D-value (microbiology)

In microbiology, in the context of a sterilization procedure, the D-value or decimal reduction time (or decimal reduction dose) is the time (or dose) required, at a given condition (e.g. temperature) or set of conditions, to achieve a log reduction, that is, to kill 90% (or 1 log) of relevant microorganisms. A D-value is denoted with the capital letter "D". Thus, after an exposure time of 1 D, only 10% of the organisms originally present in a microbial colony would remain. The term originated in assessments of microbes' thermal resistance and in thermal death time analysis; however, it now has analogous uses in other microbial resistance and death rate applications, such as for ethylene oxide and radiation processing.
Details.
Use of D-values is based on the assumption that the procedure in question causes the number of living microorganisms to decay exponentially. From this perspective, D-values can be understood as roughly analogous to half lives of radioactive substances, however a half life involves a reduction of 50% rather than 90%. The half life is actually roughly 30% () of the D-value, so if D = 10 minutes, the number of living microorganisms will be halved in about 3 minutes.
Generally, each lot of a sterilization-resistant organism will have its own specific D-value. Determining a D-value requires an experiment, but only gives the D-value under the specific conditions of that experiment. D-values are unique to the conditions of the environment that the bacteria currently exists in.
In the context of thermal analysis it is typical practice to subscript the "D" with an indication of temperature. For example, given a hypothetical organism which is reduced by 90% after exposure to temperatures of 150° C for 20 minutes, the D-value would be written as D150C = 20 minutes. In the US, the temperature is usually indicated in degrees Fahrenheit; a notation like D230 should be understood to mean D230F (D110C). When describing D-value generally for any temperature, like in the heading of a table, a common abbreviation is D"T" (where "T" stands for the temperature), where specific values for "T" may be given elsewhere. A numeric subscript may also be used to indicate some other level of reduction than 90%; for example, D10 denotes the time required for a 10% reduction.
D-values are sometimes used to express a disinfectant's efficiency in reducing the number of microbes present in a given environment.


Rhizoclosmatium

Rhizoclosmatium is a genus of fungi classified in the family Chytriomycetaceae. It was circumscribed by Danish mycologist Henning Eiler Petersen in 1903. The genus contains four species.


Mycobacterium caprae

Mycobacterium caprae is a species of bacteria in the genus "Mycobacterium" and a member of the Mycobacterium tuberculosis complex. Prior to 2003, the species was referred to as "Mycobacterium tuberculosis" subsp. caprae.
It is also synonymous with the name "Mycobacterium bovis" subsp. caprae.
"M. caprae" is a causative agent of tuberculosis in humans. The species has also been isolated from tuberculous lesions in cattle, pigs, deer, and wild boars, as well as from camels and bison.


Nikolai Cholodny

Nikolai Grigoryevich Cholodny (; 22 June 1882 – 4 May 1953) was an influential microbiologist who worked at the University of Kiev, Ukraine in the USSR during the 1930s.
He is known for the Cholodny–Went model, which he developed independently with Frits Warmolt Went of the California Institute of Technology.
Despite being associated with the same theory, the two men never actually met.
Cholodny worked in the A.V. Fomin Botanical Garden, attached to the University of Kiev.
He was one of the pioneers of the concept that microbes adhere to surfaces,
using the technique of first placing glass slides in earth for a measured time period,
then using a microscope to examine the slides.
The Prokaryote "Leptothrix cholodnii" is named after him.
In 1927 Cholodny proposed that the cells of the coleoptile are first polarized under the influence of uneven exposure to light, so growth hormone can diffuse more rapidly towards the side in the shade than in any other direction.
Went reached the same conclusion in 1928, and the two scientists' names have been attached to the controversial Cholodny–Went theory.
Bibliography.
Selected works include:
In 1937 N. G. Cholodny and E. Ch. Sankewitsch published an article on "Influence of weak electric currents upon the growth of the coleoptile" in "Plant Physiology".
The same year he published an article on "Charles Darwin and the modern theory of tropisms" in "Science" magazine.


Biology Direct

Biology Direct is an online open access scientific journal that publishes original, peer-reviewed research papers, reviews, hypotheses, comments and discovery notes in biology. The journal is published by BioMed Central.
The journal follows a peer review system which is different from the traditional peer review system, which aims to give more responsibility to authors, and reduce sources of bias. Published articles include signed reviewer reports, and responses to the reports from the authors, to provide readers with an additional guide to the article.
Based on the information presented on their website: "Biology Direct's key aim is to provide authors and readers with an alternative to the traditional model of peer review. This includes making the author responsible for selecting potentially suitable reviewers for their manuscript, from the journal's Editorial Board; making the peer review process open rather than anonymous; and making the reviewers' reports public, thus increasing the responsibility of the referees and eliminating sources of abuse in the refereeing process."


Puccinia sparganioides

Puccinia sparganioides is a parasitic fungus that causes rust disease on plants including "Spartina alterniflora".


Kyrpidia tusciae

Kyrpidia tusciae is a species of Gram positive, facultatively anaerobic, thermophilic bacterium. The cells are rod-shaped and form spores.
"K. tusciae" was first isolated from ponds in a fumerole in Tuscany, Italy. It was originally classified as "Bacillus tusciae" in 1984, but in 2011 further tests led to the creation of the genus "Kyrpidia", of which "K. tusciae" was the first and only member.
The optimum growth temperature for "K. tusciae" is 55 °C, and can grow in the 42-67 °C range. Its optimum pH is 4.2-4.8, and grows in pH range 4.2-7.5.


Joel Dudley

Joel Dudley is currently Associate Professor of Genetics and Genomic Sciences and founding Director of the Institute for Next Generation Healthcare at the Icahn School of Medicine at Mount Sinai. In March, 2018 Dr. Dudley was named Executive Vice President for Precision Health for the Mount Sinai Health System (MSHS). In 2017 he was awarded an Endowed Professorship by Mount Sinai in Biomedical Data Science. Prior to Mount Sinai, he held positions as Co-founder and Director of Informatics at NuMedii, Inc. and Consulting Professor of Systems Medicine in the Department of Pediatrics at Stanford University School of Medicine. His work is focused at the nexus of -omics, digital health, artificial intelligence (AI), scientific wellness, and healthcare delivery. His work has been featured in the Wall Street Journal, Scientific American, MIT Technology Review, CNBC, and other popular media outlets. He was named in 2014 as one of the 100 most creative people in business by Fast Company magazine. He is co-author of the book Exploring Personal Genomics from Oxford University Press. Dr. Dudley received a BS in Microbiology from Arizona State University and an MS and PhD in Biomedical Informatics from Stanford University School of Medicine.
Selected publications.
2015.
Google Scholar Citations
https://scholar.google.com/citations?user=206DEM0AAAAJ


Lavidaviridae


Cristinia

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


Malassezia japonica

Malassezia japonica is a fungus that can cause opportunistic infections in animals.


Lichenologist


Ammophila sabulosa

Ammophila sabulosa, the red-banded sand wasp, is a species of the subfamily Ammophilinae of the hunting wasp family Sphecidae. Found in northern Europe, the wasp is notable for the mass provisioning behaviour of the females, hunting caterpillars mainly on sunny days, paralysing them with a sting, and burying them in a burrow with a single egg. The species is also remarkable for the extent to which females parasitise their own species, either stealing prey from nests of other females to provision their own nests, or in brood parasitism, removing the other female's egg and laying one of her own instead.
Description.
"Ammophila sabulosa" is a large ( long) and striking solitary wasp with a very long narrow "waist" of two segments. The species can be told from "A. pubescens" (which is smaller, long) as the waist widens out very gradually into the "tail" of the abdomen. The pattern of the forewings also differs: the third submarginal cell makes broad contact with the cell to its front and the rear end of the abdomen has a faint metallic blue sheen. The whole body is black except for the front half of the "tail", which is orange.
Behaviour.
The adults fly in summer on heathland and sandy places, hunting for caterpillars. The wasp grabs the upper (dorsal) side of each caterpillar, and angles her long abdomen around under the caterpillar to sting it on its lower (ventral) side, paralyzing it. The female digs burrows in sandy ground, provisions each burrow with a food supply of paralyzed caterpillars, and lays one egg, always on the first caterpillar. A female may make up to ten nests, one at a time; about half the nests are provided with one large caterpillar, and half with two to five smaller caterpillars. The burrow is sealed with stones, twigs or pieces of earth and then covered with sand. The female camouflages the nest with debris such as pine needles and pebbles unless the surface in the area is bare sand. Females are normally active only in direct sunlight. Nests are nearly always mass provisioned, which means fully stocked with enough food to take the wasp larva through to pupation, and then permanently closed.
Brood parasitism.
Females often parasitize their own species, either stealing prey from nests of other females to provision their own nests, or in brood parasitism, removing the other female's egg and laying one of her own instead. Brood parasitism "appears to be a cheap and easy route to producing offspring", as it takes only about 30 minutes to switch eggs in an existing nest, but about 10 hours to build and provision a new nest; however, more than 80% of brood-parasitized nests were themselves parasitized by another female.
Distribution.
"Ammophila sabulosa" is widely distributed across Eurasia with records from France, the Netherlands, Germany, Austria, Hungary, Poland, Norway, Sweden and Finland, then ranging eastwards as far as the Russian Far East, with a very few records in India and Japan. It is also found in the southern half of Britain.
Former Subspecies.
Several subspecies have been described, but none of these are presently considered as conspecific with sabulosa;


Attatha ino

Attatha ino is a species of moth of the family Noctuidae. It was described by Dru Drury in 1782 from "Madras".
Description.
Upperside: Antennae brown and setaceous (bristly). Head cream coloured. Neck black. Thorax and abdomen cream coloured, the former having some black spots on it. Anterior wings cream coloured, with a large triangular black spot placed at the tips, another on the middle of the wings, extending across from the anterior edges almost to the lower corners. There are also two small ones next the shoulders. The external edges have a row of small black spots placed thereon. Posterior wings cream coloured, tinctured with red, with a faint black border, rising at the upper corners where it is broadest, and running half-way to the abdominal ones, gradually narrowing.
Underside: Palpi, breast, legs, sides and abdomen cream coloured. Wings reddish cream, without any marks; the black marks, etc. on the upperside being faintly perceived. Margins of the wings entire. Wing span inches (33 mm).


