Guilty Gear Isuka

 is a 2D fighting video game developed by Arc System Works and published by Sammy Corporation. Announced by Arc in September, it was released on December 17, 2003 in Japanese arcades as the sixth installment of the "Guilty Gear" series. Later, the game was ported for a release on the PlayStation 2 (PS2), Xbox, and Windows in Japan. The PS2 version was brought to North America by Sammy, and, in Europe, the home console version was released by 505 Game Street and the PC version by Zoo Digital Publishing.
While the gameplay remained almost the same as in previous titles, the game introduced a four-player battle mode, and the PS2 version included new features to the series, including a scrolling adventure, a customization mode, and two new characters. "Guilty Gear Isuka" received mixed critical reviews. It was praised for its visual, music and customization features. However, although some aspects of the new gameplay—such as the two fighting planes and the turn button—were praised as original, their implementation was criticized. The removal of features present in previous titles was also not well received by critics.
Gameplay.
Combat system.
The basic gameplay system of "Guilty Gear Isuka" is like the other games in the series. The game uses a four attack button configuration that consists of punch, kick, slash, and high slash. Unlike previous games, it features a "turn" button, since a character does not automatically turn around if its opponent moves to the other side of the screen. Each character (or team) starts a fight with at least a "soul"; when a character life bar is emptied, its life is filled while the player lost a soul. If the life is depleted when the player has no souls, it is defeated. It also features previous installments features like the tension gauge, which allows the player to perform super moves, and the burst gauge, which allows the player to break combinations and super moves.
Modes.
The game introduces a four-player option in Versus Mode, giving a player four characters who can fight two-on-two, three-on-one or everyone-for-themselves. There are two fighting planes, one in the foreground and the other behind it.
Another innovation was Boost Mode: a two-player, side-scrolling, arcade-style beat 'em up mode not included in the arcade version, in which a player fights enemy waves to accumulate items, health and experience. For the Xbox, this mode was adapted for online play with Xbox Live, supporting up to 16 players. Experience points from Boost Mode can be used in the new Robo-Ky II Factory mode, in which a player can customize a robot named Robo-Ky II by teaching him moves, combos, or one of 65 special attacks from other characters. In addition to the attacks, other aspects such as jump height, offense, defense, recovery time, tension, and speed can be improved.
The game also features other modes: Color Edit, a palette swap editor that allows the player to customize nearly every aspect of the characters, including buckles and hair; Training, in which a player can practice with (and against) computer-controlled opponents and Arcade, similar to the survival mode featured in other fighting games.
Playable characters.
"Guilty Gear Isuka" features twenty playable characters in its arcade version: Anji Mito, Axl Low, Baiken, Bridget, Chipp Zanuff, Dizzy, Eddie, Faust, I-No, Jam Kuradoberi, Johnny, Ky Kiske, May, Millia Rage, Potemkin, Slayer, Sol Badguy, Testament, Venom, and Zappa. Three characters were added to the PlayStation 2 edition: A.B.A, Robo-Ky, and Robo-Ky II.
Development and release.
In September 2003, Sammy Corporation announced that a new game dubbed "Guilty Gear X Series The Newest Version" would be featured at the Japan Amusement Machinery Manufacturers Association (JAMMA) arcade show; at the show, the company revealed that "Guilty Gear Isuka" would be the game's name. "In "Guilty Gear Isuka" we want to satisfy existing fighter fans with new content and never-before-seen innovations. We also want to reach out to mainstream fans to show them that, right now, the envelope in fighting games is also being pushed in two dimensions", declared Tim Pivnicny, senior VP of Sammy Studios, Inc. A PlayStation 2 version of the game was announced to be in development on March 3, 2004. An August 24 announcement said that the game would be compatible with Xbox.
"Guilty Gear Isuka" was released in Japan on December 17, 2003 by Sammy for the Atomiswave arcade cabinets, followed by the PlayStation 2 version on July 29, 2004. An Xbox version was released by Arc System Works on December 16, 2004, and Sourcenext released the game for Windows on November 25, 2005. In North America, "Guilty Gear Isuka" was released by Sammy for PlayStation 2 on November 2, 2004. In Europe, 505 Games Street released it on June 16, 2005 for PlayStation 2, and the PC version was released on April 7, 2006 by Zoo Digital Publishing (now Zushi Games). In 2007, the game was made compatible with Xbox 360. DotEmu also released "Guilty Gear Isuka" on its DRM-free shop in April 2011. On January 16, 2014, the game was released on the Steam digital distribution platform for Windows PCs. In 2020, a homebrew conversion was released for the Dreamcast.
Reception.
"Guilty Gear Isuka" was the 176th-bestselling Japanese title in 2004, with 74,270 copies sold for PlayStation 2 as of December 26. It was "Best Fighting Game" at the Best of E3 2004 Awards from IGN, and was nominated for "Best Sequel Fighting" at the 2004 National Academy of Video Game Testers and Reviewers (NAVGTR) Awards. The game received mixed reviews from critics, with a score of 75.56% at GameRankings and 73/100 at Metacritic. Allgame's Damian Francis gave the game three-and-a-half stars out of five; "Famitsu"s four reviewers scored it 7, 7, 6, and 7 (out of 10) respectively, with a total score of 27 out of 40.
Although the introduction of two planes and the turning button were considered good ideas in theory, both features were heavily criticized by reviewers. Jeremy Dunham of IGN, Manny LaMancha of "GamePro" and Benjamin Turner of GameSpy felt it difficult to fight one-on-one when a player can start a cat-and-mouse game, while GameSpot's Greg Kasavin and Brian Gee of Game Revolution found the features to cause "chaos". Turner said it deprived the player of the ability "to have a normal "Guilty Gear X2"-style match", and Dunham said the computer reacted faster. David Smith of 1UP.com called it an "irrational control scheme". The perceived poor execution of its new features led GameSpy to give it a special "It Sounded Good on Paper" award.
Conversely, other additions received more positive feedback. Dunham called the Boost and Factory modes "intriguing distractions", while Turner praised the latter for "much depth and nuance", unreached by other games. Kasavin said the Boost Mode gets boring quickly due to the lack of an objective; though Kasavin declared that the Factory Mode "is quite possibly the most interesting part of the gameplay", he criticized how it depends on playing "a mindless side-scroller over and over." The new backgrounds were commended by Dunham, Kasavin and Smith, with the latter saying that Sammy should have saved them for a better game.
The maintenance of aspects from previous titles, including its animation and soundtrack, was praised by Kasavin, Turner, and Gee. Its soundtrack was said to be "the best score in the franchise so far" by Dunham, and was rated among video game soundtracks which "never got the recognition they truly deserve" by Siliconera. LaMancha, however, criticized a lack of improvement of its animation and music compared to its gameplay. The removal of other features from previous titles was criticized: Dunham and Kasavin complained about the lack of a story mode, while Joe Juba of "Game Informer" said the series had a "magic" until "Isuka", criticizing the new additions and the absence of a traditional arcade mode. "Isuka" was well-rated on balance, but considered inferior to the previous "Guilty Gear X2 #Reload".
Other media.
Music.
, composed by Daisuke Ishiwatari, Tetsuya Ohuchi and Yoshihiro Kusano, arranged by Ohuchi and Kusano, was released on CD by Team Entertainment on April 21, 2004. An additional edition was released on iTunes on November 23, 2005; it contains six more tracks, totalizing 26 tracks.
It was well received by critics; Don Kotowski and Harry of Square Enix Music Online rated it 8 out of 10. Kotowski said Ishiwatari is the mainstream in the soundtrack, while Ohuchi and Kusano "somewhat disappoint", qualifying it as "a great album" in overall. Harry said the only thing bad about this album is its "too short" length. Writing for the same site, a reviewer dubbed GoldfishX rated it 7 out of 10, citing "it lacks the depth of previous entries in the series."
Books.
Ichijinsha released two "Guilty Gear Isuka" manga adaptations under its "DNA Media Comics" line. The first one, titled , is a "yonkoma" series released on February 25, 2004. The other series is an anthology titled , which was released on March 25 of the same year. Subsequently, on March 30, was released by Enterbrain. It is an encyclopedia compiled by "Monthly Arcadia", an Enterbrain magazine, which was released along with a DVD with commentaries on the game features. Two guidebooks were released by SoftBank Creative; and were published on August 9, and on September 6, 2004, respectively.


Oxaloacetic acid

Oxaloacetic acid (also known as oxalacetic acid or OAA) is a crystalline organic compound with the chemical formula HO2CC(O)CH2CO2H. Oxaloacetic acid, in the form of its conjugate base oxaloacetate, is a metabolic intermediate in many processes that occur in animals. It takes part in gluconeogenesis, the urea cycle, the glyoxylate cycle, amino acid synthesis, fatty acid synthesis and the citric acid cycle.
Properties.
Oxaloacetic acid undergoes successive deprotonations to give the dianion:
At high pH, the enolizable proton is ionized:
The enol forms of oxaloacetic acid are particularly stable, so much so that the two tautomers have different melting points (152 °C for the "cis" isoform and 184 °C for the "trans" isoform). This reaction is catalyzed by the enzyme oxaloacetate tautomerase. "trans"-Enol-oxaloacetate also appears when tartrate is the substrate for fumarase.
Biosynthesis.
Oxaloacetate forms in several ways in nature. A principal route is upon oxidation of -malate, catalyzed by malate dehydrogenase, in the citric acid cycle. Malate is also oxidized by succinate dehydrogenase in a slow reaction with the initial product being enol-oxaloacetate.

