Vampirococcus

Vampirococcus is an informally described genus of ovoid Gram-negative bacteria, but the exact phylogeny remains to be determined. This predatory prokaryote was first described in 1983 by Esteve et al. as small, anaerobic microbe about 0.6 μm wide before being given the name of "Vampirococcus" in 1986 by Guerrero et al. This prokaryote is a freshwater obligate predator that preys specifically on various species of the photosynthetic purple sulfur bacterium, "Chromatium". As an epibiont, "Vampirococcus" attaches to the cell surface of their prey and "sucks" out the cytoplasm using a specialized cytoplasmic bridge. They are commonly mentioned as an example of epibionts when discussing strategies employed by bacterial predators. This microbe still has yet to be classified based on genomic sequencing or 16S rRNA because it cannot be sustained long enough outside its natural environment to isolate a pure culture.
Characterization.
"Vampirococcus" is a predatory prokaryotic genus that lives in anaerobic, aquatic conditions. This bacterium is distinguished from other predatory prokaryotes because it feeds upon its prey using epibiosis (also see epibiont). "Vampirococcus" cells are small and ovoid, being only 0.6μm wide. This small size is characteristic of prokaryotes - as they are smaller than eukaryotic cells - and is beneficial for predatory species, as discussed in the Prey and Predation section below. In addition, "Vampirococcus" specifically preys upon various species within the bacterial genus, "Chromatium", a freshwater purple sulfur bacteria. Because "Chromatium" is a primary producer as a phototroph, it has been suggested that "Vampirococcus" could be considered a primary consumer as a predator of photosynthetic bacteria.
There is some disagreement in the scientific community regarding "Vampirococcus's" motility. Many papers have stated that this specific predatory prokaryote does not have cilia or flagella, rendering the prokaryote immotile. However, recent scientific papers have begun to describe "Vampirococcus" specifically with a single polar flagellum that allows it to interact with potential prey in its environment. Other recent articles have referred to "Vampirococcus" as part of a group of similar organisms known as BALOs (Bdellovibrio And Like Organisms) which are known to be very motile predatory microbes. It is difficult to find recent research specifically about "Vampirococcus" that elaborates on this topic, so the motility of this organism should be addressed with caution until further research clarifies the matter.
Genomics and phylogeny.
As of now, the genome of "Vampirococcus" has not been sequenced, and the phylogeny and taxonomy of the microbe have not been determined. Despite this fact, "Vampirococcus" has now been included in a group of microbes known as BALOs, or Bdellovibrio And Like Organisms. These organisms are Gram-negative, obligate predators that exhibit either epibiotic predation or intracellular periplasmic predation. Although these microbes are similar in function, grouping them together does not indicate any close phylogenetic or evolutionary relationships. Only a small portion of the microbes included in BALO have been genetically sequenced. Because "Vampirococcus" is difficult to culture and sustain in a laboratory outside of its natural environment. Without a pure, isolated culture of this organism, more information regarding its genome, genes, evolutionary relationships with other microbes, cellular functions, and behavior cannot be attained.
Habitat.
Currently, "Vampirococcus" has only been found in two freshwater lakes in northeastern Spain: Lake Estanya and Lake Cisó. These lakes were formed in karst areas where rocks underground have been dissolved by groundwater. High concentrations of calcium sulfate and hydrogen sulfide make the lakes anoxic, providing an anaerobic environment to sustain both "Vampirococcus" and its prey, "Chromatium." Cell concentrations of "Vampirococcus" are highest during the fall months and are indirectly proportional to the cell concentrations of "Chromatium", an indication of "Vampirococcus's" predation.
Prey and predation.
Predatory microbes attack and feed off of prey through extracellular or intracellular methods. Since predatory prokaryotes are smaller than their prey, they cannot engulf, or phagocytize, the larger bacteria. This difference in ability and size may have led to the evolution of different predation methods. "Vampirococcus" utilizes epibiotic predation to feed on specifically on various species of "Chromatium." Epibiosis is an extracellular method of predation and requires cell to cell contact between predator and prey. This is the only way in which this predatory acquires nutrients to grow. The steps of "Vampirococcus's" predation are as follows:
As stated previously, "Vampirococcus" solely preys upon species of "Chromatium", a phototrophic purple sulfur bacterium that lives in freshwater. As a bacterium, "Chromatium" is much larger than "Vampirococcus". The benefit of preying on larger microbes is the sheer abundance of nutrients and resources from one individual. In 1986, Guerrero et al. observed that a single "Chromatium" could sustain up to six "Vampirococcus" simultaneously. In contrast, predators larger than their prey must phagocytize multiple microbes in order to receive sufficient nutrition.
Reproduction.
"Vampirococcus" can exist freely in its aquatic environment without being attached to another microbe. However, this prokaryote only reproduces when it is attached to a prey bacterium which makes it an obligate predator. Reproduction occurs via binary fission to produce two daughter cells. "Vampirococcus" does not use "Chromatium's" cellular machinery to reproduce like a virus. It only uses the bacterium as a source of nutrition, and attachment is merely a requirement for reproduction.
Future research.
Research was being conducted in 2005 to evaluate whether or not predatory prokaryotes can be used in other ways to degrade biofilms and cancerous tumor cells. It has been suggested that if predatory microbes attack and kill a certain type of microbe, then they may exhibit the same behavior toward a cell with characteristics similar to their normal prey. Certain BALOs are already being considered for these specific tasks, particularly "Bdellovibrio bacteriovorus". Once "Vampirococcus" is more thoroughly researched and understood, it too could potentially be used to treat cancer or biofilms.


Prunus necrotic ringspot virus

"Prunus necrotic ringspot virus" (PNRSV) is a plant pathogenic virus causing ring spot diseases affecting species of the genus "Prunus", as well as other species such as rose ("Rosa" spp.) and hops ("Humulus lupulus"). PNRSV is found worldwide due to easy transmission through plant propagation methods and infected seed. The virus is in the family "Bromoviridae" and genus "Ilarvirus". Synonyms of PNRSV include European plum line pattern virus, hop B virus, hop C virus, plum line pattern virus, sour cherry necrotic ringspot virus, and peach ringspot virus.
Hosts and symptoms.
All cultivated species of the genus "Prunus", which includes plums, cherries, apricots, almonds, and peaches, are susceptible to one or more strains of PNRSV. Hops and rose are also susceptible to infection by the virus. Other susceptible hosts used for diagnosis include "Chenopodium quinoa" Willd., sunflower ("Helianthus annus"), and "Momordica balsamina".
Symptoms on orchard trees can include death of buds and roots, reduced tree survival and uniformity, and increased susceptibility to winter injury. Some common symptoms also include necrotic “shot holes” in leaves or rugosity and mosaic symptoms. In sweet cherries, PNRSV causes reduced leaf size and produces diffused chlorotic rings and/or spots. Generally, symptoms of PNRSV appear in the year following infection, and then becomes symptomless, although some strains cause recurrent symptoms annually. Although adult trees can show recovery from initial symptoms, keeping young trees virus-free is important because the virus can cause long-lasting stunting compared to healthy trees. It is important to note that symptom severity varies due to host cultivar and viral isolate.
Transmission and epidemiology.
PNRSV can be transmitted through plant propagation methods, making spread through tree nursery stock and root grafting in orchards problematic. The virus also has been shown to infect and transmit through pollen and seeds. PNRSV has been shown to be transmitted by bees carrying infected pollen into orchards. PNRSV infects all seed parts, therefore infection of seed can occur from an infected pollen grain, ovule, or both. Seed transmission incidence can be different among different species or varieties of hosts; host factors that control viral seed transmission, however, are unknown. Cross pollination with PNRSV infected pollen to healthy plants has shown that the virus can also infect the fruit and not just seeds. The virus can also be transmitted by thrips, however the contribution and importance of thrips transmission is unknown.
Management and control.
The most important measure in controlling PNRSV is through planting of certified virus-free trees. Tree nurseries producing propagative material can use thermotherapy (keeping cultures at 38˚ C for at least 20 days), and/or apical meristem cultures to eliminate PNRSV. Prompt removal of infected trees is often recommended as a control strategy, but is not practical for most growers. Field studies have shown that planting of same or similar cultivars near an infected orchard favored earlier infection than when different cultivars were grown, indicating that planting of unrelated cultivars could help slow spread of the virus and allow healthy trees to bear fruit before infection. Genetically engineered resistance may be a possibility for control in the future using RNA interference silencing.


Itamintho

Itamintho is a genus of parasitic flies in the family Tachinidae. There is one described species in "Itamintho", "I. erro".


