Malassezia nana

Malassezia nana is a fungus that can cause opportunistic infections in animals. It was first isolated from animals in Japan and Brazil. "M. nana" resembles "M. dermatis" and "M. sympodialis", but is distinguished from these species by its inability to use Kolliphor EL (Sigma) as the sole lipid source and to hydrolyse aesculin. The type strain of "M. nana" is NUSV 1003T(=CBS 9557T=JCM 12085T).


Bidnaviridae


Compensation (cytometry)

In cytometry, compensation is a mathematical correction of a signal overlap between the channels of the emission spectra of different fluorochromes.
The photons emitted by fluorochromes have different energies and wavelengths and as flow cytometers use photomultiplier tubes (PMT) in order to convert the photons into electrons, the detector can register the signal from more than one fluorochrome. This creates a signal overlap (spillover) which cannot be removed by the optical system and has to be corrected electronically. The compensation can be done through different flow cytometry software such as Flowjo, Flowlogic, Kaluza etc. The first data compensation was done in 1977 by Michael Loken et al. during a two colour experiment, where mouse splenocytes were stained with fluorescein and rhodamine.
Spillover.
When one cell is marked by two or more fluorochromes, the added brightness of one fluorochrome to the other creates significant background noise and affects the strength of the signal. This is called a spillover. The physical overlap between the different emission spectra of fluorochromes can activate different receptors than the ones intended for the given wavelength. The ability to correct this stems from the fact, that the overlap is a linear function, so the measured signal can be averaged and thus corrected. This correction is called compensation.
Compensation is necessary in order to be able to differentiate between populations of cells. This is done by measuring the spectral overlap of the different fluorochromes and using the measured values to create a matrix. The matrix is then inverted and gives the actual compensation values. The flow cytometer then uses these values to correct the overlap in each detector for each colour.


Rhopalomyces elegans

Rhopalomyces elegans is a common species of zygomycete fungus, and the type species of the genus "Rhopalomyces". Widely distributed, it is found in soil, rotting plant material, and animal dung. It is a facultative parasite of nematode eggs.
Taxonomy.
The species was first recorded by August Carl Joseph Corda, who isolated it from material collected from a Prague greenhouse. In 1962, Ellis and Hesseltine demonstrated a method to grow the species in pure culture by using a growth medium containing calf's liver and lamb fat. A year later, Ellis recognized four varieties of "Rhopalomyces elegans", defined by their growth in different media: "minor", "crassus", "apiculatus", and the nominate variety "elegans".
Description.
When grown in pure culture conditions on a petri dish at a temperature of , "Rhopalomyces elegans" produces hyaline (translucent), partially submerged colonies that fill the plate in about six days. The fungus produces large, dark brown conidiospores borne on a swollen vesicle at the end of a conidiophore. The vesicles measure 40–63 μm in diameter. The hyphae are very thin, measuring only 2 μm in diameter.
"Rhopalomyces magnus" is similar in morphology, but only attacks eggs of rotifers.
Ecology.
A common species, "R. elegans" is found in rotting plant material and animal debris, as well as dung associated with soil. The fungus is a parasite of nematode eggs. When it encounters an egg, it produces hyphae that form a structure on the egg surface similar to an appressorium. This structure produces a narrow infection tube that penetrates the egg shell. Once inside, fungal hyphae proliferate by branching and expanding, eventually filling the interior of the egg and absorbing the nutrients within." R. elegans" may be able to attack the larval and adult stages of some nematode species.
"Rhopalomyces elegans" can itself be parasitized by the fungi "Mycogone perniciosa" and "Verticillium psalliotae". "Verticillium psalliotae" is a saprobic soil-dwelling fungus that is a parasite of the common commercially grown button mushroom ("Agaricus bisporus"). "R. elegans" may serve as a reservoir for the pathogen, and may harbor the parasite in its thick cell walls.


Dipodascaceae

The Dipodascaceae are a family of yeasts in the order Saccharomycetales. According to the 2007 Outline of Ascomycota, the family contains four genera; however, the placement of "Sporopachydermia" and "Yarrowia" is uncertain. Species in the family have a widespread distribution, and are found in decaying plant tissue, or as spoilage organisms in the food industry.


Turnip crinkle virus

Turnip crinkle virus (TCV) is a plant pathogenic virus of the family "Tombusviridae". It was first isolated from turnip ("Brassica campestris" ssp. "rapa").
Structure.
TCV is a small (4054 base pairs), single-stranded, positive-sense RNA virus (viral RNA is in the same orientation as mRNA). It has been shown to infect various types of plant species (including "Nicotiana benthamiana") including the common plant model, "Arabidopsis thaliana". Its gRNA encodes for five proteins: p28 and p88 (replication), p8 and p9 (movement) and CP (coat protein or encapsidation). The structure of the virus was determined to 3.2 Ångstrom resolution using x-ray crystallography in 1986. It is structurally quite similar to the tomato bushy stunt virus.
A number of non-coding RNA elements have been characterised in the TCV genome; examples are hairpin 5 and the core promoter.
Replication.
Replication of the viral RNA begins with the migration of p28 to the mitochondrial membrane. p28 migrates to and invaginates the outer mitochondrial membrane; several p88 molecules are brought the newly formed vesicles. The viral RNA binds to the p28 bound to the membrane and the RNA dependent RNA polymerase, or p88, initiates replication of the positive strand RNA to produce a minus strand intermediate. The negative-strand intermediate is used as a template to produce progeny positive strand RNA. The coat proteins p8, p9, and p38, are involved in movement in the plant.
Satellite viruses.
Small, helper viruses known as satellite RNA have been found to co-infect plants only in the presence of TCV. These non-coding RNAs up-regulate the symptoms of TCV infection. The satellite RNA are dependent of the TCV and host machinery to propagate. Satellite C shares sequence homology with the 3'end of the TCV, while satellite D shares sequence homology with the 5'end of satellite C.


Malassezia sympodialis

Malassezia sympodialis is a species in the genus "Malassezia". It is characterized by a pronounced lipophily, unilateral, percurrent or sympodial budding and an irregular, corrugated cell wall ultrastructure. It is one of the most common species found on the skin of healthy and diseased individuals. It is considered to be part of the skin's normal human microbiota and begins to colonize the skin of humans shortly after birth. "Malassezia sympodialis", often has a symbiotic or commensal relationship with its host, but it can act as a pathogen causing a number of different skin diseases, such as atopic dermatitis.
History.
In 1846, Karl Ferdinand Eichstedt was the first to identify the association of fungi with pityriasis versicolor, a common infection associated with the genus "Malassezia". The name applied to the fungal agent responsible shifted multiple times over the next 150 years until the genus "Pityrosporum" was settled upon for the teleomorph, and "Malassezia" for the anamorph. Through the use of genetic sequencing, a number of new species have since been identified.
Description.
"Malassezia sympodialis" exhibits unipolar budding, similar to a number of other "Malassezia" species including "M. pachydermatis". The colonies achieve a size of 5 mm in diameter after a week of growth, and develop a soft texture and a round, smooth shape. The individual cells are oval in shape and 2.5-7.5 × 2.0-8.0 μm in size and acquire a yellowish appearance "en masse" when grown in culture at . The optimal growth of this species occurs at . A range of specialized growth media such as Cremophor EL and Leeming-Notman agar that incorporate fatty acids support the growth of "M. sympodialis". However, non-specialized growth media overlaid with sterile olive oil also support the growth of this species in culture. "Malassezia sympodialis" can be identified in the laboratory by the presence of β-glucosidase activity which causes darkening of the growth medium.
Pathogenicity in humans and animals.
The innate and adaptive immune systems are both important for the health of the skin. There are several different types of cells, such as neutrophils, that search their environment for antigens by using pattern recognition receptors and are essential in the innate immune response. "Malassezia sympodialis" causes atopic eczema in susceptible individuals. Many of the skin diseases caused by this species occur when the barrier of the skin is breached, allowing the organism to access the damaged integument, such as occurs in individuals infected with atopic eczema. The "M. sympodialis" peptide LL-37 is found in monocyte-derived dendritic cells where it is involved in initiating a Th-2 like response. The Th-2 like response is involved in the creation of IgE and is therefore important for individuals with atopic eczema. There are several factors that contribute to the development of atopic eczema, including the environment and genetics.
Human diseases.
"Malassezia sympodialis" has been identified conjunction with a number of human skin disorders include pityriasis versicolor, seborrheic dermatitis and dandruff and atopic dermatitis. There have also been reports of "M. sympodialis" in patients with granulomatous dermatitis.
Pityriasis versicolor.
Pityriasis versicolor is a skin disorder that leads to the formation of patches on the skin that are either hypo- or hyperpigemented. It may be found on oilier areas of the body including the neck and trunk. Besides "M. sympodialis", several species of "Malassezia" have been identified on individuals with the disorder including, "M. globosa", "M. slooffiae" and several others. Some believe that "M. globosa" is responsible for the disease as it has been found in higher numbers, but this has not yet been confirmed. Confirmation of the agent of disease involves microscopic examination of skin scrapings from the infected individuals for the presence of thick-walled yeast cells intermixed with broad hyphae. Ointments containing fungicidal ingredients such as selenium can be applied to the affected area. Oral medications are also used in some cases.
Seborrhoeic dermatitis and dandruff.
Seborrheic dermatitis is a skin disorder where inflammation and desquamation occurs in areas of the body with a high density of sebaceous glands, particularly the face and trunk. The dandruff form does not result in inflammation and is restricted to the scalp. Although 'M. sympodialis" has been reported as an agent of seborrhoeic dermatitis and dandruff, other species including "M. furfur" and "M. globosa" are more commonly associated with the disorder.
Atopic dermatitis.
Atopic dermatitis occurs in individuals that have an abnormal immune reaction to allergens resulting in inflammation on the affected area of the skin. This disorder is associated with "M. furfur", "M. restricta", "M. sympodialis" and a number of other species.
Animal diseases.
"Malassezia sympodialis" has been identified in high frequency on dogs that have some form of dermatitis and is found in association with other species of "Malassezia". This species has also been associated with otitis in cattle, cats and other animals.


