Teseptimavirus

Teseptimavirus (synonyms "T7 phage group", "T7-like phages", "T7-like viruses", "T7likevirus") is a genus of viruses in the order "Caudovirales", in the family "Autographiviridae", in the subfamily "Studiervirinae". Bacteria serve as the natural host, with transmission achieved through passive diffusion. There are currently 17 species in this genus, including the type species "Escherichia virus T7".
Taxonomy.
The following species are recognized:
Structure.
Sp6likeviruses are nonenveloped, with a head and tail. The head has icosahedral symmetry (T=7) approximately 60 nm in diameter. The tail is non-contractile and has six short subterminal fibers.
Genome.
Genomes are linear, around 40-42kb in length. All three viruses' genomes have been fully sequenced and are available on NCBI's website. They range between 37k and 40k nucleotides, with 42 to 60 proteins. All three complete genomes, as well as several additional "unclassified" virus genomes, are available here
Life cycle.
Viral replication is cytoplasmic. The virus attaches to the host cell adhesion receptors using its tail fibers, and ejects the viral DNA into the host periplasm via short tail system. Class I genes are transcribed by the host cell's RNA polymerase before the viral genome completely exits the capsid. Class II genes are then transcribed by T7 RNA polymerase and the host genome is degraded. Genomic DNA is replicated by T7 DNA polymerase and concatemers are formed before Class III genes are transcribed. Finally, the procapsid is assembled and packed, the tail is assembled and the mature virions are released via lysis. Bacteria serve as the natural host. Transmission routes are passive diffusion.
History.
According to ICTV's second report in 1976, the genus "T7likevirus" was first accepted under the name "T7 phage group", unassigned to an order, family, or sub-family. In ICTV's third report in 1981, the genus was classified into the family "Poloviridae". "T7 phage group" was renamed to "T7-like phages" in the sixth report in 1995. In 1998, the whole family was moved into the newly created order "Caudovirales", and the genus was renamed again in the seventh report in 1999 to "T7-like viruses". 2009 saw the genus moved into the newly created subfamily "Autographivirinae", and it was renamed again in 2012 to "T7likevirus". The genus was later renamed to Teseptimavirus under the newly established family "Autographiviridae" and subfamily "Studiervirinae".


Vibrio campbellii

Vibrio campbellii is a Gram-negative, curved rod-shaped, marine bacterium closely related to its sister species, "Vibrio harveyi". It is an emerging pathogen in aquatic organisms.
Biology.
Quorum sensing allows the bacterium to communicate with autoinducers, a chemical signaling molecule that is secreted. Some strains of "V. campellii" are known to be not luminescent; these strains are thought to be less virulent than the luminescent strains.
Bioluminescence in bacteria is due to the reaction:
FMNH− + H+ + RCHO + O2 → FMN + RCOOH + H2O + hν
and is catalyzed by the enzyme luciferase. A new luciferase was isolated from "V. campbellii" (Lux_Vc) and is similar to that of the Lux_Vh found in "V. harveyi", but is more thermodynamically stable due to the binding of reduced FMN.
The "V. campbellii" strains PEL22A, BAA-1116, AND4 are known to be mixotrophic or more specifically photo(organo)heterotrophic. This is considered a rare phenotype in "Vibrio" and is thought to be caused by their exploitation of lateral gene transfer during adaptation.
Pathogenesis.
The causes of virulence can vary depending on different strains. The PEL22A strain showed that the genes that regulate the bacteriophage CTXΦ, the main cause of virulence in "Vibrio cholerae", were present but lack the genes for cholera toxin, "ctxA" and "ctxB". The strain did contain "hlyA" gene which codes for hemolysin, an endotoxin found in most "Vibrio" species.


Tapinella (fungus)

Tapinella is a genus of three inedible fungi in the Tapinellaceae family. The genus was circumscribed by the French mycologist Jean-Edouard Gilbert in 1931.


MicrobeLibrary

MicrobeLibrary is a permanent collection of over 1400 original peer-reviewed resources for teaching undergraduate microbiology. It is provided by the American Society for Microbiology, Washington DC, United States.
Contents include curriculum activities; images and animations; reviews of books, websites and other resources; and articles from "Focus on Microbiology Education", "Microbiology Education" and "Microbe". Around 40% of the materials are free to educators and students, the remainder require a subscription. the service is suspended with the message to:


Kyrpidia spormannii

Kyrpidia spormannii is a species of Gram positive, aerobic, thermophilic bacterium. The cells are rod-shaped and form spores. It was first isolated from sediment samples from hydrothermal systems collected in the Azores. The species is named in honor of German-American microbiologist Alfred M. Spormann, in recognition of his work on the field microbial electrosynthesis.
The optimum growth temperature for "K. spormannii" is 55 °C, and can grow in the 45-65 °C range. Its optimum pH is 5.5, and grows in pH range 4.5-7.0.


Preoperational anxiety

Preoperational anxiety, or preoperative anxiety, is a common reaction experienced by patients who are admitted to a hospital for surgery. It can be described as an unpleasant state of tension or uneasiness that results from a patient's doubts or fears before an operation.
Measuring preoperative anxiety.
The State-Trait Anxiety Inventory (STAI) is a widespread method of measuring preoperative anxiety for research purposes. It consists of two 20-item scales on which patients are asked to rate particular symptoms.
The STAI is based on the theory that there are two distinct aspects of anxiety. The State scale is designed to measure the circumstantial or temporary arousal of anxiety, and the Trait scale is designed to measure longstanding personality characteristics related to anxiety. The items on each scale are based on a two-factor model: "anxiety present" or "anxiety absent".
In a 2009 paper in "The" "Journal of Nursing Measurement", researchers argued that fast-paced hospital environments make it difficult to get each patient through all 20 items, especially when other assessments must also be done. Shorter versions of the STAI have been developed. For example, Marteau and Bekker’s six-item version of the State scale was found in 2009 to have "favorable internal consistency reliability and validity when correlated with the parent 20-item State scale".
Causes of anxiety.
A variety of fears can cause preoperative anxiety. They include fear of:
Other factors in the intensity of preoperative anxiety are:
Irving Janis separates the factor trends that are commonly seen affecting anxiety into three different levels:
Effects of preoperative anxiety.
Physiological effects.
Anxiety can cause physiological responses such as tachycardia, hypertension, elevated temperature, sweating, nausea, and a heightened sense of touch, smell, or hearing.
A patient may also experience peripheral vasoconstriction, which makes it difficult for the hospital staff to obtain blood.
Psychological effects.
Anxiety may cause behavioral and cognitive changes that result in increased tension, apprehension, nervousness, and aggression.
Some patients may become so apprehensive that they cannot understand or follow simple instructions. Some may be so aggressive and demanding that they require constant attention of the nursing staff.
Behavioral strategies and trends.
In research conducted by Irving Janis, common reactions and strategies were separated into three different levels of preoperative anxiety:
Low anxiety
Patients in this category tend to adopt a joking attitude or to say things like "there’s nothing to it!" Because most pain is not preconceived by the patient, the patients tends to blame their pain on the hospital staff. In this case, the patient feels as if they have been mistreated. This is because the patient doesn't have the usual mindset that pain is an unavoidable result of an operation.
Other trends include displaying a calm and relaxed attitude during preoperative care. They don't usually experience any sleeping disturbances. They also tend to make little effort to seek more information about medical procedures. This may be due to the fact that they are unaware of the potential threats, or it may just be because they have succeeded in shutting themselves out and eliminating all thought of doubt and fear.
The main concern that low anxiety patients tend to express is finances, and they usually deny apprehension about operational dangers.
Moderate anxiety
Patients in this category may only experience minor emotional tension. The occasional worry or fear that is experienced by a patient with moderate anxiety can usually be suppressed.
Some may suffer from insomnia, but they also usually respond well to mild sedatives. Their outward manner may seem relatively calm and well controlled, except for small moments where it is apparent to others that the patient is suffering from an inner conflict. They can usually perform daily tasks, only becoming restless from time to time.
These patients are usually very motivated to develop reliable information from medical authority in order to reach a point of comfortable relief.
High anxiety
Patients in this category will usually try to reassure themselves by seeking information, but these attempts, in the long-run, are unsuccessful at helping the patient reach a comfortable point because the fear is so dominant.
It is common for patients in this level of anxiety to engage in mentally distracting activities in an attempt to get their mind off of anticipated danger. They have a hard time idealizing their situation or maintaining any sort of conception that things could turn out well in the end. This because they tend to dwell on improbable dangers.
Effects.
Preparation for surgery.
On the positive side, if a patient experiences moderate amounts of anxiety, the anxiety can aid in the preparation for surgery. On the negative side, the anxiety can cause harm if the patient experiences an excessive or diminutive amount. One reason for this is that small amounts of anxiety will not adequately prepare the patient for pain. Also, higher levels of anxiety can over-sensitize the patient to unpleasant stimuli, which would heighten their senses of touch, smell or hearing. This results in intense pain, dizziness, and nausea. It can also increase the patient’s feelings of uneasiness in the unfamiliar surroundings.
Post-operation.
Anxiety has also been proven to cause higher analgesic and anaesthetic requirement, postoperative pain, and prolonged hospital stay.
Irving L. Janis separates the effects of preoperative anxiety on postoperative reactions into three levels:
Treatment.
Treatment of preoperative anxiety may include:


