Nitrososphaera gargensis

"Nitrososphaera gargensis" is a non-pathogenic, small coccus measuring 0.9 ± 0.3 μm in diameter. "N. gargensis" is observed in small abnormal cocci groupings and uses its archaella to move via chemotaxis. Being an Archaeon, "Nitrososphaera gargensis" has a cell membrane composed of crenarchaeol, its isomer, and a distinct glycerol dialkyl glycerol tetraether (GDGT), which is significant in identifying ammonia-oxidizing archaea (AOA). The organism plays a role in influencing ocean communities and food production.
Discovery.
"Nitrososphaera gargensis" was discovered in a Garga hot spring in Siberia by Hatzenpichler and associates in 2008. The organism was isolated from a sample taken from the Siberian hot springs that was actually located in a microbial mat. Hatzenpichler et al. later grew the culture aerobically at 46℃ with ammonium and bicarbonate. In 2007, the first indications of "Nitrososphaera gargensis" were found through testing a hot spring sample for ammonia oxidizers. The researchers found ammonia-oxidizing archaea instead of the expected bacteria with this capability since no previous archaea had been found to be able to complete this process. Through analyzing 16S rRNA gene sequences and performing the scientific methods of catalyzed reporter deposition (CARD)-FISH (fluorescence "in situ" hybridization) and microautoradiography, the researchers determined that the organism in the sample was an ammonia-oxidizing archaea and classified this organism as "Candidatus Nitrososphaera gargensis".
Genomics.
"Nitrososphaera gargensis"' genome is 2.83 Mb in size with a GC content of 48%, which is much larger than most other ammonia-oxidizing archaea. The organism encodes for 3565 protein genes and 37 RNA genes. "N. gargensis" also contains a CRISPR-Cas type I system able to target viral DNA, gene duplications in its chaperones, and numerous transposase genes.
Taxonomy and phylogeny.
"N. gargensis" neighbors "Nitrosopumilus maritimus" and "Nitrososphaera viennensis" on the phylogenetic tree. Like "Nitrososphaera gargensis", both of these organisms are chemolithoautotrophic ammonia-oxidizers that thrive in hot and humid habitats. Spang et al. elucidated, in 2012, the notable similarities between "N. gargensis" and "N. viennensis" through their nitrification ability and PHA (putatively polyhydroxybutyrate) production along with other elements.
Nitrification and metabolism.
As a chemolithoautotroph, "Nitrososphaera gargensis" performs aerobic oxidation of ammonia to nitrite and breaks down cyanate for energy. "N. gargensis" also encompasses a flexible carbon metabolism, allowing for the uptake of organic material. Nitrification, the process of oxidizing ammonia to nitrate, is a significant step in the nitrogen cycle. Since nitrogen is limited in marine environments, the recent discovery of ammonia-oxidizing archaea proves to be an active source of study for researchers. "N. gargensis" possesses ammonia monooxygenase, which is the enzyme that enables the organism the ability to oxidize ammonia, or urea and potentially cyanate as other sources of ammonia.
Habitat.
"Nitrososphaera gargensis" was discovered in a Garga hot spring and most commonly resides in similar heavy metal-containing thermal springs or can be isolated from microbial mats near hot springs. Besides hot springs, other ammonia-oxidizing archaea are commonly found in soil, freshwater, and the sediments in freshwater. "N. gargensis" grows best at 46℃ and thrives on the presence of ammonia or other nitrogen sources, and it utilizes flagella to move via chemotaxis.
Current research.
Crenarchaeol isomer.
The membrane composition of ammonia-oxidizing archaea, specifically through a crenarchaeol isomer, can be used to identify them as an AOA. "N. gargensis" was the first cultivated organism with the ability to produce a significant quantity of the crenarchaeol isomer. With its ability to synthesize crenarchaeol, "N. gargensis" allows scientists to expand this synthesis also to the Group I.1b Crenarchaeota. These discoveries indicate that these organisms are significant sources of crenarchaeol in their habitats of thermophilic and terrestrial environments and corroborate the association between AOA and crenarchaeol.
Marine nitrogen cycles.
Furthermore, "Nitrososphaera gargensis" influence as an ammonia-oxidizing archaea expands from land to water since its nitrification ability plays a role in the nitrogen cycles that are present in the ocean. The nitrogen cycle determines the interplay of organisms in marine ecosystems and the activity of the ocean.
Food production and fertilizers.
Along with influencing the structure of soils and ocean communities, "Nitrososphaera gargensis" also plays a role in food production. Since nitrogen is required for food production, fertilizers containing nitrogen are used. This leads to pollution that can harm the environment and end up in wastewater. Therefore, researchers are trying to develop ways to remove the nitrogen from the affected areas. Organisms similar to "Nitrososphaera gargensis" were found to oxidize ammonia in this study, and with this knowledge, the researchers plan on coupling this ability with other processes in the nitrogen cycle in order to remove the form of nitrogen that is polluting the area. Such couplings could occur due to the fact that AOA are not affected by nitrous acid concentrations whereas nitrite-oxidizing bacteria are inhibited by this chemical. In this difference, techniques could be developed to foster deammonification, which is more cost-effective. Overall, in these studies, researchers are trying to find the correct balance in a thermophilic bioreactor in order to eliminate nitrogen.


Viridiplantae

Viridiplantae (literally "green plants") are a clade of eukaryotic organisms that comprise approximately 450,000–500,000 species and play important roles in both terrestrial and aquatic ecosystems. They are made up of the green algae, which are primarily aquatic, and the land plants (embryophytes), which emerged from within them. Green algae traditionally excludes the land plants, rendering them a paraphyletic group. Since the realization that the embryophytes emerged from within the green algae, some authors are starting to include them. They have cells with cellulose in their cell walls, and primary chloroplasts derived from endosymbiosis with cyanobacteria that contain chlorophylls a and b and lack phycobilins.
In some classification systems, the group has been treated as a kingdom, under various names, e.g. Viridiplantae, Chlorobionta, or simply Plantae, the latter expanding the traditional plant kingdom to include the green algae. Adl" et al.", who produced a classification for all eukaryotes in 2005, introduced the name Chloroplastida for this group, reflecting the group having primary chloroplasts with green chlorophyll. They rejected the name Viridiplantae on the grounds that some of the species are not plants, as understood traditionally. The Viridiplantae are made up of two clades: Chlorophyta and Streptophyta as well as the basal Mesostigmatophyceae and Chlorokybophyceae. Together with Rhodophyta and glaucophytes, Viridiplantae are thought to belong to a larger clade called Archaeplastida or Primoplantae.
A taxonomic evaluation of eukaryotes based on myosin distribution showed the Viridiplantae lost class-I myosins.
Phylogeny and classification.
Simplified phylogeny of the Viridiplantae, according to Leliaert "et al". 2012.
Cladogram.
Below is a consensus reconstruction of green algal relationships, mainly based on molecular data.
More conventionally, Mesostigmatophyceae, "Spirotaenia", and Cholokybophyceae are basal Streptophyta. Ancestrally, the green algae were flagellates.


Mupapillomavirus

Mupapillomavirus is a genus of viruses in the family "Papillomaviridae". Humans serve as natural hosts. There are three species in this genus. Diseases associated with this genus include palmoplantar warts.
Taxonomy.
The following three species are assigned to the genus:
Structure.
Viruses in "Mupapillomavirus" are non-enveloped, with icosahedral geometries, and T=7 symmetry. The diameter is around 52-55 nm. Genomes are circular, around 8kb in length.
Life cycle.
Viral replication is nuclear. Entry into the host cell is achieved by attachment of the viral proteins to host receptors, which mediates endocytosis. Replication follows the dsDNA bidirectional replication model. DNA-templated transcription, with some alternative splicing mechanism is the method of transcription. The virus exits the host cell by nuclear envelope breakdown.
Human serve as the natural host. Transmission routes are contact.


Alicyclobacillus hesperidum

Alicyclobacillus hesperidum is a species of Gram positive, strictly aerobic, bacterium. The bacteria are acidophilic and produced endospores. It was first isolated from solfataric soils in the Furnas, the Azores. The species was first described in 2000, and the name refers to the Hesperides, "mythological figures whom the Greeks believed to have lived at the Western edge of the Earth in a miraculous garden, which [the researchers] interpret as the Azores."
The optimum growth temperature for "A. hesperidum" is 50-53 °C, and can grow in the 35-60 °C range. The optimum pH is 3.5-4.0, and can grow in pH 2.5-5.5.


Xenos (insect)

Xenos is a genus of insects belonging to the family Stylopidae. The word derives from the Greek word for strange. A species of the genus is "Xenos vesparum", first described by Pietro Rossi in 1793. The females are permanent entomophagous endoparasites of "Polistes" paper wasps. They dwell their whole lives in the abdomens of wasps.


Nigrospora

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


Mycobacterium virus Jeffabunny

Mycobacterium virus Jeffabunny is a bacteriophage known to infect bacterial species of the genus "Mycobacterium".
Jeffabunny was discovered by Sir Jeffrey Rubin in 2008 in HHMI funded lab as part of SEAPHAGES.


Enterobacter

Enterobacter is a genus of common Gram-negative, facultatively anaerobic, rod-shaped, non-spore-forming bacteria of the family Enterobacteriaceae. It is the type genus of the order Enterobacterales. Several strains of these bacteria are pathogenic and cause opportunistic infections in immunocompromised (usually hospitalized) hosts and in those who are on mechanical ventilation. The urinary and respiratory tracts are the most common sites of infection. The genus "Enterobacter" is a member of the coliform group of bacteria. It does not belong to the fecal coliforms (or thermotolerant coliforms) group of bacteria, unlike "Escherichia coli", because it is incapable of growth at 44.5 °C in the presence of bile salts. Some of them show quorum sensing properties.
One clinically important species from this genus is "E. cloacae".
Researchers in 2018 reported, after detecting the presence on the International Space Station (ISS) of five "Enterobacter bugandensis" bacterial strains, none pathogenic to humans, that microorganisms on ISS should be carefully monitored to continue assuring a medically healthy environment for the astronauts.
Biochemical characteristics.
The genus "Enterobacter" ferments lactose with gas production during a 48-hour incubation at 35-37 °C in the presence of bile salts and detergents. It is oxidase-negative, indole-negative, and urease-variable.
Treatment.
Treatment is dependent on local trends of antibiotic resistance. "Enterobacter huaxiensis" and "Enterobacter chuandaensis" are two recently discovered species that exhibit especially antibiotic resistant characteristics.
Cefepime, a fourth-generation cephalosporin from the β-Lactam antibiotic class. Imipenem (a carbapenem) is often the antibiotic of choice. Aminoglycosides such as amikacin have been found to be very effective, as well. Quinolones can be an effective alternative.
Linked to obesity.
A recent study has shown that the presence of "Enterobacter cloacae" B29 in the gut of a morbidly obese individual may have contributed to the patient’s obesity. Reduction of the bacterial load within the patient’s gut, from 35% "E. cloacae" B29 to non-detectable levels, was associated with a parallel reduction in endotoxin load in the patient and a concomitant, significant reduction in weight. Furthermore, the same bacterial strain, isolated from the patient, induced obesity and insulin resistance in germfree C57BL/6J mice that were being fed a high-fat diet. The study concludes that "E. cloacae" B29 may contribute to obesity in its human hosts through an endotoxin-induced, inflammation-mediated mechanism.