It also arises from the condensation of pyruvate with carbonic acid, driven by the hydrolysis of ATP:
Occurring in the mesophyll of plants, this process proceeds via phosphoenolpyruvate, catalysed by phosphoenolpyruvate carboxylase.
Oxaloacetate can also arise from trans- or de- amination of aspartic acid.
Biochemical functions.
Oxaloacetate is an intermediate of the citric acid cycle, where it reacts with acetyl-CoA to form citrate, catalyzed by citrate synthase. It is also involved in gluconeogenesis, the urea cycle, the glyoxylate cycle, amino acid synthesis, and fatty acid synthesis. Oxaloacetate is also a potent inhibitor of complex II.
Gluconeogenesis.
Gluconeogenesis is a metabolic pathway consisting of a series of eleven enzyme-catalyzed reactions, resulting in the generation of glucose from non-carbohydrates substrates. The beginning of this process takes place in the mitochondrial matrix, where pyruvate molecules are found. A pyruvate molecule is carboxylated by a pyruvate carboxylase enzyme, activated by a molecule each of ATP and water. This reaction results in the formation of oxaloacetate. NADH reduces oxaloacetate to malate. This transformation is needed to transport the molecule out of the mitochondria. Once in the cytosol, malate is oxidized to oxaloacetate again using NAD+. Then oxaloacetate remains in the cytosol, where the rest of reactions will take place. Oxaloacetate is later decarboxylated and phosphorylated by phosphoenolpyruvate carboxykinase and becomes 2-phosphoenolpyruvate using guanosine triphosphate (GTP) as phosphate source. Glucose is obtained after further downstream processing.
Urea cycle.
The urea cycle is a metabolic pathway that results in the formation of urea using one ammonium molecule from degraded amino acids, another ammonium group from aspartate and one bicarbonate molecule. This route commonly occurs in hepatocytes. The reactions related to the urea cycle produce NADH, and NADH can be produced in two different ways. One of these uses oxaloacetate. In the cytosol there are fumarate molecules. Fumarate can be transformed into malate by the actions of the enzyme fumarase. Malate is acted on by malate dehydrogenase to become oxaloacetate, producing a molecule of NADH. After that, oxaloacetate will be recycled to aspartate, as transaminases prefer these keto acids over the others. This recycling maintains the flow of nitrogen into the cell.
Glyoxylate cycle.
The glyoxylate cycle is a variant of the citric acid cycle. It is an anabolic pathway occurring in plants and bacteria utilizing the enzymes isocitrate lyase and malate synthase. Some intermediate steps of the cycle are slightly different from the citric acid cycle; nevertheless oxaloacetate has the same function in both processes. This means that oxaloacetate in this cycle also acts as the primary reactant and final product. In fact the oxaloacetate is a net product of the glyoxylate cycle because its loop of the cycle incorporates two molecules of acetyl-CoA.
Fatty acid synthesis.
In previous stages acetyl-CoA is transferred from the mitochondria to the cytoplasm where fatty acid synthase resides. The acetyl-CoA is transported as a citrate, which has been previously formed in the mitochondrial matrix from acetyl-coA and oxaloacetate. This reaction usually initiates the citric acid cycle, but when there is no need of energy it is transported to the cytoplasm where it is broken down to cytoplasmatic acetyl -CoA and oxaloacetate.
Another part of the cycle requires NADPH for the synthesis of fatty acids. Part of this reducing power is generated when the cytosolic oxaloacetate is returned to the mitochondria as long as the internal mitochondrial layer is non-permeable for oxaloacetate. Firstly the oxaloacetate is reduced to malate using NADH. Then the malate is decarboxylated to pyruvate. Now this pyruvate can easily enter the mitochondria, where it is carboxylated again to oxaloacetate by pyruvate carboxylase. In this way, the transfer of acetyl-CoA that is from the mitochondria into the cytoplasm produces a molecule of NADH. The overall reaction, which is spontaneous, may be summarized as:
Amino acid synthesis.
Six essential amino acids and three nonessential are synthesized from oxaloacetate and pyruvate. Aspartate and alanine are formed from oxaloacetate and pyruvate, respectively, by transamination from glutamate. Asparagine, methionine, lysine and threonine are synthesized by aspartate, therefore given importance to oxaloacetate as without it, no aspartate would be formed and the following other amino acids would neither be produced.
Oxalate biosynthesis.
Oxaloacetate produces oxalate by hydrolysis.
This process is catalyzed by the enzyme oxaloacetase. This enzyme is seen in plants, but is not known in the animal kingdom.


John Oldham (poet)

John Oldham (9 August 1653 – 9 December 1683) was an English satirical poet and translator.
Life and work.
Oldham was born in Shipton Moyne, Gloucestershire, the son of John Oldham, a non-conformist minister, and grandson of John Oldham the staunch anti-papist rector of Shipton Moyne and before that of Long Newton in Wiltshire. He was educated first at Tetbury Grammar School, then at St. Edmund Hall at the University of Oxford, where the Principal was Thomas Tully, an ex-headmaster from Oldham's school at Tetbury. Tully was "a person of severe morals, puritanically inclined and a struict Calvinist.
Oldham received a B. A. degree in May 1674. He became an usher at the Whitgift School in Croydon, Surrey (now in Greater London), a position that was poorly paid, monotonous and left little time for him to compose poetry; his discontent at the time was expressed in these lines from one of his satires - "To a friend about to leave University":
"But who would be to the vile drudgery bound
Where there so small encouragement is found?
Where you for recompense for all your pains,
Shall hardly reach a common fiddler's gains?
For when you've toiled and laboured all you can,
To dung and cultivate a barren brain,
A Dancing-Master shall be better paid,
Tho' he instructs the Heels and you the Head.""
By then his poetry had already been published, and he received an unexpected visit at the school from an illustrious party including the Earl of Rochester, Charles Sedley and the Earl of Dorset (part of the "merry gang", as Andrew Marvell called them), who wished to express their appreciation of his work.
He left the Whitgift school in 1678 and took up the post of tutor to the grandsons of a retired Judge, Sir Edward Thurland, in the vicinity of Reigate in Surrey. It was during this period that he composed and had published his satires against the Jesuits, at a time when popular anger was being stirred up against Catholics in England by the "Popish plot". In 1680, he became, for a short time, tutor to the son of Sir William Hicks, through whom he made the acquaintance of the notable physician Dr. Richard Lower. Under his influence he took up the study of medicine for a year before returning to his poetic muse.
Oldham settled in London and was introduced to John Dryden, with whom he became close friends. He entered fashionable society (said to be centred on Will's Coffee House), and was approached by the Earl of Kingston-upon-Hull to be a private chaplain to his household. Oldham turned down the post but did accept the hospitality of the Earl at his seat at Holme Pierrepont Hall in Nottinghamshire.
It was here that he died of smallpox, on 9 December 1683, aged only 30. He may also have suffered from tuberculosis during his lifetime. The Earl of Kingston-upon-Hull had a monument, possibly designed by Grinling Gibbons, erected over Oldham's grave in St. Edmund's Church in Holme Pierrepont. John Dryden wrote an elegy on his death.
Oldham was a satirist who imitated the classical Satires of Juvenal. His best-known works are "A Satire Upon a Woman Who by Her Falsehood and Scorn Was the Death of My Friend", written in 1678 and "A Satire against Virtue", written in 1679. During his lifetime, his poetry was published anonymously. His translations of Juvenal were published after his death.
John Dryden was one of Oldham's admirers and upon his death Dryden expressed his admiration in "To the Memory of Mr. Oldham".
Style.
Although regarded as a vigorous and passionate satirst, Oldham is often regarded as having been hampered by a poor ear for rhyme and rhythm. As Robinson (1980) has pointed out, however, "Oldham "chose" the rugged style of most of his satires: it was not imposed upon him by incapacity or carelessness."


Amraal Lambert

Amraal Lambert, Nama name: ǂGaiǀnub, (ca. 1774 – 13 February 1864) was the first Captain of the Kaiǀkhauan (Khauas Nama), a subtribe of the Orlam, in the eastern area of Namaland, today's Namibia.
Amraal Lambert was born around 1774 near Hex River in the Clanwilliam district in the Cape Colony (today's South Africa). A Cape Khoikhoi descendant, his status was little better than that of a slave, and he was forced to work in Worcester and Cape Town in his youth. In 1814 Lambert moved to Namaland (today's eastern-central Namibia), accompanied by missionary Heinrich Schmelen, who baptised him in Bethanie in 1815. Schmelen and the Kaiǀkhauan group led by Lambert stayed together for 14 more years but Schmelen closed the missionary station in Bethanie in 1822 and travelled on. Lambert accompanied Schmelen on his travel to Walvis Bay in 1825.
Between 1830 and 1860, Amraal Lambert and his cousin Jonker Afrikaner controlled much of southern and central South-West Africa. Together they have been described as "super-power[s] in the cattle raiding business". From 1825 onwards Jonker Afrikaner and his council played a dominant political role in Damaraland and Namaland, creating a "de facto" state.
In 1840 Lambert and his people moved to Naosanabis (today Leonardville) where they allied with ǁOaseb, leader of the Khaiǁkhaun (Red Nation). In 1855 or 1856 they abandoned Naosanabis and moved to ǂKoabes. Amraal, who spoke only Afrikaans, could not pronounce the Nama name for this settlement, and changed it to its now common name Gobabis.
In the 1860s the Kaiǀkhauan were severely weakened in their political and economic power. Their cattle died of lung disease, and smallpox befell the Nama community at Gobabis. Many members of the Lambert family succumbed to the disease, among them Amraal who died on 13 February 1864 in Gobabis. His grandson Andreas Lambert succeeded him as Captain of the Kaiǀkhauan at the age of 20.


NE-tag

The NE-tag is a synthetic peptide tag (NE tag) designed as an epitope tag for detection, quantification and purification of recombinant protein. This patented peptide sequence is composed of eighteen hydrophilic amino acids. This short peptide does not adopt any significant homology to any existing proteins found in nature. This synthetic NE peptide adopts random coil conformation and showing strong immunogenicity (computational prediction). This is advantageous to offer stringent specificity to the NE-tagged proteins, which are readily to be detected, quantitated, and purified.
Detection.
The NE-tag can be specifically detected using a monoclonal anti-NE detection antibody - an affinity-purified mouse immunoglobulin, IgG1, which specifically binds to NE-tagged proteins. This peptide-to-antibody conjugation is validated in Western blotting, immunoprecipitation (IP), immunocytochemistry (IHC), and affinity purification of NE fusion proteins (i.e. affinity column).