Elaine Ingham

Elaine Ingham is an American microbiologist and soil biology researcher and founder of Soil Foodweb Inc. She is known as a leader in soil microbiology and research of the soil food web, She is an author of the USDA's "Soil Biology Primer".
Career.
On 1981, Ingham earned a PhD from the Colorado State University in microbiology with an emphasis in soil. Along with her husband Russ, who has a doctorate in zoology emphasizing nematology, she was offered a post-doctoral fellowship at the Natural Resource Ecology Lab at Colorado State University. In 1985, she accepted a Research Associate Fellowship at the University of Georgia.
In 1986, Ingham moved to Oregon State University and joined the faculty in both Forest Science and Botany and Plant Pathology. She remained on faculty until 2001.
Ingham has been an Affiliate Professor of Sustainable Living at Maharishi University of Management in Fairfield, Iowa, Adjunct Faculty at Southern Cross University in Lismore, New South Wales from 1999 to 2005, Visiting Professor with Melbourne University from 2004 to 2008, and was Program Chair of the Ecological Society of America from 1999 to 2000. She was named chief scientist at The Rodale Institute in 2011 and was later director of research and an instructor at the Agricultural Celebration Institute's farm in California.
She is the founder of Soil Foodweb Inc, which works with soil testing laboratories to assess soil biology.


Epithelial polarity

Cell polarity is a fundamental feature of many types of cells. Epithelial cells are one example of a polarized cell type, featuring distinct 'apical', 'lateral' and 'basal' plasma membrane domains. Epithelial cells connect to one another via their lateral membranes to form epithelial sheets that line cavities and surfaces throughout the animal body. Each plasma membrane domain has a distinct protein composition, giving them distinct properties and allowing directional transport of molecules across the epithelial sheet. How epithelial cells generate and maintain polarity remains unclear, but certain molecules have been found to play a key role.
A variety of molecules are located at the apical membrane, but only a few key molecules act as determinants that are required to maintain the identity of the apical membrane and, thus, epithelial polarity. These molecules are the proteins Cdc42, atypical protein kinase C (aPKC), Par6, Par3/Bazooka/ASIP. Crumbs, "Stardust" and protein at tight junctions (PATJ). These molecules appear to form two distinct complexes: an aPKC-Par3-Par6 "aPKC" (or "Par") complex that also interacts with Cdc42; and a Crumbs-Stardust-PATJ "Crumbs" complex. Of these two complexes, the aPKC complex is the most important for epithelial polarity, being required even when the Crumbs complex is not. Crumbs is the only transmembrane protein in this list and the Crumbs complex serves as an apical cue to keep the aPKC complex apical during complex cellular shape changes.
Basolateral membranes.
In the context of renal tubule physiology, the term basolateral membrane or serosal membrane refers to the cell membrane which is oriented "away" from the lumen of the tubule, whereas the term luminal membrane or apical membrane refers to the cell membrane which is oriented "towards" the lumen. The principal function of this basolateral membrane is to take up metabolic waste products into the epithelial cell for disposal into the lumen where it is transported out of the body as urine. A secondary role of the basolateral membrane is to allow the recycling of desirable substrates, such as glucose, that have been rescued from the lumen of the tubule to be secreted into the interstitial fluids.
Basal and lateral membranes share common determinants, the proteins LLGL1, DLG1, and SCRIB. These three proteins all localize to the basolateral domain and are essential for basolateral identity and for epithelial polarity.
Mechanisms of polarity.
How epithelial cells polarize is still not fully understood. Some key principles have been proposed to maintain polarity, but the mechanisms behind these principles remain to be discovered.
The first principle is positive feedback. In computer models, a molecule that can be either membrane-associated or cytoplasmic can polarize when its association with the membrane is subject to positive feedback: that membrane localization occurs most strongly where the molecule is already most highly concentrated. In similar models, researchers have shown that epithelial cells can self-assemble into a rich set of robust biological shapes. In the yeast saccharomyces cerevisiae, there is genetic evidence that Cdc42 is subject to positive feedback of this kind and can spontaneously polarize, even in the absence of an external cue. In the fruit fly Drosophila melanogaster, Cdc42 is recruited by the aPKC complex and then promotes the apical localization of the aPKC complex in a probable positive feedback loop. Thus, in the absence of Cdc42 or the aPKC complex, apical determinants cannot be maintained at the apical membrane and consequently, apical identity and polarity is lost.
The second principle is segregation of polarity determinants. The sharp distinction between apical and baso-lateral domains is maintained by an active mechanism that prevents mixing. The nature of this mechanism is not known, but it clearly depends on the polarity determinants. In the absence of the aPKC complex, the baso-lateral determinants spread into the former apical domain. Conversely, in the absence of any of Lgl, Dlg or Scrib, the apical determinants spread into the former baso-lateral domain. Thus, the two determinants behave as if they exert mutual repulsion upon one another.
The third principle is directed exocytosis. Apical membrane proteins are trafficked from the Golgi to the apical, rather than baso-lateral, membrane because apical determinants serve to identify the correct destination for vesicle delivery. A related mechanism is likely to operate for the baso-lateral membranes.
The fourth principle is lipid modification. A component of the lipid bilayer, phosphatidyl inositol phosphate (PIP) can be phosphorylated to form PIP2 and PIP3. In some epithelial cells, PIP2 is apically localised while PIP3 is basolaterally localised. In at least one cultured cell line, the MDCK cell, this system is required for epithelial polarity. The relationship between this system and the polarity determinants in animal tissues remains unclear.
Basal versus lateral.
Since basal and lateral membranes share the same determinants, another mechanism must make the difference between the two domains. Cell shape and contacts provide the likely mechanism. Lateral membranes are the site of contact between epithelial cells, whereas basal membranes connect epithelial cells to the basement membrane, an extracellular matrix layer that lies along the basal surface of the epithelium. Certain molecules, such as Integrins, localise specifically to the basal membrane and form connections with the extracellular matrix.
Epithelial cell shape.
Epithelial cells come in a variety of shapes that relate to their function in development or physiology. How epithelial cells adopt particular shapes is poorly understood, but it must involve spatial control of the actin cytoskeleton, which is central to cell shape in all plant cells.
Epithelial cadherin.
All epithelial cells express the transmembrane adhesion molecule E-cadherin, a cadherin which localises most prominently to the junction between the apical and lateral membranes. The extra-cellular domains of E-cadherin molecules from neighbouring cells bind to one another via a homotypic interaction. The intra-cellular domains of E-cadherin molecules bind to the actin cytoskeleton via the adaptor proteins alpha-catenin and beta-catenin. Thus, E-cadherin forms adherens junctions that connect the actin cytoskeletons of neighbouring cells. Adherens junctions are the primary force-bearing junctions between epithelial cells and are fundamentally important for maintaining epithelial cell shape and for dynamic changes in shape during tissue development. How E-cadherin localizes to the boundary between apical and lateral membranes is not known, but polarized membranes are essential for maintaining E-cadherin at adherens junctions.


Cell-free system

A cell-free system is an "in vitro" tool widely used to study biological reactions that happen within cells apart from a full cell system, thus reducing the complex interactions typically found when working in a whole cell. Subcellular fractions can be isolated by ultracentrifugation to provide molecular machinery that can be used in reactions in the absence of many of the other cellular components. Eukaryotic and prokaryotic cell internals have been used for creation of these simplified environments. These systems have enabled cell-free synthetic biology to emerge, providing control over what reaction is being examined, as well as its yield, and lessening the considerations otherwise invoked when working with more sensitive live cells.
Types.
Cell-free systems may be divided into two primary classifications: cell extract-based, which remove components from within a whole cell for external use, and purified enzyme-based, which use purified components of the molecules known to be involved in a given process. The cell extract-based type are susceptible to problems like quick degradation of components outside their host, as shown in a study by Kitaoka "et al." where a cell-free translation system based on "Escherichia coli" ("E. coli"), of the cell extract-based type, had the mRNA template degrade very quickly and led to the halt of protein synthesis.
Preparation.
The methods of preparation vary between situations of both types of cell-free systems.
Cell extract–based.
Nobel prize winner Eduard Buchner was arguably the first to present a cell-free system using yeast extracts, but since then alternative sources have been found. "E. coli", wheat germ, and rabbit reticulocytes have all proven useful to create cell-free systems by extraction of their interior components. "E. coli" 30S extracts have been acquired, for example, by grinding the bacteria with alumina, followed by further cleaning. Similarly, wheat germ has been ground with acid-washed sand or powdered glass to open the cell membranes up. Rabbit reticulocytes have been lysed in a solution of MgCl and had the extract filtered away from the membranes by centrifugation.
Purified enzyme–based.
Cell-free synthetic pathway biotransformation biosystems can be prepared by mixing a number of purified enzymes and coenzymes. For example, tightly coupled ribosomes, which are compact and highly active, have been extracted and refined from "E. coli" through sucrose-density-gradient centrifugation.
Uses.
Cell-free synthetic pathway biotransformation biosystems are proposed as a new low-cost biomanufacturing platform compared to microbial fermentation used for thousands of years. Cell-free biosystems have several advantages suitable in industrial applications:
Protein synthesis.
"In vitro" biosystems can be easily controlled and accessed without membranes. Notably, in work leading to a Nobel prize the Nirenberg and Matthaei experiment used a cell-free system, of the cell extract-based type, to incorporate chosen amino acids tagged radioactively into synthesized proteins with 30S extracted from "E. coli". More recent studies, such as the study done by Spirin "et al." with prokaryotic and eukaryotic version of their cell-free translation system, have also synthesized proteins with increased production, incorporating techniques like continuous flow to add materials and remove products. With such advances in yield, productivity applications have been expanded, such as the synthesis of fusion proteins to potentially serve as vaccines for B-cell lymphomas. Additionally, cell-free protein synthesis is becoming a new alternative choice for fast protein synthesis.
Metabolic manipulation.
Engineering of metabolic processes have been achieved through cell-free systems. Bujara "et al.", for example, were able to use glycolytic network extracts, consisting of enzymes from "E. coli" that produced dihydroxyacetone phosphate, to analyze in real-time the metabolite concentrations while altering enzyme levels, with the end result of optimal production of dihydroxyacetone phosphate. Further, Calhoun and Swartz were able to use a glycolytic intermediate to fuel a cell-free system, enabling relatively inexpensive ATP generation compared to reagent usage in phosphoenolpyruvate reactions.
Unnatural amino acid incorporation.
Cell-free systems have also been used to incorporate unnatural amino acids. Shimizu "et al." were able to change a stop codon to a sense codon by omitting the RF1 release factor, indicating ability to insert desired amino acids in unnatural situations. This is of use in systems where working inside a cell is problematic, such as the process of amino acid metabolism preventing specific labelling of amino acids that would be useful in multidimensional NMR spectroscopy. Kigawa "et al."were able to successfully label amino acids in a cell-free system where amino acid metabolism was no longer present, thus making such systems useful to NMR studies.