Shimwellia

Shimwellia is a genus of Gram-negative bacteria of the family Enterobacteriaceae. The two species of "Shimwellia" are "Shimwellia blattae" (formerly "Escherichia blattae") and "Shimwellia pseudoproteus" (formerly "Obesumbacterium pseudoproteus").
Species in "Shimwellia" are genetically similar to "Escherichia" but differ in notable ways. "S. blattae" can synthesize coenzyme B12 and "S. pseudoproteus" is associated with beer spoilage.


Galactomyces reessii

Galactomyces reessii is a yeast belonging to the genus "Galactomyces".
It contains an enzyme that converts 3-methylcrotonic acid to 3-hydroxy-3-methylbutyric acid aka β-hydroxy β-methylbutyric acid. It can also have an enzyme that dissolves pectin.
"Galactomyces reessii" lives naturally in soil and on decaying vegetable matter.
"Galactomyces reessii" does not consume D-mannitol. It cannot ferment glucose.


Middelburg virus

Middelburg virus (MIDV) is an alphavirus of the Old World Group that has likely endemic and zoonotic potential. It is of the viral family "Togaviridae". It was isolated from mosquitos in 1957 in South Africa, MDIV antigens have now been found in livestock, horses, and humans.
Symptoms.
Typical symptoms of MIDV include: fever, swollen/aching limbs, hyperactiveness, and depression. There is research suggesting that MIDV might cause neurologic disease. Some signs of the neurologic disease are: ataxia, paresis, seizures, and paralysis. In these cases where MIDV infection lead to neurologic disease, moderate meningoencephalitis was observed microscopically. There have also been rare cases in horses where MIDV infection has led to jaundice, laminitic stance, and aborted pregnancy.
Virus structure.
Middelburg virus is a single stranded, linearly arranged, positive stranded RNA virus. MIDV has an enveloped capsid that contains an icosahedron structure. The icosahedron has a triangulation number (T) or 4, meaning is contains 240 monomers. It is thought to be part of the Semliki Forest clade of Alphaviridae
Genome.
A complete genomic sequence was made of the originally isolated MIDV-857 strand using a RT-qPCR method. Researchers found that the genome was 11,674 nucleotides long, not including the 5'-terminal cap or polyA-tail. They found that the 5'-terminal cap and polyA-tail fell between 180-220 residues. Through this sequencing, it was determined that MIDV has a similar structure and organization of its genome in comparison to other alphaviruses. MIDV possesses the same read-through stop codon between the genes nsP3 and nsP4, which is distinctive of alphaviruses. This same study found that the MIDV E1 genes was likely formed through recombination with Semliki Forest virus, or a virus very similar to SFV. The E1 gene is a membrane fusion protein that is important in viral entry and release. Together E1 and E2 are the glycoproteins that make up the Alphavirus envelope over the nucleocapsid. A final finding of this study located a 112 nucleotide duplication in the 3' untranslated region (UTR) of the MIDV genome, insinuating that this virus is prone to duplication mutations. In a similar study, MIDV was found to have two open reading frames (ORFs). The first ORF encodes for nonstructural proteins, while the second ORF encodes the structural proteins like E1 and E2. It is important to know the sequencing to understand if certain strains act differently by causing different symptoms (i.e. only arthritis, only encephalitis, or both).
Replication cycle.
Entry.
Alphaviruses, like MIDV, use receptor-mediated endocytic uptake to get into a host cell. Since no MIDV-specific cell entry literature could be found, the Alphavirus entry information that MIDV utilizes will be stated here. After being taken in through endocytosis, a low pH triggers a membrane fusion, which delivers the viral RNA genomes into the cell's cytoplasm. It is not yet know which surface molecule acts as an Alphavirus receptor, but research is looking at cell surface heparan sulfate (HS) as a viable receptor considering its close relation to the E2 protein found on the Alphavirus envelope. Research is also looking at DC-SIGN/L-SIGN as a receptor since it binds to mannose-rich carbohydrates that are often found in mosquitos, the vectors for Alphaviruses and MIDV. Alphaviruses utilize the clathrin-mediated endocytic pathway. Since presence of the Alphavirus does not have an effect on the number of clathrin-coated vesicles, it is assumed that the alphavirus takes advantage of the cells own processes without alteration. Research has found that this endocytic uptake of alphaviruses can be stopped through injection of anti-clathrin drugs - this could be utilized in the future to make a vaccine. After endocytic uptake, the virus is quickly delivered to the early endosome compartment, where a low pH then lyses the endosome and virus, exposing the cytoplasm to viral nucleocapsid. Cholesterol is also necessary for the Alphavirus to undergo fusion. This fusion of the endosomal membrane to the viral envelope allows the release of nucleocapsid into the cytoplasm of the host cell. Almost immediately the nucleocapsid is uncoated, exposing the viral RNA to the host cytoplasm
Replication and transcription.
MIDV is a member of the family Togovirdiae which is hypothesized to use a "factory" replication process. The "factories" in this case, are the host cell's endosomes and lysosomes. The role of the endosome was explained above in the section on viral entry. The modified cellular lysosome create a new vesicular structure termed the cytopathic vacuole (CPV) which can serve as sites for viral replication and possible transcription. The relationship between the CPV and RER are believed to create a viable site for translation of structural proteins and assembly of nucleocapsids of newly synthesized viruses. In replication, the (+)ssRNA genome is translated to make a polyprotein which is in turn cleaved into the smaller structural proteins that are used in the replication and transcription of RNA. From the viral RNA, a double-stranded RNA template is made. This dsRNA template then is transcribed and replicated, which is the new mRNA that is utilized for subsequent virus generations.
Assembly and release.
The subgenomic RNA (sgRNA) that was made prior to this begins the next step in the life cycle of MIDV: assembly and release. The sgRNA codes for the structural proteins that will form the new virus. The assembly of the new viral capsid occurs in the cytoplasm. Finally, this newly synthesized capsid is enveloped by budding, a process that occurs when the virus exits the cells and is surrounded by the plasma membrane
Possible Vectors.
MIDV was first isolated from the mosquito species "Ochlerotatus caballus", since then it has been found in other mosquito species in South Africa including: "Aedes leneatopennis" and "Aedes albothorax". The virus is limited to Africa, but due to the wide range of these mosquito hosts and possible travelling of horses and livestock, there is cause to believe it might spread elsewhere. Sindbis virus, an extremely similar virus to MIDV has spread outside of Africa and effects humans. The horses themselves cannot act as vectors to spread MIDV since the concentration of virus in the host blood stream is too small to infect a mosquito.
Other host species include "Ovis aries", "Mansonia", and "Aedes vittatus".
Associated Disease.
MIDV is classified as an Old World Alphavirus which also includes Semliki Forest virus (SFV), Ndumu virus, Barmah Forest virus, and the very well-known Chikungunya virus. These diseases all have similar symptoms: arthritis, fever, and rash. Current research is also pointing to Old World Alphaviruses leading to neurologic disease like their New World counterparts .
There is a similar group of Alphavirus known as the New World Alphaviruses that also share much in common with MIDV. These include: Eastern equine encephalitis (EEE) virus, and Venezuelan equine encephalitis virus. These viruses are more notoriously associated with neurologic disease and are more likely to effect humans.
Tropism.
There is no literature on MIDV tropism, but based on the symptoms it can be deduced that the virus mostly affects host connective tissue at the joints, causing arthritis. The virus also affects epithelial tissue in the form of a rash and nervous tissue in the form of encephalitis.
Treatment.
There is no known treatment for MIDV in horses currently. Veterinarians may give anti-inflammatory drugs to affected animals to lessen the inflammatory response of the infection. Horse owners can also take preemptive measure by using long-lasting repellants and mosquito netting.


Ian Macara

Ian G. Macara is a British-American biologist, currently the Louise B. McGavock Chair at Vanderbilt University. He received his PhD from the University of Sheffield in the United Kingdom and completed postdoctoral training at Harvard University before moving to the University of Virginia, where he was the Harrison Distinguished Professor of Microbiology and Director of the Advanced Microscopy Facility. He was named the chair of the Vanderbilt Department of Cell and Developmental Biology in 2012. His research focuses on the molecules that establish Cell polarity in Epithelium, both in normal cells and in cancer.


Curtobacterium

Curtobacterium is a genus of bacteria of the order Actinomycetales. They are Gram-positive soil organisms.
An analysis of Curtobacterium sequences from around the globe revealed the genus to be a cosmopolitan terrestrial taxon, with isolates derived primarily from plant and soil habitat.


John Mekalanos

John Mekalanos is a microbiologist who is primarily known for leading one of the first teams that reported the discovery of the type VI secretion system as well as his work on the pathogenicity of the bacterial species "Vibrio cholerae", its toxin, and its secretion systems. Since 1998, he has been a member of the National Academy of Sciences.
Education.
He started his research studies as a graduate student in the labs of R. John Collier and William Robert Romig at UCLA where his research was focused on studying the genetic and biochemical analysis of the cholera toxin secreted by the bacterium "Vibrio cholerae". Highlights of his career during this time was, along with Romig, the development of a screening assay designed to isolate the tox mutants of "Vibrio cholerae" (strains with altered toxin production ability) which led to the genetic mapping of the toxin-regulatory mutants in this bacterial species.
He continued his work on cholera toxin as a post-doc at the Department of Microbiology and Molecular Genetics at Harvard Medical School with John R. Murphy, which was followed by his appointment as an assistant professor there.
Career and Research.
Early Research.
His early work as an independent researcher led to the identification of toxR, a gene that affects the expression of the cholera toxin operon ctxAB, the discovery that the Staphylococcus aureus enterotoxin A (entA) is a phage-encoded protein, and finally, the demonstration of the presence of duplications of the toxin operon in different strains of "Vibrio cholerae" that could account for the variable toxinogenicity of the strains which led to his promotion to Professor in 1986. His continued strong research output led to his appointment as Chairman of the then Department of Microbiology and Molecular Genetics (now Microbiology and Immunobiology) ten years later in 1996 and his election to the National Academy of Sciences in 1998.
T6SS Discovery.
In 2006, his group published the first account of the identification of a novel secretion system that they named the type VI secretion system, a system initially found to be capable of conferring increased virulence in non-O1/non-O139 strain strains of "V. cholerae", which was later however shown to be primarily responsible for interbacterial competition.


