Mycorrhizal fungi and soil carbon storage

Soil carbon storage is an important function of terrestrial ecosystems. Soil contains more carbon than plants and the atmosphere combined. Understanding what maintains the soil carbon pool is important to understand the current distribution of carbon on Earth, and how it will respond to environmental change. While much research has been done on how plants, free-living microbial decomposers, and soil minerals affect this pool of carbon, it is recently coming to light that mycorrhizal fungi—symbiotic fungi that associate with roots of almost all living plants—may play an important role in maintaining this pool as well. Measurements of plant carbon allocation to mycorrhizal fungi have been estimated to be 5-20% of total plant carbon uptake, and in some ecosystems the biomass of mycorrhizal fungi can be comparable to the biomass of fine roots. Recent research has shown that mycorrhizal fungi hold 50 to 70 percent of the total carbon stored in leaf litter and soil on forested islands in Sweden. Turnover of mycorrhizal biomass into the soil carbon pool is thought to be rapid and has been shown in some ecosystems to be the dominant pathway by which living carbon enters the soil carbon pool.
Outlined below are the leading lines of evidence on how different aspects of mycorrhizal fungi may alter soil carbon decomposition and storage. Evidence is presented for arbuscular and ectomycorrhizal fungi separately as they are phylogenetically distinct and often function in very different ways.
Recalcitrance of mycorrhizal tissues.
Based on the magnitude of mycorrhizal fungal inputs to the soil carbon pool, some have suggested that variation in the recalcitrance of mycorrhizal biomass may be important for predicting soil carbon storage, as it would affect the rate at which the contribution of mycorrhizal fungi to soil carbon is returned to the atmosphere. The compound glomalin, produced only by arbuscular mycorrhizal fungi, has been found to accumulate in some soils, and may be a substantial fraction of the soil carbon pool in these ecosystems. However, a recent set of experiments demonstrates the presence of arbuscular mycorrhizal fungi results in net losses of soil carbon, calling into question the role of glomalin produced by arbuscular mycorrhizal fungi leading to increased soil carbon storage. Proteomic work has revealed that most of the proteins isolated in the glomalin extraction are not of mycorrhizal origin, and therefore the contribution of this molecule to soil C storage has likely been overestimated.
Using a similar line of argument, Langley and Hungate (2003) argued that the abundance of chitin in ectomycorrhizal tissues may reduce decomposition rates of these fungi, under the assumption that chitin is recalcitrant. This possibility was tested and refuted recently. Fernandez and Koide (2012) show that chitin does not decompose more slowly than other chemical compounds in ectomycorrhizal tissues, and that chitin concentrations positively correlated with mycorrhizal biomass decomposition rates, rather than negatively.
Effects on fine root decomposition.
Mycorrhizal fungi are nutrient rich structures compared to the roots they colonize, and it is possible that mycorrhizal colonization of roots leads to increased rates of root decomposition because decomposers would have greater access to nutrients. Evidence is equivocal on this point, as ectomycorrhizal colonization does increase fine root decomposition rates substantially compared to uncolonized roots in some ecosystems, while "Pinus edulis" roots colonized predominately by ectomycorrhizal fungi from the "Ascomycota" group have been found to decompose more slowly than uncolonized controls.
In an experiment where the effect of arbuscular mycorrhizal colonization on plant decomposition was tested, only aboveground plant material was found to have decomposed faster after 3 months while root decomposition remained unchanged, even though arbuscular mycorrhizal fungi are confined to roots.
Effects on soil aggregation.
Soil aggregation can physically protect organic carbon from decay by soil microbes. More aggregate formation can result in more soil carbon storage. There is much evidence that arbuscular mycorrhizal fungi increase soil aggregate formation, and that aggregate formation may be mediated by the arbuscular mycorrhizal protein glomalin. Therefore, even if glomalin itself is not exceptionally recalcitrant and chemically resistant to decomposition (as described above) it may still contribute to soil carbon storage by physically protecting other organic matter from decomposition by promoting soil aggregation.
There is little information regarding the role of ectomycorrhizal fungi in soil aggregate stability. There are anecdotal accounts of ectomycorrhizal fungi increasing aggregation in sand in-growth bags commonly used to trap these fungi, but no current evidence that they promote aggregate formation or stability in field soils.
Stimulation of decomposition (priming).
Arbuscular mycorrhizal fungi have been shown to increase soil carbon decomposition in nutrient rich patches. Since arbuscular mycorrhizal fungi are thought to lack the ability to produce the enzymes to catalyze this decomposition it is generally thought that they stimulate free-living decomposer communities to increase activity by exuding labile energy substrates, a process termed priming. Recent lab experiments have shown that the presence of arbuscular mycorrhizal fungi increases losses of soil carbon compared to soils where arbuscular mycorrhizal fungi are excluded, and that the difference is greater under elevated CO2 when the abundance of arbuscular mycorrhizal fungi is greater.
The evidence for ectomycorrhizal priming is so far inconclusive. Field evidence suggests that ectomycorrhizal fungi may be increasing the rate of soil carbon degradation, however lab tests show that exudation from fine roots decreases with increasing ectomycorrhizal colonization, which suggests that abundance of ectomycorrhizal fungi should reduce priming effects. Brzostek et al. (2012) report variation in form of nitrogen produced in the rhizosphere of trees that vary in mycorrhizal type, however the effects of root and mycorrhizal priming could not be separated.
Inhibition of decomposition.
The first report of mycorrhizal inhibition of decomposition was in 1971 and came from ectomycorrhizal "Pinus radiata" plantations in New Zealand. Authors show that excluding roots and mycorrhizal fungi resulted in net carbon loss, and that the result could not be explained by soil disturbance effects. The mechanism presented is that ectomycorrhizal fungi can compete with free-living decomposers for nutrients, and thereby limit the rate of total decomposition. Since then there have been several other reports of ectomycorrhizal fungi reducing activity and decomposition rates of free-living decomposers and thereby increasing soil carbon storage. A theoretical ecosystem model recently demonstrated that greater access to organic nitrogen by mycorrhizal fungi should slow decomposition of soil carbon by free-living decomposers by inducing nutrient limitation. Koide and Wu (2003) made a strong case that the effect of ectomycorrhizal fungi on reducing decomposition may have more to do with competition for soil water than soil nutrients.
It is possible that arbuscular mycorrhizal fungi may be outcompeting free-living decomposers for either water or nutrients in some systems as well; however, to date there is no demonstration of this, and it seems that arbuscular mycorrhizal fungi may more often increase, rather than decrease rates of decomposition by free-living microbial decomposers.
Further reading.
Further reading on the role of arbuscular and ectomycorrhizal fungi in soil carbon storage and decomposition can be found in Zhu and Miller 2003, Ekblad et al. 2013, respectively, and the 2019 paper "Climatic controls of decomposition drive the global biogeography of forest-tree symbioses".


Pleurotoid fungi

Gilled fungi with laterally-attached fruiting bodies are said to be pleurotoid (Gr.: "pleurē" + "ōtos" + "-oid", literally "side-ear form" or "having the likeness of "Pleurotus" ssp."). Pleurotoid fungi are typically wood-decay fungi and are found on dead and dying trees and coarse woody debris. The pleurotoid form is polyphyletic, having evolved a number of times within the Basidiomycota. Many species of pleurotoid fungi are commonly referred to as "oyster" mushrooms. Laterally-attached fungi with pores rather than gills are referred to as bracket fungi.


Roe Jung-hye

Roe Jung-hye (; born 1 March 1957) is a South Korean professor of Molecular biology at Seoul National University currently serving as the 6th President of National Research Foundation of Korea - the first woman to lead the Foundation or its preceding foundations.
From 1986 Roe has been teaching at her alma mater receiving full tenure in 1997. She undertook several roles in her university such as the Vice Dean of its College of Natural Sciences and Dean of Office of Research Affairs - the first woman to run the Office. She is also leading its School of Biological Sciences and BK21 programme for Biological Sciences from 2009. Roe has been active in academia as well serving as a member of editorial board of Microbiology from 2007 to 2011, Journal of Bacteriology from 2012 to 2015 and Annual Review of Microbiology from 2012 to 2017.
In addition to academia, Roe has been active in policy making and advisory instruments of the government. Roe was a board member of now-National Research Council of Science & Technology from 2005 to 2008 and a member of Presidential Advisory Council on Science and Technology from 2008 to 2013 to which she has served as an advisor from 2013.
Roe is a member of Korean Academy of Science and Technology and a fellow of American Academy of Microbiology.
Roe holds two degrees - a bachelor in Microbiology from Seoul National University and a doctorate in Molecular biology from University of Wisconsin–Madison.


Chroogomphus subfulmineus

Chroogomphus subfulmineus is a basidiomycete fungus in the family Gomphidiaceae, described as new to science in 2018.
This species is closely related to "Chroogomphus fulmineus", but produces larger fruit bodies with generally duller colours, a deep yolk-yellow trama and an olivaceous stipe base. Microscopically, it has more narrow cystidia (av. range 13.8–14.8 μm) than "C. fulmineus" and broader spores (av. range 17.5–21.6 × 6.4–7.7 μm).
It is so far known from the island of Cyprus, Finland, and the United Kingdom.


