membrane at a structure called the porosome, in a process called exocytosis, dumping its contents out of the cell's environment.
Strict biochemical control is maintained over this sequence by usage of a pH gradient: the pH of the cytosol is 7.4, the ER's pH is 7.0, and the cis-golgi has a pH of 6.5. Secretory vesicles have pHs ranging between 5.0 and 6.0; some secretory vesicles evolve into lysosomes, which have a pH of 4.8.
Nonclassical secretion.
There are many proteins like FGF1 (aFGF), FGF2 (bFGF), interleukin-1 (IL1) etc. which do not have a signal sequence. They do not use the classical ER-Golgi pathway. These are secreted through various nonclassical pathways.
At least four nonclassical (unconventional) protein secretion pathways have been described. They include 1) direct translocation of proteins across the plasma membrane likely through membrane transporters, 2) blebbing, 3) lysosomal secretion, and 4) release via exosomes derived from multivesicular bodies. In addition, proteins can be released from cells by mechanical or physiological wounding and through nonlethal, transient oncotic pores in the plasma membrane induced by washing cells with serum-free media or buffers.
In human tissues.
Many human cell types have the ability to be secretory cells. They have a well-developed endoplasmic reticulum, and Golgi apparatus to fulfill this function. Tissues that produce secretions include the gastrointestinal tract which secretes digestive enzymes and gastric acid, the lungs which secrete surfactants, and sebaceous glands which secrete sebum to lubricate the skin and hair. Meibomian glands in the eyelid secrete meibum to lubricate and protect the eye.
In gram-negative bacteria.
Secretion is not unique to eukaryotes - it is also present in bacteria and archaea as well. ATP binding cassette (ABC) type transporters are common to the three domains of life. Some secreted proteins are translocated across the cytoplasmic membrane by the SecYEG translocon, one of two translocation systems, which requires the presence of an N-terminal signal peptide on the secreted protein. Others are translocated across the cytoplasmic membrane by the twin-arginine translocation pathway (Tat). Gram-negative bacteria have two membranes, thus making secretion topologically more complex. There are at least six specialized secretion systems in gram-negative bacteria. Many secreted proteins are particularly important in bacterial pathogenesis.
Type I secretion system (T1SS or TOSS).
Type I secretion is a chaperone dependent secretion system employing the Hly and Tol gene clusters. The process begins as a leader sequence on the protein to be secreted is recognized by HlyA and binds HlyB on the membrane. This signal sequence is extremely specific for the ABC transporter. The HlyAB complex stimulates HlyD which begins to uncoil and reaches the outer membrane where TolC recognizes a terminal molecule or signal on HlyD. HlyD recruits TolC to the inner membrane and HlyA is excreted outside of the outer membrane via a long-tunnel protein channel.
Type I secretion system transports various molecules, from ions, drugs, to proteins of various sizes (20 – 900 kDa). The molecules secreted vary in size from the small "Escherichia coli" peptide colicin V, (10 kDa) to the "Pseudomonas fluorescens" cell adhesion protein LapA of 520 kDa. The best characterized are the RTX toxins and the lipases. Type I secretion is also involved in export of non-proteinaceous substrates like cyclic β-glucans and polysaccharides.
Type II secretion system (T2SS).
Proteins secreted through the type II system, or main terminal branch of the general secretory pathway, depend on the Sec or Tat system for initial transport into the periplasm. Once there, they pass through the outer membrane via a multimeric (12–14 subunits) complex of pore forming secretin proteins. In addition to the secretin protein, 10–15 other inner and outer membrane proteins compose the full secretion apparatus, many with as yet unknown function. Gram-negative type IV pili use a modified version of the type II system for their biogenesis, and in some cases certain proteins are shared between a pilus complex and type II system within a single bacterial species.
Type III secretion system (T3SS or TTSS).
It is homologous to the basal body in bacterial flagella. It is like a molecular syringe through which a bacterium (e.g. certain types of "Salmonella", "Shigella", "Yersinia", "Vibrio") can inject proteins into eukaryotic cells. The low Ca2+ concentration in the cytosol opens the gate that regulates T3SS. One such mechanism to detect low calcium concentration has been illustrated by the lcrV (Low Calcium Response) antigen utilized by "Yersinia pestis", which is used to detect low calcium concentrations and elicits T3SS attachment. The Hrp system in plant pathogens inject harpins and pathogen effector proteins through similar mechanisms into plants. This secretion system was first discovered in "Yersinia pestis" and showed that toxins could be injected directly from the bacterial cytoplasm into the cytoplasm of its host's cells rather than simply be secreted into the extracellular medium.
Type IV secretion system (T4SS or TFSS).
It is homologous to conjugation machinery of bacteria, the conjugative pili. It is capable of transporting both DNA and proteins. It was discovered in "Agrobacterium tumefaciens", which uses this system to introduce the T-DNA portion of the Ti plasmid into the plant host, which in turn causes the affected area to develop into a crown gall (tumor). "Helicobacter pylori" uses a type IV secretion system to deliver CagA into gastric epithelial cells, which is associated with gastric carcinogenesis. "Bordetella pertussis", the causative agent of whooping cough, secretes the pertussis toxin partly through the type IV system. "Legionella pneumophila", the causing agent of legionellosis (Legionnaires' disease) utilizes a type IVB secretion system, known as the icm/dot (intracellular multiplication / defect in organelle trafficking genes) system, to translocate numerous effector proteins into its eukaryotic host. The prototypic Type IVA secretion system is the VirB complex of "Agrobacterium tumefaciens".
Protein members of this family are components of the type IV secretion system. They mediate intracellular transfer of macromolecules via a mechanism ancestrally related to that of bacterial conjugation machineries.
Function.
In short, Type IV secretion system (T4SS), is the general mechanism by which bacterial cells secrete or take up macromolecules. Their precise mechanism remains unknown. T4SS is encoded on Gram-negative conjugative elements in bacteria.T4SS are cell envelope-spanning complexes or in other words 11–13 core proteins that form a channel through which DNA and proteins can travel from the cytoplasm of the donor cell to the cytoplasm of the recipient cell. Additionally, T4SS also secrete virulence factor proteins directly into host cells as well as taking up DNA from the medium during natural transformation, which shows the versatility of this macromolecular secretion apparatus.
Structure.
As shown in the above figure, TraC, in particular consists of a three helix bundle and a loose globular appendage.
Interactions.
T4SS has two effector proteins: firstly, ATS-1, which stands for Anaplasma translocated substrate 1, and secondly AnkA, which stands for ankyrin repeat domain-containing protein A. Additionally, T4SS coupling proteins are VirD4, which bind to VirE2.
Type V secretion system (T5SS).
Also called the autotransporter system, type V secretion involves use of the "Sec" system for crossing the inner membrane. Proteins which use this pathway have the capability to form a beta-barrel with their C-terminus which inserts into the outer membrane, allowing the rest of the peptide (the passenger domain) to reach the outside of the cell. Often, autotransporters are cleaved, leaving the beta-barrel domain in the outer membrane and freeing the passenger domain. Some researchers believe remnants of the autotransporters gave rise to the porins which form similar beta-barrel structures. A common example of an autotransporter that uses this secretion system is the Trimeric Autotransporter Adhesins.
Type VI secretion system (T6SS).
Type VI secretion systems were originally identified in 2006 by the group of John Mekalanos at the Harvard Medical School (Boston, USA) in two bacterial pathogens, "Vibrio cholerae" and "Pseudomonas aeruginosa". These were identified when mutations in the Hcp and VrgG genes in "Vibrio Cholerae" led to decreased virulence and pathogenicity. Since then, Type VI secretion systems have been found in a quarter of all proteobacterial genomes, including animal, plant, human pathogens, as well as soil, environmental or marine bacteria. While most of the early studies of Type VI secretion focused on its role in the pathogenesis of higher organisms, more recent studies suggested a broader physiological role in defense against simple eukaryotic predators and its role in inter-bacteria interactions. The Type VI secretion system gene clusters contain from 15 to more than 20 genes, two of which, Hcp and VgrG, have been shown to be nearly universally secreted substrates of the system. Structural analysis of these and other proteins in this system bear a striking resemblance to the tail spike of the T4 phage, and the activity of the system is thought to functionally resemble phage infection.
Release of outer membrane vesicles.
In addition to the use of the multiprotein complexes listed above, Gram-negative bacteria possess another method for release of material: the formation of bacterial outer membrane vesicles. Portions of the outer membrane pinch off, forming nano-scale spherical structures made of a lipopolysaccharide-rich lipid bilayer enclosing periplasmic materials, and are deployed for membrane vesicle trafficking to manipulate environment or invade at host-pathogen interface. Vesicles from a number of bacterial species have been found to contain virulence factors, some have immunomodulatory effects, and some can directly adhere to and intoxicate host cells. release of vesicles has been demonstrated as a general response to stress conditions, the process of loading cargo proteins seems to be selective.
Secretion in gram-positive bacteria.
In some "Staphylococcus" and "Streptococcus" species, the accessory secretory system handles the export of highly repetitive adhesion glycoproteins.