Abyssoviridae


Byng Formation

The Byng Formation is a geologic formation in British Columbia. It preserves fossils dating back to the Ediacaran period.


Sergey Ognev

Sergey Ivanovich Ognev () (17 November 1886 in Moscow – 20 December 1951 in Moscow) was a Russian scientist, zoologist and naturalist, remembered for his work on mammalogy. He graduated from Moscow University in 1910, the same year in which he published his first monograph. In 1928, he became a professor at the Moscow State Pedagogical University. He published a variety of textbooks in zoology and economy. His magnum opus, "Mammals of Russia and adjacent territories", was never completed.


Neodasyscypha

Neodasyscypha is a genus of fungi belonging to the family Hyaloscyphaceae.
The species of this genus are found in Europe, Northern America and Australia.
Species:


Lolaniso Ismoilova

Lolaniso Ibrohimovna Ismoilova () (born October 4, 1929) is a Tajikistani biologist, active during the Soviet era.
Born into a working-class family in Dushanbe, Ismoilova graduated from the Department of Biology of the Tajikistan State University in 1953. In 1965 she joined the Communist Party of the Soviet Union. She became an assistant professor in the Department of Histology at the University in 1970, and in 1974 was promoted to become head of the Department of Biology and General Genetics of the Tajikistan State Medical Institute. She received a doctoral degree in biology in 1986. As a researcher, Ismoilova concerned herself with the structure and function of lymph nodes once they had been subjected to fire. She also studied post-traumatic postnatal issues, and did work on the restoration and transplantation of blood vessels in kidneys. Among her publications are "Environmental Upkeep and People's Health" (1984) and "A Short Russian-Tajiki-Dari Dictionary of Biology" (Dushanbe, 1973). She has published over 180 articles and papers during her career, including 24 instructional methods and two textbooks.


Quick Professor of Biology

The Quick Professorship of Biology is one of the senior professorships in biology at the University of Cambridge.
Frederick James Quick (1836–1902), a prosperous coffee merchant and senior partner in the London coffee-firm "Quick, Reek and James" at the time of his death, bequeathed the majority of his wealth to the University of Cambridge (where he had been a student at Trinity Hall, graduating in 1859) to be used in the 'study of vegetable and animal biology'. After much debate, it was decided that a new professorship should be established which would primarily cover the field of protozoology, and in 1906 George Nuttall became the first holder of the chair.
From 1907 to 1921 there was a laboratory associated with the chair, known as the Quick Laboratory: it was a single room, divided into cubicles, on the ground floor of the Cambridge Medical School building. In 1919, after an appeal for funds by the Quick Professor, the Molteno Institute of Parasitology was established. In 1920 the scope of the chair was broadened to the study of parasitology. In 1931 the chair was offered to David Keilin for study of cell biology.


Malassezia equina

Malassezia equina is a fungus first isolated in horses, which can cause opportunistic infections in animals. Its type strain is MA146=CBS 9969. This species will not grow without any lipid supplementation. It grows slowly and forms small colonies (average diameter ). In the lab, colonies will not grow at temperatures of 40 °C, differing from "M. sympodialis"-related species, such "M. dermatis" and "M. nana", which can grow at this temperature. "Malassezia caprae" cells are ovoidal.


Boothiomyces

Boothiomyces is a genus of fungi belonging to the family Terramycetaceae.
The genus has almost cosmopolitan distribution.
Species:


Epideme

"Epideme" is the seventh episode of science fiction comedy series "Red Dwarf VII" and the 43rd in the series run. It was first broadcast on the British television channel BBC2 on 28 February 1997. Written by Paul Alexander & Doug Naylor and directed by Ed Bye, the episode involves Lister contracting an intelligent, but deadly, virus.
Plot.
The crew encounters an abandoned ship, the "Leviathan", which is buried in the middle of an ice planetoid. In it, they find the frozen body of Caroline Carmen, one of Lister's former crushes. She is taken on board the "Starbug", where the crew attempts to thaw her out, but they are unable to melt the ice. That night, Carmen defrosts of her own accord and turns out to be in an advanced state of decomposition. She attacks Lister and spits part of her jaw and tongue down his throat, infecting him with Epideme, an intelligent virus (with an annoying personality) that was supposed to cure nicotine addiction, but in practice kills its victims within 48 hours, then reanimates their corpse to find a new victim to transfer itself to.
Lister tries reasoning with Epideme directly through a communication link, but has no luck in convincing the virus to leave. Kochanski comes up with a drastic plan to save Lister's life: coax the virus to move down toward Lister's hand and then cut off the hand, isolating the virus outside his body. However, they end up cutting off Lister's right arm instead of the left one as he had requested, and they only manage to dispose of part of the Epideme virus, with the end result that they only succeed in prolonging Lister's life by an hour. Lister sneaks aboard the "Leviathan" with some explosives, intending to kill both himself and Epideme, but the virus talks him out of it by revealing that the destination of the "Leviathan" was Delta VII, a research base that might have a cure.
When "Starbug" arrives at Delta VII, it turns out that the planet has been destroyed in order to deal with a massive Epideme outbreak – a fact that the virus was fully aware of, and used in its attempt to prevent Lister from killing himself. With Lister on the verge of death, Kochanski injects Lister with a drug that stops his heart, then gets his corpse to bite her left hand, infecting it. After amputating her left arm she reveals that it was actually Caroline Carmen's arm, and that her own left arm is intact. Kryten and Kochanski then revive the now virus-free but now one-armed Lister.
Production.
For Paul Alexander's second script, he used an old Jasper Carrot joke for the premise of the plot – "What if your flu could talk to you? Wouldn't it just say that it was doing its job?" Again, Naylor helped out with the script, tweaking it to conform to the "Red Dwarf" universe.
An alternate ending was scripted and filmed for the episode – involving the dead arm, containing the Epideme virus, flying through space and then towards the camera – but it was decided to end the episode just before this scene.
Of the many new props needed for the new series was a laser bone-saw – used for the scenes of severing the Epideme-infected arm. For the scene, Chloë Annett had taken several attempts to cut the arm off.
Voice artist Gary Martin played the talking virus Epideme. He was recommended by Danny John-Jules, his friend of many years' standing, and had even been with Danny when he auditioned for the role of the Cat in the mid-eighties.
Nicky Leatherbarrow also appeared, in heavy make-up, as Caroline Carmen - the initial carrier of the Epideme virus.
Reception.
Originally broadcast on the British television channel BBC2 on 28 February 1997 in the 9:00 pm evening slot, this episode's television ratings were high. Although Series VII as a whole received a mixed response from fans and critics alike, this was considered one of the better episodes.
DVDActive thought the episode was "a nice idea, and one that is well-executed ... the final scene is one of the funniest of the series." DVD Verdict thought that this episode was the first in which the character of Kochanski finally "reached her stride" after all the "attitude and aggravation during those first few shows". Sci-Fi Online noted that the episode was "particularly reminiscent of Confidence and Paranoia, since it deals with a talking disease."


Comperiella bifasciata

Comperiella bifasciata is a parasitic wasp species in the genus "Comperiella" in the family Encyrtidae. It is used in biological control of California red scale and yellow scale of citrus.
Description.
"Comperiella bifasciata" is a tiny black wasp with two white bars on the head. These are more prominent in females, which also have dark patches on the wings, giving them the appearance of having a forked tail; the wings of males are unblotched.
History.
"C. bifasciata" is a parasite of the red scale ("Aonidiella aurantii"), a major insect pest of citrus. This pest was accidentally brought into the United States in the second half of the nineteenth century, and is known there as California red scale.
In attempts to try to control the red scale, in 1908 "Comperiella bifasciata", and two other parasitic wasps, were introduced into California from Japan. It failed to become established on red scale but was found by 1931 to have become established on yellow scale ("Aonidiella citrina"). It was later established that an error had been made and that it was not parasitising "Aonidiella aurantii" in Japan, but rather "Aonidiella taxus" and "Chrysomphalus bifasciculatus". When imports of a different biological race were made from China between 1947 and 1949, the parasite did become established on red scale in California.
These two types are identical in appearance and will hybridise in the laboratory, but maintain their separate identities in the field. In the San Joaquin Valley, wasps reared from yellow scale are always of the Japanese type while those raised from red scale are the Chinese type. It seems that the hybrid is not so well adapted as either of its parents, so natural selection eliminates it, thereby preserving the two distinct types.
Ecology.
The larva of "C. bifasciata" is an endoparasite. The adult female seeks out third instar and fourth instar female scale insects, but is prepared to oviposit in any stage except females that have already produced crawlers. Each egg is laid singly and the developing larva feeds inside its host as it grows. When it pupates, black meconium pellets are deposited and get pushed to one side under the scale. When it emerges, the wasp chews a jagged-edged hole through the scale's body and scale. The mummified corpse of the scale insect, with black meconium deposits inside, usually remains stuck to the host plant.
Use in biological control.
In California, the most important parasite of yellow scale is "C. bifasciata". The California red scale is most easily controlled by using the ectoparasite "Aphytis", with "C. bifasciata" being unable to compete with "Aphytis" because the latter consumes the scale larvae including any developing "C. bifasciata" larvae that happens to be inside. However, in inland climates, such as in the San Joaquin Valley, "Aphytis" is less suitable for use and "C. bifasciata" is more effective.