Inovirus

Inovirus is a genus of viruses in the family "Inoviridae". Gram-positive and gram-negative bacteria (specifically "Enterobacteriaceae", "Pseudomonadaceae", "Spirillaceae", "Xanthomonadaceae", "Clostridium" and "Propionibacterium") serve as natural hosts in this family. The type species "Escherichia virus M13" is the only species recognized by the 2019 release of the ICTV in the genus, but this classification is out of date, and many other species are known. The name of the genus is derived from the Greek word "Ίνα" meaning 'fibre or filament'.
Virology.
"Inovirus" virions consist of a non-enveloped, worm-like chain with helical symmetry. The virions are between 760 and 1950 nm in length and 6-8 nm in width.
Their capsid consists of 5 or more proteins: gp8 (the major capsid protein); gp6, gp7 and gp8 (minor capsid proteins); and gp3 which acts as the initial host binding protein.
The genomes are circular, positive-sense, single-stranded DNA 4.4-8.5 kilobases in length. They encode 4 to 11 proteins. Replication of the genome occurs via a dsDNA intermediate and the rolling circle mechanism. Gene transcription is by the host's cellular machinery each gene having a specific promoter.
The viral protein gp2 plays an essential role in viral DNA replication. It binds to the origin of replication, and cleaves the dsDNA intermediate, allowing DNA replication to initiate at the cleavage site. After one round of rolling circle synthesis, gp2 is linked to the newly synthesized ssDNA and joins the ends of the displaced strand to generate a new circular single-stranded molecule ready to be packed into a virion.
Life cycle.
Inoviruses begin their life cycle by attaching to specific host receptors via viral protein gp3. After attachment, they insert their viral DNA into the host cell. Once inside the cell, they convert the genome into a double-stranded intermediate form which is then replicated by the host's DNA polymerase. At the same time, the host's RNA polymerase transcribes the viral genome to make mRNA and viral proteins. The replicated genomes then combine with newly synthesized viral proteins to make more viruses, which are released from the host. This replication cycle generally takes 10–15 minutes to complete.
Replication.
Genome replication is initiated when a viral endonuclease (gp2) nicks the double stranded intermediate. This nicking site is specific and the sequence around the site highly symmetrical. The activity of gp2 is regulated by two other viral proteins: gp5 (single strand binding protein) and gp10. New viral genomes are produced via the rolling circle mechanism. These new single strand DNA sequences become templates for further DNA and RNA synthesis. When sufficient gp5 has accumulated within the cell, further DNA synthesis is halted and virion assembly begins.
Virion assembly.
Virion assembly is initiated by the formation of a complex of gp1, gp7, gp9 and gp11 along with the single stranded DNA. It begins at a specific sequence within the DNA which is predicted to have a hairpin formation. Assembly continues at the membrane where ~1500 subunits of gp5 are displaced by ~2700 subunits of gp8 (the number of major capsid protein subunits per virion). This process involves both gp1 and gp11. The virion is extruded through the plasma membrane without killing the host, and is a useful model system to study transmembrane protein. Assembly is completed by the addition of the viral proteins gp3 and gp6. In hosts with both an inner and outer membrane adhesion zones are created by gp4, a process that may also involve gp1.
Virion release.
Productive infection may occur by budding from the host membrane. This pattern is typically seen in the genus "Plectivirus".
Notes.
A number of exceptions to this life cycle are known. Lysogenic species, which encode integrases, exist within this family.
The phage DNA may integrate into the host genome via site-specific homologous recombination. Most phages that do integrate into the host genome encode a recombinase. Inoviruses do not encode this enzyme. The phages that infect hosts in the genus "Vibro" highjack the chromosome dimer resolution system of their hosts in order to integrate into the genome of the host.
Relevance.
At least one of the viruses (Vibrio phage CTX) is medically important as it encodes the cholera toxin.
Inovirus has been extensively used in experimental work in microbiology.
Non biological uses.
Derivatives of phage M13 have been created for use in materials science by Angela Belcher and colleagues.


Parvarchaeum acidophilus


Mycobacterium heckeshornense

Mycobacterium heckeshornense is a species of the phylum Actinobacteria (Gram-positive bacteria with high guanine and cytosine content, one of the dominant phyla of all bacteria), belonging to the genus "Mycobacterium".
Description.
Gram-positive, nonmotile and acid-fast rods. Cells are typically rod-shaped, with some coccoid forms.
Colony characteristics
Smooth, yellow scotochromogenic colonies appear after 4 weeks of culture.
Physiology
Differential characteristics
Type strain.
Strain S369 = CCUG 51897 = DSM 44428


Euriphene doriclea

Euriphene doriclea, the Doriclea nymph, is a butterfly in the family Nymphalidae. It is found in Sierra Leone, Liberia, Ivory Coast, Ghana, Nigeria, Cameroon, Gabon, the Central African Republic, the Democratic Republic of the Congo and Uganda. The habitat consists of forests.
Description.
"Upperside:" Antennae brown. Thorax and abdomen dark brown. Wings dark clay coloured. The anterior ones having three black marks placed at the middle of the anterior edges, being about a quarter of an inch (6 mm) long, and a few very faint dark marks at the external edges. Posterior wings with only two rows of small faint dark crescents placed along the external edges.
"Underside:" Palpi, legs, breast, abdomen, and anterior wings light clay coloured; the latter having two black streaks placed close to the anterior edges, near the middle, and a shade of dark brown along the external edges. Posterior wings along the upper part light clay; but towards the abdominal corners are darker. A dark-coloured narrow band rises at the middle of the anterior edges, which runs circularly towards the abdominal groove, but is lost in the general colour of the wing before it reaches that part. About the middle of this inner compartment is a small round black spot, being the only one either on the upperside or underside. Margins of the wings entire, the posterior being slightly angulated. Wingspan inches (57 mm).


Helen Lorraine


Centralspindlin

Centralspindlin is a motor complex implicated in cell division. It contributes to virtually every step in cytokinesis, It is highly conserved in animal cells as a component of the spindle midzone and midbody. Centralspindlin is required for the assembly of the mitotic spindle as well as for microtubule bundling and anchoring of midbody microtubules to the plasma membrane. This complex is also implicated in tethering the spindle apparatus to the plasma membrane during cytokinesis This interaction permits cleavage furrow ingression. In addition, centralspindlin's interaction with the ESCRT III allows for abscission to occur.
Structure.
Centralspindlin is a heteroteramer consisting of two different subunit proteins:
Both KIF23 and RacGAP1 dimerize via their parallel coiled coil domain.
Centralspindlin oligomerizes in order to link the mitotic spindle with the plasma membrane The sequences mediating interactions between KIF23 and RacGAP1 are highly variable between species. However, a high affinity interaction between these subunits is essential for the proper functioning of the Centralspindlin complex.
Subunits.
KIF23 interacts with microtubules at sites of overlap, linking the centraspindlin complex to the mitotic spindle.
RacGAP1 recruits ECT2 to the central spindle. ECT2 is a Guanine nucleotide-exchange factor for RhoA. Cytokinesis is initiated when RhoA is activated by ECT2.
RacGAP1 is also involved in tethering the central spindle to the plasma membrane. Without this interaction, cytokinesis cannot occur.


Viduidae

The indigobirds and whydahs, together with the cuckoo-finch, make up the family Viduidae; they are small passerine birds native to Africa.
These are finch-like species which usually have black or indigo predominating in their plumage. The birds named "whydahs" have long or very long tails in the breeding male.
All are obligate brood parasites, which lay their eggs in the nests of estrildid finch species; most indigobirds use firefinches as hosts, whereas the paradise whydahs chose pytilias. Unlike the cuckoos and honeyguides, the indigobirds and whydahs do not destroy the host's eggs. Typically, they lay 2–4 eggs in with those already present. The eggs of both the host and the victim are white, although the indigobird's are slightly larger. Many of the indigo-plumaged species named "indigobirds" are very similar in appearance, with the males difficult to separate in the field, and the young and females near impossible. The best guide is often the estrildid finch with which they are associating, since each indigobird parasitises a different host species. For example, the village indigobird is usually found with red-billed firefinches. Indigobirds and whydahs imitate their host's song, which the males learn in the nest. Although females do not sing, they also learn to recognise the song, and choose males with the same song, thus perpetuating the link between each species of indigobird and firefinch. The nestling indigobirds mimic the unique gape pattern of the fledglings of the host species.
The matching with the host is the driving force behind speciation in this family, but the close genetic and morphological similarities among species suggest that they are of recent origin.
The family contains two genera:


Mycobacterium cosmeticum

Mycobacterium cosmeticum is a rapidly growing mycobacterium that was first isolated from cosmetic patients and sites performing cosmetic procedures.
Dr. Robert Cooksey and Dr. Jacobus H. de Waard, along with their research teams in the Centre for Disease Control and Preventions’s Mycobacterial lab in the USA and Instituto de Biomedicina in Caracas, Venezuela discovered the "M. cosmeticum" bacterium, which can thrive in salons, healthcare and clinic settings. This species is the newest identifiable mycobacterial organism to thrive in these settings, joining other rapid growing species, "Mycobacterium fortuitum", "Mycobacterium chelonae", and "Mycobacterium abscessu"s, that have been found in previous outbreaks. These organisms are very persistent in the environment and can survive unusually harsh environmental conditions. The antibiotic therapy can go on for many months or even years. It very often requires an incision to remove the abscess.
Etymology: cosmeticum, referring to cosmetics.
It is closely related to "Mycobacterium frederiksbergense", "Mycobacterium hodleri", "Mycobacterium diernhoferi", and "Mycobacterium neoaurum".
Description.
Microscopy
Colony characteristics
Physiology
Differential characteristics
or on media containing 5% (w/v) NaCl, the utilization of trehalose or citrate, but not sorbitol, as a sole carbon source.