Aggresome

In eukaryotic cells, an aggresome refers to an aggregation of misfolded proteins in the cell, formed when the protein degradation system of the cell is overwhelmed. Aggresome formation is a highly regulated process that possibly serves to organize misfolded proteins into a single location.
Biogenesis.
Correct folding requires proteins to assume one particular structure from a constellation of possible but incorrect conformations. The failure of polypeptides to adopt their proper structure is a major threat to cell function and viability. Consequently, elaborate systems have evolved to protect cells from the deleterious effects of misfolded proteins.
Cells mainly deploy three mechanisms to counteract misfolded proteins: up-regulating chaperones to assist protein refolding, proteolytic degradation of the misfolded/damaged proteins involving ubiquitin–proteasome and autophagy–lysosome systems, and formation of detergent-insoluble aggresomes by transporting the misfolded proteins along microtubules to a region near the nucleus. Intracellular deposition of misfolded protein aggregates into ubiquitin-rich cytoplasmic inclusions is linked to the pathogenesis of many diseases. Functional blockade of either degradative system leads to an enhanced aggresome formation. Why these aggregates form despite the existence of cellular machinery to recognize and degrade misfolded protein, and how they are delivered to cytoplasmic inclusions, are not known.
Aggresome formation is accompanied by redistribution of the intermediate filament protein vimentin to form a cage surrounding a pericentriolar core of aggregated, ubiquitinated protein. Disruption of microtubules blocks the formation of aggresomes. Similarly, inhibition of proteasome function also prevents the degradation of unassembled presenilin-1 (PSE1) molecules leading to their aggregation and deposition in aggresomes. Aggresome formation is a general response of cells which occurs when the capacity of the proteasome is exceeded by the production of aggregation-prone misfolded proteins.
Typically, an aggresome forms in response to a cellular stress which generates a large amount of misfolded or partially denatured protein: hyperthermia, overexpression of an insoluble or mutant protein, etc. The formation of the aggresome is largely believed to be a protective response, sequestering potentially cytotoxic aggregates and also acting as a staging center for eventual autophagic clearance from the cell.
An aggresome forms around the microtubule organizing center in eukaryotic cells, adjacent to or enveloping the cell's centrosomes. Polyubiquitination tags the protein for retrograde transport via HDAC6 binding and microtubule-based motor protein, dynein. Moreover, substrates can also be targeted to the aggresome by a ubiquitin-independent pathway mediated by the stress-induced co-chaperone BAG3 (Bcl-2-associated athanogene 3), which transfers misfolded protein substrates bound to HSP70 (heat-shock protein 70) directly on to the microtubule motor dynein. The protein aggregate is then transported along the microtubule and unloaded via ATPase p97 forming the aggresome. Mediators such as p62 are believed to be involved in aggresome formation in sequestering omega-somes, which bind and increase the size of the aggresome. The aggresome is eventually targeted for autophagic clearance from the cell. Some pathological proteins, such as alpha-synuclein, cannot be degraded and cause the aggresomes to form inclusion bodies (in Parkinson's disease, Lewy bodies) which contribute to neuronal dysfunction and death.
Triggering aggresome formation.
Abnormal polypeptides that escape proteasome-dependent degradation and aggregate in cytosol can be transported via microtubules to an aggresome, a recently discovered organelle where aggregated proteins are stored or degraded by autophagy. Synphilin 1, a protein implicated in Parkinson disease, was used as a model to study mechanisms of aggresome formation. When expressed in naïve HEK293 cells, synphilin 1 forms multiple small highly mobile aggregates. However, proteasome or Hsp90 inhibition rapidly triggered their translocation into the aggresome, and surprisingly, this response was independent on the expression level of synphilin 1. Therefore, aggresome formation, but not aggregation of synphilin 1, represents a special cellular response to a failure of the proteasome/chaperone machinery. Importantly, translocation to aggresomes required a special aggresome-targeting signal within the sequence of synphilin 1, an ankyrin-like repeat domain. On the other hand, formation of multiple small aggregates required an entirely different segment within synphilin 1, indicating that aggregation and aggresome formation determinants can be separated genetically. Furthermore, substitution of the ankyrin-like repeat in synphilin 1 with an aggresome-targeting signal from huntingtin was sufficient for aggresome formation upon inhibition of the proteasome. Analogously, attachment of the ankyrin-like repeat to a huntingtin fragment lacking its aggresome-targeting signal promoted its transport to aggresomes. These findings indicate the existence of transferable signals that target aggregation-prone polypeptides to aggresomes.
Human disease.
Accumulation of misfolded proteins in proteinaceous inclusions is common to many age-related neurodegenerative diseases, including Parkinson's disease, Alzheimer's disease, Huntington's disease, and amyotrophic lateral sclerosis. In cultured cells, when the production of misfolded proteins exceeds the capacity of the chaperone refolding system and the ubiquitin-proteasome degradation pathway, misfolded proteins are actively transported to a cytoplasmic juxtanuclear structure called an aggresome. Whether aggresomes are benevolent or noxious is unknown, but they are of particular interest because of the appearance of similar inclusions in protein deposition diseases. Evidence shows that aggresomes serve a cytoprotective function and are associated with accelerated turnover of mutant proteins. Experiments show that mutant androgen receptor (AR), the protein responsible for X-linked spinobulbar muscular atrophy, forms insoluble aggregates and is toxic to cultured cells. Mutant AR was also found to form aggresomes in a process distinct from aggregation. Molecular and pharmacological interventions were used to disrupt aggresome formation, revealing their cytoprotective function. Aggresome-forming proteins were found to have an accelerated rate of turnover, and this turnover was slowed by inhibition of aggresome formation. Finally, it is shown that aggresome-forming proteins become membrane-bound and associate with lysosomal structures. Together, these findings suggest that aggresomes are cytoprotective, serving as cytoplasmic recruitment centers to facilitate degradation of toxic proteins.
Proteins implicated in aggresome formation.
Histone deacetylase 6 is the protein that, in the deacetylase adaptor protein function, forms Lewy bodies (the regular wild-type protein localized to inclusion bodies). No mutation associated with disease has been linked to this protein.
Parkin is the protein that, in the protein ligase function, forms Lewy bodies (the regular wild-type protein localized to inclusion bodies). Parkinson's disease has been linked to this protein when there is a protein.
Ataxin-3 is the protein that, in the deubiquitinating enzyme function, forms SCA type-1 and 2 DRPLA intranuclear inclusions (the regular wild-type protein localized to inclusion bodies). SCA type-3 has been linked to this protein when there is a protein.
Dynein motor complex is the protein that, in the retrograde microtubule motor function, forms an unknown protein (the regular wild-type protein localized to inclusion bodies). Motor neuron degeneration has been linked to this protein when there is a protein.
Ubiquilin-1 is the protein that, in the protein turnover, intracellular trafficking function, forms Lewy bodies and neurofibrillary tangles (the regular wild-type protein localized to inclusion bodies). Alzheimer's disease (potential risk factor) has been linked to this protein when there is a protein.
Cystic fibrosis.
Cystic fibrosis transmembrane conductance regulator (CFTR) is an inefficiently folded integral membrane protein that is degraded by the cytoplasmic ubiquitin-proteasome pathway. Overexpression or inhibition of proteasome activity in transfected human embryonic kidney cells or Chinese hamster ovary cells leads to the accumulation of stable, high molecular weight, detergent-insoluble, multi-ubiquitinated forms of CFTR. Undergraded CFTR molecules accumulate at a distinct pericentriolar aggresome.
Role of the aggresome pathway in cancer.
There is emerging evidence that inhibiting the aggresome pathway leads to accumulation of misfolded proteins and apoptosis in tumor cells through autophagy.


Halorubrum salsolis

"Halorubrum salsolis" is an undescribed species of halobacteria which is known to live in the Great Salt Lake in the United States.
The microbe was named by two children who took part in a naming contest held by the discoverers of the organism in 2006; the children independently suggested "salsolis" as the species name for the microbe.
This halophilic extremophile lives in water 10 times saltier than the ocean. It contains carotenoids that make it resistant to ultraviolet rays.