Lambda phage

Enterobacteria phage λ (lambda phage, coliphage λ, officially Escherichia virus Lambda) is a bacterial virus, or bacteriophage, that infects the bacterial species "Escherichia coli" ("E. coli"). It was discovered by Esther Lederberg in 1950. The wild type of this virus has a temperate life cycle that allows it to either reside within the genome of its host through lysogeny or enter into a lytic phase, during which it kills and lyses the cell to produce offspring. Lambda strains, mutated at specific sites, are unable to lysogenize cells; instead, they grow and enter the lytic cycle after superinfecting an already lysogenized cell.
The phage particle consists of a head (also known as a capsid), a tail, and tail fibers (see image of virus below). The head contains the phage's double-strand linear DNA genome. During infection, the phage particle recognizes and binds to its host, "E. coli", causing DNA in the head of the phage to be ejected through the tail into the cytoplasm of the bacterial cell. Usually, a "lytic cycle" ensues, where the lambda DNA is replicated and new phage particles are produced within the cell. This is followed by cell lysis, releasing the cell contents, including virions that have been assembled, into the environment. However, under certain conditions, the phage DNA may integrate itself into the host cell chromosome in the lysogenic pathway. In this state, the λ DNA is called a prophage and stays resident within the host's genome without apparent harm to the host. The host is termed a lysogen when a prophage is present. This prophage may enter the lytic cycle when the lysogen enters a stressed condition.
Anatomy.
The virus particle consists of a head and a tail that can have tail fibers. The whole particle consists of 12–14 different proteins with more than 1000 protein molecules total and one DNA molecule located in the phage head. However, it is still not entirely clear whether the L and M proteins are part of the virion. All characterized lambdoid phages possess an N protein-mediated transcription antitermination mechanism, with the exception of phage HK022
The genome contains 48,490 base pairs of double-stranded, linear DNA, with 12-base single-strand segments at both 5' ends. These two single-stranded segments are the "sticky ends" of what is called the "cos" site. The "cos" site circularizes the DNA in the host cytoplasm. In its circular form, the phage genome, therefore, is 48,502 base pairs in length. The lambda genome can be inserted into the " E. coli" chromosome and is then called a prophage. See section below for details.
Life cycle.
Infection.
Lambda phage is a non-contractile tailed phage, meaning during an infection event it cannot 'force' its DNA through a bacterial cell membrane. It must instead use an existing pathway to invade the host cell, having evolved the tip of its tail to interact with a specific pore to allow entry of its DNA to the hosts.
On initial infection, the stability of cII determines the lifestyle of the phage; stable cII will lead to the lysogenic pathway, whereas if cII is degraded the phage will go into the lytic pathway. Low temperature, starvation of the cells and high multiplicity of infection (MOI) are known to favor lysogeny (see later discussion).
N antitermination.
This occurs without the N protein interacting with the DNA; the protein instead binds to the freshly transcribed mRNA. Nut sites contain 3 conserved "boxes", of which only BoxB is essential.
Lytic life cycle.
This is the lifecycle that the phage follows following most infections, where the cII protein does not reach a high enough concentration due to degradation, so does not activate its promoters.
Rightward transcription.
Rightward transcription expresses the "O", "P" and "Q" genes. O and P are responsible for initiating replication, and Q is another antiterminator that allows the expression of head, tail, and lysis genes from "PR’".
Q antitermination.
Q is similar to N in its effect: Q binds to RNA polymerase in "Qut" sites and the resulting complex can ignore terminators, however the mechanism is very different; the Q protein first associates with a DNA sequence rather than an mRNA sequence.
Leftward transcription.
Leftward transcription expresses the "gam", "red", "xis", and "int" genes. Gam and red proteins are involved in recombination. Gam is also important in that it inhibits the host RecBCD nuclease from degrading the 3’ ends in rolling circle replication. Int and xis are integration and excision proteins vital to lysogeny.
Lysogenic (or lysenogenic) life cycle.
The lysogenic lifecycle begins once the cI protein reaches a high enough concentration to activate its promoters, after a small number of infections.
The prophage is duplicated with every subsequent cell division of the host. The phage genes expressed in this dormant state code for proteins that repress expression of other phage genes (such as the structural and lysis genes) in order to prevent entry into the lytic cycle. These repressive proteins are broken down when the host cell is under stress, resulting in the expression of the repressed phage genes. Stress can be from starvation, poisons (like antibiotics), or other factors that can damage or destroy the host. In response to stress, the activated prophage is excised from the DNA of the host cell by one of the newly expressed gene products and enters its lytic pathway.
Prophage integration.
The integration of phage λ takes place at a special attachment site in the bacterial and phage genomes, called "attλ". The sequence of the bacterial att site is called "attB", between the "gal" and "bio" operons, and consists of the parts B-O-B', whereas the complementary sequence in the circular phage genome is called "attP" and consists of the parts P-O-P'. The integration itself is a sequential exchange (see genetic recombination) via a Holliday junction and requires both the phage protein Int and the bacterial protein IHF ("integration host factor"). Both Int and IHF bind to "attP" and form an intasome, a DNA-protein-complex designed for site-specific recombination of the phage and host DNA. The original B-O-B' sequence is changed by the integration to B-O-P'-phage DNA-P-O-B'. The phage DNA is now part of the host's genome.
Induction.
The classic induction of a lysogen involved irradiating the infected cells with UV light. Any situation where a lysogen undergoes DNA damage or the SOS response of the host is otherwise stimulated leads to induction.
Multiplicity reactivation and prophage reactivation.
Multiplicity reactivation (MR) is the process by which multiple viral genomes, each containing inactivating genome damage, interact within an infected cell to form a viable viral genome. MR was originally discovered with phage T4, but was subsequently found in phage λ (as well as in numerous other bacterial and mammalian viruses). MR of phage λ inactivated by UV light depends on the recombination function of either the host or of the infecting phage. Absence of both recombination systems leads to a loss of MR.
Survival of UV-irradiated phage λ is increased when the E. coli host is lysogenic for an homologous prophage, a phenomenon termed prophage reactivation. Prophage reactivation in phage λ appears to occur by a recombinational repair process similar to that of MR.
Repressor.
The repressor found in the phage lambda is a notable example of the level of control possible over gene expression by a very simple system. It forms a 'binary switch' with two genes under mutually exclusive expression, as discovered by Barbara J. Meyer.
The lambda repressor gene system consists of (from left to right on the chromosome):
The lambda repressor is a self assembling dimer also known as the cI protein. It binds DNA in the helix-turn-helix binding motif. It regulates the transcription of the cI protein and the Cro protein.
The life cycle of lambda phages is controlled by cI and Cro proteins. The lambda phage will remain in the lysogenic state if cI proteins predominate, but will be transformed into the lytic cycle if cro proteins predominate.
The cI dimer may bind to any of three operators, OR1, OR2, and OR3, in the order OR1 > OR2 > OR3.
Binding of a cI dimer to OR1 enhances binding of a second cI dimer to OR2, an effect called cooperativity. Thus, OR1 and OR2 are almost always simultaneously occupied by cI. However, this does not increase the affinity between cI and OR3, which will be occupied only when the cI concentration is high.
At high concentrations of cI, the dimers will also bind to operators OL1 and OL2 (which are over 2 kb downstream from the R operators). When cI dimers are bound to OL1, OL2, OR1, and OR2 a loop is induced in the DNA, allowing these dimers to bind together to form an octamer. This is a phenomenon called "long-range cooperativity". Upon formation of the octamer, cI dimers may cooperatively bind to OL3 and OR3, repressing transcription of cI. This "autonegative" regulation ensures a stable minimum concentration of the repressor molecule and, should SOS signals arise, allows for more efficient prophage induction.
Lytic vs. lysogenic.
An important distinction here is that between the two decisions; lysogeny and lysis on infection, and continuing lysogeny or lysis from a prophage. The latter is determined solely by the activation of RecA in the SOS response of the cell, as detailed in the section on induction. The former will also be affected by this; a cell undergoing an SOS response will always be lysed, as no cI protein will be allowed to build up. However, the initial lytic/lysogenic decision on infection is also dependent on the cII and cIII proteins.
In cells with sufficient nutrients, protease activity is high, which breaks down cII. This leads to the lytic lifestyle. In cells with limited nutrients, protease activity is low, making cII stable. This leads to the lysogenic lifestyle. cIII appears to stabilize cII, both directly and by acting as a competitive inhibitor to the relevant proteases. This means that a cell "in trouble", i.e. lacking in nutrients and in a more dormant state, is more likely to lysogenise. This would be selected for because the phage can now lie dormant in the bacterium until it falls on better times, and so the phage can create more copies of itself with the additional resources available and with the more likely proximity of further infectable cells.
A full biophysical model for lambda's lysis-lysogeny decision remains to be developed. Computer modeling and simulation suggest that random processes during infection drive the selection of lysis or lysogeny within individual cells. However, recent experiments suggest that physical differences among cells, that exist prior to infection, predetermine whether a cell will lyse or become a lysogen.
As a genetic tool.
Lambda phage has been used heavily as a model organism, and has been a rich source for useful tools in microbial genetics, and later in molecular genetics. Uses include its application as a vector for the cloning of recombinant DNA; the use of its site-specific recombinase (int) for the shuffling of cloned DNAs by the gateway method; and the application of its Red operon, including the proteins Red alpha (also called 'exo'), beta and gamma in the DNA engineering method called recombineering. The 48 kb DNA fragment of lambda phage is not essential for productive infection and can be replaced by foreign DNA. Lambda phage will enter bacteria more easily than plasmids making it a useful vector that can destroy or can become part of the host's DNA. Lambda phage can be manipulated and used as an anti-cancer vaccine, nanoparticle, targeting human aspartyl (asparaginyl) β-hydroxylase (ASPH, HAAH). Lambda phage has also been of major importance in the study of specialized transduction.


Nitrosomonas stercoris

Nitrosomonas halophila is an ammonia-oxidizing bacterium from the genus of "Nitrosomonas".
References.


Setchelliogaster

Setchelliogaster is a genus of fungi in the order Agaricales. It is "incertae sedis" with respect to familial placement within the order, although Kirk and colleagues ("Dictionary of the Fungi", 10th edition, 2008) consider it likely aligned with either the Bolbitiaceae or the Cortinariaceae. The genus is widespread in warm, dry areas, and contains five species. It was circumscribed by Czech mycologist Zdeněk Pouzar in 1958.


Candidatus Bartonella volans

""Candidatus" Bartonella volans" is a candidatus bacteria from the genus of "Bartonella" which was isolated from flying squirrels (Glaucomys volans)