Platynereis dumerilii

Platynereis dumerilii is a species of annelid polychaete worm. It was originally placed into the genus "Nereis" and later reassigned to the genus "Platynereis". "Platynereis dumerilii" lives in coastal marine waters from temperate to tropical zones. It can be found in a wide range from the Azores, the Mediterranean, in the North Sea, the English Channel, and the Atlantic down to the Cape of Good Hope, in the Black Sea, the Red Sea, the Persian Gulf, the Sea of Japan, the Pacific, and the Kerguelen Islands. "Platynereis dumerilii" is today an important lab animal, it is considered as a living fossil, and it is used in many phylogenetic studies as a model organism.
Description.
"Platynereis dumerilii" is a small marine ragworm: Males reach a length of 2 to 3 cm, while females reach a length of 3 to 4 cm. Like a number of invertebrate phyla, "Platynereis dumerilii" has an axochord, a paired longitudinal muscle that displays striking similarities to the notochord regarding position, developmental origin, and expression profile. It has the simplest eyes in the animal kingdom, each of which consists solely of a photoreceptor cell and a pigment cell.
Locomotion.
"P. dumerilii" worms have a ciliated surface which beats synchronously to drive locomotion and fluid flow. Larvae have segmental multiciliated cells that regularly display spontaneous coordinated ciliary arrests, which compose the ciliomotor circuitry in the worms. Whole-body coordination of ciliary locomotion is performed by a "stop-and-go pacemaker system".
As the worms develop, they use chaetae, and then parapodia, for locomotion. Unlike other polychaetes, in "Platynereis" larvae, the parapodia are used only for navigation while the cilia are responsible for propulsive force.
Senses.
Photoreceptor cells.
"Platynereis dumerilii" larvae possess two kinds of photoreceptor cells: Rhabdomeric and ciliary photoreceptor cells.
The ciliary photoreceptor cells are located in the deep brain of the larva. They are not shaded by pigment and thus perceive non-directional light. The ciliary photoreceptor cells resemble molecularly and morphologically the rods and cones of the human eye. Additional, they express an ciliary opsin that is more similar to the visual ciliary opsins of vertebrate rods and cones than to the visual rhabdomeric opsins of invertebrates. Therefore, it is thought that the urbilaterian, the last common ancestor of mollusks, arthropods, and vertebrates already had ciliary photoreceptor cells. The ciliary opsin is UV-sensitive ("λ"max = 383 nm), and the ciliary photoreceptor cells react on non-directional UV-light by making the larvae swimming down. This forms a ratio-chromatic depth-gauge with phototaxis of the rhabdomeric photoreceptor cells of the eyes.
A rhabdomeric photoreceptor cell forms with a pigment cell a simple eye. A pair of these eyes mediate phototaxis in the early "Platynereis dumerilii" trochophore larva. In the later nectochaete larva, phototaxis is mediated by the more complex adult eyes. The adult eyes express at least three opsins: Two rhabdomeric opsins and a Go-opsin. The three opsins there mediate phototaxis all the same way via depolarization, even so a scallop Go-opsin is known to hyperpolarize.
Chemical.
"P. dumerilii" senses chemicals with four types of organs: The antennae, the palps, the nuchal organs, and the tentacular cirri. The cirri are thin tendrils or filaments, while the nuchal organ is a singular ciliated pit.
Appendages of the worm's head and trunk provide a multisensory complex, which detects food and chemical cues such as alcohols, esters, amino acids, and sugars; as well as performing tactile function. Parts of the brain resemble the insect brain.
The antennae perform generalized chemosensation, while the palps are specialized for taste or detection of food-related chemical cues. The cirri are specialized in tactile sensation, but can also provide spatial information about chemical cues. Based on a single stimulus, the left and right cirrus can have a separate response time. The cirri are also photosensitive and involved in the "shadow reflex", a defensive withdrawal behaviour triggered by a decrease in illumination.
Conserved nuchal organs play an important sensory role in annelids, but they are less important in "P. dumerilii" than in other annelids. The antennae are the primary chemosensory organs over the palps, nuchal organs, and cirri
Habitat.
"Platynereis dumerilii" builds tubes on its substrate. The substrate may be algae-covered hard bottoms, sea grass, pelagic "Sargassum" rafts in the Sargasso Sea, or even rotting plant debris. "Platynereis dumerilii" commonly lives in depths of 0 to 5 meters, and so is typical for shallow bright infra-littoral environments. However, it has been also found on a buoy at 50 meters and on rotting seaweed at 100 m. It may also live in less favorable environments, like at thermal vents or polluted areas near sewer outfall pipes. It dominates polluted areas and acidic areas with pH values around 6.5 fitting the preferred pH value of a subpopulation of late "Platynereis dumerilii" nectochaete larvae. Larvae feed on plankton, and migrate vertically in the ocean in response to changes in light, causing a daily transport of biomass.
Reproduction and Development.
"Platynereis dumerilii" is dioecious, that means it has two separate sexes: During mating, the male swims around the female while the female is swimming in small circles. Both release eggs and sperm into the water. This is triggered by sexual pheromones. The eggs are then fertilized outside of the body in the water. "Platynereis dumerilii" has like other Nereidids no segmental gonades, the oocytes mature freely swimming in the body cavity (coelom), and stain the body of the mature female epitoke yellow.
"Platynereis dumerilii" develops very stereotypically between batches and therefore time can be used to stage "Platynereis dumerilii" larvae. However, the temperature influences the speed of development greatly. Therefore, the following developmental times are given with 18 °C as reference temperature:
After 24 hours, a fertilized egg gives rise to a trochophore larva. At 48 hours, the trochophore larva becomes a metatrochophore larva. Both trochophore and metatrochophore swim with a ring of cilia in the water and are positively phototactic. The metatrochophore has, beside the larval eyes, already the anlagen for the more complex adult eyes of the adult worm. A day later, at 72 hours after fertilization, the metatrochophore larva becomes a nectochaete larva. The nectochaete larva already has three segments, each with a pair of parapodia bearing chaetae, which serve for locomotion. The nectochaete larva can switch from positive to negative phototaxis. After five to seven days, the larvae start feeding and develop on their own speed, depending on food supply. After three to four weeks, when six segments have formed, the head is formed.
Normal development is subdivided into 16 stages. "Platynereis dumerilii" lives for 3 up to 18 months with an average lifespan of seven months. The worm reproduces only once, and dies after delivering its gametes.
Genome.
The genome of "Platynereis dumerilii" is diploid (2n chromosomes) with a haploid set of n = 14 chromosomes. It contains approximately 1 Gbp (giga base pairs) or 10 9 base pairs. This genome size is close to the average observed for other animals. However, compared to many classical invertebrate molecular model organisms, this genome size is rather large and therefore it is a challenge to identify gene regulatory elements that can be far away from the corresponding promoter. But it is intron rich unlike those of "Drosophila melanogaster" and "Caenorhabditis elegans" and thus closer to vertebrate genomes including the human genome.


Bromovirus

Bromovirus is a genus of viruses, in the family "Bromoviridae". Plants serve as natural hosts. There are six species in this genus.
Taxonomy.
The following species are assigned to the genus:
Structure.
Viruses in the genus "Bromovirus" are non-enveloped, with icosahedral geometries, and T=3 symmetry. The diameter is around 26 nm. Genomes are linear and segmented, tripartite.
Life cycle.
Viral replication is cytoplasmic. Entry into the host cell is achieved by penetration into the host cell. Replication follows the positive stranded RNA virus replication model. Positive stranded rna virus transcription, using the internal initiation model of subgenomic RNA transcription is the method of transcription. The virus exits the host cell by tubule-guided viral movement. Plants serve as the natural host. Transmission routes are mechanical and contact.
Recombination.
"Brome mosaic virus" (BMV) genomes are able to undergo RNA-RNA homologous recombination upon infection of plant cells. The RNA-dependent RNA polymerase specified by the BMV genome appears to undergo template switching (copy choice) recombination during viral RNA synthesis.


Ternatin heptapeptide

Ternatin is a mushroom heptapeptide that suppresses hyperglycemia "in vivo".