Kono Yasui

 was a Japanese biologist and cytologist. In 1927, she became the first Japanese woman to receive a doctoral degree in science. She received a Medal of Honor with Purple Ribbon and was awarded as an Order of the Precious Crown Third Class for her academic accomplishments and leadership in women’s education in Japan.
Early life and education.
Yasui was born in the town of Sanbonmatsu in Kagawa Prefecture in 1880, to the owner of a shipping business. She was the first child of nine siblings and was raised by parents who valued and emphasized education. When she was moving from lower elementary to higher elementary school, her father persuaded her to read "Encouragement of Learning", a highly influential book written by the philosopher and educator Yukichi Fukuzawa. Throughout her early education, she excelled in her studies, and was particularly gifted in science and mathematics. She graduated from Kagawa Prefecture Normal School in 1898 and the Division of Science at the Women's Higher Normal School in 1902. She taught at Gifu Girls' Higher School and Kanda Girls' School until 1905, when a graduate course was established at the Women's Higher Normal School. She was the first woman to enter the course with a major in science research; she focused on zoology and botany. She published a paper about the Weberian apparatus of carp fish in "Zoological Science" in 1905, becoming the first woman published in the journal. Her research on the aquatic fern "Salvinia natans" was published in the "Journal of Plant Sciences" and the British journal "Annals of Botany", marking the first publication of a Japanese woman's research in a foreign journal. She completed the graduate program at Women's Higher Normal School in 1907 and became an assistant professor at the school.
Academic career.
When Yasui applied to the Japanese Ministry of Education to study abroad, they were hesitant to give her permission because of their belief that “a woman cannot achieve much in science.” She was only allowed on the condition that she listed "home economics research" alongside "scientific research" on her application and that she agreed not to marry and instead commit herself to her research. She traveled to Germany and the United States in 1914 to perform cytological research at the University of Chicago. She travelled to Harvard University in 1915, where she conducted research on coal under Professor E. C. Jeffrey. She returned to Japan in June 1916 and continued researching coal at Tokyo Imperial University (now the University of Tokyo) until 1927. She taught genetics there from 1918 to 1939, and was made a professor at the Women's Higher Normal School in Tokyo in 1919. She completed her doctoral thesis, "Studies on the structure of lignite, brown coal, and bituminous coal in Japan", in 1927, becoming the first woman in Japan to complete a doctorate in science.
In 1929, Yasui founded the cytology journal "Cytologia". From 1924 onwards, she researched the genetics of poppies, corn and "Tradescantia" species, and in 1945 she began a survey of plants that had been affected by nuclear fallout after the atomic bombings of Hiroshima and Nagasaki. When Ochanomizu University was established under its current name in 1949, Yasui was appointed professor. She retired in 1952, becoming a professor emerita. By 1957 she had published a total of 99 scientific papers.
Legacy.
Kono Yasui accomplished a lot of firsts during her life and career as a biologist and cytologist. Her career lasted from the late Meiji period, through the Taisho (1912-1926), to the early Showa period (1926-1989). During this time, women were strongly oppressed in Japan and were all but outlawed from working in research and academia. She was the first Japanese woman to publish an academic paper in an international journal. Most notably, she was the first Japanese woman to receive a doctoral degree in science, and she did so at a university that did not accept female students until almost 20 years later. During her time as a teacher at Tokyo Women’s Higher Normal School, she was very strict and did not treat her students as “girls.” Outside of the laboratory and classroom, however, she was known to be kind to her juniors and students alike. She heavily valued and contributed to the advancement of women’s education in Japan. After World War II, Yasui worked to establish a national university for women. These efforts were successful, as she played a pivotal role in the transformation of Tokyo Women’s Higher Normal School to Ochanomizu University in 1949. She also donated the money received as gifts for her retirement to the Tokyo Women’s Higher Normal School as the “Yasui-Kuroda Scholarship,” which continues to provide educational opportunities for young female researchers today. Kono Yasui’s life has served as a guide and shining example to a whole generation of young women scientists.
Timeline.
(1880) February 16, Born in Kagawa Prefecture
(1905) Published first paper, “Weber’s Organ of Carp Fish,” in the Journal “Zoological Science.”
(1914) Began studying cytology at the University of Chicago
(1915) Began studying coal at Harvard University
(1929) Started the cytology journal, “Cytologia”


Halspiviridae


Virophage

Virophages are small, double-stranded DNA viral phages that require the co-infection of another virus. The co-infecting viruses are typically giant viruses. Virophages rely on the viral replication factory of the co-infecting giant virus for their own replication. One of the characteristics of virophages is that they have a parasitic relationship with the co-infecting virus. Their dependence upon the giant virus for replication often results in the deactivation of the giant viruses. The virophage may improve the recovery and survival of the host organism.
Unlike satellite viruses, virophages have a parasitic effect on their co-infecting virus. Virophages have been observed to render a giant virus inactive and thereby improve the condition of the host organism.
All known virophages are grouped into the family Lavidaviridae (from "large virus dependent or associated" + -viridae).
Discovery.
The first virophage was discovered in a cooling tower in Paris, France in 2008. It was discovered with its co-infecting giant virus, "Acanthamoeba castellanii" mamavirus (ACMV). The virophage was named Sputnik and its replication relied entirely on the co-infection of ACMV and its cytoplasmic replication machinery. Sputnik was also discovered to have an inhibitory effect on ACMV and improved the survival of the host. Other characterised virophages include Sputnik 2, Sputnik 3, Zamilon and Mavirus.
A majority of these virophages are being discovered by analyzing metagenomic data sets. In metagenomic analysis, DNA sequences are run through multiple bioinformatic algorithms which pull out certain important patterns and characteristics. In these data sets are giant viruses and virophages. They are separated by looking for sequences around 17 to 20 kbp long which have similarities to already sequenced virophages. These virophages can have linear or circular double-stranded DNA genomes. Known virophages in culture have icosahedral capsid particles that measure around 40 to 80 nanometers long, and virophage particles are so small that electron microscopy must be used to view them. Metagenomic sequence-based analyses have been used to predict around 57 complete and partial virophage genomes and in December 2019 to identify 328 high-quality (complete or near-complete) genomes from diverse habitats including the human gut, plant rhizosphere, and terrestrial subsurface, from 27 distinct taxonomic clades.
Host range and replication.
Virophages need to have a co-infecting virus in order for them to replicate. The virophages do not have the necessary enzymes to replicate on their own. Virophages use the giant viral replication machinery to replicate their own genomes and continue their existence. The host range for virophages include giant viruses with double stranded DNA genomes. Virophages use the transcriptional machinery of these giant viruses for their own replication instead of the host's transcriptional machinery. For example, the discovery of the virophage associated with the Samba virus decreased the viruses concentration in the host while the virophage was replicating using the giant virus. The host amoeba also showed a partial recovery from the infection by the Samba virus.
Genome.
Virophages have small double-stranded DNA genomes that are either circular or linear in shape. The size of these genomes can vary depending on the giant virus it infects. Most virophages have genomes around 17–30 kbp (kilobasepairs). Their genome is protected by an icosahedral capsid measuring approximately 40–80 nm in length. In contrast, their co-infecting giant virus counterparts can have genomes as large as 1–2 Mbp (megabasepairs). Some of the largest genomes of virophages are similar to the genome size of an adenovirus.
All virophages known so far have four core genes. They are the virophage-specific major and minor capsid proteins (MCP and mCP), PRO (cysteine protease), and a DNA-packaging ATPase. The two capsids are almost universally found in a conserved block. The MCP has two vertical jelly roll fold domain typical of Bamfordvirae, while the mCP (penton) has a regular jelly roll fold domain.
Taxonomy.
The family Lavidaviridae with the two genera, "Sputnikvirus" and "Mavirus", has been established by the International Committee on Taxonomy of Viruses for classification of virophages. It is the sole family under order Priklausovirales (from Lithuanian , "dependent"), which in turn is the sole order under class Maveriviricetes (from Maverick transposons).
Additionally, virophage genomes identified from metagenomes have been classified together with the isolate virophages into 27 distinct clades with consistent genome length, gene content, and habitat distribution. Some fragmentary virophage sequences were additionally reported in a Loki's Castle metagenome.


Sphaerolipoviridae

Sphaerolipoviridae is a family of double-stranded DNA viruses that infect thermophilic bacteria and halophilic archea, formally approved by the International Committee on Taxonomy of Viruses in 2015. Viruses of this family have tailless icosahedral virions with an internal lipid membrane located between the protein capsid and the double-stranded DNA genome. Overall virion organization of sphaerolipoviruses is similar to that of viruses belonging to the families "Tectiviridae", "Corticoviridae" and "Turriviridae".
There are three genera in this family. Members of the genera "Alphasphaerolipovirus" and "Betasphaerolipovirus" infect halophilic archaea, while those of the genus "Gammasphaerolipovirus" replicate in thermophilic bacteria.
The kingdom Helvetiavirae is recognized for its use of single-domain, vertically-folded jelly roll capsids.


Mycobacterium xenopi

Mycobacterium xenopi is a slow-growing scotochromogenic species of "Mycobacterium". It was first reported by Schwabacher in 1959, having been isolated in lesions found on a "Xenopus laevis", but the possibility of human infection was not confirmed until 1965. It has been cultured from hot and cold water taps, hospital hot water generators and storage tanks, and other environmental sources.
It has low pathogenicity in humans, and where infections have been found they are closely associated with immunocompromised individuals, such as an extrapulmonary malignancy, alcoholism, diabetes mellitus, or immunosuppressive therapy. Pulmonary disease may be chronic, subacute, or acute; symptoms are indistinguishable from those associated with disease caused by "M. kansasii".
Radiographic findings with "M. xenopi" pulmonary disease are variable but most often include upper lobe cavitary abnormalities similar to tuberculosis.
On solid media, there is an egg next colony produced.
Treatment is usually with macrolide, rifampin, and ethambutol with moxifloxacin.
Type strain: strain ATCC 19250 = CCUG 28011 = CCUG 31306 = CIP 104035 = DSM 43995 = NCTC 10042.


Wirthbacteria

"Candidatus" Wirthbacteria is a proposed bacterial phylum containing only one known sample from the Crystal Geyser aquifer, "Ca. Wirthibacter wanneri". This bacterium stands out in a basal position in some trees of life as it is closely related to Candidate phyla radiation but is not considered part of that clade.


