Wolbachia

Wolbachia is a genus of intracellular bacteria that infects mainly arthropod species, including a high proportion of insects, and also some nematodes. It is one of the most common parasitic microbes and is possibly the most common reproductive parasite in the biosphere. Its interactions with its hosts are often complex, and in some cases have evolved to be mutualistic rather than parasitic. Some host species cannot reproduce, or even survive, without "Wolbachia" colonisation. One study concluded that more than 16% of neotropical insect species carry bacteria of this genus, and as many as 25 to 70% of all insect species are estimated to be potential hosts.
History.
The genus was first identified in 1924 by Marshall Hertig and Simeon Burt Wolbach in the common house mosquito. They described it as "a somewhat pleomorphic, rodlike, Gram-negative, intracellular organism [that] apparently infects only the ovaries and testes". Hertig formally described the species in 1936, and proposed both the generic and specific names: "Wolbachia pipientis". Research on "Wolbachia" intensified after 1971, when Janice Yen and A. Ralph Barr of UCLA discovered that "Culex" mosquito eggs were killed by a cytoplasmic incompatibility when the sperm of "Wolbachia"-infected males fertilized infection-free eggs. The genus "Wolbachia" is of considerable interest today due to its ubiquitous distribution, its many different evolutionary interactions, and its potential use as a biocontrol agent.
Phylogenetic studies have shown that "Wolbachia persica" (now "Francisella persica") was closely related to species in the genus "Francisella" and that "Wolbachia melophagi" (now "Bartonella melophagi") was closely related to species in the genus "Bartonella", leading to a transfer of these species to these respective genera. Furthermore, unlike "Wolbachia", which need a host cell to multiply, "F. persica" and "B. melophagi" can be cultured on agar plates.
Method of sexual differentiation in hosts.
These bacteria can infect many different types of organs, but are most notable for the infections of the testes and ovaries of their hosts. "Wolbachia" species are ubiquitous in mature eggs, but not mature sperm. Only infected females, therefore, pass the infection on to their offspring. "Wolbachia" bacteria maximize their spread by significantly altering the reproductive capabilities of their hosts, with four different phenotypes:
Effects of sexual differentiation in hosts.
Several host species, such as those within the genus "Trichogramma", are so dependent on sexual differentiation of "Wolbachia" that they are unable to reproduce effectively without the bacteria in their bodies, and some might even be unable to survive uninfected.
One study on infected woodlice showed the broods of infected organisms had a higher proportion of females than their uninfected counterparts.
"Wolbachia", especially "Wolbachia"-caused cytoplasmic incompatibility, may be important in promoting speciation. Wolbachia strains that distort the sex ratio may alter their host's pattern of sexual selection in nature, and also engender strong selection to prevent their action, leading to some of the fastest examples of natural selection in natural populations.
The male killing and feminization effects of "Wolbachia" infections can also lead to speciation in their hosts. For example, populations of the pill woodlouse, "Armadillidium vulgare" which are exposed to the feminizing effects of "Wolbachia", have been known to lose their female-determining chromosome. In these cases, only the presence of "Wolbachia" can cause an individual to develop into a female. Cryptic species of ground wētā ("Hemiandrus maculifrons" complex) are host to different lineages of "Wolbachia" which might explain their speciation without ecological or geographical separation.
Fitness advantages by "Wolbachia" infections.
"Wolbachia" infection has been linked to viral resistance in "Drosophila melanogaster", "Drosophila simulans", and mosquito species. Flies, including mosquitoes, infected with the bacteria are more resistant to RNA viruses such as Drosophila C virus, norovirus, flock house virus, cricket paralysis virus, chikungunya virus, and West Nile virus.
In the common house mosquito, higher levels of "Wolbachia" were correlated with more insecticide resistance.
In leafminers of the species "Phyllonorycter blancardella", "Wolbachia" bacteria help their hosts produce green islands on yellowing tree leaves, that is, small areas of leaf remaining fresh, allowing the hosts to continue feeding while growing to their adult forms. Larvae treated with tetracycline, which kills "Wolbachia", lose this ability and subsequently only 13% emerge successfully as adult moths.
"Muscidifurax uniraptor, a" parasitoid wasp, also benefits from hosting "Wolbachia" bacteria.
In the parasitic filarial nematode species responsible for elephantiasis, such as "Brugia malayi" and "Wuchereria bancrofti", "Wolbachia" has become an obligate endosymbiont and provides the host with chemicals necessary for its reproduction and survival. Elimination of the Wolbachia symbionts through antibiotic treatment therefore prevents reproduction of the nematode, and eventually results in its premature death.
Some "Wolbachia" species that infect arthropods also provide some metabolic provisioning to their hosts. In "Drosophila melanogaster", "Wolbachia" is found to mediate iron metabolism under nutritional stress and in "Cimex lectularius", the "Wolbachia" strain "cCle" helps the host to synthesize B vitamins.
Some "Wolbachia" strains have increased their prevalence by increasing their hosts' fecundity. "Wolbachia" strains captured from 1988 in southern California still induce a fecundity deficit, but nowadays the fecundity deficit is replaced with a fecundity advantage such that infected "Drosophila simulans" produces more offspring than the uninfected ones.
Life-history consequences of "Wolbachia" infection.
"Wolbachia" often manipulates host reproduction and life-history in a way that favours its own propagation. In the Pharaoh ant, "Wolbachia" infection correlates with increased colony-level production of reproductives (i.e., greater reproductive investment), and earlier onset of reproductive production (i.e., shorter life-cycle). Infected colonies also seem to grow more rapidly. There is substantial evidence that the presence of "Wolbachia" that induce parthenogenesis have put pressure on species to reproduce primarily or entirely this way.
Additionally, "Wolbachia" has been seen to decrease the lifespan of "Aedes aegypti", carriers of mosquito-borne diseases, and it decreases their efficacy of pathogen transmission because older mosquitoes are more likely to have become carriers of one of those diseases. This has been exploited as a method for pest control.
Genomics.
The first "Wolbachia" genome to be determined was that of one that infects "D. melanogaster" fruit flies. This genome was sequenced at The Institute for Genomic Research in a collaboration between Jonathan Eisen and Scott O'Neill. The second "Wolbachia" genome to be determined was one that infects "Brugia malayi" nematodes. Genome sequencing projects for several other "Wolbachia" strains are in progress. A nearly complete copy of the "Wolbachia" genome sequence was found within the genome sequence of the fruit fly "Drosophila ananassae" and large segments were found in seven other "Drosophila" species.
In an application of DNA barcoding to the identification of species of "Protocalliphora" flies, several distinct morphospecies had identical cytochrome c oxidase I gene sequences, most likely through horizontal gene transfer (HGT) by "Wolbachia" species as they jump across host species. As a result, "Wolbachia" can cause misleading results in molecular cladistical analyses. It is estimated that between 20 and 50 percent of insect species have evidence of HGT from "Wolbachia"—passing from microbes to animal (i.e. insects).
Horizontal gene transfer.
"Wolbachia" species also harbor a bacteriophage called bacteriophage WO or phage WO. Comparative sequence analyses of bacteriophage WO offer some of the most compelling examples of large-scale horizontal gene transfer between "Wolbachia" coinfections in the same host. It is the first bacteriophage implicated in frequent lateral transfer between the genomes of bacterial endosymbionts. Gene transfer by bacteriophages could drive significant evolutionary change in the genomes of intracellular bacteria that were previously considered highly stable or prone to loss of genes over time.
Small RNA.
The small non-coding RNAs WsnRNA-46 and WsnRNA-59 in "Wolbachia" were detected in "Aedes aegypti" mosquitoes and "Drosophila melanogaster". The small RNAs (sRNAs) may regulate bacterial and host genes. Highly conserved intragenic region sRNA called ncrwmel02 was also identified in "Wolbachia pipientis." It is expressed in four different strains in a regulated pattern that differs according to the sex of the host and the tissue localisation. This suggested that the sRNA may play important roles in the biology of "Wolbachia."
Relation to human-related infections.
Disease vector.
Outside of insects, "Wolbachia" infects a variety of isopod species, spiders, mites, and many species of filarial nematodes (a type of parasitic worm), including those causing onchocerciasis (river blindness) and elephantiasis in humans, as well as heartworms in dogs. Not only are these disease-causing filarial worms infected with "Wolbachia", but "Wolbachia" also seems to play an inordinate role in these diseases.
A large part of the pathogenicity of filarial nematodes is due to host immune response toward their "Wolbachia". Elimination of "Wolbachia" from filarial nematodes generally results in either death or sterility of the nematode. Consequently, current strategies for control of filarial nematode diseases include elimination of their symbiotic "Wolbachia" via the simple doxycycline antibiotic, rather than directly killing the nematode with far more toxic antinematode medications.
Disease prevention.
Naturally existing strains of "Wolbachia" have been shown to be a route for vector control strategies because of their presence in arthropod populations, such as mosquitoes. Due to the unique traits of "Wolbachia" that cause cytoplasmic incompatibility, some strains are useful to humans as a promoter of genetic drive within an insect population. "Wolbachia"-infected females are able to produce offspring with uninfected and infected males; however, uninfected females are only able to produce viable offspring with uninfected males. This gives infected females a reproductive advantage that is greater the higher the frequency of "Wolbachia" in the population. Computational models predict that introducing "Wolbachia" strains into natural populations will reduce pathogen transmission and reduce overall disease burden. An example includes a life-shortening "Wolbachia" that can be used to control dengue virus and malaria by eliminating the older insects that contain more parasites. Promoting the survival and reproduction of younger insects lessens selection pressure for evolution of resistance.
In addition, some "Wolbachia" strains are able to directly reduce viral replication inside the insect. For dengue they include wAllbB and wMelPop with "Aedes aegypti", wMel with "Aedes albopictus". and "Aedes aegypti". A trial in an Australian city with 187,000 inhabitants plagued by dengue had no cases in four years, following introduction of mosquitoes infected with "Wolbachia". Earlier trials in much smaller areas had been carried out, but the effect in a larger area had not been tested. There did not appear to be any environmental ill-effects. The cost was A$15 per inhabitant, but it was hoped that it could be reduced to US$1 in poorer countries. The "strongest evidence yet" to support the "Wolbachia" technique was found in its first randomized controlled trial, conducted between 2016 and 2020 in Yogyakarta, an Indonesian city of about 400,000 inhabitants. In August 2020, the trial's Indonesian lead scientist Adi Utarini announced that the trial showed a 77% reduction in dengue cases compared to the control areas.
"Wolbachia" has also been identified to inhibit replication of chikungunya virus (CHIKV) in "A. aegypti". The Wmel strain of "Wolbachia pipientis" significantly reduced infection and dissemination rates of CHIKV in mosquitoes, compared to "Wolbachia" uninfected controls and the same phenomenon was observed in yellow fever virus infection converting this bacterium in an excellent promise for YFV and CHIKV suppression.
"Wolbachia" also inhibits the secretion of West Nile virus (WNV) in cell line Aag2 derived from "A. aegypti" cells. The mechanism is somewhat novel, as the bacteria actually enhances the production of viral genomic RNA in the cell line "Wolbachia". Also, the antiviral effect in intrathoracically infected mosquitoes depends on the strain of "Wolbachia", and the replication of the virus in orally fed mosquitoes was completely inhibited in wMelPop strain of "Wolbachia".
"Wolbachia" infection can also increase mosquito resistance to malaria, as shown in "Anopheles stephensi" where the "w"AlbB strain of "Wolbachia" hindered the lifecycle of "Plasmodium falciparum".
However, "Wolbachia" infections can enhance pathogen transmission. "Wolbachia" has enhanced multiple arboviruses in "Culex tarsalis" mosquitoes. In another study, West Nile Virus (WNV) infection rate was significantly higher in "Wolbachia"-infected mosquitoes compared to controls.
"Wolbachia" may induce reactive oxygen species-dependent activation of the Toll (gene family) pathway, which is essential for activation of antimicrobial peptides, defensins, and cecropins that help to inhibit virus proliferation. Conversely, certain strains actually dampen the pathway, leading to higher replication of viruses. One example is with strain wAlbB in "Culex tarsalis", where infected mosquitoes actually carried the west nile virus (WNV) more frequently. This is because wAlbB inhibits REL1, an activator of the antiviral Toll immune pathway. As a result, careful studies of the "Wolbachia" strain and ecological consequences must be done before releasing artificially-infected mosquitoes in the environment.
Deployments.
In 2016 it was proposed to combat the spread of the Zika virus by breeding and releasing mosquitoes that have intentionally been infected with an appropriate strain of "Wolbachia". A contemporary study has shown that Wolbachia has the ability to block the spread of Zika virus in mosquitoes in Brazil.
In October 2016, it was announced that US$18 million in funding was being allocated for the use of "Wolbachia"-infected mosquitoes to fight Zika and dengue viruses. Deployment is slated for early 2017 in Colombia and Brazil.
In July 2017, Verily, the life sciences arm of Google's parent company Alphabet Inc., announced a plan to release about 20 million Wolbachia-infected "Aedes aegypti" mosquitoes in Fresno, California, in an attempt to combat the Zika virus. Singapore's National Environment Agency has teamed up with Verily to come up with an advanced, more efficient way to release male Wolbachia mosquitoes for Phase 2 of its study to suppress the urban "Aedes aegypti" mosquito population and fight dengue.
In November 3, 2017, the US Environmental Protection Agency (EPA) registered Mosquito Mate, Inc. to release Wolbachia-infected mosquitoes in 20 US states and the District of Columbia.
Effect on the sex-differentiation enzyme aromatase.
The enzyme aromatase is found to mediate sex-change in many species of fish. "Wolbachia" can affect the activity of aromatase in developing fish embryos.