Actinobacillus equuli

Actinobacillus equuli is a gram-negative, non-motile rod bacteria from the family Pasteurellaceae.
"A. equuli" is classified as a bio-containment level 2 organism under the U.S. Public Health Service Guidelines. Biochemical differentiation tests with positive results are: catalase, urease and oxidase tests. "Actinobacillus equuli" subspecies "equuli" is not hemolytic and is found in equine and porcine hosts. Another subspecies exists and is classified as "Actinobacillus equuli" subsp. "haemolyticus" which is positive for hemolysis and is found in horses and very rarely in rabbits. Occasionally, humans can become infected with "A. equuli," more commonly as a result from destruction to the skin barrier, such as a horse bite.
"A. equuli" can commonly be isolated from the upper respiratory tract and oral cavity of adult healthy horses and can be important for diseases of foals, adult horses and pigs. It is a commensal bacteria unless it multiplies to overwhelming numbers, at which point it will cause disease. Specifically, "A. equuli" is known to cause neonatal sepsis in foals, known as Sleepy Foal Disease. Less commonly, "A. equuli" will cause disease in adult horses, resulting in respiratory infections. "A." equuli also has the capability to cause kidney damage, arthritis and septicemia in affected pigs. The subspecies "A. equuli" subsp. "haemolyticus" results in similar pathogenesis as "A. equuli" subsp. "equuli" in horses. Due to these diseases and conditions, "A. equuli" can result in great economic losses especially in the equine industry.
Taxonomy and genome.
Taxonomy.
It was previously thought that this bacteria was limited to the species level, however it is now divided into two subspecies of "Actinobacillus" "equuli" which include: "A." "equuli" subsp". equuli", and "A." "equuli" subsp". haemolyticus". Differentiation between these two subspecies can be done via biochemical tests including a CAMP test, and haemolytic properties. "A." "equuli" subsp". equuli" is non-haemolytic and CAMP negative, while "A". "equuli" subsp". haemolyticus" is haemolytic and CAMP positive.
Isolation of the subspecies "equuli" have been found in both horses and pigs, but only subspecies "haemolyticus" has been isolated from horses.
Genome.
"Actinobacillus" "equuli" genome's size is approximately 1.7 GDa and contains 40% guanine and cytosine in its genetic makeup.
"A." "equuli" type strains include: ATCC 19392, CCUG 2041, GIP 103284, DSM 19655, JCM 2432, LMG 3736, and NCTC 8529. The 16S rRNA gene for "A." "equuli" is AF381186, this helps classification of the bacteria to the species level but not to the subspecies level. This information helped determine that this species is closely related to "Actinobacillus" "suis" and "Actinobacillus" "hominus". Another 16s rRNA study determined that an "A". "equuli" type strain was 98.3% similar to "A". "lignieresii" but are of different species.
Isolation of the subspecies "equuli" in the UK and Australia determined that it contained strains NCTC 8529T, and I 5445/4. "A." "equuli" subspecies "haemolyticus" contain strains: T 355/87, F 92, Ac 7 F 119, F 154, and F 490. PCR testing that results in the presence of the RTX gene allows differentiation to be made between the two subspecies, as only A. "equuli" "subsp. equuli" contains the RTX gene.
To differentiate similar strains of "A. equuli" from other genera originally thought to be "A". "equuli", ribotyping can be performed. The characteristic of being L-arabinose positive was thought to be an important taxonomic characteristic to classify "A." "equuli" strains from others. Many different strains of "A." "equuli" were determined through ribotyping, indicating that this species is diverse.
Epidemiology.
Horses.
"A. equuli" is found on a variety of mucosal surfaces in the horse; it is considered to be part of the normal flora and an opportunistic pathogen. Despite it being a component of the normal flora, an mean isolation frequency as low as 37% (n =174) in adult horses and foals was detected in one study. However, the isolation frequency varied from 12-88% between farms. "A. equuli" does not have a preference for age, breed or gender, suggesting that husbandry practices may play a role in isolation frequency. An important aspect of the isolation frequency is that a horse or foal will not be culture positive every time it is swabbed, making it hard to determine the correct isolation frequency.
"A. equuli" is the causative agent in sleepy foal syndrome, which has been documented throughout the world. It is important to note that "A. equuli" does not only cause sleepy foal syndrome in foals, it is also a causative agent of pneumonia, muscular degeneration and jaundice in foals. On necropsy, foals were found to have the highest distribution of the bacteria in their synovial fluid, followed by the thoracic fluid and the liver. Important risk factors for foals acquiring an infection with "A. equuli" include failure of passive transfer, unsanitary foaling environments, and the presence of immunosuppressive conditions. Foals can become infected in-utero, during parturition or shortly after birth. Adults horses have similar diseases associated with "A. equuli" infections, including septicemia, respiratory and bone/joint diseases. Less common forms of infection can manifest as cutaneous abscess, pharyngitis, guttural pouch eustachitis, pericarditis, mastitis, urethritis, and lymphadenitis. Risk factors for developing infections in adult horses differs from that of foals, these factors include: stress, concurrent bacterial and/or viral infections, and discontinuities in the mucosa membranes allowing the bacteria entry into the body's internal compartment.
Swine.
Infections in swine are more common in European countries compared to the North American Countries. Infections in the United States are extremely rare with only 2 cases reported prior to 2008 and there was a 30 year period leading up to 2008 in which there were no cases documented. There has only ever been one case reported in Manitoba, Canada in 2010. However, infections may have occurred but were unreported. An infection with "A. equuli" in swine commonly yields septicemia, metritis, and can result in abortion. It was once thought pigs acquired the infection directly from horses, but there has been reports of swine developing infections on farms that housed horses prior to housing swine, and there has also been one case in which the swine infected had no association with horses. Owning to the fact that the exact source of the infection in swine is not known, the risk factors are also relativity unknown.
Microbiology.
Morphology and culture growth.
"Actinobacillus equuli" are rod-shaped bacteria that measure an average of 1 μm in length. According to a study of the complete genome of "A. equuli", this microbe can be cultured on blood agar at an optimal temperature of 37 °C, but is able to grow in temperatures ranging from 20 °C to 44 °C. Two studies noted that the colonies of "A. equuli" are circular, smooth in texture and produce a slimy, viscous material that gives the colonies a gelatinous and glossy appearance. In addition to its mesophilic properties, "A. equuli" can grow at a pH of 6.0 to 8.4 which allows the organism to inhabit the intestine and survive in various structures such as the heart and adrenal gland. "A. equuli" is a facultative anaerobe and is moderately fastidious, therefore culture growth in the laboratory may be challenging.
Biochemical tests.
As part of the genus "Actinobacillus", "Actinobacillus equuli" is gram negative. "A. equuli" displays negative results after inoculation into motility agar indicating a lack of motility. "A. equuli" is equipped with catalase and urease enzymes and therefore yield positive results for these tests. Although facultatively anaerobic, "A. equuli" can survive in environments exposed to oxygen as it contains the enzyme cytochrome oxidase for use in the electron transport chain. Differentiation between "A. equuli" subsp. "equuli" and "A. equuli" subsp. "haemolyticus" can be made using sheep's blood agar or the CAMP test upon the absence or presence of beta-haemolysis, respectively.
"A. equuli" has varying results for sugar fermentation. "A. equuli" subsp. "equuli" is not capable of fermenting cellobiose, whereas the opposite is true for "A. equuli" subsp. "haemolyticus," indicated by a negative and positive result for the cellobiose fermentation test, respectively. However, both subspecies are positive for lactose fermentation, which is indicated by using phenol red lactose broth. Gram negative lactose fermenters typically display positive results on MacConkey agar, however, a study on equine actinobacilli resulted in the lack of growth on MacConkey agar, which may suggest that "A. equuli" is too fastidious to grow on this medium. To add, "A. equuli" ferments D-glucose as indicated by a positive result for the oxidative-fermentation glucose test performed using Hugh-Leifson medium. Both subspecies yield a positive result for both raffinose and D-galactose fermentation and displays mixed results for D-mannitol fermentation, where only some biovars of "A. equuli" subsp. "haemolyticus" displayed a negative result while others were positive for D-mannitol fermentation.
"A. equuli" is negative for the methyl red test, which indicates that this microbe does not use the mixed acid fermentation pathway. "A. equuli" also displays a negative Voges-Proskauer test because "A. equuli" does not use the 2,3-butanediol fermentation pathway resulting in the absence of acetoin production. As demonstrated by a negative Simmon's citrate test result, "A. equuli" is not able to use citrate as its sole carbon source for energy.
Pathogenesis.
Horses.
The major host for "A. equuli" is horses and under physiological conditions, "A. equuli" is part of horses' mucosal microbiota and does not normally cause clinical symptoms and/or lesions. However, when mucous membranes become compromised (wound penetration, ulcers/erosions) it allows for resident "A. equuli" to establish infection in the horses' internal environment. "A. equuli's" penetration into the body's internal environment has been reported to cause septicemia in newborn foals (also called sleepy foal disease) and localized infections in adult horses or in more severe cases acute or chronic peritonitis. It is unknown at this time if there are certain strains of "A. equuli" that have a greater virulence for adult horses and/or foals.
One study emphasized the contribution of "A. equuli" to the development of equine valvular endocarditis, where an isolate grown from the bacterial samples of an vegetative equine heart showed stunning resemblance with the phenotypical characteristics of a pure culture of "A. equuli" subsp. equuli. Although the exact source of infection is not yet known for horses with valvular endocarditis, it has been suggested that this microbe may be distributed through the body by the migration of "Strongylus vulgaris", a common pasture parasite that inhabits the intestinal mucosa of horses and can migrate intravascularly to various organs of the body.
The pathogenicity and virulence factors of "A. equuli" are not well known, but following PCR analysis it has been determined that both subspecies ("equuli" and "haemolyticus") have the RTX toxin gene which is capable of causing host species specific toxicity.
Swine.
"A. equuli" has been found occasionally to cause disease in sows and their piglets however, like in horses, the pathogenicity is not well known. Unlike horses, PCR analysis did not find the "aqxA" gene and therefore concluded that only subspecies "equuli" and not subspecies "haemolyticus" causes disease in pigs. In sows, "A. equuli" is thought to cause disease as both a primary and a secondary pathogen. In piglets, since they usually show clinical signs within hours up to 4 days after parturition, it is hypothesized that the piglets are infected in utero. Nasal, fecal and vaginal swabs of infected sows were performed and pure cultures of "A. equuli" were only found in the vaginal swabs, supporting the hypothesis of in utero infection. Navel swabs and blood tests were performed on affected piglets and no "A. equuli" was cultured and bacteremia was not found. The pathogenicity causing the variation in clinical manifestations between cases of swine affected with "A. equuli" is not well understood.
The virulence factors of "A. equuli" in swine is also not well known.
Rabbits.
There has been one case that found a rabbit presenting for necropsy, had a secondary infection caused by "A. equuli." The rabbit was diagnosed with acute hepatitis characteristic of Tyzzer's disease caused by "Clostridium piliforme". However, samples of the lungs and liver of the rabbit also resulted in the culture of "A. equuli" subspecies "haemolyticus". "A. equuli" was determined to be a secondary opportunistic invader in this rabbit.
Clinical signs.
Horses.
Acute signs: moderate to severe abdominal pain (colic), inappetence, intestinal stasis, lethargy.
Chronic signs: weight loss
Less frequently "A. equuli" has also been known to cause respiratory tract disease, abortion, haemorrhagic diatheses, pericarditis, periorchitis, enteritis, and peritonitis.
Sleepy foal syndrome: The acute form of sleepy foal syndrome presents as sepsis that can lead to death. Acutely infected foals appear dull, can have pneumonia and are neutropenic. However, in some cases a chronic form of the disease can manifest in the kidneys, lungs, and joints resulting in lesions to the affected areas.
Necropsies of horses infected with "A. equuli" showed consistent diffuse, bilateral, multifocal renal infarcts affecting the renal cortices. Fibrinous exudate and pulmonary edema was also a common finding.
Swine.
Acute Signs in sows: Most commonly lethargy, inappetence, sudden death. Less commonly causes recumbency, hyperesthesia, pneumonia, bronchitis, surface wound infections, metritis, and septicemia.
Acute signs in piglets: lethargy, +/- pyrexia, severe arthritis (causing them to be non-weight bearing on that limb), encephalitis (although only neurological signs were lateral recumbency), septicemia and sudden death.
Chronic signs of piglets and sows: Poor doing and weight loss leading to culling or euthanasia
Sow Necropsies: Sows most commonly had dehydration, subcutaneous hemorrhage, embolic infarcts consisting of neutrophils and basophilic bacilli in the renal cortex. Embolic infarcts were also found in liver, lungs spleen, adrenal gland. Sows were concluded to have died of renal infarcts.
Gilt Necropsy: A gilt was found to have liquefactive necrosis in the epicardium of both auricles of the heart, valvular endocarditis of both mitral and tricuspid valves and thrombus of the right atrial wall. She had recently aborted her pregnancy and within the amniotic sacs of the aborted fetuses, a brown serous fluid was found. The gilt was concluded to have died of "A. equuli" causing valvular endocarditis and metritis with secondary septicemia.
Piglet Necropsies (6 hours to 4 days old belonging to infected sows): Piglets had petechial hemorrhage and multiple bacterial emboli in the renal cortex +/- multifocal purulent nephritis. Piglets were also found to have severe diffuse fibrinopurulent arthritis in one or more joints. Some piglets have additionally had a mild purulent encephalitis and perivasculitis of the vessels in the brain.
Prevention and treatment.
Horses.
"A. equuli" causing sleepy foal syndrome in neonatal horses is most often attributed to the mother, as "A. equuli" is part of the normal microflora of the mare which makes it difficult to prevent exposure of the foal to "A. equuli." In a majority of reported cases, sleepy foal syndrome is more than likely a direct result of failure of passive transfer thus, it is important that neonatal foals receive colostrum to reduce the incidence of the disease caused by "A. equuli." Reducing environmental contamination when the foal is born has also shown to be effective at reducing the incidence of disease. In adult horses, there has been a reported case of infection caused by "A. equuli" associated with gastrointestinal ulceration possibly due to the use of phenylbutazone for extended periods of time. Ulceration of the GI mucosa can allow "A. equuli" to set up an opportunistic infection. Limiting the duration or dose of phenylbutazone could reduce the chance of ulceration and thus an infection. Preventative treatments can also include minimizing the risk of infection with other parasites or pathogens that could weaken the immune system or cause physical damage that allows "A. equuli" to set up an infection. Some studies have found that "A. equuli" infections have been established after exposure with "Strongylus vulgaris" as the migrating larvae can transport "A. equuli" to various parts of the body resulting in infection. Overall, ensuring the health of the horse is maintained has shown to be the best strategy to reduce infection with "A. equuli".
Treatment and supportive care of a horses infected with "A. equuli" has been shown to be very effective when detected early, resulting in low incidences of death associated with infection. One study involving 51 horses with peritonitis associated with "A. equuli," found treatment with procaine penicillin or procaine penicillin and gentamicin sulphate to be effective. However, antimicrobial sensitivity testing of 14 cultures showed 1 culture to be resistant to penicillin, 1 resistant to trimethoprin-sulphaimidine and 1 resistant to a combination of penicillin and trimethoprin-sulphaimidine. Thus the study recommended the treatment with procaine penicillin and gentamicin sulphate in cases of antimicrobial resistance. In neonatal foals with sleepy foal syndrome, treatment failure resulting in fatal outcome has been recorded because of the severity of the condition and an inability of the neonate to successfully mount an immune response against the pathogen due to failure of passive transfer. In other cases, treatment of sleepy foal syndrome included antibiotic treatment with amoxicillin-clavulanic acid and amikacin sulfate along with fluid therapy.
Swine.
During the outbreak at the swine farm in Canada, both preventative antibiotic therapy in the water and feed of the entire herd and individual therapy of the clinically affected sows was administered. Susceptibility testing showed that "A. equuli" was sensitive to ampicillin, tetracycline, trimethoprim, ceftiofur, neomycin and spectinomycin. Clinically affected sows were determined by failure to rise when stimulated and temperature, and were additionally treated with antibiotics and anti-inflammatories. Some of the clinically affected sows who survived the initial infection were euthanized or culled due to wasting and poor-doing. Sow mortality ranged from an average of 8 deaths per day at the beginning of the outbreak, to 2 deaths/day by day 50 of the infection.
Prevention of "A. equuli" spread in swine operations with herd outbreak from the infected to the non-infected sows or newly introduced gilts was mitigated by the development of a herd-specific killed vaccine.
Zoonotic potential.
"A. equuli" commonly affects equine hosts. Occasionally, "A. equuli" has been found to cause disease in sows and their newborn piglets. There was one case describing a rabbit who was infected with "A. equuli."
Humans have also been found to have infections caused by "A. equuli" after being bit by a horse. One case study described a stable hand who had been bitten by a horse 12 hours prior, presenting to the hospital with a red and swollen laceration on the dorsal side of his hand. "A. equuli-"like species was cultured from the wound and was determined to cause the infection along with "A. lignieresii." Additionally, there has been one case of a 13 year old boy who developed meningitis and sepsis from "A. equuli." The boy had visited a farm 3 days prior but denied coming into direct contact with horses or pigs. Furthermore, a blood sample from a 53 year old butcher with septicemia was found to contain "A. equuli" after the individual had lacerated his left thumb. Prior to the discovery, "A. equuli" had never been recorded in the blood of a human with septicemia.
Susceptibility and resistance.
Susceptibility testing performed found that "A. equuli" was sensitive to ampicillin, tetracycline, trimethorprin, ceftiofur, neomycin, cefotaxime, ceftazidime, imipenem, meropenem, ciprofloxacin, levofloxacin, piperacillin-tazobactam, tigecycline and spectinomycin.
However, after conducting susceptibility testing, one study found "A. equuli" resistance to penicillin, ampicillin, streptomycin, neomycin, chloramphenicol, methicillin, and nalidixic acid. The study also found susceptibility of "A. equuli" to gentamicin, tetracycline, nitrofurantoin, polymyxin B, sulphonamides, trimethoprin with sulphonamides, carbenicillin, cephalotin, and amoxycillin with clavulanic acid. The study did note it had differing results in susceptibility tests than other studies had reported, which could be a result of regional or strain differences or differences in the methods of the susceptibility testing between studies. Additional reports have found "A. equuli" resistance to oxacillin and trimethoprin-sulphaimidine along with developed resistance to tetracycline after one month of use in sows.