Plasmodium (life cycle)

A plasmodium is a living structure of cytoplasm that contains many nuclei, rather than being divided into individual cells each with a single nucleus.
Plasmodia are best known from slime molds, but are also found in parasitic Myxosporea, and some algae such as the Chlorarachniophyta.
Structure.
A plasmodium is an amoeboid, multinucleate, and naked mass of cytoplasm that contains many diploid nuclei. The resulting structure, a coenocyte, is created by many nuclear divisions without the process of cytokinesis, which in other organisms pulls newlydivided cells apart. In some cases, the resulting structure is a syncytium, created by the fusion of cells after division. Under suitable conditions, plasmodia differentiates and forms fruiting bodies bearing spores at their tips.
Taxonomic distribution.
The term plasmodium, introduced by Leon Cienkowski, usually refers to the feeding stage of slime molds; these are macroscopic mycetozoans.
The multinucleate developmental stages of some intracellular parasites, namely Microsporidia (now in Fungi) and Myxosporidia (now in Cnidaria), former cnidosporans, are also sometimes called plasmodia.
Similarly, in Rhizaria, the amoeboid, multinucleate protoplasts of some Cercozoan algae, e.g. Chlorarachniophyta, are called plasmodia. These lack cell walls; the syncytia are created by cell fusion. Some plasmodiophorids and haplosporidians are other multinucleated rhizarians.


Fimbriimonas ginsengisoli

Fimbriimonas ginsengisoli is a Gram-negative bacterium and also the first representative of the new class "Fimbriimonadia" 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 "F. ginsengisoli's" relative, "Armatimonas rosea's" discovery.
Discovery.
"F. ginsengisoli" was originally isolated from a soil sample from a ginseng field in the Pocheon province, South Korea. Cultivation took place on one-half strength R2A agar.
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".
"Armatimonas rosea" an aerobic, Gram-negative, pink pigmented, nonmotile, ovoid/rod shaped bacterium, was isolated from the rhizoplane of an aquatic plant "Phragmites australis" in Japan. It is the first representative of the phylum "Armatimonadetes".
Characteristics.
When grown on one-half strength R2A, colonies were ivory pigmented, circular, raised, contained a greasy surface, highly mucoid, and relatively small (1–2 mm) in size after two weeks of incubation at 30 °C. "F. ginsengisoli" has an optimum temperature at 30 °C with a range of 15-30 °C. The optimum pH for growth was 7.0 with a range of 6.0-8.5. Supplementary NaCl was not needed for growth but concentrations up to 1% could be tolerated.
When examined by phase-contrast and transmission electron microscopy cells were observed to be nonmotile, rod shaped, with sizes ranging from 0.5-0.7 µm in width and 2.5-5.0 µm in length. "F. ginsengisoli" carried peritrichous fibrils, which were very fine and hairy and projected out from the cell wall. Spore formation was not observed.
When investigated in one-half R2A media, cultures of "F. ginsengisoli" were observed to be strictly aerobic with no evidence of growth under anaerobic conditions. It is negative for the oxidase test, but positive for the catalase test. It could not use most substrates tested as a sole carbon source but could use peptone, casamino acids or yeast extract as sole carbon sources. The strain did not degrade DNA, starch, xylan, or cellulose.
References.
1. Tamaki, Hideyuki, et al. "Armatimonas rosea gen. nov., sp. nov., of a novel bacterial phylum, Armatimonadetes phyl. nov., formally called the candidate phylum OP10." International Journal of Systematic and Evolutionary Microbiology 61.6 (2011): 1442-1447.http://ijs.sgmjournals.org/content/61/6/1442.short
2. Lee, Kevin C-Y., et al. "Chthonomonas calidirosea gen. nov., sp. nov., an aerobic, pigmented, thermophilic micro-organism of a novel bacterial class, Chthonomonadetes classis nov., of the newly described phylum Armatimonadetes originally designated candidate division OP10." International Journal of Systematic and Evolutionary Microbiology 61.10 (2011): 2482-2490.http://ijsb.sgmjournals.org/content/61/10/2482.short
3. Im, Wan-Taek, et al. "Description of Fimbriimonas ginsengisoli gen. nov., sp. nov. within the Fimbriimonadia class nov., of the phylum Armatimonadetes."Antonie van Leeuwenhoek (2012): 1-11. https://doi.org/10.1007%2Fs10482-012-9739-6


Cleavage furrow

In cell biology, the cleavage furrow is the indentation of the cell's surface that begins the progression of cleavage, by which animal and some algal cells undergo cytokinesis, the final splitting of the membrane, in the process of cell division. The same proteins responsible for muscle contraction, actin and myosin, begin the process of forming the cleavage furrow, creating an actomyosin ring. Other cytoskeletal proteins and actin binding proteins are involved in the procedure.
Mechanism.
Plant cells do not perform cytokinesis through this exact method but the two procedures are not totally different. Animal cells form an actin-myosin contractile ring within the equatorial region of the cell membrane that constricts to form the cleavage furrow. In plant cells, Golgi vesicle secretions form a cell plate or septum on the equatorial plane of the cell wall by the action of microtubules of the phragmoplast. The cleavage furrow in animal cells and the phragmoplast in plant cells are complex structures made up of microtubules and microfilaments that aide in the final separation of the cells into two identical daughter cells.
Cell cycle.
The cell cycle begins with interphase when the DNA replicates, the cell grows and prepares to enter mitosis. Mitosis includes four phases, prophase, metaphase, anaphase, and telophase. Prophase is the initial phase when spindle fibers appear that function to move the chromosomes toward opposite poles. This spindle apparatus consists of microtubules, microfilaments and a complex network of various proteins. During metaphase, the chromosomes line up using the spindle apparatus in the middle of the cell along the equatorial plate. The chromosomes move to opposite poles during anaphase and remain attached to the spindle fibers by their centromeres. Animal cell cleavage furrow formation is caused by a ring of actin microfilaments called the contractile ring, which forms during early anaphase. Myosin is present in the region of the contractile ring as concentrated microfilaments and actin filaments are predominant in this region. The actin filaments here are both pre-existing and new. Cleavage is driven by these motor proteins, actin and myosin, which are the same proteins involved with muscle contraction. During cellular cleavage, the contractile ring tightens around the cytoplasm of the cell until the cytoplasm is pinched into two daughter cells. During the final phase of mitosis, telophase, the furrow forms an intercellular bridge using mitotic spindle fibers. Phosphatidylethanolamine (PE) has been shown to be present during this time which indicates that is may play a role in movement between the plasma membrane and contractile ring. The bridge is then broken and resealed to form two identical daughter cells during cytokinesis. The breakage is formed by microtubules and the resealing is negated by Calcium dependent exocytosis using Golgi vesicles. In comparison, the plant cell septum and the animal cell mid-zone are analogous. Both require vesicular secretions by the Golgi apparatus for resealing and formation of the cytoskeletal network in addition to microtubules and microfilaments for division and movement. The cleavage furrow mechanism in animal cells is a complex network of actin and myosin filaments, Golgi vesicles and Calcium dependent channels enabling the cell to break apart, reseal and form new daughter cells with complete membranes.


Mycobacterium botniense

Mycobacterium botniense is a slowly growing "Mycobacterium", which produces a yellow pigment. It was first isolated from a stream of water. "M. botniense" is most closely related to "Mycobacterium xenopi". Etymology: botniense; of Botnia, referring to the Latin name of the province of Finland from which the isolation was made.
Description.
Microscopy
Colony characteristics
Physiology
Differential characteristics