DNA re-replication

DNA re-replication (or simply rereplication) is an undesirable and possibly fatal occurrence in eukaryotic cells in which the genome is replicated more than once per cell cycle. Rereplication is believed to lead to genomic instability and has been implicated in the pathologies of a variety of human cancers. To prevent rereplication, eukaryotic cells have evolved multiple, overlapping mechanisms to inhibit chromosomal DNA from being partially or fully rereplicated in a given cell cycle. These control mechanisms rely on cyclin-dependent kinase (CDK) activity. DNA replication control mechanisms cooperate to prevent the relicensing of replication origins and to activate cell cycle and DNA damage checkpoints. DNA rereplication must be strictly regulated to ensure that genomic information is faithfully transmitted through successive generations.
Initiating Replication at Origins.
Replication of DNA always begins at an origin of replication. In yeast, the origins contain autonomously replicating sequences (ARS), distributed throughout the chromosome about 30 kb from each other. They allow replication of DNA wherever they are placed. Each one is 100-200 bp long, and the A element is one of the most conserved stretches. Along with other conserved B elements, they form the section where the ORCs assemble to begin replication. The repetition of these sequences may be the most important to origin recognition.
In animal cells, replication origins may seem to be randomly placed throughout the chromosome, sometimes even acting as ARSs, but local chromatin structure plays a large role in determining where replication will occur. The replication origins are not distributed evenly throughout the chromosome. Replicon clusters, containing 20-80 origins per cluster, are activated at the same time during S phase. Although they are all activated during S phase, heterochromatin tends to be replicated in late S phase, as they are more difficult to access than euchromatin. Epigenetic factors also have a large influence on what gets replicated and when it gets replicated.
Origin licensing.
All known mechanisms that prevent DNA rereplication in eukaryotic organisms inhibit origin licensing. Origin licensing is the preliminary step for normal replication initiation during late G1 and early S phase and involves the recruitment of the pre-replicative complex (pre-RC) to the replication origins. Licensing begins with the binding of the multi-subunit ATPase, the origin recognition complex (ORC), to the DNA at the replication origins. Once bound to chromatin the ORC recruits the AAA+ ATPase Cdc6 and the coiled-coil domain protein Cdt1. Cdt1 binding and the ATPase activity of ORC and Cdc6 facilitate the loading of the minichromosome maintenance (MCM) proteins 2-7 onto the chromatin. The MCM complex is the DNA helicase that opens the helix at the replication origin and unwinds the two strands as the replication forks travel along the DNA. Elevated CDK activity at the end of G1 triggers the firing of the origins and the dismantling of the pre-RCs. High CDK levels, which are maintained until the end of mitosis, inhibit or destroy pre-RC components and prevent the origin from relicensing. A new MCM complex cannot be loaded onto the origin until the pre-RC subunits are reactivated with the decline of CDK activity at the end of mitosis. Thus, CDKs serve a dual role in the regulation of eukaryotic DNA replication: elevated CDK activity initiates replication at the origins and prevents rereplication by inhibiting origin re-licensing. This ensures that no replication origin fires twice in the same cell cycle.
Two-state model for DNA replication regulation.
Early experimental evidence on the regulation of DNA replication suggests that replication origins exist in one of two states during the cell cycle: a prereplicative state in G1 and a postreplicative state from the moment of initiation until passage through mitosis. Origins of replication alternate between these two distinct states during the cell cycle. A licensing factor which is required for replication initiation binds to origins in the prereplicative state. At the G1/S transition, the factor is inactivated and cannot be restored until the cell cycle has concluded. The identification and characterization of the ORC, Cdc6, Cdt1, and the MCM complex proteins as the licensing factor gives credence to this model and suggests a means by which the oscillatory nature of CDKs in the cell cycle can regulate rereplication.
Replication regulation.
Budding yeast.
Rereplication regulation is best understood in budding yeast. "Saccharomyces cerevisiae" cells prevent rereplication by directly regulating pre-RC assembly through the CDK-mediated phosphorylation of the pre-RC components Cdc6, MCM2-7, and the ORC subunits. The phosphorylation of these components is initiated at the onset of S phase and is maintained throughout the rest of the cell cycle as CDK activity remains high. Phosphorylated Cdc6 is bound by the ubiquitin-protein ligase SCF which leads to its proteolytic degradation. CDK-dependent phosphorylation of the MCM2-7 proteins results in the complex's export from the nucleus. (Cdt1 which associates with the MCM complex is similarly exported from the nucleus). Phosphorylation of the ORC subunits presumably disrupts the ORC's ability to bind other pre-RC components. Thus, multiple mechanisms ensure that the pre-RC cannot be reassembled on postreplicative origins.
Note: Since origins fire at different times throughout S phase, it is crucial that the inhibitory mechanisms that prevent new MCM2-7 recruitment do not destabilize existing pre-RCs. Pre-RCs can remain assembled on origins that haven't fired even though rereplication inhibitory mechanisms are inhibiting or destroying pre-RC components.
Other organisms.
Although CDK regulation of pre-RC assembly appears to be highly evolutionarily conserved, some differences across organisms are noted. In multicellular eukaryotes pre-RC assembly is regulated by the anaphase-promoting complex (APC) in addition to CDKs. APC, an E3 enzyme, ubiquitinates the protein geminin and targets it for degradation. Geminin normally prevents origin licensing by binding to and inhibiting Cdt1. In G1, APC activity is adequate to suppress the accumulation of geminin, thereby indirectly promoting pre-RC assembly. At the end of G1, APC is inactivated and geminin can accumulate and prevent origin re-licensing.
Cdt1 is usually upregulated by E2F-mediated transcriptional activation and by binding of human acetylase to Orc1. Proteolytic degradation of Cdt1 is a conserved mechanism in various higher order eukaryotes as well. Cdt1 is degraded through the Cul4–Ddb1–Cdt2 E3 ubiquitin ligase complex so that DNA licensing control is maintained in S and G2. Cdt1 is an important regulatory protein, and evolution has led to different pathways of regulation in different organisms. Overexpression of Cdt1 or incactivation of Geminin can lead to re-replication, as undegraded Cdt1 will induce pre-RC assembly.
Pre-RC regulation in most animals is still not well understood.
Consequences of rereplication in eukaryotic cells.
Rereplication and mitotic failure are generally not programmed events, but rather result spontaneously from defects in the cell cycle machinery. Rereplication appears to give rise to dsDNA breaks which triggers a DNA damage response and arrests cells in G2. The checkpoint effectively causes a permanent cell cycle arrest and eventual apoptosis.
Rereplication can be experimentally induced by simultaneously disrupting several of the mechanisms that prevent origin re-licensing. For example, deregulation of the ORC, MCM2-7 and Cdc6 mechanisms can induce rereplication in budding yeast cells.
Note: Recent evidence suggests that although overlapping, the multiple replication regulation mechanisms should not be considered as functionally redundant; although a single mechanism may repress rereplication at greater than 99% efficiency, it may not be sufficient to maintain genome stability over many generations. Instead, it is believed that the multiplicative effect of many overlapping mechanisms is what sufficiently prevents rereplication and ensures the faithful transmission of a cell's genome.
Preventing Rereplication.
Cells with replication stress activate replication checkpoints so that S phase is delayed and slows down the transition to G2/M phase. When replicative stress is recognized by U-2-OS cells, human osteosarcoma cell lines with wild-type retinoblastoma (RB) and p53, the ATM/ATR-regulated DNA damage network is activated. This checkpoint response activates due to overexpression of cyclin E, which has been shown to be important in regulating the licensing system. When cyclin E is overexpressed in U-2-OS cell lines, the ATM/ATR-regulated DNA damage network results in increases in Ser 15-phosphorylated p53, γ-H2AX, and Ser 966-phosphorylated cohesin SMC1. The DNA re-replication response is different from the response taken when damage is due to oxygen radical generation. Damage from oxygen radical generations leads to a response from the Myc oncogene, which phosphorylates p53 and H2AX.
The ATM/ATR DNA damage network will also respond to cases where there is an overexpression of Cdt1. Overexpression of Cdt1 leads to accumulation of ssDNA and DSBs. Ataxia telangiectasia and Rad3 related (ATR) is activated earlier when it detects ssDNA in the earlier phases of DNA re-replication. ATR phosphorylates downstream replication factors, such as RPA2 and MCM2 or through modulation of Rb or p53. Ataxia telangiectasia mutated (ATM) activates after a larger amount of DSBs is detected at later stages of DNA re-replication. While ATM plays a role in cell cycle arrest, apoptosis, and senescence, it is also suspected to play a role in mediating DSB repair, but the exact mechanisms are not understood yet.
Rereplication in cancer.
Rereplication has been implicated in tumorigenesis in model organisms and humans. Replication initiation proteins are overexpressed in tissue samples from several types of human cancers and experimental overexpression of Cdt1 and Cdc6 can cause tumor development in mouse cells. Similarly, Geminin ablation in knockout mice has been reported to enhance tumor formation. Further, these studies indicate that rereplication can result in an increase in aneuploidy, chromosomal fusions, and DNA breaks. A thorough understanding of the regulatory replication mechanisms is important for the development of novel cancer treatments.
In yeast, increased activity of G1 CDK activity usually inhibits the assembly of pre-RCs and entry into S phase with less active origins, but in cancer cells, p53 and Rb/E2F pathways are deregulated and allow entry into S phase with a reduced amount of active origins. This leads to double-strand breaks in the DNA, increased recombination, and incorrect chromosomal arrangements. The mechanism by which this damage occurs is still not known. One possibility is that reduced origin activation leads to incomplete DNA replication. Significant re-replication is only observed when all CDK regulatory pathways are inhibited.
In mammalian cells, Cdt1 and Cdc6 are much more important to re-replication regulation. Overexpression of Cdt1 and Cdc6 were found in 43/75 cases of non-small cell lung carcinomas. Targeting Cdc6 or ORC in mammalian cells does not cause substantial re-replication. Overexpression of Cdt1, on the other hand, can lead to potentially lethal re-replication levels on its own. This response is seen only in cancer cells. Overexpression of E2F family members contributes to an increase in Cdt1 and Cdc6 expression. Loss of p53 regulation in cells can also be observed frequently in cell lines that overexpress Cdt1 or Cdc6.
Endoreduplication.
For the special case of cell cycle-regulated DNA replication in which DNA synthesis is uncoupled from cell cycle progression refer to endoreduplication. Endoreduplication is an important and widespread mechanism in many cell types. It does not adhere to many of the cell cycle checkpoints and damage controls in regularly dividing cells, but it does not result in uncontrolled re-replication. Endoreduplication is a controlled process and occurs to perform a specific cell function. In some cells, it has been proposed that endoreduplication is used as a way to store nucleotides for embryogenesis and germination. In other cases, endoreduplication may be used in cells that are only used for storage of nutrients. Despite its useful functioning in many cells, endoreduplication has also been observed in cancerous cells, and it is not fully understood whether endoreduplication leads to cancerous behavior or whether other mutations lead to endoreduplication. Other mechanisms may be involved in mediating these changes.


Pierella nereis

Pierella nereis is a butterfly species from the subfamily Satyrinae in the family Nymphalidae. It was first described by Dru Drury in 1782 from Brazil.
Description.
Upperside: Antennae black. Head, thorax, abdomen grey brown. Anterior wings grey brown, thin, and slightly diaphanous, with a small light-coloured bar running from the anterior edge near the tips to the posterior. Posterior wings having one-third next the body grey brown, divided by a line drawn across the wings from the anterior to the abdominal edges; next to this is an angulated white patch, the rest of these wings being orange coloured, with two black eyespots, having white centres, placed one at the upper, the other at the abdominal corners, the former having a small white spot joining to its upper part. The edges of these wings are bordered with dark brown.
Underside: Palpi, legs, breast, and abdomen cream coloured. Anterior wings next the tips tinged with red brown; the remainder of the wings being of the same colour as on the upperside. Posterior wings next the body pale clay, which occupies half the wings; below which is a white bar, the remainder of the wings being dark orange: the two black eyespots are very small on this side, and the white spot above them not so distinct. These wings are larger than is generally observed among insects of this tribe, and are dentated, the anterior ones being entire. Wingspan 3 inches (76 mm).