Soybean rust

Soybean rust is a disease that affects soybeans and other legumes. It is caused by two types of fungi, "Phakopsora pachyrhizi", commonly known as Asian soybean rust and "Phakopsora meibomiae", commonly known as New World soybean rust. "P. meibomiae" is the weaker pathogen of the two and generally does not cause widespread problems. The disease has been reported across Asia, Australia, Africa, South America and the United States.
Importance.
Soybean is one of the most important commercial crops around the world and in the United States. Asian soybean rust is the major disease that affects soybeans. It causes lesions on the leaves of soybean plants and eventually kills the plants. The disease has caused serious yield loss of soybeans. In the areas where this disease is common, the yield losses can be up to 80%. In 2002, USDA reported 10-60% yield losses in South America and Africa.
Host and symptoms.
Soybean rust is caused by two types of fungi, "Phakopsora pachyrhizi" and "Phakopsora meibomiae". It affects several important commercial plants, however, most notable for soybeans. Asian Soybean Rust can infect and reproduce on 90 known plant species, 20 of which are found in the United States, such as, soybeans, dry beans, kidney beans, peas, leguminous forage crops such as trefoil and sweet clover and weeds such as kudzu.
At the early stage of Asian Soybean Rust, it causes yellow mosaic discoloration on the upper surfaces of older foliage. At this stage, it is usually hard to identify since the symptoms are relatively small and poorly defined.
Later as the disease continues to progress, the leaves will turn yellow and there will be lesions mostly on the undersides of the leaves and sometimes on petioles, stems or pods and premature defoliation can also be observed.
Asian Soybean Rust produces two types of lesions. Lesions at the later stage will turn from gray to tan or reddish brown. Mature tan lesions consist of small pustules surrounded by discolored necrotic areas. Tan spores can be found at the necrotic areas on the underside of the leaf. In the case of reddish brown lesions, there are larger reddish brown necrotic areas with few pustules and visible spores on the underside of the leaf. A good way to distinguish Asian Soybean Rust from other diseases is to look at the pustules it produces. ASR pustules usually do not have the yellow halo which is typical of bacterial pustules. Besides, ASR pustules are raised and can be commonly found on the underside of the leaf which makes it different from the lesions caused by spot diseases.
Soybean plants are one of ASR's most known hosts and are susceptible at any stage in the life cycle. However, symptoms are most commonly found during or after flowering. ASR infection will reduce pod production and fill.
Environment.
Asian Soybean Rust (ASR) was first detected in Asia. It has been found in many countries around the world since then. For example, Australia, China, Korea, India, Japan, Nepal, Taiwan, Thailand, the Philippines, Mozambique, Nigeria, Rwanda, Uganda, Zimbabwe, South Africa, Brazil, Argentina, and Paraguay. This disease was first detected in the Caribbean in Puerto Rico in 1976 and first reported in the continental United States in 2004.
Asian Soybean Rust favors environments that are humid and warm. A continuous period of wetness on leaves will aid the growth of this disease since this situation is required for spores to germinate. Therefore, is most likely to appear under conditions of and a relative humidity of 75% to 80%. Therefore, ASR is a more serious problem in tropical and subtropical areas in Asia, Africa, Australia and South America. It is unable to survive the cold winters of northern habitats.
Disease cycle.
Soybean rust is spread by windblown spores and has caused significant crop losses in many soybean-growing regions of the world. Windblown spores can travel for great distances and are released in cycles of seven days to two weeks. It is likely that ASR will survive on vast acreages of naturalized kudzu in the southern U.S. and thereby establish a permanent presence in the continental U.S. It is commonly believed that the disease was carried from Venezuela to the United States by Hurricane Ivan.
"P. pachyrhizi" is an obligate parasite, meaning that it must have live, green tissue to survive. For this reason ASR is something that will blow in every year, as cold winters will push it back. It can overwinter in southern states, so long as it has a living host.
ASR overwinters on live host legumes and sporulates the following spring. It cannot survive on dead tissue or crop residues.
Additional hosts can serve as overwintering reservoirs for the pathogen and allow for build-up of inoculum, in those environs free from freezing temperatures. The pathogen is well adapted for long-distance dispersal, because spores can be readily carried long distances by the wind to new, rust-free regions.
Overwintering sites of soybean rust are restricted to areas with very mild winters, such as the gulf coasts of Florida, the very southernmost areas of Texas, or in Mexico. Soybean rust will not survive over the winter in the North Central region because it can't live and reproduce without green living tissue.
Spores of the soybean rust pathogen are transported readily by air currents and can be carried hundreds of miles in a few days. Weather conditions will determine when and where the spores travel from south to north.
Rust spores, called urediniospores, are able to penetrate the plant cells directly, rather than through natural openings or through wounds in the leaf tissue. Thus infection is relatively quick: about 9 to 10 days from initial infection to the next cycle of spore production.
Rust is a multi-cyclic disease. After the initial infection is established, the infection site can produce spores for 10 to 14 days. Abundant spore production occurs during wet leaf periods (in the form of rain or dew) of at least 8 hours and moderate temperatures of .
The process.
The infection process starts when urediniospores germinate to produce a single germ tube that grows across the leaf surface, until an appressorium forms. Appressoria form over anticlinal walls or over the center of epidermal cells, but rarely over stomata. Penetration of epidermal cells is by direct penetration through the cuticle by an appressorial peg. When appressoria form over stomata, the hyphae penetrate one of the guard cells rather than entering the leaf through the stomatal opening. This rust and related species are unique in their ability to directly penetrate the epidermis; most rust pathogens enter the leaf through stomatal openings and penetrate cells once inside the leaf. The direct penetration of the epidermal cells and the non-specific induction of appressoria in the infection process of "P. pachyrhizi" may aid in understanding the broad host range of the pathogen and may have consequences in the development of resistant cultivars.
Uredinia can develop 5 to 8 days after infection by urediniospores. The first urediniospores can be produced as early as 9 days after infection, and spore production can continue for up to 3 weeks. Uredinia may develop for up to 4 weeks after a single inoculation, and secondary uredinia will arise on the margins of the initial infections for an additional 8 weeks. Thus, from an initial infection, there could be first generation pustules that maintain sporulation for up to 15 weeks. Even under dry conditions this extended sporulation capacity allows the pathogen to persist and remain a threat. If conditions for re-infection are sporadic throughout the season, significant inoculum potential still remains from the initial infection to reestablish an epidemic. Successful infection is dependent on the availability of moisture on plant surfaces. At least 6 hours of free moisture is needed for infection with maximum infections occurring with 10 to 12 hours of free moisture. Temperatures between are ideal for infection.
Management and control.
Disease control options for ASR are limited. Rust descends in clouds of spores across the countryside. Cultural practices such as row spacing and crop rotations have little effect. Resistant cultivars do exist, carrying what are called "Rpp" genes. When weather and disease infection conditions are favorable, the occurrence of ASR can be widespread. Thus, remedial control measures—using fungicides as protective sprays—are the main effective disease control method.
Synthetic fungicides are the primary disease control option for protection against Asian soybean rust. The cost of spraying is estimated to be about $15 to $20 per acre; however, two or three sprays may be needed over the course of the growing season. These are significant additional production costs for soybean growers.
Fungicide screening trials to determine disease control efficacy have been field conducted in South America and South Africa. These reports are available on the Web through USDA's Integrated Pest Management Information Centers. These research trials form the basis for fungicidal recommendations in the U.S.
Recent research from Washington State University indicates that the herbicide Glyphosate may be effective in dealing with the fungus.
Rust-resistant varieties of soybeans are currently in development by both public universities and private industry.
In some regions, the selection of winter cover crops and forage legumes may be effected, since they can serve as host plants. Resistance genes ("Rpp"s) have been identified and host resistance is expected to be an effective, long-term solution for soybean rust in the future. Until resistant commercial varieties are in place, the management of rust depends on judicious use of fungicides.
When untreated, soybean rust causes yield losses due to premature defoliation, fewer seeds per pod and decreased number of filled pods per plant.


Dermabacteraceae

Dermabacteraceae is an Actinomycete family.
Phylogeny.
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI)
and the phylogeny is based on 16S rRNA-based LTP release 106 by The All-Species Living Tree Project
Notes<br>
♠ Strains found at the National Center for Biotechnology Information (NCBI) but not listed in the List of Prokaryotic names with Standing in Nomenclature (LPSN)


Ronidovirineae

Ronidovirineae is a suborder of RNA viruses in the order "Nidovirales" which infects arthropods. Host organisms include crusteceans such as prawns.


Brachybacterium aquaticum

Brachybacterium aquaticum is a species of Gram positive, strictly aerobic, pale yellow-pigmented bacterium. The cells are coccoid during the stationary phase, and irregular rods during the exponential phase. It was first isolated from a seawater sample collected from the coastal region of Kovalam, India off the Indian Ocean. The name is derived from Latin "aquaticum" (living in water).
The optimum growth temperature for "B. aquaticum" is 30 °C, but can grow in the 20-37 °C range. The optimum pH is 8.0 and can grow in pH 7.0-11.0.


Mycobacterium brumae

Mycobacterium brumae is a rapidly growing environmental mycobacterial species identified in 1993. Aside from one 2004 report of a catheter related bloodstream infection no other infections by this organism have been reported. It was first isolated from water, soil and one human sputum sample in Spain.
Description.
Microscopy
Colony characteristics
Physiology


Cokeromyces recurvatus

Cokeromyces recurvatus is a pathogenic fungus. Described as a new species in 1950, it was isolated from rabbit dung collected in Illinois.
It appears similar to "Coccidioides immitis".


Clarence Odbody

Clarence Odbody (born May 1653) is a fictional guardian angel in Frank Capra's 1946 film "It's a Wonderful Life", where he was portrayed by Henry Travers, and in the 1990 sequel, "Clarence", where he was played by Robert Carradine.
Odbody is loosely based on "a stranger", a character in Philip Van Doren Stern's 1943 booklet "The Greatest Gift".
In 1977's "It Happened One Christmas", a remake of the 1946 film, a gender-reversed Clarence appeared as Clara Oddbody, played by Cloris Leachman. The 1986 musical "A Wonderful Life" features Odbody, who was played by David Hyde Pierce in its 2005 rendition.
Biography.
In "It's a Wonderful Life".
On Christmas Eve, 1945, George Bailey, a banker in the town of Bedford Falls facing financial ruin and disgrace, is contemplating committing suicide by jumping off a bridge into an icy river because the payout on his $15,000 life insurance policy would solve the problems confronting his business and family. Two celestial beings observe this, and decide to send an angel to save George. For this task, the only available angel is Clarence Odbody, an AS2 (Angel Second Class), who after 200 years has yet to win his wings. To prepare for this assignment, Clarence is shown several scenes from George's life that show some of his selfless acts. Sent to Earth, Clarence finds George standing on a bridge about to leap into the river. Before George can jump off, Clarence jumps in the water, which prompts George to dive in to rescue him.
Clarence introduces himself as they are drying out in the tollhouse keeper's shack (whereupon the tollboy flees in fright). George expresses a wish that he had never been born, and Clarence grants his wish to show George what the world would be like had George never existed. George discovers that his war-hero brother, Harry, had drowned in a frozen lake as a child, as George was not there to save him, and as a result, the soldiers Harry saved from two kamikaze planes died too. He sees that his old boss Emil Gower, the town druggist, served twenty years in prison for manslaughter since George was not around to prevent him from accidentally poisoning a child's prescription. George finds his wife Mary unmarried and childless. He sees that the town has been renamed "Pottersville" in honor of the wealthy but heartless, Henry F. Potter, who appears to have taken over the town, turning it into a sleazy and dangerous place filled with whiskey joints, crime, pawnshops, violence, seedy entertainment establishments, and unhappy people with meaningless, amoral lives. As George comes to realize the positive effects that he has had on others' lives, he regrets his wish. Clarence then restores George to his previous life, a life which he now greatly appreciates. Clarence gives George his copy of "The Adventures of Tom Sawyer". A bell on the family Christmas Tree rings, signifying that Clarence has finally won his wings.
In "Clarence".
As shown in the 1990 film "Clarence", in December 1989, Clarence again comes to Earth to assist a human, Rachel Logan, who is in need of his care. Asked to help her by his fellow angel, Logan's deceased husband, he assists her to again appreciate life and her children, and saves her from suicide by bringing her to heaven for a brief visit with her husband. During his time on Earth he also shows that he has the power to take on the looks of a human, in this case, Rachel's son Brent, whom he portrays so the boy doesn't get expelled from high school.
2011 novel.
"The Last Temptation of Clarence Odbody" is a 2011 novel written by John Pierson which imagines the future lives of various "It's a Wonderful Life" characters if George had not survived his jump into the river.