Eukaryote

Eukaryotes () are organisms whose cells have a nucleus enclosed within a nuclear envelope. Eukaryotes belong to the domain Eukaryota or Eukarya; their name comes from the Greek εὖ ("eu", "well" or "good") and κάρυον ("karyon", "nut" or "kernel"). The domain Eukaryota makes up one of the three domains of life; the prokaryotes Bacteria and Archaea make up the other two domains. The eukaryotes are usually now regarded as having emerged in the Archaea or as a sister of the now cultivated Asgard archaea. Eukaryotes represent a tiny minority of the number of organisms; however, due to their generally much larger size, their collective global biomass is estimated to be about equal to that of prokaryotes. Eukaryotes emerged approximately 2.1-1.6 billion years ago, during the Proterozoic eon, likely as flagellated phagotrophs.
Eukaryotic cells typically contain other membrane-bound organelles such as mitochondria and Golgi apparatus; and chloroplasts can be found in plants and algae. Prokaryotic cells may contain primitive organelles. Eukaryotes may be either unicellular or multicellular, and include many cell types forming different kinds of tissue; in comparison, prokaryotes are typically unicellular. Animals, plants, and fungi are the most familiar eukaryotes; other eukaryotes are sometimes called protists.
Eukaryotes can reproduce both asexually through mitosis and sexually through meiosis and gamete fusion. In mitosis, one cell divides to produce two genetically identical cells. In meiosis, DNA replication is followed by two rounds of cell division to produce four haploid daughter cells. These act as sex cells or gametes. Each gamete has just one set of chromosomes, each a unique mix of the corresponding pair of parental chromosomes resulting from genetic recombination during meiosis.
History of the concept.
The concept of the eukaryote has been attributed to the French biologist Edouard Chatton (1883–1947). The terms prokaryote and eukaryote were more definitively reintroduced by the Canadian microbiologist Roger Stanier and the Dutch-American microbiologist C. B. van Niel in 1962. In his 1937 work "Titres et Travaux Scientifiques", Chatton had proposed the two terms, calling the bacteria prokaryotes and organisms with nuclei in their cells eukaryotes. However he mentioned this in only one paragraph, and the idea was effectively ignored until Chatton's statement was rediscovered by Stanier and van Niel.
In 1905 and 1910, the Russian biologist Konstantin Mereschkowski (1855–1921) argued that plastids were reduced cyanobacteria in a symbiosis with a non-photosynthetic (heterotrophic) host that was itself formed by symbiosis between an amoeba-like host and a bacterium-like cell that formed the nucleus. Plants had thus inherited photosynthesis from cyanobacteria.
In 1967, Lynn Margulis provided microbiological evidence for endosymbiosis as the origin of chloroplasts and mitochondria in eukaryotic cells in her paper, "On the origin of mitosing cells." In the 1970s, Carl Woese explored microbial phylogenetics, studying variations in 16S ribosomal RNA. This helped to uncover the origin of the eukaryotes and the symbiogenesis of two important eukaryote organelles, mitochondria and chloroplasts. In 1977, Woese and George Fox introduced a "third form of life", which they called the Archaebacteria; in 1990, Woese, Otto Kandler and Mark L. Wheelis renamed this the Archaea.
In 1979, G. W. Gould and G. J. Dring suggested that the eukaryotic cell's nucleus came from the ability of Firmicute bacteria to form endospores. In 1987 and later papers, Thomas Cavalier-Smith proposed instead that the membranes of the nucleus and endoplasmic reticulum first formed by infolding a prokaryote's plasma membrane. In the 1990s, several other biologists proposed endosymbiotic origins for the nucleus, effectively reviving Mereschkowski's theory.
Cell features.
Eukaryotic cells are typically much larger than those of prokaryotes, having a volume of around 10,000 times greater than the prokaryotic cell. They have a variety of internal membrane-bound structures, called organelles, and a cytoskeleton composed of microtubules, microfilaments, and intermediate filaments, which play an important role in defining the cell's organization and shape. Eukaryotic DNA is divided into several linear bundles called chromosomes, which are separated by a microtubular spindle during nuclear division.
Internal membrane.
Eukaryote cells include a variety of membrane-bound structures, collectively referred to as the endomembrane system. Simple compartments, called vesicles and vacuoles, can form by budding off other membranes. Many cells ingest food and other materials through a process of endocytosis, where the outer membrane invaginates and then pinches off to form a vesicle. It is probable that most other membrane-bound organelles are ultimately derived from such vesicles. Alternatively some products produced by the cell can leave in a vesicle through exocytosis.
The nucleus is surrounded by a double membrane known as the nuclear envelope, with nuclear pores that allow material to move in and out. Various tube- and sheet-like extensions of the nuclear membrane form the endoplasmic reticulum, which is involved in protein transport and maturation. It includes the rough endoplasmic reticulum where ribosomes are attached to synthesize proteins, which enter the interior space or lumen. Subsequently, they generally enter vesicles, which bud off from the smooth endoplasmic reticulum. In most eukaryotes, these protein-carrying vesicles are released and further modified in stacks of flattened vesicles (cisternae), the Golgi apparatus.
Vesicles may be specialized for various purposes. For instance, lysosomes contain digestive enzymes that break down most biomolecules in the cytoplasm. Peroxisomes are used to break down peroxide, which is otherwise toxic. Many protozoans have contractile vacuoles, which collect and expel excess water, and extrusomes, which expel material used to deflect predators or capture prey. In higher plants, most of a cell's volume is taken up by a central vacuole, which mostly contains water and primarily maintains its osmotic pressure.
Mitochondria.
 Mitochondria are organelles found in all but one eukaryote. Mitochondria provide energy to the eukaryote cell by oxidising sugars or fats and releasing energy as ATP. They have two surrounding membranes, each a phospholipid bi-layer; the inner of which is folded into invaginations called cristae where aerobic respiration takes place.
The outer mitochondrial membrane is freely permeable and allows almost anything to enter into the intermembrane space while the inner mitochondrial membrane is semi permeable so allows only some required things into the mitochondrial matrix.
Mitochondria contain their own DNA, which has close structural similarities to bacterial DNA, and which encodes rRNA and tRNA genes that produce RNA which is closer in structure to bacterial RNA than to eukaryote RNA. They are now generally held to have developed from endosymbiotic prokaryotes, probably proteobacteria.
Some eukaryotes, such as the metamonads such as "Giardia" and "Trichomonas", and the amoebozoan "Pelomyxa", appear to lack mitochondria, but all have been found to contain mitochondrion-derived organelles, such as hydrogenosomes and mitosomes, and thus have lost their mitochondria secondarily. They obtain energy by enzymatic action on nutrients absorbed from the environment. The metamonad "Monocercomonoides" has also acquired, by lateral gene transfer, a cytosolic sulfur mobilisation system which provides the clusters of iron and sulfur required for protein synthesis. The normal mitochondrial iron-sulfur cluster pathway has been lost secondarily.
Plastids.
Plants and various groups of algae also have plastids. Plastids also have their own DNA and are developed from endosymbionts, in this case cyanobacteria. They usually take the form of chloroplasts which, like cyanobacteria, contain chlorophyll and produce organic compounds (such as glucose) through photosynthesis. Others are involved in storing food. Although plastids probably had a single origin, not all plastid-containing groups are closely related. Instead, some eukaryotes have obtained them from others through secondary endosymbiosis or ingestion. The capture and sequestering of photosynthetic cells and chloroplasts occurs in many types of modern eukaryotic organisms and is known as kleptoplasty.
Endosymbiotic origins have also been proposed for the nucleus, and for eukaryotic flagella.
Cytoskeletal structures.
Many eukaryotes have long slender motile cytoplasmic projections, called flagella, or similar structures called cilia. Flagella and cilia are sometimes referred to as undulipodia, and are variously involved in movement, feeding, and sensation. They are composed mainly of tubulin. These are entirely distinct from prokaryotic flagellae. They are supported by a bundle of microtubules arising from a centriole, characteristically arranged as nine doublets surrounding two singlets. Flagella also may have hairs, or mastigonemes, and scales connecting membranes and internal rods. Their interior is continuous with the cell's cytoplasm.
Microfilamental structures composed of actin and actin binding proteins, e.g., α-actinin, fimbrin, filamin are present in submembranous cortical layers and bundles, as well. Motor proteins of microtubules, e.g., dynein or kinesin and actin, e.g., myosins provide dynamic character of the network.
Centrioles are often present even in cells and groups that do not have flagella, but conifers and flowering plants have neither. They generally occur in groups that give rise to various microtubular roots. These form a primary component of the cytoskeletal structure, and are often assembled over the course of several cell divisions, with one flagellum retained from the parent and the other derived from it. Centrioles produce the spindle during nuclear division.
The significance of cytoskeletal structures is underlined in the determination of shape of the cells, as well as their being essential components of migratory responses like chemotaxis and chemokinesis. Some protists have various other microtubule-supported organelles. These include the radiolaria and heliozoa, which produce axopodia used in flotation or to capture prey, and the haptophytes, which have a peculiar flagellum-like organelle called the haptonema.
Cell wall.
The cells of plants and algae, fungi and most chromalveolates have a cell wall, a layer outside the cell membrane, providing the cell with structural support, protection, and a filtering mechanism. The cell wall also prevents over-expansion when water enters the cell.
The major polysaccharides making up the primary cell wall of land plants are cellulose, hemicellulose, and pectin. The cellulose microfibrils are linked via hemicellulosic tethers to form the cellulose-hemicellulose network, which is embedded in the pectin matrix. The most common hemicellulose in the primary cell wall is xyloglucan.
Differences among eukaryotic cells.
There are many different types of eukaryotic cells, though animals and plants are the most familiar eukaryotes, and thus provide an excellent starting point for understanding eukaryotic structure. Fungi and many protists have some substantial differences, however.
Animal cell.
All animals are eukaryotic. Animal cells are distinct from those of other eukaryotes, most notably plants, as they lack cell walls and chloroplasts and have smaller vacuoles. Due to the lack of a cell wall, animal cells can transform into a variety of shapes. A phagocytic cell can even engulf other structures.
Plant cell.
Plant cells are quite different from the cells of the other eukaryotic organisms. Their distinctive features are:
Fungal cell.
The cells of fungi are similar to animal cells, with the following exceptions:
Other eukaryotic cells.
Some groups of eukaryotes have unique organelles, such as the cyanelles (unusual chloroplasts) of the glaucophytes, the haptonema of the haptophytes, or the ejectosomes of the cryptomonads. Other structures, such as pseudopodia, are found in various eukaryote groups in different forms, such as the lobose amoebozoans or the reticulose foraminiferans.
Reproduction.
Cell division generally takes place asexually by mitosis, a process that allows each daughter nucleus to receive one copy of each chromosome. Most eukaryotes also have a life cycle that involves sexual reproduction, alternating between a haploid phase, where only one copy of each chromosome is present in each cell and a diploid phase, wherein two copies of each chromosome are present in each cell. The diploid phase is formed by fusion of two haploid gametes to form a zygote, which may divide by mitosis or undergo chromosome reduction by meiosis. There is considerable variation in this pattern. Animals have no multicellular haploid phase, but each plant generation can consist of haploid and diploid multicellular phases.
Eukaryotes have a smaller surface area to volume ratio than prokaryotes, and thus have lower metabolic rates and longer generation times.
The evolution of sexual reproduction may be a primordial and fundamental characteristic of eukaryotes. Based on a phylogenetic analysis, Dacks and Roger proposed that facultative sex was present in the common ancestor of all eukaryotes. A core set of genes that function in meiosis is present in both "Trichomonas vaginalis" and "Giardia intestinalis", two organisms previously thought to be asexual. Since these two species are descendants of lineages that diverged early from the eukaryotic evolutionary tree, it was inferred that core meiotic genes, and hence sex, were likely present in a common ancestor of all eukaryotes. Eukaryotic species once thought to be asexual, such as parasitic protozoa of the genus "Leishmania", have been shown to have a sexual cycle. Also, evidence now indicates that amoebae, previously regarded as asexual, are anciently sexual and that the majority of present-day asexual groups likely arose recently and independently.
Classification.
In antiquity, the two lineages of animals and plants were recognized. They were given the taxonomic rank of Kingdom by Linnaeus. Though he included the fungi with plants with some reservations, it was later realized that they are quite distinct and warrant a separate kingdom, the composition of which was not entirely clear until the 1980s. The various single-cell eukaryotes were originally placed with plants or animals when they became known. In 1818, the German biologist Georg A. Goldfuss coined the word "protozoa" to refer to organisms such as ciliates, and this group was expanded until it encompassed all single-celled eukaryotes, and given their own kingdom, the Protista, by Ernst Haeckel in 1866. The eukaryotes thus came to be composed of four kingdoms:
The protists were understood to be "primitive forms", and thus an evolutionary grade, united by their primitive unicellular nature. The disentanglement of the deep splits in the tree of life only really started with DNA sequencing, leading to a system of domains rather than kingdoms as top level rank being put forward by Carl Woese, uniting all the eukaryote kingdoms under the eukaryote domain. At the same time, work on the protist tree intensified, and is still actively going on today. Several alternative classifications have been forwarded, though there is no consensus in the field.
Eukaryotes are a clade usually assessed to be sister to Heimdallarchaeota in the Asgard grouping in the Archaea. In one proposed system, the basal groupings are the Opimoda, Diphoda, the Discoba, and the Loukozoa. The Eukaryote root is usually assessed to be near or even in Discoba.
A classification produced in 2005 for the International Society of Protistologists, which reflected the consensus of the time, divided the eukaryotes into six supposedly monophyletic 'supergroups'. However, in the same year (2005), doubts were expressed as to whether some of these supergroups were monophyletic, particularly the Chromalveolata, and a review in 2006 noted the lack of evidence for several of the supposed six supergroups. A revised classification in 2012 recognizes five supergroups.
There are also smaller groups of eukaryotes whose position is uncertain or seems to fall outside the major groups – in particular, Haptophyta, Cryptophyta, Centrohelida, Telonemia, Picozoa, Apusomonadida, Ancyromonadida, Breviatea, and the genus "Collodictyon". Overall, it seems that, although progress has been made, there are still very significant uncertainties in the evolutionary history and classification of eukaryotes. As Roger & Simpson said in 2009 "with the current pace of change in our understanding of the eukaryote tree of life, we should proceed with caution." Newly identified protists, purported to represent novel, deep-branching lineages, continue to be described well into the 21st century; recent examples including "Rhodelphis", putative sister group to Rhodophyta, and "Anaeramoeba", anaerobic amoebaflagellates of uncertain placement.
Phylogeny.
The rRNA trees constructed during the 1980s and 1990s left most eukaryotes in an unresolved "crown" group (not technically a true crown), which was usually divided by the form of the mitochondrial cristae; see crown eukaryotes. The few groups that lack mitochondria branched separately, and so the absence was believed to be primitive; but this is now considered an artifact of long-branch attraction, and they are known to have lost them secondarily.