St. Nicholas Magazine

St. Nicholas Magazine was a popular monthly American children's magazine, founded by Scribner's in 1873. The first editor was Mary Mapes Dodge, who continued her association with the magazine until her death in 1905. Dodge published work by the country's best writers, including Louisa May Alcott, Frances Hodgson Burnett, Mark Twain, Laura E. Richards and Joel Chandler Harris. Many famous writers were first published in "St. Nicholas League", a department that offered awards and cash prizes to the best work submitted by its juvenile readers. Edna St. Vincent Millay, F. Scott Fitzgerald, E. B. White, and Stephen Vincent Benet were all St. Nicholas League winners.
"St. Nicholas Magazine" ceased publication in 1940. A revival was attempted in 1943, but only a few issues were published before "St. Nicholas" folded once more.
Founding.
In 1870 Roswell Smith, cofounder of the magazine publishing company Scribner & Company, contacted Mary Mapes Dodge to inquire if she would be interested in working for a projected new children's magazine. At the time Dodge was an associate editor of the weekly periodical "Hearth and Home", as well as the author of children's novels, including the best-seller "Hans Brinker, or the Silver Skates".
Dodge had specific ideas about what a children's magazine should and shouldn't be. She felt it must not be "a milk-and-water variety of the periodicals for adults. In fact, it needs to be stronger, truer, bolder, more uncompromising than the other... Most children...attend school. Their heads are strained and taxed with the day's lessons. They do not want to be bothered nor amused nor petted. They just want to have their own way over their own magazine."
The first issue of "St. Nicholas: Scribner's Illustrated Magazine for Girls and Boys" was dated November, 1873. It had 48 pages and a press run of 40,000 copies. Although "St. Nicholas" never reached the high circulation numbers of some other magazines (in the 1890s "The Youth's Companion" had 500,000 subscribers compared with St Nicholas's 100,000 in Christmas 1883 ), within a few years it had acquired numerous competing children's periodicals. Magazines that merged with "St. Nicholas" were "Our Young Folks" and "The Children's Hour" in 1874, "The Schoolday Magazine" and "The Little Corporal" in 1875, and "Wide Awake" in 1878 .
From the start, "St. Nicholas" was beautifully printed with illustrations from a consistent group of artists and wood engravers, such as Walter James Fenn, used by Scribner & Company's other magazine, "Scribner's Monthly".
"St. Nicholas League".
In 1899 "St. Nicholas League" began. It was one of the magazine's most important departments, and had the motto of "Live to learn and learn to live." Each month contests were held for the best poems, stories, essays, drawings, photographs, and puzzles submitted by the magazine's young readers. Winners received gold badges, runners-up received silver badges, and "honor members", winners of both gold and silver badges, were sent cash prizes.”There is no doubt about it,” E.B. White wrote. “The fierce desire to write and paint that burns in our land today, the incredible amount of writing and painting that still goes on in the face of heavy odds, are directly traceable to St Nicholas.”
Many "St. Nicholas League" winners went on to achieve prominence. The most prolific poetry contest winner was Edna St. Vincent Millay, who had seven poems published in the "League". E.B. White and Bennett Cerf won essay contests. William Faulkner made the honor roll for his drawings, and F. Scott Fitzgerald was honored for a photograph.
People.
Mary Mapes Dodge as editor.
From 1873 until 1881, Mary Mapes Dodge was involved with the day-to-day operations of all aspects of "St. Nicholas". She created the magazine departments, wrote the monthly column Jack-in-the-Pulpit, and contributed many stories and poems.
In the first issue she explained why she chose "St. Nicholas" for the name of the magazine:
In order to retain her juvenile readers for many years, Dodge created departments for different age groups. For Very Little Folks (1873–1897) was a page of simple stories printed in large type. The Puzzle Box contained riddles, math and word games. Young Contributors Department (begun in 1875) encouraged the writing skills of older children. The Agassiz Association was begun in 1885 to develop the awareness of nature, and the importance of conservation. Hundreds of Agassiz chapters were organized across the nation, and reports of activities were printed in the department.
Dodge knew many famous writers, and was able to persuade them to submit their work to her magazine. Frances Hodgson Burnett's novel "Little Lord Fauntleroy" first appeared as a "St. Nicholas" serial, beginning in the November 1885 issue. Her novella "Sara Crewe" appeared in the December 1887 issue. Other novels to be serialized in "St. Nicholas" were Louisa May Alcott's "Eight Cousins" and Mark Twain's "Tom Sawyer Abroad". Dodge asked Rudyard Kipling to do a fiction series, and he sent her the "Jungle Book" stories.
Within a few years, "St. Nicholas" increased in size to 96 pages, and reached a circulation of 70,000 subscribers.
In 1881, the Scribner publishing house withdrew from ownership of its two magazines, and they were purchased by The Century Company. "Scribner's Monthly" became "Century Magazine", and "St. Nicholas: Scribner's Illustrated Magazine for Girls and Boys" became "St. Nicholas: An Illustrated Magazine for Young Folks". The printing and art facilities of the prosperous new owner was made available to "St. Nicholas", and the magazine continued to thrive.
Dodge's eldest son, Harry, died in 1881. In her grief she relinquished much of her responsibilities to her assistant editor, William Fayal Clarke. Though no longer in control of all day-to-day operations, Dodge continued working at "St. Nicholas" until her death in 1905.
William Fayal Clarke as editor.
William Fayal Clarke was twenty years old when, in 1874, he joined the staff of "St. Nicholas". In 1878 he was promoted to associate editor. Starting in 1881, he took on more responsibilities when, upon the death of her son, Mary Mapes Dodge limited her work load.
As editor, Clarke placed more emphasis on departments, perhaps because he lacked Dodge's close ties to famous authors. Departments devoted to short plays, science and philately (stamp collecting) were added to "St. Nicholas". Circulation remained at about 70,000.
In 1927, Clarke stepped down as editor. He retired in 1928, after 54 years with the magazine. Within a few years, "St. Nicholas" began a steady decline in circulation.
Final years.
In November 1927 George F. Thomson, the former editor of "Our Young Folks" (a magazine taken over by "St. Nicholas" in 1874) became editor. He was replaced after two years, and a rapid turnover of editors began.
In 1930 "St. Nicholas" was sold to American Education Press, and the magazine's full name was changed to "St. Nicholas for Boys and Girls". In 1935 "St. Nicholas" was sold to Educational Publishing Corporation.
Editors under the last two owners were Albert Gallatin Lanier (1930), May Lamberton Becker (1930–32), Eric J. Bender (1932–34), Chesla Sherlock (1935), Vertie A. Coyne (1936–40), and Juliet Lit Sterne (1943).
In 1940 the format was changed to a large-print picture-and-story-magazine, aimed at beginner readers. Slick paper was replaced with soft paper. The last issue was February 1940.
In 1943 "St. Nicholas" was brought back, in a format similar to early days. It failed after four issues.
Availability of issues and stories.
A popular service provided to "St. Nicholas" subscribers was that, for a small fee, six issues could be sent off to be bound into a hard-back volume, with crimson covers and a gold-stamped title. These bound volumes are available through used book sellers.
Many anthologies of favorite "St. Nicholas" stories have been compiled. The two best-known collections were edited by Henry Steele Commager and published by Random House (the head of Random House, Bennett Cerf, had once been a "St. Nicholas" subscriber and contributor to the famous "St. Nicholas League"). The "St. Nicholas Anthology" came out in 1948, followed by "The Second St. Nicholas Anthology" in 1950. "Treasury of Best-Loved Stories, Poems Games & Riddles from St. Nicholas Magazine," edited by Commager, was published in 1978 by Greenwich House. The first two volumes were reprinted by Greenwich House in 1982 and 1984. In addition, Burton Frye compiled "A St. Nicholas Anthology: the Early Years" for Meredith House in 1969.
In 2003 and again in 2004, William F. Buckley Jr. edited "The National Review Treasury of Classic Children's Literature" and "The National Review Treasury of Classic Children's Literature: Volume Two," both with stories gathered from "St. Nicholas."
A number of "St. Nicholas" issues can be downloaded free of charge. Sources shown in External Links are Project Gutenberg and "A Tribute to St. Nicholas: A Magazine for Young Folks", which contains a menu of online links.


Toward a New Philosophy of Biology

Toward a New Philosophy of Biology: Observations of an Evolutionist (published by Harvard University Press, Cambridge, Massachusetts, in 1988) is a book by Harvard evolutionary biologist Ernst Mayr.
A collection of 28 essays, five previously unpublished, grouped into ten categories—Philosophy, Natural Selection, Adaptation, Darwin, Diversity, Species, Speciation, Macroevolution, and Historical Perspective. The book, "Mayr" notes in the Forward, is an attempt "to strengthen the bridge between biology and philosophy, and point to the new direction in which a new philosophy of biology will move."