Dover Demon

The Dover Demon is a creature reportedly sighted in the town of Dover, Massachusetts on April 21 and April 22, 1977.
Sightings.
17-year-old William "Bill" Bartlett claimed that while driving on April 21, 1977, he saw a large-eyed creature "with tendril-like fingers" and glowing eyes on top of a broken stone wall on Farm Street in Dover, Massachusetts. 15-year-old John Baxter reported seeing a similar creature on Miller Hill Road the same evening. Another 15-year-old, Abby Brabham, claimed to have seen the creature the following night on Springdale Avenue.
The teenagers all drew sketches of the alleged creature. Bartlett wrote on his sketch, "I, Bill Bartlett, swear on a stack of Bibles that I saw this creature." According to the "Boston Globe", "the locations of the sightings, plotted on a map, lay in a straight line over 2 miles".
Some suggested that the creature may have been a foal or a moose calf. Police told the Associated Press that creatures reported by the teenagers "were probably nothing more than a school vacation hoax."
In popular culture.
In 2009, The Dover Demon was featured in an episode of the American horror television series "Lost Tapes", which aired on "Animal Planet".
The Dover Demon appears as a character in the American comic book series Proof, which features various other creatures of cryptozoology. In the comic, it is a creature able to see into the future. It appears in another similar comic book series called The Perhapanauts. The Dover Demon would further make brief appearances in the comic books "The Pound: Ghouls Night Out", and "Hack/Slash: Entry Wound".


Actinophryida


Amalgaviridae

Amalgaviridae is a family of double-stranded RNA viruses. Member viruses infect plants and are transmitted vertically via seeds. The name derives from "amalga"m (blend, mix) which refers to amalgaviruses possessing characteristics of both partitiviruses and totiviruses. There are ten species in the family.
Genome.
Amalgavirus genomes are monopartite and about 3.5 kilobases in length. They have two partially overlapping open reading frames which encode the RNA-dependent RNA polymerase (RdRp) and a putative capsid protein.
Evolution.
It has been suggested that amalgaviruses have evolved via recombination between viruses with double-stranded and negative-strand RNA genomes. Phylogenetic analysis indicates that the amalgavirus RdRp forms a sister clade to the corresponding RdRp protein of partitiviruses ("Partitiviridae") which have segmented (bipartite) dsRNA genomes and infect plants, fungi and protists. By contrast, the putative capsid protein of amalgaviruses is homologous to the nucleocapsid proteins of negative-strand RNA viruses of the genera "Phlebovirus" ("Bunyaviridae") and "Tenuivirus".
Taxonomy.
The family "Amalgaviridae" has two genera and ten species:
"Amalgavirus"
"Zybavirus"


Helopeltis antonii

Helopeltis antonii, also known as the tea mosquito bug, are heteropterans found within the Miridae family. They have a relatively large geographical distribution and are a known pest of many agricultural “cash” crops such as cocoa, cashew, and tea. Subsequently, their impact negatively influences economic growth within the regions in which they inhabit. Thus, their impact on humans has caused them to be of great interest biologically, resulting in significant environmental implications.
Distribution.
"Helopeltis antonii" are found in a region known as the old-world tropics which encompasses places such as India, Northern Australia, Guinea, Vietnam, Tanzania, Nigeria, and Indonesia. More specifically, they are more concentrated in the agricultural regions of the old-world tropics. In India their distribution is primarily found within the “cashew belt” which is located along the western coast and central regions of the country due to its high affinity for these plants. However, different nations grow certain crops in various locations within their borders. Crops that "H. antonii" prefer will ultimately determine their specific distribution within a country.
Identification of distribution.
"H. antonii" are often mistaken and misidentified with other "Helopeltis" species. Thus, identifying the exact geographical range of "H. antonii" has become a difficult process. However, recent advances in species identification though DNA barcoding has made it much easier. DNA barcoding is a rapid and relatively inexpensive identification technique that locates unique genetic markers in their DNA allowing for the accurate identification of not only "H. antonii", but other species as well.
Mating.
Reproduction for "H. antonii" occurs in 4 stages—arousal, mounting, copulation, and termination of copulation—and occurs year-round. Mounting, arousal, and termination of copulation occurs within a short time frame; copulation is much longer and more variable in length. Mating typically occur in shaded, covered areas
Arousal.
Arousal consists of both chemical and tactile stimuli. Pheromones play an important role in the chemical attraction of females for mating. Although these chemical cues are important, physical cues comprise the bulk of mate attraction and arousal. Males are the sole initiators for reproductive encounters. This first done through sexual identification of a female partner. Sexual identification is only possible when in close proximity of each other. Once a female is located, the male makes contact with the female by gently probing her body with his antennae. Receptive females remain passive, permitting the male to proceed. In contrast, non-receptive females move to escape any further male interaction.
Mounting.
Following the initial arousal, the process of mounting ensues. Males mount females on the posterior region of her body allowing the erect male rostrum to stroke the dorsal side of the female, just below the thoracic shield. This stroking behaviour quiets the female and allows for easier insertion of the male aedeagus into the female genital aperture. If insertion is not achieved the male begins a left to right stroking motion to aid in its insertion. Females can also kick or shake males off to prevent further progression of mating. When this occurs, males are quick to remount and re-attempt insertion of their aedeagus into the female genital aperture. Successful insertion leads to copulation.
Copulation.
Once insertion has been established the male twists around in an end-to-end fashion to allow for copulation. Once in this end-to-end position, both the male and female remain still until copulation has completed. This can last anywhere from 10 minutes to 2 hours.
Termination of copulation.
Following copulation, they abruptly disjoin, however, detachment can be often difficult due to the males' twisted position. Once separated both the male and female begin to feed and clean their own genitals and antenna—this feeding and cleaning behaviour typically occurs within a few steps from the site of copulation. Females do not respond to any other mating advances immediately following copulation. However, females typically reproduce more than once during their lifetime. Interspecific mating has been known to occur between "Helopeltis" species, specifically between "H. antonii" and "H. theivora". However, their mating results in the production of unviable eggs. The production of eggs following interspecific mating between "H. antonii" and "H. bradyi" has not been observed. This ability and inability to engage in interspecific mating is due to the difference in genital structure between females. Females of both "H. antonii" and "H. theivora" have sclerotized rings that are not fused, whereas, the females of "H. bradyi" have fused sclerotized rings in its genitalia. This difference acts like a “lock and key” model for genitalia.
Oviposition.
Males and females are able to reproduce and lay viable eggs after their first day of sexual maturity. Unmated females are capable of laying eggs; however, they are sterile. The sex ratio of males to females does not influence the number of eggs a female can lay but environments with a high ratio reduces female longevity due to mating exhaustion. Females that reproduce more than once lay a larger number of eggs during oviposition. Females probe plant tissues with the tip of their rostrum to find a suitable site for the deposition of their eggs. The exact reason behind site choice is unknown, but once found the female bends her abdomen to establish contact between her ovipositor and the plant tissue. The ovipositor is then inserted into the plant tissue and the eggs are deposited, below the epidermis and parenchymatous tissue of the plant, via abdominal contractions. The eggs are ovo-elongate and silvery-white in colour and are approximately 1.0x0.3mm in size. Abundance of eggs laid is also weather dependent. Conditions that yield higher temperatures and increased sun exposure result in a higher abundance; whereas cooler temperatures, less available sunlight, and increased rain exposure reduces abundance.
Development.
"H. antonii" experiences partial metamorphosis, otherwise known as hemimetabolous development, which is characterized by it transition from an egg to nymph and eventually into a matured adult. This developmental pattern takes about 25 days from the time the eggs are laid to adulthood. The eggs take eggs 12–13 days to hatch followed by 12–13 days of progressive nymph instars. "H. antonii" experience 5 instars in total before reaching adulthood. During the first instar, the body appears light orange in colour and progresses to a deep orange in the second instar. During the third instar, the body beings to develop wing buds and a scutellar horn. Wing pads become visibly prominent as the fourth instar emerges. Finally, in the fifth instar, the wing pads cover half of the abdomen—with the wings being transparent—and the body is light brown in colour but darkens via sclerotization. Additionally, in the fifth instar, the dorsum of the thorax appears red in colour, the tergum of the abdomen a dull white, the dorsal abdominal segment a deep orange colour, and overlapped hemi-elytra covers over the abdomen with its distal end containing a triangular blackish-brown colouration.
The less-matured first, second and third instars tend to group close to each other and remain in proximity of their hatch site for feeding. In contrast, the more matured fourth and fifth instars tend to be more dispersed and feed in areas farther from their hatch site as a result. Matured females have a characteristic white patch present on their fifth abdominal segment.
Environmental influence.
Although colouration is an important identifying feature of "H. antonii" it is subject to variation due to variations in temperature and sunlight exposure. Red colour morphs tend to peak in abundance during October and reach their minimum abundance during February (for males) and June (for females). Black colour morphs peak during June for both sexes. A brownish-black colour morph is also seen within the population, but its abundance is low, and its frequency remains constant throughout the year.
Diet and feeding.
"H. antonii" are herbivorous insects that have been known to feed on more than 100 different plant species. The sites of feeding, on these plant hosts, are not localized. Rather, both adult and nymphs feed on various sites ranging from tender shoots, buds, stems, and even their fruiting bodies to obtain sap. "H. antonii" possess modified mouthparts which work to form a long straw-like structure known as a “stylet”. This modified mouth part enables them to suck up sap from deep within the plant tissues that would not otherwise be as easily accessible.
Seasonal Consumption.
"H. antonii" feed on both native plants as well as agriculturally grown crops. However, their availability changes with the seasons. This change in availability is due to the different growth cycles host plants experience throughout the year. As host plants enter their fruiting or flushing stages, they begin to have a higher rates of sap production and as a result become targeted by "H. antonii." In native, non-cultivated, habitats there appears to be a preference for certain types of host plants even when many others are present. During January to February "Annona" is preferred, from March to April neem is preferred, from May to August papaya is preferred, and from September to December Singapore cherry is preferred. In addition to the consumption of native plant species, agricultural “cash crops” such black pepper, cashew, cocoa, and tea as are often at high risk for consumption and damage due to their large-scale cultivation and ease of accessibility. However, their feeding schedule on these is agricultural crops are more restricted based due to growing and harvest seasons.
Plant preference.
Like the seasonal preference of plants, preference is also seen in consumption habits of fruits with respect to different plants. For example, in custard apples the immature fruits are preferred over the matured fruits. Whereas in the Singapore cherries there is no observed feeding preference for immature or mature fruits.
Biological mechanics.
Feeding requires the insertion of their stylet into the plant tissues. This insertion results in the secretion of saliva. Present within their saliva are toxic substances that cause death of plant tissues following feeding. However, the biochemical understanding of the toxin's toxicology and function within the saliva is poorly understood and is a site of current research.
Predators.
Being a pest to many agricultural crops, resulting in severe destruction of plants following their consumption, have since made "H. antonii" a major target in hopes to reduce their prevalence in the agricultural industry. The use of insecticides and pesticides have long been used in an attempt to manage and reduce the damaging effects of "H. antonii" feeding. However, the effectiveness of these chemicals are concentration and volume dependent with respect to the type being used. Some of these pesticides have a prevalence of 500 liters per hectare at concentrations ranging from 50g/L-500g/L. The use of such chemical agents poses a risk not only to the environment but to humans as well—as exposure and administration levels continue to increase so too does its level of toxicity. Additionally, many countries that import these crops do not import those that have traces of pesticides. Thus, natural predators and parasitoids have been looked to for their biological control properties to prevent the use of these harmful chemicals.
Biological control.
"H. antonii" are subject to both predation and parasitism via parasitoids. Parasitoids of both nymph and adult morphs include Hymenoptera (Braconidae, Platygastridae) and Diptera (Sarcophagidae). Predators are more extensive in diversity and consist of Hymenoptera (Formicidae, Vespidae), Coleoptera, Mantodea, and Odonata.
Of specific interest and use are hymenopteran parasitoids, specifically, "Telenomus cupis" due to their high specificity and specialization on "H. antonii" eggs. The employment of these parasitoid specialists has significantly decreased the abundance of "H. antonii" eggs to effectively reduce their devastating impact on agricultural crops. Additionally, these hymenopteran parasitoids are one of the few parasitoids that are active year-round.
The combined use of pesticides and biological control agents are less effective in reducing the number of "H. antonii" within agricultural systems. This is because these pesticides also act against biological control agents—reducing their effectiveness. Additionally, the biological control agents tend to be more affected by pesticides than "H. antonii." Biological predators and parasitoids are more affected than "H. antonii" due to their increase locomotory abilities causing them to be exposed to larger amounts of the synthetic pesticides found on crops. The extensive and prolonged use of pesticides and its lesser effect on "H. antonii", when compared to its biological control agents, raises concerns regarding pesticide resistance. However, such evidence has yet to suggest the acquisition of pesticide resistance in "H. antonii."
Ecological and economic damage.
"H. antonii" foraging behaviour, especially on commercially produced crops, has devastating impacts on overall crop yields showing yield reduction of as much as 35-75 percent. As more of the native landscape becomes converted into agricultural lands it provides an increased food supply for them. This increased food supply allows for an increase in population. As their population increases more plant tissues are subject to damage and injury. Thus, injured plants are no longer able to allocate their desired resources into fruit/seed production, rather, they are forced to allocate resources and energy into damage control and repair. This alternative allocation of resources is what causes the observed yield reductions. Poor yields result in poor economic outcomes for producers which also has adverse consequences for consumers such as increased prices, as well as an overall reduction in the number and overall quality of available products.
Foraging behaviour of "H. antonii" causes necrotic lesions to develop on plant tissues at feeding sites which can cause the death to new plant buds. Bud death inhibits plants from producing fruit—decreasing yield. Similarly, feeding on premature and mature fruits causes fruit desiccation resulting in a reduction in size and quality—as seen in cashew plants.
Fungal contribution.
Although feeding results in necrotic lesioning and desiccation, it is not the only factor that impacts yield. Following foraging, fungal pathogens can enter the wound tissues more readily and cause die-back of shoots and is the primary cause of inflorescence blight. Even though fungal blight is a common occurrence in various plants, the wounds caused by "H. antonii" in plant tissues exacerbates and accelerates its effects. Die-back from blight also limits the plant's ability to produce products and grow—further perpetuating yield loss.