, there is widespread agreement that the Rhizaria belong with the Stramenopiles and the Alveolata, in a clade dubbed the SAR supergroup, so that Rhizaria is not one of the main eukaryote groups; also that the Amoebozoa and Opisthokonta are each monophyletic and form a clade, often called the unikonts. Beyond this, there does not appear to be a consensus.
It has been estimated that there may be 75 distinct lineages of eukaryotes. Most of these lineages are protists.
The known eukaryote genome sizes vary from 8.2 megabases (Mb) in "Babesia bovis" to 112,000–220,050 Mb in the dinoflagellate "Prorocentrum micans", showing that the genome of the ancestral eukaryote has undergone considerable variation during its evolution. The last common ancestor of all eukaryotes is believed to have been a phagotrophic protist with a nucleus, at least one centriole and cilium, facultatively aerobic mitochondria, sex (meiosis and syngamy), a dormant cyst with a cell wall of chitin and/or cellulose and peroxisomes. Later endosymbiosis led to the spread of plastids in some lineages.
Five supergroups.
A global tree of eukaryotes from a consensus of phylogenetic evidence (in particular, phylogenomics), rare genomic signatures, and morphological characteristics is presented in Adl "et al." 2012 and Burki 2014/2016 with the picozoa having emerged within the Archaeplastida, and Cryptista as its sister. Possibly, TSAR is sister to the Haptista.
In some analyses, the Hacrobia group (Haptophyta + Cryptophyta) is placed next to Archaeplastida, but in other ones it is nested inside the Archaeplastida. However, several recent studies have concluded that Haptophyta and Cryptophyta do not form a monophyletic group. The former could be a sister group to the SAR group, the latter cluster with the Archaeplastida (plants in the broad sense).
The division of the eukaryotes into two primary clades, bikonts (Archaeplastida + SAR + Excavata) and unikonts (Amoebozoa + Opisthokonta), derived from an ancestral biflagellar organism and an ancestral uniflagellar organism, respectively, had been suggested earlier. A 2012 study produced a somewhat similar division, although noting that the terms "unikonts" and "bikonts" were not used in the original sense.
A highly converged and congruent set of trees appears in Derelle et al. (2015), Ren et al. (2016), Yang et al. (2017) and Cavalier-Smith (2015) including the supplementary information, resulting in a more conservative and consolidated tree. It is combined with some results from Cavalier-Smith for the basal Opimoda. The main remaining controversies are the root, and the exact positioning of the Rhodophyta and the bikonts Rhizaria, Haptista, Cryptista, Picozoa and Telonemia, many of which may be endosymbiotic eukaryote-eukaryote hybrids. Archaeplastida acquired chloroplasts probably by endosymbiosis of a prokaryotic ancestor related to a currently extant cyanobacterium, "Gloeomargarita lithophora".
Cavalier-Smith's tree.
Thomas Cavalier-Smith 2010, 2013, 2014, 2017 and 2018 places the eukaryotic tree's root between Excavata (with ventral feeding groove supported by a microtubular root) and the grooveless Euglenozoa, and monophyletic Chromista, correlated to a single endosymbiotic event of capturing a red-algae. He et al. specifically supports rooting the eukaryotic tree between a monophyletic Discoba (Discicristata + Jakobida) and an Amorphea-Diaphoretickes clade.
Origin of eukaryotes.
The origin of the eukaryotic cell is a milestone in the evolution of life, since eukaryotes include all complex cells and almost all multicellular organisms. A number of approaches have been used to find the first eukaryote and their closest relatives. The last eukaryotic common ancestor (LECA) is the hypothetical last common ancestor of all eukaryotes that have ever lived, and was most likely a biological population.
Eukaryotes have a number of features that differentiate them from prokaryotes, including an endomembrane system, and unique biochemical pathways such as sterane synthesis. A set of proteins called eukaryotic signature proteins (ESPs) was proposed to identify eukaryotic relatives in 2002: they have no homology to proteins known in other domains of life by then, but they appear to be universal among eukaryotes. They include proteins that make up the cytoskeleton, the complex transcription machinery, membrane-sorting systems, the nuclear pore, as well as some enzymes in the biochemical pathways.
Fossils.
The timing of this series of events is hard to determine; Knoll (2006) suggests they developed approximately 1.6–2.1 billion years ago. Some acritarchs are known from at least 1.65 billion years ago, and the possible alga "Grypania" has been found as far back as 2.1 billion years ago. The "Geosiphon"-like fossil fungus "Diskagma" has been found in paleosols 2.2 billion years old.
Organized living structures have been found in the black shales of the Palaeoproterozoic Francevillian B Formation in Gabon, dated at 2.1 billion years old. Eukaryotic life could have evolved at that time. Fossils that are clearly related to modern groups start appearing an estimated 1.2 billion years ago, in the form of a red algae, though recent work suggests the existence of fossilized filamentous algae in the Vindhya basin dating back perhaps to 1.6 to 1.7 billion years ago.
Biomarkers suggest that at least stem eukaryotes arose even earlier. The presence of steranes in Australian shales indicates that eukaryotes were present in these rocks dated at 2.7 billion years old, although it was suggested they could originate from samples contamination.
Whenever their origins, eukaryotes may not have become ecologically dominant until much later; a massive uptick in the zinc composition of marine sediments has been attributed to the rise of substantial populations of eukaryotes, which preferentially consume and incorporate zinc relative to prokaryotes.
In April 2019, biologists reported that the very large medusavirus, or a relative, may have been responsible, at least in part, for the evolutionary emergence of complex eukaryotic cells from simpler prokaryotic cells.
Relationship to Archaea.
The nuclear DNA and genetic machinery of eukaryotes is more similar to Archaea than Bacteria, leading to a controversial suggestion that eukaryotes should be grouped with Archaea in the clade Neomura. In other respects, such as membrane composition, eukaryotes are similar to Bacteria. Three main explanations for this have been proposed:
Alternative proposals include:
Assuming no other group is involved, there are three possible phylogenies for the Bacteria, Archaea and Eukaryota in which each is monophyletic. These are labelled 1 to 3 in the table below. The eocyte hypothesis is a modification of hypothesis 2 in which the Archaea are paraphyletic. (The table and the names for the hypotheses are based on Harish and Kurland, 2017.)
In recent years, most researchers have favoured either the three domains (3D) or the eocyte hypothesis. An rRNA analyses supports the eocyte scenario, apparently with the Eukaryote root in Excavata. A cladogram supporting the eocyte hypothesis, positioning eukaryotes within Archaea, based on phylogenomic analyses of the Asgard archaea, is:
In this scenario, the Asgard group is seen as a sister taxon of the TACK group, which comprises Crenarchaeota (formerly named eocytes), Thaumarchaeota, and others. This group is reported contain many of the eukaryotic signature proteins and produce vesicles.
In 2017, there has been significant pushback against this scenario, arguing that the eukaryotes did not emerge within the Archaea. Cunha "et al." produced analyses supporting the three domains (3D) or Woese hypothesis (2 in the table above) and rejecting the eocyte hypothesis (4 above). Harish and Kurland found strong support for the earlier two empires (2D) or Mayr hypothesis (1 in the table above), based on analyses of the coding sequences of protein domains. They rejected the eocyte hypothesis as the least likely. A possible interpretation of their analysis is that the universal common ancestor (UCA) of the current tree of life was a complex organism that survived an evolutionary bottleneck, rather than a simpler organism arising early in the history of life. On the other hand, the researchers who came up with Asgard re-affirmed their hypothesis with additional Asgard samples.
Details of the relation of Asgard archaea members and eukaryotes are still under consideration, although, in January 2020, scientists reported that "Candidatus Prometheoarchaeum syntrophicum", a type of cultured Asgard archaea, may be a possible link between simple prokaryotic and complex eukaryotic microorganisms about two billion years ago.
Endomembrane system and mitochondria.
The origins of the endomembrane system and mitochondria are also unclear. The phagotrophic hypothesis proposes that eukaryotic-type membranes lacking a cell wall originated first, with the development of endocytosis, whereas mitochondria were acquired by ingestion as endosymbionts. The syntrophic hypothesis proposes that the proto-eukaryote relied on the proto-mitochondrion for food, and so ultimately grew to surround it. Here the membranes originated after the engulfment of the mitochondrion, in part thanks to mitochondrial genes (the hydrogen hypothesis is one particular version).
In a study using genomes to construct supertrees, Pisani "et al." (2007) suggest that, along with evidence that there was never a mitochondrion-less eukaryote, eukaryotes evolved from a syntrophy between an archaea closely related to Thermoplasmatales and an alphaproteobacterium, likely a symbiosis driven by sulfur or hydrogen. The mitochondrion and its genome is a remnant of the alphaproteobacterial endosymbiont. The majority of the genes from the symbiont have been transferred to the nucleus. They make up most of the metabolic and energy-related pathways of the eukaryotic cell, while the information system (DNA polymerase, transcription, translation) is retained from archaea.
Hypotheses.
Different hypotheses have been proposed as to how eukaryotic cells came into existence. These hypotheses can be classified into two distinct classes – autogenous models and chimeric models.
Autogenous models.
Autogenous models propose that a proto-eukaryotic cell containing a nucleus existed first, and later acquired mitochondria. According to this model, a large prokaryote developed invaginations in its plasma membrane in order to obtain enough surface area to service its cytoplasmic volume. As the invaginations differentiated in function, some became separate compartments – giving rise to the endomembrane system, including the endoplasmic reticulum, golgi apparatus, nuclear membrane, and single membrane structures such as lysosomes.
Mitochondria are proposed to come from the endosymbiosis of an aerobic proteobacterium, and it is assumed that all the eukaryotic lineages that did not acquire mitochondria became extinct. Chloroplasts came about from another endosymbiotic event involving cyanobacteria. Since all known eukaryotes have mitochondria, but not all have chloroplasts, the serial endosymbiotic theory proposes that mitochondria came first.
Chimeric models.
Chimeric models claim that two prokaryotic cells existed initially – an archaeon and a bacterium. The closest living relatives of these appears to be Asgardarchaeota and (distantly related) the alphaproteobacteria called the proto-mitochondrion. These cells underwent a merging process, either by a physical fusion or by endosymbiosis, thereby leading to the formation of a eukaryotic cell. Within these chimeric models, some studies further claim that mitochondria originated from a bacterial ancestor while others emphasize the role of endosymbiotic processes behind the origin of mitochondria.
The inside-out hypothesis.
The inside-out hypothesis suggests that the fusion between free-living mitochondria-like bacteria, and an archaeon into a eukaryotic cell happened gradually over a long period of time, instead of in a single phagocytotic event. In this scenario, an archaeon would trap aerobic bacteria with cell protrusions, and then keep them alive to draw energy from them instead of digesting them. During the early stages the bacteria would still be partly in direct contact with the environment, and the archaeon would not have to provide them with all the required nutrients. But eventually the archaeon would engulf the bacteria completely, creating the internal membrane structures and nucleus membrane in the process.
It is assumed the archaean group called halophiles went through a similar procedure, where they acquired as much as a thousand genes from a bacterium, way more than through the conventional horizontal gene transfer that often occurs in the microbial world, but that the two microbes separated again before they had fused into a single eukaryote-like cell.
An expanded version of the inside-out hypothesis proposes that the eukaryotic cell was created by physical interactions between two prokaryotic organisms and that the last common ancestor of eukaryotes got its genome from a whole population or community of microbes participating in cooperative relationships to thrive and survive in their environment. The genome from the various types of microbes would complement each other, and occasional horizontal gene transfer between them would be largely to their own benefit. This accumulation of beneficial genes gave rise to the genome of the eukaryotic cell, which contained all the genes required for independence.
The serial endosymbiotic hypothesis.
According to serial endosymbiotic theory (championed by Lynn Margulis), a union between a motile anaerobic bacterium (like "Spirochaeta") and a thermoacidophilic crenarchaeon (like "Thermoplasma" which is sulfidogenic in nature) gave rise to the present day eukaryotes. This union established a motile organism capable of living in the already existing acidic and sulfurous waters. Oxygen is known to cause toxicity to organisms that lack the required metabolic machinery. Thus, the archaeon provided the bacterium with a highly beneficial reduced environment (sulfur and sulfate were reduced to sulfide). In microaerophilic conditions, oxygen was reduced to water thereby creating a mutual benefit platform. The bacterium on the other hand, contributed the necessary fermentation products and electron acceptors along with its motility feature to the archaeon thereby gaining a swimming motility for the organism.
From a consortium of bacterial and archaeal DNA originated the nuclear genome of eukaryotic cells. Spirochetes gave rise to the motile features of eukaryotic cells. Endosymbiotic unifications of the ancestors of alphaproteobacteria and cyanobacteria, led to the origin of mitochondria and plastids respectively. For example, "Thiodendron" has been known to have originated via an ectosymbiotic process based on a similar syntrophy of sulfur existing between the two types of bacteria – "Desulfobacter" and "Spirochaeta".
However, such an association based on motile symbiosis has never been observed practically. Also there is no evidence of archaeans and spirochetes adapting to intense acid-based environments.
The hydrogen hypothesis.
In the hydrogen hypothesis, the symbiotic linkage of an anaerobic and autotrophic methanogenic archaeon (host) with an alphaproteobacterium (the symbiont) gave rise to the eukaryotes. The host utilized hydrogen (H2) and carbon dioxide () to produce methane while the symbiont, capable of aerobic respiration, expelled H2 and as byproducts of anaerobic fermentation process. The host's methanogenic environment worked as a sink for H2, which resulted in heightened bacterial fermentation.
Endosymbiotic gene transfer acted as a catalyst for the host to acquire the symbionts' carbohydrate metabolism and turn heterotrophic in nature. Subsequently, the host's methane forming capability was lost. Thus, the origins of the heterotrophic organelle (symbiont) are identical to the origins of the eukaryotic lineage. In this hypothesis, the presence of H2 represents the selective force that forged eukaryotes out of prokaryotes.
The syntrophy hypothesis.
The syntrophy hypothesis was developed in contrast to the hydrogen hypothesis and proposes the existence of two symbiotic events. According to this model, the origin of eukaryotic cells was based on metabolic symbiosis (syntrophy) between a methanogenic archaeon and a deltaproteobacterium. This syntrophic symbiosis was initially facilitated by H2 transfer between different species under anaerobic environments. In earlier stages, an alphaproteobacterium became a member of this integration, and later developed into the mitochondrion. Gene transfer from a deltaproteobacterium to an archaeon led to the methanogenic archaeon developing into a nucleus. The archaeon constituted the genetic apparatus, while the deltaproteobacterium contributed towards the cytoplasmic features.
This theory incorporates two selective forces at the time of nucleus evolution
6+ serial endosymbiosis scenario.
A complex scenario of 6+ serial endosymbiotic events of archaea and bacteria has been proposed in which mitochondria and an asgard related archaeota were acquired at a late stage of eukaryogenesis, possibly in combination, as a secondary endosymbiont. The findings have been rebuked as an artefact.


