Robert Petre, 8th Baron Petre

Robert James Petre, 8th Baron Petre (3 June 1713 – 2 July 1742) was a renowned horticulturist and a British peer.
Lord Petre was the son of Robert Petre, 7th Baron Petre (1689–1713) and his wife Catherine Walmesley (1697 – 31 January 1785), heiress of the Walmesley family of Lancashire. Petre was born three months after his father's death and spent his childhood at Ingatestone Hall, instead of at Thorndon Hall, the family seat, as his grandmother was still in residence there.
Botany and horticulture.
He developed an interest in botany and horticulture as a child, and by his teenage years was friends with some of the most eminent botanists, horticulturists and landscapers of the day, including; Philip Miller, keeper of the Chelsea Physic Garden, Philip Southcote, a leading pioneer of landscape design, and Peter Collinson, the Quaker haberdasher turned horticulturist who was to remain a lifelong friend and colleague. In 1727, when he was 14, he received, as a Christmas gift from Ralph Howard, one of his mother's suitors, a specially made pruning knife and saw, which, it is recorded, was "well taken".
Robert's interest in botany and horticulture was practical as well as academic. By 1729, it seems that, at least in part, he had taken over the management of his grandmother's gardens at Thorndon. The old lady herself evidently had a keen interest in horticulture, growing orange trees, 'jesamines' and myrtles in her greenhouses. In 1732 released from guardianship, his mother handed over to him by special permission the family estates. Now in complete control of Ingatestone and Thorndon halls, Robert was able to give full expression to his enthusiasms and immediately embarked on an ambitious plan to remodel both the house and the park, which had been held in trust for him since his father's death.
John Martin, visiting in 1729, was amazed by what he saw; he confessed he had never witnessed the like of the 'stoves' or hothouses and found in them some species that he, a professional botanist, had never seen before. The raising of exotic species from seed was a particular passion of the time, encouraged by the work of Philip Miller in developing the technique of using beds of tanner's bark to achieve safely and efficiently the high soil temperatures required and Robert had adopted the technique to spectacular effect. Writing to Carl Linnaeus some years later, Peter Collinson exclaims, "Such stoves the world never saw, nor may ever again".
The Great Stove, reputed to be the largest hothouse in the world, was fully high and contained trees and shrubs 10 to tall including specimens of guava, papaw, plantain, hibiscus, "Hernandia" (jack-in-a-box), ceroid cacti, sago palm, annatto (a red berry used for edible dye) and bamboo cane. The walls were hung with trellises covered with passion flowers, a wide variety of clematis and creeping cereus.
There were also two other stoves maintained at a slightly lower temperature for more temperate plants, a house long exclusively for the cultivation of bananas and pineapples and another the same size for storing apples. From these stoves came the first camellia to flower in England and, in 1739, a gift of bananas sent to Sir Hans Sloane (along with "2 uncommon fowls of the widgeon kind").
Nonetheless, there were failures too; Robert was particularly fond of the white lilac and, on one occasion, culled sufficient seed to raise in his nursery 5,000 new plants. Unfortunately, the principles of plant genetics and cross-pollination were then little understood; all but twenty of them bore purple blossom.
Between 1740 and 1742, some 60,000 trees of at least 50 species were planted at Thorndon Hall. For the most part, these were arranged in mixed thickets, with dark green foliage contrasting with light green and blue green with yellow green, the whole set off by highlights of white bark or leaves with white undersides. This style of planting was not in itself a new idea but was made, in this case, particularly striking by the variety of effects achieved by the wide range of species including: acacias, "Acer" (Virginia), camphor tree, cedar (Lebanon), red cedar, cherry (Pennsylvanian), oak (Carolina), and tulip trees.
By 1762, however, Collinson, on a visit to Thorndon, found a scene of desolation: the house was falling down, the nurseries overgrown and the stoves empty, apart from two date palms, a cactus and a few sickly shrubs.
The redesign of the estate by his son swept away much of Lord Petre's work, only traces of the plantings, the two mounts adjacent to the present house and the ruins of the ziggurat by the old mill pond can be found today. The menagerie only survives in the name of Menagerie Plantation. Furthermore, Robert's impressive botanic library, including 17 folio volumes of dried specimens, were sold, together with the rest of the family library by the unworldly 13th lord and his mahogany cabinet with 20 drawers stuffed with botanic curiosities was turned into a wardrobe and the contents thrown away.
Marriage and issue.
On 2 May 1732 at St Paul's Cathedral, Robert married Lady Henrietta Anna Mary Barbara Radcliffe, (Mary), (1716 – 31 January 1760), only daughter of the Earl of Derwentwater (1689–1716) and Anna Maria Webb (1690–1723) and great granddaughter of Charles II and Moll Davis. The couple had four children;
As a young couple, the parents took up residence at Thorndon Hall. Mary had her father's remains put in the mausoleum at Thorndon. There is no entry about the funeral in the register; Rector Ewer was then an old man, and there are only four burials entered for that year. Perhaps the burial was secret. The sympathies of the Petre family may well have been with the old and young Pretenders, and although he had the bells of Ingrave Church cast at Ingatestone, their success would have meant the supremacy once more of the Roman hierarchy; but it does not appear that they took any active part in the risings. He did maintain four missions, beside the one at Thorndon; Lord Petre maintained three at Ingatestone Hall, Writtle Park and Crondon Hall.
Death.
Like his father, Lord Petre succumbed at an early age to smallpox. He died on 2 July 1742 at Ingatestone Hall, soon after his 29th birthday, and was buried in the family vault at Ingatestone. His son being but an infant, there was no one else to carry forward his plans for the estates, and his widow then resided at Ingatestone Hall, where she died in 1760. She is the last Dowager Lady Petre who has lived in the old family mansion. At his death, Robert's nurseries contained some 219,925 plants and his personal catalogue, now in the Passmore Edwards Museum, lists 696 species.
Accolades.
When Robert was 18, he was elected a fellow of the Royal Society – not in itself an exceptional honour since peers of the realm had an automatic right to membership but it is a mark of the esteem in which he was already held that his sponsor was John Martin, future professor of botany at Cambridge. Furthermore, less than two years later, a Caribbean genus of the verbena family, which the plant collector, Dr. William Houston had identified, was named "Petrea" in Robert's honour.
On his death, the following poem, signed by Janus the Younger (probably a pseudonym for Philip Southcote), appeared in the "Daily Advertiser":
Less sentimentally, his friend, Peter Collinson wrote of Petre in 1744;
And on the fly leaf of his catalogue of the plants in Thorndon Garden is inscribed this tribute;
Lord Petre was commemorated in a stucco monument by the French sculptor Louis-Francois Roubiliac which was housed in the Temple of Death in the country garden of Jonathan Tyers, the proprietor of Vauxhall Gardens. The garden was at Denbies, near Dorking. The monument represented an angel blowing the last trump causing a stone pyramid to crumble to pieces and the corpse within it to throw aside the grave clothes and prepare to arise "with a mixture of joy and astonishment". The epitaph was written by Mr. Robson, tutor to Petre's children:
Over the door of the temple, were further verses written by Robson, warning the reader to prepare for death. Robson was Lord Petre's chaplain and tutor to his sons.