Brood parasite

Brood parasites are organisms that rely on others to raise their young. The strategy appears among birds, insects and fish. The brood parasite manipulates a host, either of the same or of another species, to raise its young as if it were its own, using brood mimicry, for example by having eggs that resemble the host's (egg mimicry).
Brood parasitism relieves the parasitic parents from the investment of rearing young or building nests for the young, enabling them to spend more time on other activities such as foraging and producing further offspring. Bird parasite species mitigate the risk of egg loss by distributing eggs amongst a number of different hosts. As this behaviour damages the host, it often results in an evolutionary arms race between parasite and host as the pair of species coevolve.
The strength of defenses and counter-adaptation rely on the host/parasitic species' ability to evolve; some host species have very strong rejection defenses resulting in the parasitic species evolving to have very close mimicry. In other species, hosts do not show rejection defenses and as a result, the parasitic species will show no evolved trait (example: egg mimicry).
Birds.
In many monogamous bird species, there are extra-pair matings resulting in males outside the pair bond siring offspring and used by males to escape from the parental investment in raising their offspring. This form of cuckoldry is taken a step further when females of the goldeneye ("Bucephala clangula") often lay their eggs in the nests of other individuals. Intraspecific brood parasitism is seen in a number of duck species, where females often lay their eggs in the nests of others.
Interspecific brood-parasites include the indigobirds, whydahs, and honeyguides in Africa, cowbirds, Old World cuckoos, black-headed ducks, and some New World cuckoos in the Americas. Seven independent origins of obligate interspecific brood parasitism in birds have been proposed. While there is still some controversy over when and how many origins of interspecific brood parasitism have occurred, recent phylogenetic analyses suggest two origins in Passeriformes (once in New World cowbirds: Icteridae, and once in African Finches: Viduidae); three origins in Old World and New World cuckoos (once in Cuculinae, Phaenicophaeinae, and in Neomorphinae-Crotophaginae); a single origin in Old World honeyguides (Indicatoridae); and in a single species of waterfowl, the black-headed duck ("Heteronetta atricapilla").
Most avian brood parasites are specialists which parasitize only a single host species or a small group of closely related host species, but four out of the five parasitic cowbirds (all except the screaming cowbird) are generalists which parasitize a wide variety of hosts; the brown-headed cowbird has 221 known hosts. They usually lay only one egg per nest, although in some cases, particularly the cowbirds, several females may use the same host nest.
The common cuckoo presents an interesting case in which the species as a whole parasitizes a wide variety of hosts, including the reed warbler and dunnock, but individual females specialize in a single species. Genes regulating egg coloration appear to be passed down exclusively along the maternal line, allowing females to lay mimetic eggs in the nest of the species they specialize in. Females generally parasitize nests of the species which raised them. Male common cuckoos fertilize females of all lines, which maintains sufficient gene flow among the different maternal lines to prevent speciation.
The mechanisms of host selection by female cuckoos are somewhat unclear, though several hypotheses have been suggested in attempt to explain the choice. These include genetic inheritance of host preference, host imprinting on young birds, returning to place of birth and subsequently choosing a host randomly ("natal philopatry"), choice based on preferred nest site (nest-site hypothesis), and choice based on preferred habitat (habitat-selection hypothesis). Of these hypotheses the nest-site selection and habitat selection have been most supported by experimental analysis.
Adaptations for parasitism.
Among specialist avian brood parasites, mimetic eggs are a nearly universal adaptation. The generalist brown-headed cowbird may have evolved an egg coloration mimicking a number of their hosts. Size may also be important for the incubation and survival of parasitic species; it may be beneficial for parasitic eggs to be similar in size to the eggs of the host species.
The eggshells of brood parasites are often thicker than those of the hosts. For example, the eggs of cuckoos are about thicker than those the great reed warbler. The function of this thick eggshell is debated. One hypothesis, the puncture resistance hypothesis, states that the thicker eggshells serve to prevent hosts from breaking the eggshell, thus killing the embryo inside. This is supported by a study in which marsh warblers damaged their eggs more often when attempting to break cuckoo eggs, but incurred less damage when trying to puncture great reed warbler eggs put in the nest by researchers. Another hypothesis is the laying damage hypothesis, which postulates that the eggshells are adapted to damage the eggs of the host when the former is being laid, and prevent the parasite's eggs from being damaged when the host lays its eggs. In support of this hypothesis, eggs of the shiny cowbird parasitizing the house wren and the chalk-browed mockingbird and the brown-headed cowbird parasitizing the house wren and the red-winged blackbird damaged the host's eggs when dropped, and sustained little damage when host eggs were dropped on them.
Most avian brood parasites have very short egg incubation periods and rapid nestling growth. In many brood parasites, such as cuckoos and honeyguides, this short egg incubation period is due to internal incubation periods up to 24 hours longer in cuckoos than hosts. Some non-parasitic cuckoos also have longer internal incubation periods, suggesting that this longer internal incubation period was not an adaptation following brood parasitism, but predisposed birds to become brood parasites. This is likely facilitated by a heavier yolk in the egg providing more nutrients. Being larger than the hosts at growth is a further adaptation to being a brood parasite.
Mafia hypothesis.
There is a question as to why the majority of the hosts of brood parasites care for the nestlings of their parasites. Not only do these brood parasites usually differ significantly in size and appearance, but it is also highly probable that they reduce the reproductive success of their hosts. The "mafia hypothesis" evolved through studies in an attempt to answer this question. This hypothesis revolves around host manipulations induced by behaviors of the brood parasite. Upon the detection and rejection of a brood parasite's egg, the host's nest is destroyed and nestlings injured or killed. This threatening response indirectly enhances selective pressures favoring aggressive parasite behavior that may result in positive feedback between mafia-like parasites and compliant host behaviors.
There are two avian species that have been speculated to portray this mafia-like behavior: the brown-headed cowbird of North America, "Molothrus ater", and the great spotted cuckoo of Europe, "Clamator glandarius". The great spotted cuckoo lays the majority of its eggs in the nests of the European magpie, "Pica pica". It repeatedly visits the nests that it has parasitised, a precondition for the mafia hypothesis. An experiment was run by Soler "et al." from April to July 1990 – 1992 in the high-altitude plateau Hoya de Guadix, Spain. They observed the effects of the removal of cuckoo eggs on the reproductive success of the magpie and measured the magpie's reaction; the egg was considered accepted if it remained in the nest, ejected if gone in between visits, or abandoned if eggs were present but cold. If any nest contents were gone between consecutive visits, the nests were considered to have been depredated. The magpie's reproductive success was measured by number of nestlings that survived to their last visit, which was just before the nestling had been predicted to fledge from the nest. The results from these experiments show that after the removal of the parasitic eggs from the great spotted cuckoo, these nests are predated at much higher rates than those where the eggs were not removed. Through the use of plasticine eggs that model those of the magpie, it was confirmed that the nest destruction was caused by the great spotted cuckoo. This destruction benefits the cuckoo, for the possibility of re-nesting by the magpie allows another chance for the cuckoo egg to be accepted.
A similar experiment was done in 1996–2002 by Hoover "et al." on the relationship between the parasitic brown-headed cowbird and a host, the prothonotary warbler, "Protonotaria citrea". In their experiment, researchers manipulated the cowbird egg removal and cowbird access to the warbler's predator–proof nests. They found that 56% of egg-ejected nests were predated upon, in comparison to 6% of non-ejected nests when cowbirds were not prevented from getting to the hosts' nest; nearly all nests protected from cowbirds fledged warblers successfully. Of the nests that were rebuilt by hosts that had previously been predated upon, 85% of those were destroyed. The number of young produced by the hosts that ejected eggs dropped 60% compared to those that accepted the cowbird eggs.
Nest-site hypothesis.
In this hypothesis, female cuckoos select a group of host species with similar nest sites and egg characteristics to her own. This population of potential hosts is monitored and a nest is chosen from within this group.
Research of nest collections has illustrated a significant level of similarity between cuckoo eggs and typical eggs of the host species. A low percentage of parasitized nests were shown to contain cuckoo eggs not corresponding to the specific host egg morph. In these mismatched nests a high percent of the cuckoo eggs were shown to correlate to the egg morph of another host species with similar nesting sites. This has been pointed to as evidence for nest- site selection.
A criticism of the hypothesis is that it provides no mechanism by which nests are chosen, or which cues might be used to recognize such a site.
Parental-care parasitism.
Parental-care parasitism emphasizes the relationship between the host and the parasite in brood parasitism. Parental-care parasitism occurs when individuals raise offspring of other unrelated individuals. The host are the parents of offspring and the parasites are individuals who take advantage of either the nest or eggs within the family construct. Such dynamics occur when the parasites attempt to reduce their parental investment so they can invest the extra energy into other endeavors.
Cost to the hosts.
Given the harm that avian brood parasites can do to their hosts' reproductive success, hosts have come up with various defenses against this unique threat. Given that the cost of egg removal concurrent with parasitism is unrecoverable, the best strategy for hosts is to avoid parasitism in the first place. This can take several forms, including selecting nest sites which are difficult to parasitize, starting incubation early so they are sitting on the nests when parasites visit them early in the morning, and aggressively defending their territory. Despite providing intensive parental care, in Prothonotary Warblers, where conspecific brood parasitism occurs, there was no cost for host females in terms of annual survival probability.
Hosts reject offspring.
The host may be the one that ultimately ends up raising offspring after they return from foraging. Once parasitism has occurred, the next most optimal defense is to eject the parasitic egg. According to parental investment theory, the host can possibly adopt some defense to protect their own eggs if they distinguish which eggs are not theirs. Recognition of parasitic eggs is based on identifying pattern differences or changes in the number of eggs. This can be done by grasp ejection if the host has a large enough beak, or otherwise by puncture ejection. Ejection behaviour has some costs however, especially when host species have to deal with mimetic eggs. Hosts may mistake one of their own eggs for a parasite's on occasion and eject it, and may damage their own eggs while trying to eject a parasite's egg.
Among hosts not exhibiting parasitic egg ejection, some abandon parasitized nests and start over again. However, at high enough parasitism frequencies, this becomes maladaptive as the new nest will most likely also be parasitized. Some host species modify their nests to exclude the parasitic egg, either by weaving over the egg or in some cases rebuilding a new nest over the existing one. For instance, American coots may kick the parasites' eggs out, or build a new nest beside the brood nests where the parasites’ babies starve to death. In the Western Bonelli's warbler "Phylloscopus bonelli", a small host, experimental parasitism revealed that small dummy parasitic eggs were always ejected, whilst with large dummy parasitic eggs nest desertion more frequently occurred.
Cost to the parasites.
While parental-care parasitism significantly increased the breeding number of the parasite, only about half of the parasite eggs survived. Parasitism for the individual (the brood parasite) also has significant drawbacks. As an example, the parasitic offspring of the bearded tits, "Panurus biarmicus", compared to the offspring in non-parasitic nests, tend to develop much more slowly and often don't reach full maturity. Parasitic females however can adopt either floater traits or nesting traits. Floater females are entirely dependent on others to raise their eggs because they do not have their own nests. Hence, they reproduce significantly less because the hosts reject their ‘intruder’ eggs or they may just miss the egg-laying period of the bird they are trying to pass their eggs to. Nesting females who have their own nests may also be parasitic due to temporary situations like sudden loss of nests, or they lay surplus eggs, which overload their parental care ability.
Hosts raise offspring.
Sometimes hosts are completely unaware that they are caring for a bird that is not their own. This most commonly occurs because the host cannot differentiate the parasitic eggs from their own. It may also occur when hosts temporarily leave the nest after laying the eggs. The parasites lay their own eggs into these nests so their nestlings share the food provided by the host. It may occur in other situations. For example, female eiders would prefer to lay eggs in the nests with one or two existing eggs of others because the first egg is the most vulnerable to predators. The presence of others’ eggs reduces the probability that a predator will attack her egg when a female eider leaves the nest after laying the first egg.
Sometimes, the parasitic offspring kills the host nest-mates during competition for resources. As an example, the parasite offspring of the cowbird chick kill the host nest-mates if food intake for each of them is low, but do not do so if the food intake is adequate, as a result of their interactions with co-inhabitants of the nest.
Fish.
Mouthbrooding parasites.
A mochokid catfish of Lake Tanganyika, "Synodontis multipunctatus", is a brood parasite of several mouthbrooding cichlid fish. The catfish eggs are incubated in the host's mouth, and—in the manner of cuckoos—hatch before the host's own eggs. The young catfish eat the host fry inside the host's mouth, effectively taking up virtually the whole of the host's parental investment.
"Nest" parasites.
A cyprinid minnow, "Pungtungia herzi" is a brood parasite of the percichthyid freshwater perch "Siniperca kawamebari", which live in the south of the Japanese islands of Honshu, Kyushu and Shikoku, and in South Korea. Host males guard territories against intruders during the breeding season, creating a patch of reeds as a spawning site or "nest". Females (one or more per site) visit the site to lay eggs, which the male then defends. The parasite's eggs are smaller and stickier than the host's. 65.5% of host sites were parasitised in a study area.
Insects.
Kleptoparasites.
There are many different types of cuckoo bees, all of which lay their eggs in the nest cells of other bees, but they are normally referred to as kleptoparasites (Greek: klepto-, to steal), rather than as brood parasites, because the immature stages are almost never fed directly by the adult hosts. Instead, they simply take food gathered by their hosts. Examples of cuckoo bees are "Coelioxys rufitarsis", "Melecta separata", "Nomada" and "Epeoloides".
Kleptoparasitism in insects is not restricted to bees; several lineages of wasp including most of the Chrysididae, the cuckoo wasps, are kleptoparasites. The cuckoo wasps lay their eggs in the nests of other wasps, such as those of the potters and mud daubers.
True brood parasites.
True brood parasitism is rare among insects. Cuckoo bumblebees (the subgenus "Psithyrus") are among the few insects which, like cuckoos and cowbirds, are fed by adult hosts. Their queens kill and replace the existing queen of a colony of the host species then use the host workers to feed their brood.
A true brood-parasitic wasp is "Polistes sulcifer". This paper wasp has lost the ability to build its own nest, and relies on its host, "Polistes dominula", to raise its brood. The adult host feeds the parasite larvae directly, unlike typical kleptoparasitic insects.
Host insects are sometimes tricked into bringing offspring of another species into their own nests, as with the parasitic butterfly, "Phengaris rebeli", and the host ant "Myrmica schencki". The butterfly larvae release chemicals that confuse the host ant into believing that the "P. rebeli" larvae are actually ant larvae. Thus, the "M. schencki" ants bring back the "P. rebeli" larvae to their nests and feed them, much like the chicks of cuckoos and other brood-parasitic birds. This is also the case for the parasitic butterfly, "Niphanda fusca", and its host ant "Camponotus japonicus". The butterfly releases cuticular hydrocarbons (CHCs) that mimic the CHCs of the host male ant. The ant then brings the third instar larva back into its own nest and raises them until pupation.


Clostridium cellobioparum

Clostridium cellobioparum is a species of anaerobic cellulose-degrading Gram-positive bacterium found in the bovine rumen belonging to the family Clostridiaceae.


Hypoviridae


Palpitomonas bilix

Palpitomonas bilix is a protist species first described in 2010.