Choristocarpaceae

Choristocarpaceae is a family in the order Discosporangiales of the brown algae (class Phaeophyceae). The family contains a single genus, "Choristocarpus".


Alphaguttavirus

Alphaguttavirus is a genus of viruses, in the family "Guttaviridae". "Sulfolobus newzealandicus" serve as natural hosts. There is currently only one species in this genus: the type species "Sulfolobus newzealandicus droplet-shaped virus".
Taxonomy.
Group: dsDNA
Structure.
Viruses in the genus "Alphaguttavirus" are enveloped. The diameter is around 70-95 nm, with a length of 110-185 nm. Genomes are circular, around 20kb in length.
Life cycle.
DNA-templated transcription is the method of transcription. "Sulfolobus newzealandicus" serve as the natural host.


Mallomonas hexareticulata

Mallomonas hexareticulata is a species of heterokont algae. It is a tiny free-living cell, about the width of a human hair. It has ornate scales and bristles, as well as long spines. It is a relatively common part of lake or pond plankton. It differs from its cogenerates by the number, distribution, and size of its base plate pores, the secondary structures on the scale surfaces, together with characteristics of its bristles.


Mycobacterium tusciae

Mycobacterium tusciae is a slow-growing, scotochromogenic mycobacterium first isolated from a lymph node of an immunocompromised child and subsequently from tap water and from a respiratory specimen of a patient with chronic fibrosis.
Etymology: tusciae referring to the Italian region of Tuscany, where the organisms were first isolated.
Description.
Microscopy
Colony characteristics
Physiology
streptomycin.
Pathophysiology
Differential characteristics


Moraxella osloensis

Moraxella osloensis is a Gram-negative oxidase-positive, aerobic bacterium within the family Moraxellaceae in the gamma subdivision of the purple bacteria.
"M. osloensis" is a mutualistic symbiont of the slug-parasitic nematode "Phasmarhabditis hermaphrodita". In nature, "Phasmarhabditis hermaphrodita" vectors "M. osloensis" into the shell cavity of the slug host in which the bacteria multiply and kill the slug.
Lifecycle.
This bacterium has been identified as one of the natural symbionts of a bacteria-feeding nematode, "Phasmarhabditis hermaphrodita" (Rhabditida: Rhabditidae), which is an endoparasite of slugs, including the slug "Deroceras reticulatum" (grey garden slug) which is one of the most serious agricultural and garden slug pests.
In nature, bacteria colonize the gut of nematode-infective juveniles which represent a specialized stage of development adapted for survival in the unfavorable environment. The infective juveniles seek out and enter the slug's shell cavity through the posterior mantle region. Once inside the shell cavity, the bacteria are released, and the infective juveniles resume growth, feeding on the multiplying bacteria. The infected slugs die in 4–10 days, and the nematodes colonize the entire carcass and produce next-generation infective juveniles, which leave the carcass to seek a new host. The bacteria are responsible for killing the slugs; nematodes without bacteria do not cause death.
Biochemistry.
The lipopolysaccharide, that is an endotoxin, from "M. osloensis" is a molluscicide for "Deroceras reticulatum" when applied by injection.
The lethality of these nematodes to slugs has been shown to correlate with the number of "M. osloensis" cells carried by infective juveniles. Tan and Grewal (2001) demonstrated that the 72-hour-old "M. osloensis" cultures inoculated into the shell cavity were highly pathogenic to the slug. They further reported that "M. osloensis" produced an endotoxin which was identified to be a rough type lipopolysaccharide with a molecular weight of 5300 KD, and the purified lipopolysaccharide was toxic to the slug with an estimated 50% lethal dose of 48 μg when injected into the shell cavity.
Infections of humans.
Although "M. osloensis" rarely infects humans, it can sometimes be found in a variety of tissues, where it sometimes causes disease. Antibiotics are usually effective against such infections.
Smelliness.
"M. osloensis" has been found to be the bacterium responsible for locker-room smell or shower-curtain odor.
Classification.
The species "M. osloensis" was proposed in 1967; the bacteria which are now considered to be "M. osloensis" would previously have been considered to be "Moraxella nonliquefaciens" or "Mima polymorpha" (var.) "oxidans".
References.
This article incorporates CC-BY-2.0 text from the reference.


Luteimonas lutimaris

Luteimonas lutimaris is yellow-pigmented, Gram-negative, strictly aerobic bacterium. Its type strain is G3(T) (= KACC 14929(T) = JCM 16916(T)).


Gongronella

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


Hoard (video game)

Hoard (trademarked as HOARD) is an action-strategy video game developed by Canadian studio Big Sandwich Games Inc. It was released in November 2010 in North America on PlayStation Network, and April 4, 2011 for the PC and Mac on Steam and was released on June 2, 2011 on the PAL PlayStation Network regions.
Gameplay.
"Hoard" is an action strategy game that combines elements of a dual-stick shooter with those of a real-time strategy game. Each player controls a dragon that has the ability to fly, breathe fire, and perform several special abilities with the help of powerups.
The core mode of the game, called "Treasure", challenges the player to collect as much gold as possible over a 10-minute period. Gold is earned in a variety of ways, the simplest being to use fire breath to destroy merchant wagons or buildings and then pick up the treasure chests that appear. Dragons have a limited carrying capacity, so from time to time the player must return to the dragon's hoard and deposit the gold there.
When certain key thresholds of gold have been collected at the hoard, the dragon "levels up" and is awarded with upgrade points which can be distributed amongst four key abilities: speed, fire breath, carrying, and armor. Upgrading each of these improves the dragon's abilities, which can have a major effect on game strategy.
In addition to destroying things for gold, the player can earn gold in other ways such as kidnapping princesses for ransom, capturing wizard gems, and scaring villages into offering tribute. The player can also steal gold from other dragons and their hoards.
Treasure mode is the main mode of the game with over 20 maps available. Other modes include Princess Rush (be the first to ransom 15 princesses), Hoard (survival), and Co-Op Treasure mode (all dragons share a hoard and work together).
"Hoard" supports four players at a time, working competitively or co-operatively.
Global leaderboards are present in the PlayStation 3 version and will be in the PC (Steam) version.
Strategic depth.
"Hoard" is somewhat unusual in that it contains elements of deep strategy and systems interactions typically absent from action-oriented shooters.
The medieval kingdom simulates with its own simple commerce, and the player's interaction with the kingdom can have a large effect on how much gold the player is able to score. Farms and towns can be destroyed regularly, or left to grow to become prosperous. Generally, the bigger towns, castles, wizards towers and similar structures become, the more valuable they are but as a result are also better defended. Individual town buildings are also important, as the presence of markets or taverns help determine wagon value, number of thieves produced, and so on.
Dragon upgrade choices are also integral to the game's strategy. In single player scenarios with only one dragon, the player is motivated to play strategically to maximize points. In multiplayer scenarios, upgrading leads to interaction mechanics with strategies and counter-strategies similar to an RTS or fighting game.
Player progression and rewards.
"Hoard" contains approximately 100 "badges", or mini-objectives which challenge the player to complete tasks of varying difficulty throughout normal play.
Badges award the player with experience points, which raise the player's dragon profile level. This is a title-only award that does not confer any game abilities.
In the PlayStation 3 version, "Hoard" contains 11 trophies worth a total of 315 points.
Development.
"Hoard" was released for the PlayStation 3 on November 2, 2010. The PSP version of "Hoard" was released on March 22, 2011 in the United States.
Reception.
Review aggregator Metacritic rated the PlayStation 3 version of "Hoard" at 75 percent and the PC version at 65 percent.
"IGN" awarded "Hoard" "Best Quick Fix" in their PlayStation 3 Best of 2010 Awards, and also nominated the game for "Best Competitive Multiplayer."