Panayiotis Zavos

Panayiotis Michael Zavos (), or Panos Zavos (, ), is a physiologist who was born in Cyprus and later emigrated to the United States. Zavos has been the subject of controversy for making unsubstantiated claims that he can clone human beings.
Academic career.
Zavos received a Bachelor of Science in biology-chemistry in 1970, a Master of Science in biology-physiology in 1972, and an Education Specialist in Science (Ed.S.) in 1976 from Emporia State University in Emporia, Kansas. He earned a doctorate in animal physiology in 1978 from the University of Minnesota. He also received an MBA in 2008. He received the Distinguished Alumnus Award from Emporia State University
Zavos is Professor Emeritus in reproductive physiology at the University of Kentucky. He was named as an Honorary Professor by the Chinese Academy of Sciences, and as a Professor Emeritus by the Venkateshwara Institute of Medicine in India. He has served as a member of the International Advisory Committee of the Middle East Fertility Society.
Cloning claims.
Zavos claims to have created and implanted cloned human embryos. However, Zavos' claims were roundly dismissed after he failed to produce any proof and have been widely condemned by doctors, politicians, and religious and pressure groups.
Professor Hans Evers, chairman of the European Society of Human Reproduction and Embryology, stated: “All the scientific evidence so far indicates that it is completely impossible to clone humans. Anyone claiming that he is going to clone a human does not know what he is talking about. All these guys, including Zavos are doing damage to the profession and goodwill we have built up for many years in the area of fertility treatments."
Professor Robert Winston, emeritus professor of fertility studies at Imperial College London, said "I do not know of any credible evidence that suggests Dr Zavos can clone a human being. This seems to be yet another one of his claims to get repeated publicity".
Arthur Caplan, a bioethicist at the University of Pennsylvania said of Zavos, "I think he is the most dangerous of the current fringe proponents of cloning, because he knows more, stretches the facts, and seems to be wallowing in a mix of publicity and fund-raising that rests on a foundation of hype."
UK Health Secretary John Reid condemned Zavos' attempts to create a cloned human baby as a "gross misuse of genetic science".
Spyros Simitis, the brother of former Greek Prime Minister Costas Simitis, characterized Zavos's claims as "scientific barbarism". He said that if human cloning were to become reality, it would mean the "end of human freedom and evolution". He also referred to the possible use of cloning by governments for controlling and shaping society according to the government's will.


Diplocystaceae

Diplocystaceae (alternatively spelled Diplocystidaceae or Diplocystidiaceae) is a family of fungi in the Boletales order. The family was described by mycologist Hanns Kreisel in 1974.


Ourmiavirus

Ourmiavirus is a genus of positive-strand RNA viruses. Cucurbits, cherry, and cassava serve as natural hosts. There are three species in this genus. Diseases associated with this genus include: OuMV: yellowing and chlorotic spot symptoms.
Structure.
Viruses in the genus "Ourmiavirus" are non-enveloped, with icosahedral and bacilliform geometries, and T=1 symmetry. The diameter is around 18 nm, with a length of 30 nm.
Genome.
Genomes are linear and segmented, around 2.8kb in length.
Life cycle.
Viral replication is cytoplasmic. Entry into the host cell is achieved by penetration into the host cell. Replication follows the positive stranded RNA virus replication model. Positive stranded RNA virus transcription is the method of transcription. The virus exits the host cell by tubule-guided viral movement. Cucurbits, cherry, and cassava serve as the natural host.
Taxonomy.
The genus has three species:


Pest (organism)