Chondroblast

Chondroblasts, or perichondrial cells, is the name given to mesenchymal progenitor cells in situ which, from endochondral ossification, will form chondrocytes in the growing cartilage matrix. Another name for them is subchondral cortico-spongious progenitors. They have euchromatic nuclei and stain by basic dyes.
These cells are extremely important in chondrogenesis due to their role in forming both the chondrocytes and cartilage matrix which will eventually form cartilage. Use of the term is technically inaccurate since mesenchymal progenitors can also technically differentiate into osteoblasts or fat. Chondroblasts are called chondrocytes when they embed themselves in the cartilage matrix, consisting of proteoglycan and collagen fibers, until they lie in the matrix lacunae. Once they embed themselves into the cartilage matrix, they grow the cartilage matrix by growing more cartilage extracellular matrix rather than by dividing further.
Structure.
Within adults and developing adults, most chondroblasts are located in the perichondrium. This is a thin layer of connective tissue which protects cartilage and is where chondroblasts help to expand cartilage size whenever prompted to by hormones such as GH, TH, and glycosaminoglycans. They are located on the perichondrium because the perichondrium, located on the outside of developing bone, is not as heavily ensheathed in cartilage extracellular matrix as the interior and because here where capillaries are located. The type of growth maintained by chondroblasts is called appositional bone growth and increases the birth of the affected tissue. It is important to note that perichondrium, and thus chondroblasts, are not found on the articular cartilage surfaces of joints.
Matrix formation and composition.
The extracellular matrix secreted by chondroblasts is composed of fibers, collagen, hyaluronic acid, proteoglycans, glycoproteins, water, and a host of macromolecules. Within finished cartilage, collagen fibers compose 10-20% of the volume, water 65-80%, and the proteoglycan-hyaluronic acid aggregates the remaining portion. Due to the proliferative nature of Chondroblasts, cells compose a larger portion of the composition than what is normally found within completed cartilage.
Collagen Type II fibers are responsible for giving the future cartilage matrix its tensile strength. The structure of these fibers, like the majority of collagen fibers, forms a triple helix structure.
Proteoglycans resist the compression generally put upon cartilage and generate the swelling pressure responsible for stress shielding the matrix from compression loading. They attach themselves to up to 100 Chondroitin sulfate molecules and up to 50 keratan sulfate glycoaminoglycan chains. These chains together are attached to a hyaluronic acid backbone which, in conjunction with the collagen fibrils, create an interstitial intrafibrillar space in which water is held in by the negative charge of the proteoglycans.
Development.
As suggested in the name, mesenchymal progenitors originate from the mesoderm. These cells, when forming from the mesoderm, specifically form from embryonic stem cells via induction through BMP4 and fibroblast growth factor FGF2 while the fetus is inside the womb. It has been suggested that differentiating embryonic stem cells with these growth factors could prevent stem cells, once injected into potential patients, from forming teratomas, or stem cell caused tumors.
Signaling, transcription and environmental factors responsible for chondroblast creation.
Transcription factors.
An important genetic component of this process is Sox9, a HMG box transcription factor, which marks progenitor cells for chondrogenic differentiation. Inactivation of the Sox9 gene will result in the loss of all Cartilage, and thus Chondroblast, formation. This factor is also expressed alongside Sox5 and Sox6.
Runx2 is another important genetic component of Chondroblast formation. It has been found that expressing this gene will result in the suppression of the differentiation of chondroblasts. Expression of this gene will also prompt already formed cartilage to undergo endochondral ossification which will prompt the cartilage to form bone.
It is important to note here that these genes are not the only factors which determine whether chondroblasts will form. General inactivation or activation of these gene doesn't turn all affected cells into one type or another. Extrinsic environmental factors act upstream in determining what cell type will form out of any particular mesenchymal progenitor cell.
Wnt/β-catenin signaling.
Wnt14 is controlled by Col2a1 and is put through the β-Catenin mediated Wnt pathway. Higher levels of Wnt14 prevented chondrocyte differentiation whereas lower levels appeared to allow it. If the Wnt/ β-Catenin pathway is upregulated, then endochondral ossification is encouraged which promotes ossification of the formed cartilage. This pathway is a canonical Wnt pathway because of the β-Catenin that accumulates once Wnt14 signalling is initiated. After Wnt14 is initiated, phosphorylation of the β-Catenin that would normally mark the protein for destruction is suppressed which allows it to accumulate and eventually go into the cell nucleus to bind to the LEF/TCF transcription factors which lead both to the destruction of any remaining phosphorylated β-Catenin as well as the differentiation of mesenchymal progenitor cells into osteoblasts.
Testing of this pathway has indicated that the Wnt/β-Catenin increases β-Catenin levels before the activation of the Runx2 and Osx transcription factors which seems to suggest that early β-Catenin levels can be a sign of whether an early mesenchymal progenitor cell will progress to a chondrocyte or to an osteoblast.
Retinoic acid.
Retinoic acid, part of a family of molecules called retinoids, need to be repressed in order for Chondroblasts to form. A 2003 study using transgenic mice with a weak, constitutively active retinoic acid receptor found that retinoids maintain cells within condensations in a prechondrogenic, mesenchymal cell state which prevents cell differentiation. It has also been suggested that the inhibition of receptor mediated retinoid signaling induces Sox9 expression which is considered a “master switch” for the differentiation of chondroblasts.
Environmental factors.
Differentiation of chondroblasts is favored in an environment with high compressive force and low partial oxygen pressure which combine to inhibit protein 3, a protein which inhibits cartilage differentiation. These preferences are important since mature cartilage tissue is avascular and thus would be ill-suited to a high oxygen environment.
Function.
Chondroblasts appear to migrate to cartilage whenever chondrocytes are destroyed via mechanical force. Remaining chondrocytes divide in order to form more chondroblasts. HMGB-1, a growth factor which promotes chondrocyte division while receptors for advanced glycation products (RAGE) mediated chemotaxis to clean up cell debris resulting from the damage. Chondroblasts then secrete cartilage matrix around themselves in order to reform the lost cartilage tissue.
However, regeneration is still too slow for patient care to effectively rely on this mechanism of repair. Part of this inability to regenerate quickly from injury results from the relative avascular nature of cartilage as compared to other connective tissues of the human body.
Pathology.
Chondroblastomas can sometimes form, which are benign tumors that form at the sites of endochondral ossification due to over stimulation of the chondroblasts. When they form, they are usually found on the upper or lower tibia as well as the upper humerus where chondroblast activity is most apparent. Rarely, they can be found on the feet, hands, flat bones, or spine. 30–50% of these sarcomas have an accompanying osteoblastoma which is similarly benign.
Chondrosarcoma is a more malignant type of tumor, but most are low grade tumors and often appear in the axial skeletal region. It constitutes 20% of skeletal system tumors in the United States.


Killing the Dragon

Killing the Dragon is the ninth studio album by American heavy metal band Dio. It was released May 21, 2002 through Spitfire Records and was produced by frontman Ronnie James Dio. The album was reissued in 2007 in a two-CD package with "Magica". It was remastered in 2019 and reissued in 2020 with updated album art and a bonus disc containing six tracks recorded live on the "Killing the Dragon" tour.
Symbolism.
In an interview on the TV show "Uranium", Dio stated that the "dragon" of the album title refers to technology. He expressed concern with it threatening society in the future. Dio elaborated that the title track refers to "those who perpetrate injustices and what the world is doing to stop them. In fantasy tales, dragons were notorious for stealing children and feeding them to their babies. During the first part of the song, I sing 'Someone has taken a child.' The second part is about a cruel feudal lord. The third part is about 'electronic serfdom.'" He also expressed belief that the computer has become a god in modern society. "It is a small god with an electrical heart (...) It is time to rebel against it."
Members.
"Killing the Dragon" introduces guitarist Doug Aldrich to the band. He had previously performed with Burning Rain and subsequently went on to join the band Whitesnake. Previous guitarist, Craig Goldy, co-wrote some of the songs before leaving the band. He returned for 2004's "Master of the Moon". It is their final album with bassist Jimmy Bain.
Music video.
The song "Push" was a hit and had a music video that featured Tenacious D performing a humorous cover of Ronnie James Dio's biggest song from his time with Black Sabbath, "Heaven and Hell". Dio approaches them to tell them that he will pay them to play Tenacious D music. Apparently, according to an interview with Dio in 2005, during filming of this music video, Ronnie James Dio became friends with Tenacious D frontman Jack Black, who told Dio about his plans to make a Tenacious D film and asked him to perform in the film if anything became of it. In 2005, Dio received a letter from Black informing him that production of the film was starting and requested that he play himself. This film is "Tenacious D in The Pick of Destiny". The video was directed by Bill Schacht (who has directed other videos for Alice Cooper, Amon Amarth, Sister Sin, Yngwie Malmsteen, Saxon, etc.) for Aestheticom. The video was listed as No. 54 most metal moment of all time on a VH1 100 Most Metal Moments show, hosted by Eddie Trunk.
Aborted Hear 'n Aid sequel project.
The song, "Throw Away Children", from this album was slated to appear in a sequel project to Hear 'n Aid but was aborted due to various reasons.
Track listing.
All lyrics by Ronnie James Dio, music as stated. The "Limited Tour Edition" came in a slipcase with poster and added two bonus tracks. These bonus tracks are Ronnie James Dio performing live with Deep Purple and first appeared on Deep Purple's 2001 album "Live at the Rotterdam Ahoy". The "The Limited Tour Edition" bonus tracks are not included on the 2020 reissue.
The 2020 reissue has a printing error on the vinyl and CD variants; the song "Guilty" is printed as "Guitly".
Personnel.
Dio
Additional musicians
Production


Phaeosaccion

Phaeosaccion is a genus of algae with monostromatic tubular to saccate thalli, up to long and to wide. It is the sole genus in the family Phaeosaccionaceae. It is olive brown and resembles young plants of "Scytosiphon". The sole species in the genus is Phaeosaccion collinsii, a species of marine algae. It was first identified in a publication by W.G. Farlow in the article "Notes on New England algae" published in "Bulletin of the Torrey Botanical Club" in 1882. It was named in honor of Frank Shipley Collins. "Phaeosacchion collinsii" is red listed in Iceland as a vulnerable species (VU).


Wood Canyon Formation

The Wood Canyon Formation is a geologic formation in the northern Mojave Desert of Inyo County, California and Nye County and Clark County, Nevada.
It can be seen in the Panamint Range and Funeral Mountains adjoining Death Valley, within Death Valley National Park; and in the Spring Mountains in Clark County.
Geology.
The 570+ million years old formation underlies the Zabriskie Quartzite Formation, and overlies the Stirling Quartzite Formation.
It has members of quartzite, shale, sandstone, and dolomite.
Fossils.
It preserves scattered olenellid trilobite and archaeocyathid fossils in upper part of formation, dating back to the Ediacaran period of the Neoproterozoic Era and Lower Cambrian Period of the Paleozoic Era.


Gomphidius borealis

Gomphidius borealis is a mushroom in the family Gomphidiaceae that is found in Siberia.


Clostridium saccharobutylicum

Clostridium saccharobutylicum is an indole and notably acetone, butanol and ethanol-producing bactera, with type strain DSM 13864T (= ATCC BAA-117T). Its genome has been sequenced.