Candida lusitaniae

Candida lusitaniae is a species of yeast in the genus "Candida".
"C. lusitaniae" was first identified as a human pathogen in 1979.
"C. lusitaniae" was initially described as a rare cause of fungemia, with fewer than 30 cases reported between 1979 and 1990. However, there has been a marked increase in the number of recognized cases of candidemia due to this organism in the last two decades. Bone marrow transplantation and high-dose cytoreductive chemotherapy have both been identified as risk factors for infections with this organism.
These patients are often neutropenic for extended periods of time, leaving them susceptible to bacterial and fungal infections, including Candidal infections. Some investigators have theorized that the widespread use of Amphotericin B empiric antifungal therapy selects for infections with "Candida lusitaniae".


Dicranophora fulva

Dicranophora fulva is a mold of the family Mucoraceae. The species was described as new to science in 1886 by German mycologist Joseph Schröter, who first discovered it near Baden in 1877. Its species name is derived from the Latin "fulvus" "brown". The yellow mold has been reported from Europe and the United States. Although it is wide-ranging, it is not common. It grows exclusively on the decaying fruit bodies of Boletales. Known hosts include "Suillus bovinus", "S. cavipes", "S. grevillei", "Paxillus involutus", "Chroogomphus rutilus", and "Leccinum scabrum". It was not recorded after 1935 until Hermann Voglmayr and Irmgard Krisai-Greilhuber encountered it on a fungal field trip in southeastern Styria in 1994. Initially unable to identify it, they solved the mystery after checking older literature.
"Dicranophora fulva" was illustrated by botanist Charles Geoffrey Dobbs in 1938. The mold produces two types of sporangia: one type is tree-like in shape, with mostly single-spored sporangiola; the other type has a morphology more typical of the Mucorales. Zygospores produced by the fungus have irregular surface crevices. It appears to require high humidity and ample moisture, cool temperatures and abundant bolete mushrooms to flourish, a set of conditions more likely to occur in montane regions, which might explain the lack of records for this species. The mold becomes dormant in the autumn, but the circumstances that induce it to germinate are unknown.
It is unclear whether "Dicranophora fulva" is a mycoparasite (living off living material) or saprotrophite (living off dead or decaying material). It was initially thought to be the former, as are many Mucorales. However it is readily cultured on a wide variety of substrates such as bread and is hence suspected of being saprotrophic.


Index Fungorum

Index Fungorum is an international project to index all formal names (scientific names) in the fungus kingdom. the project is based at the Royal Botanic Gardens, Kew, one of three partners along with Landcare Research and the Institute of Microbiology, Chinese Academy of Sciences.
It is somewhat comparable to the International Plant Names Index (IPNI), in which the Royal Botanic Gardens is also involved. A difference is that where IPNI does not indicate correct names, the "Index Fungorum" does indicate the status of a name. In the returns from the search page a currently correct name is indicated in green, while others are in blue (a few, aberrant usages of names are indicated in red). All names are linked to pages giving the correct name, with lists of synonyms.
Index Fungorum is one of three nomenclatural repositories recognized by the Nomenclature Committee for Fungi; the others are "MycoBank" and "Fungal Names".
Current names in "Index Fungorum" ("Species Fungorum").
The main part of "Index Fungorum" is intended to be a global list of all fungus names which have ever been validly defined, but many of them are conflicting or no longer used. "Species Fungorum" is a closely related project based at the Royal Botanical Gardens, Kew supported by CABI to decide a consistent subset of the "Index Fungorum" names which can be recommended as currently valid. It is possible to search in either the "Index Fungorum" or the "Species Fungorum" list separately and the "Index Fungorum" results also give a cross-reference to "Species Fungorum" where an entry is available - names without such a reference are generally only of historical interest and should not be considered reliable for present use.
Life Science Identifiers (LSIDs).
"Index Fungorum" provides Life Science Identifiers (LSIDs) for records in its database.
Services.
"Index Fungorum" provides a SOAP protocol web service for searching its database and retrieving records. A WSDL file describing the services is available.


Lycoperdon lividum

Lycoperdon lividum, commonly known as the grassland puffball, is a type of puffball mushroom in the genus "Lycoperdon". It is found in Europe, where it grows on sandy soil in pastures, dunes, and heaths, especially in coastal areas. It fruits in autumn. It was first described scientifically in 1809 by Christian Hendrik Persoon.