A pest is any animal or plant harmful to humans or human concerns. The term is particularly used for creatures that damage crops, livestock, and forestry or cause a nuisance to people, especially in their homes. Humans have modified the environment for their own purposes and are intolerant of other creatures occupying the same space when their activities impact adversely on human objectives. Thus, an elephant is unobjectionable in its natural habitat but a pest when it tramples crops.
Some animals are disliked because they bite or sting; snakes, wasps, ants, bed bugs, fleas and ticks belong in this category. Others enter the home; these include houseflies, which land on and contaminate food, beetles, which tunnel into the woodwork, and other animals that scuttle about on the floor at night, like cockroaches, which are often associated with unsanitary conditions.
Agricultural and horticultural crops are attacked by a wide variety of pests, the most important being insects, mites, nematodes and gastropod molluscs. The damage they do results both from the direct injury they cause to the plants and from the indirect consequences of the fungal, bacterial or viral infections they transmit. Plants have their own defences against these attacks but these may be overwhelmed, especially in habitats where the plants are already stressed, or where the pests have been accidentally introduced and may have no natural enemies. The pests affecting trees are predominantly insects, and many of these have also been introduced inadvertently and lack natural enemies, and some have transmitted novel fungal diseases with devastating results.
Humans have traditionally performed pest control in agriculture and forestry by the use of pesticides; however, other methods exist such as mechanical control, and recently developed biological controls.
Concept.
A pest is any living thing, whether animal, plant, or fungus, which humans consider troublesome to themselves, their possessions, or the environment. It is a loose concept, as an organism can be a pest in one setting but beneficial, domesticated, or acceptable in another. Microorganisms, whether bacteria, microscopic fungi, protists, or viruses that cause trouble, on the other hand, are generally thought of as causes of disease (pathogens) rather than as pests. An older usage of the word "pest" is of a deadly epidemic disease, specifically plague. In its broadest sense, a pest is a competitor to humanity.
Animals as pests.
Animals are considered pests or vermin when they injure people or damage crops, forestry, or buildings. Elephants are regarded as pests by the farmers whose crops they raid and trample. Mosquitoes and ticks are vectors that can transmit ailments but are also pests because of the distress caused by their bites. Grasshoppers are usually solitary herbivores of little economic importance until the conditions are met for them to enter a swarming phase, become locusts and cause enormous damage. Many people appreciate birds in the countryside and their gardens, but when these accumulate in large masses, they can be a nuisance. Flocks of starlings can consist of hundreds of thousands of individual birds, their roosts can be noisy and their droppings voluminous; the droppings are acidic and can cause corrosion of metals, stonework, and brickwork as well as being unsightly. Pigeons in urban settings may be a health hazard, and gulls near the coast can become a nuisance, especially if they become bold enough to snatch food from passers-by. All birds are a risk at airfields where they can be sucked into aircraft engines. Woodpeckers sometimes excavate holes in buildings, fencing and utility poles, causing structural damage; they also drum on various reverberatory structures on buildings such as gutters, down-spouts, chimneys, vents and aluminium sheeting. Jellyfish can form vast swarms which may be responsible for damage to fishing gear, and sometimes clog the cooling systems of power and desalination plants which draw their water from the sea.
Many of the animals that we regard as pests live in our homes. Before humans built dwellings, these creatures lived in the wider environment, but co-evolved with humans, adapting to the warm, sheltered conditions that a house provides, the wooden timbers, the furnishings, the food supplies and the rubbish dumps. Many no longer exist as free-living organisms in the outside world, and can therefore be considered to be domesticated. The St Kilda house mouse rapidly became extinct when the last islander left the island of St Kilda, Scotland in 1930, but the St Kilda field mouse survived.
Plants as pests.
Plants may be considered pests, for example, if they are invasive species or weeds. There is no universal definition of what makes a plant a pest. Some governments, such as that of Western Australia, permit their authorities to prescribe as a pest plant "any plant that, in the local government authority's opinion, is likely to adversely affect the environment of the district, the value of property in the district, or the health, comfort or convenience of the district’s inhabitants." An example of such a plant prescribed under this regulation is caltrop, "Tribulus terrestris", which can cause poisoning in sheep and goats, but is mainly a nuisance around buildings, roadsides and recreation areas because of its uncomfortably sharp spiny burrs.
Other organisms as pests.
Some definitions encompass any hazardous or problematic organism, and so often include fungi, oomycetes, bacteria, and viruses.
Ecology.
The term "plant pest", mainly applied to insect micropredators of plants, has a specific definition in terms of the International Plant Protection Convention and phytosanitary measures worldwide. A pest is any species, strain or biotype of plant, animal, or pathogenic agent injurious to plants or plant products.
Plant defences against pests.
Plants have developed strategies that they use in their own defence, be they thorns (modified stems) or spines (modified leaves), stings, a thick cuticle or waxy deposits, with the second line of defence being toxic or distasteful secondary metabolites. Mechanical injury to the plant tissues allows the entry of pathogens and stimulates the plant to mobilise its chemical defences. The plant soon seals off the wound to reduce further damage.
Plants sometimes take active steps to reduce herbivory. "Macaranga triloba" for example has adapted its thin-walled stems to create ideal housing for an ant "Crematogaster" spp., which, in turn, protects the plant from herbivores. In addition to providing housing, the plant also provides the ant with its exclusive food source in the form of food bodies located on the leaf stipules. Similarly, several "Acacia" tree species have developed stout spines that are swollen at the base, forming a hollow structure that provides housing for ants which protect the plant. These "Acacia" trees also produce nectar in nectaries on their leaves as food for the ants.
Economic impact.
In agriculture and horticulture.
Together pests and diseases cause up to 40% yield losses every year. The animal groups of the greatest importance as agricultural pests are (in order of economic importance) insects, mites, nematodes and gastropod molluscs.
Insects are responsible for two major forms of damage to crops. First, there is the direct injury they cause to the plants as they feed on the tissues; a reduction in leaf surface available for photosynthesis, distortion of growing shoots, a diminution of the plant's growth and vigour, and the wilting of shoots and branches caused by the insects' tunneling activities. Secondly there is the indirect damage, where the insects do little direct harm, but either transmit or allow entry of fungal, bacterial or viral infections. Although some insects are polyphagous, many are restricted to one specific crop, or group of crops. In many cases it is the larva that feeds on the plant, building up a nutritional store that will be used by the short-lived adult; sawfly and lepidopteran larvae feed mainly on the aerial portions of plants while beetle larvae tend to live underground, feeding on roots, or tunnel into the stem or under the bark. The true bugs, Hemiptera, have piercing and sucking mouthparts and live by sucking sap from plants. These include aphids, whiteflies and scale insects. Apart from weakening the plant, they encourage the growth of sooty mould on the honeydew the insects produce, which cuts out the light and reduces photosynthesis, stunting the plant's growth. They often transmit serious viral diseases between plants.
The mites that cause most trouble in the field are the spider mites. These are less than in diameter, can be very numerous, and thrive in hot, dry conditions. They mostly live on the underside of leaves and puncture the plant cells to feed, with some species forming webbing. They occur on nearly all important food crops and ornamental plants, both outdoors and under glass, and include some of the most economically important pests. Another important group of mites is the gall mites which affect a wide range of plants, several mite species being major pests causing substantial economic damage to crops. They can feed on the roots or the aerial parts of plants and transmit viruses. Some examples are the big bud mite that transmits the reversion virus of blackcurrants, the coconut mite which can devastate coconut production, and the cereal rust mite which transmits several grass and cereal viruses. Being exceedingly minute, many plant mites are spread by wind, although others use insects or other arthropods as a means to disperse.
The nematodes (eelworms) that attack plants are minute, often too small to be seen with the naked eye, but their presence is often apparent in the galls or "knots" they form in plant tissues. Vast numbers of nematodes are found in soil and attack roots, but others affect stems, buds, leaves, flowers and fruits. High infestations cause stunting, deformation and retardation of plant growth, and the nematodes can transmit viral diseases from one plant to another. When its populations are high, the potato cyst nematode can cause reductions of 80% in yield of susceptible potato varieties. The nematode eggs survive in the soil for many years, being stimulated to hatch by chemical cues produced by roots of susceptible plants.
Slugs and snails are terrestrial gastropod molluscs which typically chew leaves, stems, flowers, fruit and vegetable debris. Slugs and snails differ little from each other and both do considerable damage to plants. With novel crops being grown and with insect pests having been brought more under control by biological and other means, the damage done by molluscs becomes of greater significance. Terrestrial molluscs need moist environments; snails may be more noticeable because their shells provide protection from desiccation, while most slugs live in soil and only come out to feed at night. They devour seedlings, damage developing shoots and feed on salad crops and cabbages, and some species tunnel into potatoes and other tubers.
Weeds.
A weed is a plant considered undesirable in a particular situation; the term has no botanical significance. Often, weeds are simply those native plants that are adapted to grow in disturbed ground, the disturbance caused by ploughing and cultivation favouring them over other species. Any plant is a weed if it appears in a location where it is unwanted; Bermuda grass makes a good lawn plant under hot dry conditions but become a bad weed when it out-competes cultivated plants.
A different group of weeds consists of those that are invasive, introduced, often unintentionally, to habitats to which they are not native but in which they thrive. Without their original competitors, herbivores, and diseases, they may increase and become a serious nuisance. One such plant is purple loosestrife, a native of Europe and Asia where it occurs in ditches, wet meadows and marshes; introduced into North America, it has no natural enemies to keep it in check and has taken over vast tracts of wetlands to the exclusion of native species.
In forestry.
In forestry, pests may affect various parts of the tree, from its roots and trunk to the canopy far overhead. The accessibility of the part of the tree affected may make detection difficult, so that a pest problem may already be far advanced before it is first observed from the ground. The larch sawfly and spruce budworm are two insect pests prevalent in Alaska and aerial surveys can show which sections of forest are being defoliated in any given year so that appropriate remedial action can be taken.
Some pests may not be present on the tree all year round, either because of their life cycle or because they rotate between different host species at different times of the year. The larvae of wood-boring beetles may spend years excavating tunnels under the bark of trees, and only emerge into the open for brief periods as adults, to mate and disperse. The import and export of timber has inadvertently assisted some insect pests to establish themselves far from their country of origin. An insect may be of little importance in its native range, being kept under control by parasitoid wasps, predators, and the natural resistance of the host trees, but be a serious pest in a region into which it has been introduced. This is the case with the emerald ash borer, an insect native to north-eastern Asia, which, since its arrival in North America, has killed millions of ash trees.
In buildings.
Animals able to live in the dry conditions found in buildings include many arthropods such as beetles, cockroaches, moths, and mites. Another group, including termites, woodworm, longhorn beetles, and wood ants cause structural damage to buildings and furniture. The natural habitat of these is the decaying parts of trees. The deathwatch beetle infests the structural timbers of old buildings, mostly attacking hardwood, especially oak. The initial attack usually follows the entry of water into a building and the subsequent decay of damp timber. Furniture beetles mainly attack the sapwood of both hard and soft wood, only attacking the heartwood when it is modified by fungal decay. The presence of the beetles only becomes apparent when the larvae gnaw their way out, leaving small circular holes in the timber.
Carpet beetles and clothes moths cause non-structural damage to property such as clothing and carpets. It is the larvae that are destructive, feeding on wool, hair, fur, feathers and down. The moth larvae live where they feed, but the beetle larvae may hide behind skirting boards or in other similar locations between meals. They may be introduced to the home in any product containing animal fibres including upholstered furniture; the moths are feeble fliers but the carpet beetles may also enter houses through open windows. Furniture beetles, carpet beetles and clothes moths are also capable of creating great damage to museum exhibits, zoological and botanical collections, and other cultural heritage items. Constant vigilance is required to prevent an attack, and newly acquired items, and those that have been out on loan, may need quarantining before being added to the general collection.
There are over four thousand species of cockroach worldwide, but only four species are commonly regarded as pests, having adapted to live permanently in buildings. Considered to be a sign of unsanitary conditions, they feed on almost anything, reproduce rapidly and are difficult to eradicate. They can passively transport pathogenic microbes on their body surfaces, particularly in environments such as hospitals, and are linked with allergic reactions in humans.
Various insects attack dry food products, with flour beetles, the drugstore beetle, the sawtoothed grain beetle and the Indianmeal moth being found worldwide. The insects may be present in the warehouse or maybe introduced during shipping, in retail outlets, or in the home; they may enter packets through tiny cracks or may chew holes in the packaging. The longer a product is stored, the more likely it is to become contaminated, with the insects often originating from dry pet foods.
Some mites, too, infest foodstuffs and other stored products. Each substance has its own specific mite, and they multiply with great rapidity. One of the most damaging is the flour mite, which is found in grain and may become exceedingly abundant in poorly stored material. In time, predatory mites usually move in and control the flour mites.
Countermeasures.
Pest control in agriculture and horticulture.
The control of pests in crops is as old as civilisation. The earliest approach was mechanical, from ploughing to picking off insects by hand. Early methods included the use of sulphur compounds, before 2500 BC in Sumeria. In ancient China, insecticides derived from plants were in use by 1200 BC to treat seeds and to fumigate plants. Chinese agronomy recognised biological control by natural enemies of pests and the varying of planting time to reduce pests before the first century AD. The agricultural revolution in Europe saw the introduction of effective plant-based insecticides such as pyrethrum, derris, quassia, and tobacco extract. The phylloxera (a powdery mildew) damage to the wine industry in the 19th century resulted in the development of resistant varieties and grafting, and the accidental discovery of effective chemical pesticides, Bordeaux mixture (lime and copper sulphate) and Paris Green (an arsenic compound), both very widely used. Biological control also became established as an effective measure in the second half of the 19th century, starting with the vedalia beetle against cottony cushion scale. All these methods have been refined and developed since their discovery.
Pest control in forestry.
Forest pests inflict costly damage, but treating them is often unaffordable, given the relatively low value of forest products compared to agricultural crops. It is also generally impossible to eradicate forest pests, given the difficulty of examining entire trees, and the certainty that pesticides would damage many forest organisms other than the intended pests. Forest integrated pest management therefore aims to use a combination of prevention, cultural control measures, and direct control (such as pesticide use). Cultural measures include choosing appropriate species, keeping competing vegetation under control, ensuring a suitable stocking density, and minimizing injury and stress to trees.
Pest control in buildings.
Pest control in buildings can be approached in several ways, depending on the type of pest and the area affected. Methods include improving sanitation and garbage control, modifying the habitat, and using repellents, growth regulators, traps, baits and pesticides. For example, the pesticide Boron can be impregnated into the fibres of cellulose insulation to kill self-grooming insects such as ants and cockroaches. Clothes moths can be controlled with airtight containers for storage, periodic laundering of garments, trapping, freezing, heating and the use of chemicals. Traditional mothballs deter adult moths with strong-smelling naphthalene; modern ones use volatile repellents such as 1,4-Dichlorobenzene. Moth larvae can be killed with insecticides such as permethrin or pyrethroids. However, insecticides cannot safely be used in food storage areas; alternative treatments include freezing foods for four days at or baking for half an hour at to kill any insects present.
In mythology, religion, folklore and culture.
Pests have attracted human attention from the birth of civilisation. Plagues of locusts caused devastation in the ancient Middle East, and were recorded in tombs in Ancient Egypt from as early as 2470 BC, and in the Book of Exodus in the Bible, as taking place in Egypt around 1446 BC. Homer's "Iliad" mentions locusts taking to the wing to escape fire. Given the impact of agricultural pests on human lives, people have prayed for deliverance. For example, the 10th century Greek monk Tryphon of Constantinople is said to have prayed "Snails, earwigs and all other creatures, hurt not the vines, nor the land nor the fruit of the trees, nor the vegetables ... but depart into the wild mountains."
The 11th-century Old English medical text "Lacnunga" contained charms and spells to ward off or treat pests such as "wid smeogan wyrme", "penetrating worms", in this case requiring a charm to be sung, accompanied by covering the wound with spittle, pounded green centaury, and hot cow's urine.
The 20th century "prayer against pests" including the words "By Your power may these injurious animals be driven off so that they will do no harm to any one and will leave our fields and meadows unharmed" was printed in the 1956 "Rural Life Prayerbook".


SoyBase Database

SoyBase is a database created by the United States Department of Agriculture. It contains genetic information about soybeans. It includes genetic maps, information about Mendelian genetics and molecular data regarding genes and sequences. It was started in 1990 and is freely available to individuals and organizations worldwide.
History.
SoyBase was instituted by the Corn Insects and Corn Genetics Research Unit (CICGRU) in Ames, Iowa as a central repository for the soybean genetics community's published information. Originally, the database concentrated on genetic information such as genetic linkage maps and other Mendalian information. SoyBase genetic maps are a manually-curated composite of all published mapping and QTL studies, and thus provide a species level view of markers and QTL.
In 2010 the soybean genome sequence was released along with gene models and many other types of genome annotations that were integrated in to SoyBase. SoyBase genetic linkage maps were integral to the assembly of the soybean genome.
In 2018 the database received approximately 63,000 page requests from 2,600 users per month from 130 countries. About 40 organizations in the United States and 82 foreign educational institutions access SoyBase yearly. SoyBase supplies data to U.S. and foreign government organizations and corporate entities.
Data submission and release policy.
Data is accepted from the original source generators only. Users that independently identify data for inclusion into the database can contact SoyBase directly. A number Excel-based spreadsheet templates are available to facilitate the inclusion of data into SoyBase.
All data in SoyBase are available without restrictions. A number of data sub-setting and download tools are provided, and when needed ad hoc subsets of the data can be requested from the SoyBase Curator.
Search tool.
The SoyBase Database Search Tool uses a text entry box for queries. Results are returned as text and as displays. Results display soybean genetic (and genomic) data using Generic Model Organism Database (GMOD) open-source software. In addition to SoyBase, objects identified by exact lexical matches to the query term, the tool also uses a soybean-specific ontology to identify biologically-related SoyBase objects.
Some SoyBase sequence data and annotations are available through an InterMine instance (SoyMine), which is a collaboration with the Legume Information System Project.
Graphical displays.
Genetic maps contain information on markers (SSR, RFLP, SNP, etc.), genes, and biparental and Genome-wide Association Study (GWAS) Quantitative Trait Loci (QTL). Soybean genetic maps are displayed using the CMap comparative genetic map viewer. Soybean genomic sequence and gene model data are displayed using the GBrowse sequence viewer. Other genome annotations in this viewer include epigenetic data such as DNA methylation and gene expression data of various soybean strains subjected to different treatments and from different soybean tissues/cultivars. Metabolic data and biochemical pathway information is displayed using Pathway Tools. Soybean metabolic pathway information (SoyCyc) was inferred by the Plant Metabolic Network project and was used to populate PathwayTools displays.