Haemoproteus crumenium

Haemoproteus crumenium is a haemoproteid parasite first described in 1905. Birds of the family Ciconiidae serve as the host. From an early stage of development it tends to take up a lateral position within infected cells. While it usually has an irregular outline while developing, by maturity it has clearly rounded ends. Even fully-grown it almost never takes up more than two-thirds of the cell it hosts in.


Coriobacteriia

The Coriobacteriia are a class of Gram-positive bacteria within the Actinobacteria phylum. Species within this group are nonsporulating, strict or facultative anaerobes that are capable of thriving in a diverse set of ecological niches. "Gordonibacter" species are the only members capable of motility by means of flagella within the class.
Several species within the Coriobacteriia class have been implicated with human diseases that range in severity. "Atopobium", "Olsenella", and "Cryptobacterium" species have responsible for human oral infections including periodontitis, halitosis, and other endodontic infections. "Eggerthella" species have been associated with severe blood bacteraemia and ulcerative colitis.
Taxonomy.
The class Coriobacteriia currently consists of 16 genera within two orders and three families. The order Coriobacteriales consists of two families, the Coriobacteriaceae and Atopobiaceae. The family Coriobacteriaceae contains the genera "Collinsella", "Coriobacterium", "Enorma", "Parvibacter", and "Senegalimassilia", while the Atopobiaceae contain "Atopobium" and "Olsenella". The Eggerthellales consist of a single family (Eggerthellaceae) and the remaining Coriobacteriia genera ("Adlercreutzia" , "Asaccharobacter", "Cryptobacterium", "Denitrobacterium", "Eggerthella", "Enterorhabdus", "Gordonibacter", "Paraeggerthella", and "Slackia").
Molecular signatures and phylogenetic position.
Historically, all Coriobacteriia species were placed within a single order (Coriobacteriales) and a single family (Coriobacteriaceae). This view, however, was not reflective of accurate evolutionary interrelationships within the class. The current taxonomic view is justified by the presence of several conserved signature indels (CSIs) that have been found at the different taxonomic ranks. These CSIs are specific and represent synapomorphic characteristics that can be used to distinguish groups within the Coriobacteriia, both at the family and order levels. The distinction of the orders within the Coriobacteriia is also supported phylogenetic tree branching and by consistent characteristics; members belonging to the Coriobacteriales are glucose-fermenting, saccharolytic species while the Eggerthellales order has species that are consistently unable to ferment glucose and are asaccharolytic.
CSIs have also been used to resolve the phylogenetic position of the Coriobacteriia among all bacteria where they have been found exclusively for all species within the class, delineating them from other Actinobacteria. The Coriobacteriia are an early branching lineage within the Actinobacteria phylum The deep branching of the class has led to dispute over its membership within the phylum and whether or not it is a true actinobacterial group. A CSI in the form of a single amino acid insert in the enzyme deoxyuridine 59-triphosphate (dUTP) nucleotidohydrolase has been found that is shared by all Coriobacteriia members, as well as several Actinobacteria species, and absent from all other bacteria. This CSI provides unambiguous support for Coriobacteriia’s membership within the Actinobacteria.
Phylogeny.
The currently accepted taxonomy is based on the National Center for Biotechnology Information (NCBI).


Helminthosporium

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


Clostridium septicum

Clostridium septicum is a gram positive, spore forming, obligate anaerobic bacterium.
"Clostridium septicum" can cause gas gangrene, but unlike other Clostridium species like "Clostridium perfringens", no trauma is necessary at the site of the infection. It is thought that the infection is established by hematogenous spread from the gastrointestinal tract. Gas gangrene caused by "Clostridium septicum" is associated with colorectal cancer and other defects of the bowel.
"Clostridium septicum" causes myonecrosis through the release of exotoxins such as the alpha toxin, lethal toxin, and hemolytic toxin
General and morphological information.
"C. septicum" is a large, gram-positive, rod-shaped bacterium that is a member of the normal gut flora in humans as well as other animals. "C. septicum" are spore formers, with a terminal spore that gives them their drumstick-like shape. They are also motile bacteria, using peritrichous flagellae to navigate from one environment to the next. "C. septicum" are fermentative anaerobes and therefore can live off of a variety of substrates like sugars, amino acids and other organic compounds, generating molecular hydrogen gas and carbon dioxide as byproducts of cellular respiration.
"C. septicum" can cause infection quickly if the gut tissue becomes necrotic or inflamed. "C. septicum" produces four toxins; alpha, beta, gamma and delta, with alpha toxin being necrotic and lethal. Their anaerobic nature creates susceptibility in areas of decreased blood flow. Although rare, "C. septicum" infections are often found in individuals with a recent history of trauma, surgery, peripheral vascular disease, diabetes, colon cancer, skin infections or burns and septic abortions.
Ecology and habitat.
"C. septicum" is a resident bacterium of the human microflora, however it can be found in almost any anoxic habitat in which exists organic compounds. Under unfavorable conditions, "C. septicum" forms endospores allowing it to survive under harsh conditions such as extreme temperature, dry land, and nutrient-deficient habitats.
Pathogenesis.
As of 2006, between 1000 and 3000 cases of clostridial myonecrosis were reported in the United States each year, typically accompanied by another pre-existing medical condition. C. septicum is one of several bacteria responsible for myonecrosis, otherwise known as gas gangrene. Infection by "C. septicum" was once thought to be extremely rare, however anaerobic laboratory techniques allowed for the discovery of the true potential of this infectious microbe. Infections are typically seen in settings of immunodeficiency, trauma, surgery, malignancy, skin infections/burns, and septic abortions. Sites prone to infection are those with poor vascular supply, although because of pH, electrolyte and osmotic differences, the colon may promote the growth of "C. septicum" better than most other anatomical regions. One of the more aggressive progenitors of gas gangrene, "C. septicum" infection progresses very rapidly, with a mortality rate of approximately 79% in adults, typically occurring within 48 hours of infection. The greatest survival rates are typically seen in patients without pre-existing medical conditions, and with infection localized to the extremities. Gas gangrene proceeds via disruption of blood flow to the infected site, resulting in diminished levels of oxygen and nutrients ultimately causing premature cell death and tissue necrosis. Four toxins have been isolated from "C. septicum": the lethal alpha toxin, DNase beta-toxin, hyaluronidase gamma toxin, and the thiol-activated/septicolysin delta toxin. Alpha toxin causes intravascular hemolysis and tissue necrosis and is well known as the main virulent factor in "C. septicum". Symptoms of infection include pain, described as a heaviness or pressure that is disproportionate to physical findings, tachycardia, and hypotension. Tissue necrosis then causes edema and ischemia resulting in metabolic acidosis, fever, and kidney failure. The carbon dioxide and hydrogen produced during cellular respiration move through tissue planes, causing their separation, producing features characteristic of palpable emphysema. This also results in a magenta-bronze skin discoloration and bulla filled with a foul-smelling serosanguinous fluid.
Association with malignancy.
"C. Septicum" derived gas gangrene has shown strong correlations with increased levels of malignancy. Generally, patients with "C. septicum" infections present colonic carcinoma or a tumor that has metastasized to the colon. One particular study by Alpern and Dowell noted 85% comorbidity with malignancy, while another study by Koransky et al. noted 71% comorbidity. This relationship suggests the opportunistic nature of this pathogen raising the possibility that immunosuppression plays a key role in the ability of "C. septicum" to cause infection. It seems likely that either the treatment or the malignancy itself impairs the immune function of the gastrointestinal mucosa allowing "C. septicum" to gain access to the circulatory system.
Alpha toxin.
The alpha toxin produced by "C. septicum" is the underlying cause of gas gangrene, otherwise known as myonecrosis; a disease characterized by extensive tissue destruction, edema, thrombosis, and fluid-filled bullae. Alpha toxin is a pore-forming toxin exotoxin that is secreted as a protoxin that requires proteolytic cleavage of a 5kDa peptide from its carboxy-terminal in order to become active. Cleavage is typically initiated by the cell surface protease furin. Once activated, the toxin can oligomerize and form ion-permeable pores through the cell membrane. Pores formed by alpha toxin are approximately 1.5 nm in diameter, allowing the release of potassium ions from erythrocytes, thus disrupting the ionic equilibrium within the cell. Alpha toxin binds GPI-anchored cell surface receptors including the human folate receptor (hFR) as well as the neuronal molecules contactin and Thy-1 (CD90).
Alpha-toxin and aerolysin.
Quite surprisingly, the alpha toxin of "C. septicum" is not related to the alpha toxin of "C. perfringens" (another bacterium implicated in the pathogenesis of gas gangrene). "C. septicum" alpha toxin does, however, exhibit similarities to aerolysin, another beta-pore forming toxin. Alpha toxin and aerolysin share approximately 72% sequence similarity and have numerous functional similarities as well. Both proteins require cleavage by furin, or a furin-like protease, and then oligomerize to form transmembrane pores. Similarities between the two toxins have also been discovered through analysis of the crystal structure of aerolysin. Aerolysin is a bilobar protein consisting of four domains (D1-D4). The smallest lobe of aerolysin is missing in the alpha toxin of "C. septicum", implying that the alpha toxin is monolobar with three domains, similar to domains D2-D4 in aerolysin. Further research has led to the conclusions that the D1 domain is involved in receptor-binding and the D3 domain functions to prevent premature oligomerization of alpha toxin.
Diagnosis and treatment.
If left untreated, the mortality rate for "C. septicum" infection nears 100%. A study by Cline and Turnbull offers that diagnosis be based on findings of pain disproportionate to clinical findings or injury, marked tachycardia, discolored or edematous skin, and a gram-stain of bullous drainage showing gram-positive bacilli without spores and few leukocytes. Physical manifestations of infection include pain caused by infiltration of the infected muscle with edema and gas, tachycardia, muscle and skin discoloration, and the presence of a brown, watery discharge with a foul smell within the wounds. Treatment for "C. septicum" infection includes antibiotic administration, surgical intervention, and hyperbaric oxygen therapy (HBOT). For antibiotic selection, usual anaerobic coverage can include penicillin, metronidazole or clindamycin. There are no CLSI standards for susceptibility testing so antibiotic selection is often made based on local patterns of resistance. In a Canadian survey from 2000 to 2006, 19 isolates were tested and 9 (47%) were resistant to clindamycin and 1 (5%) was resistant to both metronidazole and clindamycin. None had reduced susceptibility to penicillin. The Infectious Diseases Society of America (IDSA) recommends that for gas gangrene where clostridium has been identified as the cause that both penicillin and clindamycin be used. Often in severe cases amputation becomes the only viable option remaining to clear the infection.
Other animals.
In sheep, "C. septicum" causes a disease known as braxy; affected animals are generally found dead.