Avesthagen

Avesthagen Limited is an integrated systems biology platform company headquartered in Bangalore, India. It was founded as an academic startup in 1998 by Villoo Morawala-Patell, a Rockefeller Fellow and grantee within NCBS-UAS, Bangalore. Avesthagen started business operations on March 21, 2001 with Series-A round investment led by ICICI Ventures and Tata Industries. Dr.Villoo Morawala Patell, is the Chairperson and Managing Director of Avesthagen Limited.
The company developed a unique portfolio of high-potential pharmaceutical, nutrition and agro-industrial bio-based products and continues to create novel products through Co"nvergence of food, pharma and population genetics leading to "Predictive, Preventive, Personalized" Healthcare and Food security". The goal of PPP healthcare is to use the advanced tools of molecular genetics to predict how patients will respond to drugs, reducing harm and increasing benefit. The dual combination of diagnostic and treatment technologies is at the heart of personalized medicine and will continue to transform modern healthcare dramatically.
The Avestagenome Project
The Avestagenome Project, founded by Dr.Villoo Morawala Patell was created to identify genetic risk factors within the Parsi population that predispose individuals to cancers and high morbidity diseases. Its database of genomic variants derived from the Parsi control population is used with other populations to identify early intervention and improve disease prevention strategies to deliver improved health outcomes. The endogamous Parsi community is characterized by greater longevity, fewer cases of lung, head, neck and esophageal cancers. At the same time, there is increased prevalence of Parkinson's & Alzheimer's diseases, cardiovascular disease, breast and prostate cancer, and male and female infertility. A pilot study by Avesthagen Limited into the prevalence of breast cancer biomarkers and metabolite signatures indicated unique signatures that are currently undergoing further validation in larger cohorts
The Parsi people, followers of Zoroastrianism, strongly advocate a responsible attitude towards the environment and respect to the elements of creation – fire, water, air, earth, and ether/space - with a special emphasis on fire, the purest of elements and an essential for all rituals and prayers. Veneration for fire has kept the vast majority of Parsis from smoking for centuries. Family pressure coupled with religious restrictions ensured a nearly smoke-free community. This makes the Parsi people and Avesthagen's Biobank the ideal control population to act as the reference standard for research into tobacco-related cancers and diseases
Since 2008, the Avestagenome Project has collected blood samples and extensive patient data from over 4,500 members of the Zoroastrian-Parsi community with a target of 15,000 Parsis globally by 2021. The molecular basis of longevity and age-related disorders, prioritising cancers, cardiovascular disease, diabetes and neurological disorders will be investigated in this cohort specifically. The project will provide insights into disease prediction and accelerate identification and development of biomarkers, predictive diagnostic tests, new drugs and therapies. In 2019, this initiative received support by the Foundation for a Smoke Free World (FSFW), a US-based, independent non-profit organization that aims to end smoking in this generation. FSFW has awarded Dr.Villoo Morawala-Patell,a grant of 2.29M USD to explore “Cancer risk in smoking subjects assessed by next generation sequencing profile of circulating free DNA and RNA.” The work carried out at Avesthagen Limited will combine liquid biopsy, next-generation sequencing (NGS), state-of-the-art bioinformatics, artificial intelligence and machine learning to identify predictive and early-stage biomarkers of cancers in smokers. The project will use non-Parsi smoker and non-smoker samples from the wider Indian and other populations to gain further insights into the evidence behind such data.
Recent Publications
AGENOME-ZPMS-HV2a-1: The first complete Zoroastrian Parsi Mitochondrial Reference Genome
In a new paper, available on bioRxiv in 2020, Avesthagen researchers characterized the genetic traits specific to the Zoroastrian-Parsi population—a community that has historically abstained from smoking. Because of this unique social practice, Zoroastrian-Parsi genes may help scientists characterize biomarkers predictive of diseases caused by tobacco use, such as lung, head and neck, and esophagus cancers.
To obtain a complete picture of population-specific variants, the Avesthagen team analyzed one hundred Zoroastrian-Parsi mitochondrial genomes to generate a “consensus genome.” This is a process that combines genetic information from a large number of individuals to determine the genetic traits typical to that population. The mitochondrial DNA of one hundred Zoroastrian-Parsi individuals sequenced created the “consensus mitochondrial genome” (AGENOME-ZPMCG V 1.0). For practical reasons, maternally-inherited mitochondrial DNA is often used for this type of analysis. The researchers also did phylogenetic mapping to determine the ancestry of the Zoroastrian-Parsi community and found a largely Persian origin, attesting to their historical migration from ancient Persia.
The researchers identified a total of 420 mitochondrial variants in the hundred Zoroastrian-Parsi genomes. Analysis of the variants revealed genetic indicators of longevity and of diseases that tend to emerge later in life. The genomes showed, for example, variants linked to colon and prostate cancer, as well as neurodegenerative conditions like Parkinson's disease. Because these diseases typically affect older individuals, indicators of their presence corroborate apparent longevity in the Zoroastrian-Parsi community.
The researchers found no indicators of tobacco-related diseases that often cause premature death. The genomes had a low frequency of mutations linked to carcinogen-induced diseases, such as lung cancer.
Dynamic Methylome Modification associated with mutational signatures in ageing and etiology of disease
More recently, in 2020, Avesthagen released a pre-print of their recent work on the whole genome methylation and variant analysis in one Zoroastrian-Parsi non-smoking individual, collected at an interval of 12 years apart on biorXiv titled "Dynamic Methylome Modification associated with mutational signatures in ageing and etiology of disease". The work identified 5258 disease relevant genes differentially methylated across this individual over 12 years and 24,948 genes corresponding to 4,58,148 variants specific to ZPMetG-Hv2a-1B, indicative of variants that accrued over time providing an understanding of the ageing methylome over time through the interplay between differentially methylated genes and variants in the etiology of disease.
AVGEN Pharma
AVGEN Pharma, Avesthagen's biopharmaceuticals business develops a comprehensive range of biosimilars and antibody therapeutics for a spectrum of diseases including oncology, auto-immune, cardiovascular–targeted biologics. AVGEN Pharma owns 8 biosimilar molecules with patents, processes, manufacturing rights for global licensing and sales & marketing rights. The biosimilars listed below have completed preclinical trials and are ready to enter clinical trials for validation.
Avesta Nordic Research Private Limited
Avesthagen's subsidiary, Avesta Nordic Research Private Limited engages primarily in the research, development, manufacturing and commercialization of our Food for Medicine portfolio of novel bioactives, functional food products and dietary supplements targeting the growing population of health conscious consumers around the globe. Avesthagen's research programs have led to a portfolio of scientifically validated botanical bioactive ingredients exclusively derived from traditional Indian medicine. Avesta Nordic's Functional ingredients, such as Teestar®, Cincata®, Bonapure™ & Bonaphyte™ have scientifically and some of them clinically validated health benefits to promote wellness through prevention of specific degenerative conditions: diabetes, obesity, metabolic syndromes, cardiovascular disorders and bone loss.
Avesthagen's DHA from algal sources will also provide the much need omega-3 fatty acids to vegetarians. The company is in the process of developing a manufacturing alliance for AvestaDHA and has developed a marketing alliances for its bioactives and DHA with a large beverage player in India, a large MNC retailer and a large Indian conglomerate.
The key products and product candidates are based upon, or include as a primary ingredient, scientifically and clinically validated plant extracts, or "bioactives", sourced from traditional Indian medicine which we have researched and developed using ADePt, Avesta Nordic's proprietary bioactive discovery engine and information management platform and MetaGrid, the proprietary bioactive testing methodology. In May 2008, we launched Teestar, our first ADePt and MetaGrid derived bioactive, which we clinically demonstrated to reduce blood glucose levels.
AVA Seeds
Avesthagen's subsidiary, AVA Seeds is engaged in the development of novel seed research, application of molecular markers and transgene based technologies to develop more productive food, feed, fuel and fiber based products to meet the growing needs of farmers, processors and consumers globally.
AVA Seeds® has developed cutting edge GMO technologies such as enhanced nutritional value, and sustainable green technology viz., biofuels and Environmentally Adapted Crop Technology for traits such as drought stress, salinity stress, nitrogen use efficiency.
The R&D focus and intellectual property has been developed around genes and promoters that enable the synthetic production of proteins and the generation of a specific GMO plant. In this respect, the company has developed a process patent on first, transformation of pearl millet and secondly, a modified tobacco plant reducing nicotine by c.80%.
The focus of AVA Seeds is in the following areas:
Nutrition-FIT
AVA Seeds project for the production of gene-modified seeds with enhanced nutritional value is the development of high-lycopene tomatoes. The company has produced a tomato variant through the introduction of a gene from rice, which on a greenhouse trial scale, has shown significantly increased levels of lycopene.
Hybrid-FIT
The development of male sterile hybrid variants of plants is an essential step in the development of enhanced seeds and transgenic variants. By creating male sterile variants with the desired traits, the developer of such variants can ensure that all of the produced seeds contain the desired trait and that the desired trait will not be diluted or lost due to naturally occurring crossbreeding.
AVA Seeds has developed a unique male sterility system for rice focused on the role of the mitochondria in the reproductive cycle of rice. By inserting a gene that inhibits certain respiratory functions of the mitochondria, we have created transgenic rice plants which are male sterile.
Tomatoes. Presently, a male sterile system does not exist in nature for the cultivated tomato, "Lycoperison esculentum".  AVA Seeds has a strategy to develop male sterile hybrid line of tomatoes based on the same core technology applied for the development of male sterile rice. The process currently awaits evaluation in greenhouse trials.
AVA Seeds under the Oil world Program is developing transgenic Jathropha plants that have an increased oil yield for the production of biodiesel and also pearl millet, a grain whose fiber contains an enzyme that would facilitate cellulosic ethanol production without the use of external enzymes, thereby making the process faster and more cost effective than the sugarcane model, resulting in more sustainable cellulosic ethanol.
The company as part of its sustainability initiative developed BioPercept, a biocompostable plastic made from renewable resources that breaks down and decomposes, under industrial composting conditions, within 120 days.
DHA Program
Docosahexaenoic acid, or DHA and acid alpha linolenic acid, or ALA are two of the Omega 3 acids, and which have shown a variety of positive health effects. This program is aimed at introducing key step genes for oil quality into mustard and sunflower with the goal of developing variants of the plants that produce these Omega 3 acids.  Avesthagen Limited has isolated the gene sequence of the marine organism schizochytrium that is required for the production of the Omega 3 fatty acids ALA, and DHA and is currently working on transforming mustard, by inserting the relevant isolated genes, to develop a variant that produces DHA, and on transforming Sunflower to develop variants that produce ALA and DHA.
Jatropha
Jatropha is a popular oilseed crop with potential for use in the production of biofuels. The oil content of Jatropha seeds ranges from around 30–35% and is inedible. This oil has traditionally been used as a fuel in domestic lighting and as a raw material for soap making. As a triglyceride, this oil is a poor fuel substitute due to its high viscosity, low flow rate, low volatility and poor cold flow rates. Derivatives of this oil, however, commonly referred to as “biodiesel” may be blended with diesel in varying proportions or used directly as a diesel substitute in compression-ignition engines.
Avesthagen Limited aims to develop high oil-yielding Jatropha curcas plants by transgenic manipulation of oil biosynthesis with oil-enhancing genes in addition to expanding its pipeline to other seeds, including sunflower, mustard and tobacco and intend to commence work on maize and cotton.
Transgenic plants that produce docosahexaenoic acid, commonly known as DHA, which is an omega-3 fatty acid. We have isolated the genes that produce DHA and ALA in schizochytrium, a marine organism, and have commenced the transformation of such genes into mustard. We are also developing yeast variety to produce DHA directly in a high-throughput manner in controlled environment.
Jatropha variants with increased oil yields for the production of biofuels. Jatropha seeds can be grown on marginal land and are a candidate for the production of biofuels. They have a naturally occurring oil content ranging from around 30–35% and their oil is inedible.
Criticisms
In 2012, the company ran out of money and saw a number of exits by senior executives. Also in 2012, several former staff filed criminal and civil charges against the company.