Ascoidea asiatica

Ascoidea asiatica is a species of yeast in the Ascoideaceae family discovered in 1964.
Biochemistry.
In 2018, it was reported by researchers at the University of Bath and the Max-Planck Institute for Biophysical Chemistry that the CUG sense codon in this yeast is translated by two different tRNAs, one coding for serine and one for leucine, with approximately equal probability. This is the first reported instance of a proteome that is stochastically encoded from the genome. This codon is rarely used in this species, which has led to the suggestion that stochastic encoding is deleterious to the organism.


Trichura coarctata

Trichura coarctata is a moth in the subfamily Arctiinae. It was described by Dru Drury in 1773. It is found in Brazil (Para, Pernambuco).
Description.
Upperside: Antennae pectinated, and thickest in the middle. Head black, with a blue spot in front. Neck blue. Thorax black, with an orange spot on each shoulder. Abdomen black; smallest next the thorax, with a row of golden-blue spots on each side, and another at the top; at the extremity is placed a hairy bristle, about a quarter the length of the abdomen. Wings yellowish and transparent. The anterior having a black narrow border running round all their edges, except the anterior ones; and in the middle of each is an oblong black spot, joining to the anterior edge, which reaches almost halfway across the wing. Posterior wings with a black border along the abdominal edges and the upper corners; the anterior and external edges having none. The extremity of the body of the male is furnished with a villose tail, as long as the body.
Underside: Palpi externally white but internally black. Tongue curled up. Breast black, the sides being blue. Legs black. Thighs white within, and blue without. Abdomen, next the thorax, white; the remainder being black, with four white spots on each side; that next the anus being the smallest. Wings as on the upperside; except the anterior, which have a yellowish border running along the posterior edges. Wingspan inches (45 mm).


African Natural History

African Natural History was a scientific journal published by Iziko Museums (Cape Town). It took the place of the "Annals of the South African Museum", which has been discontinued. Now the journal has been discontinued.


Trioecy

Trioecy (or subdioecy) is an extremely rare reproductive system characterized by the coexistence of males, females, and hermaphrodites. It has been found in both plants and animals. Trioecy has been estimated to occur in about 3.6% of flowering plants. Although most reports of trioecy are misinterpretions of gynodioecy.
Evolution of trioecy.
Trioecy is usually viewed as evolutionarily unstable. Its exact stability over evolution is unclear, but many speculate it is a transient state. Trioecy is often associated with evolutionary transitioning from Gynodioecy to Dioecy. Other studies support show that trioecious populations originated from gonochoristic ancestors which were invaded by a mutant selfing hermaphrodite, creating a trioecious population.
Species that exhibit trioecy.
The following species have been observed to exhibit a trioecious breeding system.
Plants.
Trioecy, is a relatively common sexual system in plants. The following list gives some examples:


Young Woman with Unicorn

Portrait of Young Woman with Unicorn is a painting by Raphael, which art historians date "c." 1505-1506. It is in the Galleria Borghese in Rome. The painting was originally oil on panel, and was transferred to canvas during conservation work in 1934. It was in the course of this work that overpainting was removed, revealing the unicorn, and removing the wheel, cloak, and palm frond that had been added by an unknown painter during the mid-17th century.
The composition of the picture--placing the figure in a loggia opening out onto a landscape, the three-quarter length format-- was apparently inspired by the "Mona Lisa", painted by Leonardo between 1503 and 1506. Christof Thoenes observes: "However unabashedly Raphael adopts the pose, compositional framework and spatial organization of the Leonardo portrait...the cool watchfulness in the young woman's gaze is very different" from the "enigmatic ambiguity" of Mona Lisa.
The work was of uncertain attribution until recent times. In the 1760 inventory of the Gallery, the subject of the painting was identified as Saint Catherine of Alexandria and attributed to Perugino. A restoration of the painting in 1934–36 confirmed art historian Roberto Longhi's attribution of the work to Raphael, and the removal of heavy repainting revealed the unicorn, traditionally a symbol of chastity in medieval romance, in place of a Saint Catherine wheel. Restoration work on the painting in 1959 revealed through radiography the image of a small dog, a symbol of conjugal fidelity, under the unicorn. It served as a sketch for the final appearance of the unicorn.


Granulicatella adiacens

Granulicatella adiacens is a fastidious Gram-positive cocci (pairs, chains) and is part of the nutritionally variant streptococci (NVS). Like other constituents of the NVS, it can cause bacteremia and infective endocarditis (IE), with significant morbidity and mortality. NVS has less often been implicated in a variety of other infections, including those of the orbit, nasolacrimal duct and breast implants. It is a commensal of the human mouth, genital, and intestinal tracts, although it is rarely implicated in infections, in part due to it being a fastidious organism and rarely being identified in the laboratory environment. However, its identification has become more frequent with use of commercial mediums and automated identification systems. Because it has been difficult to identify, it has been considered one of the causes of culture negative IE. Identifying "G. adiacens" can allow more appropriate selection of antibiotics, especially when susceptibility testing is not available.
Clinical relevance.
Infective endocarditis.
Of human diseases caused by "G. adiacens", infective endocarditis (IE) is the most common. Among the members of the genus "Granulicatella", "G. adiacens" seems to be more capable of causing IE, possibly due to its capacity to bind to the cardiac valvular tissue. IE from NVS species has been described as indolent-onset, often in the setting of preexisting heart valve damage. The aortic and mitral valves are most commonly affected. More often than not, IE due to NVS produces detectable vegetations, although other classic IE signs (e.g., Osler nodes) are usually not present. Treatment failure is frequently observed, and approximately 1/4 of cases require prosthetic valve replacement.
Antibiotic treatment.
The "Granulicatella" genus is more resistant to antibiotics than viridans streptococci (another common cause of IE), although it is still often susceptible to clindamycin, erythromycin, rifampicin and vancomycin.
Malodorous breath.
"Granulicatella spp". have been associated with malodorous breath (halitosis) in Japan.
Laboratory identification.
It grows best on media supplemented with thiol or pyridoxal. Phenotypic identification of this genus is difficult, but feasible with automated identification systems. 16S rRNA gene sequencing is confirmatory.
Classification history.
In 1961, a new type of viridans streptococci was classified as "nutritionally variant streptococci" (NVS). In 1989, NVS was subdivided into "Streptococcus defectiva" and "Streptococcus adiacens", which in 1995 were relocated to create a new genus "Abiotrophia". In 2000, three members of the "Abiotrophia" genus were reclassified into the genus "Granulicatella" ("Granulicatella adiacens", "balaenopterae" and "elegans").


Mycobacterium hiberniae

Mycobacterium hiberniae is a species of the phylum Actinobacteria (Gram-positive bacteria with high guanine and cytosine content, one of the dominant phyla of all bacteria), belonging to the genus "Mycobacterium".
Etymology Hibernia, Latin for Ireland where it was first isolated.
Description.
Polymorphic, beaded, gram-positive, nonmotile and acid-fast rods (0.9 µm x 1.2-1.5 µm).
Colony characteristics
Physiology
Differential characteristics
Type strain.
Strain Hi 11 = ATCC 49874 = CIP 104537 = DSM 44241 = JCM 13571.


Hyphomicrobiales

The Hyphomicrobiales are an order of Gram-negative Alphaproteobacteria.
The rhizobia, which fix nitrogen and are symbiotic with plant roots, appear in several different families. The four families "Nitrobacteraceae", "Hyphomicrobiaceae", "Phyllobacteriaceae", and "Rhizobiaceae" contain at least several genera of nitrogen-fixing, legume-nodulating, microsymbiotic bacteria. Examples are the genera "Bradyrhizobium" and "Rhizobium". Species of the "Methylocystaceae" are methanotrophs; they use methanol (CH3OH) or methane (CH4) as their sole energy and carbon sources. Other important genera are the human pathogens "Bartonella" and "Brucella", as well as "Agrobacterium" (useful in genetic engineering).
Taxonomy.
Provisional Taxa.
These taxa have been published, but have not been validated according to the Bacteriological Code.
Phylogeny.
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature and the phylogeny is based on whole-genome sequences.
Natural genetic transformation.
Natural genetic transformation has been reported in at least four "Hyphomicrobiales" species: "Agrobacterium tumefaciens", "Methylobacterium organophilum", "Ensifer adhaerens", and "Bradyrhizobium japonicum". Natural genetic transformation is a sexual process involving DNA transfer from one bacterial cell to another through the intervening medium, and the integration of the donor sequence into the recipient genome by homologous recombination.


Enaphalodes atomarius

Enaphalodes atomarius is a species of beetle in the family Cerambycidae. It was described by Dru Drury in 1773 from New York City.
Description.
Head brownish black, covered with short yellowish-grey pile. Thorax dirty black, covered with yellow-grey pile; cylindrical, and without any spines or risings. Antennae dusky brown; having a spine on each joint, except that next to the head, and about the length of the insect. Scutellum very small. Elytra black, mottled with yellow grey; being margined at the sides and suture, and not reaching or covering the anus, each having two spines at the extremity. Abdomen and breast greyish brown, as are the legs, each of which is furnished with a spine at the tip of the tibiae. Length of body inch (17 mm).