Boletinus

Boletinus is a genus of fungi belonging to the family Suillaceae.
The genus was first described by Károly Kalchbrenner in 1867.
The genus has cosmopolitan distribution.
Species:


Luteimonas vadosa

Luteimonas vadosa is aerobic, Gram-negative, yellow-pigmented, nonmotile, rod-shaped bacterium. Its type strain is KMM 9005(T) ( = NRIC 0881(T) = JCM 18392(T)).


Blastodinium

Blastodinium (also known as Blastodiniphycaea) is a diverse genus of dinoflagellates and important parasites of planktonic copepods. They exist in either a parasitic stage, a trophont stage, and a dinospore stage. Although morphologically and functionally diverse, as parasites they live exclusively in the intestinal tract of copeods.
Etymology.
"Blastodinium" is made up of the Greek prefix ‘blasto-’, meaning to germ/bud. This likely refers to its dinospore stage following "Blasdotinium" reproduction, where sporocytes appear to bud out of a cuticle.
History of knowledge.
The "Blastodinium" taxonomy is entirely based on their morphology at the trophont stage with "B. pruvoti" being the type species of the group. In 1920, Chatton proposed 3 main groups which are consistent with today's molecular data; Spinoulsum, Contorum, and Mangini. Upon their discovery, it was recognized that "Blastodinium" organisms had features that distinguished them from the majority of dinoflagellates in the "Dinophyceae" class. These include their parasitic lifestyle and the lack of histones in their temporary dinokaryon (dinospore) stage. Thus, the genus was placed in a separate class, "Blastodiniphyceae", which contained the single order, "Blastodiniales". However, the "Blastodinium’s" dinospore's thecal plate pattern is still noticeably similar to the thecal patterning on dinophyceae dinoflagellates, highlighting the close relationship between the lineages.
"Blastodinium" exhibit the two features that link all members of the "Blastodiniale" order; a parasitic life mode and the presence of a temporary dinokaryon at some life cycle stage. However, "Blastodinium" classification as a monophyletic group is only moderately supported, as small subunit rDNA sequences between some of the genus's species have a relatively large difference.
Habitat and ecology.
"Blastodinium" live most of their life as parasites in the guts of marine planktonic copepods. Although some "Blastodinium" species are capable of photosynthesis through the copepod's transparent gut, they acquire most of its nutrients from their host.
"Blastodinium" infection only occurs in juvenile copepods or adult females, since infected male juveniles are unable to molt into an adult stage. When infected, castration of female copepods is commonly observed, along with a general reduction in copepod size and survival. This is likely due to food limitations from the blocked alimentary tract and the added competition against the protist for organic matter.
Morphology.
"Blastodinium" are typically motile and bi-flagellated. These organisms exhibit three life stages; a parasitic stage (also known as trophocyte), a trophont stage, and a sporocyte (dinospore) stage. Most trophonts and dinospores are greenish brown in color, indicating the presence of a plastid. These stages also have thecal plates, which contain trichocyst pores scattered along the surface.
Trophocytes are binucleated and have large Golgi apparati composed of many dictyosomes. Instead of fully functioning chloroplasts, they possess etioplasts and small underdeveloped plastids. Thus, trophocytes perform limited photosynthesis despite being highly metabolically active. Unlike the typical dinoflagellate morphology, trophocytes are multicellular and composed of hundreds of non-flagellated cells. Sometimes, young trophocytes possess an anterior beak, although its function is unknown.
The trophont stage is a multicellular growth stage, composed of many individual cells wrapped by a cellulosic layer.
Dinospores are free-swimming flagellates that exhibit the typical morphology of dinoflagellates. Although initially binucleated, they later divide into four uni-nucleated dinospores. They have clear thecal plates with a dense covering of papillae. They are ellipsoid in shape and have well developed plastids located at the cell's periphery.
Nucleus.
"Blastodinium" have a dinokaryon nucleus, characterized by a lack of histones and permanently condense chromosomes. "Blastodinium" perform closed mitosis, in which their nuclear envelope remains intact to aid in the orientation and segregation of chromosomes. Mitosis does not involve kinetochores or centrioles, as their chromosomes are attached to the inner membrane. During asexual reproduction, their mitosis stages follow one another in the absence of interphase.
Life cycle.
The infection cycle first starts with the ingestion of a free-swimming dinospore by a copepod. Rather than being digested, the dinospore grows and developed into a parasitic trophocyte. At this stage, it takes residence in the copepod's gut lumen, where it competes for nutrients and organic matter.
Following infection, the trophocyte will engage in asexual reproduction by palintomy. During this, the trophocyte divides via binary fission into a secondary trophocyte and a germ cell. The germ cell will then divide into many sporocytes. The secondary trophocyte may divide into a tertiary trophocyte and another germ cell, which may then produce a second layer of sporocytes. These repeated binary fissions continue in the absence of an intermediate growth stage, to get multiple layers of the multicellular growth that is the trophont. All of this occurs within a common cuticle, whose rupture results in the release of sporocytes through the copepod anus and into the environment. Although initially non-motile, sporocytes later develop a flagellum and take on the general morphology of a typical dinoflagellate.


Heart of Europe Bio-Crystallography Meeting

The Heart of Europe Bio-Crystallography Meeting (short HEC-Meeting) is an annual academic conference on structural biology, in particular protein crystallography. Researchers from universities, other research institutions and industry from Austria, Czech Republic, Germany and Poland meet to present and discuss current topics of their research. The talks are predominantly given by PhD students (doctoral students). An exception is the invited HEC lecture, which is held by a renowned scientist of the research field. The format of the HEC meeting has been adopted from the eleven years older Rhine-Knee Regional Meeting on Structural Biology.
History of the HEC-Meeting.
The HEC-Meeting dates back to an initiative in the year 1998 of Manfred Weiss and Rolf Hilgenfeld, who were researchers at the Institute for Molecular Biotechnology (IMB) in Jena and intended to establish a meeting format similar to the Rhine-Knee Regional Meeting on Structural Biology in the New Länder. Both conferences are regional meetings of German scientists together with scientific research groups of the neighbouring countries. Nine groups from Germany (the new states and West-Berlin), Poland and Czech Republic participated in the first HEC-Meeting from 8 to 10 October 1998. Later also groups from Austria and the Old Federal States participated.
Former HEC-Meetings:


Cardiobacterium

Cardiobacterium is a Gram-negative bacillus (rod-shaped) bacterium commonly grouped with other bacteria into the HACEK group. Species of "Cardiobacterium" include "Cardiobacterium hominis" and "Cardiobacterium valvarum".


Striped cuckoo

The striped cuckoo ("Tapera naevia") is a near-passerine bird, the only member of the genus "Tapera". This resident cuckoo is found from Mexico and Trinidad south to Bolivia and Argentina.
The striped cuckoo is found in open country with trees or shrubs, and the edges of mangrove forests. It is among the very few brood parasitic cuckoos of the Americas (only other are "Dromococcyx"), and typical hosts are spinetails, but often also wrens, and other species with domed nests. The female cuckoo lays one, sometimes two, white or bluish eggs in the host's large stick nest. The eggs hatch in 15 days, with a further 18 days until the cuckoo fledges. The young spinetails disappear.
This species is about long and weighs . The adult is mainly grey-brown above, streaked with black and buff. It has a pale supercilium and a chestnut and black crest which is raised as part of its display. The underparts are off-white and the tail is long and graduated. Immature birds are spotted with buff and are more rufous on the back and wings.
The striped cuckoo eats large insects, often taken off the ground. This is a solitary and fairly shy species which tends to keep to the cover of bushes, although it will sing from more open perches. It has a whistled call usually of two or three notes, "wu-weee" or "wu-wu-wee", and can be attracted by imitations of this.
Brazilian folklore.
This bird is very important in Brazilian folklore, being related to the legend of the saci, or matita-perê. Other than saci, the bird is also known as matinta-pereira, pitica (Pará), crispim, fenfém, martim-pererê, matimpererê, matintapereira, matintaperera, matitaperê, peitica, peito-ferido, roceiro-planta, seco-fico, sede-sede, saci-do-campo, sem-fim, fém-fém, tempo-quente, bulhões, bolinhas, feijão, feijoada, jotalhão, gansolino, peixe-frito (Bahia), e peixe-frito-seu-veríssimo.
Matita-pereira is famously mentioned in Tom Jobim's song "Águas de Março".


Paul Fagot

Jacques Sébastien François Léonce Marie Paul Fagot (1842–1908) was a French malacologist who often published under the name Paul Fagot.
Life and career.
Fagot was part of a "New School" of naturalists, which included Jules-René Bourguignat, Aristide-Horace Letourneux, Jules François Mabille, and Étienne Alexandre Arnould Locard. Species of land snails that were named and described by Fagot include "Aegopinella epipedostoma", "Pyrenaearia navasi", and "Pyrenaearia cotiellae".


Cyanothrichaceae


Luteimonas marina

Luteimonas marina is a bacterium. Its type strain is FR1330(T) (=KCTC 12327(T) =JCM 12488(T) =IMSNU 60306(T)).


Pasteuriaceae

The Pasteuriaceae are a family of nonmotile Gram-positive bacteria. They are moderately to strongly resistant to heat. Species in this family produce a septate mycelium with one refractile endospore. The mycelium grows bigger on one end to form sporangia and sometimes endospores. The size of the endospores is different for each species of the genus "Pasteuria". Species of the family of Pastueriaceae are endoparasitic in plant, soil, and freshwater invertebrates.
Parasitism.
Bacteria of the Pasteuriaceae family are endoparasitic within nematodes or cladoceran hosts. After the infection, the host gets castrated by the parasite and shows gigantism. The infection pathway is not fully discovered yet. The core of the endospores is covered by glycoproteins that are presumed to be involved in the attachment of the endospores to the invertebrates host.


Fibrillanosema crangonycis

Fibrillanosema crangonycis is a species of fungus in the phylum Microsporidia. This species is morphologically identical to uncharacterized microsporidia from populations of North American amphipods. It is, however, distinct from microsporidia found in European populations of amphipods.