Frank DeStefano

Frank DeStefano FACPM is a medical epidemiologist and researcher at the Centers for Disease Control and Prevention, where he is director of the Immunization Safety Office.
Education.
Frank DeStefano graduated from Cortland (NY) High School in 1970. DeStefano graduated from Cornell University in 1974, receiving a Bachelor of Science degree, and the University of Pittsburgh School of Medicine, from which he received a medical degree in 1978. He received his MPH at Johns Hopkins University School of Hygiene and Public Health in 1984.
Research.
DeStefano is an author of a number of scientific studies concluding that vaccines, in particular thimerosal-containing ones, do not cause autism. In March 2013, for example, DeStefano was the lead author on a study in the Journal of Pediatrics, which concluded that exposure of children to particular ingredients in vaccines, namely proteins and polysaccharides, did not increase their risk of autism. In addition, DeStefano et al. concluded that children with autism had received the same number of antigens as children without. This study received widespread media attention.
As director of the ISO, his research focuses primarily on alleged and real adverse reactions to vaccines, and how common these reactions are. As mentioned above, some of DeStefano's research pertains to the use of thiomersal in vaccines; for example, he co-authored a study in 2003 in Pediatrics which concluded that there was no consistent association between thimerosal-containing vaccines and neurodevelopmental disorders. In addition, he was the final author of a study on the alleged link between thimerosal and autism, authored by the Vaccine Safety Datalink team, published in the New England Journal of Medicine. This study concluded that "Our study does not support a causal association between early exposure to mercury from thimerosal-containing vaccines and immune globulins and deficits in neuropsychological functioning at the age of 7 to 10 years."
Other topics he has published research on include Guillain–Barré syndrome, as well as the potential link between seizures and the whole-cell pertussis vaccine or MMR vaccine. More generally, with regard to the VSD, he published a study in 2001 summarizing the ability of the project to reveal potential risks associated with vaccination, especially intussusception, through conduction of a population-based cohort study.
Originally, however, DeStefano's research focused on the safety of contraceptives, a topic he researched from 1982 to 1984 as a medical officer at the National Institutes of Health. Also in 1982, he joined the CDC as a senior epidemiologist in the Agent Orange projects.
Career.
After completing a residency in pediatrics at the University of Rochester School of Medicine, he joined the Epidemic Intelligence Service in 1979. In 1982, he completed a CDC residency in preventive medicine. In 2004, DeStefano was appointed acting chief of the Immunization Safety Branch of the National Immunization Program, now known as the National Center for Immunization and Respiratory Diseases. From 1992 to 1996, DeStefano held a post at the Marshfield Medical Research Foundation in Marshfield, Wisconsin. In 1996, he returned to the CDC.


Voclosporin

Voclosporin, sold under the brand name Lupkynis, is a calcineurin inhibitor used as an immunosuppressant medication. It was approved by the U.S. Food and Drug Administration (FDA) for the treatment of lupus nephritis (LN) on January 22, 2021.
It is an analog of ciclosporin that has enhanced action against calcineurin and greater metabolic stability. Voclosporin was discovered by Robert T. Foster and his team at Isotechnika in the mid 1990s. Isotechnika was founded in 1993 and merged with Aurinia Pharmaceuticals in 2013. In Jan. 2021, Aurinia Pharmaceuticals received approval from the Food & Drug Administration to sell the drug Lupkynis.
Initially, voclosporin was a mixture of equal proporations of "cis" and "trans" geometric isomers of amino acid-1 modified cyclosporin. Later, in collaboration with Roche in Basel, Switzerland, voclosporin's manufacturing was changed to yield the predominantly "trans" isomer which possesses most of the beneficial effect of the drug (immunosuppression) in the treatment of organ transplantation and autoimmune diseases.