Etest

Etest (previously known as the Epsilometer test) is a way of determining antimicrobial sensitivity by placing a strip impregnated with antimicrobials onto an agar plate. A strain of bacterium or fungus will not grow near a concentration of antibiotic or antifungal if it is sensitive. For some microbial and antimicrobial combinations, the results can be used to determine a minimum inhibitory concentration (MIC). Etest is a proprietary system manufactured by bioMérieux. It is a laboratory test used in healthcare settings to help guide physicians by indicating what concentration of antimicrobial could successfully be used to treat patients' infections.
Use.
Etest is a quantitative technique for determining the antibiotic sensitivity and minimum inhibitory concentration (in µg/mL) of some bacteria including Gram-negative and Gram-positive aerobic bacteria such as Enterobacteriaceae, "Pseudomonas", "Burkholderia", "Staphylococcus", and "Enterococcus" species and fastidious bacteria, such as anaerobes, "N. gonorrhoeae", "S. pneumoniae", "Streptococcus" and "Haemophilius" species. It can also be used to determine MICs against certain fungi.
Procedure.
Etest is a pre-prepared non-porous plastic reagent strip with a predefined gradient of antibiotic, covering a continuous concentration range. It is applied to the surface of an agar plate inoculated with the test strain, where there is release of the antimicrobial gradient from the plastic carrier to the agar to form a stable and continuous gradient beneath and in nearby to the strip.
The time taken for a plate to be ready depends on the bacterium that is being tested, and the conditions of the agar plate. The predefined Etest gradient remains stable for at least 18 to 24 hours; that is, a period that covers the critical times of many species of fastidious and non-fastidious organisms.
After the test, the bacterial growth becomes visible after incubation and a symmetrical inhibition ellipse centered along the strip is seen. The MIC value is read from the scale in terms of µg/mL where the ellipse edge intersects the strip. After the required incubation period, the minimum inhibitory value is read where the edge of the inhibition ellipse intersects the side of the strip. The plate should not be read if the culture appears mixed or if the lawn of growth is too light or too heavy.
Etest MIC endpoints are usually clear-cut although different growth/inhibition patterns may be seen depending on the antifungal or antibiotic used.
Selection of agar medium.
Etest can be used with many different kinds of AST agar medium as long as the medium supports good growth of the test organism and does not interfere with the activity of the antimicrobial agent. However, to maximise reproducibility, the medium chosen should fulfil the basic requirements for a susceptibility test medium. The following AST media are recommended for use with Etest:
These media may require supplemental nutrients to obtain enhanced growth of nutritionally fastidious organisms such as pneumococci, streptococci, "Abiotrophia", "Haemophilus", gonococci, meningococci and "Campylobacter". In general, media recommendations from the Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) are considered appropriate for Etest.
Availability.
Etest products for more than 100 antimicrobial agents, including antibiotics, antifungal agents and antimycobacterial agents are available. In addition, specific Etest products are available for the detection of specific resistance mechanisms [e.g. ESBL (Extended Spectrum Beta-Lactamase), MBL (Metallo Beta-Lactamase), AmpC Beta-Lactamase and VISA/h VISA].
Etest has been FDA cleared and CE marked for many organisms by comparing to conventional broth/agar dilution reference methods and shown to have excellent correlation.
Etest equipment.
The Etest family of instruments is designed to simplify the daily use of Etest. Simplex C76, Nema C88, and Retro C80 are easy to use, reducing operator fatigue, saving time and improving the quality of results by increasing reproducibility. Etest and related instruments offer one of the most efficient methods for generating on-scale MIC values across 15 doubling dilutions for susceptibility testing of a wide range of drug-bug combinations, including fastidious organisms.
History.
The Etest strip was first described in 1988 and was introduced commercially in 1991 by AB BIODISK. bioMérieux acquired AB BIODISK in 2008 and continues to manufacture and market this product range under the mark Etest.
During the 1950s, Hans Ericsson (Professor of microbiology at the Karolinska Hospital and Karolinska Institute, Stockholm), the scientific founder of AB BIODISK, developed a method to standardize the disk diffusion test and to improve its reproducibility and reliability for clinical susceptibility predictions. The inhibition zone sizes from disk test results were compared to minimum inhibitory concentration (MIC) values based on the reference agar dilution procedure. The correlation between zone sizes and MIC values was then assessed using regression analysis and regression lines were used for extrapolating zone interpretive limits that corresponded to the MIC breakpoint values that defined susceptible, intermediate and resistant categorical results.
Etest was first presented at the Interscience Conference on Antimicrobial Agents and Chemotherapy (ICAAC) in Los Angeles in 1988 as a novel gradient concept for MIC determinations. In September 1991, Etest was launched globally as a MIC product after receiving the USA Food and Drug Administration (FDA) clearance.


Strigocossus crassa

Strigocossus crassa is a moth in the family Cossidae. It is found in Cameroon, the Democratic Republic of Congo, Ghana, Nigeria, Sierra Leone and South Africa.
Description.
Upper side: antennae filiform, whiteish at the base, black at the tips. Head whiteish, small. Thorax whiteish, having two black tufts of hair on the shoulders, and two next the abdomen; upper part yellowish brown. Abdomen dark brown, almost black, being ringed and edged with dark grey. Anterior wings whiteish, intermixed with many patches and irregular spots of grey and dark brown. Posterior wings darkish grey brown, but lighter along the posterior edges.
Under side: all the parts on this side are of a dark yellow brown, of the same colour with the upper side of the inferior wings. Abdomen rather lighter, with a dark brown line running along its middle from the thorax to the anus. Wingspan 7 inches (178 mm).


Fort Morgan virus

Fort Morgan virus is an RNA virus in the genus "Alphavirus". It is an Alphavirus isolated from nesting Cliff Swallows, House Sparrows and from cimicid bugs in eastern Colorado for which the name Fort Morgan virus was proposed.


Thysania zenobia

Thysania zenobia, the owl moth, is a species of moth in the family Erebidae. The species was first described by Pieter Cramer in 1776, and is native to North and South America and the Caribbean.
Description.
Upperside: Antennae setaceous and dark brown. Head the same. Thorax and abdomen grey: having a tuft of black hairs standing between them. General colour grey, faintly tinged with red. Anterior wings with a remarkable irregular black bar running from the tips to the shoulders, crossing the thorax horizontally, and parallel with the anterior edges; on the middle of this edge is a triangular dark brown spot edged with black, and nearer the body is a smaller one of the same shape and colour: a second narrower black line is situate about half an inch below, and parallel with the first, rising on the posterior edges, and extending across the wings almost to the external ones. Posterior wings with a black irregular bar arising near the external corners, and crossing them in a straight direction, meeting at the extremity of the abdomen; just above this, and almost close to it, is a very small and narrow waved black line running parallel with it, but towards the end suddenly turns off, and reaches the anterior edges. Besides the above markings there are a number of lighter and darker shades interspersed on the different parts of the wings. They are so ugly and nasty.
Underside: Palpi reddish, the extremities brown. Tongue spiral. Legs dark brown, mottled with red. Breast, abdomen, and sides red. Wings greyish red, with black indented lines and bars running parallel with the edges of the wings, and regularly placed one above another. Anterior wings having a black spot near their centre shaped like a kidney bean, with a small round one at a little distance nearer the body. Posterior having likewise a small black spot about half an inch from the base. Margins of the wings rather deeply scolloped. Wingspan inches (140 mm).
See also.
Other moths which are called "owl moth" include:


Enterobacteriaceae

Enterobacteriaceae is a large family of Gram-negative bacteria. It was first proposed by Rahn in 1936, and now includes over 30 genera and more than 100 species. Its classification above the level of family is still a subject of debate, but one classification places it in the order Enterobacterales of the class Gammaproteobacteria in the phylum Proteobacteria.
Enterobacteriaceae includes, along with many harmless symbionts, many of the more familiar pathogens, such as "Salmonella", "Escherichia coli", "Klebsiella", and "Shigella". Other disease-causing bacteria in this family include "Enterobacter" and "Citrobacter". Members of the Enterobacteriaceae can be trivially referred to as enterobacteria or "enteric bacteria", as several members live in the intestines of animals. In fact, the etymology of the family is enterobacterium with the suffix to designate a family (aceae)—not after the genus "Enterobacter" (which would be "Enterobacteraceae")—and the type genus is "Escherichia".
Morphology.
Members of the Enterobacteriaceae are bacilli (rod-shaped), and are typically 1–5 μm in length. They typically appear as medium to large-sized grey colonies on blood agar, although some can express pigments.
Most have many flagella used to move about, but a few genera are nonmotile. Most members of Enterobacteriaceae have peritrichous, type I fimbriae involved in the adhesion of the bacterial cells to their hosts.
They are not spore-forming.
Metabolism.
Like other proteobacteria, enterobactericeae have Gram-negative stains, and they are facultative anaerobes, fermenting sugars to produce lactic acid and various other end products. Most also reduce nitrate to nitrite, although exceptions exist. Unlike most similar bacteria, enterobacteriaceae generally lack cytochrome c oxidase, there are exceptions.
Catalase reactions vary among Enterobacteriaceae.
Ecology.
Many members of this family are normal members of the gut microbiota in humans and other animals, while others are found in water or soil, or are parasites on a variety of different animals and plants.
Model organisms and medical relevance.
"Escherichia coli" is one of the most important model organisms, and its genetics and biochemistry have been closely studied.
Some enterobacteria are important pathogens, e.g. "Salmonella", or "Shigella" e.g. because they produce endotoxins. Endotoxins reside in the cell wall and are released when the cell dies and the cell wall disintegrates. Some members of the "Enterobacteriaceae" produce endotoxins that, when released into the bloodstream following cell lysis, cause a systemic inflammatory and vasodilatory response. The most severe form of this is known as endotoxic shock, which can be rapidly fatal.
Genera.
Validly published genera.
The following genera have been validly published, thus they have "Standing in Nomenclature". The year the genus was proposed is listed in parentheses after the genus name.
Proposed genera.
The following genera have been effectively, but not validly, published, thus they do not have "Standing in Nomenclature". The year the genus was proposed is listed in parentheses after the genus name.
Identification.
To identify different genera of Enterobacteriaceae, a microbiologist may run a series of tests in the lab. These include:
In a clinical setting, three species make up 80 to 95% of all isolates identified. These are "Escherichia coli", "Klebsiella pneumoniae", and "Proteus mirabilis". However, "Proteus mirabilis" is now considered a part of the Morganellaceae, a sister clade within the Enterobacterales.
Antibiotic resistance.
Several Enterobacteriaceae strains have been isolated which are resistant to antibiotics including carbapenems, which are often claimed as "the last line of antibiotic defense" against resistant organisms. For instance, some "Klebsiella pneumoniae" strains are carbapenem resistant.