Doratomyces

Doratomyces (Dor-ah-toe-mice’-ees) is a genus of the fungi imperfecti, closely related to "Scopulariopsis". Their conidiophores gather together to form a stalk-like inflorescence known as a synnema or coremia; "Scopulariopsis" being distinguished in their lack of such a structure.
Usually associated with decay, they are usually found in association with dead wood, rotting plants, and in soil or dung. Economically, they can cause rot in potatoes, oats and corn.


Typhedanus crameri

Typhedanus crameri is a species of butterfly in the family Hesperiidae, native to Central America and Suriname. It was described by Pieter Cramer in 1777 using the name "Papilio orion", which was preoccupied (see "Scolitantides orion"). A replacement name honouring Cramer was designated in 1960.
Description.
Upper side. Antennae black. Thorax, abdomen, and wings dark olive brown. Anterior wings having a small narrow transparent white line crossing them from the anterior edges to the lower corners, intersected by the brown tendons of the wings. Posterior wings terminating in two white, short, and broad tails.
Under side. Palpi white. Breast, abdomen, and wings coloured as on the upper side; the posterior differing merely in having their outward edges bordered with white. Wing-span 2 inches (50 mm).


Alphacarmotetravirus


Picobirnaviridae


Blochmannia

Blochmannia is a genus of symbiotic bacteria found in carpenter ant. There are over 1000 species of these ants and, as of 2014, of the over 30 species of carpenter ant that have been investigated, all contain some form of "Blochmannia". The bacteria filled cells currently known as members of the genus "Blochmannia" were first discovered by zoologist F. Blochmann in the ovaries and midguts of insects in the 1880s. In 2000 "Candidatus Blochmannia" was proposed as its own genus.
Endosymbiosis, or when the "Blochmannia" bacteria and the ant hosts became bonded, occurred around 30–40 million years ago. In comparing two species of "Blochmannia" that diverged evolutionarily around 15-20 million years ago, the extreme similarity between their genes means "Blochmannia" bacteria have high levels of genetic conservation. The high amounts of genetic conservation suggest that the "Blochmannia" genes lack some recombination mechanisms.
"Blochmannia" bacteria are found in the midguts of carpenter ants, as well as the ovaries of the female carpenter ants. "Blochmannia" is important in synthesizing essential and non essential amino acids, including tyrosine, and it helps the ant to process nitrogen. The "Blochmannia" bacteria improves the ants’ nutrition and, in doing this, it is also important to the overall health of the ant colony. According to the study by Zientz et al., "Blochmannia" improves the health of the colony of ants as a whole because worker ants use a "trophallaxis and regurgitation" system to provide the colony with food. When control colonies which had "Blochmannia" were compared to groups where the worker ants had been given antibiotics to reduce their levels of "Blochmannia" , the health of the control colony was superior. Zientz proposes that this superior fitness of the control ant colonies is likely due to "Blochmannia" improving the nutritional quality of the food that worker ants supply to the young ants, as the health effects of "Blochmannia" appear to decrease with the ant's maturation.
"Blochmannia" bacteria are sensitive to heat. In one experiment, when exposed to an increased heat of 99.87 °F (37.7 °C) for 4 weeks, over 99% of "Blochmannia" disappeared. However, even after 16 weeks exposure of this heat exposure, trace small amounts of "Blochmannia" survived. According to researchers Fan and Wernegreen, this experiment suggests that the "Blochmannia" in ants could be vulnerable to the effects of global warming.


Savagella


List of human microbiota

This article lists some of the species recognized as belonging to the human microbiome.
Skin.
Candida parapsilosis
Vagina.
The vaginal microbiota in pregnancy varies markedly during the entire time of gestation. The species and diversity of the microorganisms may be related to the various levels of hormones during pregnancy.
Uterus.
The healthy uterine microbiome has been identified and over 278 genera have been sequenced.
Ovarian follicle.
The ovarian follicle microbiome has been studied using standard culturing techniques. It has been associated with the outcomes of assisted reproductive technologies and birth outcomes. Positive outcomes are related to the presence of "Lactobacilli spp" while the presence of "Propionibacterium" and "Actinomyces" were related to negative outcomes. Also, the microbiome can vary from one ovary to the other. Studies are ongoing in the further identification of those bacteria present.
Male reproductive tract.
The microbiome present in seminal fluid has been evaluated. Using traditional culturing techniques the microbiome differs between men who have acute prostatitis and those who have chronic prostatitis. Identification of the seminal fluid microbiome has become one of the diagnostic tools used in treating infertility in men that do not display symptoms of infection or disease. The taxa Pseudomonas, Lactobacillus, and Prevotella display a negative effect on the quality of sperm. The presence of "Lactobacillus spp" in semen samples is associated with a very high normal sperm count.


Aseptic sampling

Aseptic sampling is the process of aseptically withdrawing materials used in biopharmaceutical processes for analysis so as not contaminate or alter the sample or the source of the sample. Aseptic samples are drawn throughout the entire biopharmaceutical process (cell culture/fermentation, buffer & media prep, purification, final fill and finish). Analysis of the sample includes sterility, cell count/cell viability, metabolites, gases, osmolality and more.
Aseptic sampling techniques.
Biopharmaceutical drug manufacturers widely use aseptic sampling devices to enhance aseptic technique. The latest innovations of sampling devices harmonize with emerging trends in disposability, enhance operating efficiencies and improve operator safety.
Turn-key aseptic sampling devices.
Turn-key Aseptic Sampling Devices are ready-to-use sampling devices that require little or no equipment preparation by the users. Turn-key devices help managers reduce labor costs, estimated to represent 75% to 80% of the cost of running a biotech facility.
Turn-key aseptic sampling devices include:
To protect the integrity of the sample and to ensure it is truly representative of the time the sample is taken, the sampling pathway should be fully contained and independent of other sampling pathways.
Cannula(needle) based aseptic sampling devices.
In a cannula-based aseptic sampling system, a needle penetrates an elastomeric septum. The septum is in direct contact with the liquid so that the liquid flows out of the equipment through the needle. Iterations of this technique are used in medical device industries but don't usually include equipment combining the needle and the septum. Introducing a potentially non-sterile needle into the bioprocessing equipment violates good aseptic technique. With a cannula based aseptic sampling device the needle and septa are combined into a hermetically sealed aseptic sampling device.


Euphaedra eleus

Euphaedra eleus, the Eleus orange forester, is a butterfly in the family Nymphalidae. It is found in Guinea, Sierra Leone, Liberia, Ivory Coast, Ghana, Nigeria, Cameroon, Gabon, the Republic of the Congo, Angola, the Democratic Republic of the Congo and Uganda. The habitat consists of primary forests and secondary forests with a closed canopy.
Adults mimic the day-flying moth "Scopula helcita".
The larvae feed on "Phialodiscus unijugatus", "Deinbollia", "Allophylus" and "Paullinia" species.
Description.
Upperside. Antennae black, with two small white spots at the base. Thorax and abdomen black, spotted with two rows of white spots, in pairs, from the neck to the anus; those on the abdomen being the least. Half the superior wings next the tips black, with two white streaks thereon placed obliquely; the other half next to the body dirty orange, the anterior edges being black. Posterior wings dirty orange, bordered along the external edges with black, whereon is a row of seven oval white spots on each wing, placed at equal distances.
Underside. Palpi and breast orange. Forelegs orange, the rest white. Wings on this side dark orange coloured. The white streaks near the tips of the anterior ones are very plain. Anterior edges of the posterior wings white, and the row of white spots along the external edges are here very conspicuous, each being verged with black. Wingspan inches (88 mm).


Lentithecium

Lentithecium is a genus of fungi belonging to the family Lentitheciaceae.
The species of this genus are found in Europe.
Species:


Mononivirinae


Serpulaceae

The Serpulaceae are a family of fungi in the Boletales order. According to the "Dictionary of the Fungi" (10th edition, 2008), the family contains 4 genera and 20 species. However, a molecular phylogenetics study showed that the genus "Neopaxillus", which was formerly placed in this family, belongs in the family Crepidotaceae in the order Agaricales.


B. Mario Pinto

Dr. B. Mario Pinto is a Canadian chemical biologist, academic and the former President of the Natural Sciences and Engineering Research Council of Canada (NSERC). Prior to his appointment at NSERC, Pinto served as a chemistry professor and as the Vice-President of Research at Simon Fraser University. He is a fellow of the Royal Society of Canada, Chemical Institute of Canada and the American Chemical Society.
He resigned as president of NSERC on September 21, 2018.
He was appointed Deputy Vice Chancellor (Research) of Griffith University, Brisbane, Australia, on October 3, 2019, to commence in February 2020.
Education.
Pinto received his undergraduate degree and doctorate from Queen's University in Ontario. He completed his post-doctoral work at the Centre national de la recherche scientifique in France and the National Research Council of Canada in Ottawa. Pinto has published over 225 papers.