Candidatus Savagella


Deuterosome

In cell biology, a deuterosome is a protein structure within a multiciliated cell (such as an epithelial cell of respiratory tract) that produces multiple centrioles.
Most cells in human body possess one primary cilium, a relatively small protrusion of the cell membrane that looks like a stick or a finger under the electron microscope. Primary cilium is typically used by the cell as a sensory organelle, or antenna. Some cells, however, have numerous cilia which they use to generate directed fluid flow. The examples include epithelial cells of the respiratory tract in which multiple cilia are used for mucus clearance, the oviduct, in which cilia help the egg migrate to the uterus, and others.
Each cilium has a basal body formed from a centriole to which it is anchored and from which it starts to grow after each cell division, when a new daughter cell is formed. Centrioles typically replicate once during cell division, thus allowing for only one cilium for a daughter cell. Multiciliated cells, on the other hand, need to produce more than 100 centrioles in order to grow multiple cilia. This problem is solved by the existence of deuterosome, a structure thought to be formed from amorphous filamentous material and able to make many centrioles at once.
The evidence of the existence of deuterosome first came from electron microscopy work in various multiciliated tissues. It was found that both centriole duplication and "de novo" generation of centrioles occurs in such cells. The generation of new centrioles which will serve as basal bodies for multiple cilia is due to a cytoplasmic structure, which was termed the “deuterosome” by Sorokin.


Alicyclobacillus contaminans

Alicyclobacillus contaminans is a species of Gram positive, strictly aerobic, bacterium. The bacteria are acidophilic and produce endospores. It was first isolated during a survey from both orange juice, and soil in Fuji City, Japan. The species was first described in 2007, and the name is derived from the Latin "contaminans" (contaminating).
The optimum growth temperature for "A. contaminans" is 50-55 °C, and can grow in the 35-60 °C range. The optimum pH is 4.0-4.5, and cannot grow at pH 3.0 or pH 6.0.
"A. contaminans" was found during a Japanese survey of various beverages and environments, which also discovered 5 other species of "Alicyclobacillus": "A. fastidiosus", "A. kakegawensis", "A. macrosporangiidus", "A. sacchari", and "A. shizuokensis".


Cortinarius catarracticus

Cortinarius catarracticus is a species of potentially lethal fungus in the family Cortinariaceae native to South Australia.


Xanthotype sospeta

Xanthotype sospeta, the crocus geometer, is a species of moth in the family Geometridae. It was first described by Dru Drury in 1773 from Jamaica. It is also found in North America, where it has been recorded from Nova Scotia to southern British Columbia, south to Colorado and Georgia. The habitat consists of deciduous and mixedwood forests.
Description.
Upperside: antennae filiform. Head pale yellow. Eyes dark brown. Tongue spiral. Thorax, abdomen, and wings pale yellow. On the posterior edges of the anterior wings are placed two faint brown streaks; one, which is smallest, being about a quarter of an inch from the shoulders, the other the same distance from the lower corners; about the same distance from the tips, on the anterior edges, is placed another very small one. Posterior wings having likewise two of these faint spots, one on the anterior, the other on the abdominal edges.
Underside: sides, breast, and abdomen pale yellow. Legs brown and yellow. Wings pale yellow, with the same spots and marks as on the upper side, but more distinct. The wings are a little angulated. Wingspan nearly inches (62 mm).
Biology.
The larvae are feed on a wide variety of low-growing shrubs and herbs, including "Salix", "Cornus" and "Viburnum" species. They are twig mimics.


Acrocerinae

Acrocerinae is a subfamily of Acroceridae. They are small distinctive flies whose larvae are endoparasites of spiders. Adults hunchback-flies visit flowers to feed on nectar. Traditionally the subfamily included the genera now placed in Cyrtinae and Ogcodinae, but the subfamily in this sense was found to be polyphyletic and was split up in 2019.
Systematics.
The subfamily includes two extant genera and one extinct:
The extinct fly genus †"Burmacyrtus" was originally placed in this subfamily as well, but according to Gillung & Winterton (2017) it is not considered an acrocerid.


Chroogomphus

Chroogomphus is a genus of mushrooms commonly known as pine-spikes or spike-caps based on their shape and because they are often found growing in association with pine trees. The genus is distributed throughout the Northern Hemisphere including North America, the Caribbean, Europe, and Asia.
Taxonomy.
These fungi are members of the family Gomphidiaceae which are agaricoid members of the Boletales (suborder Suillineae). Related to the genus "Gomphidius" (in which they were once classified), "Chroogomphus" are distinguished from "Gomphidius" by their lack of a partial veil.
The genus name is derived from the Greek χρω- chroo-, meaning 'skin' or 'colour', and 'γομφος' "gomphos" meaning 'plug' or 'large wedge-shaped nail'.
Ecology.
Members of this genus have been thought to be ectomycorrhizal with various species of pine, however, there is now evidence that all members of the Gomphidiaceae are parasitic upon other boletes. Specifically, "Chroogomphus" species are thought to be parasitic on various conifer-associated "Suillus" species, with this parasitism often being highly species-specific. In the Pacific Northwest of North America, "C. tomentosus" is found with western hemlock ("Tsuga heterophylla") and Douglas-fir ("Pseudotsuga menziesii"), while "C. helveticus" of Europe is found in conifer forests containing spruce ("Picea" ssp.).
Species.
"Chroogomphus rutilus" (image), found in Europe, is the type species for this genus. It has been the subject of investigation as the source of antibiotics, as well as other potentially useful secondary compounds.
The cap is up to 10 cm in diameter and red-brown in colour. The widely spaced gills are brownish-orange and with black to brownish-yellow spores. The stalk is brownish-yellow and tapers toward the base. The flesh is orange to salmon-coloured and turns violet when chewed.
"Chroogomphus ochraceus" (image) of North America is very similar in habit and appearance to "C. rutilus", and the latter name has often been misapplied to "C. ochraceus".
"Chroogomphus vinicolor" (image), another North American species, is likewise similar to "C. rutilus", although "C. vinicolor" tends to be smaller. The cap color is variable in both species, with "C. vinicolor" being, as its scientific name suggests, more wine-colored while "C. rutilus" is usually more brown. The most distinctive differences between these three species are microscopic.
Other species within genus "Chroogomphus" include:
Edibility.
"Chroogomphus rutilus", "C. ochraceus", "C. oregonensis", "C. tomentosus", and "C. vinicolor" are edible and may be interchangeable for culinary purposes. They are not, however, regarded as flavorful and possess neither a distinctive taste nor odor. One food writer states about "C. rutilus" and "C. vinicolor":


Stirling Quartzite Formation

The Stirling Quartzite Formation is a geologic formation in the northern Mojave Desert of Inyo County, California and Nye County and Clark County, Nevada.
It can be seen in the Panamint Range and Funeral Mountains adjoining Death Valley within Death Valley National Park; and in the Spring Mountains in Clark County.
Geology.
The formation underlies the Wood Canyon Formation.
It preserves fossils dating back to the Ediacaran period of the Neoproterozoic Era.