Melinoessa fulvescens

Melinoessa fulvescens is a species of moth in the family Geometridae, native to Sierra Leone and Gambia. It was described by Dru Drury in 1782 as "Phalaena fulvata", a name which was pre-occupied (see "Cidaria fulvata"). The current, slightly different, specific name was given by L. B. Prout in 1916.
Description.
Upper Side. Antennae setaceous and yellow. Thorax and abdomen yellow. Wings deep straw-coloured, the anterior having a small black spot placed near the middle of the anterior edges. A small narrow line of a silverish colour runs along the external edges of these wings, beginning near the tips, and continuing along the edges of the posterior ones, ends at the abdominal corners.
Under Side. Breast, legs, and abdomen whiteish. Wings coloured as on the upper side, but dappled with minute reddish streaks. Margins of the wings entire. Wing-span somewhat more than 1½ inches (40 mm).


Deltapapillomavirus

Deltapapillomavirus is a genus of viruses, in the family "Papillomaviridae". Ruminants serve as natural hosts. There are seven species in this genus. Diseases associated with this genus include: warts (papillomas and fibropapillomas) of the skin and alimentary tract (rarely cancers of the alimentary tract and urinary bladder); possibly responsible for the skin tumour equine sarcoid in horses and donkeys.
Taxonomy.
The following seven species are assigned to the genus:
Structure.
Viruses in "Deltapapillomavirus" are non-enveloped, with icosahedral geometries. The diameter is around 60 nm. Genomes are circular, around 8kb in length.
Life cycle.
Viral replication is nuclear. Entry into the host cell is achieved by attachment of the viral proteins to host receptors, which mediates endocytosis. Replication follows the dsDNA bidirectional replication model. Dna templated transcription, with some alternative splicing mechanism is the method of transcription. The virus exits the host cell by nuclear envelope breakdown.
Ruminants serve as the natural host. Transmission routes are contact.


Macroglossum passalus

Macroglossum passalus, the black-based hummingbird hawkmoth, is a moth of the family Sphingidae described by Dru Drury in 1773. It is known from Sri Lanka, India, Thailand, south-eastern China, Taiwan, southern Japan, Indonesia (Sumatra, Java) and the Philippines.
The wingspan is 52–62 mm. Adults are attracted to the flowers of "Duranta erecta" and "Lantana camara". They are on wing at dawn and dusk.
Larvae have been recorded feeding on "Daphniphyllum calycinum" in Hong Kong, "Photinia glabra" in Japan and "Photinia lindleyana" in India.
Description.
Upperside: antennae brown, and thickest near their extremities. Head and thorax greyish brown, with a dark line running down the middle. Abdomen red brown, with two yellow spots on each side. Tail broad and hairy. Anterior wings, next the body, dark chocolate, occupying a third part; next to this they are of a light red brown, growing darker as it approaches the tips. Inferior wings yellow next the shoulders; the apical half being of a fine dark chocolate.
Underside: head white. Tongue curled up. Breast and thighs yellow clay coloured. Legs, sides, and abdomen dark clay coloured. Wings, next the body, yellow clay coloured; the remaining parts being red brown, with a faint darker border along the external edges. Wingspan 2 inches (50 mm).


Autographiviridae

Autographiviridae is a family of viruses in the order "Caudovirales". Bacteria serve as natural hosts. There are 373 species in this family, assigned to 9 subfamilies and 133 genera.
History.
Since the 1990s, the term "T7 supergroup" has been coined for the expanding group of bacteriophages related to coliphage T7, as members of the family "Podoviridae". Enterobacteriaceae phages SP6 and K1-5 were the first to be considered as an estranged subgroup of the "T7 supergroup". "Pseudomonas" phage phiKMV also shared commonalities at the genome organizational level. As such, based on the available morphological and proteomic data, this clade of viruses was established as a subfamily of the family "Podoviridae". The subfamily was later raised to the level of family in 2019.
Etymology.
The name of this family, termed "Autographiviridae", refers to the “auto-graphein” or “self-transcribing” phages which encode their own (single subunit) RNA polymerase, a common characteristic among its members.
Structure.
Viruses in Autographiviridae are non-enveloped, with icosahedral and Head-tail geometries, and T=7 symmetry. The diameter is around 60 nm. Genomes are linear, around 40-42kb in length.
Life cycle.
Viral replication is cytoplasmic. DNA templated transcription is the method of transcription. The virus exits the host cell by lysis, and holin/endolysin/spanin proteins. Bacteria serve as the natural host. Transmission routes are passive diffusion.
Taxonomy.
The following subfamilies are recognized:
The following genera are unassigned to a subfamily:


Peripolesis

Peripolesis is the process in which a cell attaches itself to another cell. This is differentiated from "emperipolesis", which is when one cell is engulfed by another.
Peripolesis is thought to be a physiological mechanism involved in regulating some processes of immune response. It was observed between lymphocytes and macrophages following skin grafts between subjects, and after immune challenge with antigens. Peripolesis was also observed in lung alveoli, where the peripolesed macrophages were not injured, but the cell membrane did appear to be temporarily altered. In patients with active sarcoidosis, which is characterized by lymphocyte-macrophage cooperation, lymphocyte peripolesis appeared to occur in clusters and could last for minutes to hours. The lymphocytes could be seen moving around a macrophage while maintaining contact.


Actinosphaerium


Encephalitozoon intestinalis

Encephalitozoon intestinalis is a parasite. It can cause microsporidiosis.
It is notable as having one of the smallest genome among known eukaryotic organisms, containing only 2.25 million base pairs. Its genome was completely sequenced in 2010.
"E. intestinalis" originally named Septata intestinalis, was reclassified based on morphologic, antigenic
and molecular similarities with other species of the genus Encephalitozoon. Recently, Some domestic
and wild animals have been found to be naturally infected with "E. intestinalis" and some other
microsporidian species.
"E. intestinalis" is transmitted in contaminated water. It causes Gastro-Intestinal tract infection which
subsequently leads to diarrhea and circulates to the ocular, genitourinary and respiratory tracts.
Research has proven that "E. intestinalis" infection can increase host cell nuclear mutation rate.
Disease.
Microsporidia are obligate intracellular opportunistic fungi that cause significant pathology in
immunocompromised (simply put: having an impaired immune system) hosts. Like other
obligate intracellular pathogens, "microsporidia" exert significant stress on infected host cells.
"Microsporidia" infection alters host cell cycle regulation and can lead to development of
multinucleated host cells.
Genome.
Compared to "E. cuniculi" which encodes about 2000 massive genes at 2.9 Mbp, "E. intestinalis" had a reduced gene complement and genome size (2.3 Mbp) because of a high degree of host dependency. "E. intestinalis" lack large gene blocks of sequence in its subtelomeric regions unlike "E.
cuniculi". However, "E. intestinalis" and "E. cuniculi" share a conserved gene content, order and density
over most of their genomes which have similar GC content. They also contain the same
complement of transfer RNAs and ribosomal RNAs.
Detection.
The assay is adaptable to the clinical laboratory and represents the first real‐time PCR assay
designed to detect Encephalitozoon species. Melting temperature analysis of the amplicons
allows for the differentiation of three Encephalitozoon species (E. intestinalis, E. cuniculi, and E.hellem).
Prevention and Treatment.
Frequent washing of hands and limited exposure to animals is highly recommended especially for
people with immunesystem deficiency. Treatment of Microsporidia can vary depending on the
species involved. Intravenous fluid administration, electrolyte repletion, dietary and nutritional
regimens can be helpful to patients with diarrhea while antiretroviral therapy can help improve
immune system function.


Alicyclobacillus shizuokensis

Alicyclobacillus shizuokensis is a species of Gram positive, strictly aerobic, bacterium. The bacteria are acidophilic and produce endospores. It was first isolated from soil in a crop field in Shizuoka, Japan. The species was first described in 2007, and the name refers to the city from which it was first isolated.
The optimum growth temperature for "A. shizuokensis" is 45-50 °C, and can grow in the 35-60 °C range. The optimum pH is 4.0-4.5, and cannot grow at pH 3.0 or pH 6.5.
"A. shizuokensis" was found during a Japanese survey of various beverages and environments, which also discovered 5 other species of "Alicyclobacillus": "A. contaminans", "A. fastidiosus", "A. kakegawensis", "A. macrosporangiidus", and "A. sacchari".