Taiva shrew tenrec

The taiva shrew tenrec ("Microgale taiva") is a species of mammal in the family Tenrecidae. It is endemic to Madagascar. Its natural habitats are subtropical or tropical moist lowland forest and subtropical or tropical moist montane forest. It is threatened by habitat loss.


Stem Cell Research (journal)

Stem Cell Research is a peer-reviewed open access scientific journals of cell biology. The journal was established in 2007, and is currently published 8 times per year by Elsevier. The current editor-in-chief is Thomas Zwaka (Icahn School of Medicine at Mount Sinai).
Abstracting and indexing.
The journal is abstracted and indexed in the following bibliographic databases:
According to the "Journal Citation Reports", the journal has a 2018 impact factor of 3.929.


Yinsheng Wang

Yinsheng Wang is a Professor of Chemistry and the Director for the ETOX (Environmental Toxicology) Graduate Program at the University of California Riverside. His current research involves the use of a multi-pronged approach encompassing mass spectrometry, synthetic chemistry, and molecular biology, for understanding the biological consequences of DNA damage and the molecular mechanisms of actions of anti-cancer drugs and environmental toxicants.
He obtained his B.S., M.S., and Ph.D. in Chemistry from Shandong University (1993), Dalian Institute of Chemical Physics (1996), and Washington University in St. Louis (2001), respectively. He joined the faculty of the University of California Riverside in 2001.
He has received several awards including a Research Award (2005) and the Biemann Medal (2013) from the American Society for Mass Spectrometry, and the inaugural "Chemical Research in Toxicology" Young Investigator Award (2012), cosponsored by the Division of Chemical Toxicology of the American Chemical Society and the ACS journal "Chemical Research in Toxicology". He is also a fellow for the American Association for the Advancement of Sciences (since 2012).


2,alpha-DMT

2,alpha-DMT, or 2,α-dimethyltryptamine, is a tryptamine and a lesser-known psychedelic drug. It is the 2,a-dimethyl analog of DMT. 2,α-DMT was first synthesized by Alexander Shulgin. In his book "TiHKAL" ("Tryptamines I Have Known and Loved"), Shulgin lists the dosage as 300-500 mg, and the duration as 7–10 hours. 2,α-DMT causes mydriasis and paresthesia. It also produces a calm, drunk-like feeling. Very little data exists about the pharmacological properties, metabolism, and toxicity of 2,α-DMT.


Bacteriochlorophyll

Bacteriochlorophylls (BChl) are photosynthetic pigments that occur in various phototrophic bacteria. They were discovered by C. B. van Niel in 1932. They are related to chlorophylls, which are the primary pigments in plants, algae, and cyanobacteria. Organisms that contain bacteriochlorophyll conduct photosynthesis to sustain their energy requirements, but do not produce oxygen as a byproduct. They use wavelengths of light not absorbed by plants or Cyanobacteria. Replacement of Mg2+ with protons gives bacteriophaeophytin (BPh), the phaeophytin form.
Structure.
Bacteriochlorophylls "a", "b", and "g" are bacteriochlorins, meaning their molecules have a bacteriochlorin macrocycle ring with two reduced pyrrole rings (B and D). Bacteriochlorophylls "c", "d", "e", and "f" are chlorins, meaning their molecules have a chlorin macrocycle ring with one reduced pyrrole ring (D).
Bacteriochlorophylls "c" to "f" occur in the form of closely related homologs with different alkyl groups attached to pyrrole rings B and C and are illustrated above in their simplest versions, esterified with the sesquiterpene alcohol farnesol. Bacteriochlorophyll "g" has a vinyl group in ring (A).
Biosynthesis.
There are a large number of known bacteriochlorophylls but all have features in common since the biosynthetic pathway involves chlorophyllide "a" as an intermediate. Isobacteriochlorins, in contrast, are biosynthesised from uroporphyrinogen III in a separate pathway that leads, for example, to siroheme, cofactor F430 and cobalamin.


3,4-Dihydroxymandelic acid

3,4-Dihydroxymandelic acid (DHMA, DOMA) is a metabolite of norepinephrine.


Peer Bork

Peer Bork (born 4 May 1963) is a German bioinformatician. He is Director of Scientific Activities at the European Molecular Biology Laboratory (EMBL) in Heidelberg, in south-west Germany.
Bork received his PhD in biochemistry in 1990 from the Leipzig University and his habilitation in theoretical biophysics in 1995 from the Humboldt University of Berlin. He was appointed a Group Leader at EMBL in 1995. He has worked on the microbiomes of humans and other animals.
He is on the board of editorial reviewers of "Science", and is a senior editor of the journal "Molecular Systems Biology".
In 2000 Bork was elected as a Member of the European Molecular Biology Organization, and in 2008 he received the "Nature" "mid-career achievement" award for science mentoring in Germany. He was appointed a member of the German National Academy of Sciences Leopoldina in 2014. He received an honorary doctorate from the University of Würzburg in 2014 and the University of Utrecht in 2017.
In 2021, Bork was awarded the 'Novozymes Prize' "for developing groundbreaking, publicly available and integrative bioinformatic tools" by the Novo Nordisk Foundation. He was also awarded the 2021 International Society for Computational Biology 'Accomplishments by a Senior Scientist Award' for "tremendous contributions to bioinformatics on a plethora of fronts within the field".


PNGase F

Peptide:N-glycosidase F, commonly referred to as PNGase F, is an amidase of the peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase class. PNGase F works by cleaving between the innermost GlcNAc and asparagine residues of high mannose, hybrid, and complex oligosaccharides from N-linked glycoproteins and glycopeptides. This results in a deaminated protein or peptide and a free glycan.
PNGase F has a molecular weight of 35,500 and consists of a polypeptide chain of 314 amino acids. The optimal pH for enzyme activity is 8.6. However, the activity is stable for a wide variety of conditions and reagents. PNGase F maintains 60% activity from pH 6.0 to pH 9.5. It is able to deglycosylate in the absence of denaturants, but needs extensive incubation and larger amounts of the enzyme to cleave native proteins.
Other endoglycosidases, similar to PNGase F, include endoglycosidase F1, endoglycosidase F2, endoglycosidase F3, and endoglycosidase H. These endoglycosidases have more specificity in cleavage and are less sensitive to protein conformation than PNGase F. All of these endoglycosidases, including PNGase F, can be purified from an almond emulsion or "flavobacterium meningosepticum".
Mechanism.
PNGase F catalyzes the cleavage of an internal glycoside bond in an oligosaccharide. It cleaves all asparagine-linked complex, hybrid, or high mannose oligosaccharides unless the core GlcNAc contains an alpha 1,3- fucose. The asparagine residue, from which the glycan is removed, is deaminated to aspartic acid. PNGase F requires a minimum of two GlcNAc oligosaccharide residues attached to the asparagine in order for catalysis to occur. This enzyme utilizes a catalytic triad of cysteine-histidine-aspartate in its active site, which is a common motif for amidases. This motif contains a nucleophile, a proton donor, and a positive charge to stabilize the tetrahedral intermediate. The crystal structure of PNGase F from flavobacterium miningosepticum, with 1.8 Å resolution, was found to be folded in two domains, each with an eight-stranded antiparallel β barrel, or jelly roll, configuration. This structure is similar to lectins and glucanases, suggesting similarities with lectins and other carbohydrate-binding proteins.
Applications and uses.
Biologically, deficiencies in endoglycosidases can lead to several diseases, including lysosomal storage diseases and multisystem diseases, most of which involve the nervous system. N-linked glycans can provide structural components of cell walls and extracellular matrices, modify protein stability and solubility, direct trafficking of other glycoproteins, and mediate cell signaling (cell-cell interactions and cell-matrix interactions). N-linked glycosylation can be seen in antibodies, on cell surfaces, and on various proteins throughout the matrix. Alterations in glycosylation are often acquired in cases of cancer and inflammation, which may have important functional consequences.
To that end, PNGase F and other endoglycosidases can be used to study oligosaccharides and characterize glycoproteins. PNGase F lacks selectivity for outer carbohydrate structure, resulting in broad specificity, making it a useful tool for investigating glycoprotein structure and function. In most instances, proteins of interest are denatured and treated with PNGase F. Following this, they are either subjected to gel electrophoresis, in which protein migration changes due to the deglycosylation by PNGase F, or are analyzed via mass spectrometry, by which the oligosaccharide can be characterized and the protein or peptide fragment from which it came can be characterized.