Naomi A. H. Millard

Naomi Adeline Helen Millard, née Bokenham (16 July 1914, Green Point, Cape Town – 12 June 1997) was a South African biologist, one of the founders of the Zoological Society of South Africa and the Zoologica Africana Journal.
Life.
Naomi Adeline Helen Bokenham was on 16 July 1914 in Green Point, Cape Town. She graduated the Wynberg Girls’ High School and entered the University of Cape Town in 1932, completing a master's degree in 1935.
In 1938, Bokenham married Arthur Millard and later settled in Pillans Road, Rosebank, raising a son and a daughter.
In 1942, Millard was awarded a Ph.D. degree, and in 1946, she was appointed to the permanent staff as a lecturer.
Career.
In 1951, Millard published "Observations and experiments on fouling organisms in table Bay Harbour, south Africa in Transactions of the Royal Society of South Africa". By 1952, she was awarded a University Fellowship for the number and quality of her scientific publications. In 1958, Millard was promoted to a senior lectureship and in 1963 became a Fellow of the Royal Society of South Africa.
From 1961 to 1972 Millard was an Honorary secretary of the Zoological Society of South Africa Executive Council. In 1967, Millard published a work "Hydrois from the south-west Indian Ocean. Annals of the South African Museum".
In 1971, she retired from the University and joined the staff of the South African Museum as marine biologist studying South African hydroids.
In 1972-1977 Millard was a Journal Editor of Zoological Society of South Africa Executive Council. Another Millard's work on hydroids was published in 1977 - "Hydroids from the Kerguelen and Crozet shelves, collected by the cruise MD.03 of the Marion-Dufresne. Ann. S. Afr. Mus". During her career she described over 100 South African taxa.
In 1980, Millard was awarded the Gold Medal of the Zoological Society of Southern Africa.
Naomi A. H. Millard died on 12 June 1997.


Arcanobacterium

Arcanobacterium () is a genus of bacteria. They are gram-positive, non–acid fast, nonmotile, facultatively anaerobic, and non–endospore forming. They are widely distributed in nature in the microbiota of animals (including the human microbiota) and are mostly innocuous. Some can cause disease in humans and other animals (for example, "Arcanobacterium haemolyticum" infections). As with various species of a microbiota (including their cousins in the genera "Corynebacterium" and "Trueperella"), they usually are not pathogenic but can occasionally opportunistically capitalize on atypical access to tissues (via wounds) or weakened host defenses.
Taxonomy.
As explained by Yassin et al., the genus "Arcanobacterium" was first described by Collins et al. in 1982 to accommodate bacterial strains previously assigned to the genus "Corynebacterium" variously (and controversially) as "C. pyogenes hominis" and then "C. haemolyticum", thenceforth to be known as "Arcanobacterium haemolyticum". The name (from "arcanus" + "bacterium") means "secretive bacterium" or "enigmatic/mysterious bacterium". In 2011, Yassin et al., on the basis of 16S rRNA signature nucleotide comparisons, menaquinone and phospholipid compositions, and Christie–Atkins–Munch-Petersen (CAMP) tests, proposed that four species—"A. haemolyticum", "A. hippocoleae", "A. phocae", and "A. pluranimalium"—should continue to be affiliated with the genus "Arcanobacterium", whereas the species "A. abortisuis", "A. bernardiae", "A. bialowiezense", "A. bonasi", and "A. pyogenes" should be reclassified as members of a new genus, "Trueperella", as "Trueperella abortisuis" comb. nov., "Trueperella bernardiae" comb. nov., "Trueperella bialowiezensis" comb. nov., "Trueperella bonasi" comb. nov., and "Trueperella pyogenes" comb. nov. Therefore, they provided an emended description of the genus "Arcanobacterium".
In 2001, Lawson et al. reported that "A. pluranimalium" sp. nov. had been isolated from a harbour porpoise and a deer. In 2002, Hoyles et al. reported that "A. hippocoleae" sp. nov. had been isolated from a vaginal discharge of a horse.
In 2012, Hijazin et al. reported that "A. canis" sp. nov. had been isolated from otitis externa in a dog. In 2013 the same group (with Hijazin, Sammra, and others) reported that "A. phocisimile" sp. nov. had been isolated from harbor seals. In 2015, the same group (with Sammra and others) reported that "A. pinnipediorum" sp. nov. had also been isolated from a harbor seal.
Species.
"A. abortisuis" (now "Trueperella abortisuis")

"A. bernardiae" (formerly "Actinomyces bernardiae"; now "Trueperella bernardiae")

"A. bialowiezense" (now "Trueperella bialowiezense")

"A. bonasi" (now "Trueperella bonasi")

"A. canis"

"A. haemolyticum"

"A. hippocoleae"

"A. phocae"

"A. phocisimile"

"A. pinnipediorum"

"A. pluranimalium"

"A. pyogenes" (formerly "Actinomyces pyogenes"; now "Trueperella pyogenes")


Candidatus Holdemania massiliensis


Cucullanus gymnothoracis

Cucullanus gymnothoracis is a species of parasitic nematodes. It is an endoparasite of the lipspot moray "Gymnothorax chilospilus". The species has been described in 2018 by František Moravec & Jean-Lou Justine from material collected off New Caledonia in the South Pacific Ocean.
"Cucullanus gymnothoracis" was considered somewhat similar to "Cucullanus austropacificus", but differs from this species in the absence of cervical alae and the posterior cloacal outgrowth, in the shape and size of the anterior cloacal outgrowth and shorter spicules 1.12 mm long.


Gaertneriomyces

Gaertneriomyces is a genus of fungi belonging to the family Spizellomycetaceae.
The species of this genus are found in Southeastern Asia and Australia.
Species:


Pilobolaceae

The Pilobolaceae are a family of fungi in the Mucorales order. Generally, species in this family have a widespread distribution, although there are some that are restricted to tropical and subtropical regions. This family includes two genera: "Pilobolus", and "Utharomyces".
Morphology.
All species produce unusual, phototrophic sporangiophores. These sporangiophores give rise to dark-colored, columellate sporagia covered in calcium oxalate crystals. In "Pilobolus" and "Utharomyces", inflated structures filled with yellow cartenoid pigments give rise to the sporophores; these two genera also produce subsporangiul vesicles. Zygospores are formed on apposed, entwined suspensors, usually at or below the dung.
Ecology.
All species grow on dung but can rarely be isolated from the soil. "Pilobolus" are common on many types of herbivore dung, while "Utharomyces" grows on rodent dung. "Utharomyces" appears to be restricted to the tropics.
Dispersal.
This family has spectacular means of dispersal. Many species require passage through the gut of an herbivore in order for the spores to germinate. The problem is that many animals tend to avoid eating their own dung. To compensate, remarkable mechanisms of spore dispersal are used.
In "Pilobolus", the subsporangial swelling acts as a lens to focus light on light-sensitive pigments at the base of the swelling. Turgor pressure builds inside of the swelling until it ruptures, and the sporangium is hurled for 2 meters. The calcium oxalate crystals helps it adhere to the surface it lands on, and if the surface is wet, the crystals allow the sporangium to rotate. This rotation allows the mucus surrounding the spores (under the crystals) to glue it to surface where it will await ingestion by an herbivore. Nematodes have been observed climbing the sporangiophore or swimming inside of it to catch a ride on the sporangium. While many species may do this, it seems only "Dictyocaulus vivipores", cattle lungworm, are able to survive the trip.
Mechanisms of dispersal are less known in these genera. In both genera, the sporangiophore, guided by light, elongates until the sporangium is brought into contact with a solid surface. In "Pilobolus", contact with the surface causes a rupture at the columella, which releases the sporangium, which adheres to the new surface. In "Utharomyces", contact with the surface ruptures the subsporangial swelling. This releases cytoplasm, which is used to glue the upper portion of the swelling containing the sporangium to the substrate.