Cell disruption

Cell disruption is a method or process for releasing biological molecules from inside a cell.
Methods.
The production of biologically interesting molecules using cloning and culturing methods allows the study and manufacture of relevant molecules. Except for excreted molecules, cells producing molecules of interest must be disrupted. This page discusses various methods. Another method of disruption is called cell unroofing.
Bead method.
A common laboratory-scale mechanical method for cell disruption uses glass, ceramic or steel beads, 0.1 to 2 mm in diameter, mixed with a sample suspended in aqueous media. First developed by Tim Hopkins in the late 1970s, the sample and bead mix is subjected to high level agitation by stirring or shaking. Beads collide with the cellular sample, cracking open the cell to release intercellular components. Unlike some other methods, mechanical shear is moderate during homogenization resulting in excellent membrane or subcellular preparations. The method, often called "beadbeating", works well for all types of cellular material - from spores to animal and plant tissues. It is the most widely used method of yeast lysis, and can yield breakage of well over 50% (up to 95%). It has the advantage over other mechanical cell disruption methods of being able to disrupt very small sample sizes, process many samples at a time with no cross-contamination concerns, and does not release potentially harmful aerosols in the process.
In the simplest example of the method, an equal volume of beads are added to a cell or tissue suspension in a test tube and the sample is vigorously mixed on a common laboratory vortex mixer. While processing times are slow, taking 3-10 times longer than that in specialty shaking machines, it works well for easily disrupted cells and is inexpensive.
Successful beadbeating is dependent not only design features of the shaking machine (which take into consideration shaking oscillations per minute, shaking throw or distance, shaking orientation and vial orientation), but also the selection of correct bead size (0.1–6 mm diameter), bead composition (glass, ceramic, steel) and bead load in the vial.
In most laboratories, beadbeating is done in batch sizes of one to twenty-four sealed, plastic vials or centrifuge tubes. The sample and tiny beads are agitated at about 2000 oscillations per minute in specially designed reciprocating shakers driven by high power electric motors. Cell disruption is complete in 1–3 minutes of shaking. Significantly faster rates of cell disruption are achieved with a beadbeater variation called SoniBeast. Differing from conventional machines, it agitates the beads using a vortex motion at 20,000 oscl/min. Larger beadbeater machines that hold deep-well microtiter plates also shorten process times, as do Bead Dispensers designed to quickly load beads into multiple vials or microplates. Pre-loaded vials and microplates are also available.
All high energy beadbeating machines warm the sample about 10 degrees/minute. This is due to frictional collisions of the beads during homogenization. Cooling of the sample during or after beadbeating may be necessary to prevent damage to heat-sensitive proteins such as enzymes. Sample warming can be controlled by beadbeating for short time intervals with cooling on ice between each interval, by processing vials in pre-chilled aluminum vial holders or by circulating gaseous coolant through the machine during beadbeating.
A different beadbeater configuration, suitable for larger sample volumes, uses a rotating fluorocarbon rotor inside a 15, 50 or 200 ml chamber to agitate the beads. In this configuration, the chamber can be surrounded by a static cooling jacket. Using this same rotor/chamber configuration, large commercial machines are available to process many liters of cell suspension. Currently, these machines are limited to processing monocellular organisms such as yeast, algae and bacteria.
Cryopulverization.
Samples with a tough extracellular matrix, such as animal connective tissue, some tumor biopsy samples, venous tissue, cartilage, seeds, etc., are reduced to a fine powder by impact pulverization at liquid nitrogen temperatures. This technique, known as cryopulverization, is based on the fact that biological samples containing a significant fraction of water become brittle at extremely cold temperatures. This technique was first described by Smucker and Pfister in 1975, who referred to the technique as cryo-impacting. The authors demonstrated cells are effectively broken by this method, confirming by phase and electron microscopy that breakage planes cross cell walls and cytoplasmic membranes.
The technique can be done by using a mortar and pestle cooled to liquid nitrogen temperatures, but use of this classic apparatus is laborious and sample loss is often a concern. Specialised stainless steel pulverizers generically known as Tissue Pulverizers are also available for this purpose. They require less manual effort, give good sample recovery and are easy to clean between samples.
Advantages of this technique are higher yields of proteins and nucleic acids from small, hard tissue samples - especially when used as a preliminary step to mechanical or chemical/solvent cell disruption methods mentioned above.
High Pressure Cell Disruption.
Since the 1940s high pressure has been used as a method of cell disruption, most notably by the French Pressure Cell Press, or French Press for short. This method was developed by Charles Stacy French and utilises high pressure to force cells through a narrow orifice, causing the cells to lyse due to the shear forces experienced across the pressure differential. While French Presses have become a staple item in many microbiology laboratories, their production has been largely discontinued, leading to a resurgence in alternate applications of similar technology.
Modern physical cell disruptors typically operate via either pneumatic or hydraulic pressure. Although pneumatic machines are typically lower cost, their performance can be unreliable due to variations in the processing pressure throughout the stroke of the air pump. It is generally considered that hydraulic machines offer superior lysing ability, especially when processing harder to break samples such as yeast or Gram-positive bacteria, due to their ability to maintain constant pressure throughout the piston stroke. As the French Press, which is operated by hydraulic pressure, is capable of over 90% lysis of most commonly used cell types it is often taken as the gold standard in lysis performance and modern machines are often compared against it not only in terms of lysis efficiency but also in terms of safety and ease of use. Some manufacturers are also trying to improve on the traditional design by altering properties within these machines other than the pressure driving the sample through the orifice. One such example is Constant Systems, who have recently shown that their Cell Disruptors not only match the performance of a traditional French Press, but also that they are striving towards attaining the same results at a much lower power.
Pressure Cycling Technology ("PCT"). PCT is a patented, enabling technology platform that uses alternating cycles of hydrostatic pressure between ambient and ultra-high levels (up to 90,000 psi) to safely, conveniently and reproducibly control the actions of molecules in biological samples, e.g., the rupture (lysis) of cells and tissues from human, animal, plant, and microbial sources, and the inactivation of pathogens. PCT-enhanced systems (instruments and consumables) address some challenging problems inherent in biological sample preparation. PCT advantages include: (a) extraction and recovery of more membrane proteins, (b) enhanced protein digestion, (c) differential lysis in a mixed sample base, (d) pathogen inactivation, (e) increased DNA detection, and (f) exquisite sample preparation process control.
The Microfluidizer method used for cell disruption strongly influences the physicochemical properties of the lysed cell suspension, such as particle size, viscosity, protein yield and enzyme activity. In recent years the Microfluidizer method has gained popularity in cell disruption due to its ease of use and efficiency at disrupting many different kinds of cells. The Microfluidizer technology was licensed from a company called Arthur D. Little and was first developed and utilized in the 1980s, initially starting as a tool for liposome creation. It has since been used in other applications such as cell disruption nanoemulsions, and solid particle size reduction, among others.
By using microchannels with fixed geometry, and an intensifier pump, high shear rates are generated that rupture the cells. This method of cell lysis can yield breakage of over 90% of E. coli cells.
Many proteins are extremely temperature-sensitive, and in many cases can start to denature at temperatures of only 4 degrees celsius. Within the microchannels, temperatures exceed 4 degrees celsius, but the machine is designed to cool quickly so that the time the cells are exposed to elevated temperatures is extremely short (residence time 25 ms-40 ms). Because of this effective temperature control, the Microfluidizer yields higher levels of active proteins and enzymes than other mechanical methods when the proteins are temperature-sensitive.
Viscosity changes are also often observed when disrupting cells. If the cell suspension viscosity is high, it can make downstream handling—such as filtration and accurate pipetting—quite difficult. The viscosity changes observed with a Microfluidizer are relatively low, and decreases with further additional passes through the machine.
In contrast to other mechanical disruption methods the Microfluidizer breaks the cell membranes efficiently but gently, resulting in relatively large cell wall fragments (450 nm), and thus making it easier to separate the cell contents. This can lead to shorter filtration times and better centrifugation separation.
Microfluidizer technology scales from one milliliter to thousands of liters.
Nitrogen decompression.
For nitrogen decompression, large quantities of nitrogen are first dissolved in the cell under high pressure within a suitable pressure vessel. Then, when the gas pressure is suddenly released, the nitrogen comes out of the solution as expanding bubbles that stretch the membranes of each cell until they rupture and release the contents of the cell.
Nitrogen decompression is more protective of enzymes and organelles than ultrasonic and mechanical homogenizing methods and compares favorably to the controlled disruptive action obtained in a PTFE and glass mortar and pestle homogenizer. While other disruptive methods depend upon friction or a mechanical shearing action that generate heat, the nitrogen decompression procedure is accompanied by an adiabatic expansion that cools the sample instead of heating it.
The blanket of inert nitrogen gas that saturates the cell suspension and the homogenate offers protection against oxidation of cell components. Although other gases: carbon dioxide, nitrous oxide, carbon monoxide and compressed air have been used in this technique, nitrogen is preferred because of its non-reactive nature and because it does not alter the pH of the suspending medium. In addition, nitrogen is preferred because it is generally available at low cost and at pressures suitable for this procedure.
Once released, subcellular substances are not exposed to continued attrition that might denature the sample or produce unwanted damage. There is no need to watch for a peak between enzyme activity and percent disruption. Since nitrogen bubbles are generated within each cell, the same disruptive force is applied uniformly throughout the sample, thus ensuring unusual uniformity in the product. Cell-free homogenates can be produced.
The technique is used to homogenize cells and tissues, release intact organelles, prepare cell membranes, release labile biochemicals, and produce uniform and repeatable homogenates without subjecting the sample to extreme chemical or physical stress.
The method is particularly well suited for treating mammalian and other membrane-bound cells. It has also been used successfully for treating plant cells, for releasing virus from fertilized eggs and for treating fragile bacteria. It is not recommended for untreated bacterial cells. Yeast, fungus, spores and other materials with tough cell walls do not respond well to this method.