ESAT-6

ESAT-6, the 6 kDa early secretory antigenic target produced by "Mycobacterium tuberculosis", is a secretory protein and potent T cell antigen. It is used in tuberculosis diagnosis by the whole blood interferon γ test QuantiFERON-TB Gold, in conjunction with CFP-10 and TB7.7.
ESAT-6 has been shown to directly bind to the TLR2 receptor, inhibiting downstream signal transduction.


Paenibacterin

Paenibacterin is a mixture of antimicrobial lipopeptides isolated from "Paenibacillus thiaminolyticus". It contains three isomeric compounds which differ by the fatty acid side chain.


Primer extension

Primer extension is a technique whereby the 5' ends of RNA can be mapped - that is, they can be sequenced and properly identified.
Primer extension can be used to determine the start site of transcription (the end site cannot be determined by this method) by which its sequence is known. This technique requires a radiolabelled primer (usually 20 - 50 nucleotides in length) which is complementary to a region near the 3' end of the mRNA. The primer is allowed to anneal to the RNA and reverse transcriptase is used to synthesize cDNA from the RNA until it reaches the 5' end of the RNA. By denaturing the hybrid and using the extended primer cDNA as a marker on an electrophoretic gel, it is possible to determine the transcriptional start site. It is usually done so by comparing its location on the gel with the DNA sequence (e.g. Sanger sequencing), preferably by using the same primer on the DNA template strand. The exact nucleotide by which the transcription starts at can be pinpointed by matching the labelled extended primer with the marker nucleotide, who are both sharing the same migration distance on the gel.
Primer extension offers an alternative to a nuclease protection assay (S1 nuclease mapping) for quantifying and mapping RNA transcripts. The hybridization probe for primer extension is a synthesized oligonucleotide, whereas S1 mapping requires isolation of a DNA fragment. Both methods provide information where a mRNA starts and provide an estimate of the concentration of a transcript by the intensity of the transcript band on the resulting autoradiograph. Unlike S1 mapping, however, primer extension can only be used to locate the 5’-end of an mRNA transcript because the DNA synthesis required for the assay relies on reverse transcriptase (only polymerizes in the 5’ → 3’ direction).
Primer extension is unaffected by splice sites and is thus preferable in situations where intervening splice sites prevent S1 mapping. Finally, primer extension is more accurate than S1 mapping because the S1 nuclease used in S1 mapping can “nibble off” ends of the RNA-DNA hybrid or fail to degrade the single-stranded regions completely, making a transcript either appear shorter or longer.


MinC

The MinC protein is one of three proteins in the Min system encoded by the "minB" operon and which is required to generate pole to pole oscillations prior to bacterial cell division as a means of specifying the midzone of the cell. This function is achieved by preventing the formation of the divisome Z-ring around the poles.
History.
When initially discovered in "E.coli", MinC was believed to form a stable cap by binding with MinD at the bacterial caps in a stable and static manner, thereby specifying the mid-zone of the cell by lower-concentration or lack of this complex in that region, alleviating inhibition of Z-ring formation. However, Raskin & de Boer applied live-cell imaging with GFP fusion proteins to reveal a dynamic interaction of the Min proteins, demonstrating that MinC and MinD, with the essential help of MinE, actually rapidly oscillate between the two poles in a non-static manner. MinC is found in diverse genera, including Neisseria, Bacillus, and Synechocystis, but is absent in an equally wide assortment of genera (e.g. Caulobacter, Mycobacterium). Many bacteria that lack MinC carry alternative proteins that can position their Z-ring.
Function.
MinC is known to dimerize and functions as an FtsZ protein inhibitor, antagonizing its structure assembly when in a high enough concentration. The protein has the ability to disassemble the ZapA, ZapB and ZipA proteins which preferentially bind to the FtsZ scaffold protein and which are needed to initiate cell division.
Concentrations of MinC are lowest at the mid-zone of bacterial cells, thereby permitting septum formation and scaffold assembly at the cellular mid-zone since the Min System proteins (MinCDE) are lowest in concentration in this region, alleviating the physical inhibition on the proteins required to initiate division.


Hugh Whitehead (scientist)

Hugh Robinson Whitehead (11 November 1899 – 13 March 1983) was a notable New Zealand biochemist, microbiologist and scientific administrator. He was born in Leeds, Yorkshire, England, in 1899. He was the director of the Dairy Research Institute in Palmerston North.
In the 1964 Queen's Birthday Honours, Whitehead was appointed an Officer of the Order of the British Empire.


PSI-Missing

"PSI-missing" is the sixth single released by the J-pop singer, Mami Kawada. This single was released on October 29, 2008, one year after the release of her fifth single, "Joint". The song was used as the first opening theme for the anime series "A Certain Magical Index".
The B-side was used as an insert song on the twelfth episode of "A Certain Magical Index".
The single came in a limited CD+DVD edition (GNCV-0009) and a regular CD edition (GNCV-0010). The DVD contains the promotional video for "PSI-missing".
Reception.
It peak ranked 14th on the weekly Oricon albums chart and remained on the chart for fourteen weeks.


Hermona Soreq

Hermona Soreq (חרמונה שורק) is an Israeli professor of Molecular Neuroscience at The Hebrew University of Jerusalem. Best known for her work on the signaling of acetylcholine and its relevance in stress responses and neurodegenerative diseases such as Parkinson's and Alzheimer's.
Biography.
Soreq (née Even) was born in Tel-Aviv. She completed her B.Sc. in Biochemistry and Microbiology at the Hebrew University, M.Sc. in Biochemistry from Tel-Aviv University and Ph.D. in Biochemistry from the Weizmann Institute in 1976. From 1977 to 1979, she was a post-doctoral Fogarty fellow, in Molecular Cell Biology, at the Rockefeller University, New York.
Scientific career.
Soreq started her scientific career in the Weizmann Institute, where she served as Senior Scientist and then Associate Professor (1979-1986). In 1986 she became an Associate Professor of Molecular Biology in the Department of Biological Chemistry at the Hebrew University of Jerusalem. In 1989 she gained her professorship there and set up her laboratory. She has run her lab there, ever-since. She served as the head of the Silberman Institute of Life Sciences at the Hebrew University (1995-2000). In 2000 she was elected as President of the Israeli Society of Biochemistry and Molecular Biology, and served as such till 2002. In 2005 she was elected to serve a term of 3 years as the first female Dean of the Hebrew University's Faculty of Science.
Today, Soreq is The Charlotte Schlesinger Professor of Molecular Neuroscience at the Silberman Institute for Life Sciences and a founding member of the Hebrew University’s Edmond and Lily Safra Center for Brain Sciences, where she heads the Soreq group. Her major research interests are MicroRNAs (miRs) and other non-coding RNA regulators of gene expression, including transfer RNA fragments (tRFs). Soreq combines advanced sequencing technologies with computational neuroscience and transgenic engineering tools to investigate miR and tRF functions in the healthy and diseased brain and body, with a focus on acetylcholine (ACh)-related processes. Her studies found primate-specific "CholinomiR" silencers of multiple genes that compete with each other on suppressing their targets and discovered cholinergic brain-to-body regulation of anxiety and inflammation. In human volunteers, Soreq found cholinergic-associated pulse increases under fear of terror; and identified massive CholinomiRs decline in Alzheimer’s brains, which accompanies changes in long non-coding RNAs and points at Statins intervention with the onset of Parkinson’s disease and modifications in pseudogenes expression. In engineered mice, Soreq studies CholinomiR and CholinotRF responders to stress, epilepsy, inflammation and ischemic stroke; and found liver fattening, trait anxiety, blood pressure and inflammation under inherited interference with acetylcholinesterase (AChE)-targeting CholinomiRs. Soreq has found CholinomiR differences between brains of men and women with schizophrenia and bipolar disorder, and CholinomiRs decline accompanied by CholinotRF increases in blood cells from stroke patients; together, her work leads to precision medicine-driven prevention and/or intervention with diseases involving impaired ACh signaling.
Major landmarks of the Soreq group in the cholinergic field.
She is the author of over 280 peer-reviewed journal articles and 8 books
Awards and honors.
Soreq served on the boards of the Hebrew University, the Technion (Israel Institute of Technology) and Yissum (the Research Development Company of the Hebrew University). She was also an Adjunct Research professor at the Arizona State University Biodesign Institute.
Her awards and honors include:
She has also received honorary Doctorates from the University of Erlangen, Nűremberg, Germany (2007), Ben-Gurion University of the Negev, Israel (2007) and the University of Stockholm, Sweden, (1996)


Fluprazine

Fluprazine (DU-27,716) is a drug of the phenylpiperazine class. It is a so-called serenic or antiaggressive agent. It is closely related to several other piperazines, including eltoprazine and batoprazine, and TFMPP, as well as more distantly to the azapirones such as buspirone. The pharmacology of fluprazine is unknown, but it is likely to act as an agonist at the 5-HT1A and 5-HT1B receptors like its sister compound eltoprazine.