Adipogenesis

Adipogenesis is the formation of adipocytes (fat cells) from stem cells. It involves 2 phases, determination, and terminal differentiation. Determination is mesenchymal stem cells committing to the adipocyte precursor cells, also known as preadipocytes which lose the potential to differentiate to other types of cells such as chondrocytes, myocytes, and osteoblasts. Terminal differentiation is that preadipocytes differentiate into mature adipocytes. Adipocytes can arise either from preadipocytes resident in adipose tissue, or from bone-marrow derived progenitor cells that migrate to adipose tissue.
Introduction.
Adipocytes play a vital role in energy homeostasis and process the largest energy reserve as triglycerol in the body of animals. Adipocytes stay in a dynamic state, they start expanding when the energy intake is higher than the expenditure and undergo mobilization when the energy expenditure exceeds the intake. This process is highly regulated by counter regulatory hormones to which these cells are very sensitive. The hormone insulin promotes expansion whereas the counter hormones epinephrine, glucagon, and ACTH promote mobilization. Adipogenesis is a tightly regulated cellular differentiation process, in which mesenchymal stem cells committing to preadipocytes and preadipocytes differentiating into adipocytes. Cellular differentiation is a change of gene expression patterns which multipotent gene expression alters to cell type specific gene expression. Therefore, transcription factors are crucial for adipogenesis. Transcription factors, peroxis proliferator-activated receptor γ (PPARγ) and CCAAT enhancer-binding proteins (C/EBPs) are main regulators of adipogenesis. Comparing with cells from other lineage, the in vitro differentiation of fat cells is authentic and recapitulates most of the characteristic feature of in vivo differentiation. The key features of differentiated adipocytes are growth arrest, morphological change, high expression of lipogenic genes and production of adipokines like adiponectin, leptin, resistin (in the mouse, not in humans) and TNF-alpha.
Differentiation.
In vitro studies on differentiation have used the pre-committed preadipocyte lineage, such as 3T3-L1 and 3T3-F442A cell line, or preadipocytes isolated from the stromal-vascular fraction of white adipose tissue. In vitro differentiation is a highly ordered process. Firstly, proliferating preadipocytes arrest growth usually by contact inhibition. The growth arrest followed by the earliest events, including a morphological change of preadipocyte from the fibroblast-shape to the round-shape and the induction of transcription factors C/EBPβ, and C/EBPδ. The second phase of growth arrest is the expression of two key transcription factors PPARγ and C/EBPα which promote expression of genes that confer the characteristics of mature adipocytes. These genes include adipocyte protein (aP2), insulin receptor, glycerophosphate dehydrogenase, fatty acid synthase, acetyl CoA carboxylase, glucose transporter type 4 (Glut 4) and so on. Through this process, lipid droplets accumulate in the adipocyte. However, preadipocytes cell lines have difficult to different to differentiate into adipocytes. Preadipocytes display CD45− CD31− CD34+ CD29+ SCA1+ CD24+ surface markers can proliferate and differentiate to adipocytes in vivo.
Transcriptional regulations.
PPARγ.
PPARγ is a member of the nuclear-receptor superfamily and is the master regulator of adipogenesis. PPARγ heterodimerizes with retinoid X receptor (RXR) and then binds to DNA, which activates the promoters of the downstream genes. PPARγ induces fat-cell specific genes, including aP2, adiponectin and phosphoenolpyruvate carboxykinase (PEPCK). PPARg activation has effects on several aspects of the mature adipocyte characteristics such as morphological changes, lipid accumulation, and the acquisition of insulin sensitivity. PPARγ is necessary and sufficient to promote fat cell differentiation. PPARγ is required for embryonic stem cells (ES cells) differentiation to adipocytes. The expression of PPARγ itself is sufficient to convert fibroblast into adipocytes in vitro. Other pro-adipogenic factors like C/EBPs and Krüppel-like factors (KLFs) have been shown to induce the PPARγ promoter. Moreover, PPARγ is also required to maintain the expression of genes that characterize the mature adipocyte. Thiazolidinediones (TZDs), antidiabetic agents which well used differentiation cocktail in vitro, promoting the activity of PPARγ.
C/EBPs.
C/EBPs, transcription factors, are members of the basic-leucine zipper class. cAMP, an inducer of adipogenesis, can promote expression of C/EBPβ and C/EBPδ. At the early stage of differentiation, the transient increase of C/EBPβ and C/EBPδ mRNA and protein levels are thought to activate the adipogenic transcription factors, PPARγ and C/EBPα. PPARγ and C/EBPα can feedback to induce the expression of each other as well as their downstream genes. C/EBPα also plays an important role in the insulin sensitivity of adipocytes. However, C/EBPγ suppresses differentiation which might due to inactivation by C/EBPβ.
Transcriptional cascade.
Although PPARγ and C/EBPα are master regulators of adipogenesis, other transcription factors function in the progression of differentiation. Adipocyte determination and differentiation factor 1 (ADD1) and sterol regulatory element binding protein 1 (SREBP1) can activate PPARγ by the production of an endogenous PPARγ ligand or directly promote the expression of PPARγ. cAMP-responsive element binding protein promotes differentiation, while the activation of PPARγ and C/EBPα is also responsive to negative regulation. T-cell factor/lymphoid enhancer-binding factor (TCF/LEF), GATA2/3, retinoic acid receptor α, and SMAD6/7 don't affect the expression of C/EBPβ and C/EBPδ but inhibit the induction of PPARγ and C/EBPα.
Other regulations.
Products of endocrine system such as insulin, IGF-1, cAMP, glucocorticoid, and triiodothyronine effectively induce adipogenesis in preadipocytes.
Insulin and IGF1.
Insulin regulates adipogenesis through insulin-like growth factor 1 (IGF1) receptor signaling. Insulin/IGF1 promotes the induction transcription factors regulating terminal differentiation.
Wnt signaling.
Wnt/β-catenin signaling suppresses adipogenesis, by promoting the differentiation of mesenchymal stem cells into myocytes and osteocytes but blocking the commitment to the adipocytic lineage. Wnt/β-catenin inhibits the differentiation of preadipocytes by inhibiting the induction of PPARγ and C/EBPα.
BMPs.
Bone morphogenetic proteins (BMPs) are transforming growth factor β (TGFβ) superfamily members. BMP2 can either stimulates the determination of multipotent cells or induce osteogenesis through different receptor heteromers. BMPs also promotes the differentiation of preadipocytes.
Senescent cells.
Senescent adipose progenitor cells in subcutaneous adipose tissue has been shown to suppress adipogenic differentiation. Reduced adipogenesis in obese persons is due to increased senescent cells in adipose tissue rather than reduced numbers of stem/progenitor cells.