Sabellidites

Sabellidites is a genus of annelid from the Ediacaran period. It is among the oldest annelid body fossils.


Velarivirus

Velarivirus is a genus of viruses, in the family "Closteroviridae". Plants serve as natural hosts. There are eight species in this genus. Diseases associated with this genus include: GLRaV-7: symptomless in white-berried grapevine cultivar from Albania. However, it induces leafroll symptoms onto grafted cv. cabernet.
Taxonomy.
The following species are assigned to the genus:
Structure.
Viruses in the genus "Velarivirus" are non-enveloped, with filamentous geometries. These viruses are about 1500-1700 nm long. Genomes are linear, around 16-17kb in length. The genome codes for 10 proteins.
Life cycle.
Viral replication is cytoplasmic. Entry into the host cell is achieved by penetration into the host cell. Replication follows the positive stranded RNA virus replication model. Positive stranded RNA virus transcription is the method of transcription. The virus exits the host cell by tubule-guided viral movement.
Plants serve as the natural host. Transmission routes are mechanical.


Ca. Epixenosoma ejectans


Phenetics

In biology, phenetics ( - to appear) , also known as taximetrics, is an attempt to classify organisms based on overall similarity, usually in morphology or other observable traits, regardless of their phylogeny or evolutionary relation. It is closely related to numerical taxonomy which is concerned with the use of numerical methods for taxonomic classification. Many people contributed to the development of phenetics, but the most influential were Peter Sneath and Robert R. Sokal. Their books are still primary references for this sub-discipline, although now out of print.
Phenetics has largely been superseded by cladistics for research into evolutionary relationships among species. However, certain phenetic methods, such as neighbor-joining, have found their way into phylogenetics, as a reasonable approximation of phylogeny when more advanced methods (such as Bayesian inference) are too computationally expensive.
Phenetic techniques include various forms of clustering and ordination. These are sophisticated ways of reducing the variation displayed by organisms to a manageable level. In practice this means measuring dozens of variables, and then presenting them as two- or three-dimensional graphs. Much of the technical challenge in phenetics revolves around balancing the loss of information in such a reduction against the ease of interpreting the resulting graphs.
The method can be traced back to 1763 and Michel Adanson (in his "Familles des plantes") because of two shared basic principles — overall similarity and equal weighting — and modern pheneticists are sometimes called "neo-Adansonian"s.
Difference from cladistics.
Phenetic analyses are unrooted, that is, they do not distinguish between plesiomorphies, traits that are inherited from an ancestor, and apomorphies, traits that evolved anew in one or several lineages. A common problem with phenetic analysis is that basal evolutionary grades, which retain many plesiomorphies compared to more advanced lineages, appear to be monophyletic. Phenetic analyses are also liable to be misled by convergent evolution and adaptive radiation. Cladistic methods have attempted to solve those problems.
Consider for example songbirds. These can be divided into two groups – Corvida, which retains ancient characters in phenotype and genotype, and Passerida, which has more modern traits. But only the latter are a group of closest relatives; the former are numerous independent and ancient lineages which are about as distantly related to each other as each single one of them is to the Passerida. In a phenetic analysis, the large degree of overall similarity found among the Corvida will make them appear to be monophyletic too, but their shared traits were present in the ancestors of "all" songbirds already. It is the loss of these ancestral traits rather than their presence that signifies which songbirds are more closely related to each other than to other songbirds. However, the requirement that taxa be monophyletic – rather than paraphyletic as in the case of the Corvida – is itself part of the cladistic view of Taxonomy, not necessarily followed to an absolute degree by other schools.
The two methodologies are not mutually exclusive. There is no reason why, e.g., species identified using phenetics cannot subsequently be subjected to cladistic analysis, to determine their evolutionary relationships. Phenetic methods can also be superior to cladistics when only the "distinctness" of related taxa is important, as the computational requirements are lower.
The history of pheneticism and cladism as rival taxonomic systems is analysed in David Hull's 1988 book "Science as a Process".
Today.
Traditionally there was a great deal of heated debate between pheneticists and cladists, as both methods were initially proposed to resolve evolutionary relationships. Perhaps the "high-water mark" of phenetics were the DNA-DNA hybridization studies by Charles G. Sibley, Jon E. Ahlquist and Burt L. Monroe Jr., from which resulted the 1990 Sibley-Ahlquist taxonomy for birds. Highly controversial at its time, some of its findings (e.g. the Galloanserae) have been vindicated, while others (e.g. the all-inclusive "Ciconiiformes" or the "Corvida") have been rejected. However, with computers growing increasingly powerful and widespread, more refined cladistic algorithms became available and could put the suggestions of Willi Hennig to the test. The results of cladistic analyses turned out to be superior to those of phenetic methods – at least when it came to resolving phylogenies.
Many systematists continue to use phenetic methods, particularly in addressing species-level questions. While a major goal of taxonomy remains describing the 'tree of life' – the evolutionary path connecting all species – in fieldwork one needs to be able to separate one taxon from another. Classifying diverse groups of closely related organisms that differ very subtly is difficult using a cladistic approach. Phenetics provides numerical tools for examining overall patterns of variation, allowing researchers to identify discrete groups that can be classified as species.
Modern applications of phenetics are common in botany, and some examples can be found in most issues of the journal "Systematic Botany". Indeed, due to the effects of horizontal gene transfer, polyploid complexes and other peculiarities of plant genomics, phenetic techniques in botany – though less informative altogether – may, in these special cases, be less prone to errors compared with cladistic analysis of DNA sequences.
In addition, many of the techniques developed by phenetic taxonomists have been adopted and extended by community ecologists, due to a similar need to deal with large amounts of data.