Liraglutide

Liraglutide, sold under the brand name Victoza among others, is a medication used to treat diabetes mellitus type 2 and obesity. In diabetes it is a less preferred agent compared to metformin. Its effects on long-term health outcomes like heart disease and life expectancy are unclear. It is given by injection under the skin.
Common side effects include low blood sugar, nausea, dizziness, abdominal pain, and pain at the site of injection. Other serious side effects may include medullary thyroid cancer, angioedema, pancreatitis, gallbladder disease, and kidney problems. Use in pregnancy and breastfeeding is of unclear safety. Liraglutide is a glucagon-like peptide-1 receptor agonist (GLP-1 receptor agonist) also known as incretin mimetics. It works by increasing insulin release from the pancreas and decreases excessive glucagon release.
Liraglutide was approved for medical use in the European Union in 2009, and in the United States in 2010. In 2018, it was the 143rd most commonly prescribed medication in the United States, with more than 4million prescriptions.
Medical uses.
Liraglutide is a medication used for the treatment of type 2 diabetes or obesity.
Type 2 diabetes.
Liraglutide improves control of blood glucose. As of 2017 it is unclear if incretin mimetics like liraglutide affect a person's risk of death.
In diabetes it is a less preferred agent. It may be used in those in who metformin and another antidiabetic medication such as a sulfonylurea are not sufficient.
Obesity.
Liraglutide may also be used together with diet and exercise for chronic weight management in adult patients. The body mass index (BMI) needs to be greater than 30 kg/m2, or greater than 27 kg/m2 together with high blood pressure, type 2 diabetes mellitus, or dyslipidemia.
It is unknown if the weight loss will be permanent. Appetite suppression may be temporary and appetite might return even if one continues to use liraglutide after 56 weeks.
Adverse effects.
Thyroid cancer.
At exposures eight times greater than those used in humans, liraglutide caused a statistically significant increase in thyroid tumors in rats. The clinical relevance of these findings is unknown. In clinical trials, the rate of thyroid tumors in patients treated with liraglutide was 1.3 per 1000 patient years (4 people) compared to 1.0 per 1000 patients (1 person) in comparison groups. The sole person in the comparator group and four of the five persons in the liraglutide group had serum markers (elevated calcitonin) suggestive of pre-existing disease at baseline.
The FDA said serum calcitonin, a biomarker of medullary thyroid cancer, was slightly increased in liraglutide patients, but still within normal ranges, and it required ongoing monitoring for 15 years in a cancer registry.
Pancreatitis.
In 2013, a group at Johns Hopkins reported an apparently statistically significant association between hospitalization for acute pancreatitis and prior treatment with GLP-1 derivatives (such as exenatide) and DPP-4 inhibitors (such as sitagliptin). In response, the United States FDA and the European Medicines Agency conducted a review of all available data regarding the possible connection between incretin mimetics and pancreatitis or pancreatic cancer. In a joint 2014 letter to the New England Journal of Medicine, the agencies concluded that "A pooled analysis of data from 14,611 patients with type 2 diabetes from 25 clinical trials in the sitagliptin database provided no compelling evidence of an increased risk of pancreatitis or pancreatic cancer" and "Both agencies agree that assertions concerning a causal association between incretin-based drugs and pancreatitis or pancreatic cancer, as expressed recently in the scientific literature and in the media, are inconsistent with the current data. The FDA and the EMA have not reached a final conclusion at this time regarding such a causal relationship. Although the totality of the data that have been reviewed provides reassurance, pancreatitis will continue to be considered a risk associated with these drugs until more data are available; both agencies continue to investigate this safety signal."
Pharmacodynamics.
Liraglutide is an acylated glucagon-like peptide-1 (GLP-1) agonist, derived from human GLP-1-(7-37), a less common form of endogenous GLP-1.
It reduces meal-related hyperglycemia (for 24 hours after administration) by increasing insulin secretion (only) when required by increasing glucose levels, delaying gastric emptying, and suppressing prandial glucagon secretion.
Liraglutide leads to insulin release in pancreatic beta cells in the presence of elevated blood glucose. This insulin secretion subsides as glucose concentrations decrease and approach euglycemia (normal blood glucose level). It also decreases glucagon secretion in a glucose-dependent manner and delays gastric emptying. Unlike endogenous GLP-1, liraglutide is stable against metabolic degradation by peptidases, with a plasma half-life of 13 hours.
Pharmacokinetics.
Endogenous GLP-1 has a plasma half-life of 1.5–2 minutes due to degradation by the ubiquitous enzymes, dipeptidyl peptidase-4 (DPP4) and neutral endopeptidases (NEP). The half-life after intramuscular injection is approximately half an hour, so even administered this way, it has limited use as a therapeutic agent. The metabolically active forms of GLP-1 are the endogenous GLP-1-(7-36)NH2 and the more rare GLP-1-(7-37). The prolonged action of liraglutide is achieved by attaching a fatty acid molecule at one position of the GLP-1-(7-37) molecule, enabling it to both self-associate and bind to albumin within the subcutaneous tissue and bloodstream. The active GLP-1 is then released from albumin at a slow, consistent rate. Albumin binding also results in slower degradation and reduced renal elimination compared to that of GLP-1-(7-37).
Society and culture.
Brand names.
Liraglutide is marketed under the brand name Victoza in the U.S., U.K. UAE, Kuwait, India, Iran, Canada, Europe and Japan. It has been launched in Germany, Italy, Denmark, the Netherlands, the United Kingdom, Ireland, Sweden, Japan, Canada, the United States, France, Malaysia and Singapore. Liraglutide is also known to be marketed as Saxenda in Australia, Iran, Israel, Canada, Brazil, Switzerland and the U.S.
Marketing.
Liraglutide was approved by the FDA in 2014 and by the European Medicines Agency in 2015, for adults with a body mass index (BMI) of 30 or greater (obesity) or a BMI of 27 or greater (overweight) who have at least one weight-related condition. Liraglutide was approved by the FDA in 2019 for treatment of children 10 years or older with type 2 diabetes, making it the first non-insulin drug approved to treat type 2 diabetes in children since metformin was approved in 2000.
Novo Nordisk stated that it plans to use 500 of its 3,000-strong sales force in the United States to promote Saxenda in 2015, because it is considered to have the potential for sales of $1 billion a year within 8–10 years of launch around the world. Analysts at Citi Research concur, assuming that the drug will reach less than 0.5 percent of the 107 million people in the United States classified as obese, and a daily price of $30 over 6 to 12 months' use. The company estimates that it has spent about $1 billion over ten years to take Saxenda from research to marketing.
Controversy.
In 2010, Novo Nordisk breached the ABPI's code of conduct by failing to provide information about side effects, and by promoting it prior to being granted market authorization.
In 2012, the non-profit consumer advocacy group Public Citizen petitioned the U.S. Food and Drug Administration (FDA) to immediately remove liraglutide from the market because they concluded that risks of thyroid cancer and pancreatitis outweigh any documented benefits.
In 2017, Novo Nordisk agreed to pay $58.65 million to settle multiple whistleblower lawsuits alleging that the company had illegally marketed, promoted, and sold Victoza for off-label uses (such as for type 1 diabetes ) in violation of the Federal Food, Drug, and Cosmetic Act and the False Claims Act. Novo Nordisk paid an additional $1.45 million to the states of California and Illinois to settle whistleblower cases alleging fraud against private commercial health insurers.
Novo-Nordisk applied to the USFDA in April 2019 for approval of oral semaglutide.