Anncaliia

Anncaliia is a genus of aquatic unicellular parasite in the division microsporidium.


Mycobacterium gordonae

Mycobacterium gordonae is a species of "Mycobacterium" named for Ruth E. Gordon. It is a species of the phylum actinobacteria (Gram-positive bacteria with high guanine and cytosine content, one of the dominant phyla of all bacteria), belonging to the genus "Mycobacterium".
Description.
Gram-positive, nonmotile and moderate to long acid-fast rods.
Colony characteristics
Physiology
Differential characteristics
Type strain.
Strain ATCC 14470 = CCUG 21801 = CCUG 21811 = CIP 104529 = DSM 44160 = JCM 6382 = NCTC 10267.


Jerzy Jurka

Jerzy Władysław Jurka (June 4, 1950 – July 19, 2014) was a Polish-American computational and molecular biologist. He served as the assistant director of research at the Linus Pauling Institute prior to founding the Genetic Information Research Institute. He collaborated with several notable scientists including Linus Pauling, George Irving Bell, Roy Britten, Temple Smith, and Emile Zuckerkandl. His Erdős number is 3, using the path through Temple Smith and Stanislaw Ulam.
Research.
Dr. Jurka is best known for his work on eukaryotic transposable elements (TEs), including the discovery of the major families of Alu elements. He also proposed the mechanism of Alu proliferation and discovered their paternal transmission. The majority of known types of class II TEs, or DNA transposons, were discovered or co-discovered by his team at the Genetic Information Research Institute, based on DNA sequence analysis. The first one, reported in 2001 with Vladimir Kapitonov, became known as "Helitron", which is playing a major role in genomic evolution.
In 2006 they reported a study of a new, self-synthesizing transposable element called Polinton or Maverick, which is present many diverse eukaryotes. More recently, Jurka and his co-workers presented a hypothesis that links the origin of repetitive families (TE families), to population subdivision and speciation based on classical concepts of population genetics.
Jerzy Jurka is the founder of Repbase , which he developed since 1990 with his team and other contributors. Repbase is the primary reference database of TEs used in DNA annotation and analysis.


Tequintavirus

Tequintavirus (synonyms "T5-like phages", "T5-like viruses", "T5likevirus") is a genus of viruses in the order "Caudovirales", in the family "Demerecviridae". Bacteria serve as the natural host, with transmission achieved through passive diffusion. There are currently 22 species in this genus, including the type species "Escherichia virus T5".
Taxonomy.
The following species are recognized:
Structure.
Tequintaviruses are nonenveloped, with a head and tail. The head is icosahedral (T=13) and is about 90 nm in diameter. The tail is about 180 nm long, 9 nm wide. It has three long, kinked terminal fibers around 120 nm in length, and a single straight central fiber attached to a conical tip.
Genome.
Genomes are linear, around 121kb in length. The type species, Enterobacteria phage T5, and several other species have been fully sequenced. The genomes range between roughly 108-121 thousand nucleotides, with about 140 to 170 predicted open reading frames. The complete genomes, as well as two other similar, unclassified genomes are available here.
Life cycle.
The virus attaches to the host cell's adhesion receptors using its terminal fibers, and degrades the cell wall using viral exolysin enough to eject the viral DNA into the host cytoplasm via long flexible tail ejection system. Replication follows the DNA strand displacement, via replicative transposition model. DNA-templated transcription is the method of transcription. Once the viral genes have been replicated, the procapsid is assembled and packed. The tail is then assembled and the mature virions are released via lysis. Bacteria serve as the natural host. Transmission routes are passive diffusion.
History.
According to ICTV's 1996 report, the genus "T5likevirus" was first accepted under the name "T5-like phages", assigned only to family "Siphoviridae". The whole family was moved to order "Caudovirales" in 1998, and the genus was renamed to "T5-like viruses" in ICTV's 7th Report in 1999. In 2012, it was renamed again to "T5likevirus". The genus was later renamed to Tequintavirus and placed in the newly established family "Demerecviridae".


Ismarus (wasp)

Ismarus is a genus of wasps belonging to the family Ismaridae, and presently the sole extant genus in the family (a second genus was recently removed). About 50 species are known in this small relictual group, all of which appear to be hyperparasitoids that parasitize Dryinidae (that attack leafhoppers).
"Ismarus" was formerly included in the family Diapriidae, but differ from diapriid wasps by lacking a facial projection from which the antenna arise, and characterized by various degrees of fusion of the metasomal terga.


Saxicolous lichen

A saxicolous lichen is a lichen that grows on rock. The prefix "sax" from the Latin means "rock" or "stone".


Zoi Lygerou

Zoi Lygerou is a Greek associate professor of biology at the Medical School University of Patras whose works have been published in such journals as the European Journal of Biochemistry, Journal of Cell Science, the Molecular and Cellular Biology journal, Journal of Biological Chemistry, and both Science and Nature journals among others. In 1991 she got her first degree at the University of Athens followed by a Ph.D. from the University of Heidelberg four years later. She also used to be a postdoc at the Imperial Cancer Research Fund of London under guidance from Paul Nurse. On April 12, 1996 she and her colleagues (along with David Tollervey) have discovered that the minimum amount of enzymes are required for the eukaryotes' ribosomal RNA.


Dinoroseobacter shibae

Dinoroseobacter shibae is a facultative anaerobic anoxygenic photoheterotroph belonging to the family, Rhodobacteraceae. First isolated from washed cultivated dinoflagellates, they have been reported to have mutualistic as well as pathogenic symbioses with dinoflagellates.
Cell morphology and physiology.
"D. shibae" cells are Gram-negative cocci, or occasionally ovoid rods that measure 0.3 – 0.7 μm in width and 0.3 – 1.0 μm in length. They are motile and have a single polar flagellum.
When grown in the dark, colonies have a distinct pink or light red pigmentation, while under strong illumination they are beige. They contain bacteriochlorophyll a and the carotenoid pigment spheroidenone and have absorption spectrum peaks at 804 and 868 nm. The carotenoid leads to an extended absorption spectrum including 400 – 600 nm. "D. shibae" cells use light as a supplementary energy source and don't use it to fix inorganic carbon. Colonies grown on complex agar media appear deep red in color.
"D. shibae" is a facultative anaerobe that requires 1-7% salinity and grows between 15 and 38 °C with an optima temperature of 33 °C. Its optimal pH range is 6.5 – 9.0. While most of the organisms in the Roseobacter clade are obligate aerobes, "D. shibae" is able to grow anaerobically using electron acceptors nitrate and dimethyl sulfoxide. It has a complete denitrification pathway for energy production. A variety of organic substrates including acetate, succinate, fumarate, malate, lactate, citrate, glutamate, pyruvate, glucose, fructose and glycerol can support heterotrophic growth. Like others in the Roseobacter clade, ethanol, methanol and butyrate do not support growth.
"D. shibae" can synthesize vitamins <chem>B_1</chem> and <chem>B_{12}</chem>, of which its dinoflagellate host is auxotrophic.
Environment and ecology.
Members of the Roseobacter clade are widely associated with marine phytoplankton such as dinoflagellates and diatoms in the water column as well as shallow sediments. They play important roles in the carbon cycle by assimilating dissolved organic matter produced by phytoplankton and also in the sulfur cycle by removing DMS from the algal osmolyte dimethylsulfoniopropionate (DMSP). Their close association with eukaryotic phytoplankton is supported by phylogenomic evidence suggesting that the Roseobacter lineage diverged from other Alphaproteobacteria at the same moment as the Mesozoic radiation of phytoplankton.
Traits involved in symbioses of "D. shibae" include flagelar synthesis and type IV secretion system under the control of N-acyl homoserine lactone intercellular signal molecules (quorum sensing).
"D. shibae" forms symbioses with "Prorocentrum minimum", a toxic red tide-forming dinoflagellate, as well as other dinoflagellates associated with toxic algal blooms. In a mutualistic association, the "P. minimum" provides carbon sources and some vitamins essential for growth, and while "D. shibae" provides vitamins <chem>B_1</chem> and <chem>B_{12}</chem>. In co-culture, this mutualism changes to pathogenicity as the bacteria induce death in the algae cells, but algicidal compounds produced by "D. shibae" have yet to be identified. "P. minimum" has a global marine distribution, suggesting that its symbiont does as well.
Genome.
"D. shibae’s" genome is 4417 kbp long, which is in line with other Roseobacter clade genomes. Included in this count are its large circular genome and five circular plasmids. The GC-content of "D. shibae" is 66%.
Based on comparative sequence analysis of the circular plasmids, they were likely acquired through conjugation and two sister plasmids contain the vir operon encoding the type IV secretion system required for the formation of sex pili. Other traits encoded on the plasmids include degradation of aromatic compounds and carbon monoxide oxidation.
As opposed to ABC transporters, the "D. shibae" genome suggests a preference for tripartite ATP-independent periplasmic transporters (TRAP) for uptake of nutrients like C4-dicarboxylates, pyruvate, glutamate, sialic acid, ectoine and 2,3-diketogulonate. "D. shibae’s" genome encodes for 27 complete TRAP systems.
Discovery and Isolation.
"D. shibae" was first isolated in 2003 with two strains, both isolated from washed single cells of cultivated marine dinoflagellates ("Prorocentrum lima" and "Alexandrium ostenfeldii").
Etymology.
The genus "Dinoroseobacter" name originates from the Greek dinos meaning whirling rotation and the first part of Dinophyceae (dinoflagellates) from which it was isolated, and "Roseobacter" a bacterial genus with similar traits. Shibae was named after Professor Tsuneo Shiba who discovered the marine aerobic anoxygenic phototrophic bacteria.


Propionispora

"Propionispora" is a genus of Firmicutes bacteria classified within the class Negativicutes.