Morganellaceae

The Morganellaceae are a family of Gram-negative bacteria that include some important human pathogens formerly classified as Enterobacteriaceae. This family is a member of the order Enterobacterales in the class Gammaproteobacteria of the phylum Proteobacteria. Genera in this family include the type genus "Morganella", along with "Arsenophonus, Cosenzaea, Moellerella, Photorhabdus, Proteus, Providencia" and "Xenorhabdus".
Human pathogens.
A number of Morganellaceae bacterial species are opportunistic human pathogens, including "Proteus", "Providencia", and occasionally "Morganella" in nosocomial settings.
"Proteus".
Three "Proteus" species "P. vulgaris", "P. mirabilis", and "P. penneri" are opportunistic human pathogens, most commonly resulting in urinary tract infections. "Proteus vulgaris" is commonly found in the intestine in various animals, and is shed into manure and soil.
About 10–15% of kidney stones are struvite stones, caused by alkalinization of the urine by the action of the urease enzyme of "Proteus" (and other) bacterial species.
"Providencia".
"Providencia rettgeri" is a common cause of traveller's diarrhea.
Insect pathogens and symbionts.
A number of Morganellaceae have intimate relationships with insects and other invertebrates.
"Arsenophonus".
"Arsenophonus" are endosymbiotic bacteria of various insects. In Nasonia parasitic wasps, "Arsenophonus nasoniae" acts as a reproductive manipulator by killing developing male wasps. This promotes an increased frequency of females in the population, which are the only biological sex that transmits "Arsenophonus" to the next generation. This type of interaction is referred to as "male-killing or son-killing."
In flies and Lice, "Arsenophonus"-like bacteria act as primary symbionts faithfully transmitted from generation to generation. In such relationships, the primary endosymbiont commonly supplements the host's metabolism by providing essential vitamins and nutrients that the host cannot synthesize itself.
"Photorhabdus and Xenorhabdus".
"Photorhabdus" and "Xenorhabdus" are bacterial associates of entomopathogenic nematodes. These nematodes infect insects and regurgitate their "Photorhabdus" or "Xenorhabdus" bacteria into the insect blood (also called hemolymph). The bacteria then suppress the insect's immune response, increasing the success of the nematode parasite. As a result of this highly effective evolutionary strategy, entomopathogenic nematodes are commonly used as biological control agents against insect pests like corn rootworms.
"Providencia".
"Providencia" are common bacterial species in the microbiome of "Drosophila" fruit flies. In "Drosophila melanogaster", "Providencia rettgeri" is a common pathogen isolated from wild-caught flies. The fly immune system defends against this infection using a highly specific antimicrobial peptide that is required for defence against "P. rettgeri", but not other "Providencia" species.


Cellular waste product

Cellular waste products are formed as a by-product of cellular respiration, a series of processes and reactions that generate energy for the cell, in the form of ATP. One example of cellular respiration creating cellular waste products are aerobic respiration and anaerobic respiration.
Each pathway generates different waste products.
Aerobic respiration.
When in the presence of oxygen, cells use aerobic respiration to obtain energy from glucose molecules.
Simplified Theoretical Reaction: C6H12O6 (aq) + 6O2 (g) → 6CO2 (g) + 6H2O (l) + ~ 30ATP
Cells undergoing aerobic respiration produce 6 molecules of carbon dioxide, 6 molecules of water, and up to 30 molecules of ATP (adenosine triphosphate), which is directly used to produce energy, from each molecule of glucose in the presence of surplus oxygen.
In aerobic respiration, oxygen serves as the recipient of electrons from the electron transport chain. Aerobic respiration is thus very efficient because oxygen is a strong oxidant.
Aerobic respiration proceeds in a series of steps, which also increases efficiency - since glucose is broken down gradually and ATP is produced as needed, less energy is wasted as heat. This strategy results in the waste products H2O and CO2 being formed in different amounts at different phases of respiration. CO2 is formed in Pyruvate decarboxylation, H2O is formed in oxidative phosphorylation, and both are formed in the citric acid cycle.
The simple nature of the final products also indicates the efficiency of this method of respiration. All of the energy stored in the carbon-carbon bonds of glucose is released, leaving CO2 and H2O. Although there is energy stored in the bonds of these molecules, this energy is not easily accessible by the cell. All usable energy is efficiently extracted.
Anaerobic respiration.
Anaerobic respiration is done by aerobic organisms when there is not sufficient oxygen in a cell to undergo aerobic respiration as well as by cells called anaerobes that selectively perform anaerobic respiration even in the presence of oxygen.
In anaerobic respiration, weak oxidants like sulfate and nitrate serve as oxidants in the place of oxygen.
Generally, in anaerobic respiration sugars are broken down into carbon dioxide and other waste products that are dictated by the oxidant the cell uses. Whereas in aerobic respiration the oxidant is always oxygen, in anaerobic respiration it varies. Each oxidant produces a different waste product, such as nitrite, succinate, sulfide, methane, and acetate.
Anaerobic respiration is correspondingly less efficient than aerobic respiration. In the absence of oxygen, not all of the carbon-carbon bonds in glucose can be broken to release energy. A great deal of extractable energy is left in the waste products.
Anaerobic respiration generally occurs in prokaryotes in environments that do not contain oxygen.
Fermentation.
Fermentation is another process by which cells can extract energy from glucose. It is not a form of cellular respiration, but it does generate ATP, break down glucose, and produce waste products.
Fermentation, like aerobic respiration, begins by breaking glucose into two pyruvate molecules. From here, it proceeds using endogenous organic electron receptors, whereas cellular respiration uses exogenous receptors, such as oxygen in aerobic respiration and nitrate in anaerobic respiration. These varied organic receptors each generate different waste products.
Common products are lactic acid, lactose, hydrogen, and ethanol. Carbon dioxide is also commonly produced.
Fermentation occurs primarily in anaerobic conditions, although some organisms such as yeast use fermentation even when oxygen is plentiful.
Lactic Acid Fermentation.
Simplified Theoretical Reaction: C6H12O6 formula_1 2C3H6O3 + 2 ATP (120 kJ)
Lactic Acid Fermentation is commonly known as the process by which mammalian muscle cells produce energy in anaerobic environments, as in instances of great physical exertion, and is the simplest type of fermentation. It starts along the same pathway as aerobic respiration, but once glucose is converted to pyruvate proceeds down one of two pathways and produces only two molecules of ATP from each molecule of glucose. In the homolactic pathway, it produces lactic acid as waste. In the heterolactic pathway, it produces lactic acid as well as ethanol and carbon dioxide.
Lactic acid fermentation is relatively inefficient. The waste products lactic acid and ethanol have not been fully oxidized and still contain energy, but it requires the addition of oxygen to extract this energy.
Generally, lactic acid fermentation occurs only when aerobic cells are lacking oxygen. However, some aerobic mammalian cells will preferentially use lactic acid fermentation over aerobic respiration. This phenomenon is called the Warburg effect and is found primarily in cancer cells. Muscles cells under great exertion will also use lactic acid fermentation to supplement aerobic respiration. Lactic acid fermentation is somewhat faster, although less efficient, than aerobic respiration, so in activities like sprinting it can help quickly provide needed energy to muscles.
Secretion and effects of waste products.
Cellular respiration takes place in the cristae of the mitochondria within cells. Depending on the pathways followed, the products are dealt with in different ways.
CO2 is excreted from the cell via diffusion into the blood stream, where it is transported in three ways:
H2O also diffuses out of the cell into the bloodstream, from where it is excreted in the form of perspiration, water vapour in the breath, or urine from the kidneys. Water, along with some dissolved solutes, are removed from blood circulation in the nephrons of the kidney and eventually excreted as urine.
The products of fermentation can be processed in different ways, depending on the cellular conditions.
Lactic acid tends to accumulate in the muscles, which causes pain in the muscle and joint as well as fatigue. It also creates a gradient which induces water to flow out of cells and increases blood pressure. Research suggests that lactic acid may also play a role in lowering levels of potassium in the blood. It can also be converted back to pyruvate or converted back to glucose in the liver and fully metabolized by aerobic respiration.


Benjamin Arthur Bensley

Benjamin Arthur Bensley (1875–1934) was a Canadian mammologist.
He was born in Hamilton, Ontario to Robert Daniel and Caroline Vandeleur Bensley. He was best known for his work on marsupials and a standard text "Practical Anatomy of the Rabbit". Bensley headed the department of biology at the University of Toronto after graduating from the same institution and completing his doctorate at the University of Columbia.
He spent about two years in London, from 1901, studying marsupials at the British Museum. In 1903 he returned to the University of Toronto as a lecturer and in 1914 was made head of the Biology Department.
He was the first director of the Royal Ontario Museum of Zoology, appointed on its founding in October 1913.
He died on January 20, 1934 at his home in Toronto. He was survived by his wife, Ruth Horton, and his son, Dr. Edward Bensley.


Tapinellaceae

The Tapinellaceae are a family of fungi in the order Boletales. Members of this family are: "Bondarcevomyces", "Pseudomerulius", and "Tapinella".