Host microbe interactions in Caenorhabditis elegans

"Caenorhabditis elegans"- microbe interactions are defined as any interaction that encompasses the association with microbes that temporarily or permanently live in or on the nematode "C. elegans." The microbes can engage in a commensal, mutualistic or pathogenic interaction with the host. These include bacterial, viral, unicellular eukaryotic, and fungal interactions. In nature "C. elegans" harbours a variety of different microbes. In contrast, "C. elegans" strains that are cultivated in laboratories for research purposes have lost the natural associated microbial communities and are commonly maintained on a single bacterial strain, "Escherichia coli" OP50.
However, E. coli OP50 does not allow for reverse genetic screens because RNAi libraries have only been generated in strain HT115. This limits the ability to study bacterial effects on host phenotypes. The host microbe interactions of C. elegans are closely studied because of their orthologs in humans. Therefore, the better we understand the host interactions of C. elegans the better we can understand the host interactions within the human body.
Natural ecology.
"C. elegans" is a well-established model organism in different research fields, yet its ecology however is only poorly understood. They have a short development cycle only lasting three days with a total life span of about two weeks."C. elegans" were previously considered a soil-living nematode, but in the last 10 years it was shown that natural habitats of "C. elegans" are microbe-rich, such as compost heaps, rotten plant material, and rotten fruits. Most of the studies on "C. elegans" are based on the N2 strain, which has adapted to laboratory conditions. Only in the last few years the natural ecology of "C. elegans" has been studied in more detail and one current research focus is its interaction with microbes. As "C. elegans" feeds on bacteria (microbivory), the intestine of worms isolated from the wild is usually filled with a large number of bacteria. In contrast to the very high diversity of bacteria in the natural habitat of "C. elegans", the lab strains are only fed with one bacterial strain, the Escherichia coli derivate OP50
. OP50 was not co-isolated with "C. elegans" from nature, but was rather used because of its high convenience for laboratory maintenance. Bleaching is a common method in the laboratory to clean "C. elegans" of contaminations and to synchronize a population of worms. During bleaching the worms are treated with 5N NaOH and household bleach, leading to the death of all worms and survival of only the nematode eggs. The larvae hatching from these eggs lack any microbes, as none of the currently known "C. elegans"-associated microbes can be transferred vertically. Since most laboratory strains are kept under these gnotobiotic conditions, nothing is known about the composition of the "C. elegans" microbiota. The ecology of "C. elegans" can only be fully understood in the light of the multiple interactions with the microorganisms, which it encounters in the wild. The effect of microbes on "C. elegans" can vary from beneficial to lethal.
Beneficial microbes.
In its natural habitat "C. elegans" is constantly confronted with a variety of bacteria that could have both negative and positive effects on its fitness. To date, most research on "C. elegans"-microbe interactions focused on interactions with pathogens. Only recently, some studies addressed the role of commensal and mutualistic bacteria on "C. elegans" fitness. In these studies, "C. elegans" was exposed to various soil bacteria, either isolated in a different context or from "C. elegans" lab strains transferred to soil. These bacteria can affect "C. elegans" either directly through specific metabolites, or they can cause a change in the environmental conditions and thus induce a physiological response in the host.
Beneficial bacteria can have a positive effect on the lifespan, generate certain pathogen resistances, or influence the development of "C. elegans".
Lifespan extension.
The lifespan of "C. elegans" is prolonged when grown on plates with "Pseudomonas sp." or "Bacillus megaterium" compared to individuals living on "E.coli". The lifespan extension mediated by "B. megaterium" is greater than that caused by "Pseudomonas sp.". As determined by microarray analysis (a method, which allows the identification of "C. elegans" genes that are differentially expressed in response to different bacteria), 14 immune defence genes were up-regulated when "C. elegans" was grown on "B. megaterium", while only two were up-regulated when fed with "Pseudomonas sp." In addition to immune defence genes, other upregulated genes are involved in the synthesis of collagen and other cuticle components, indicating that the cuticle might play an important role in the interaction with microbes. Although some of the genes are known to be important for "C. elegans" lifespan extension, the precise underlying mechanisms still remain unclear.
Protection against microbes.
The microbial communities residing inside the host body have now been recognized to be important for effective immune responses. Yet the molecular mechanisms underlying this protection are largely unknown. Bacteria can help the host to fight against pathogens either by directly stimulating the immune response or by competing with the pathogenic bacteria for available resources. In "C. elegans", some associated bacteria seem to generate protection against pathogens. For example, when "C. elegans" is grown on "Bacillus megaterium" or "Pseudomonas mendocina", worms are more resistant to infection with the pathogenic bacterium "Pseudomonas aeruginosa" [21], which is a common bacterium in "C. elegans’ "natural environment and therefore a potential natural pathogen. This protection is characterized by prolonged survival on "P. aeruginosa" in combination with a delayed colonization of "C. elegans" by the pathogen. Due to its comparatively large size "B. megaterium" is not an optimal food source for "C. elegans", resulting in a delayed development and a reduced reproductive rate. The ability of "B. megaterium" to enhance resistance against the infection with "P. aeruginosa" seems to be linked to the decrease in reproductive rate. However, the protection against "P. aeruginosa" infection provided by "P. mendocina" is reproduction independent, and depends on the p38 mitogen-activated protein kinase pathway." P. mendocina" is able to activate the p38 MAPK pathway and thus to stimulate the immune response of "C. elegans" against the pathogen. A common way for an organism to protect itself against microbes is to increase fecundation to increase the surviving individuals in the face of an attack. This defense against parasites are genetically linked to stress response pathways and dependent on the innate immune system.
Effects on development.
Under natural conditions it might be advantageous for "C. elegans" to develop as fast as possible to be able to reproduce rapidly. The bacterium "Comamonas" DA1877 accelerates the development of "C. elegans". Neither TOR (target of rapamycin), nor insulin signalling seem to mediate this effect on the accelerated development. It is thus possible that secreted metabolites of "Comamonas", which might be sensed by "C. elegans", lead to faster development. Worms that were fed with "Comamonas" DA1877 also showed a reduced number of offspring and a reduced lifespan. Another microbe that accelerates C. elegans' growth are L . sphaericus. This bacteria significantly increased the growth rate of C. elegans when compared to their normal diet of E. coli OP50. C. elegans are mostly grown and observed in a controlled laboratory with a controlled diet, therefore, they may show differential growth rates with naturally occurring microbes.
Pathogenic microbes.
In its natural environment "C. elegans" is confronted with a variety of different potential pathogens. "C. elegans" has been used intensively as a model organism for studying host-pathogen interactions and the immune system. These studies revealed that "C. elegans" has well-functioning innate immune defenses. The first line of defense is the extremely tough cuticle that provides an external barrier against pathogen invasion. In addition, several conserved signaling pathways contribute to defense, including the DAF-2/DAF-16 insulin-like receptor pathway and several MAP kinase
pathways, which activate physiological immune responses. Finally, pathogen avoidance behavior represents another line of "C. elegans" immune defense. All these defense mechanisms do not work independently, but jointly to ensure an optimal defense response against pathogens. Many microorganisms were found to be pathogenic for "C. elegans" under laboratory conditions. To identify potential "C. elegans" pathogens, worms in the L4 larval stage are transferred to a medium that contains the organism of interest, which is a bacterium in most cases. Pathogenicity of the organism can be inferred by measuring the lifespan of worms. There are several known human pathogens that have a negative effect on "C. elegans" survival. However, only very few natural "C. elegans" pathogens are currently known.
Eukaryotic microbes.
One of the best studied natural pathogens of "C. elegans" is the microsporidium "Nematocida parisii", which was directly isolated from wild-caught "C. elegans". "N. parisii" is an intracellular parasite that is exclusively transmitted horizontally from one animal to another. The microsporidian spores are likely to exit the cells by disrupting a conserved cytoskeletal structure in the intestine called the terminal web. It seems that none of the known immune pathways of "C. elegans" is involved in mediating resistance against "N. parisii". Microsporidia were found in several nematodes isolated from different locations, indicating that microsporidia are common natural parasites of "C. elegans". The "N. parisii"-"C. elegans" system represents a very useful tool to study infection mechanisms of intracellular parasites. Additionally, a new species of microsporidia was recently found in a wild caught "C. elegans" that genome sequencing places in the same genus "Nematocida" as prior microsporidia seen in these nematodes. This new species was named "Nematocida displodere," after a phenotype seen in late infected worms that explode at the vulva to release infectious spores. "N. displodere" was shown to infect a broad range of tissues and cell types in "C. elegans", including the epidermis, muscle, neurons, intestine, seam cells, and coelomocytes. Strangely, the majority of intestinal infection fails to grow to later parasite stages, while the muscle and epidermal infection thrives. This is in stark contrast to "N. parisii" which infects and completes its entire life cycle in the "C. elegans" intestine. These related "Nematocida" species are being used to study the host and pathogen mechanisms responsible for allowing or blocking eukaryotic parasite growth in different tissue niches.
Another eukaryotic pathogen is the fungus "Drechmeria coniospora", which has not been directly co-isolated with "C. elegans" from nature, but is still considered to be a natural pathogen of "C. elegans". "D. coniospora" attaches to the cuticle of the worm at the vulva, mouth, and anus and its hyphae penetrate the cuticle. In this way "D. coniospora" infects the worm from the outside, while the majority of bacterial pathogens infect the worm from the intestinal lumen.
Viral pathogens.
In 2011 the first naturally associated virus was isolated from "C. elegans" found outside of a laboratory. The Orsay virus is an RNA virus that is closely related to nodaviruses. The virus is not stably integrated into the host genome. It is transmitted horizontally under laboratory conditions. An antiviral RNAi pathway is essential for "C. elegans" resistance against Orsay virus infection. To date there has not been a virus, other intracellular pathogens, or multicellular parasite that have been able to affect the nematode. Because of this we cannot use "C. elegans" as an experimental system for these interactions. In 2005, two reports have shown that vesicular stomatitis virus (VSV), an arbovirus with a many invertebrate and vertebrate host range, could replicate in primary cells derived from C. elegans embryos.
Bacterial pathogens.
Two bacterial strains of the genus "Leucobacter" were co-isolated from nature with the two "Caenorhabditis" species "C. briggsae" and "C. n. spp 11", and named Verde 1 and Verde 2. These two "Leucobacter" strains showed contrasting pathogenic effects in "C. elegans". Worms that were infected with Verde 2 produced a deformed anal region (“Dar” phenotype), while infections with Verde 1 resulted in slower growth due to coating of the cuticle with the bacterial strain. In liquid culture Verde 1 infected worms stuck together with their tails and formed so called “worm stars”. The trapped worms cannot free themselves and eventually die. After death "C. elegans" is then used as a food source for the bacteria. Only larvae in the L4 stage seem to be able to escape by autotomy. They split their bodies into half, so that the anterior half can escape. The “half-worms” remain viable for several days.
The Gram-positive bacterium "Bacillus thuringiensis" is likely associated with "C. elegans" in nature. "B. thuringiensis" is a soil bacterium that is often used in infection experiments with "C. elegans". It produces spore-forming toxins, called crystal (Cry) toxins, which are associated with spores. These are jointly taken up by "C. elegans" orally. Inside the host, the toxins bind to the surface of intestinal cells, where the formation of pores in intestinal cells is induced, causing their destruction. The resulting change in milieu in the gut leads to germination of the spores, which subsequently proliferate in the worm body. An aspect of the "C. elegans"–"B. thuringiensis" system is the high variability in pathogenicity between different strains. There are highly pathogenic strains, but also strains that are less or even non-pathogenic.


Megabirnavirus


All That the Rain Promises and More...

All That the Rain Promises, and More... is a wild mushroom identification and field guide by American mycologist David Arora and published in 1991 by Ten Speed Press in Berkeley, California. The book includes detailed descriptions of more than 200 edible and poisonous mushroom species, as well as recipes, stories, and information on uses of various species such as for dying hair and clothing or playing games. In the preface, Arora writes, "In leafing through these pages, you may wonder what all the 'fanciful,' 'foolish,' or (shudder) 'extraneous' material is doing in a factual guide. After all, it is the practical, hands-on, how-to-identify information that makes this book useful and gives it substance. But I ask: is it any stranger or less desirable to sprinkle the facts with flakes of fancy than it is to liven up solemn, substantial fare like potatoes with something fancier and more flavorful, like wild mushrooms?"
The book is the second major work by David Arora. "Mushrooms Demystified" was published in 1979, also by Ten Speed Press.
The book was generally well received among critics. Writing for "The New York Times", critic Roger McKnight wrote that the book "is certainly the best guide to fungi, and may in fact be a long lasting masterpiece in guide writing for all subjects."


Alphanodavirus

Alphanodavirus is a genus of non-enveloped positive-strand RNA viruses in the family "Nodaviridae". Insects, mammals, and fishes serve as natural hosts. Diseases associated with this genus include: Nodamura virus paralysis in infected wax moth larvae. Member viruses can also provoke paralysis and death to suckling mice and suckling hamsters. There are five species in this genus.
Structure.
Viruses in the genus "Alphanodavirus" are non-enveloped, with icosahedral geometries, and T=3 symmetry. The diameter is around 30 nm. Genomes are linear and segmented, bipartite, around 21.4kb in length.
Life cycle.
Viral replication is cytoplasmic. Entry into the host cell is achieved by penetration into the host cell. Replication follows the positive-strand RNA virus replication model. Positive-strand RNA virus transcription, using the internal initiation model of subgenomic RNA transcription is the method of transcription. Member viruses are released by lysis of the infected host cell. Insects, mammals, and fishes serve as the natural host.
Taxonomy.
The genus has five species:


Funneliformis

Funneliformis is a genus of fungi in the family Glomeraceae. All species are arbuscular mycorrhizal (AM) fungi that form symbiotic relationships (mycorrhizaa) with plant roots. The genus was circumscribed in 2010 by Arthur Schüßler and Christopher Walker, with "Funneliformis mosseae" (originally described in 1968 as a species of "Endogone") as the type species. The generic name refers to the funnel-shaped spore base present in several species.


Spironematellaceae


Pneumocystis murina

Pneumocystis murina is a species of fungus, first isolated from laboratory mice, hence its name.


Candida rhizophoriensis

Candida rhizophoriensis is a yeast species first found in the Florida Everglades.


Planomicrobium

Planomicrobium (formerly "Planococcus") is a genus of gram-positive bacteria. It includes the hydrocarbon-degrading strain "P. alkanoclasticum" MAE2.


Zanardinia

Zanardinia is a monotypic genus of seaweed in the brown algae (class Phaeophyceae). The only species, Zanardinia typus, commonly known as penny weed, is native to the northeastern Atlantic Ocean and the Mediterranean Sea.
Description.
This brown alga is loosely secured to the rock by the felted rhizoids on the underside. Young individuals are circular and have a smooth surface and a double fringe of short hairs round the margin. Older individuals may be up to across and be fan-shaped or have broad blades with irregular margins. The consistency of the thallus is cartilaginous or leathery, and the colour is yellowish-brown or olive brown. Portions that become detached and wash up on the shore may crinkle as they dry and resemble pieces of blackish leather. This species could be confused with "Cutleria adspersa", but that species tends to grow in brightly-lit, very shallow places while "Z. typus" prefers deeper, shadier habitats. Also, the upper and lower surfaces of the thallus of "C. adspersa" appear similar, but "Z. typus" has a distinctively-felted under surface.
Distribution and habitat.
"Zanardinia typus" is found in the northeastern Atlantic Ocean and the Mediterranean Sea, its range including southwestern Britain and Ireland, the Atlantic coast of France, Spain and Portugal, the western Mediterranean Sea, the Adriatic Sea and the Black Sea. It grows on rock and silty boulders in the shallow subtidal zone at depths down to about .
Biology.
Growth in this species is "trichothallic", meaning that it occurs at the base of the marginal hairs. The edge of the thallus is two cells thick, and in the growth zone, the cells divide several times to form a thickened area with an upper cortex with about five rows of cells, a central parenchyma composed of long, thick-walled cells, and a lower cortex, with one or two rows of cells from which the rhizoids emerge. There is an alternation of generations in this brown alga into sporophytes and gametophytes, although these are similar in appearance. The reproductive organs differentiate on the upper surface of the thallus. The alga can also reproduce vegetatively, with cup-shaped new growths developing on old fronds.