Pixie Hollow Games

Pixie Hollow Games is a 30-minute television special broadcast on November 19, 2011, on Disney Channel. Based on the "Disney Fairies" franchise, it was produced by DisneyToon Studios and animated by Prana Studios. It features the voices of Mae Whitman, Lucy Liu, Raven-Symoné, Megan Hilty, Angela Bartys, and others, as Tinker Bell and the other fairies of Pixie Hollow in Never Land, taking part in an Olympic-style competition. It is based loosely on J. M. Barrie's Peter Pan stories, by way of Disney's animated adaptation.
It was originally intended as the last of five feature-length films in the Tinker Bell series of direct-to-DVD 3D animated films, with the title "Tinker Bell: Race through the Seasons", and a release date in 2012. However, the movie was rescheduled and retooled as a TV special instead of a film-length movie. Unlike the previous feature films in this series, Tinker Bell is not a central featured character in this special release.
Plot.
Rosetta is busy helping to set up flowers for the big night, when she meets a new garden fairy named Chloe. Chloe announces she has been training for the Pixie Hollow Games and is excited to be competing. Even though the garden fairies have little hope of winning and haven't ever won, Chloe is confident that she and her partner can turn things around and end their losing streak. When it comes time for the team selection, Chloe has already volunteered and Rosetta is selected to be her partner.
On the night of the games, Rosetta wears a fancy gown, certain that she and Chloe will be eliminated after one round. The storm fairies, Rumble and Glimmer, are the heavy favorites to win the competition due to their winning streak and having winners rings for almost every finger. The first event is leapfrogging. Rosetta refuses to get onto the frog, but finally does when the spectators yell in protest, leading to total chaos on the racetrack.
The next day, Rosetta and Chloe continue to compete in a series of games, such as dragonfly water skiing, twig-spheres, and mouse polo, slowly moving up in the standings during each game. The final challenge (a teacup race) arrives. Chloe dives down the chute with no trouble, but Rosetta nervously crawls down the chute, to Chloe's dismay. Rosetta's actions put them in last place, causing Chloe to start doubting her. Meanwhile, other teams start dropping which leaves only the garden and storm fairies.
Rosetta and Chloe take the mudslide mountain shortcut and successfully make it over thanks to Tinker Bell. However, in the last leg of the race, Rumble uses Glimmer's lightning ability to zap one of the wheels causing the girls' cart to crash. Glimmer is appalled. Seeing their cart destroyed, Rosetta and Chloe push their cart over the finish line and finish together. While Rumble celebrates his victory, Queen Clarion announces that the garden fairies are the winners. Rumble protests, until she shows him that Glimmer abandoned him just before the finish line for cheating, giving the victory to the garden fairies. Rosetta and Chloe broke their losing streak and they celebrate with their friends.
Music.
The score to the special is composed by Joel McNeely, who scored the first three "Tinker Bell" films. Zendaya sings the theme song (written by Brendan Milburn and Valerie Vigoda of GrooveLily), which is called "Dig Down Deeper".
Zendaya performed "Dig Down Deeper" in the 2011 Macy's Thanksgiving Day Parade.
In Spain, the main theme was played by Lydia Fairen.
Release.
The special debuted in the United States on The Disney Channel on November 19, 2011.
The special was included as a bonus feature on the Blu-ray releases of "Secret of the Wings" in 2012. A standalone DVD was released on August 20, 2013.
Sequel.
A fourth full-length "Tinker Bell" film, "Secret of the Wings", was originally announced to be released before the special, but was instead released on October 23, 2012.


Ampelovirus

Ampelovirus is a genus of viruses, in the family "Closteroviridae". Plants serve as natural hosts. There are 13 species in this genus. Diseases associated with this genus include: yellowing and necrosis, particularly affecting the phloem.
Taxonomy.
The following species are assigned to the genus:
Structure.
Viruses in the genus "Ampelovirus" are non-enveloped, with flexuous and Filamentous geometries. The diameter is around 10-13 nm, with a length of 1400-2200 nm. Genomes are linear, around 17.9kb in length. The genome codes for 13 proteins.
Life cycle.
Viral replication is cytoplasmic. Entry into the host cell is achieved by penetration into the host cell. Replication follows the positive stranded RNA virus replication model. The virus exits the host cell by tubule-guided viral movement. Plants serve as the natural host. Transmission routes are mechanical.


EIF4G

Eukaryotic translation initiation factor 4 G (eIF4G) is a protein involved in eukaryotic translation initiation and is a component of the eIF4F cap-binding complex. Orthologs of eIF4G have been studied in multiple species, including humans, yeast, and wheat. However, eIF4G is exclusively found in domain Eukarya, and not in domains Bacteria or Archaea, which do not have capped mRNA. As such, eIF4G structure and function may vary between species, although the human eIF4G 1 has been the focus of extensive studies.
Across species, eIF4G strongly associates with eIF4E, the protein that directly binds the mRNA cap. Together with the RNA helicase protein eIF4A, these form the eIF4F complex.
Within the cell eIF4G is found primarily in the cytoplasm, usually bound to eIF4E; however, it is also found in the nucleus, where its function is unknown. It may have a role in nonsense-mediated decay.
History.
eIF4G stands for eukaryotic initiation factor 4 gamma (typically gamma is now replaced by G in the literature). It was initially isolated by fractionation, found present in fraction 4 gamma, and was involved in eukaryotic translation initiation.
Binding partners.
eIF4G has been found to associate with many other proteins besides those of the eIF4F complex, including MNK-1, CBP80, CBP20, PABP, and eIF3. eIF4G also directly binds mRNA and has multiple positively charged regions for this function. Several IRESs also bind eIF4G directly, as do BTE CITEs.
In translation initiation.
eIF4G is an important scaffold for the eIF4F complex and aids in recruiting the 40S ribosomal subunit to mRNA.
There are three mechanisms that the 40S ribosome can come to recognize the start codon: scanning, internal entry, and shunting. In scanning, the 40S ribosome slides along the RNA until it recognizes a start site (typically an AUG sequence in "good context"). In internal entry, the 40S ribosome does not start from the beginning (5' end) of the mRNA but instead starts from somewhere in the middle. In shunting, after the 40S ribosome starts sliding along the mRNA it "jumps" or skips large sections; the mechanism for this is still unclear. eIF4G is required for most types of initiation, except in special cases such as internal initiation at the HCV IRES or Cripavirus IRES.
eIF4G is an initiation factor involved in the assembly of the 43S and 48S 43S_preinitiation_complex. This particular initiation factor binds to the PABPI (PolyA binding protein I), which is in turn binds the messenger RNA's poly(A) tail and eIF3, which is bound to the incoming small ribosomal subunit (40S).
In disease.
eIF4G has been implicated in breast cancer. It appears in increased levels in certain types of breast cancer and increases production of mRNAs that contain IRESs; these mRNAs produce hypoxia- and stress-related proteins that encourage blood vessel invasion (which is important for tumorigenesis).
Role in aging.
Regulation of translation initiation by eIF4G is vital for protein synthesis in developing organisms, for example yeast and nematodes. Deletion of eIF4G is lethal in yeast. In the roundworm C. elegans, knockout of eIF4G leads to animals that cannot develop past the early larval stage (L2) of development. The critical role of eIF4G in development appears to be reversed in adulthood, when eIF4G dysregulation negatively impacts lifespan and increases susceptibility to certain aging-related diseases (see eIF4G in diseases above). Inhibiting eIF4G during adulthood in C. elegans drastically extends lifespan, comparable to the lifespan increase exhibited during dietary restriction. In addition, inhibiting eIF4G reduces overall protein translation, while preferentially translating mRNA of genes important for responding to stress and against those associated with growth and reproduction. Thus eIF4G appears to control differential mRNA translation during periods or growth and stress, which may ultimately lead to age-related decline.
Importance in virology.
As previously mentioned, eIF4G is bound by certain IRESs, which were initially discovered in viruses. Some viral IRESs directly bind eIF4G and co-opt it to gain access to the ribosome. Some cellular mRNAs also contain IRESs (including eIF4G itself).
Some viral proteases cleave off part of eIF4G, that contains the eIF4E binding region. This has the effect of preventing most cellular mRNAs from binding eIF4G; however, a few cellular mRNAs with IRESs still translate under these conditions.
One example of an eIF4G binding site in a viral IRES is in the EMCV IRES (nucleotides 746-949).