Lactic acid bacteria

Lactobacillales are an order of gram-positive, low-GC, acid-tolerant, generally nonsporulating, nonrespiring, either rod-shaped (bacilli) or spherical (cocci) bacteria that share common metabolic and physiological characteristics. These bacteria, usually found in decomposing plants and milk products, produce lactic acid as the major metabolic end product of carbohydrate fermentation, giving them the common name lactic acid bacteria (LAB).
Production of lactic acid has linked LAB with food fermentations, as acidification inhibits the growth of spoilage agents. Proteinaceous bacteriocins are produced by several LAB strains and provide an additional hurdle for spoilage and pathogenic microorganisms. Furthermore, lactic acid and other metabolic products contribute to the organoleptic and textural profile of a food item. The industrial importance of the LAB is further evidenced by their generally recognized as safe (GRAS) status, due to their ubiquitous appearance in food and their contribution to the healthy microbiota of animal and human mucosal surfaces. The genera that comprise the LAB are at its core "Lactobacillus", "Leuconostoc", "Pediococcus", "Lactococcus", and "Streptococcus", as well as the more peripheral "Aerococcus", "Carnobacterium", "Enterococcus", "Oenococcus", "Sporolactobacillus", "Tetragenococcus", "Vagococcus", and "Weissella". All but "Sporolactobacillus" are members of the Lactobacillales order, and all are members of the Firmicutes phylum.
Although lactic acid bacteria are generally associated with the order Lactobacillales, bacteria of the genus Bifidobacterium (phylum Actinobacteria) also produce lactic acid as the major product of carbohydrate metabolism.
Characteristics.
The lactic acid bacteria (LAB) are either rod-shaped (bacilli), or spherical (cocci), and are characterized by an increased tolerance to acidity (low pH range). This aspect helps LAB to outcompete other bacteria in a natural fermentation, as they can withstand the increased acidity from organic acid production (e.g., lactic acid). Laboratory media used for LAB typically include a carbohydrate source, as most species are incapable of respiration. LAB are catalase-negative. LAB are amongst the most important groups of microorganisms used in the food industry. Their relative simple metabolism has also prompted their use as microbial cell factories for the production of several commodities for the food and non-food sectors
Metabolism.
Two main hexose fermentation pathways are used to classify LAB genera. Under conditions of excess glucose and limited oxygen, homolactic LAB catabolize one mole of glucose in the Embden-Meyerhof-Parnas pathway to yield two moles of pyruvate. Intracellular redox balance is maintained through the oxidation of NADH, concomitant with pyruvate reduction to lactic acid. This process yields two moles of ATP per mole of glucose consumed. Representative homolactic LAB genera include "Lactococcus", "Enterococcus", "Streptococcus", "Pediococcus", and group I lactobacilli
Heterofermentative LAB use the pentose phosphate pathway, alternatively referred to as the pentose phosphoketolase pathway. One mole of glucose-6-phosphate is initially dehydrogenated to 6-phosphogluconate and subsequently decarboxylated to yield one mole of CO2. The resulting pentose-5-phosphate is cleaved into one mole glyceraldehyde phosphate (GAP) and one mole acetyl phosphate. GAP is further metabolized to lactate as in homofermentation, with the acetyl phosphate reduced to ethanol via acetyl-CoA and acetaldehyde intermediates. In theory, end products (including ATP) are produced in equimolar quantities from the catabolism of one mole of glucose. Obligate heterofermentative LAB include "Leuconostoc", "Oenococcus", "Weissella", and group III lactobacilli
Some members of "Lactobacillus" appear also able to perform aerobic respiration, making them facultative anaerobes instead of aerotolerant ones like the rest of the order. Using oxygen helps these bacteria deal with stress better.
"Streptococcus" reclassification.
In 1985, members of the diverse genus "Streptococcus" were reclassified into "Lactococcus", "Enterococcus", "Vagococcus", and "Streptococcus" based on biochemical characteristics, as well as molecular features. Formerly, streptococci were segregated primarily based on serology, which has proven to correlate well with the current taxonomic definitions. Lactococci (formerly Lancefield group N streptococci) are used extensively as fermentation starters in dairy production, with humans estimated to consume 1018 lactococci annually. Partly due to their industrial relevance, both "L. lactis" subspecies ("L. l. lactis" and "L. l. cremoris") are widely used as generic LAB models for research. "L. lactis" ssp. "cremoris", used in the production of hard cheeses, is represented by the laboratory strains LM0230 and MG1363. In similar manner, "L. lactis" ssp. "lactis" is employed in soft cheese fermentations, with the workhorse strain IL1403 ubiquitous in LAB research laboratories. In 2001, Bolotin "et al." sequenced the genome of IL1403, which coincided with a significant shift of resources to understanding LAB genomics and related applications.
Phylogeny.
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature
and the phylogeny is based on 16S rRNA-based LTP release 106 by 'The All-Species Living Tree' Project.
Lactobacillales part 2 (continued).
Notes:<br>
♠ Strains found at the National Center for Biotechnology Information, but not listed in the List of Prokaryotic names with Standing in Nomenclature
Bacteriophages.
A broad number of food products, commodity chemicals, and biotechnology products are manufactured industrially by large-scale bacterial fermentation of various organic substrates. Because enormous amounts of bacteria are being cultivated each day in large fermentation vats, the risk that bacteriophage contamination rapidly brings fermentations to a halt and cause economical setbacks is a serious threat in these industries. The relationship between bacteriophages and their bacterial hosts is very important in the context of the food fermentation industry. Sources of phage contamination, measures to control their propagation and dissemination, and biotechnological defense strategies developed to restrain phages are of interest. The dairy fermentation industry has openly acknowledged the problem of phage contamination, and has been working with academia and starter culture companies to develop defence strategies and systems to curtail the propagation and evolution of phages for decades.
Bacteriophage–host interaction.
The first contact between an infecting phage and its bacterial host is the attachment of the phage to the host cell. This attachment is mediated by the phage's receptor binding protein (RBP), which recognizes and binds to a receptor on the bacterial surface. RBPs are also referred to as host-specificity protein, host determinant, and antireceptor. For simplicity, the RBP term will be used here. A variety of molecules have been suggested to act as host receptors for bacteriophages infecting LAB; among those are polysaccharides and (lipo)teichoic acids, as well as a single-membrane protein. A number of RBPs of LAB phages have been identified by the generation of hybrid phages with altered host ranges. These studies, however, also found additional phage proteins to be important for successful phage infection. Analysis of the crystal structure of several RBPs indicates that these proteins share a common tertiary folding, and support previous indications of the saccharide nature of the host receptor. Gram-positive LAB have a thick peptidoglycan layer, which must be traversed to inject the phage genome into the bacterial cytoplasm. Peptidoglycan-degrading enzymes are expected to facilitate this penetration, and such enzymes have been found as structural elements of a number of LAB phages.
Uses.
Probiotics.
Probiotics are products aimed at delivering living, potentially beneficial, bacterial cells to the gut ecosystem of humans and other animals, whereas prebiotics are indigestible carbohydrates delivered in food to the large bowel to provide fermentable substrates for selected bacteria. Most strains used as probiotics belong to the genus "Lactobacillus". (Other probiotic strains used belong to the genus "Bifidobacterium").
Probiotics have been evaluated in research studies in animals and humans with respect to antibiotic-associated diarrhea, travellers' diarrhea, pediatric diarrhea, inflammatory bowel disease, and irritable bowel syndrome. In the future, probiotics possibly will be used for different gastrointestinal diseases, vaginosis, or as delivery systems for vaccines, immunoglobulins, and other therapies.
Foods.
The quest to find food ingredients with valuable bioactive properties has encouraged interest in exopolysaccharides from LAB. Functional food products that offer health and sensory benefits beyond their nutritional composition are becoming progressively more important to the food industry. The sensory benefits of exopolysaccharides are well established, and there is evidence for the health properties that are attributable to exopolysaccharides from LAB. However, there is a wide variation in molecular structures of exopolysaccharides and the complexity of the mechanisms by which physical changes in foods and bioactive effects are elicited.
In a study for postharvest food product safety conducted with 119 LAB isolated from the rhizosphere of olive trees and desert truffles, mostly within the genera of "Enterococcus" and "Weissella", researchers found strong antibacterial activity against "Stenotrophomonas maltophilia", "Pantoea agglomerans", "Pseudomonas savastanoi", "Staphylococcus aureus" and "Listeria monocytogenes", and anti-fungal activity against "Botrytis cinerea", "Penicillium expansum", "Verticillium dahliae" and "Aspergillus niger".
Fertilizer.
Researchers have studied the impact of lactic acid bacteria on indeoleacetic acid production, phosphate solubilization, and nitrogen fixation on citrus. While most of the bacterial isolates, were able to produce IAA, phosphate-solubilization was limited to only one of the eight LAB isolates.
Fermentation.
Lactic acid bacteria are used in the food industry for a variety of reasons such as the production of cheese and yogurt products. This process has been going on for thousands of years by human ancestors. But, some of the beverages we enjoy today are produced by using lactic acid bacteria. Popular drinks such as kombucha have known to have traces of "lactobacillus" and "pediococcus" once the drink is made. Even the beer and wine-making process utilizes certain lactic acid bacteria mostly "lactobacillus". The interesting relationship between lactic acid bacteria and yeast can be observed in the wine-making process. The LAB is used to start the wine-making process by starting the malolactic fermentation. After the malolactic fermentation, yeast cells are used to start the alcoholic fermentation process in grapes. The malolactic fermentation mechanism is mainly transformation of L-malic acid (dicarboxylic acid) to an lactic acid (monocarboxylic acid). This change occurs due to the presence of malolactic and malic enzymes. All malic acid are degraded and this increase the pH levels which changes the taste of the wine. Not only do they start the process but they are responsible for the different aromas produced in wine by the nutrients presence and the quality of the grapes. Also, the presence of different strains can change the desirability of aromas' presence. The different availability of enzymes that contribute to the vast spectrum of aromas in wine are associated with glycosidases, "β"-glucosidases, esterases, phenolic acid decarboxylases and citrate lyases. By using molecular biology, researchers can help pick out different desirable strains that help improve the quality of wine and help with the removable of the undesirable strains. The same can be said about brewing beer as well which uses yeast with some breweries using lactic acid bacteria to change the taste of their beer.
Lactic acid bacteria and dental plaque.
LAB are able to synthesize levans from sucrose, and dextrans from glucose. Glucans, such as dextran, enable bacteria to adhere to the surface of teeth, which in turn can cause tooth decay through the formation of dental plaque and production of lactic acid. While the primary bacteria responsible for tooth decay is "Streptococcus mutans", LAB are among the most common oral bacteria which cause dental cavities.


Chytridium

Chytridium is a genus of fungi in the family Chytridiaceae.
With the culture and characterization of "Chytridium olla", the type species of the order, the limits of the Chytridiales were established.


Kuraishia

Kuraishia is a genus of two species of ascomycetous yeasts in the family Saccharomycetaceae. The type species "Kuraishia capsulata" was originally described as a member of "Hansenula" (now "Pichia") in 1953. "K. molischiana" was described as new to science in 2004. The complete genome sequence of "K. capsulata" was reported in 2013. K. capsulata produces extracellular exopolysahharide, phosphomannan, as an external phosphorus reserve.


Hypsizygus tessellatus

Hypsizygus tesselatus (Buna shimeji) is an edible mushroom native to East Asia. It is cultivated locally in temperate climates in Europe, North America and Australia and sold fresh in super markets. In nature, shimeji are gilled mushrooms that grow on wood. Most often the mushroom is found on beech trees, hence the common name, beech mushroom. They are often small and thin in appearance and popular in many nations across the world.
Two variations are known:
Cooking.
Being tough when raw, the Shimeji should be cooked, having a bitter taste when raw which disappears completely upon cooking. The cooked mushroom has a firm, slightly crunchy texture and a nutty flavor. Preparation makes the mushroom easier to digest. It is often eaten with stir-fried foods including wild game and seafood. It is used in soups, stews and sauces. When prepared alone, Shimeji mushrooms can be sautéed as a whole, including the stem or stalk (only the very end cut off), using a higher temperature; or, they can be slow roasted on a low temperature with a small amount of butter or cooking oil. Shimeji is used in soups, nabe and takikomi gohan.