Brachybacterium

Brachybacterium is a genus of Gram positive, nonmotile bacteria. The cells are coccoid during the stationary phase, and irregular rods during the exponential phase. The genus name comes from Greek word "brachy", meaning short, and Latin "bacterium", meaning rods, referencing the short rods noted during the exponential phase.
The type strain of the genus, "Brachybacterium faecium", was first isolated from poultry deep litter in 1966 along with several other species. Speciation of the strains was performed in 1975, but three of the strains did not cluster with any known taxon. In 1988, further work was performed on the previously unclassified organisms, and the current genus was proposed. "Brachybacteria" have been isolated from a stool sample of a healthy three-year-old girl, garden soil, Beaufort cheese, medieval wall paintings, a mouse liver, roots, salt fermented seafood, oil-contaminated coastal sand, sediment samples, and seawater. A strain of "Brachybacterium" has been indicated as the cause of bloodborne infection in an 83 year-old man.


Alicyclobacillus sendaiensis

Alicyclobacillus sendaiensis is a species of Gram positive, strictly aerobic, bacterium. The bacteria are acidophilic and produced endospores. It was first isolated from soil in Aoba-yama Park,
Sendai, Japan. The species was first described in 2003, and the name refers to the city from which it was first isolated. It was found during a survey in search of bacteria that produce thermostable collagenase.
The optimum growth temperature for "A. sendaiensis" is 55 °C, and can grow in the 40-65 °C range. The optimum pH is 5.5, and can grow in pH 2.5-6.5.


Vitreoscilla

Vitreoscilla is a genus of Gram-negative aerobic bacterium. The bacterial haemoglobin (VHb) was first discovered from "Vitreoscilla", and VHb is found to have a wide range of biological and biotechnological applications including promotion of cell growth, protein synthesis, metabolite productivity, respiration, cellular detoxification, fermentation, and biodegradation.
Etymology.
The generic name is derived from the Latin adjective "vitreus", which means clear or transparent; and the noun "oscillum", meaning a swing. Thus "Vitreoscilla" is used to describe the bacterium as the transparent swing or oscillator, the way it exhibits locomotion.
Species.
There are three valid species under the genus, namely
Structure.
Members of "Vitreoscilla" are obligate aerobic bacteria, which are morphologically colourless filaments that contain cells with diameters of 1-3 μm and 1-12 μm long. Each filament may contain from 1 to 40 cells. Locomotion is by gliding, and no special locomotor organelles are present. The cell walls are composed of the amino acids alanine, glutamate, and diaminopimelic acid, with approximate molar ratios of 2:1:1.
Importance.
"Vitreoscilla" bacteria have a unique property in that they produces a type of haemoglobin, VHb. This molecule unlike classic haemoglobin is composed only of a single globin molecule. VHb is known to have a wide variety of functions including improving cell growth, protein synthesis, enhanced metabolism, nitric oxide detoxification, increase respiration and production of ethanol. Some of these properties have been exploited as potential benefits in biotechnology and industry.


Metasphaeria

Metasphaeria is a genus of fungi belonging to the family Saccotheciaceae.
The genus has cosmopolitan distribution.
Species.
Species:


Lycoperdon pulcherrimum

Lycoperdon pulcherrimum is a type of puffball mushroom in the genus "Lycoperdon". It was first described scientifically in 1873 by Miles Joseph Berkeley and Moses Ashley Curtis. The fungus is found in the southern United States.


Infestation

Infestation is the state of being invaded or overrun by pests or parasites. It can also refer to the actual organisms living on or within a host.
Terminology.
In general, the term "infestation" refers to parasitic diseases caused by animals such as arthropods (i.e. mites, ticks, and lice) and worms, but excluding (except) conditions caused by protozoa, fungi, bacteria, and viruses, which are called infections.
External and internal.
Infestations can be classified as either external or internal with regards to the parasites' location in relation to the host.
External or ectoparasitic infestation is a condition in which organisms live primarily on the surface of the host (though porocephaliasis can penetrate viscerally) and includes those involving mites, ticks, head lice and bed bugs.
An internal (or endoparasitic) infestation is a condition in which organisms live within the host and includes those involving worms (though swimmer's itch stays near the surface).
Medically, the term "infestation" is often reserved only for external ectoparasitic infestations while the term "infection" refers to internal endoparasitic conditions.


Pseudomonas luteola

Pseudomonas luteola is an opportunistic pathogen, found ubiquitously in damp environments. Originally designated in the genus "Chryseomonas", the species has since been reassigned to the genus "Pseudomonas".
Morphology.
"Pseudomonas luteola" is a Gram-negative, motile aerobe. Its motility is created by multitrichous flagella. They grow as rods of 0.8 μm to 2.5 μm. Colonies produce a yellow-orange pigment. Optimal temperature for growth is 30 °C. Importantly for classification, it grows best on heart infusion agar supplemented with 5% horse blood. It is also able to grow on TSA, Nutrient Agar, Mac Conkey or CASA Agar.
Biosorption.
"Pseudomonas luteola" can absorb certain heavy metals such as Cr(VI) and Al(III). Both ions are found in industrial wastewaters. These metals are specifically targeted by P. luteola strain TEM05. Under relatively acidic conditions (pH: 4 and 5 for each ion respectively). Experiments indicated a maximum adsorption capacity of 55.2 mg g−1 for Al(III) and 3.0 mg g−1 for Cr(VI).
This same strain is also known to produce an exopolysaccharide (EPS) utilized in the adsorption of nickel and copper. In order to adsorb Ni and Cu at significant levels, the strain must be immobilized in a calcium alginate beads. With this enhancement, maximum adsorption capacities range from 45.87–50.81 mg g−1 and 52.91–61.73 mg g−1, respectively.
Pathenogenicity.
The pathogenic form of "Pseudomonas luteola" is a saprophyte. It is an opportunistic pathogen that can cause bacteremia, meningitis, prosthetic valve endocarditis, peritonitis in humans and animals. "P. luteola" is registered by the CDC as group Ve-1. Most strains are susceptible to broad-spectrum antibiotics, such as cephalosporins, aminosids, and ciprofloxacin. However, infections associated with foreign material are highly resistant, and infected prostheses have to be removed if possible.


Macanavirus

Macanavirus is a genus of viruses, in the family "Tombusviridae". Plants serve as natural hosts. There is only one species in this genus: "Furcraea necrotic streak virus". Diseases associated with this genus include: macana disease.
Structure.
Viruses in "Macanavirus" are non-enveloped, with icosahedral and spherical geometries, and T=3 symmetry. The diameter is around 28 nm. Genomes are linear, around 4kb in length.
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, using the premature termination model of subgenomic RNA transcription is the method of transcription. The virus exits the host cell by tubule-guided viral movement. Plants serve as the natural host.


Hemimastix


Methylobacterium fujisawaense

Methylobacterium fujisawaense is a facultatively anaerobic, Gram-negative, rod-shaped bacteria. It is catalase-positive and oxidase-negative. It produces pink-pigment on microbiological agar media (TSA and R2A, etc.). This bacteria is facultatively methylotrophic and is widely distributed in nature. They can be isolated from soil and on occasion freshwater environments, including drinking water.
Commonly, "M. fujisawaense" bacteria is not established as pathogenic; however, rarely it may cause human infection/disease, mostly in immunocompromised patients.


Andy Park (Mr. Christmas)

Andy Park is an electrician from Melksham, Wiltshire, England, who styles himself "Mr. Christmas" after claiming to have celebrated Christmas Day every day since 14 July 1993.
Personal life.
Over the years Park has sent himself more than 235,500 Christmas cards.
In 2005, he released a single entitled "It's Christmas Every Day", with a video featuring Mike Read and produced by Andy Whitmore.
He claims that each day he eats breakfast (turkey sandwich and mince pies), then goes to work, until returning around at lunchtime to eat a full roast turkey dinner before watching a recording of the Queen's Christmas speech, sherry in hand.
In an interview published in 2006, Park was quoted as saying that, over the previous 13 years, he had consumed 4,380 turkeys (one a day), 87,600 mince pies (20 a day), 2,190 pints of gravy (half a pint a day), 26,280 roast potatoes (six a day), 30,660 stuffing balls, 219,000 mushy peas, 4,380 bottles of champagne, 4,380 bottles of sherry and 5,000 bottles of wine. However, in 2001, he was warned by his doctor that the diet was affecting his health after his weight increased to .
Mr Christmas also sent in his song via post to The Scott Mills show on BBC Radio 1 and was opened live on air on 9 August 2018. It was played until listeners text in requesting the song to be stopped. Chris Stark and Scott Mills exchanged talks over how it could be a number one if it was recorded in a studio.
In the media.
On 15 December 2007, in an interview on the BBC Radio 4 programme "Saturday Live", Park said he was still celebrating every day.
On 22 December 2009, he appeared on talkSPORT radio. He was a guest on the "Ian Collins' Late Show" to discuss his lifestyle.
In 2009, Park appeared in former Radio 1 DJ Mike Read's Christmas single, "My Christmas Card To You".
On 8 December 2015, Park appeared on the Channel 5 documentary "Crackers about Christmas". The show explains how Park wanted his single to reach Christmas number one and he still follows his daily routine now in 2015, however, following recent reports in the "Daily Mirror", he has decided to stop celebrating daily after Christmas 2015 due to wiping out his savings and being at risk of losing his home. However, after just two weeks of abstention, Park returned to celebrating every day, citing his love for the holiday being too great.