Entamoeba gingivalis

Entamoeba gingivalis is an opportunistic Amoebozoa (reported by some as an effect of disease; not a cause [hence status as a commensal]) and is the first amoeba in humans to be described.
It is found in the mouth
inside the gingival pocket biofilm near the base of the teeth, and in periodontal pockets. "Entamoeba gingivalis" is found in 95% of people with gum disease and rarely in people with healthy gums. Cyst formation is not present; therefore transmission is direct from one person to another by kissing, or by sharing eating utensils. Only the trophozoites are formed and the size is usually 20 micrometers to 150 micrometers in diameter. "Entamoeba gingivalis" have pseudopodia that allow them to move quickly and phagocytise the nucleus of polynuclear neutrophils by exonucleophagy in periodontal disease. Their spheroid nucleus is 2 micrometers to 4 micrometers in diameter and contains a small central endosome. There are numerous food vacuoles, which consists mostly of phagocitised PMN nucleus, blood cells, and bacteria.
Media.
The main activity of the amoeba "Entamoeba gingivalis" in the infected periodontal crevices, besides moving, consists in feeding on the nucleus of white blood cells. The amoeba penetrates into the cytoplasm to reach the nucleus and literally suctions its contents via the negative pressure of the pseudopod. The food so gulped down is gradually digested inside the endoplasm. Phagocytosis can sometimes continue for more than 20 polynuclear neutrophil nuclei. This activity leaves a denucleated cell, unable to achieve either its NETS activity or its preprogrammed apoptosis. It will release PMN-uncontrolled proteolytic enzymes on surrounding tissues and could be considered a pathogen from this vampirising activity.


Cladochytrium

Cladochytrium is a genus of fungi. It is the type genus of the family Cladochytriaceae.


Mycobacterium obuense

Mycobacterium obuense is a species of soil-dwelling scotochromogenic "Mycobacterium". The cell wall of "M. obuense" contains 1-tetradecanol, 2-octadecanol, and 2-eicosanol, and triacylated lipoproteins.
Use in Immunomodulatory therapy.
Preparations of heat-killed Mycobacterium obuense (such as IMM-101) are immunomodulatory and have been used to direct the immune response in the treatment of cancers - notably pancreatic cancer and malignant melanoma. Recent trials have been directed towards the treatment of colorectal cancer. It has been shown that human myeloid dendritic cells, (antigen-presenting cells that serve as a bridge linking the adaptive and innate immune system), can detect mycobacterial triacylated lipoproteins via TLR2 and TLR1.


Clostridium baratii

Clostridium baratii is an anaerobic, motile, gram-positive bacterium. It is a rare cause of infant botulism, in which newborns or infants lose their muscle tone, and develop trouble feeding due to a difficulty in breathing, which can be fatal. Newborns can recover spontaneously or as in two known cases improve with injected botulism antitoxin. , the environmental source of this bacterium is unknown, despite extensive investigations when cases have occurred. It is named after Barat who is a French bacteriologist.
Diagnosis.
The diagnosis must be suspected based on the constellation of symptoms. "Clostridium baratii" infection is proven when it is grown on a petri dish and isolated from a stool culture. This takes a minimum of 48 hours and more, because the bacterium needs to grow in the absence of oxygen, that is under anaerobic conditions.
Symptoms and signs of infection.
Newborns symptoms are that they develop constipation, are fussy, and feed poorly. Signs of the disease reported by caregivers are "excessive crying, reluctance to suck, and difficulty in swallowing milk". Within hours an infant can become less responsive to stimuli and "floppy", that is its muscle tone diminishes.
Epidemiology.
The CDC reported in 2015, that through 2013, only 14 cases of "C. baratii" type F infant botulism had been reported in the United States.
As opposed to the classic cause of botulism, "C. botulinum", its environmental source is unknown. Therefore, it is unclear how to prevention infection. When very young infants become floppy and their breathing fails (progressive respiratory failure) health care practitioners should consider this disease as a possible diagnosis.


Mycobacterium confluentis

Mycobacterium confluentis is a non-pathogenic bacterium of the oral cavity.
Description.
Gram-positive, nonmotile, acid-fast coccobacillus (0.5-0.8 µm x 0.7-1.7 µm), does not form spores, capsules or aerial hyphae.
Pathogenesis.
Not associated with disease. Biosafety level 1.
Type strain.
First isolated from sputum, Koblenz, Germany.
strain 1389/90 = ATCC 49920 = CIP 105510 = DSM 44017 = JCM 13671.


Mycorrhizal network

 Mycorrhizal networks (also known as common mycorrhizal networks or CMN) are underground hyphal networks created by mycorrhizal fungi that connect individual plants together and transfer water, carbon, nitrogen, and other nutrients and minerals.
The formation of these networks is context-dependent, and can be influenced by factors such as soil fertility, resource availability, host or myco-symbiont genotype, disturbance and seasonal variation
By analogy to the many roles intermediated by the World Wide Web in human communities, the many roles that mycorrhizal networks appear to play in woodland have earned them a colloquial nickname: "the Wood Wide Web".
Substances transferred.
Several studies have demonstrated that mycorrhizal networks can transport carbon, phosphorus, nitrogen, water, defense compounds, and allelochemicals from plant to plant. The flux of nutrients and water through hyphal networks has been proposed to be driven by a source–sink model, where plants growing under conditions of relatively high resource availability (e.g., high-light or high-nitrogen environments) transfer carbon or nutrients to plants located in less favorable conditions. A common example is the transfer of carbon from plants with leaves located in high-light conditions in the forest canopy, to plants located in the shaded understory where light availability limits photosynthesis.
Types.
There are two main types of mycorrhizal networks: arbuscular mycorrhizal networks and ectomycorrhizal networks.
Benefits for plants.
Several positive effects of mycorrhizal networks on plants have been reported. These include increased establishment success, higher growth rate and survivorship of seedlings; improved inoculum availability for mycorrhizal infection; transfer of water, carbon, nitrogen and other limiting resources increasing the probability for colonization in less favorable conditions. These benefits have also been identified as the primary drivers of positive interactions and feedbacks between plants and mycorrhizal fungi that influence plant species abundance.
Mycoheterotrophic and mixotrophic plants.
Myco-heterotrophic plants are plants that are unable to photosynthesize and instead rely on carbon transfer from mycorrhizal networks as their main source of energy. This group of plants includes about 400 species. Some families that include mycotrophic species are: Ericaceae, Orchidaceae, Monotropaceae, and Gentianaceae. In addition, mixotrophic plants also benefit from energy transfer via hyphal networks. These plants have fully developed leaves but usually live in very nutrient and light limited environments that restrict their ability to photosynthesize.
Importance at the forest community level.
Connection to mycorrhizal networks creates positive feedbacks between adult trees and seedlings of the same species and can disproportionally increase the abundance of a single species, potentially resulting in monodominance. Monodominance occurs when a single tree species accounts for the majority of individuals in a forest stand. McGuire (2007), working with the monodominant tree "Dicymbe corymbosa" in Guyana demonstrated that seedlings with access to mycorrhizal networks had higher survival, number of leaves, and height than seedlings isolated from the ectomycorrhizal networks.
Introduction.
The importance of mycorrhizal networks facilitation is no surprise. Mycorrhizal networks help regulate plant survival, growth, and defense. Understanding the network structure, function and performance levels are essential when studying plant ecosystems. Increasing knowledge on seed establishment, carbon transfer and the effects of climate change will drive new methods for conservation management practices for ecosystems.
Seedling establishment.
Seedling establishment research often is focused on forest level communities with similar fungal species. However mycorrhizal networks may shift intra- and interspecific interactions that may alter pre-established plants physiology. Shifting competition can alter the evenness and dominance of the plant community. Discovery of seedling establishment showed seedling preference is near existing plants of con-or heterospecific species and seedling amount is abundant. Many believe the process of new seedlings becoming infected with existing mycorrhizae expedite their establishment within the community. The seedling inherit tremendous benefits from their new formed symbiotic relation with the fungi. The new influx of nutrients and water availability, help the seedling with growth but more importantly help ensure survival when in a stressed state. Mycorrhizal networks aid in regeneration of seedlings when secondary succession occurs, seen in temperate and boreal forests.
Several studies have focused on relationships between mycorrhizal networks and plants, specifically their performance and establishment rate. Douglas fir seedlings' growth expanded when planted with hardwood trees compared to unamended soils in the Oregon Mountains. Douglas firs had higher rates of ectomycorrhizal fungal diversity, richness, and photosynthetic rates when planted alongside root systems of mature Douglas firs and "Betula papyrifera" than compared to those seedlings who exhibited no or little growth when isolated from mature trees. The Douglas fir was the focus of another study to understand its preference for establishing in an ecosystem. Two shrub species, "Arctostaphylos" and "Adenostoma" both had the opportunity to colonize the seedlings with their ectomycorrhizae fungi. "Arctostaphylos" shrubs colonized Douglas fir seedlings who also had higher survival rates. The mycorrhizae joining the pair had greater net carbon transfer toward the seedling. The researchers were able to minimize environmental factors they encountered in order to avoid swaying readers in opposite directions.
In burned and salvaged forest, "Quercus rubrum L." establishment was facilitated when acorns were planted near "Q. montana" but did not grow when near arbuscular mycorrhizae "Acer rubrum L." Seedlings deposited near "Q. montana" had a greater diversity of ectomycorrhizal fungi, and a more significant net transfer of nitrogen and phosphorus contents demonstrating ectomycorrhizal fungi formation with the seedling helped with their establishment. Results demonstrated with increasing density; mycorrhizal benefits decrease due to an abundance of resources that overwhelmed their system resulting in little growth as seen in "Q. rubrum".
Mycorrhizae networks decline with increasing distance from parents, but rate of survival was unaffected. This indicated that seedling survival has a positive relation with decreasing competition as networks move out farther.
One study displayed the effects of ectomycorrhizal networks in plants who face primary succession. In his experiment, Nara transplanted "Salix reinii" seedlings inoculated with different ectomycorrhizal species. He found that mycorrhizal networks are the connection of ectomycorrhizal fungi colonization and plant establishment. Results showed increased biomass and survival of germinates near the inoculated seedlings compared to inoculated seedlings.
Studies have found that association with mature plant equates with higher survival of the plant and greater diversity and species richness of the mycorrhizal fungi. However, these studies have not considered the threshold status of competing for resources and the benefit for the mycorrhizal networks.
Carbon transfer.
Carbon transfer has been demonstrated by experiments using isotopic 14C and following the pathway from ectomycorrhizal conifer seedlings to another using mycorrhizal networks. The experiment showed a bidirectional movement of the 14C within ectomycorrhizae species. Further investigation of bidirectional movement and the net transfer was analyzed using pulse labeling technique with isotopes 13C and 14C in ectomycorrhizal species Douglas fir and "Betula payrifera" seedlings. Results displayed an overall net balance of carbon transfer between the two until the second year where the Douglas fir received carbon from "B. payrifera". Detection of the isotopes was found in receiver plant shorts, expressing carbon transfer from fungus to plant tissues.
When ectomycorrhizal fungi receiver end of the plant has limited sunlight availability, there was an increase in carbon transfer, indicating a source-sink gradient of carbon among plants and shade surface area regulates carbon transfer.
Water transfer.
Isotopic tracers and fluorescent dyes have been used to establish the water transfer between conspecific or heterospecific plants. The hydraulic lift aids in water transfer from deep-rooted trees to seedlings. Potentially indicating this could be a problem within drought-stressed plants which form these mycorrhizal networks with neighbors. The extent would depend on the severity of drought and tolerance of another plant species.