Sicus ferrugineus

Sicus ferrugineus is a species of fly from the genus "Sicus" in the family Conopidae.
Distribution and habitat.
This species is common throughout much of Europe. These conopids mainly inhabit hedgerows and flower meadows.
Description.
The adults grow up to long. The body is mainly reddish-brown or yellow-brown. The head is yellow, quite large and inflated-looking, with a kind of bubble at the front and narrow cheeks. The short antennae are brown, their second segment has the same length or it is longer than the third. The large eyes are reddish. The legs and also the last abdomen segments are often darkened. The abdomen is long, round in cross-section, the seventh segment is oblong and conical. When in resting position the abdomen is usually folded forward. In the females theca is hardly distinguishable. The wings are transparent, but reddish-yellow colored at the base.
Biology.
They can be encountered from May through September, feeding on nectar or pollen of various Asteraceae species ("Hieracium pilosella", Thistle, "Cirsium" species, etc.), Apiaceae species (Parsley "Petroselinum" sp, . "Heracleum sphondylium"), Onagraceae ("Chamerion angustifolium"), Lamiaceae ("Teucrium scorodonia") and Rosaceae species (Blackberries, "Rubus fruticosus" sp.).
Their larvae are endoparasites of bumble bees of the genus "Bombus" ("B. lapidarius", "B. terrestris ", "B. hortorum", "B. pascuorum", etc.). They pupate and overwinter in their victims.


Tropical acid weed


Gracilibacteria

Gracilibacteria is a bacterial candidate phylum formerly known as GN02, BD1-5, or SN-2. It is part of the Candidate Phyla Radiation and the Patescibacteria group.
The first representative of the Gracilibacteria phylum was reported in 1999 after being recovered from a deep-sea sediment sample. The representative 16S rRNA sequence was referred to as "BD1-5" (sample BD1, sequence 5) and while it was noted that it displayed low sequence identity to any known 16S rRNA gene, it was not proposed as a new phylum at this time. In 2006, representatives of Gracilibacteria were recovered from a hypersaline microbial mat from Guerrero Negro, Baja California Sur, Mexico and proposed as a new phylum "GN02". The BD1-5/GN02 phylum was renamed "Gracilibacteria" in 2013.
The first Gracilibacteria genome was recovered from an acetate-amended aquifer (Rifle, CO, USA) using culture-independent, genome-resolved metagenomic techniques in 2012. Genomic analyses suggest that members of the Gracilibacteria phylum have limited metabolisms and are likely symbionts or endosymbionts. Members of Gracilibacteria use an alternative genetic code in which UGA encodes the glycine amino acid instead of a stop codon


Candidate division

A candidate division, candidate phylum or candidate division-level is a lineage of prokaryotic organisms for which until recently no cultured representatives have been found, but evidence of the existence of the clade has been obtained by 16S rRNA and metagenomic analysis of environmental samples. The term candidatus in fact means a species for which there is insufficient information to call it a new species according to the International Code of Nomenclature of Bacteria


Archaeosphaeroides

Archaeosphaeroides is an extinct genus of bacteria from the Ediacaran.


Mycobacterium genavense

Mycobacterium genavense is a slow-growing 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".
Description.
Nonmotile, acid-fast coccobacilli (1.0 µm x 2.0 µm). No formation of spores, capsules or aerial hyphae.
Colony characteristics
Physiology
Differential characteristics
Type strain.
Strain 2289 = ATCC 51234


Leptotrichia buccalis

Leptotrichia buccalis is an anaerobic, Gram-negative rod bacteria. It is a constituent of normal oral flora.
"Leptotrichia buccalis" can be clearly identified using live blood analysis in dark field. They have a distinct form, which separates them from other rod forms.
Morphology.
"Leptotrichia" species are typically large, fusiform-shaped, non-sporulating, and non-motile rods. <ref>


Mortierellales

Mortierellales is a fungal order.


Lycoperdon umbrinum

Lycoperdon umbrinum, commonly known as the umber-brown puffball, is a type of Puffball mushroom in the genus "Lycoperdon". It is found in China, Europe, and North America.
Description.
This species has a fruit body that is shaped like the top or a pear, with a short, partly buried stipe. It is tall and broad. The fruit body is initially pale brown then reddish to blackish brown, and the outer wall has slender, persistent spines up to 1 mm long. Spores are roughly spherical, 3.5–5.5 µm in diameter, with fine warts and a pedicel that is 0.5–15 µm long. It is uncommon and found mostly in coniferous woods on sandy soils.
The species is considered edible.


Moraxella

Moraxella is a genus of gram-negative bacteria in the family Moraxellaceae. It is named after the Swiss ophthalmologist Victor Morax. The organisms are short rods, coccobacilli, or as in the case of "Moraxella catarrhalis", diplococci in morphology, with asaccharolytic, oxidase-positive, and catalase-positive properties. "M. catarrhalis" is the clinically most important species under this genus.
Roles in disease.
The organisms are commensals of mucosal surfaces and sometimes give rise to opportunistic infection.


Francisco J. Blanco

Francisco Jose Blanco is a structural biologist working as Group Leader at the Centro de investigación Cooperativa en biociencias CIC bioGUNE, Biscay, Spain. His research utilizes Nuclear Magnetic Resonance spectroscopy to characterize protein structure and protein folding. His major contributions to the field of protein folding include the study of the formation and stability of isolated β-hairpin structures, and the analysis of the folding pathway of the SH3 domain from the α-spectrin protein. His 68 structural biology papers listed in Web of Science have been cited over 2500 times, giving him an h-index of 27.


DsDNA-RT virus


Labyrnavirus

Labyrnavirus is a monotypic genus of viruses in the order "Picornavirales". Protist and labyrinthulomycetes serve as natural hosts, notably "Aurantiochytrium". There is only one species in this genus: "Aurantiochytrium single-stranded RNA virus 01".
Structure.
Viruses in "Labyrnavirus" are non-enveloped, with icosahedral, spherical, and round geometries, and T=pseudo3 symmetry. The diameter is around 25 nm. Genomes are linear and non-segmented, around 9kb in length. The genome has three open reading frames.
Life cycle.
Viral replication is cytoplasmic. Entry into the host cell is achieved by attachment of the virus to host receptors, which mediates endocytosis. Replication follows the positive stranded RNA virus replication model. Positive stranded RNA virus transcription is the method of transcription. Protist and labyrinthulomycetes serve as the natural host.


Races of the Dragon

Races of the Dragon is an optional supplemental source book for the 3.5 edition of the "Dungeons & Dragons" fantasy role-playing game.
Contents.
This book contains info on two new races. This book offers a new race that works well with the "Dungeons & Dragons" sorcerers, a class that uses magical power derived from having dragon blood. The book also contains new prestige classes, feats, and spells.
Publication history.
"Races of the Dragon" was written by Gwendolyn F.M. Kestrel, Jennifer Clarke Wilkes, and Kolja Raven Liquette, and was published in January 2006. Cover art was by Steve Prescott, with interior art by Steven Belledin, Ed Cox, Daarken, Wayne England, Emily Fiegenschuh, Carl Frank, Dan Frazier, Brian Hagan, Ralph Horsley, Chris Malidore, Jim Nelson, and Eric Polak.
Gwendolyn Kestrel explains the inspiration for the book's material: "Dragons are a rich part of the "Dungeons & Dragons" game history. There's plenty of material in the game system to serve as inspiration. Of course, we wanted to go beyond what we had done before. While familiar with both "Savage Species" and "Unearthed Arcana", I didn't directly go to these books for inspiration for "Race of the Dragon"."


Olpidium

Olpidium is a fungal genus in the family Olpidiaceae. Members of "Olpidium" are zoosporic pathogens of plants, animals, fungi, and oomycetes.
Morphology.
"Olpidium" species exist as spherical zoosporangia inside the cells of their host. Zoospores emerge from a single discharge tube and have a single, posterior whiplash flagellum. Resting spores can be smooth or ornamented.
Ecology.
"Olpidium" species infect a wide variety of plants, animals, protists, and fungi and are fairly common in aquatic and terrestrial ecosystems. Most of what is known about the genus comes from those species that infect higher plants, especially crops.
In higher plants, infection with "Olpidium" often causes little to no symptoms. An exception is "Olpidium viciae", which causes broadbean blister. However, "Olpidium" species can vector plant viruses. For example, "Olpidium brassicae" transmits big-vein virus and big-vein associated varicosavirus among lettuce plants, and transmits tobacco mosaic virus among tobacco plants. "Olpidium bornovanus" or "Olpidium cucurbitacearum" serves as a vectors for a number of curcubit viruses.
Taxonomy.
The genus "Olpidium" was placed in the Olpidiaceae in the Chytridiales. Later some species, notably "O. brassicae", were moved to the genus "Pleotrachelus", but these were later moved back into the genus. Based on zoospore ultrastructure, Donald J. S. Barr moved the genus into Spizellomycetales In studies using molecular phylogenetics, "O. brassicae", "O. virulentus", and "O. bornovanus" were found to cluster with members of the former Zygomycota not with members of Chytridiomycota. One researcher, has elevated "Olpidium" to the level of phylum (Olpidiomycota) and split the genus into several genera. While nomenclaturaly valid and accepted by some researchers, others view these changes as controversial and unsupported.