Systems biomedicine

Systems biomedicine, also called systems biomedical science, is the application of systems biology to the understanding and modulation of developmental and pathological processes in humans, and in animal and cellular models. Whereas systems biology aims at modeling exhaustive networks of interactions (with the long-term goal of, for example, creating a comprehensive computational model of the cell), mainly at intra-cellular level, systems biomedicine emphasizes the multilevel, hierarchical nature of the models (molecule, organelle, cell, tissue, organ, individual/genotype, environmental factor, population, ecosystem) by discovering and selecting the key factors at each level and integrating them into models that reveal the global, emergent behavior of the biological process under consideration.
Such an approach will be favorable when the execution of all the experiments necessary to establish exhaustive models is limited by time and expense (e.g., in animal models) or basic ethics (e.g., human experimentation).
In the year of 1992, a paper on system biomedicine by Kamada T. was published (Nov.-Dec.), and an article on systems medicine and pharmacology by Zeng B.J. was also published (April) in the same time period.
In 2009, the first collective book on systems biomedicine was edited by Edison T. Liu and Douglas A. Lauffenburger.
In October 2008, one of the first research groups uniquely devoted to systems biomedicine was established at the European Institute of Oncology. One of the first research centers specialized on systems biomedicine was founded by Rudi Balling. The Luxembourg Centre for Systems Biomedicine is an interdisciplinary center of the University of Luxembourg. The first centre devoted to spatial issues in systems biomedicine has been recently established at Oregon Health and Science University.
The first peer-reviewed journal on this topic, Systems Biomedicine, was recently established by Landes Bioscience.


Effusibacillus lacus

Effusibacillus lacus is a species of Gram positive, facultatively anaerobic, thermophilic bacterium. The cells are rod-shaped and form spores. It was first isolated from freshwater lake sediment from Lake Mizugaki, Japan. The species name is derived from "lacus" (of a lake).
The species was among the first grouped into the newly create genus "Effusibacillus", along with two other species that were reclassified from "Alicyclobacillus", "E. consociatus" and "E. pohliae". "E. lacus" is the type strain for the genus.
The optimum growth temperature for "E. lacus" is 50-52 °C, and can grow in the 28-60 °C range. Its optimum pH is 7.25-7.50, and grows in pH range 7.0-8.5.


Inkcap

Inkcap may refer to any of a number of toadstools of the genera "Coprinus", "Coprinellus" and "Coprinopsis".
The best known, and very good to eat:
The next best known, and also "conditionally" edible:
Also any of the following, many of which are poisonous:


Cylindromyia bicolor

Cylindromyia bicolor is a European species of fly in the family Tachinidae.
Distribution.
This species is present in Europe, in Russia, in the Middle Asia and in Iran.
Habitat.
These insects mainly inhabit dry meadows, bushes, edges of wood, marshes, parks and gardens.
Description.
"Cylindromyia bicolor" can reach a length of . These small flies have a grayish thorax and very elongated, cylindrical red abdomen, with a black longitudinal band at the base and discal bristles at the tergites 2 - 4. The large compound eyes are dark brown. Wings are partly smoked. Calyptra are large and white. Legs are black.
Biology.
Adults can be found from mid July to October, with a peak in August. They feed on nectar and pollen of flowers of various local plants, but especially on Apiaceae. Larvae of this species are endoparasites of "Rhaphigaster nebulosa" (Pentatomidae). The females lay their eggs on their hosts, usually one egg per bug. Then the larvae enter by the abdomen the interior of juvenile pentatomids, where they develop. They pupape on the ground after winter.


Enterobacter cowanii

Enterobacter cowanii is a Gram-negative, motile, facultatively-anaerobic, rod-shaped bacterium of the genus "Enterobacter". The species is typically associated with natural environments and is found in soil, water, and sewage. "E. cowanii" is associated with plant pathogens that exhibit symptoms of severe defoliation and plant death. This species, originally referred to as NIH Group 42, was first proposed in 2000 as a potential member of the family Enterobacteriaceae. The name of this species honors S. T. Cowan, an English bacteriologist, for his significant contributions to the field of bacterial taxonomy.
Phenotypic characterization.
"Enterobacter cowanii" is phenotypically defined as being a Gram-negative, motile, and facultative anaerobic bacterium. The morphology of this bacterium is described as being cream colored when cultured on non-selective, YDC (Yeast extract-dextrose-CaCO3) medium. When tested for enzyme production, "E. cowanii" is asparagine and catalase positive, while also being urease and oxidase negative. When originally introduced as NIH Group 42, seventy traditional phenotypic characteristics were determined and listed by Kohaku et al.
Genotypic characterization.
The diversity of strains present in the "Enterobacter cowanii" species have been confirmed through analysis of DNA G+C content and DNA-DNA Hybridization results, which involves the hybridizing (annealing) of putative strains to "E. cowanii" LMG 23569T. A DNA similarity of 70% or greater indicates that strains of interest are the same species. When testing for DNA-DNA similarity comparing the "rpoB" gene of "E. cowanii", the strains BCC 009, BCC 011, BCC 078 showed 76% to 92% DNA similarity.
N.B. Using a multilocus sequence analysis (MLSA) approach, based on partial sequencing of protein-encoding genes (gyrB, rpoB, infB and atpD), this species has been reclassified to the genus "Kosakonia", so that its name is more properly given as "Kosakonia cowanii".
Microbiology.
Isolates of "Enterobacter cowanii" were extracted from leaf tissue of the "Eucalyptus" trees. To determine the overall relatedness of the isolated strains, 16S rRNA gene sequencing was utilized. The 16S rRNA gene is commonly implemented for sequencing and inferring relatedness of isolates, because it is highly conserved. Phylogenetically related strains of "E. cowanii", determined through 16S rRNA gene sequencing and rpoB gene sequencing, include BCC 078, BCC 074, BCC 008, BCC 011 and BCC 009.
Diversity.
When comparing the DNA from a representative strain of NIH Group 42 and DNA from 35 other species of "Enterobacteriaceae" by DNA-DNA hybridization, it was found that the degree of reassociation ranged from 5–38% at 70 °C. Because of its unique phenotypic characteristics and its distinct separation from other species of "Enterobacteriaceae" by DNA hybridization, there is sufficient evidence that constitutes "E. cowanii" a separate species in the family Enterobacteriaceae.


Armatimonas rosea

Armatimonas rosea is a Gram-negative bacterium and also the first species to be characterized within the phylum Armatimonadetes. The Armatimonadetes were previously known as candidate phylum OP10. OP10 was composed solely of environmental 16S rRNA gene clone sequences prior to "A. rosea's" discovery.
Discovery.
"A. rosea" was originally isolated from the rhizoplane of the aquatic plant "Phragmites australis" inhabiting a freshwater lake in the Yamanashi prefecture in Japan. Cultivation and isolation were completed in a low nutrient medium, DTS.
Relatives.
The environmental 16S rRNA gene sequences belonging to the phylum "Armatimonadetes" are currently sorted into six groups. Groups 2, 5, and 6 consist solely of sequences. Group 1 contains "Armatimonadetes rosea", Group 3 contains "Chthonomonadetes calidirosea", and Group 4 contains "Fimbriimonas ginsengisoli".
"Chthonomonas calidirosea" strain T49T, an aerobic, saccharolytic, obligately thermophilic, motile, non-spore-forming bacterium, was isolated from geothermally heated soil at Hell's Gate, Tikitere, New Zealand. It is the first representative of a new class in the phylum "Armatimonadetes". It represents the first cultured representative of the "Chthonomonadetes", corresponding with Group 3 of the phylum "Armatimonadetes".
"Fimbriimonas ginsengisoli", an aerobic, non-motile, mesophilic, rod-shaped bacterium, was isolated from a ginseng field soil sample. It represents the first cultured representative of the "Fimbriimonadia" class, corresponding with Group 4 of the phylum"Armatimonadetes".
Characteristics.
When grown on the relatively low-nutrient medium, R2A, colonies were pink pigmented, circular, smooth, significantly hard, relatively small (1–2 mm) in size after one week of incubation at 30 °C. "A.rosea" has an optimum temperature at 30–35 °C with a range of 20–40 °C. The optimum pH for growth was 6.5 with a range of 5.5–8.5. It is able to tolerate NaCl concentrations up to 0.5%.
When examined by phase-contrast and transmission electron microscopy cells were observed to be nonmotile, ovoid to rod shaped, with sizes ranging from 1.4 to 1.8 µm in width and 2.4–3.2 µm in length. Neither spores nor flagella were observed.
When investigated in R2A media, cultures of "A. rosea" were observed to be aerobic and chemoheterotrophic with no evidence of growth under anaerobic conditions. It is negative for the following tests: nitrate respiration, fermentative growth, catalase, and cytochrome oxidase.