Hamid Nawab

S. Hamid Nawab is Professor of Electrical and Computer Engineering and Biomedical Engineering at Boston University who is a researcher, educator, and engineer in the signal processing and machine perception subfields of Electrical Engineering and their application to the machine/computer analysis of complex biosignals from auditory, speech, and neuromuscular systems.
Education.
Nawab received his BS degree in Electrical Engineering, MS degree in Electrical Engineering and Computer Science, and PhD degree in Electrical Engineering from Massachusetts Institute of Technology (M.I.T.) in 1977, 1979 and 1982.
Career.
Nawab is an elected fellow of the American Institute of Medical and Biological Engineering (AIMBE) for contributions to the analysis of complex biosignals from speech, auditory, and neuromuscular systems; AIMBE fellows represent the top 2% of medical and biological engineers. Key journal articles written by Nawab include those on "Integrated Processing and Understanding of Signals", "Decomposition of Surface EMG Signals", "Approximate Signal Processing", "Direction Determination of Wideband Signals" (winner of 1988 "Paper Award" from IEEE Signal Processing Society in the "Multidimensional Signal Processing" Category), and "Signal Reconstruction from Short-time Fourier Transform Magnitude". Among his other major written works is the book "Symbolic and Knowledge-Based Signal Processing" at the intersection of signal processing and artificial intelligence research, as well as the textbook "Signals and Systems" that he co-authored with Alan V. Oppenheim and Alan S. Willsky. This textbook has been adopted around the world with its international edition and its Chinese edition. Nawab is currently a tenured full professor at Boston University where his earned honors include the university-wide Metcalf Award for Excellence in Teaching. He has held visiting professorships in Electrical Engineering at M.I.T. (1994–95) and in Computer Science at University of Massachusetts, Amherst (1989–90).
Personal life.
Nawab is a Pakistani-American who currently lives in Andover MA with his wife and son. He has lived in the Greater Boston area since 1974 when he first arrived in the US to attend College.


Gaston, Count of Marsan

Gaston de Lorraine (Gaston Jean Baptiste Charles; 7 February 1721 – 2 May 1743) was a French nobleman and member of a cadet branch of the House of Lorraine. He was the last Count of Marsan. His wife was Marie Louise de Rohan.
Biography.
The eldest son of Charles Louis de Lorraine and his wife Élisabeth de Roquelaure, he was one of four children. He bore the first names [Gaston Jean Bapiste] as his great grandfather Gaston Jean Baptiste de Roquelaure, father of the maréchal de Roquelaure.
His father was known as the "Prince de Pons" and Gaston was styled the Count of Marsan ("comte de Marsan") from birth. As a male line descendant of the House of Guise (cadet branch of the House of Lorraine) he was a Foreign Prince residing at the royal court of Versailles and had the right to the style of Highness.
His older sister "Louise" Henriette Gabrielle married into the prestigious House of La Tour d'Auvergne, sovereigns of the Duchy of Bouillon.
At the age fifteen, he was married to Marie Louise de Rohan. Marie Louise was the daughter of Jules, Prince of Soubise and his wife Anne Julie de Melun. The only daughter of five children, her older brother was the famous Maréchal de Soubise. The couple were married on 4 June 1736. The wedding nuptials were carried out in the chapel of the "hôtel de Mayenne" by her great uncle the Cardinal de Soubise.
In 1736, the year of his marriage, Gaston was put on campaign as an Aide-de-camp to his father. The previous year, he was given his own regiment the "Marsan regiment". On 20 February 1743 he was created a Brigadier of the Kings armies. Some three months later he died of smallpox in Strasbourg leaving his childless wife a widow at the age of twenty two. He was buried in the Strasbourg Cathedral.
His wife never remarried and outlived him till 1801. She was later the Governess to the Children of France and as such, the governess of the future Louis XVI, Louis XVIII and Charles X the grandsons of Louis XV. His wife's parents also died of smallpox within a week of each other in May 1724.