Candidatus Legionella jeonii

"Candidatus" Legionella jeonii is a "candidatus" species of bacteria from the genus "Legionella". Previously known as X-bacterium"', "Candidatus" Legionella jeonii grows symbiotically in "Amoeba proteus". This endosymbiotic relationship was first noticed by Kwang Jeon and Joan Lorch in 1966.
A more recent reference dropped "Candidatus" from its name.


Methanoregula

In the taxonomy of microorganisms, Candidatus Methanoregula is a genus of the Methanomicrobiales. It was is isolated from an acidic peat bog. It produces methane at the lowest pH of any known organism.


Lycoperdon echinatum

Lycoperdon echinatum, commonly known as the spiny puffball or the spring puffball, is a type of puffball mushroom in the genus "Lycoperdon". The saprobic species has been found in Africa, Europe, Central America, and North America, where it grows on soil in deciduous woods, glades, and pastures. It has been proposed that North American specimens be considered a separate species, "Lycoperdon americanum", but this suggestion has not been followed by most authors. Molecular analysis indicates that "L. echinatum" is closely related to the puffball genus "Handkea".
The fruit bodies of "L. echinatum" are wide by tall, supported by a small base, and densely covered with spines that are up to long. The spines can fall off in maturity, leaving a net-like pattern of scars on the underlying surface. Initially white in color, the puffballs turn a dark brown as they mature, at the same time changing from nearly round to somewhat flattened. Young specimens of "L. echinatum" resemble another edible spiny puffball, "Lycoperdon pulcherrimum", but the latter species does not turn brown as it ages. The fruit bodies are edible when young, when the interior is white and firm and before it has turned into a powdery brown mass of spores. Laboratory tests have shown that extracts of the fruit bodies can inhibit the growth of several bacteria that are pathogenic to humans.
Taxonomy and phylogeny.
The species was first described by Christian Hendrik Persoon in 1797. It was later reduced to a variety of "Lycoperdon gemmatum" (as "L. gemmatum" var. "echinatum"; "L. gemmatum" is now known as "Lycoperdon perlatum") by Elias Magnus Fries, but American mycologist Charles Horton Peck, who extensively studied the North American distribution of the genus, raised it again to species level in 1879. He thought it worthy of status as a species distinct from "L. gemmatum" because of the different character of its warts, its much spinier appearance, and the smoother surface of the peridium underneath the spines. Miles Joseph Berkeley and Christopher Edmund Broome wrote of the fungus in 1871, but believed their specimen, collected from Reading, Berkshire, by Hoyle, represented a new species, which they called "Lycoperdon Hoylei". They wrote that their specimen agreed "exactly with an authentic specimen of Persoon's "L. echinatum" externally, who could, however, scarcely have overlooked the lilac spores." Despite the apparent difference in spore color, "L. Hoylei" is currently considered synonymous with "L. echinatum". "Utraria echinata", named by Lucien Quélet in 1873, is another synonym for "L. echinatum".
In 1972, Vincent Demoulin described the species "Lycoperdon americanum" on the basis of a specimen found in North Carolina. Although he believed it to be a unique species, several authors consider it synonymous with "L. echinatum". Phylogenetic analysis of the sequence and secondary structure of the ribosomal RNA (rRNA) genes coding for the internal transcribed spacer units suggests that "Lycoperdon echinatum" forms a clade with the puffball genus "Handkea", separate from the type species of "Lycoperdon", "Lycoperdon perlatum". In previous analyses that used only the rRNA sequences for phylogenetic comparison, "L. echinatum" formed a clade with "L. mammiforme", "L. foetidum", and "Bovistella radicata" (now known as "Lycoperdon radicatum"), but separate from "L. pyriforme".
The species is commonly known as the "spiny puffball" or the "spring puffball"; Peck referred to the species as the "echinate puff-ball". The specific epithet "echinatum" is derived from the Greek word "echinos" (εχινος) meaning "hedgehog" or "sea-urchin".
Description.
The fruit bodies of "L. echinatum" are wide by tall, and are roughly spherical, or pear-shaped. The exterior surface is crowded with spines that may be up to long. According to Curtis Gates Lloyd, American specimens have more slender spines than European ones. Initially white and becoming dark brown in maturity, the spines are often joined at the tips in groups of three or four. In this form the puffballs resemble acorn caps of burr oak, with which they may readily be confused. The spines slough off in age, revealing a somewhat net-like or reticulated surface. The fruit body has a small base that is an off-white or purple-gray color, and it may be attached to the growing surface by thin white cords (rhizomorphs). The internal contents of the puffball contain the gleba, a mass of spores and associated spore-producing cells. In young specimens the gleba is white and firm, but as the puffball ages, it turns yellowish and then brown to purple-brown and powdery. Mature specimens develop a pore at the top of the fruit body through which spores are released when hit by falling raindrops.
The spores of "L. echinatum", roughly spherical with warts on the surface, have diameters between 4 and 6 µm. The capillitia (coarse thick-walled hyphae in the gleba) are elastic, brown in color, contain small pores, and are 5–8 µm thick. The basidia (the spore-bearing cells) may be attached to two to four spores, and the sterigmata (tapered spine-like projections from the basidia that attach the spores) are up to 5 µm long.
Like most other puffball species, "L. echinatum" is edible when still young and while the gleba is still white and firm. Consumption of older specimens with a non-white gleba, or where the gleba has turned into a powdery spore mass, may cause stomach upsets. This species has a mild taste, and no distinguishable odor, although one source describes the smell of dried fruit bodies as similar to "old ham". One source notes that it is "well flavoured and tender when cooked", while another describes the texture (of edible puffballs in general) as "somewhat like French toast". Antonio Carluccio recommends sautéeing puffballs with other mushrooms. To avoid possible confusion with potentially deadly "Amanita" species, it is recommended to slice young puffballs with a longitudinal cut to ensure that the flesh is devoid of any internal structures.
Similar species.
"Lycoperdon pulcherrimum" closely resembles "L. echinatum", but its spines are stouter, do not turn brown in age, and the surface of the fruit body underneath the spines is smooth, not pitted. Alexander H. Smith noted that in youth, they are "difficult if not impossible to distinguish from each other, but this will cause no inconvenience to those collecting for the table, since both are edible." In some areas the two species appear to intergrade, as specimens may be found whose spines turn brown but do not fall off. Young specimens of "L. pedicellatum" may also be difficult to distinguish from "L. echinatum", but the former has a smooth outer surface when mature, and has spores attached to a pedicel (a narrow extension of the basidium on which the sterigmata and spores are formed) that is about 4–5 times as long as the spore. "Lycoperdon compactum", found only in New Zealand, also resembles "L. echinatum" in appearance, but differs in having smaller spores, capillitia that are hyaline (translucent) and septate (with partitions that divide the capillitia into compartments).
Habitat, distribution, and ecology.
"Lycoperdon echinatum" can be found either solitary or in small groups. It typically grows on the ground in deciduous forests and grassy areas, glades and pastures, on moss, humus, or woody debris. The fungus has been noted to have a preference for beech woods. Fruit bodies may make their appearance anytime from the late spring to autumn. Older specimens are more likely to be overlooked, as their brown color blends into the surrounding environment of dead leaves and dead wood. The puffball is used by various species of scuttle flies (family Phoridae) as larval food.
This species has been collected from eastern central Africa, China, Costa Rica, Iran, Japan, and Europe (including Britain, Bulgaria, the Czech Republic, Finland, Germany, Italy, Slovakia, Spain, Sweden, and Switzerland). In North America, it is "locally frequent" east of the Rocky Mountains.
It is considered a threatened species in the Åland Islands of Finland. A study of the species' distribution in Sweden reported that in the 1940s and 50s, it grew in beech woods with broad-leaved grasses and herbs in topsoils with soil pH levels between 5.0 and 6.6, but the populations have since decreased owing to soil acidification during the last several decades. Fruit bodies collected near arsenic-contaminated sites have been shown to bioaccumulate arsenic, largely in the form of arsenobetaine.
Antimicrobial activity.
Using a standard laboratory method to determine antimicrobial susceptibility, methanol-based extracts of "Lycoperdon umbrinum" fruit bodies were shown in a 2005 study to have "significant" antibacterial activity against various human pathogenic bacteria, including "Bacillus subtilis", "Escherichia coli", "Salmonella typhimurium", "Staphylococcus aureus", "Streptococcus pyogenes", and "Mycobacterium smegmatis". An earlier study (2000) had identified weak antibacterial activity against "Enterococcus faecium" and "Staphylococcus aureus". Although the specific compounds responsible for the antimicrobial activity have not been identified, chemical analysis confirms the presence of terpenoids, a class of widely occurring organic chemicals that are being investigated for their potential use as antimicrobial drugs.


Vibrion

Vibrion may also refer to: the singular form of "vibrio", a genus of anaerobic bacteria with a comma-like shape.
Vibrion is an antiquated term for microorganisms, especially pathogenic ones; see Germ theory of disease. The term was specifically used in reference to motile microorganisms, and the name of the genus "Vibrio" derives from this term. The term is closely tied to the history of the study of cholera. It was used in biological literature between the late 19th century and the 1920s.
Early Identification and Characterization of "Vibrio" bacteria.
Bacteria with the same characteristics as those of the genus "Vibrio" were discovered independently multiple times, but only later findings were able to connect these bacteria with cholera, tetanus, and other diseases.
Leeuwenhoek may have observed "Vibrio" bacteria after his discovery of “animalcules” described in his letters to the Royal Society. He described microorganisms with the same appearances and behaviors as bacteria belonging to the genus "Vibrio". Bacteria of this genus were later anonymously described as “Capillary Eels” in the 1703 issue of "Philosophical Transactions" by a “Sir C. H.” because of their thin, wormlike appearance. Additionally, the naturalist O. F. Müller documented eight species of the genus "Vibrio" in his work on infusoria.
History of the Term.
In 1854, the Italian anatomist Filippo Pacini coined the term "vibrions" in a paper he published during the third Cholera pandemic arguing that they were the main agents causing cholera. He drew his conclusion from his observations of the thin, wormlike bacteria present in the blood and stool of cholera patients, especially characteristic of late-stage infections. The "Vibrio cholerae" identified by Pacini were rediscovered by Robert Koch in 1884, who was unaware of Pacini's work; he called them “Comma Bacillus” and received worldwide fame as a result of his discovery.
The term “vibrion” was subsequently used by Louis Pasteur in 1861 in naming a bacterium he discovered, "Vibryon butyrique", which was capable of surviving in an environment without oxygen. This bacterium was then identified as the same bacterium which had been discovered by two other scientists and renamed "Clostridium butyricum".
By the 20th century "vibrion" came to be used as a general term for motile microorganisms with an elongated, wormlike shape associated with pathogenic illnesses such as cholera and tetanus. It was also incorporated in the names created for several bacteria by microbiologists at the time, such as in the name "Vibrion septique" from a 1922 paper in "The" "Journal of Medical Research." In an issue of the journal "Modern Medicine" from 1893, the term "cholera vibrion" is used to refer to "Vibrio cholerae". In the same journal from 1893, the term "vibrion" is said to be dated, which highlights the brevity of the time period in which the word was used.
The term "vibrion" was out of use by the late 1920s and does not appear on its own in subsequent biological literature. This is largely due to the more extensive development of bacterial taxonomy towards the turn of the 19th century, which gave bacteriologists a more specific way to classify microorganisms. The term "vibrion" was adapted into the name of the "Vibrio" prokaryotic genus.