Citrus greening disease

Citrus greening disease (; or HLB) is a disease of citrus caused by a vector-transmitted pathogen. The causative agents are motile bacteria, "Candidatus" Liberibacter spp. The disease is vectored and transmitted by the Asian citrus psyllid, "Diaphorina citri", and the African citrus psyllid, "Trioza erytreae", also known as the two-spotted citrus psyllid. It has also been shown to be graft-transmissible. Three different types of HLB are currently known: The heat-tolerant Asian form, and the heat-sensitive African and American forms. The disease was first described in 1929 and first reported in China in 1943. The African variation was first reported in 1947 in South Africa, where it is still widespread. Eventually, it affected the United States, reaching Florida in 2005. Within three years, it had spread to the majority of citrus farms. The rapid increase in this disease has threatened the citrus industry not only in Florida, but the entire US. As of 2009, 33 countries have reported HLB infection in their citrus crop.
Symptoms.
HLB is distinguished by the common symptoms of yellowing of the veins and adjacent tissues; followed by splotchy mottling of the entire leaf, premature defoliation, dieback of twigs, decay of feeder rootlets and lateral roots, and decline in vigor, ultimately followed by the death of the entire plant. Affected trees have stunted growth, bear multiple off-season flowers (most of which fall off), and produce small, irregularly shaped fruit with a thick, pale peel that remains green at the bottom and tastes very bitter. Common symptoms can often be mistaken for nutrient deficiencies; however, the distinguishing factor between nutrient deficiencies is the pattern of symmetry. Nutrient deficiencies tend to be symmetrical along the leaf vein margin, while HLB has an asymmetrical yellowing around the vein. The most noticeable symptom of HLB is greening and stunting of the fruit, especially after ripening.
Transmission.
HLB was originally thought to be a viral disease, but was later discovered to be caused by bacteria, carried by insect vectors. HLB infection can arise in various climates and is often associated with different species of psyllid insects. For example, citrus crops in Africa become infected under cool conditions as the bacteria are transmitted by the African citrus psyllid "Trioza erytreae", an invasive insect that favors cool and moist conditions for optimal growth. Citrus crops in Asia, however, are often infected under warm conditions as the bacteria are transmitted by the Asian citrus psyllid "Diaphorina citri".
The young larval stage is the most suitable for acquisition of "Ca." L. asiaticus by the Asian citrus psyllid "Diaphorina citri", and some cultivars show greater efficiency in transmitting the disease to the vector than others. Temperature also shows a great influence in the parasite-host relationship between the bacteria and the insect vector, affecting how it is acquired and transmitted by the insects.
The causative agents are fastidious phloem-restricted, Gram-negative bacteria in the gracilicutes clade. The Asian form, "Ca." L. asiaticus is heat tolerant. This means the greening symptoms can develop at temperatures up to 35 °C. The African form, "Ca." L. africanus, and American form, "Ca." L. americanus, are heat sensitive, thus symptoms only develop when the temperature is in the range 20–25 °C. Although "T. erytreae" is the natural vector of African citrus greening and "D. citri" is the natural vector of American and Asian citrus greening, either psyllid can in fact transmit either of the greening agents under experimental conditions.
Distribution.
Distribution of the Asian citrus psyllid that is a vector of the citrus greening disease, is primarily in tropical and subtropical Asia. It has been reported in all citrus-growing regions in Asia except mainland Japan. The disease has affected crops in China, India, Sri Lanka, Malaysia, Indonesia, Myanmar, the Philippines, Pakistan, Thailand, the Ryukyu Islands, Nepal, Saudi Arabia, and Afghanistan. Areas outside Asia have also reported the disease: Réunion, Mauritius, Brazil, Paraguay, and Florida in the U.S. since 2005, and in several municipalities in Mexico since 2009 On March 30, 2012, citrus greening disease was confirmed in a single citrus tree in Hacienda Heights, Los Angeles County, California. The first report of HLB in Texas occurred on January 13, 2012 from a Valencia sweet orange tree in a commercial orchard in San Juan, Texas. Prospects are bleak for the ubiquitous backyard citrus orchards of California as residential growers are unlikely to consistently use the pesticides which provide effective control in commercial orchards.
The distribution of the African citrus psyllid includes Africa, Madeira, Saudi Arabia, Portugal, and Yemen This species is sensitive to high temperatures and will not develop at temperatures greater than 25 °C. It is also a vector of the African strain of "huanglongbing" ("Candidatus" Liberibacter africanus), which is also sensitive to heat. This strain of HLB is reported to occur in Africa, (Burundi, Cameroon, Central African Republic, Comoros, Ethiopia, Kenya, Madagascar, Malawi, Mauritius, Reunion, Rwanda, South Africa, St. Helena (unconfirmed), Swaziland, Tanzania, Zimbabwe), Saudi Arabia, and Yemen. The disease was not reported in the EU or USA as of 2004; however see above.
Control.
Some cultural practices can be effective in monitoring this disease. Cultural methods include antibacterial management, sanitation, removal of infected plants, frequent scouting, and most importantly, crisis declaration. Tracking the disease will help prevent further infection in other affected areas and help mitigate more local infections if detected early enough. The Asian citrus psyllid has alternative hosts that may attract psyllids to citrus plants in the vicinity such as "Murraya paniculata", "Severinia buxifolia", and other plants in the family Rutaceae.
No cure for citrus greening disease is known, and efforts to control it have been slow because infected citrus plants are difficult to maintain, regenerate, and study. Ongoing challenges associated with mitigating disease at the field-scale include seasonality of the phytopathogen ("Candidatus" Liberibacter spp.) and associated disease symptoms, limitations for therapeutics to contact the phytopathogen "in planta", adverse impacts of broad-spectrum treatments on plant-beneficial microbiota, and potential implications on public and ecosystem health.
No naturally immune citrus cultivars have been identified; however, creating genetically modified citrus may be a possible solution, but questions of its acceptability to consumers exist. A researcher at Texas AgriLife Research reported in 2012 that incorporating two genes from spinach into citrus trees improved resistance to citrus greening disease in greenhouse trials. Field tests by Southern Gardens Citrus of oranges with the spinach genes in Florida are ongoing.
A resistant variety of mandarin orange called 'Bingo' has been bred at the University of Florida. Other varieties can have a partial tolerance to the disease.
Antibiotics.
Researchers at the Agricultural Research Service of the United States Department of Agriculture have used lemon trees infected with citrus greening disease to infect periwinkle plants in an effort to study the disease. Periwinkle plants are easily infected with the disease and respond well when experimentally treated with antibiotics. Researchers are testing the effect of penicillin G sodium and biocide 2,2-dibromo-3-nitrilopropionamide as potential treatments for infected citrus plants based on the positive results that were observed when applied to infected periwinkle. In June 2014, the USDA allocated an additional US$31.5 million to expand research combating citrus greening disease.
Certain antibiotics, specifically streptomycin and oxytetracycline, may be effective in the fight against citrus greening disease and have been used in the United States but have been banned in Brazil and the European Union. In 2016, the EPA allowed use of streptomycin and oxytetracyclin on orchards with citrus fruits like grapefruits, oranges and tangerines in Florida on an emergency basis, this approval was expanded and broadened to other states for oxytetracycline in December 2018. Further expansion of medically important antibiotics is proposed by the EPA but opposed by the FDA and CDC, primarily as antibiotic resistance can be expected to develop and impact human health.
Peptide.
University of California scientists have discovered a peptide that prevented and treated citrus greening disease in greenhouse trials; as of 2021, it is being tested in field trials. The university entered into an exclusive license with Invaio to develop an enhanced injectable version of the product.


Leucopaxillus gentianeus

Leucopaxillus gentianeus is a bitter-tasting, inedible mushroom commonly known as the bitter false funnelcap, or the bitter brown leucopaxillus. A common synonym is "Leucopaxillus amarus". The bitter taste is caused by a triterpene called cucurbitacin B. The species was first described in 1873 as "Clitocybe gentianea" by French mycologist Lucien Quélet. František Kotlaba transferred it to "Leucopaxillus" in 1966.
The pileus ranges from wide and the stipe from long.


Spiraviridae

Spiraviridae is a family of viruses that replicate in hyperthermophilic archaea of the genus "Aeropyrum", specifically "Aeropyrum pernix". The family contains one genus, "Alphaspiravirus", which contains one species, "Aeropyrum coil-shaped virus". The virions of Aeropyrum coil-shaped virus (ACV) are non-enveloped and in the shape of hollow cylinders that are formed by a coiling fiber that consists of two intertwining halves of the circular DNA strand inside a capsid. An appendage protrudes from each end of the cylindrical virion. The viral genome is ((+)ssDNA) and encodes for significantly more genes than other known ssDNA viruses. ACV is also unique in that it appears to lack its own enzymes to aid replication, instead likely using the host cell's replisomes. ACV has no known relation to any other archaea-infecting viruses, but it does share its coil-like morphology with some other archaeal viruses, suggesting that such viruses may be an ancient lineage that only infect archaea.
Taxonomy.
Family: Spiraviridae
Characteristics.
Structure.
Virions of ACV are non-enveloped and in the shape of hollow cylinders approximately 230±10 by 19±1 nanometers (nm) in size. The cylindrical shape is formed by the coiling of a nucleoprotein filament as a helical spring. This coil-like structure is itself formed by two intertwining halves of a circular, ssDNA molecule in another helical shape that is covered by capsid proteins. Each end of the cylindrical virion has an appendage about 20±2 nm in length protruding from the virion at a 45° angle relative to the axis of the virion. For about 80% of virions, the appendages protrude from the same face of the virion. The virion is flexible, capable of contracting and stiffening upon being dehydrated. Virions have two major proteins with molecular masses of about 23 and 18.5 kilodaltons (kDa) and a few minor proteins with molecular masses of 5–13 kDa. Approximately 40 discs or turns of the helix are distinguishable for the length of the virion. The coil-like morphology of ACV is characteristic of certain archaeal viruses, not being found among bacterial and eukaryotic viruses.
Genome.
ACV contains a single molecule of circular, positive-sense, single-stranded DNA ((+)ssDNA) that is 24,893 nucleotides in length. The GC-content of the genome is 46.7%. The genome is predicted to have 57 open reading frames (ORFs) larger than 40 codons, such ORFs comprising 93.5% of the genome. All but one ORF has the same directionality as the DNA strand, indicating that the genome is positive-sense. The number of predicted genes is much greater than other known ssDNA viruses. These include genes that encode for a putative trypsin-like serine protease, a tyrosine recombinase, two thioredoxin-like proteins, proteins involved in carbohydrate metabolism, and DNA-binding proteins.
Replication.
ACV does not encode any identifiable DNA or RNA polymerases, nor does it encode any proteins homologous to known Rep proteins used by most known ssDNA viruses in replication. As such, ACV is likely to replicate in a manner that depends on the host replisome. After replication, virions leave the host cell without the host cell undergoing lysis, or cell death.
Evolution.
ACV has no known relation to any other viruses. However, some other archaeal viruses also have coil-shaped virions like ACV, which may indicate such morphology is an ancient form that is not represented among viruses that infect eukaryotes and other prokaryotes.
History.
ACV was first isolated from a sample of "Aeropyrum pernix" ("A. pernix") taken from the coastal Yamagawa Hot Spring, where the temperature can reach 109° Celsius, in Japan in 2010. As "A. pernix" was the only organism present in the culture, it was recognized as the host of ACV. ACV could not be replicaed in other strains of "A. pernix" or in "Aeropyrum camini", so the original "A. pernix" culture was used for study. The family, genus, and species were recognized by the International Committee on Taxonomy of Viruses (ICTV) in 2013.


Narnavirus

Narnavirus is a genus of positive-strand RNA viruses, in the family Narnaviridae. Fungi serve as natural hosts. There are two species in this genus. Narnaviruses have been shown to be required for sexual reproduction of "Rhizopus microsporus".
Structure.
Narnaviruses have no true virion. They do not have structural proteins or a capsid.
Genome.
Narnaviruses have nonsegmented, linear, positive-sense, single-stranded RNA genomes. The genome has one open reading frame which encodes the RNA-dependent RNA polymerase (RdRp). The genome is associated with the RdRp in the cytoplasm of the fungi host and forms a naked ribonucleoprotein complex.
Life cycle.
Viral replication is cytoplasmic. Replication follows the positive-strand RNA virus replication model. Positive-strand RNA virus transcription is the method of transcription. The virus exits the host cell by cell-to-cell movement. Fungi serve as the natural host. Transmission routes are parental and sexual.
Taxonomy.
The genus has the following two species:


Sue Jones (computational biologist)

Susan Jones is a British computational biologist and bioinformatics group leader at the James Hutton Institute.
Biography.
Education.
In 1990, she received her Bachelor of Science in Biology from the University of York.
In 1995, she earned her Doctor of Philosophy in Bioinformatics/ Biochemistry from University College London.
Career.
She began her scientific career as a research fellow at University College London, Cancer Research UK and EMBL-EBI.
She went on to hold bioinformatics lecturer and bioinformatics senior lecturer positions at the University of Sussex.
From 2011 to 2020, Jones was a senior scientist in computational biology at the James Hutton Institute in Dundee, United Kingdom. Since 2020, she is the bioinformatics group leader there.
Publications.
Jones has over 60 publications. Some of them have been cited over 3000 times each.