Turnip crinkle virus (TCV) repressor of minus strand synthesis H5

The TCV hairpin 5 (H5) is an RNA element found in the turnip crinkle virus. This RNA element is composed of a stem-loop that contains a large symmetrical internal loop (LSL). H5 can repress minus-strand synthesis when the 3' side of the LSL pairs with the 4 bases at the 3'-terminus of the RNA(GCCC-OH).


The CRISPR Journal

The CRISPR Journal is a peer-reviewed scientific journal published every two months by Mary Ann Liebert. It covers research on all aspects of CRISPR research, including its uses in synthetic biology and genome editing. Its editor-in-chief is Rodolphe Barrangou. The journal's editorial board includes key pioneers of CRISPR technology Jennifer Doudna, Emmanuelle Charpentier, and George Church. The inaugural issue of the journal was published in February, 2018.


Kazachstania exigua

Kazachstania exigua is a yeast species that commonly occurs in olive brine and in some kefir cultures. It is one of the yeast species used in the production of sourdough. It is acid-tolerant and maltose-negative.


False morel

The name false morel is given to several species of mushroom which bear a resemblance to the highly regarded true morels of the genus "Morchella". Like "Morchella", false morels are members of the Pezizales, but within that group represent several unrelated taxa scattered through the families Morchellaceae, Discinaceae, and Helvellaceae, most often "Gyromitra". "Verpa" species by contrast are in the Morchellaceae and are true morels.
Compared to morels.
When gathering morels for the table, care must be taken to distinguish them from the poisonous "false morels", a term loosely applied to describe "Gyromitra esculenta", "Verpa bohemica", and other morel lookalikes. Although false morels are sometimes eaten without ill effect, they can cause severe gastrointestinal upset, loss of muscular coordination (including cardiac muscle), or even death. Incidents of poisoning usually occur when they are eaten in large quantities, inadequately cooked, or over several days in a row. False morels contain gyromitrin, an organic carcinogenic poison, hydrolyzed in the body into monomethylhydrazine (MMH). "Gyromitra esculenta" in particular, has been reported to be responsible for up to 23% of mushroom fatalities each year in Poland. "G. esculenta"—regarded as delicious—is known to be potentially deadly when eaten fresh, but research in the 1990s showed that toxins remain even after proper treatment. While many people eat false morels without apparent harm, some people have developed acute toxicity and recent evidence suggests that there may be long-term health risks as well.
The key morphological features distinguishing false morels from true morels are as follows:


Yingvirus

Yingvirus is a genus of negative-strand RNA viruses which infect invertebrates. Member viruses have bisegmented genomes. It is the only genus in the family Qinviridae, which is the only family in Muvirales, which is the only order in Chunqiuviricetes. There are eight species in the genus.
Etymology.
The name "Yingvirus" derives from (), the ancestral name of Duke Mù of Qín during the Spring and Autumn period, along with "-virus" the suffix for a virus genus. "Qinviridae" gets its name from (), meaning Qín State, added to "-viridae" the suffix for a virus family. "Muvirales" is from (), again for Duke Mù of Qín, along with "-virales" the suffix for a virus order. "Chunqiuviricetes" is from (), or Spring and Autumn period, attached to "-viricetes" the suffix for a virus class.
Genome.
Yingviruses have linear, negative-sense, bisegmented RNA genomes. Genome lengths for four member species are:
Taxonomy.
The following species are recognized:


Curtobacterium flaccumfaciens

Curtobacterium flaccumfaciens is a Gram-positive bacterium that causes disease on a variety of plants. Gram-positive bacterium characteristics include small irregular rods, lateral flagella, the ability to persist in aerobic environments, and cells containing catalase. In the interest of studying pathogenicity in plants, the species "Curtobacterium flaccumfaciens" is broken down further into pathovars, which help to better describe the pathogen.
Hosts and symptoms.
"Curtobacterium flaccumfacien" is a bacterial wilt pathogen. The hallmark symptoms of bacterial wilt are leaf and petiole wilting. Chlorosis of the leaf and tissue occurs due to the lack of water transport. "Curtobacterium flaccumfaciens" as a species has a wide host range not limited to kidney beans, soybeans, tulips, and tomatoes. However, the species is artificially separated into a pathovar based on host range and symptoms.
One of the economically important pathovars is "Curtobacterium flaccumfaciens pv. Flaccumfaciens". This pathovar is classified as bacterial wilt and has a primary host range of the genus "Phaseolus" (beans), but the pathogen can infect many other species of the "Fabaceae". In beans the symptoms can be devastating to the crop yield. These beans have severe foliage wilting and chlorosis.
One ornamental example is "Curtobacterium flaccumfaciens pv. oortii". The primary host are plants from the genus "Tulipa" (Tulip). Although the host range differs, the symptoms are relatively similar. During flowering typical symptoms of dehydration are observed. Similarly to beans, the tulips get wilt. In severe cases, the plant eventually fails to recover from wilting and dies.
Disease cycle.
Survival
"Curtobacterium flaccumfaciens" can overwinter in plant debris, diseased plants, wild hosts, seeds, or vegetative propagative organs. The bacteria can survive only a couple of weeks as free bacteria in soil. Multiple factors go into survival of a bacterial population, including temperature, humidity, and soil characteristics. Infected seeds cannot be used for susceptible bean crops because "Curtobacterium flaccumfaciens pv. flaccumfaciens" has been known to survive in dried bean pods from five years and up to 24 years in laboratory conditions. Different pathovars survive in slightly different ways. For example, "Curtobacterium flaccumfaciens pv. oortii" survive in the vegetative propagative organs (bulbs) rather than in the seeds, like "Curtobacterium flaccumfaciens pv. flaccumfaciens".
Dispersal
Curtobacterium flaccumfaciens causes wilting at high populations and disperses in many ways. The bacteria multiply relatively quickly which increases the possibility that "Curtobacterium flaccumfaciens" can shed from dying or dead plant material. The pathogen is normally dispersed via agricultural practices such as, planting saved seed and through farm equipment. In the case of beans & tulips these practices move the propagule during overwriting phase of their life cycles. This is effective dispersal for the pathogen.
Infection
"Curtobacterium flaccumfaciens" usually enters the plant though a wound. Natural wounds (created by excision of flowers or genesis of lateral roots) and unnatural wounds could become entry sites. There are no reports of vectors, but the nematode "Meloidogyne incognita" may assist entry by providing unnatural wounds.
Management.
Management varies for each between hosts. For this purpose, we will look specifically at the detection and control methods of "Curtobacterium flaccumfaciens pv. flaccumfaciens". Since most plant pathogens are Gram-negative detection of Gram-positive bacterium, using methods such as the KOH test, is a beginners diagnostic tool used to identify this bacterium. Bacteria may be detected beneath the seedcoat by means of a combined cultural and slide agglutination test. Bean seed from countries where the disease is known to occur should be inspected for discoloration of the seedcoat. Immunofluorescence staining can also be used to detect the bacterium in contaminated seed lots. Control may be affected by using disease-free seed and crop rotations. Seeds grown in dry climates are usually free from infection and are, therefore, recommended for distribution. The strongest control regulations handed down by the European and Mediterranean Plant Protection (EPPO) to date was a quarantine procedure. There is little resistance available commercially to "Curtobacterium flaccumfaciens pv. flaccumfaci"ens and antibiotics are ineffective.