Octaethylporphyrin

Octaethylporphyrin (H2OEP) is an organic compound that is a relative of naturally occurring heme pigments. The compound is used in the preparation of models for the prosthetic group in heme proteins. It is a dark purple solid that is soluble in organic solvents. When treated with ferric chloride in hot acetic acid solution, it forms the square pyramidal complex Fe(OEP)Cl. It also forms the square planar complexes Ni(OEP) and Cu(OEP).
Unlike naturally occurring porphyrins, the conjugate base of H2OEP has four-fold symmetry, which simplifies spectroscopic analysis. In contrast to tetraphenylporphyrin and related analogues, H2OEP features unprotected meso positions. In this way, it is a more accurate model for naturally occurring porphyrins.
H2OEP is prepared by condensation of 3,4-diethylpyrrole with formaldehyde.


Guilty Gear Dust Strikers

, or Guilty Gear DS, is a fighting game of the "Guilty Gear" series for the Nintendo DS. It is modeled after "Guilty Gear Isuka", and also allows for four player fights. It was the first versus fighting game for the Nintendo DS to be released outside Japan.
"Guilty Gear: Dust Strikers" is also the first "Guilty Gear" game so far to have mini-games, ranging from the Balance Game where the player must help a chibi Jam balance the falling items with her plate, to Venom's Billiards, which puts the player and opponent in a pool-style game. The boss of the game's Story and Arcade modes is Gig, an immense insect-like monster with an angel attached to its bottom half. The game has 21 playable characters in all, but only twenty story modes, as Robo-Ky has no story mode.
Reception.
"Guilty Gear Dust Strikers" received "mixed or average reviews", according to Metacritic.


Hymenobacter psychrophilus

Hymenobacter psychrophilus is a Gram-negative, psychrophilic, aerobic, rod-shaped and non-motile bacterium from the genus of Hymenobacter which has been isolated from soil from an industrial site in Bozen in Italy.


Time-resolved RNA sequencing

Time-resolved RNA sequencing methods are applications of RNA-seq that allow for observations of RNA abundances over time in a biological sample or samples. Second-Generation DNA sequencing has enabled cost effective, high throughput and unbiased analysis of the transcriptome. Normally, RNA-seq is only capable of capturing a snapshot of the transcriptome at the time of sample collection. This necessitates multiple samplings at multiple time points, which increases both monetary and time costs for experiments. Methodological and technological innovations have allowed for the analysis of the RNA transcriptome over time without requiring multiple samplings at various time points.
Background.
While DNA encodes all of the functional elements of life, the information encoded must be converted into functional form. Following the central dogma of molecular biology, messenger RNA encodes genetic information for producing proteins, which, alongside functional RNA carry out the majority of cellular processes required for life. Changes in RNA abundance may be used as a measurement of changes in cellular behavior, such as heat stress, infection by virus, or oncogenesis. Knowledge of how the transcriptome changes during cellular processes allows for greater understanding of the exact mechanisms underlying these processes.
Originally, transcriptome-wide RNA abundance could only be assessed using methods such as DNA microarrays or serial analysis of gene expression (SAGE). These methods are prohibitive in differing regards; microarrays, while cheap, provide inconsistent results and SAGE is based on sanger sequencing, which provides limited throughput. Using second generation sequencing, instead of measuring relative hybridization of sequences to probes in the case of microarrays or sequencing short segments in the case of SAGE, a researcher can simply sequence the bulk RNA within a sample and measure relative abundances of specific types of RNA by comparing the number of times each RNA molecule was sequenced in a given sample.
Normally, in a traditional RNA-seq, microarray, or SAGE experiment RNA is extracted from a biological sample such as cultured cells, and the RNA is analyzed using the chosen method. The data obtained from such an experiment corresponds to abundance of RNA under the given experimental conditions at the time of harvest. For many applications, such as comparing the abundance of mRNA molecules between cells exposed to a drug and those not exposed to the drug, this type of experimental approach is sufficient. However, many cellular processes of scientific and medical interest are processes which occur over time, such as cellular differentiation or phagocytosis. Studying such processes requires analysis of RNA abundance across a series of time points.
Methods.
Time series samples.
Sample preparation and data processing.
The simplest approach towards assessing RNA abundance over time is to simply use multiple samples which are treated in exactly the same way, except for the duration of treatment. For example, to investigate a biological process which is estimated to occur for an hour, a researcher might design an experiment where the process is triggered for five minutes, 15 minutes, 30 minutes, 45 minutes, one hour, and two hours in separate cell culture samples before harvesting the cells for RNA-seq analysis. The researcher would then have measurements of the transcriptome at each of these time points, and comparing between these samples would indicate which cellular processes are activated and deactivated over time.
Strengths.
This method is the most common for measurement of RNA over time in cell culture models, mainly due to its simplicity. Each biological sample need only be processed in exactly the same way, and the factor of time is easily adjusted in most experimental protocols. Furthermore, since each time point is its own sample, more RNA can be harvested and sequenced for a study.
Weaknesses.
The requirement of multiple samples for time-resolved data collection increases the cost of the experiment as well as introducing a greater potential for technical errors. While the price of massively parallel sequencing has decreased greatly since its introduction, it is still prohibitively expensive for many laboratories to conduct large scale RNA-seq studies. This issue is compounded by additional time points increasing the number of samples by a multiple of the number of time points; using two time points rather than one doubles the number of samples required in an experiment. Consequently, many studies which use time series RNA-seq become limited in either their sample size, which reduces statistical power, or the number of time points, which reduces their time resolution, or both. Finally, by requiring a greater number of biological samples, there is greater risk for human error to affect the results, which may lead to spurious conclusions
Affinity Purification.
Sample preparation and data processing.
In this approach, cell culture samples are cultured with tagged nucleotides which allow for selective purification of newly synthesized RNA molecules. One popular approach is pulse labeling with 4-thiouridine (4-sU), a uracil analogue that is incorporated in newly synthesized RNA molecules. In this type of experiment, a researcher would supplement cells with 4-sU at the time of the experiment or shortly beforehand. When the experimental treatment presumably affects RNA expression, newly synthesized RNA would be labeled with 4-sU. Newly synthesized RNA is labeled with a reactive thiol group, making it possible to link useful molecules to the RNA. Biotin is a popular molecule for use in this type of assay, as it is inexpensive and binds incredibly strongly and selectively to streptavidin. Incubation of biotinylated RNA with beads containing streptavidin allows for the selective purification of newly synthesized RNA. From here, newly synthesized and total RNA are sequenced separately and compared for differences.
Strengths.
Affinity purification makes use of the incredibly popular biotin-streptavidin system for fractionation of biological materials. Binding of biotin to streptavidin is incredibly strong (Kd < 10−14 mol/L). It is also highly specific, which results in minimal background signal from non-specific binding events. Furthermore, time resolution is obtained in a single biological sample, resulting in reduced biological variability compared to using separate samples for each time point.
Weaknesses.
The weaknesses of this method are mainly centered around efficiency. One major difficulty is uptake of 4-sU into cultured cells. If 4-sU is given too early, then it will be incorporated into RNA that was not synthesized before the cell began responding to the experimental conditions. If it is given too late, then early stages of the cellular response are not captured by the experiment. The rate of uptake of 4-sU can be measured, but this requires additional experiments to determine optimal dosage and time. Furthermore, these parameters need to be measured in the specific cell lines of interest, as different cell lines may take up 4-sU more slowly than others.
RNA is known to be prone to degradation "in vitro". It is common for experimental protocols involving RNA to include a number of steps to reduce chances of Ribonuclease contamination or spontaneous degradation of samples, as RNA quality affects RNA-seq results. Metabolic labeling involves a number of additional steps that must be performed in the laboratory on RNA that is in solution. Since metabolic labeling requires that the RNA be kept unfrozen in liquid solution, some level of spontaneous degradation is unavoidable, although it is usually not to such an extent that results are affected. Of greater risk is the chances of ribonuclease contamination, which would render a sample useless, wasting time and resources. It is important for researchers working with RNA in any capacity to minimize unnecessary handling of RNA due to these risks. One additional drawback of using this method is, given equivalent sample size, more sequencing runs are required compared to a time-series experiment. This is because multiple RNA samples corresponding to the initial time point must be sequenced.
Research suggests that 4-sU labeling may result in transcriptional changes on its own, which would affect any results obtained using this method.
Nucleotide Conversion.
Sample preparation and data processing.
Nucleotide conversion works by converting some nucleotides in newly synthesized RNA into others, which can be detected through sequencing. Timelapse-seq is an example of such an approach. As in affinity purification, cells are incubated with 4-sU. After extraction of RNA from samples, they are treated with 2,2,2-trifluoroethylamine and sodium periodate, which converts 4-sU into trifluoroethyl cytosine, a cytosine analogue that is sequenced as a cytosine nucleotide instead of uracil. During sequence alignment and data processing, the U-to-C conversions are used to quantify the number of transcripts that are newly synthesized compared to bulk RNA.
Strengths.
This method shares many strengths with affinity purification; notably the fact that multiple samples are not required for a time-series. This method eliminates the need for multiple sequencing runs for multiple time points, as all RNA is run together on the sequencing instrument and labeled RNA is separated from nonlabeled "in silico". This reduces sequencing costs significantly, as now time resolution may be obtained without the need for additional samples or additional sequencing runs. Furthermore, by sequencing multiple time points together, technical variability introduced by sample processing is further reduced in addition to the reduced biological variability provided through the 4-sU experimental strategy.
Weaknesses.
As with strengths, this method shares many weaknesses with affinity purification methods. Notably, 4-sU uptake and increased sample handling. Since Timelapse-seq relies upon synthetic chemistry methods to convert nucleotides, incomplete reactions result in an underestimation of the abundance of newly synthesized RNA and may result in variability between samples.
Nascent Transcript Sequencing.
Sample preparation and data processing.
Unlike metabolic labeling, nascent transcript sequencing (NET-seq) directly sequences transcripts that are still undergoing transcription by RNA polymerase II. This method allows for the study of the dynamics of transcription elongation, which is not possible with metabolic labeling techniques. For a NET-seq experiment, cells are treated as with a standard RNA-seq experiment until they are lysed. Lysis is performed such that RNA-protein complexes remain intact, and RNA polymerase II is immunoprecipitated from the lysate. RNA that was undergoing transcription from DNA is still attached to RNA polymerase and is subsequently eluted from the polymerase and sequenced.
Strengths.
Since NET-seq extracts transcripts that have not completed transcription, it is possible to obtain single-nucleotide resolution on the most recently synthesized nucleotide of transcripts. This is valuable in the study of phenomena such as transcriptional kinetics. Furthermore, it allows for the study of unstable transcripts which are degraded shortly after transcription. The general approach of immunoprecipitating RNA-binding proteins has great utility in understanding other areas of RNA biology, such as splicing.
Weaknesses.
This method relies upon immunoprecipitation of RNA polymerase II. There are a number of issues with immunoprecipitation, including non-specific binding interactions which may result in the immunoprecipitation of off-target RNA molecules.
The temporal resolution of NET-seq is limited to transcription elongation. While comparing relative abundances between transcripts using NET-seq is possible, it is not the intention of the method.
Future Directions.
Aside from time-series sampling, there are currently no methods for comparing more than two time points. Metabolic labeling experiments are only capable of comparing RNA abundances before and after pulse-labeling. It is of interest to be able to observe modifications to the transcriptome over a series of time points in a single sample, as this would provide increased time resolution in studies. Existing methods of metabolic labeling are of interest for this; if multiple different metabolic labels were used at differing time points this may allow for intermediate time points to be investigated. However, such approaches must be developed with care, as biases in labeling methods and sample processing steps could contribute to misleading results if data from different methods are compared to one another.
Metabolic labeling with 4-sU has been reported to affect cellular phenotype. In current practice, this is unavoidable and is tolerated as the obtained data still fit current biological models, as well as the fact that 4-sU samples are compared with 4-sU samples in most cases. However, this has the potential to result in spurious conclusions, especially if there is any interaction between the effect of 4-sU and the chosen experimental condition. It is not possible to distinguish differences in RNA levels as being due to the experimental conditions being studied or being the result of 4-sU treatment. Identification of labeling chemicals that do not affect cellular phenotype would eliminate these issues altogether.