Crameria amabilis

Crameria is a monotypic moth genus in the family Noctuidae erected by Jacob Hübner in 1819. Its only species, Crameria amabilis, was first described by Dru Drury in 1773.
Description.
Upperside: head brown. Antennae filiform. Thorax and abdomen yellow brown. Superior wings fine darkish red, with several yellow spots thereon of different shapes, each encircled with black; the posterior and external edges having yellow margins. Posterior wings deep yellow, inclining to orange, with a black oval spot near the middle of each. Along the external edges is a black margin, reaching from the upper to the abdominal corners; the upper edge being scalloped.
Underside: legs, sides, thorax, and abdomen pale orange. Anterior wings entirely pale orange and dusky black, without any mixture of red, etc. Posterior wings as on the upperside; the colours being less distinct. Margins of the wings entire.
Wingspan inches (38 mm).
Distribution.
It is found in Angola, Benin, Burundi, Cameroon, the Democratic Republic of the Congo, Eritrea, Ethiopia, Gabon, Ghana, Ivory Coast, Kenya, Malawi, Mali, Nigeria, Rwanda, Senegal, Sierra Leone, South Africa, Sudan, Tanzania, the Gambia, Uganda, Zambia and Zimbabwe.


Exosporium

The exosporium is the outer surface layer of mature spores. In plant spores it is also referred to as the exine. Some bacteria also produce endospores with an exosporium, of which the most commonly studied are "Bacillus" species, particularly "Bacillus cereus" and the anthrax-causing bacterium "Bacillus anthracis". The exosporium is the portion of the spore that interacts with the environment or host organism, and may contain spore antigens. Exosporium proteins, such as Cot protein, are also discovered related to strains of B. anthracis and B.cereus. This Cot protein share similar sequences with other spore coat proteins, and their putative determinants are believed to include bxpC, lunA, exsA, etc.
In Bacillus anthraces, salt and detergent washing of exosporium fragments can identify proteins that are likely to represent structural or integral exosporium proteins. Seven proteins have been identified in washed exosporium: alanine racemase, inosine hydrolase, ExsF, CotY, ExsY, CotB, and a novel protein, ExsK. CotY, ExsY and CotB are homologues of Bacillus subtilis outer spore coat proteins, but ExsF and ExsK are specific to B. anthracis and other members of the Bacillus cereus group.
The protein ywdL has been identified in "B. cereus" as important for exosporium formation. In the absence of the ywdL gene, a fragile and easily damaged exosporium is formed, which can be damaged by mechanical disruption such as freeze-thaw cycles. However, ywdL is not required to maintain the internal organization of the exosporium. ΔywdL spores have abnormal germination properties, such as the inability to respond to standard chemical means of inducing germination by treatment with calcium dipicolinate.


Serratia marcescens

Serratia marcescens () is a species of rod-shaped, Gram-negative bacteria in the family Yersiniaceae. It is a facultative anaerobe and an opportunistic pathogen. It was discovered in 1819 by Bartolomeo Bizio in Padua, Italy. "S. marcescens" is commonly involved in hospital-acquired infections (HAIs), particularly catheter-associated bacteremia, urinary tract infections, and wound infections, and is responsible for 1.4% of HAI cases in the United States. It is commonly found in the respiratory and urinary tracts of hospitalized adults and in the gastrointestinal systems of children.
Due to its abundant presence in the environment, and its preference for damp conditions, "S. marcescens" is commonly found growing in bathrooms (especially on tile grout, shower corners, toilet water lines, and basins), where it manifests as a pink, pink-orange, or orange discoloration and slimy film feeding off phosphorus-containing materials or fatty substances such as soap and shampoo residue.
Once established, complete eradication of the organism is often difficult, but can be accomplished by application of a bleach-based disinfectant. Rinsing and drying surfaces after use can also prevent the establishment of the bacterium by removing its food source and making the environment less hospitable.
"S. marcescens" may also be found in environments such as dirt, supposedly "sterile" places , and the subgingival biofilm of teeth. Due to this, and because "S. marcescens" produces a reddish-orange tripyrrole dye called prodigiosin, it may cause staining of the teeth. The biochemical pathway for the production of prodigiosin by "S. marcescens" has been characterized by analyzing what intermediates become accumulated in specific mutants.
Identification.
"S. marcescens" is a motile organism and can grow in temperatures ranging from 5–40 °C and in pH levels ranging from 5 to 9. It is differentiated from other Gram-negative bacteria by its ability to perform casein hydrolysis, which allows it to produce extracellular metalloproteinases which are believed to function in cell-to-extracellular matrix interactions. Since this bacterium is a facultative anaerobe, meaning that it can grow in either the presence of oxygen (aerobic) or in the absence of oxygen (anaerobic), it is capable of nitrate reduction under anaerobic conditions. Therefore, nitrate tests are positive since nitrate is generally used as the final electron acceptor rather than oxygen. "S. marcescens" also exhibits tyrosine hydrolysis and citrate degradation. Citrate is used by "S. marcescens" to produce pyruvic acid, thus it can rely on citrate as a carbon source and test positive for citrate utilization. In identifying the organism, one may also perform a methyl red test, which determines if a microorganism performs mixed-acid fermentation. "S. marcescens" results in a negative test. Another determination of "S. marcescens" is its capability to produce lactic acid by oxidative and fermentative metabolism. Therefore, "S. marcescens" is lactic acid O/F+.
Pathogenicity.
In humans, "S. marcescens" can cause an opportunistic infection in several sites, including the urinary tract, respiratory tract, wounds, and the eye, where it may cause conjunctivitis, keratitis, endophthalmitis, and tear duct infections. It is also a rare cause of endocarditis and osteomyelitis (particularly in people who use intravenous drugs recreationally), pneumonia, and meningitis. Most "S. marcescens" strains are resistant to several antibiotics because of the presence of R-factors, which are a type of plasmid that carry one or more genes that encode resistance; all are considered intrinsically resistant to ampicillin, macrolides, and first-generation cephalosporins (such as cephalexin).
In elkhorn coral, "S. marcescens" is the cause of the disease known as white pox disease. In silkworms, it can also cause a lethal disease, especially in association with other pathogens.
In research laboratories employing "Drosophila" fruit flies, infection of them with "S. marcescens" is common. It manifests as a pink discoloration or plaque in or on larvae, pupae, or the usually starch and sugar-based food (especially when improperly prepared).
A rare clinical form of gastroenteritis occurring in early infancy caused by infection with" S. marcescens".
The red color of the diaper can be mistaken for hematuria (blood in the urine), which may cause unnecessary investigations by the physicians.
"S. marcescens" causes cucurbit yellow vine disease, leading to sometimes serious losses in melon fields.
Professor Jim Burritt and his students at the University of Wisconsin-Stout have discovered a new strain of "S. marcescens" in bee blood (haemolymph) from hives decimated by winterkill. His research findings have been published and the new strain was named sicaria, which means assassin in Latin. The professor states that "S. marcescens sicaria" "may contribute to the wintertime failure of honey bee colonies".
History.
Possible role in medieval miracles.
Because of its red pigmentation, caused by expression of the dye prodigiosin, and its ability to grow on bread, "S. marcescens" has been evoked as a naturalistic explanation of medieval accounts of the "miraculous" appearance of blood on the Corporal of Bolsena. This followed celebration of a mass at Bolsena in 1263, led by a Bohemian priest who had doubts concerning transubstantiation, or the turning of bread and wine into the Body and Blood of Christ during the mass. During the mass, the Eucharist appeared to bleed and each time the priest wiped away the blood, more would appear. This event is celebrated in a fresco in the Apostolic Palace in the Vatican City, painted by Raphael.
Discovery.
"S. marcescens" was discovered in 1819 by Venetian pharmacist Bartolomeo Bizio, as the cause of an episode of blood-red discoloration of polenta in the city of Padua. Bizio named the organism four years later in honor of Serafino Serrati, a physicist who developed an early steamboat; the epithet "marcescens" (Latin for "decaying") was chosen because of the dyestuff's rapid deterioration (Bizio's observations led him to believe that the organism decayed into a mucilage-like substance upon reaching maturity). "Serratia" was later renamed "Monas prodigiosus" and "Bacillus prodigiosus" before Bizio's original name was restored in the 1920s.
Uses and misuse.
Role in biowarfare testing.
Until the 1950s, "S. marcescens" was erroneously believed to be a nonpathogenic "saprophyte", and its reddish coloration was used in school experiments to track infections. During the Cold War, it was used as a simulant in biological warfare testing by the U.S. military, which studied it in field tests as a substitute for the tularemia bacterium, which was being weaponized at the time.
On 26 and 27 September 1950, the U.S. Navy conducted a secret experiment named "Operation Sea-Spray" in which balloons filled with "S. marcescens" were released and burst over urban areas of the San Francisco Bay Area in California. Although the Navy later claimed the bacteria were harmless, beginning on September 29, 11 patients at a local hospital developed very rare, serious urinary tract infections. One of the afflicted patients, Edward J. Nevin, died. Cases of pneumonia in San Francisco also increased after "S. marcescens" was released. (That the simulant bacteria caused these infections and death has never been conclusively established.) Nevin's son and grandson lost a lawsuit they brought against the government between 1981 and 1983, on the grounds that the government is immune, and that the chance that the sprayed bacteria caused Nevin's death was minute. The bacterium was also combined with phenol and an anthrax simulant and sprayed across south Dorset by US and UK military scientists as part of the DICE trials which ran from 1971 to 1975.
Since 1950, "S. marcescens" has steadily increased as a cause of human infection, with many strains resistant to multiple antibiotics. The first indications of problems with the influenza vaccine produced by Chiron Corporation in 2004 involved "S. marcescens" contamination.
Contaminated injectables.
In early 2008, the U.S. Food and Drug Administration issued a nationwide recall of one lot of Pre-Filled Heparin Lock Flush Solution USP. The heparin IV flush syringes had been found to be contaminated with "S. marcescens", which resulted in patient infections. The Centers for Disease Control and Prevention confirmed growth of "S. marcescens" from several unopened syringes of this product.
"S. marcescens" has also been linked to 19 cases in Alabama hospitals in 2011, including 10 deaths. All of the patients involved were receiving total parenteral nutrition at the time, and this is being investigated as a possible source of the outbreak.
Ground-water flow tracing.
Because of its ability to be grown on agar plates into even, well coloured lawns, and the existence of a phage specific to "S. marscecens", it has been used to trace water flows in Karst limestone systems. Known quantities of phage are injected into a fixed point in the Karst water system and the outflow of interest are monitored by conventional small-volume sampling at fixed time intervals. In the laboratory, the samples are poured onto grown "S. marscecens" lawns and incubated. Colourless plaques in the lawns indicate the presence of phage. The method was claimed to be sensitive at very high dilutions because of the ability to detect single phage particles.