Riboviria

Riboviria is a realm of viruses that includes all viruses that use a homologous RNA-dependent polymerase for replication. It includes RNA viruses that encode an RNA-dependent RNA polymerase; and, it includes reverse-transcribing viruses (with either RNA or DNA genomes) that encode an RNA-dependent DNA polymerase. RNA-dependent RNA polymerase (RdRp), also called RNA replicase, produces RNA (ribonucleic acid) from RNA. RNA-dependent DNA polymerase (RdDp), also called reverse transcriptase (RT), produces DNA (deoxyribonucleic acid) from RNA. These enzymes are essential for replicating the viral genome and transcribing viral genes into messenger RNA (mRNA) for translation of viral proteins.
"Riboviria" was established in 2018 to accommodate all RdRp-encoding RNA viruses and was expanded a year later to also include RdDp-encoding retroviruses. These two groups of viruses are assigned to two separate kingdoms: "Orthornavirae" for RdRp-encoding RNA viruses, and "Pararnavirae" for RdDp-encoding viruses, i.e. all reverse-transcribing viruses. Both groups are likely descended from non-viral elements that encode reverse transcriptase, though the exact origin of "Orthornavirae" is unclear. While the realm has few prokaryotic viruses, it includes most eukaryotic viruses, including most human, animal, and plant viruses.
Many of the most widely known viral diseases are caused by viruses in "Riboviria", which includes coronaviruses, ebola virus, HIV, influenza viruses, and the rabies virus. These viruses and others have been prominent throughout history, including "Tobacco mosaic virus", which was the first virus to be discovered. Many reverse transcribing viruses notably become integrated into the genome of their host as part of their replication cycle. As a result of that, it is estimated that about 7–8% of the human genome originates from these viruses.
Etymology.
"Riboviria" is a portmanteau of "ribo", referencing ribonucleic acid, and the suffix -"viria", which is the suffix used for virus realms.
Characteristics.
All members of "Riboviria" contain a gene that encodes for an RNA-dependent polymerase, also called RNA-directed polymerase. There are two types of RNA-dependent polymerases: RNA-dependent RNA polymerase (RdRp), also called RNA replicase, which synthesizes RNA from RNA, and RNA-dependent DNA polymerase (RdDp), also called reverse transcriptase (RT), which synthesizes DNA from RNA. In a typical virus particle, called a virion, the RNA-dependent polymerase is bound to the viral genome in some manner and begins transcription of the viral genome after entering a cell. As part of a virus's life cycle, the RNA-dependent polymerase also synthesizes copies of the viral genome as part of the process of creating new viruses.
Viruses that replicate via RdRp belong to three groups in the Baltimore classification system, all of which are in the kingdom "Orthornavirae": single-stranded RNA (ssRNA) viruses, which are either positive (+) or negative (-) sense, and double-stranded RNA viruses (dsRNA). +ssRNA viruses have genomes that can functionally act as mRNA, and a negative sense strand can also be created to form dsRNA from which mRNA is transcribed from the negative strand. The genomes of -ssRNA viruses and dsRNA viruses act as templates from which RdRp creates mRNA.
Viruses that replicate via reverse transcription belong to two Baltimore groups, both of which are in the kingdom "Pararnavirae": single-stranded RNA (ssRNA-RT) viruses, all of which belong to the order "Ortervirales", and double-stranded DNA (dsDNA-RT) viruses, which belong to the family "Caulimoviridae", also in "Ortervirales", and the family "Hepadnaviridae" of the order "Blubervirales". ssRNA-RT viruses have their positive-sense genome transcribed by RdDp to synthesize a negative sense complementary DNA (-cDNA) strand. The +RNA strand is degraded and later replaced by RdDp with a +DNA strand to synthesize a linear dsDNA copy of the viral genome. This genome is then integrated into the host cell's DNA.
For dsDNA-RT viruses, a pregenomic +RNA strand is transcribed from the relaxed circular DNA (rcDNA), which is in turn used by RdDp to transcribe a -cDNA strand. The +RNA strand is degraded and replaced in a similar manner as +ssRNA-RT viruses to synthesize the rcDNA. The rcDNA genome is later repaired by the host cell's DNA repair mechanisms to synthesize a covalently closed circular DNA (cccDNA) genome. The integrated genome of +ssRNA-RT viruses and the cccDNA of dsDNA-RT viruses are then transcribed into mRNA by the host cell enzyme RNA polymerase II.
Viral mRNA is translated by the host cell's ribosomes to produce viral proteins. In order to produce more viruses, viral RNA-dependent polymerases use copies of the viral genome as templates to replicate the viral genome. For +ssRNA viruses, an intermediate dsRNA genome is created from which +ssRNA is synthesized from the negative strand. For -ssRNA viruses, genomes are synthesized from complementary positive sense strands. dsRNA viruses replicate their genomes from mRNA by synthesizing a complementary negative sense strand to form genomic dsRNA. For dsDNA-RT viruses, pregenomic RNA created from the cccDNA is retrotranscribed into new dsDNA genomes. For +ssRNA-RT viruses, the genome is replicated from the integrated genome. After replication and translation, the genome and the viral proteins are assembled into complete virions, which then leave the host cell.
Phylogenetics.
Both kingdoms in "Riboviria" show a relation to the reverse transcriptases of group II introns that encode RTs and retrotransposons, which are self-replicating DNA sequences, the latter of which self-replicate via reverse transcription and integrate themselves into other parts of the same DNA molecule. Reverse transcribing viruses, assigned to "Pararnavirae", appear to have evolved from a retrotransposon on a single occasion. The origin of the RdRps of "Orthornavirae" is less clear due to a lack of information, but two scenarios have been suggested. The most likely scenario is that the RdRps of viruses in "Orthornavirae" originated from the reverse transcriptase of a bacterial group II intron shortly before the emergence of eukaryotes. The other possibility is that the RdRps of "Orthornavirae" originated before the last universal common ancestor (LUCA) and that they preceded the retroelement reverse transcriptases.
With regard to the second possibility, it has been noted that the capsid proteins of leviviruses, which infect bacteria, have no homologues with cellular organisms and other viruses. Furthermore, it has been claimed that the RdRps of other RNA viruses are more similar to reverse transcriptases than they are to the RdRps of leviviruses and their relatives in the phylum "Lenarviricota". From that, it has been proposed that numerous lineages of prokaryotic RNA viruses may have gone extinct when they lost competition with prokaryotic DNA viruses, after which RNA viruses reemerged once they began to infect eukaryotes.
It is also probable that there are RNA viruses that infect archaea based on metagenomic samples. Phylogenetic analysis of extracted sequences suggests that they are the most divergent RNA viruses and that they may be ancestors of eukaryotic RNA viruses, especially those of "Pisuviricota", "Kitrinoviricota", "Duplornaviricota", and "Negarnaviricota", which do not have an apparent prokaryotic ancestor. The discovery of these viruses could change the ideas about the origin of RNA viruses.
Classification.
"Riboviria" contains two kingdoms: "Orthornavirae" and "Pararnavirae". "Orthornavirae" contains multiple phyla and unassigned taxa, whereas "Pararnavirae" is monotypic down to the rank of class. This taxonomy can be visualized hereafter.
Additionally, "Riboviria" contains two "incertae sedis" families and four "incertae sedis" genera. Additional information about them is needed to know their exact placement in higher taxa. They are listed hereafter (-"viridae" indicates family and -"virus" indicates genus).
"Riboviria" partially merges Baltimore classification with virus taxonomy, including the Baltimore groups for RNA viruses and reverse transcribing viruses in the realm. Baltimore classification is a classification system used for viruses based on their manner of mRNA production, often used alongside standard virus taxonomy, which is based on evolutionary history. All members of five Baltimore groups belong to "Riboviria": Group III: dsRNA viruses, Group IV: +ssRNA viruses, Group V: -ssRNA viruses, Group VI: ssRNA-RT viruses, and Group VII: dsDNA-RT viruses. Realms are the highest level of taxonomy used for viruses and "Riboviria" is one of four, the other three being "Duplodnaviria", "Monodnaviria", and "Varidnaviria".
Most identified eukaryotic viruses are RNA viruses, and for that reason most eukaryotic viruses belong to "Riboviria", including most human, animal, and plant viruses. Prokaryotic RNA viruses are seemingly rare as only two such families have been identified: +ssRNA "Leviviridae", whose origin is unclear, and dsRNA "Cystoviridae", who appear to be related to reoviruses, which infect eukaryotes. Other major branches of eukaryotic viruses include herpesviruses in "Duplodnaviria", the kingdom "Shotokuvirae" in "Monodnaviria", and various viruses in "Varidnaviria".
Interactions with hosts.
Disease.
Viruses in "Riboviria" are associated with a wide range of diseases, including many of the most widely known viral diseases. Notable disease-causing viruses in the realm include:
Animal viruses in "Riboviria" include orbiviruses, which cause various diseases in ruminants and horses, including "Bluetongue virus", "African horse sickness virus", "Equine encephalosis virus", and "epizootic hemorrhagic disease virus". The vesicular stomatitis virus causes disease in cattle, horses, and pigs. Bats harbor many viruses including ebolaviruses and henipaviruses, which also can cause disease in humans. Similarly, arthropod viruses in the "Flavivirus" and "Phlebovirus" genera are numerous and often transmitted to humans. Coronaviruses and influenza viruses cause disease in various vertebrates, including bats, birds, and pigs. The family "Retroviridae" contains many viruses that cause leukemia, immunodeficiency, and other cancers and immune system-related diseases in animals.
Plant viruses in the realm are numerous and infect many economically important crops. Tomato spotted wilt virus is estimated to cause more than 1 billion USD in damages annually, affecting more than 800 plant species including chrysanthemum, lettuce, peanut, pepper, and tomato. "Cucumber mosaic virus" infects more than 1,200 plant species and likewise causes significant crop losses. "Potato virus Y" causes significant reductions in yield and quality for pepper, potato, tobacco, and tomato, and "Plum pox virus" is the most important virus among stone fruit crops. "Brome mosaic virus", while not causing significant economic losses, is found throughout much of the world and primarily infects grasses, including cereals.
Endogenization.
Many reverse transcribing viruses, called retroviruses, in "Riboviria" are able to become integrated into the DNA of their host. These viruses become endogenized as part of their replication cycle. Namely, the viral genome is integrated into the host genome by the retroviral enzyme integrase, and viral mRNA is produced from that DNA. Endogenization is a form of horizontal gene transfer between unrelated organisms, and it is estimated that about 7–8% of the human genome consists of retroviral DNA. Endogenization can also be used to study the evolutionary history of viruses, showing an approximate time period when a virus first became endogenized into the host's genome as well as the rate of evolution for the viruses since endogenization first occurred.
History.
Diseases caused by viruses in "Riboviria" have been known for much of recorded history, though their cause was only discovered in modern times. "Tobacco mosaic virus" was discovered in 1898 and was the first virus to be discovered. Viruses transmitted by arthropods have been central in the development of vector control, which often aims to prevent viral infections. In modern history, numerous disease outbreaks have been caused by various members of the realm, including coronaviruses, ebola, and influenza. HIV especially has had dramatic effects on society as it causes a sharp decline in life expectancy and significant stigma for infected persons.
For a long time, the relation between many viruses in "Riboviria" couldn't be established due to the high amount of genetic divergence among RNA viruses. With the development of viral metagenomics, many additional RNA viruses were identified, helping to fill in the gaps of their relations. This led to the establishment of "Riboviria" in 2018 to accommodate all RdRp-encoding RNA viruses based on phylogenetic analysis that they were related.
A year later, all reverse transcribing viruses were added to the realm. The kingdoms were also established in 2019, separating the two RNA-dependent polymerase branches. When the realm was founded, it mistakenly included two viroid families, "Avsunviroidae" and "Pospiviroidae", and the genus "Deltavirus", which were promptly removed in 2019 because they use host cell enzymes for replication.