DSIF

In gene expression, DSIF (DRB Sensitivity Inducing Factor) is a protein that can either negatively or positively affect transcription by RNA polymerase II (Pol II). In one case of negative regulation, it can interact with negative elongation factor (NELF) to promote the stalling of Pol II at some genes. This stalling is relieved by P-TEFb. In humans, DSIF is composed of hSPT4 and hSPT5 (SPT4 and SPT5 are homologs in yeast).
The complex locks the RNAP clamp into a closed state to prevent the elongation complex (EC) from dissociating. The Spt5 NGN domain helps anneal the two strands of DNA upstream. The single KOW domain in bacteria and archaea anchors a ribosome to the RNAP.
In bacteria, the homologous complex only contains "NusG", a Spt5 homolog. Archaea have both proteins.


Elwira Lisowska

Professor Elwira Lisowska (born May 6, 1930) is a Polish biochemist. She made significant contributions to the biochemistry of human blood groups, especially MNS and P1PK blood group systems, and to the immunochemical characterization of glycopeptide antigens.
Early life and education.
Lisowska was born in Przemyśl. She studied chemistry at the Wrocław University of Science and Technology. As a student she became interested in biomedical research, and worked with Tadeusz Baranowski in the Department of Physiological Chemistry. She moved to the Hirszfeld Institute of Immunology and Experimental Therapy where she started to work on blood group antigens. She earned her doctoral degree in 1962, and in the years 1969-1970 she spent one year as a post-dotoral fellow at Massachusetts General Hospital, where she worked with Roger W. Jeanloz.
Research and career.
For many years Lisowska worked on the M and N antigens. She identified that these antigens were carried by the glycosylated protein of the erythrocyte membrane called glycophorins. At first it was understood that the M and N antigens had carbohydrate character, but later it emerged that there were differences in amino acid sequence of polypeptide chain. Lisowska was the first to show that there was a difference between the amino acid residues at positions 1 and 5 of M and N antigens.
Beyond her work on M and N antigens, Lisowska solved the mystery of NOR polyagglutination, elucidated the structure of NOR antigen, which is the cause of NOR polyagglutination and a member of the human P1PK antigen system. and showed that the NOR antigen is recognized by antibodies present in most of human sera. In addition, she showed that carcinoembryonic antigen forms dimers in solution and was the first to demonstrate that human Band 3 anion transport protein is proteolytically degraded during the lifespan of erythrocyte. She characterized several lectins, including "Vicia graminea" lectin which is specific for human N blood group antigen, described novel methods of lectin modifications and proved that they are valuable tools in glycoconjugate research. She participated in elucidation of structure and function of glycans from human glycophorin A and glycophorin C. She obtained and characterized several monoclonal antibodies recognizng M and N blood group antigens, as well as other fragments of glycophorin A. These studies were important in characterization of antigenic properties of human glycophorins.
She became head of Laboratory of Tissue Immunochemistry (later Laboratory of Glycoconjugate Immunochemistry) at the Hirszfeld Institute of Immunology and Experimental Therapy in 1973. In 1980 she became full professor. In the years 1992–2000 she was deputy director of the Hirszfeld Institute of Immunology and Experimental Therapy. She was a promoter of 9 Ph.D. theses. Elwira Lisowska served also as editor of the journal "Archivum Immunologiae et Therapiae Experimentalis" (1980–2016), "European Journal of Biochemistry" (1979–1987), "Glycoconjugate Journal" (1984–1990), "Acta Biochimica Polonica" (1977–2015), and "Advances of Clinical and Experimental Medicine" (2000–2003). In 2001 Elwira Lisowska retired from the Hirszfeld Institute of Immunology and Experimental Therapy.


MMP23B

Matrix metalloproteinase-23 is an enzyme that in humans is encoded by the "MMP23B" gene.
Function.
This gene (MMP23B) encodes a member of the matrix metalloproteinase (MMP) family, and it is part of a duplicated region of chromosome 1p36.3. Proteins of the matrix metalloproteinase (MMP) family are involved in the breakdown of extracellular matrix in normal physiological processes, such as embryonic development, reproduction, and tissue remodeling, as well as in disease processes, such as arthritis and metastasis. This gene belongs to the copy of the duplicated region of the gene that is closer to the end of the chromosome (more telemeric).
MMP23B is strongly expressed in ovary and heart.


Holo-ACP synthase

In enzymology, a holo-ACP synthase () is an enzyme that catalyzes the chemical reaction
Thus, the two substrates of this enzyme are 2'-(5"-triphosphoribosyl)-3'-dephospho-CoA and apo-citrate lyase, whereas its two products are holo-citrate lyase and diphosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing nucleotide groups (nucleotidyltransferases). The systematic name of this enzyme class is 2'-(5"-triphosphoribosyl)-3'-dephospho-CoA:apo-citrate lyase adenylyltransferase. Other names in common use include 2'-(5"-phosphoribosyl)-3'-dephospho-CoA transferase, 2'-(5"-triphosphoribosyl)-3'-dephospho-CoA:apo-citrate lyase, and CitX. This enzyme participates in two-component system - general.
Structural studies.
As of late 2007, only one structure has been solved for this class of enzymes, with the PDB accession code .


Biotin hydrazide

Biotin hydrazide is a biotinyl derivative that can be used as a probe for the determination of protein carbonylation. It readily forms Schiff bases with carbonyl groups.


Long-chain-aldehyde dehydrogenase

Fatty aldehyde dehydrogenase (or Long-chain-aldehyde dehydrogenase) is an aldehyde dehydrogenase enzyme that in human is encoded in the ALDH3A2 gene on chromosome 17.
Aldehyde dehydrogenase enzymes function to remove toxic aldehydes that are generated by the metabolism of alcohol and by lipid peroxidation.
Structure.
The ALDH3A2 belongs to the aldehyde dehydrogenase superfamily and is a membrane-associated protein typically containing 485 residues. The mature protein functions as a dimer. The structure was resolved using X-ray crystallography at 2.1 Angstrom resolution. It contains an element in the C-terminal region referred to as a "gatekeeper" helix, which is adjacent to the membrane-anchored transmembrane domain and the catalytic core. The gatekeeper helix appears to control access of molecular substrates to the catalytic core and allows efficient transit between membranes and catalytic sites.
Function.
ALDH3A2 catalyzes the oxidation of long-chain aliphatic aldehydes into fatty acids. It is known to act on a variety of both saturated and unsaturated aliphatic aldehydes between 6 and 24 carbons in length, as well as dihydrophytal, a 20-carbon branched chain aldehyde. It requires NAD+ as a co-factor. The encoded enzyme is responsible for conversion of the sphingosine 1-phosphate (S1P) degradation product hexadecenal to hexadecenoic acid. ALD3H2 is expressed in the human liver and has been found to localize the microsome fraction inside the cell.
At least two alternative splicing isoforms of ALDH3A2 are known to exist. The alternative transcript differs by an additional exon and anchors differently to the endoplasmic reticulum vs. the peroxisome
Clinical significance.
Mutations and deletions of in the ALDH3A2 gene have been widely associated with the autosomal recessive Sjögren-Larsson syndrome, an autosomal recessive neurocutaneous disease. Multiple mutations have been found in different families, including those that molecularly disrupts the protein dimerization interface or reduces mRNA stability. Absence or insufficiency of ALDH3A2 protein products in mutant cells are known to cause abnormal metabolism of sphingosine 1-phosphate to ether-linked glycerolipids and the abnormal accumulation of lipid precursors.