Bymovirus

Bymovirus is a genus of viruses, in the family "Potyviridae". Plants serve as natural hosts. There are currently six species in this genus including the type species Barley yellow mosaic virus.
Taxonomy.
Group: ssRNA(+)
Structure.
Viruses in Bymovirus are non-enveloped, with flexuous and Filamentous geometries. The diameter is around 12-15 nm, with a length of 500-600 and 200-300 nm. Genomes are linear and bipartite, around 23.5-3.8kb in length.
Life cycle.
Viral replication is cytoplasmic. Entry into the host cell is achieved by penetration into the host cell. Replication follows the positive stranded RNA virus replication model. Positive stranded rna virus transcription is the method of transcription. The virus exits the host cell by tubule-guided viral movement.
Plants serve as the natural host. The virus is transmitted via a vector (fungus; plasmodiophorales). Transmission routes are vector, mechanical, and oral.


Candidatus Bartonella ancashi


Earth Microbiome Project

The Earth Microbiome Project (EMP) is an initiative founded by Janet Jansson, Jack Gilbert and Rob Knight in 2010 to collect natural samples and to analyze the microbial community around the globe.
Microbes are highly abundant, diverse, and have an important role in the ecological system. For example, the ocean contains an estimated 1.3 × 1028 archaeal cells, 3.1 × 1028 bacterial cells, and 1 × 1030 virus particles. The bacterial diversity, a measure of the number of "types" of bacteria in a community, is estimated to be about 160 for a mL of ocean water, 6,400–38,000 for a g of soil, and 70 for a mL of sewage works. Yet , it was estimated that the total global environmental DNA sequencing effort had produced less than 1 percent of the total DNA found in a liter of seawater or a gram of soil, and the specific interactions between microbes are largely unknown.
The EMP aims to process as many as 200,000 samples in different biomes, generating a complete database of microbes on earth to characterize environments and ecosystems by microbial composition and interaction. Using these data, new ecological and evolutionary theories can be proposed and tested.
Actors.
The non-governmental international project was launched in 2010. As of January 2018, it listed 161 institutions, all of them universities and university-affiliated institutions, except for IBM Research and the Atlanta Zoo. Crowdsourcing has come from John Templeton Foundation, the W. M. Keck Foundation, the Argonne National Laboratory by the U.S. Dept. of Energy, the Australian Research Council, the Tula Foundation, and the Samuel Lawrence Foundation. Companies have provided in-kind support including MO BIO Laboratories, Luca Technologies, Eppendorf, Boreal Genomics, Illumina, Roche and Integrated DNA Technologies.
Goals.
The primary goal of the Earth Microbiome Project (EMP) has been to survey microbial composition in many environments across the planet, across time as well as space, using a standard set of protocols. The development of standardized protocols is vital, because variations in sample extraction, amplification, sequencing and analysis introduce biases that would invalidate comparisons of microbial community structure.
Another important goal is to determine how reconstruction of microbial communities is affected by analytic biases. The rate of technological advance is rapid, and it is necessary to understand how data using updated protocols will compare with data collected using earlier techniques. Information from this project will be archived in a database to facilitate analysis. Other outputs will include a global atlas of protein function and a catalog of reassembled genomes classified by their taxonomic distributions.
Methods.
Standard protocols for sampling, DNA extraction, 16S rRNA amplification, 18S rRNA amplification, and "shotgun" metagenomics have been developed or are under development.
Sample collection.
Samples will be collected using appropriate methods from various environments including deep ocean, fresh water lakes, desert sand, and soil. Standardized collection protocols will be used when possible, so that the results are comparable. Microbes from natural samples cannot always be cultured. Because of this, metagenomic methods will be employed to sequence all the DNA or RNA in a sample in a culture-independent fashion.
Wet lab.
The wet lab usually needs to perform a series of procedures to select and purify the microbial portion of the samples. The purification process may be very different according to the type of sample. DNA will be extracted from soil particles, or microbes will be concentrated using a series of filtration techniques. In addition, various amplification techniques may be used to increase DNA yield. For example, non-PCR based Multiple displacement amplification is preferred by some researchers. DNA extraction, the use of primers, and PCR protocols are all areas that, in order to avoid bias, need to be performed following carefully standardized protocols.
Sequencing.
Depending on the biological question, researchers can choose to sequence a metagenomic sample using two main approaches. If the biological question to be resolved is, what types of organisms are present and in what abundance, the preferred approach would be to target and amplify a specific gene that is highly conserved among the species of interest. The 16S ribosomal RNA gene for bacteria and the 18S ribosomal RNA gene for protists are often used as target genes for this purpose. The advantage of targeting a specific gene is that the gene can be amplified and sequenced at a very high coverage. This approach is called "deep sequencing", which allows rare species to be identified in a sample. However, this approach will not enable assembly of any whole genomes, nor will it provide information on how organisms may interact with each other. The second approach is called shotgun metagenomics, in which all the DNA in the sample is sheared and the random fragments sequenced. In principle, this approach allows for the assembly of whole microbial genomes, and it allows inference of metabolic relationships. However, if most of microbes are uncharacterised in a given environment, "de novo" assembly will be computationally expensive.
Data analysis.
EMP proposes to standardize the bioinformatics aspects of sample processing.
Data analysis usually includes the following steps: 1) Data clean up. A pre-procedure to clean up any reads with low quality scores removing any sequences containing "N" or ambiguous nucleotides and 2) Assigning taxonomy to the sequences which is usually done using tools such as BLAST or RDP. Very often, novel sequences are discovered which cannot be mapped to existing taxonomy. In this case, taxonomy is derived from a phylogenetic tree which is created with the novel sequences and a pool of closely related known sequences.
Depending on the sequencing technology and the underlying biological question, additional methods may be employed. For example, if the sequenced reads are too short to infer any useful information, an assembly will be required. An assembly can also be used to construct whole genomes, which will provide useful information on the species. Furthermore, if the metabolic relationships within a microbial metagenome are to be understood, DNA sequences need to be translated into amino acid sequences, for example with using gene prediction tools such as GeneMark or FragGeneScan.
Project output.
The four key outputs from the EMP have been:
Challenges.
Large amounts of sequence data generated from analyzing diverse microbial communities are a challenge to store, organize and analyse. The problem is exacerbated by the short reads provided by the high-throughput sequencing platform that will be the standard instrument used in the EMP project. Improved algorithms, improved analysis tools, huge amounts of computer storage, and access to many thousands of hours of supercomputer time will be necessary.
Another challenge will be the large number of sequencing errors that are expected. Next-generation sequencing technologies provide enormous throughput but lower accuracies than older sequencing methods. When sequencing a single genome, the intrinsic lower accuracy of these methods is far more than compensated for by the ability to cover the entire genome multiple times in opposite directions from multiple start points, but this capability provides no improvement in accuracy when sequencing a diverse mixture of genomes. The question will be, how can sequencing errors be distinguished from actual diversity in the collected microbial samples?
Despite the issuance of standard protocols, systematic biases from lab to lab are expected. The need to amplify DNA from samples with low biomass will introduce additional distortions of the data. Assembly of genomes of even the dominant organisms in a diverse sample of organisms requires gigabytes of sequence data.
The EMP must avoid a problem that has become prevalent in the public sequence databases. With the advancement in high-throughput sequencing technologies, many sequences are entering public databases with no experimentally determined function, but which have been annotated on the basis of observed homologies with a known sequence. The first known sequence is used to annotate the first unknown sequence, but what is happening is that the first unknown sequence is being used to annotate the second unknown sequence and so on. Sequence homology is only a modestly reliable predictor of function.


Gymnopaxillus

Gymnopaxillus is a genus of fungi in the family Serpulaceae. According to the "Dictionary of the Fungi" (10th edition, 2008), the family contains four species found in temperate South America and Australia. "Gymnopaxillus" was circumscribed by mycologist Egon Horak in 1966 with "G. morchelliformis" as the type species. "G. crubensis", described from Argentina, was added in 1989, while the Australasian species "G. nudus" and
"G. vestitus" were added to the genus in 2001.


Coriobacteridae


Kaisha Atakhanova

Kaisha Atakhanova (born 18 July 1957) is a biologist from Karaganda, Kazakhstan, specializing in the genetic effects of nuclear radiation. Due to her civil society activism, she was awarded the international Goldman Environmental Prize in 2005 for leading a campaign to prevent nuclear waste from being commercially imported into Kazakhstan.
Atakhanova is founder and former leader of the "Karaganda Ecological Center" (known as "EcoCenter").
Early life.
Atakhanova was born in Karaganda, Kazakhstan. Her father was a coal miner and also fought in the Second World War. Growing up, she felt comfortable in nature and had a strong interest in animals, which led her to study biology and become an environmental activist.
The effects of radiation have affected her family, as both her parents and her sister have died from cancer. Her only other sibling, a brother, was also diagnosed with cancer.
Career and research.
Upon graduating in biology from Karaganda State University, Atakhanova began environmental and biological research. Following her interest on the effects of nuclear waste in Kazakhstan, she specialized in the genetic effects of nuclear radiation on amphibians, focusing primarily on frogs.
She did research in the "Semipalatinsk Test Sit", also known as the polygon, which was a testing site for Soviet nuclear weapons. Through this research, she was able to study the effects of radiation on people and animals that had been directly affected.
In 1992, she founded the "Karaganda Ecological Center" ("EcoCenter)", which allowed her to work directly with people who have been exposed to radiation. The purpose of this was to inform people of how the exposure to radiation could impact their living conditions. Through the EcoCenter, Atakhanova was able to lead a successful campaign to prevent nuclear waste from being commercially imported and disposed of in Kazakhstan.
Personal Accomplishments.
Atakhanova is the founder of the "Karaganda Ecological Center", or "EcoCenter", which focuses on environmental protection and promoting grassroots democracy. She is also a founding member of the "Women's Earth Alliance" ("WEA"), an organization that seeks to empower women and equip them with the skills and tools needed to protect the earth.