DMSO reductase

DMSO reductase is a molybdenum-containing enzyme that catalyzes reduction of dimethyl sulfoxide (DMSO) to dimethyl sulfide (DMS). This enzyme serves as the terminal reductase under anaerobic conditions in some bacteria, with DMSO being the terminal electron acceptor. During the course of the reaction, the oxygen atom in DMSO is transferred to molybdenum, and then reduced to water.
DMSO reductase (DMSOR) and other members of the DMSO reductase family are unique to bacteria and archaea. Enzymes of this family in anaerobic oxidative phosphorylation and inorganic-donor-based lithotrophic respiration. These enzymes have been engineered to degrade oxoanions.
DMSOR catalyzes the transfer of two electrons and one oxygen atom in the reaction: The active site of DMSOR contains molybdenum, which is otherwise rare in biology.
Tertiary structure and active site.
As for other members of DMSO reductase family, the tertiary structure of DMSOR is composed of Mo-surrounding domains I-IV, with domain IV heavily interacting with pyranopterindithiolene Mo-cofactors (P- and Q-pterin) of the active site. Members of the DMSO reductase family differ in terms of their active sites. In the case of DMSOR, the Mo center is found to two dithiolene provided by two pyranopterin cofactors. These organic cofactors, called molybdopterins, are linked to GMP to create a dinucleotide form. An additional fifth cap-like ligand is the side-chain O of serine-147 residue, further classifying the enzyme as Type III DMSO reductase. InType I and II serine is replaced by cysteine and aspartate residues, respectively. Depending on the redox state of the Mo, which fluctuates between IV, V, or VI as the reaction progresses, the active site Mo core can also be ligated to an oxygen atom of an aqua-, hydroxo-, or oxo-group, respectively. Studies have shown that the particular identity of the amino-acid used to coordinate the Mo core greatly influences Mo redox midpoint potential and protonation state of the oxygen-group ligation, which are key determinants in the enzyme's mechanism for catalysis.
Mechanism.
Initial isotopic DMSO18 studies established a double-oxotransferase mechanism for DMSOR of "R. sphaeroides". In this mechanism the labeled O18 is transferred from substrate to Mo, which then transfers the O18 to 1,3,5-triaza-7-phosphaadamantane (PTA) to yield PTAO18. In an analogous mechanism, DMSO transfers O to Mo, and the resulting Mo(VI)O center is reduced, yielding water.
Studies on synthetic Mo bis-dithiolene complexes suggest that be oxygen-transfer, electron transfer. Using S K-edge XAS and DFT, these model studies point to concerted S-O scission and electron transfer. Rates are proportion to decreasing substrate X-O bond strength and increasing substrate proton affinity.
X-ray crystallography established that the overall tertiary structure of the enzyme remains constant through the reaction progression. However, several different experiments conducted on DMSOR of "R. sphaeroides" reported different results for the coordination activity of the four potential dithiolene ligands. While one x-ray crystallography investigation concluded equidistant coordination of all four Mo-S ligands in the oxidized form, which is supported by numerous x-ray absorption spectroscopy (XAS) studies, a different study characterized asymmetrical Mo-S distances. Both studies as well as electron paramagnetic resonance (EPR) studies have predicted that the Mo active site is highly flexible in terms of position and degree of potential ligand coordinations.
The data that suggested two significantly asymmetric pyranopterin cofactors were used to propose a reaction mechanism. In the fully oxidized Mo VI form of the active site, the oxo-group and serine ligands were coordinated at 1.7 A distances from the Mo center. S1 and S2 of the P-pterin and S1 of the Q-pterin were locationed 2.4 A away from the Mo, and S2 of Q-pterin was located 3.1 A away. This pterin asymmetry may be the result of the trans-effect of the oxo-group weakening the S2-Mo bond, which is located directly opposite the oxo-group.
In contrast, the structure of the fully reduced Mo IV form of the active site showed S1 and S2 P-pterin and S1 Q-pterin maintained full coordination, however the S2 of the Q-pterin shifted away from the metal center, indicating decreased coordination. This shift in ligand-Mo bond length is consistent with the proposed mechanism of direct oxygen transfer from the DMSO substrate to the Mo. A weaker dithiolene coordination in the reduced enzyme form could facilitate direct binding of the S=O. In the reduction of Mo and protonation of the oxo-group, it is proposed that a cytochrome electron source could bind to a depression above the active site and directly reduce the Mo center, or alternatively this cytochrome could bind to a well-solvated polypeptide loop in proximity to the Q-pterin, and Q-pterin could mediate this electron transfer.
Cellular location and regulation.
In "R. sphaeroides", DMSOR is a single-subunit, water-soluble protein that requires no additional cofactors beyond pterin. In "E. coli", DMSOR is embedded within the membrane and has three unique subunits, one of which includes the characteristic pterin cofactor, another which contains four 4Fe:4S clusters, and a final transmembrane subunit that binds and oxidizes menaquinol. The transfer of an e- from menaquinol to the 4Fe:4S clusters and finally to the pterin-Mo active site generates a proton gradient used for ATP generation.
DMSOR regulated predominantly at a transcriptional level. It is encoded by the dor gene and expressed when activated by a signal cascade, which is under the regulation of DorS, DorR, and DorC proteins. A study of lacZ fusions (reporter genes) to corresponding dorS, dorR, and dorC promoters concluded that expression of DorR and DorC increased in reduced oxygen environments, but DorS expression was unaffected by oxygen concentration. DorC expression also increased with increasing concentrations of DMSO.
Environmental impact.
DMS, a product of DMSOR, is a component of the sulfur cycle. DMS is oxidized to Methanesulfonates, which nucleate cloud condensation over open oceans, where the alternative source of nucleation, dust, is absent. Cloud formation is a key component in increasing earth's albedo and regulating atmospheric temperature, thus this enzyme and the reaction it catalyzes could prove helpful on the climate control frontier.