Mycobacterium mucogenicum

Mycobacterium mucogenicum
Etymology: mucogenicum, from the organism's highly mucoid appearance.
Description.
Gram-positive, nonmotile, curved and acid-fast rods.
Colony characteristics
Physiology


Asian koel

The Asian koel ("Eudynamys scolopaceus") is a member of the cuckoo order of birds, the Cuculiformes. It is found in the Indian Subcontinent, China, and Southeast Asia. It forms a superspecies with the closely related black-billed koels, and Pacific koels which are sometimes treated as subspecies. The Asian koel like many of its related cuckoo kin is a brood parasite that lays its eggs in the nests of crows and other hosts, who raise its young. They are unusual among the cuckoos in being largely frugivorous as adults. The name "koel" is echoic in origin with several language variants. The bird is a widely used symbol in Indian and Nepali poetry.
Description.
The Asian koel is a large and long-tailed cuckoo measuring and weighing . The male of the nominate race is glossy bluish-black, with a pale greenish grey bill, the iris is crimson, and it has grey legs and feet. The female of the nominate race is brownish on the crown and has rufous streaks on the head. The back, rump and wing coverts are dark brown with white and buff spots. The underparts are whitish, but is heavily striped. The other subspecies differ in colouration and size. The upper plumage of young birds is more like that of the male and they have a black beak.
They are very vocal during the breeding season (March to August in the Indian Subcontinent), with a range of different calls. The familiar song of the male is a repeated "koo-Ooo". The female makes a shrill "kik-kik-kik..." call. Calls vary across populations.
They show a pattern of moult that differs from those of other parasitic cuckoos. The outer primaries show a transilient (alternating) ascending moult (P9-7-5-10-8-6) while the inner primaries are moulted in stepwise descending order (1-2-3-4).(Payne citing Stresemann and Stresemann 1961)
Taxonomy.
The Asian koel was originally described by Carl Linnaeus as "Cuculus scolopaceus" based on a specimen he received from the Malabar region. The species has variations within its wide range with several island populations and a number of taxonomic variations have been suggested. The black-billed koel ("E. melanorhynchus") of the Sulawesi region and the Pacific koel of Australasia are sometimes considered conspecific with the Asian koel in which case the "combined" species is known as the common koel. Due to differences in plumage, colour of bill and voice, the three are increasingly treated as separate species. Alternatively, only the black-billed koel has been considered as a separate species, or the Asian koel has included all subspecies otherwise included in the Pacific koel, except for the subspecies breeding in Australia, which then has the name Australian koel ("E. cyanocephalus").
The Asian koel has several geographic forms that have well marked plumage differences or have been geographically isolated with little gene flow. The following is a list of named subspecies with their distributions and synonyms as given by Payne:
Distribution and habitat.
The Asian koel is a bird of light woodland and cultivation. It is a mainly resident breeder in tropical southern Asia from Iran, Pakistan, India, Bangladesh and Sri Lanka to southern China and the Greater Sundas. They have great potential in colonizing new areas, and were among the pioneer birds to colonize the volcanic island of Krakatau. They first arrived in Singapore in the 1980s and became very common birds.
Some populations may make long-distance movements being found in places like Australia.
Behaviour.
The Asian koel is a brood parasite, and lays its single egg in the nests of a variety of birds, including the jungle crow, and house crow. In Sri Lanka before 1880 it was only known to parasitize the jungle crow, later shifting to the house crow. A study in India found 5% of "Corvus splendens" and 0.5% of "Corvus macrorhynchos" nests parasitized.
In Bangladesh, they parasitise long-tailed shrike ("Lanius schach"), common myna ("Acridotheres tristis") and house crows ("Corvus splendens") at about 35.7, 31.2 and 10.8% rates respectively. Host nests at low heights and nearer to fruit trees tended to be preferred by koels. In southern Thailand and the Malay Peninsula, koels have shifted host from crows to mynas ("Acridotheres" sp.) as the latter became more common in the late 1900s. In the Indian Subcontinent they have sometimes been found to parasitize the black drongo, the European magpie and possibly the black-headed oriole. Males may distract the hosts so that the female gets a chance to lay an egg in the nest. More often however, the female visits the nest of the host alone. The koel is not known to lay eggs in an empty host nest and a study in Pakistan found that the first koel eggs were laid, on average, within one and half days of the laying of the host's first egg. The chicks of the koel hatched about 3 days ahead of the host chicks. Koels usually lay only an egg or two in a single nest but as many as seven to eleven eggs have been reported from some host nests. A female may remove a host egg before laying. Eggs hatch in 12 to 14 days. The young koel does not always push out eggs or evict the host chicks, and initially calls like a crow. The young fledge in 20 to 28 days. Unlike some other cuckoos, the young do not attempt to kill the host chicks, a trait that is shared with the channel-billed cuckoos which are also largely frugivorous as adults. It has been suggested that koels, like some other brood parasites do not evict the host chicks due presumably due to the higher cost of evicting nestmates. A small parasite may not be able to evict large host eggs or chicks from a deep Corvid nest without risking starvation and possibly accidental self-eviction. An alternative hypothesis that retaining host chicks might benefit the koel chicks did not gain much support. Adult female parents have been known to feed young koels in the nests of the hosts, a behaviour seen in some other brood parasitic species as well. Adult males have however not been noted to feed fledglings.
The Asian koel is omnivorous, consuming a variety of insects, caterpillars, eggs and small vertebrates. Adults feed mainly on fruit. They will sometimes defend fruiting trees that they forage in and chase away other frugivores. They have been noted to be especially important in the dispersal of the sandalwood tree ("Santalum album") in India. Large seeded fruits are sometimes quickly regurgitated near the parent tree while small seeded fruits are ingested and are likely to be deposited at greater distances from the parent tree. They have a large gape and are capable of swallowing large fruits including the hard fruit of palms such as "Arenga" and "Livistona". They have been known to occasionally take eggs of small birds.
They feed on the fruits of "Cascabela thevetia" which are known to be toxic to mammals.
A number of parasites of the species have been described, including malaria-like protozoa, lice and nematodes.
In culture.
The word "koel" is onomatopoeic in origin. The Sanskrit name of "Kokila" and words in several Indian languages are similarly echoic. Being familiar birds with loud calls, references to them are common in folklore, myth and poetry. It is traditionally held in high regard for its song and revered in the Manusmriti, with a decree protecting them from harm. The Vedas, Sanskrit literature dated to about 2000 BC referred to it as "Anya-Vapa" which has been translated as "that which was raised by others" (or "sown for others to reap"). This has been interpreted as the earliest knowledge of brood parasitism. It has been chosen as the state bird by the Indian union territory of Puducherry.
These birds were once very popular in India as cagebirds. Feeding even on boiled rice, these hardy birds lived in captivity for as long as 14 years.


Candidatus Bartonella mayotimonensis

""Candidatus" Bartonella mayotimonensis" is a candidatus bacteria from the genus of "Bartonella" which can cause endocarditis in humans


Gyroporus brunneofloccosus

Gyroporus brunneofloccosus is a species of bolete fungus in the family Gyroporaceae. Described as new to science in 2003, it is found in China.


Candidatus Bartonella woyliei

""Candidatus" Bartonella woyliei" is a candidatus bacteria from the genus of "Bartonella" which was isolated from the fleas "Pygiopsylla hilli" and "Ixodes australiensis".


Symmachia menetas

Symmachia menetas is a species in the butterfly family Riodinidae found in Brazil and Suriname. It was first described by Dru Drury in 1782.
Description.
Upperside. Antennae black. Front of the head yellow. Thorax black, with two yellow streaks at the base of the wings. Abdomen dark brown. Half of the superior wings black, beginning at the shoulders, and running to the external edges, on which are seven cream-coloured spots variously shaped. The other half of these wings is scarlet, without any marks. Posterior wings entirely scarlet, edged with black.
Underside. Palpi cream coloured. Breast and abdomen light yellow. Legs black, but underneath pale yellow. Wings coloured as on the upperside. Margins of the wings entire. Wingspan inches (33 mm).


Agaricus inapertus

Agaricus inapertus is a species of secotioid fungus in the genus "Agaricus". It was first described by American mycologists Rolf Singer and Alexander H. Smith in 1958 as "Endoptychum depressum". Molecular analysis later proved it to be aligned with "Agaricus", and it was formally transferred in a 2003 publication.


Bartonella japonica

Bartonella japonica is a species of proteobacteria in the genus "Bartonella". A strain of this species was originally isolated from the blood of a small Japanese field mouse ("Apodemus argenteus").


Megamonas

Megamonas is a genus of Firmicutes bacteria classified within the class Negativicutes.
Phylogeny.
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI)
and the phylogeny is based on 16S rRNA-based LTP release 111 by The All-Species Living Tree Project


Nitrosomonas eutropha

Nitrosomonas eutropha is an ammonia-oxidizing, Gram-negative bacterium from the genus of "Nitrosomonas".
Starting in 2014, it was being tested by the biotech company AOBiome for its possible health benefits on skin. AOBiome started a Phase II trial of an intranasal formulation of the bacteria for migraines.


Cnuibacter

Cnuibacter is a genus of bacteria. Cells are Gram-positive rods, strictly aerobic, non-sporeforming, and non-motile.
The genus was proposed in 2016, when the only species of the genus, "Cnuibacter physcomitrellae", was isolated from "Physcomitrella patens", or spreading earthmoss. The genus is named after Capital Normal University (CNU) in Beijing, China.