Cell synchronization

Cell synchronization is a process by which cells in a culture at different stages of the cell cycle are brought to the same phase. Cell synchrony is a vital process in the study of cells progressing through the cell cycle as it allows population-wide data to be collected rather than relying solely on single-cell experiments. The types of synchronization are broadly categorized into two groups; physical fractionization and chemical blockade.
Physical Separation.
Physical fractionation is a process by which continuously dividing cells are separated into phase-enriched populations based on characteristics such as the following:
Given that cells take on varying morphologies and surface markers throughout the cell cycle, these traits can be used to separate by phase. There are two commonly used methods.
Centrifugal Elutriation.
(Previously called: counter streaming centrifugation) Centrifugal elutriation can be used to separate cells in different phases of the cell cycle based on their size and sedimentation velocity (related to sedimentation coefficient). Because of the consistent growth patterns throughout the cell cycle, centrifugal elutriation can separate cells into G1, S, G2, and M phases by increasing size (and increasing sedimentation coefficients) with diminished resolution between G2 and M phases due to cellular heterogeneity and lack of a distinct size change.
Larger cells sediment faster, so a cell in G2, which has experienced more growth time, will sediment faster than a cell in G1 and can therefore be fractionated out. Cells grown in suspension tend to be easier to elutriate given that they do not adhere to one another and have rounded, uniform shapes. However, some types of adherent cells can be treated with trypsin and resuspended for elutriation as they will assume a more rounded shape in suspension.
Flow Cytometry and Cell Sorting.
Flow cytometry allows for detection, counting, and measurement of the physical and chemical properties of cells. Cells are suspended in fluid and put through the flow cytometer. Cells are sent one at a time through a laser beam and the light scatter is measured by a detector. Cells or their components can be labeled with fluorescent markers so that they emit different wavelengths of light in response to the laser, allowing for additional data collection.
For quantitative cell cycle analysis, cells are usually fixed with ethanol and stained with DNA-binding dyes like propidium iodide, Hoechst 33342, DAPI, 7-Aminoactinomysin D, Mithramycin, DRAQ5, or TO-PRO-3, allowing for determination of phase by DNA quantity. However, if these cells have been fixed, they are dead and cannot be maintained for continued growth. Cells can also be resuspended in media and dyed with non-toxic dyes to maintain living cultures. Cells can also be genome edited such that some cellular proteins are made with conjugated fluorescent tags such as GFP, mCherry, and Luciferase that can be used to detect and quantify those components. For example, chimeric histone H2B-GFP constructs can be made and used to measure DNA content and determine replication status as a means of discerning cell phase. Light scatter measurements can be used to determine characteristics like size, allowing for distinction of cell phase without tagging.
Flow cytometers can be used to collect multiparameter cytometry data, but cannot be used to separate or purify cells. Fluorescence-activated cell sorting (FACS) is a technique for sorting out the cells based on the differences that can be detected by light scatter (e.g. cell size) or fluorescence emission (by penetrated DNA, RNA, proteins or antigens). The system works much like flow cytometry, but will also charge each cell droplet after it has been measured based on a defined parameter. The charged droplet will then encounter an electrostatic deflection system that will sort the cell to a different container based on that charge. This allows cells to be separated on the basis of fluorescent content or scatter.
To summarize, flow cytometry alone can be used to gather quantitative data about cell cycle phase distribution, but flow cytometry in coordination with FACS can be used to gather quantitative data and separate cells by phase for further study. Limitations include:
Chemical blockade.
The addition of exogenous substrates can be used to block cells in certain phases of the cell cycle and frequently target cell cycle checkpoints. These techniques can be carried out "in vitro" and do not require removal from the culture environment. The most common type of chemical blockade is arrest-and-release, which involves treatment of a culture with a chemical block and subsequent release by washing or addition of a neutralizing agent for the block. While chemical blockade is typically more effective and precise than physical separation, some methods can be imperfect for various reasons, including:
Arrest in M.
Mitotic arrest can be achieved through many methods and at various points within M-phase, including the G2/M transition, the metaphase/anaphase transition, and mitotic exit.
Nocodazole.
Nocodazole is a rapidly-reversible inhibitor of microtubule polymerization that can be used to arrest cells before Anaphase at the spindle assembly checkpoint in the metaphase/anaphase transition. The microtubule poison works by blocking the formation of the mitotic spindles that attach to and pull apart sister chromatids in dividing cells. Cells will remain arrested until the nocodazole has been washed out. Nocodazole does not appear to disrupt interphase metabolism, and released cells return to normal cell cycle progression. Because microtubules are vital in other cellular functions, sustained use of nocodazole can result in disruption of those functions, causing cell death.
Inhibition of CDK1.
CDK1 is necessary for the transition from G2 to M phase. RO-3306 is a selective CDK1 inhibitor that can reversibly arrest cells at the G2/M border. RO-3306 synchronized >95% of cycling cells (including cancer cells), and released cells rapidly enter mitosis.
Roscovitine.
Roscovitine can be used to inhibit the activity of cyclin-dependent kinases (CDKs) by competing with ATP in the ATP-binding region of the kinase. Its effects are potent, arresting cells by knocking down the function of CDKs necessary for cell cycle progression. Roscovitine can be used to arrest cells in G0/G1, G1/S, or G2/M transitions.
Colchicine.
Colchicine arrests cells in metaphase and is a microtubule poison preventing mitotic spindle formation, much like nocodazole. It works by depolymerizing tubulin in microtubules, blocking progression to anaphase through sustained arrest at the spindle assembly checkpoint.
Arrest in S (G1/S arrest).
Arrest in S phase typically involves inhibition of DNA synthesis as the genome is being replicated. Most methods are reversible through washing.
Double thymidine block.
High concentrations of thymidine interrupt the deoxynucleotide metabolism pathway through competitive inhibition, thus blocking DNA replication. A single treatment with thymidine arrests cells throughout S phase, so a double treatment acts to induce a more uniform block in early S phase. The process begins with a treatment with thymidine, washing of the culture, followed by another thymidine treatment.
Hydroxyurea.
Hydroxyurea decreases the production of dNTPs by inhibiting the enzyme ribonucleotide reductase. This serves to halt DNA synthesis by depriving DNA polymerase of dNTPs at replication forks. Hydroxyurea is also used to treat certain types of cancer and blood disorders.
Aphidicolin.
Aphidocolin is a fungus-derived tetracyclic diterpenoid that acts as a selective inhibitor for DNA polymerase α. This enzyme is necessary for replicative DNA synthesis, but does not disrupt DNA repair synthesis or mitochondrial DNA replication.
Arrest in G1.
A single commonly-used chemical method exists for synchronization of cells in G1. It involves Lovastatin, a reversible competitive inhibitor of 3-hydroxy-3-methylglutaryl-coenzyme A reductase, an enzyme vital in the production of mevalonic acid. Mevalonic acid is a key intermediate in the mevalonate pathway responsible for synthesis of cholesterol. Addition of cholesterol to Lovastatin-treated cells does not undo the arrest affect, so Lovastatin appears to inhibit the formation of some early intermediate in the pathway that is essential for progression through early G1.
Other Methods of Synchronization.
Mitotic Selection.
Mitotic selection is a drug-free procedure for the selection of mitotic cells from a monolayer undergoing exponential growth. During mitosis, cells undergo changes in morphology, and mitotic selection takes advantage of this in adherent cells grown in a monolayer. The cells become more spherical, decreasing the surface area of cell membrane attached to the culture plate. Mitotic cells can therefore be completely detached by gently shaking and collected from the supernatant.
Nutrient/Serum Deprivation.
Elimination of serum from the culture medium for about 24 hours results in the accumulation of cells at the transition between G0 quiescence and early G1. This arrest is easily reversible through addition of serum or the deprived nutrient. Upon release, progression through the cell cycle is variable, as some cells remain quiescent while others proceed through the cell cycle at variable rates.
Contact Inhibition.
Contact inhibition occurs when cells are allowed to grow to high or full confluence, maximizing cell-to-cell contact. This triggers arrest in early G1 in normal cells. Arrest is reversed by replating cells at a lower density. Because of the proliferation-promoting mutations intrinsic to cancer, tumor cell lines are not usually able to undergo contact inhibition, though there are exceptions.


Bidensovirus

Bidensovirus is a genus of single stranded DNA viruses that infect invertebrates. The species in this genus were originally classified in the family "Parvoviridae" (subfamily "Densovirinae") but were moved to a new genus because of significant differences in
the genomes.
Taxonomy.
There is one species in this genus currently recognised: "Bombyx mori bidensovirus".
Host.
As the name suggests this virus infects "Bombyx mori", the silkworm.
Virology.
The virions are icosahedral, non enveloped and ~25 nanometers in diameter. They contain two structural proteins.
The genome is bipartite, unique among ssDNA viruses, with two linear segments of ~6 and 6.5 kilobases (kb). These segments and the complementary strands are that are packaged separately giving rise to 4 different types of full particles.
Both segments have an ambisense organization, coding for a structural protein in one sense and the non-structural proteins on the complementary strand.
The open reading frame 4 (VD1-ORF4) is 3318 nucleotides (bases) in length and encodes a predicted () 1105 amino acid protein which has a conserved DNA polymerase motif. It appears to encode at least 2 other proteins including one of ~53 kDa that forms part of the virion.
Evolution.
Comprehensive analysis of bidnavirus genes has shown that these viruses have evolved from a parvovirus ancestor from which they inherit a jelly-roll capsid protein and a superfamily 3 helicase. It has been further suggested that the key event that led to the separation of the bidnaviruses from parvoviruses was the acquisition of the PolB gene. A likely scenario has been proposed under which the ancestral parvovirus genome was integrated into a large virus-derived DNA transposon of the Polinton/Maverick family (polintoviruses) resulting in the acquisition of the polintovirus PolB gene along with terminal inverted repeats. Bidnavirus genes for a minor structural protein (putative receptor-binding protein) and a potential novel antiviral defense modulator were derived from dsRNA viruses ("Reoviridae") and dsDNA viruses ("Baculoviridae"), respectively.


Clostridium colicanis

Clostridium colicanis is an anaerobic, motile, gram-positive bacterium.


Pyramidelloidea

Pyramidelloidea is a superfamily of mostly very small sea snails, marine gastropod mollusks and micromollusks within the clade Panpulmonata.
This is a voluminous taxon: above the species level close to 400 named taxa are referred to this gastropod superfamily.
Pyramidelloidea has both fossil and recent members. They live as ectoparasites on bivalve molluscs and polychaete worms, and have a sharp, piercing stylet instead of a radula.
Distribution.
This taxon is found worldwide.
Taxonomy.
1999 taxonomy.
Taxonomy by Schander, Van Aartsen & Corgan (1999):
2005 taxonomy.
Pyramidelloidea has been classified within the informal group Lower Heterobranchia in the taxonomy of Bouchet & Rocroi (2005).
Taxonomy of Bouchet & Rocroi, 2005:
2010 taxonomy.
Jörger et al. (2010) have redefined major groups within the Heterobranchia and they moved Pyramidelloidea to Panpulmonata.


Mucophilus

Mucophilus is a fungal genus in the Chytridiales of uncertain familial placement. A monotypic genus, it contains the single species Mucophilus cyprini, described from Germany by Marianne Plehn in 1920.


Candidatus Bartonella thailandensis

""Candidatus" Bartonella thailandensis" is a candidatus bacteria from the genus of "Bartonella" which was isolated in Thailand.
References.


Actinomyces israelii

Actinomyces israelii is a species of Gram-positive, rod-shaped bacteria within the genus "Actinomyces". Known to live commensally on and within humans, "A. israelii" is an opportunistic pathogen and a cause of actinomycosis. Many physiologically diverse strains of the species are known to exist, though not all are strict anaerobes. It was named after the German surgeon James Adolf Israel (1848–1926), who studied the organism for the first time in 1878.
Pathogenesis.
Actinomycosis is most frequently caused by "A. israelii". It is a normal colonizer of the vagina, colon, and mouth. Infection is established first by a breach of the mucosal barrier during various procedures (dental, gastrointestinal), aspiration, or pathologies such as diverticulitis. The chronic phase of this disease is also known as the "classic phase" because the acute, early phase is often missed by health care providers. This is characterized by slow, contiguous growth that ignores tissue planes and forms a sinus tract that can spontaneously heal and recur, leading to a densely fibrotic lesion. This lesion is often characterized as "wooden". Sulfur granules form in a central purulence surrounded by neutrophils. This conglomeration of organisms is virtually diagnostic of "A. israelii."
Treatment.
"A. israelii" is curable and can be treated with antibiotics. Both a sodium hypochlorite solution and calcium hydroxide can be highly effective in killing "A. israelii" when it has caused infection in the mouth.


Biology Open

Biology Open (BiO) is an online-only peer-reviewed Open Access scientific journal published by The Company of Biologists. It launched in 2011 and publishes original research in all areas of the biological and biomedical sciences. "Biology Open" is partnered with Publons, is part of the Review Commons initiative and has two-way integration with bioRxiv.
Content.
"Biology Open" considers original research, Methods & Techniques papers, papers on computational analysis, replication studies and reports presenting negative results.
The journal operates on a continuous publication model. The final version of record is immediately released online as soon as it is ready.
All papers are published as Open Access articles under the CC-BY licence.
Abstracting and indexing.
"Biology Open" is abstracted and/or indexed by:
It is a member of OASPA (Open Access Scholarly Publishers Association) and is indexed in the DOAJ (Directory of Open Access Journals).
"Biology Open" is a signatory of the San Francisco Declaration on Research Assessment (DORA).
Management.
The founding Editor-in-Chief was Jordan Raff, from 2011-2018.
Steven Kelly has been the Editor-in-Chief since 2018.


Blueflower Formation

The Blueflower Formation is a geologic formation in Northwest Territories. It preserves fossils dating back to the Ediacaran period.


Aplyccavirus