Bupicomide

Bupicomide is a chemical compound created and manufactured by Lanospharma Laboratories Company, Ltd. It is used experimentally as a beta blocker and clinically as a strong vasodilator with the noted side effects of reduced systolic, diastolic and mean arterial pressure.
Synthesis.
As the result of the screening program examining microbial fermentation products for pharmacological activity (other than antibiotic activity), fusaric acid was isolated from "Fusarium oxysporum" following the discovery that extracts were potent inhibitors of DBH, and thus interfered with the biosynthesis of the pressor neurohormone, norepinephrine. To refine this lead, amidation via the acid chloride was carried out to give antihypertensive analog bupicomide.


Little gastrin I

Little gastrin I is a form of gastrin commonly called as gastrin-17. This is a protein hormone, secreted by the intestine.
Gastrin II has identical amino acid composition to Gastrin I, the only difference is that the single tyrosine residue is sulfated in Gastrin II.


Molybdopterin-synthase adenylyltransferase

Molybdopterin-synthase adenylyltransferase (, "MoeB", "adenylyltransferase and sulfurtransferase MOCS3") is an enzyme with systematic name "ATP:molybdopterin-synthase adenylyltransferase". This enzyme catalyses the following chemical reaction
This enzyme adenylates the C-terminus of the small subunit of the molybdopterin synthase.


Spiruchostatin

Spiruchostatins are a group of chemical compounds isolated from "Pseudomonas sp." as gene expression-enhancing substances. They possess novel bicyclic depsipeptides involving 4-amino-3-hydroxy-5-methylhexanoic acid and 4-amino-3-hydroxy-5-methylheptanoic acid residues. The two main forms are spiruchostatin A and spiruchostatin B.
History.
Since the early 1960s, small organic molecules derived naturally from microbes and plants have provided a number of useful cancer chemotherapeutic drugs. The search for naturally occurring lead compounds of this type has continued in recent years, with the constituents of marine fauna and flora as well as those of terrestrial microorganisms and plants being investigated for their anticancer activities. Natural products (NPs) are small molecules produced by living organisms. The term “secondary metabolite” is often used to differentiate NPs from other molecules that are synthesized in the course of primary metabolism.
Uses.
Spiruchostatin A is a natural compound that is showing positive signs of development as a prodrug. Very often, prodrugs are made by simple addition of groups, such as acetyl or alkyl chains, to the drug through amide or ester formation. Similarly, in nature there are examples in which protecting groups are added to an NP, as a strategy for self resistance. This evolutionary trait allows the organism to carry the toxic compound harmlessly until the target is presented that activates the NP.
Synthesis.
Spiruchostatin A is a member of a class of cyclic, cysteine-containing, depsipeptidic natural products. Due to their histone deacetylase (HDAC) inhibitory activity, tremendous effort has been thrust into the synthesis of these compounds and their analogs as potential chemotherapeutic targets. In human cancers, HDACs are often over-expressed and are recruited to reduce the transcription of tumor suppressor genes and other cell growth regulators. HDAC inhibitors are therefore thought to increase the expression of tumor suppressor genes, and they are an emerging compound class in the treatment of cancers, with several agents either approved or in development.


Prokaryotic ubiquitin-like protein

Prokaryotic ubiquitin-like protein (Pup) is a functional analog of ubiquitin found in the prokaryote "Mycobacterium tuberculosis". Like ubiquitin, Pup serves to direct proteins to the proteasome for degradation. However, the enzymology of ubiquitylation and pupylation is different, owing to their distinct evolutionary origins. In contrast to the three-step reaction of ubiquitylation, pupylation requires only two steps, and thus only two enzymes are involved in pupylation. The enzymes involved in pupylation are descended from glutamine synthetase.
Similar to ubiquitin, Pup is attached to specific lysine residues of substrate proteins by isopeptide bonds; this is called pupylation. It is then recognized by the protein Mycobacterium proteasomal ATPase (Mpa), in a mechanism that induces folding of Pup. Mpa delivers the substrate protein to the proteasome for degradation by coupling of ATP hydrolysis.
The discovery of Pup indicates that like eukaryotes, bacteria may use a small-protein modifier to control protein stability.
The Pup gene encodes a 64–amino acid protein with a molecular size of about 6.9 kDa.
Pup is an intrinsically disordered protein. In 2010, scientists at the Brookhaven National Laboratory determined the X-ray crystal structure of the complex between Pup and its delivery enzyme Mpa and found that Pup binding to Mpa induces the folding of a unique alpha-helix.
In 2017, the presence of Pup homologs in bacterial species outside of the group of gram-positive bacteria was reported. The Pup homologs were termed UBact (for Ubiquitin Bacterial), although the distinction has not been proven to be phylogenetically supported by a separate evolutionary origin and is without experimental evidence. UBact is a homolog of Pup, and is found in several phyla of gram-negative bacteria (Pup is found predominantly in the gram-positive bacterial phylum Actinobacteria).