Thermogenesis

Thermogenesis is the process of heat production in organisms. It occurs in all warm-blooded animals, and also in a few species of thermogenic plants such as the Eastern skunk cabbage, the Voodoo lily, and the giant water lilies of the genus "Victoria". The lodgepole pine dwarf mistletoe, "Arceuthobium americanum", disperses its seeds explosively through thermogenesis.
Types.
Depending on whether or not they are initiated through locomotion and intentional movement of the muscles, thermogenic processes can be classified as one of the following:
Shivering.
One method to raise temperature is through shivering. It produces heat because the conversion of the chemical energy of ATP into kinetic energy causes almost all of the energy to show up as heat. Shivering is the process by which the body temperature of hibernating mammals (such as some bats and ground squirrels) is raised as these animals emerge from hibernation.
Non-shivering.
Non-shivering thermogenesis occurs in brown adipose tissue (brown fat) that is present in almost all eutherians (swine being the only exception currently known). Brown adipose tissue has a unique uncoupling protein (thermogenin, also known as uncoupling protein 1) that allows the uncoupling of protons (H+) moving down their mitochondrial gradient from the synthesis of ATP, thus allowing the energy to be dissipated as heat.
In this process, substances such as free fatty acids (derived from triacylglycerols) remove purine (ADP, GDP and others) inhibition of thermogenin, which causes an influx of H+ into the matrix of the mitochondrion and bypasses the ATP synthase channel. This uncouples oxidative phosphorylation, and the energy from the proton motive force is dissipated as heat rather than producing ATP from ADP, which would store chemical energy for the body's use. Thermogenesis can also be produced by leakage of the sodium-potassium pump and the Ca2+ pump. Thermogenesis is contributed to by futile cycles, such as the simultaneous occurrence of lipogenesis and lipolysis or glycolysis and gluconeogenesis. In a broader context, futile cycles can be influenced by activity/rest cycles such as the Summermatter cycle.
Acetylcholine stimulates muscle to raise metabolic rate.
The low demands of thermogenesis mean that free fatty acids draw, for the most part, on lipolysis as the method of energy production.
A comprehensive list of human and mouse genes regulating cold-induced thermogenesis (CIT) in living animals ("in vivo") or tissue samples ("ex vivo") has been assembled and is available in CITGeneDB.
Regulation.
Non-shivering thermogenesis is regulated mainly by thyroid hormone and the sympathetic nervous system. Some hormones, such as norepinephrine and leptin, may stimulate thermogenesis by activating the sympathetic nervous system. Rising insulin levels after eating may be responsible for diet-induced thermogenesis (thermic effect of food).
Progesterone also increases body temperature.


Arsenophonus arthropodicus

"Candidatus" Arsenophonus arthropodicus is a Gram-negative and intracellular secondary (S) endosymbiont that belongs to the genus "Arsenophonus". This bacterium is found in the Hippoboscid louse fly, "Pseudolynchia canariensis". S-endosymbionts are commonly found in distinct tissues. Strains of recovered "Arsenophonus" found in arthropods share 99% sequence identification in the 16S rRNA gene across all species. "Arsenophonus"-host interactions involve parasitism and mutualism, including a popular mechanism of "male-killing" found commonly in a related species, "Arsenophonus nasoniae". This species is considered ""Ca." A. arthropodicus" due it being as of yet uncultured.
Isolation and genome identification.
Isolation.
Amplified 16S rRNA gene sequences of "Phoenix canariensis" pupal DNA showed "Arsenophonus" detection in hemocytes, gut, fat body, and reproductive tissues indicating distribution of bacterium throughout hosts tissues. Lab cultured bacteria found in these tissues show extracellular and intracellular attachment indicating "Ca." A. arthropodicus can initiate intracellular infection in the host cells "in vitro".
A primary culture of "P. canariensis" pupae was used to enrich "Ca." A. arthropodicus through Gram-positive inhibitor vancomycin and Gram-negative sensitive antibacterial cationic peptides. Ancestral species identification also provides insight into "Arsenophonus" being a monophyletic clade.
Genome identification.
Contents of the "Ca." A. arthropodicus genome are a single chromosome and multiple extrachromosomal elements. Through the use of restriction enzymes Notl and Ascl the approximate chromosome size is 3.51 Mbp. Two species were identified from enrichments based on the behavior of extrachromosomal DNA under alkaline lysis, restriction enzymes, and agarose gel electrophoresis .


Chrysophyta

Chrysophyta or golden algae is a term used to refer to certain heterokonts.
It can be used to refer to:


Lycoperdon

Lycoperdon is a genus of puffball mushrooms. The genus has a widespread distribution and contains about 50 species. In general, it contains the smaller species such as the pear-shaped puffball and the gem-studded puffball. It was formerly classified within the now-obsolete order Lycoperdales, as the type genus which, following a restructuring of fungal taxonomy brought about by molecular phylogeny, has been split. "Lycoperdon" is now placed in the family Agaricaceae of the order Agaricales.
The scientific name has been created with Greek words ("lycos" meaning "wolf" and "perdon" meaning "to break wind") and based on several European dialects in which the mushroom name sounds like "wolf-farts".
Most species are edible, ranging from mild to tasting distinctly of shrimp.


Acaulospora longula

Acaulospora longula is a species of fungi in the family Acaulosporaceae. It forms arbuscular mycorrhiza and vesicles in roots. Found in Colombia in soil with native grasses, the species was described as new to science in 1984.


Stappogiedde Formation

The Stappogiedde Formation is a geologic formation in Norway. It preserves fossils dating back to the Ediacaran period.


Mycobacterium wolinskyi

Mycobacterium wolinskyi is a rapidly growing mycobacterium most commonly seen in post-traumatic wound infections, especially those following open fractures and with associated osteomyelitis. "Mycobacterium wolinskyi" is clearly clinically significant, and occurs in the same settings as "Mycobacterium smegmatis" and members of the "Mycobacterium fortuitum" complex; they differ from members of the "Mycobacterium fortuitum" complex in the type of chronic lung disease they produce, with essentially all cases occurring in the setting of chronic lipoid pneumonia, either secondary to chronic oil ingestion or chronic aspiration (usually achalasia). Etymology: Wolinsky, named after Emanuel Wolinsky in honour of, and in recognition for, significant contributions to the study of the non-tuberculous mycobacteria.
Description.
Microscopy
Colony characteristics
Physiology


Pluralibacter gergoviae

Pluralibacter gergoviae (formerly Enterobacter gergoviae) is a Gram-negative, motile, facultatively-anaerobic, rod-shaped bacterium. "P. gergoviae" is of special interest to the cosmetics industry, as it displays resistance to parabens, a common antimicrobial agent added to cosmetic products.
Background.
"Enterobacter gergoviae" was first proposed as a novel species in 1980. The species name is derived from the Gergovie plateau, which is located near Clermont-Ferrand University Hospital; the type strain was isolated at this hospital during a nosocomial outbreak of "P. gergoviae." In 2013, the species was reclassified into the novel genus, "Pluralibacter", and is the type species for the genus.
"P. gergoviae" has been isolated from maize, grapes, coffee beans, spring water, fruit flies, and pink bollworms. It is an uncommon human pathogen, most commonly as an opportunistic nosocomial infection. One hospital in Spain reported the organism to represent 0.4% of clinical "Enterobacter" isolates. Risk factors include prolonged hospital stays, "immunosuppression, the presence of a foreign device, prior use of anti-microbial agents in the patient involved, and extremes of age." In the cosmetic industry, "P. gergoviae" has been implicated in recalls of eye cream, children's shampoo, skin cream, and hand cleaning paste.
"P. gergoviae" is resistant to penicillins (specifically benzylpenicillin, oxacillin), macrolides (with the exception of azithromycin), lincosamides (specifically lincomycin and clindamycin), streptogramins, rifampicin, fusidic acid, and fosfomycin. "P. gergoviae" is also resistant to cefoxitin, likely due to β-lactamase production.