Enterobacter cloacae

Enterobacter cloacae is a clinically significant Gram-negative, facultatively-anaerobic, rod-shaped bacterium.
Microbiology.
In microbiology labs, "E. cloacae" is frequently grown at 30 °C on nutrient agar or at 35 °C in tryptic soy broth. It is a rod-shaped, Gram-negative bacterium, is facultatively anaerobic, and bears peritrichous flagella. It is oxidase-negative and catalase-positive.
Industrial use.
"Enterobacter cloacae" has been used in a bioreactor-based method for the biodegradation of explosives and in the biological control of plant diseases.
Safety.
"E. cloacae" is considered a biosafety level 1 organism in the United States and level 2 in Canada.
Genomics.
A draft genome sequence of "Enterobacter cloacae" subsp. "cloacae" was announced in 2012. The bacteria used in the study were isolated from giant panda feces.
Clinical significance.
"Enterobacter cloacae" is a member of the normal gut flora of many humans and is not usually a primary pathogen. Some strains have been associated with urinary tract and respiratory tract infections in immunocompromised individuals. Treatment with cefepime and gentamicin has been reported.
A 2012 study in which Enterobacter cloacae transplanted into previously germ-free mice resulted in increased obesity when compared with germ-free mice fed an identical diet, suggesting a link between obesity and the presence of Enterobacter gut flora.
Species of the "E. cloacae" complex.
"E. cloacae" was described for the first time in 1890 by Jordan[201] as "Bacillus cloacae", and then underwent numerous taxonomical changes, becoming 'Bacterium cloacae' in 1896 (Lehmann and Neumann), "Cloaca cloacae" in 1919 (Castellani and Chalmers), it was identified as 'Aerobacter cloacae' in 1923 (Bergey et al.), "Aerobacter cloacae" in 1958 (Hormaeche and Edwards) and "E. cloacae" in 1960 (Hormaeche and Edwards), by which it is still known today.[7] "E. cloacae" is ubiquitous in terrestrial and aquatic environments (water, sewage, soil and food). These strains occur as commensal microflora in the intestinal tracts of humans and animals[1] and play an important role as pathogens in plants and insects. This diversity of habitats is mirrored by the genetic variety of the nomenspecies "E. cloacae".[6] "E. cloacae" is also an important nosocomial pathogen responsible for bacteremia and lower respiratory tract, urinary tract and intra-abdominal infections, as well as endocarditis, septic arthritis, osteomyelitis and skin and soft tissue infections. The skin and the GI tract are the most common sites through which "E. cloacae" can be contracted.[1,29]
"E. cloacae" tends to contaminate various medical, intravenous and other hospital devices. Nosocomial outbreaks have also been associated with colonization of certain surgical equipment and operative cleaning solutions. Another potential reservoir for nosocomial bacteremia is the heparin solution used to irrigate certain intravascular devices continually. This fluid had been implicated as a reservoir for outbreaks of device-associated bacteremia in several instances.[30]
In recent years, E. cloacae has emerged as one of the most commonly found nosocomial pathogen in neonatal units, with several outbreaks of infection being reported.[31] In 1998, van Nierop et al. reported an outbreak in a neonatal intensive care unit with nine deaths,[32] and in 2003, Kuboyama et al. reported three outbreaks with 42 systemic infections and a mortality of 34%.[33] This microorganism may be transmitted to neonates through contaminated intravenous fluids, total parenteral nutrition solutions and medical equipment. Many single-clone outbreaks, probably caused by cross-transmission via healthcare workers, have been described, suggesting that inpatients can also act as a reservoir.[31] The type strains of the species are E. cloacae ATCC 49162 and 13047. This latter strain is the first complete genome sequence of the "E. cloacae" species and the type strain is "E. cloacae" subsp. "cloacae".
The complete "E. cloacae" subsp. "cloacae" ATCC 13047 genome contains a single circular chromosome of 5,314,588 bp and two circular plasmids, pECL_A and pECL_B, of 200,370 and 85,650 bp (GenBank accession numbers CP001918, CP001919 and CP001920, respectively).[34]
The other genomes of "E. cloacae" that have been sequenced are deposited in GenBank under accession numbers CP002272, CP002886, FP929040 and AGSY00000000.
"E. asburiae" is named after Mary Alyce Fife-Asbury, an American bacteriologist who made many important contributions to the classification of Enterobacteriaceae, particularly in describing new "Klebsiella" and "Salmonella" serotypes,[35–37] new genera and new species.[38–42] "E. asburiae" sp. nov. was described in 1986 based on the enteric group 17.[43] This group was defined in 1978 as a group of biochemically similar strains isolated from different human specimens[44] and sent to the CDC. Before the designation of 'enteric group 17', these strains had been reported as unidentified or atypical Citrobacter or Enterobacter strains.[44] After several studies, it was shown that these strains represent a single new species in the genus "Enterobacter", which was named "E. asburiae".
"E. asburiae" strains have been isolated from the soil and implicated in the mobilization of phosphate for plant nutrition from calcium phosphate, but most E. asburiae species have been isolated from human sources. The type strain of the species "E. asburiae" is ATCC 35953 and was isolated from lochia exudates of a 22-year-old woman in the USA.[43] The only sequenced strain of "E. asburiae" is LF7a, which contains a circular DNA (4,812,833 bp) and two circular plasmids, pENTAS01 (166,725 bp) and pENTAS02 (32,574 bp), which were submitted by Lucas et al. in 2011 to the US DOE Joint Genome Institute (CA, USA; GenBank accession numbers CP003026.1, CP003027.1 and CP003028.1, respectively).
"E. hormaechei" is named after Estenio Hormaeche, a Uruguayan microbiologist who (with PR Edwards) proposed and defined the genus "Enterobacter".[7] The name "E. hormaechei" was formerly called enteric group 75, which contained 11 strains that were sent to the CDC for identification between 1973 and 1984. Twelve additional strains were received from 1985 to 1987, three of which were blood isolates. "E. hormaechei" was first described on the basis of 23 isolates sent to the CDC for identification. At that time, they could not be assigned to a species since they were negative in the D-sorbitol and melibiose tests and did not fit the biochemical profile of any established Enterobacter species. The species "E. hormaechei" was proposed to be lactose-, D-sorbitol-, raffinose-, melibiose- and esculin-negative and 87% dulcitol-positive. These species were originally defined by O'Hara et al. when a large hybridization group of enteric organisms was isolated and found to be associated with bloodstream infections.[10]
The type strain of "E. hormaechei" is ATCC 49162 and was isolated from the sputum of a man in California in 1977.[10] The whole-genome shotgun sequencing project was submitted in 2011 to the Human Genome Sequencing Center (TX, USA; GenBank accession number AFHR00000000).
"E. hormaechei" consists of three different subspecies: "E. hormaechei" subsp. "oharae", "E. hormaechei" subsp. "hormaechei" and "E. hormaechei" subsp. "steigerwaltii", which corresponds to genetic clusters VI, VII and VIII, respectively.[8] The differentiation of these subspecies is based on their particular properties and biochemical tests.[11]
"E. hormaechei" is commonly isolated as a nosocomial pathogen of clinical significance;[45,46] it has been reported in several outbreaks of sepsis in neonatal intensive care units in the USA[47] and in Brazil, where the outbreak originated from contaminated parenteral nutrition.[48]
"E. kobei" is named after Kobe City (Japan), where the type strain of this species was isolated. "E. kobei" was first described by Kosako et al. based on a collection of 23 strains with the general traits of "E. cloacae" and the common phenotypic difference of being Voges–Proskauer-negative.[49] The name "E. kobei" is proposed for a group of organisms referred to as NIH group 21 at the NIH, Tokyo. It was later found that NIH group 21 also resembled the CDC enteric group 69,[50] and "E. kobei" was compared with the latter. On the basis of DNA relatedness, both organisms could be included in a single taxon. However, the CDC enteric group 69 was described as positive in Voges–Proskauer and yellow pigmentation,[50] whereas all strains of E. kobei were Voges–Proskauer- and pigmentation-negative. These findings suggest that the relationship of both organisms is at the subspecies or biogroup level. The type strain of E. kobei is NIH 1485–1479 and was isolated by blood culture of a diabetic patient.
"E. ludwigii", named after Wolfgang Ludwig, a microbiologist working in bacterial systematics[51] and who developed the ARB databases as well as making them public.[52] This description is based on the phylogenetic analyses of partial hsp60 sequence data collected in a population genetic study,[6] as well as on DNA–DNA hybridization assays and phenotypic characterizations.
The type strain EN-119T was isolated from midstream urine of an 18-year-old male patient with a nosocomial urinary tract infection while he was hospitalized at the Grosshadern University-Hospital Munich, Germany. The GenBank accession number of the 16S rDNA of strain EN-119T is AJ853891.[12]
"E. nimipressuralis" The species "E. nimipressuralis" was originally defined by Brenner et al. and was formerly called "Erwinia nimipressuralis", which was isolated from nonclinical sources (e.g., elm trees with a disease called wet wood).[43] "Erwinia nimipressuralis" was inserted in the Approved Lists of Bacterial Names in 1980. This microorganism is biochemically similar to "E. cloacae", but it is different for acid production from sucrose and raffinose, whereas "E. cloacae" is positive in these tests. The type strain of "E. nimipressuralis" is ATCC 9912 and isolated from the elm Ulmus spp. in the USA (GenBank accession number AJ567900).
"E. cloacae subsp.cloacae strain PR-4 was isolated and identified by 16S rDNA gene sequence with phylogenetic tree view from explosive laden soil by P Ravikumar (GenBank accession number KP261383).
E. cloacae SG208 identified as a predominant microorganism in mixed culture isolated from petrochemical sludge, IOCL, Guwahati is responsible for degradation of benzene was reported by Padhi and Gokhale (2016)[137].


Microbial food web

The microbial food web refers to the combined trophic interactions among microbes in aquatic environments. These microbes include viruses, bacteria, algae, heterotrophic protists (such as ciliates and flagellates).
In aquatic environments, microbes constitute the base of the food web. Single celled photosynthetic organisms such as diatoms and cyanobacteria are generally the most important primary producers in the open ocean. Many of these cells, especially cyanobacteria, are too small to be captured and consumed by small crustaceans and planktonic larvae. Instead, these cells are consumed by phagotrophic protists which are readily consumed by larger organisms. Viruses can infect and break open bacterial cells and (to a lesser extent), planktonic algae (a.k.a. phytoplankton). Therefore, viruses in the microbial food web act to reduce the population of bacteria and, by lysing bacterial cells, release particulate and dissolved organic carbon (DOC). DOC may also be released into the environment by algal cells. One of the reasons phytoplankton release DOC termed "unbalanced growth" is when essential nutrients (e.g. nitrogen and phosphorus) are limiting. Therefore, carbon produced during photosynthesis is not used for the synthesis of proteins (and subsequent cell growth), but is limited due of a lack of the nutrients necessary for macromolecules. Excess photosynthate, or DOC is then released, or exuded.
The microbial loop describes a pathway in the microbial food web where DOC is returned to higher trophic levels via the incorporation into bacterial biomass.