Run-off transcription

A run-off transcription assay is an assay in molecular biology which is conducted "in vitro" to identify the position of the transcription start site (1 base pair upstream) of a specific promoter along with its accuracy and rate of "in vitro" transcription.
Run-off transcription can be used to quantitatively measure the effect of changing promoter regions on in vitro transcription levels, Because of its in vitro nature, however, this assay cannot accurately predict cell-specific gene transcription rates, unlike in vivo assays such as nuclear run-on.
To perform a run-off transcription assay, a gene of interest, including the promoter, is cloned into a plasmid. The plasmid is digested at a known restriction enzyme cut site downstream from the transcription start site such that the expected mRNA run-off product would be easily separated by gel electrophoresis.
DNA needs to be highly purified prior to running this assay.
 To initiate transcription, radiolabeled UTP, the other nucleotides, and RNA polymerase are added to the linearized DNA. Transcription continues until the RNA polymerase reaches the end of the DNA where it simply “runs off” the DNA template, resulting in an mRNA fragment of a defined length. This fragment can then be separated by gel electrophoresis, alongside size standards, and autoradiographed. The corresponding size of the band will represent the size of the mRNA from the restriction enzyme cut site to the transcription start site (+1). The intensity of the band will indicate the amount of mRNA produced.
Additionally, it can be used to detect whether or not transcription is carried out under certain conditions (i.e. in the presence of different chemicals).


Erik Tambuyzer

Erik Tambuyzer (born 1949) is a Belgian bio-engineer and businessman. He is Chairman of the Board of the Flemish Center for Medical Innovation (CMI).
Education.
Tambuyzer holds a doctoral degree in bio-industrial sciences from the Katholieke Universiteit Leuven, (Leuven, Belgium).
Career.
Having started his professional career at Baxter Healthcare (Baxter-Travenol in Europe) in 1977, Tambuyzer pursued his career six years later at Innovi NV (Brussels, Belgium), a technology management and consultancy company. He also worked as a consultant on biotechnology for minister-president Gaston Geens of the Flemish government. In 1985 he made the business plan and co-founded, together with Hugo Van Heuverswyn, the healthcare biotech company Innogenetics NV (Ghent, Belgium), of which he was General Manager until 1992, at which time he joined Genzyme. He was Senior Vice President Corporate Affairs for Genzyme Europe and International, and a member of the European Management Committee of Genzyme Corporation until 2010, when he joined the Flemish Center for Medical Innovation (CMI).
Tambuyzer is a founding Board member and past Chairman of EuropaBio, the European Association for Bioindustries, and founder of the Ethics Working Group of this Association, as well as the Chair of the joint EBE/EFPIA-EuropaBio Orphan medicines Task Force. He is also Vice-Chair of EPPOSI, the European Platform for Patients' Organizations, Science & Industry. He published on policies regarding orphan medicines and advanced therapies in Europe and internationally, on the European Clinical Trial Directive, and on the impact of biotechnology on healthcare systems.