Mycobacterium agri

Mycobacterium agri 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.
Microscopy
Colony characteristics
Physiology
Pathogenesis.
Not associated with disease.


Chaenotheca chlorella

Chaenotheca chlorella is a species of lichen belonging to the family Coniocybaceae.
Synonym:


Dale Clayton

Dale Hartwell Clayton (born October 23, 1957), a parasitologist and professor of evolution at the University of Utah. Clayton is the taxonomist of "Strigiphilus garylarsoni".
Information.
Dale Clayton named the new species of feather louse after his favorite cartoonist, Gary Larson. Clayton has been interested in the relationships between parasites and their hosts since he was in high school. He was so intrigued with these relationships that he was able to use the research that he gathered in a high school science fair project in his Ph.D. thesis. The information was on the impact of parasites on avian conditions. He is specifically interested in the factors that allow parasite specificity, specification, co-specification, competition, and adaptive radiation. Thus far, his favorite research has been on birds and their feather-feeding lice.
Career.
Dale Clayton teaches the following classes:
Education.
Dale Clayton has received his education from the following institutions:
Honors.
Dale Clayton has received the following honors:


Amoeba

An amoeba (; less commonly spelt ameba or amœba; plural "am(o)ebas" or "am(o)ebae" ), often called an amoeboid, is a type of cell or unicellular organism which has the ability to alter its shape, primarily by extending and retracting pseudopods. Amoebae do not form a single taxonomic group; instead, they are found in every major lineage of eukaryotic organisms. Amoeboid cells occur not only among the protozoa, but also in fungi, algae, and animals.
Microbiologists often use the terms "amoeboid" and "amoeba" interchangeably for any organism that exhibits amoeboid movement.
In older classification systems, most amoebae were placed in the class or subphylum Sarcodina, a grouping of single-celled organisms that possess pseudopods or move by protoplasmic flow. However, molecular phylogenetic studies have shown that Sarcodina is not a monophyletic group whose members share common descent. Consequently, amoeboid organisms are no longer classified together in one group.
The best known amoeboid protists are "Chaos carolinense" and "Amoeba proteus", both of which have been widely cultivated and studied in classrooms and laboratories. Other well known species include the so-called "brain-eating amoeba" "Naegleria fowleri", the intestinal parasite "Entamoeba histolytica", which causes amoebic dysentery, and the multicellular "social amoeba" or slime mould "Dictyostelium discoideum".
Shape, movement and nutrition.
Amoebae do not have cell walls, which allows for free movement. Amoebae move and feed by using pseudopods, which are bulges of cytoplasm formed by the coordinated action of actin microfilaments pushing out the plasma membrane that surrounds the cell. The appearance and internal structure of pseudopods are used to distinguish groups of amoebae from one another. Amoebozoan species, such as those in the genus "Amoeba", typically have bulbous (lobose) pseudopods, rounded at the ends and roughly tubular in cross-section. Cercozoan amoeboids, such as "Euglypha" and "Gromia", have slender, thread-like (filose) pseudopods. Foraminifera emit fine, branching pseudopods that merge with one another to form net-like (reticulose) structures. Some groups, such as the Radiolaria and Heliozoa, have stiff, needle-like, radiating axopodia (actinopoda) supported from within by bundles of microtubules.
Free-living amoebae may be "testate" (enclosed within a hard shell), or "naked" (also known as , lacking any hard covering). The shells of testate amoebae may be composed of various substances, including calcium, silica, chitin, or agglutinations of found materials like small grains of sand and the frustules of diatoms.
To regulate osmotic pressure, most freshwater amoebae have a contractile vacuole which expels excess water from the cell. This organelle is necessary because freshwater has a lower concentration of solutes (such as salt) than the amoeba's own internal fluids (cytosol). Because the surrounding water is hypotonic with respect to the contents of the cell, water is transferred across the amoeba's cell membrane by osmosis. Without a contractile vacuole, the cell would fill with excess water and, eventually, burst. Marine amoebae do not usually possess a contractile vacuole because the concentration of solutes within the cell are in balance with the tonicity of the surrounding water.
Diet.
The food sources of amoebae vary. Some amoebae are predatory and live by consuming bacteria and other protists. Some are detritivores and eat dead organic material.
Amoebae typically ingest their food by phagocytosis, extending pseudopods to encircle and engulf live prey or particles of scavenged material. Amoeboid cells do not have a mouth or cytostome, and there is no fixed place on the cell at which phagocytosis normally occurs.
Some amoebae also feed by pinocytosis, imbibing dissolved nutrients through vesicles formed within the cell membrane.
Size range.
The size of amoeboid cells and species is extremely variable. The marine amoeboid "Massisteria voersi" is just 2.3 to 3 micrometres in diameter, within the size range of many bacteria. At the other extreme, the shells of deep-sea xenophyophores can attain 20 cm in diameter. Most of the free-living freshwater amoebae commonly found in pond water, ditches, and lakes are microscopic, but some species, such as the so-called "giant amoebae" "Pelomyxa palustris" and "Chaos carolinense", can be large enough to see with the naked eye.
Amoebae as specialized cells and life cycle stages.
Some multicellular organisms have amoeboid cells only in certain phases of life, or use amoeboid movements for specialized functions. In the immune system of humans and other animals, amoeboid white blood cells pursue invading organisms, such as bacteria and pathogenic protists, and engulf them by phagocytosis.
Amoeboid stages also occur in the multicellular fungus-like protists, the so-called slime moulds. Both the plasmodial slime moulds, currently classified in the class Myxogastria, and the cellular slime moulds of the groups Acrasida and Dictyosteliida, live as amoebae during their feeding stage. The amoeboid cells of the former combine to form a giant multinucleate organism, while the cells of the latter live separately until food runs out, at which time the amoebae aggregate to form a multicellular migrating "slug" which functions as a single organism.
Other organisms may also present amoeboid cells during certain life-cycle stages, e.g., the gametes of some green algae (Zygnematophyceae) and pennate diatoms, the spores (or dispersal phases) of some Mesomycetozoea, and the sporoplasm stage of Myxozoa and of Ascetosporea.
Amoebae as organisms.
Early history and origins of Sarcodina.
The earliest record of an amoeboid organism was produced in 1755 by August Johann Rösel von Rosenhof, who named his discovery "Der Kleine Proteus" ("the Little Proteus"). Rösel's illustrations show an unidentifiable freshwater amoeba, similar in appearance to the common species now known as Amoeba proteus. The term "Proteus animalcule" remained in use throughout the 18th and 19th centuries, as an informal name for any large, free-living amoeboid.
In 1822, the genus "Amiba" (from the Greek ἀμοιβή "amoibe", meaning "change") was erected by the French naturalist Bory de Saint-Vincent. Bory's contemporary, C. G. Ehrenberg, adopted the genus in his own classification of microscopic creatures, but changed the spelling to "Amoeba".
In 1841, Félix Dujardin coined the term "sarcode" (from Greek σάρξ "sarx", "flesh," and εἶδος "eidos", "form") for the "thick, glutinous, homogenous substance" which fills protozoan cell bodies. Although the term originally referred to the protoplasm of any protozoan, it soon came to be used in a restricted sense to designate the gelatinous contents of amoeboid cells. Thirty years later, the Austrian zoologist Ludwig Karl Schmarda used "sarcode" as the conceptual basis for his division Sarcodea, a phylum-level group made up of "unstable, changeable" organisms with bodies largely composed of "sarcode". Later workers, including the influential taxonomist Otto Bütschli, emended this group to create the class Sarcodina, a taxon that remained in wide use throughout most of the 20th century.
Within the traditional Sarcodina, amoebae were generally divided into morphological categories, on the basis of the form and structure of their pseudopods. Amoebae with pseudopods supported by regular arrays of microtubules (such as the freshwater Heliozoa and marine Radiolaria) were classified as ; whereas those with unsupported pseudopods were classified as . The Rhizopods were further subdivided into lobose, filose, and reticulose amoebae, according to the morphology of their pseudopods.
Dismantling of Sarcodina.
In the final decade of the 20th century, a series of molecular phylogenetic analyses confirmed that Sarcodina was not a monophyletic group. In view of these findings, the old scheme was abandoned and the amoebae of Sarcodina were dispersed among many other high-level taxonomic groups. Today, the majority of traditional sarcodines are placed in two eukaryote supergroups: Amoebozoa and Rhizaria. The rest have been distributed among the excavates, opisthokonts, and stramenopiles. Some, like the Centrohelida, have yet to be placed in any supergroup.
Classification.
Recent classification places the various amoeboid genera in the following groups:
Some of the amoeboid groups cited (e.g., part of chrysophytes, part of xanthophytes, chlorarachniophytes) were not traditionally included in Sarcodina, being classified as algae or flagellated protozoa.
Pathogenic interactions with other organisms.
Some amoebae can infect other organisms pathogenically, causing disease:
Meiosis.
Recent evidence indicates that several Amoebozoa lineages undergo meiosis.
Orthologs of genes employed in meiosis of sexual eukaryotes have recently been identified in the "Acanthamoeba" genome. These genes included "Spo11, Mre11, Rad50, Rad51, Rad52, Mnd1, Dmc1, Msh" and "Mlh". This finding suggests that the ‘'Acanthamoeba'’ are capable of some form of meiosis and may be able to undergo sexual reproduction.
The meiosis-specific recombinase, Dmc1, is required for efficient meiotic homologous recombination, and "Dmc1" is expressed in "Entamoeba histolytica". The purified Dmc1 from "E. histolytica" forms presynaptic filaments and catalyses ATP-dependent homologous DNA pairing and DNA strand exchange over at least several thousand base pairs. The DNA pairing and strand exchange reactions are enhanced by the eukaryotic meiosis-specific recombination accessory factor (heterodimer) Hop2-Mnd1. These processes are central to meiotic recombination, suggesting that "E. histolytica" undergoes meiosis.
Studies of "Entamoeba invadens" found that, during the conversion from the tetraploid uninucleate trophozoite to the tetranucleate cyst, homologous recombination is enhanced. Expression of genes with functions related to the major steps of meiotic recombination also increase during encystations. These findings in "E. invadens", combined with evidence from studies of "E. histolytica" indicate the presence of meiosis in the "Entamoeba".
"Dictyostelium discoideum" in the supergroup Amoebozoa can undergo mating and sexual reproduction including meiosis when food is scarce.
Since the Amoebozoa diverged early from the eukaryotic family tree, these results suggest that meiosis was present early in eukaryotic evolution. Furthermore, these findings are consistent with the proposal of Lahr et al. that the majority of amoeboid lineages are anciently sexual.