CellSqueeze

Cell Squeeze® is the commercial name for a method for deforming a cell as it passes through a small opening, disrupting the cell membrane and allowing material to be inserted into the cell. It is an alternative method to electroporation or cell-penetrating peptides and operates similarly to a french cell press that temporarily disrupts cells, rather than completely bursting them.
Method.
The cell-disrupting change in pressure is achieved by passing cells through a narrow opening in a microfluidic device. The device is made up of channels etched into a wafer through which cells initially flow freely. As they move through the device, the channel width gradually narrows. The cell's flexible membrane allows it to change shape and become thinner and longer, allowing it to squeeze through. As the cell becomes more and more narrow, it shrinks in width by about 30 to 80 percent its original size and the forced rapid change in cell shape temporarily creates holes in the membrane, without damaging or killing the cell.
While the cell membrane is disrupted, target molecules that pass by can enter the cell through the holes in the membrane. As the cell returns to its normal shape, the holes in the membrane close. Virtually any type of molecule can be delivered into any type of cell. The throughput is approximately one million per second. Mechanical disruption methods can cause fewer gene expression changes than electrical or chemical methods. This can be preferable in studies that require the gene expression to be controlled at all times.
Applications.
Like other cell permeablisation techniques, it enables intracellular delivery materials, such as proteins, siRNA, or carbon nanotubes. The technique has been used for over 20 cell types, including embryonic stem cells and naïve immune cells. Initial applications focused on immune cells, for example delivering:
Commercialization.
The process was originally developed in 2013 by Armon Sharei and Andrea Adamo, in the lab of Langer and Jensen at Massachusetts Institute of Technology. In 2014 Sharei founded SQZBiotech® to demonstrate the technology. That year, SQZBiotech® won the $100,000 grand prize in the annual startup competition sponsored by Boston-based accelerator MassChallenge.
Boeing and the Center for the Advancement of Science in Space CASIS awarded the company the CASIS-Boeing Prize for Technology in Space to support the use of Cell Squeeze® on the International Space Station (ISS).


Massospora

Massospora is a genus of fungi within the order Entomophthorales of the Zygomycota. It includes more than a dozen obligate, sexually transmissible pathogenic species that infect adult gregarious cicadas (Hemiptera) worldwide. At least two species are known to produce psychoactive compounds during infection.


Kickxellales

The Kickxellales are an order of fungi classified under Kickxellomycotina. It contains the single family Kickxellaceae.
It is not monophyletic.


Rhodotorula cladiensis

Rhodotorula cladiensis is a yeast species first found in the Florida Everglades.


Mycobacterium chlorophenolicum

Mycobacterium chlorophenolicum 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".
Type strain: strain PCP-I = ATCC 49826 = CIP 104189 = DSM 43826 = HAMBI 2278 = IEGM 559 = IFO (now NBRC) 15527 = JCM 7439 = NRRL B-16528.


Ichthyochytrium

Ichthyochytrium is a fungal genus in the Chytridiales of uncertain familial placement. A monotypic genus, it contains the single rare species Ichthyochytrium vulgare, described from Germany by Marianne Plehn in 1920. A parasite of freshwater fishes, it forms spherical bodies measuring 5–20 µm that have refractive granules. It typically attacks the lung and gills.


Serous fluid

In physiology, the term serous fluid or serosal fluid (originating from the Medieval Latin word "serosus", from Latin "serum") is any of various body fluids resembling serum, that are typically pale yellow and transparent and of a benign nature. The fluid fills the inside of body cavities. Serous fluid originates from serous glands, with secretions enriched with proteins and water. Serous fluid may also originate from mixed glands, which contain both mucous and serous cells. A common trait of serous fluids is their role in assisting digestion, excretion, and respiration.
In medical fields, especially cytopathology, serous fluid is a synonym for effusion fluids from various body cavities. Examples of effusion fluid are pleural effusion and pericardial effusion. There are many causes of effusions which include involvement of the cavity by cancer. Cancer in a serous cavity is called a serous carcinoma. Cytopathology evaluation is recommended to evaluate the causes of effusions in these cavities.
Examples.
Saliva consists of mucus and serous fluid; the serous fluid contains the enzyme amylase, which is important for the digestion of carbohydrates. Minor salivary glands of von Ebner present on the tongue secrete the lipase. The parotid gland produces purely serous saliva. The other major salivary glands produce mixed (serous and mucus) saliva.
Another type of serous fluid is secreted by the serous membranes (serosa), two-layered membranes which line the body cavities. Serous membrane fluid collects on microvilli on the outer layer and acts as a lubricant and reduces friction from muscle movement. This can be seen in the lungs, with the pleural cavity.
Pericardial fluid is a serous fluid secreted by the serous layer of the pericardium into the pericardial cavity. The pericardium consists of two layers, an outer fibrous layer and the inner serous layer. This serous layer has two membranes which enclose the pericardial cavity into which is secreted the pericardial fluid.
Blood serum is the component of blood that is neither a blood cell, nor a clotting factor. Blood serum and blood plasma are similar, but serum does not contain any clotting factors, such as fibrinogen, prothrombin, thromboplastin and many others. Serum includes all proteins not used in coagulation (clotting), and all the electrolytes, antibodies, antigens, hormones, and any exogenous substances, like drugs and microorganisms.