Acarospora citrina

Acarospora citrina is a lichen in the family, Acarosporaceae, first described as "Urceolaria citrina" by
Thomas Taylor in 1847. It was assigned to the genus, "Acarospora", in 1913 by Alexander Zahlbruckner.
This lichen has been found in all mainland states of Australia, on rocks in sclerophyll woodland.


Aster (cell biology)

An aster is a cellular structure shaped like a star, consisting of a centrosome and its associated microtubules during the early stages of mitosis in an animal cell. Asters do not form during mitosis in plants. Astral rays, composed of microtubules, radiate from the centrosphere and look like a cloud. Astral rays are one variant of microtubule which comes out of the centrosome; others include kinetochore microtubules and polar microtubules.
During mitosis, there are five stages of cell division: Prophase, Prometaphase, Metaphase, Anaphase, and Telophase. During prophase, two aster-covered centrosomes migrate to opposite sides of the nucleus in preparation of mitotic spindle formation. During prometaphase there is fragmentation of the nuclear envelope and formation of the mitotic spindles. During metaphase, the kinetochore microtubules extending from each centrosome connect to the centromeres of the chromosomes. Next, during anaphase, the kinetochore microtubules pull the sister chromatids apart into individual chromosomes and pull them towards the centrosomes, located at opposite ends of the cell. This allows the cell to divide properly with each daughter cell containing full replicas of chromosomes. In some cells, the orientation of the asters determines the plane of division upon which the cell will divide.
Astral microtubules.
Astral microtubules are a subpopulation of microtubules, which only exist during and immediately before mitosis. They are defined as any microtubule originating from the centrosome which does not connect to a kinetochore. Astral microtubules develop in the actin skeleton and interact with the cell cortex to aid in spindle orientation. They are organized into radial arrays around the centrosomes. The turn-over rate of this population of microtubules is higher than any other population.
The role of astral microtubules is assisted by dyneins specific to this role. These dyneins have their light chains (static portion) attached to the cell membrane, and their globular parts (dynamic portions) attached to the microtubules. The globular chains attempt to move towards the centrosome, but as they are bound to the cell membrane, this results in pulling the centrosomes towards the membrane, thus assisting cytokinesis.
Astral microtubules are not required for the progression of mitosis, but they are required to ensure the fidelity of the process. The function of astral microtubules can be generally considered as determination of cell geometry. They are absolutely required for correct positioning and orientation of the mitotic spindle apparatus, and are thus involved in determining the cell division site based on the geometry and polarity of the cells.
The maintenance of astral microtubules is dependent on the integrity of centrosome. It is also dependent on several microtubule-associated proteins such as EB1 and adenomatous polyposis coli (APC).
Growth of Microtubules
Polymerization and nucleation are the two microscopic processes in with the growth of asters occur. At the negative ends of the aster , centrosomes will nucleate (form a nucleus) and anchor to the microtubules. At the positive end, polymerization of the aster will occur towards the outer. Cortical Dyenein, a motor protein moves along the microtubules of the cell and plays a key role in the growth and inhibition of aster microtubules. A dyenein that is barrier-attached can inhibit and trigger growth.


Bacteroides caccae

Bacteroides caccae is a saccharolytic gram-negative bacterium from the genus Bacteroides. They are obligate anaerobes first isolated from human feces in the 1980s. Prior to their discovery, they were known as the 3452A DNA homology group. The type strain is now identified as ATCC 43185.
Cell morphology and physiology.
"Bacteroides caccae" is a saccharolytic anaerobic, nonmotile Gram-negative bacteria. They have a DNA GC content of 40-46 mol %. Growth occurs at human temperature (37 °C) under anaerobic conditions. There is no growth at 25 °C or 45 °C. Its cell shapes are rods that are 1.4-1.6 by 2.5-12 µm in size. The rods are found in single cells or in pairs. In a broth culture mixed with a fermentable carbohydrate, the cells will appear vacuolated or beaded. The surface colonies of cells grown on BHI blood agar plates following 48 hours of incubation show a circular cell of 0.5–1 mm in diameter. In addition, colonies are convex, gray, translucent, shiny, and smooth. Growth on rabbit blood shows slight hemolysis. In glucose broth, the cultures appear turbid with a smooth sediment and a final pH range of 5 – 5.2.
The type strain reduces neutral red but does not produce hydrogen sulfide. Growth on peptone-yeast extract-glucose broth cultures with 20% bile yields vast amounts of acetate and succinate but minor amounts of propionate and isovalerate. Lactate and threonine are not used by the type strain. "B. caccae" produces a trace amount of (0.1%) of hydrogen. They hydrolyze esculin, weakly digest gelatin, and are susceptible to chloramphenicol and clindamycin, but not susceptible to penicillin G and tetracycline.
Pathogenicity.
For the onset of intestinal bowel diseases (IBD) such as Crohn's disease (CD) or Ulcerative colitis (UC), commensal enteric bacteria are generally required as a pathogenic factor. "B. caccae" contains a TonB-linked outer membrane protein called OmpW that has only been characterized in this particular strain. The OmpW protein contains features similar to a bacterial TonB-linked outer membrane protein which allows the bacteria to increase its ability of iron or vitamin uptake in an environment where it lacks these variables. The TonB-linked outer membrane protein contains a TonB box that is highly conserved and also present in OmpW. OmpW may play a role in facilitating the organism's ability to uptake substrates that are important for commensal bacterial survival in the intestine. The immunological finding of OmpW is an elevation of anti-OmpW IgA levels in some patients with Crohn's disease in comparison to these IgA levels in patients with ulcerative colitis or healthy subjects. More remains to be elucidated on its potential pathogenicity with regards to OmpW. In addition, "B. caccae" has also been found in cultures from infections in the appendix and the abdomen (peritoneal)
Metabolism.
"Bacteroides caccae" was specified as being a fiber-degrading microbial specialist in the microbiomes of Western individuals. In a study geared at determining the fermentation of pectin in "B. caccae" from a rabbit cecum, it was determined that cultures grown with pectin produced more acetate than formate, lactate, fumarate, and succinate as opposed to those cultures grown on glucose which yielded vast amounts of lactate. This elucidates the metabolism of a plant fiber by a human commensal. In addition, "B. caccae" showed no growth on arabinan (a pectin), arabinoxylan (wheat), xylan, xyloglucan, glucomannan, galactomannan, B-glucan, lichenin, and laminarin. They do grow on host-derived glycans like neutral mucin O-glycans, chondroitin sulfate, and hyaluronic acid. The monosaccharides that induce growth are arabinose, fructose, fucose, galactose, galacturonic acid, glucose, glucuronic acid, glucosamine, mannose, N-acetylgalactosamine, N-acetylglucosamine, N-acetylneuraminic acid, rhamnose, ribose, and xylose


Cyanothecaceae


Systems Biology Ireland

Systems Biology Ireland (SBI) is a Science Foundation Ireland (SFI) funded Centre for Science, Engineering and Technology research initiative between the University College Dublin (UCD) and the National University of Ireland, Galway (NUI Galway). It is based on the Belfield campus of UCD, and works in the areas of systems biology, systems medicine and personalised medicine.
SBI designs new therapeutic approaches to cancer, its research enabling the development of technologies that can be used for early identification of responsive patient groups and accelerated discovery of new combination therapies.
Principal investigators.
Director: Prof. Walter Kolch

Deputy Director: Prof. Boris Kholodenko
Principal investigators:

Prof. Frank Barry

Prof. Guenther Eissner

Prof. Des Higgins

Dr. Heinz-Peter Nasheuer

Prof. Tim O'Brien

Prof. Cormac Taylor


Redondoviridae

Redondoviruses (members of the Redondoviridae) are a family of human-associated DNA viruses. Their name derives from the inferred circular structure of the viral genome (“” means round in Spanish). Redondoviruses have been identified in DNA sequence based surveys of samples from humans, primarily samples from the oral cavity and upper airway.
Virology.
Taxonomy.
Redondoviruses are assigned to a new family by the International Committee on Taxonomy of Viruses (ICTV), the "Redondoviridae".
Classification.
The family "Redondoviridae" is divided into two species, "Brisavirus" and "Vientovirus". The names derive from the words for breeze and wind in Spanish (“” and “"viento"”), denoting the association with the human airway. Multiple strains have been proposed on the basis of viral genome structure.
The redondoviruses are members of the Circular Rep-Containing Single Stranded (CRESS) DNA Virus group.
Genome.
The redondovirus genome is circular, and by analogy to other CRESS viruses likely single stranded. Genomes range in size from about 3.0 to 3.1 kilobases. The genome encodes three inferred proteins:
Epidemiology.
Distribution.
Redondovirus genomes have been reported primarily from human samples surveyed using metagenomic DNA sequencing. They have been found primarily in oral and airway specimens.
Disease associations.
It is unknown whether redondoviruses cause human disease. Some CRESS viruses are known pathogens, such as porcine circovirus type 2
Redondoviruses have been reported associated with periodontitis. In one study, the levels fell with successful treatment. Abundance of redondovirus genomes has also been found to be high in some intensive care unit patients. At present the basis of these disease associations is unclear.


Diplocystis

Diplocystis is a genus of fungi in the Diplocystaceae family. The single species in the genus, Diplocystis wrightii, has been shown using phylogenetic analysis to be a member of the Sclerodermatineae suborder of the Boletales. The species was originally described in 1869 by Miles Joseph Berkeley and Moses Ashley Curtis, from specimens collected in the Caribbean.


Xipapillomavirus

Xipapillomavirus is a genus of viruses, in the family "Papillomaviridae". Bovine serve as natural hosts. There are five species in this genus. Diseases associated with this genus include: true papillomas on the cutaneous or mucosal surfaces of cattle.
Taxonomy.
The following five species are assigned to the genus:
Structure.
Viruses in "Xipapillomavirus" are non-enveloped, with icosahedral geometries, and T=7 symmetry. The diameter is around 52-55 nm. Genomes are circular, around 7kb in length. The genome has 6 open reading frames.
Life cycle.
Viral replication is nuclear. Entry into the host cell is achieved by attachment of the viral proteins to host receptors, which mediates endocytosis. Replication follows the dsDNA bidirectional replication model. DNA-templated transcription, with some alternative splicing mechanism is the method of transcription. The virus exits the host cell by nuclear envelope breakdown.
Bovine serve as the natural host. Transmission routes are contact.