L-lysine oxidase

In enzymology, a L-lysine oxidase () is an enzyme that catalyzes the chemical reaction
The 3 substrates of this enzyme are L-lysine, O2, and H2O, whereas its 3 products are 6-amino-2-oxohexanoate, NH3, and H2O2.
This enzyme belongs to the family of oxidoreductases, specifically those acting on the CH-NH2 group of donors with oxygen as acceptor. The systematic name of this enzyme class is L-lysine:oxygen 2-oxidoreductase (deaminating). Other names in common use include L-lysine alpha-oxidase, and L-lysyl-alpha-oxidase. This enzyme participates in lysine degradation.


Jacqueline Lees

Jacqueline A. Lees is a British biochemist.
Lees is the Virginia and D.K. Ludwig Professor for Cancer Research and Associate Director of the Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology. She received her BSc degree from the University of York in 1986, and her PhD from the University of London in 1990, both in biochemistry. She was a postdoc in the laboratory of Ed Harlow, first at Cold Spring Harbor and then at Massachusetts General Hospital, before joining the faculty at MIT in 1994.
Research.
Lees’ research is focused on identifying the proteins and pathways that play a key role in tumorigenicity and establishing the mechanism of their action in both normal and tumor cells. Her lab at MIT uses a combination of molecular and cellular analyses and mutant mouse models. She is also known for her work with Nancy Hopkins on genetic screens in zebrafish. Lees studies how the E2F family of mammalian transcription factors contributes to the regulation of cellular proliferation during normal development and tumorigenesis. Her work has shown that certain E2Fs, despite substantial biochemical similarities, play radically different biological roles.


HgcE RNA

The HgcE RNA (also known as Pf3 RNA) gene is a non-coding RNA that was identified computationally and experimentally verified in AT-rich hyperthermophiles. The genes in the screen were named hgcA through hgcG ("high GC"). The HgcE has been renamed as Pf3 and identified as an H/ACA snoRNA that is suggested to target 23S rRNA for pseudouridylation. This RNA contains two K-turn motifs. It was later identified as Pab105 H/ACA snoRNA with rRNA targets.


Diamphotoxin

Diamphotoxin is a toxin produced by larvae and pupae of the beetle genus "Diamphidia". Diamphotoxin is a hemolytic, cardiotoxic, and highly labile single-chain polypeptide bound to a protein that protects it from deactivation.
Diamphotoxin increases the permeability of cell membranes of red blood cells. Although this does not affect the normal flow of ions between cells, it allows "all" small ions to pass through cell membranes easily, which fatally disrupts the cells' ion levels. Although diamphotoxin has no neurotoxic effect, its hemolytic effect is lethal, and may reduce hemoglobin levels by as much as 75%.
The San people of Southern Africa use diamphotoxin as an arrow poison for hunting game. The toxin paralyses muscles gradually. Large mammals hunted in this way die slowly from a small injection of the poison.
Several leaf beetles species of genus "Leptinotarsa" produce a similar toxin, "leptinotarsin".


Phenylalanine ammonia-lyase

Phenylalanine ammonia lyase () is an enzyme that catalyzes a reaction converting -phenylalanine to ammonia and "trans"-cinnamic acid. Phenylalanine ammonia lyase (PAL) is the first and committed step in the phenyl propanoid pathway and is therefore involved in the biosynthesis of the polyphenol compounds such as flavonoids, phenylpropanoids, and lignin in plants.<ref name="struct/catalyt"></ref><ref name="struct/character"></ref> Phenylalanine ammonia lyase is found widely in plants, as well as some bacteria, yeast, and fungi, with isoenzymes existing within many different species. It has a molecular mass in the range of 270–330 kDa. The activity of PAL is induced dramatically in response to various stimuli such as tissue wounding, pathogenic attack, light, low temperatures, and hormones. PAL has recently been studied for possible therapeutic benefits in humans afflicted with phenylketonuria. It has also been used in the generation of -phenylalanine as precursor of the sweetener aspartame.
The enzyme is a member of the ammonia lyase family, which cleaves carbon–nitrogen bonds. Like other lyases, PAL requires only one substrate for the forward reaction, but two for the reverse. It is thought to be mechanistically similar to the related enzyme histidine ammonia-lyase (EC:4.3.1.3, HAL). The systematic name of this enzyme class is -phenylalanine ammonia-lyase (trans-cinnamate-forming). Previously, it was designated , but that class has been redesignated as EC 4.3.1.24 (phenylalanine ammonia-lyases), (tyrosine ammonia-lyases), and (phenylalanine/tyrosine ammonia-lyases). Other names in common use include tyrase, phenylalanine deaminase, tyrosine ammonia-lyase, -tyrosine ammonia-lyase, phenylalanine ammonium-lyase, PAL, and -phenylalanine ammonia-lyase.
Mechanism.
Phenylalanine ammonia lyase is specific for -phe, and to a lesser extent, -tyrosine. The reaction catalyzed by PAL is a spontaneous elimination reaction rather than an oxidative deamination.
The cofactor 3,5-dihydro-5-methyldiene-4"H"-imidazol-4-one (MIO) is involved in the reaction and sits atop the positive pole of three polar helices in the active site, which helps to increase its electrophilicity. MIO is attacked by the aromatic ring of -phe, which activates the C-H bond on the β carbon for deprotonation by a basic residue. The carbanion intermediate of this E1cB-elimination reaction, which is stabilized by partial positive regions in the active site, then expels ammonia to form the cinnamate alkene. The mechanism of the reaction of PAL is thought to be similar to the mechanism of the related enzyme histidine ammonia lyase.
A dehydroalanine residue was long thought to be the key electrophilic catalytic residue in PAL and HAL, but the active residue was later found instead to be MIO, which is even more electrophilic. It is formed by cyclization and dehydration of conserved Ala-Ser-Gly tripeptide segment. The first step of MIO formation is a cyclization-elimination by an intramolecular nucleophilic attack of the nitrogen of Gly204 at the carbonyl group of Ala202. A subsequent water elimination from the side chain of Ser203 completes the system of crossconjugated double bonds. Numbers are given for the phenylalanine ammonia lyase from "Petroselinum" "crispum" (PDB 1W27). Although MIO is a polypeptide modification, it was proposed to call it a prosthetic group, because it has the quality of an added organic compound.
PAL is inhibited by trans-cinnamic acid, and, in some species, may be inhibited by "trans-"cinnamic acid derivatives. The unnatural amino acids -Phe and -Tyr, the enantiomeric forms of the normal substrate, are competitive inhibitors.
Structure.
Phenylalanine ammonia lyase is composed of four identical subunits composed mainly of alpha-helices, with pairs of monomers forming a single active site. Catalysis in PAL may be governed by the dipole moments of seven different alpha helices associated with the active site. The active site contains the electrophilic group MIO non-covalently bonded to three helices. Leu266, Asn270, Val269, Leu215, Lys486, and Ile472 are located on the active site helices, while Phe413, Glu496, and Gln500 contribute to the stabilization of the MIO cofactor. The orientation of dipole moments generated by helices within the active site generates an electropositive region for ideal reactivity with MIO. The partially positive regions in the active site may also help stabilize the charge of a carbanion intermediate. PAL is structurally similar to the mechanistically related histidine ammonia lyase, although PAL has approximately 215 additional residues.
Function.
Phenylalanine ammonia lyase can perform different functions in different species. It is found mainly in some plants and fungi (i.e. yeast). In fungal and yeast cells, PAL plays an important catabolic role, generating carbon and nitrogen. In plants it is a key biosynthetic enzyme that catalyzes the first step in the synthesis of a variety of polyphenyl compounds and is mainly involved in defense mechanisms. PAL is involved in 5 metabolic pathways: tyrosine metabolism, phenylalanine metabolism, nitrogen metabolism, phenylpropanoid biosynthesis, and alkaloid biosynthesis.
Disease relevance.
Enzyme substitution therapy using PAL to treat phenylketonuria (PKU), an autosomal recessive genetic disorder in humans in which mutations in the phenylalanine hydroxylase (PAH, EC 1.14.16.1) gene inactivate the enzyme is being explored. This leads to an inability of the patient to metabolize phenylalanine, causing elevated levels of Phe in the bloodstream (hyperphenylalaninemia) and mental retardation if therapy is not begun at birth.
In May 2018, the FDA approved pegvaliase, a recombinant PEGylated phenylalanine ammonia-lyase for the treatment of PKU that had been developed by Biomarin.
Research.
Artificial sweeteners.
The reverse reaction catalyzed by PAL has been explored for use to convert "trans"-cinnamic acid to -phenylalanine, which is a precursor of the sweetener aspartame. This process was developed by Genex Corporation but was never commercially adopted.
Unnatural amino acid synthesis.
Analogous to how aspartame is synthesized, PAL is also used to synthesize unnatural amino acids from various substituted cinnamic acids for research purposes. Steric hindrance from arene substitution limits PAL's utility for this purpose however. For instance, when "Rhodotorula glutinis" was used to affect this biotransformation the enzyme was discovered to be intolerant of all "para" substituents other than F, presumably due to the element's small atomic radius. "Meta" and "ortho" positions were found to be more tolerant, but still limited by, larger substituents. For instance the enzyme's active site permitted "ortho" methoxy substitution but forbade "meta" ethoxy. Other organisms with different versions of the enzyme may be less limited in this way.
Structural studies.
As of late 2007, 5 structures have been solved for this class of enzymes, with PDB accession codes , , , , and .