Mycobacterium fallax

Mycobacterium fallax is a species of the phylum Actinobacteria (Gram-positive bacteria with high guanine and cytosine content, one of the dominant phyla of all bacteria), belonging to the genus "Mycobacterium".
Description.
Gram-positive, nonmotile and acid-fast rods (0.5 – 1 µm long) except for a small number (less than 20%) of cyanophil forms.
Colony characteristics
Physiology
Differential characteristics


Malassezia vespertilionis

Malassezia vespertilionis is a species of yeast-like fungus that grows on the skin of bats. It was described as a new species in 2018. The holotype was obtained from a swab of wing skin of a hibernating northern long-eared bat ("Myotis septentrionalis") collected in Wisconsin. The species epithet "vespertilionis" uses the Latin "vespertilio" (bat) to refer to the host.
Additional isolates were collected from various bat species in several locations in the United States – Alabama, California, Kentucky, Missouri, New York, Pennsylvania, and Wisconsin. Other bat species that harbor the fungus are the California myotis ("Myotis californicus"), the fringed myotis ("Myotis thysanodes"), the Indiana bat ("Myotis sodalis"), the little brown bat ("Myotis lucifugus"), the gray bat ("Myotis grisescens"), and the silver-haired bat ("Lasionycteris noctivagans"). The fungus appears to be fairly common on bats found in the United States, occurring in 28% of 264 individuals sampled.
Description.
When grown on Leeming and Notman agar (LNA), colonies of "Malassezia vespertilionis" are about in diameter after 10 days of growth at ; this increases to about after 40 days. The fungus was able to grow at a variety of temperatures ranging from , but grew best at . The cells have an ellipsoid or ovoid shape (in rare instances they are spherical), ranging in size from 2–3 by 2–4 μm, although 2 by 3 μm is the usual size.


Discoplastis

Discoplastis is a genus of algae belonging to the family Phacidae.
The species of this genus are found in Europe, Northern America, Southeastern Asia and Australia.
Species:


Cucullanus petterae

Cucullanus petterae is a species of parasitic nematodes. It is an endoparasite of fish, the Honeycomb grouper "Epinephelus merra" (Serranidae, Perciformes), which is the type-host, and the Blacktip grouper "Epinephelus fasciatus". The species has been described in 2020 by František Moravec & Jean-Lou Justine from material collected off New Caledonia in the South Pacific Ocean.
The name of the species honours Annie Petter, eminent French nematodologist (1932-2017).


Mycobacterium cookii

Mycobacterium cookii is a species of the phylum Actinobacteria (Gram-positive bacteria with high guanine and cytosine content, one of the dominant phyla of all bacteria), belonging to the genus "Mycobacterium".
Description.
Gram-positive, nonmotile and polymorphic acid-fast rods (0.8 µm x 1.4–1.9 µm). Forms clumps, but not cords or cross bands. Does not form spores, capsules and aerial hyphae.
Colony characteristics
Physiology
Differential characteristics
Type strain.
Strain NZ2 = ATCC 49103 = CIP 105396 = DSM 43922 = JCM 12404.


Uaithne

In Irish mythology, Uaithne () is The Dagda's harper. Uaithne (Uaitniu) could mean "wood", "work", "pillar" or "harmony". Those different meanings could be the consequence of successive metaphors.
The Dagda's harp is called Daur da Bláo, The Oak of Two Blossoms, and sometimes Coir cethar chuir, the Four Angled Music.
After the Second Battle of Mag Tuired the Fomorians had taken The Dagda's harp with them. The Dagda found it in a feasting-house wherein Bres and his father Elathan were also. The Dagda had bound the music so that it would not sound until he would call to it. After he called to it, it sprang from the wall, came to the Dagda and killed nine men on its way.
"An Uaithne" is also the original name of Irish choir Anúna.
In The Cattle-Raid of Fraech, its name is given as meaning 'Child-Birth', and that Boannd has three sons that were the three 'chants' of Uaithne. The Sorrow-strain, Joy-strain and Sleep strain, stating the origin of these three as "The time the woman was at the bearing of children it had a cry of sorrow with the soreness of the pangs at first: it was smile and joy it played in the middle for the pleasure of bringing forth the two sons: it was a sleep of soothingness played the last son, on account of the heaviness of the birth, so that it is from him that the third of the music has been named."