Paraves

Paraves are a widespread group of theropod dinosaurs that originated in the Late Jurassic period. In addition to the extinct dromaeosaurids, troodontids, anchiornithids, and scansoriopterygids, the group also contains the avialans, among which are the over ten thousand species of living birds. Early members of Paraves are well known for the possession of an enlarged claw on the second digit of the foot, which was held off the ground when walking in some species.
Description.
Like other theropods, all paravians are bipedal, walking on their two hind legs.
The teeth of primitive paravians were curved and serrated, but not blade-like except in some specialized species such as "Dromaeosaurus albertensis". The serrations on the front edge of dromaeosaurid and troodontid teeth were very small and fine, while the back edge had serrations which were very large and hooked.
Most of the earliest paravian groups were carnivorous, though some smaller species (especially among the troodontids and early avialans) are known to have been omnivores, and it has been suggested that an omnivorous diet was the ancestral state for this group, with strict carnivory evolving in some specialized lineages. Fossils also suggest that legs and feet covered with feathers was an ancestral condition, possibly having originated in the Coelurosauria, even if this trait was later lost in more advanced birds.
Wings.
Paravians generally have long, winged forelimbs, though these have become smaller in many flightless species and some extinct lineages that evolved before flight. The wings usually bore three large, flexible, clawed fingers in early forms. The fingers became fused and stiffened and the claws highly reduced or lost in some advanced lineages. An increasingly asymmetric wrist joint, a trend that can be traced back to primitive coelurosaurs, allowed the forelimbs to elongate and an elaboration of their plumage, traits that made the evolution of flapping flight possible.
Many early members of Paraves had both well-developed wings and long feathers on the hind legs, which in some cases, formed a second set of airfoils. These species, most famously represented by "Microraptor gui", have often been referred to as "four winged dinosaurs". Though it has been suggested that these hind wings would have prevented some paravians from getting around on the ground, and that they must have lived in trees, there is very little evidence that any of the earliest paravians were capable of climbing. This apparent paradox was addressed by later studies which showed that early paravians like "Microraptor" were capable of flapping flight and powered launching from the ground into the air without relying on climbing. "Microraptor" in particular also seems to represent a case of flight evolving independently of the bird lineage within Paraves.
Feet and sickle claw.
Most theropods walked with three toes contacting the ground, but fossilized footprint tracks confirm that many basal paravians, including dromaeosaurids, troodontids, and some early avialans, held the second toe off the ground in a hyperextended position, with only the third and fourth toes bearing the weight of the animal. This is called functional didactyly. The enlarged second toe bore an unusually large, curved sickle-shaped claw (held off the ground or 'retracted' when walking). This claw was especially large and flattened from side to side in the large-bodied predatory eudromaeosaurs. In these early species, the first toe (hallux) was usually small and angled inward toward the center of the body, but only became fully reversed in more specialized members of the bird lineage. One species, "Balaur bondoc", possessed a first toe which was highly modified in parallel with the second. Both the first and second toes on each foot of "B. bondoc" were held retracted and bore enlarged, sickle-shaped claws.
One of the best-known features of paravians is the presence of an enlarged and strongly curved "sickle claw" on a hyper-extendible second toe, modified to hold the sickle claw clear of the ground when walking, most notably developed in the dromaeosaurids and troodontids. While this characteristic claw and its associated modifications to the anatomy of the foot (such as a shortened metatarsus in eudromaeosaurs) had been known since the mid-20th century, their possible functions were the subject mainly of speculation, and few actual studies were published. Initial speculation regarded the claws as slashing implements used to disembowel large prey. In this scenario, the shortened upper foot would serve as an anchor point for powerful tendons to improve kicking ability. However, subsequent studies of the actual claw shape showed that the underside of the claw was only weakly keeled and would not have been an effective cutting instrument. Instead, it appeared to be more of a hooking implement. Manning et al. suggested in 2006 that the claws were similar to crampons and were used for climbing, and in the case of larger species or individuals, climbing up the flanks of very large prey.
A larger study of sickle-claw function, published in 2011 by Fowler and colleagues, concluded that the earlier study by Manning and colleagues was correct and that the "sickle claws" would have been ineffective as cutting weapons. They compared the claw and overall foot anatomy of various primitive species with modern birds to shed light on their actual function. Fowler and colleagues showed that many modern predatory birds also have enlarged claws on the second toes. In modern raptors, these claws are used to help grip and hold prey of sizes smaller than or equal to the predator, while the birds use their body weight to pin their prey to the ground and eat it alive. Fowler and colleagues suggested that this behavior is entirely consistent with the anatomy of advanced dromaeosaurids like "Deinonychus", which had slightly opposing first toes and strong tendons in the toes and foot. This makes it likely that advanced dromaeosaurids also used their claws to puncture and grip their prey to aid in pinning it to the ground, while using shallow wing beats and tail movements to stabilize themselves. Other lines of evidence for this behavior include teeth which had large, hooked serrations only on the back edge (useful in pulling flesh upward rather than slicing it) and large claws on the wings (for greater maneuvering of prey while mantling it with the wings).
In more primitive dromaeosaurids and in troodontids, the feet were not as specialized and the claws were not as large or as hooked. Additionally, the toe joints allowed more range of motion than the simple up-down movements of advanced dromaeosaurids. This makes it likely that these species specialized in smaller prey that could be pinned using only the inner toes, not requiring the feet to be as strong or sturdy.
Dichotomy in body sizes.
The most extreme examples of miniaturization and progenesis are found in Paraves. The ancestors of Paraves first started to shrink in size in the early Jurassic 200 million years ago, and fossil evidence shows that this theropod line evolved new adaptations four times faster than other groups of dinosaurs, and was shrinking 160 times faster than other dinosaur lineages were growing. Turner "et al". (2007) suggested that extreme miniaturization was ancestral for the clade, whose common ancestor has been estimated to have been around long and in mass. In Eumaniraptora, both Dromaeosauridae and Troodontidae went later through four independent events of gigantism, three times in dromaeosaurids and once in troodontids, while the body mass continued to decrease in many forms within Avialae. Fossils show that all the earliest members of Paraves found to date started out as small, while Troodontidae and Dromaeosauridae gradually increased in size during the Cretaceous period.
Evolution.
Relationships.
Paraves is a branch-based clade defined to include all dinosaurs which are more closely related to birds than to oviraptorosaurs. The ancestral paravian is the earliest common ancestor of birds, dromaeosaurids, and troodontids which was not also ancestral to oviraptorosaurs. Paravians comprises three major sub-groups: Avialae, including "Archaeopteryx" and modern birds, as well as the dromaeosaurids and troodontids, which may or may not form a natural group.
The name 'Paraves' (Greek "par(a)":near + Latin "aves", plural of "avis":bird) was coined by Paul Sereno in 1997. The clade was defined by Sereno in 1998 as a branch-based clade containing all Maniraptora closer to Neornithes (which includes all the birds living in the world today) than to "Oviraptor".
In 1997, a node-based clade called Eumaniraptora ("true maniraptorans") was named by Padian, Hutchinson and Holtz. They defined their clade to include only avialans and deinonychosaurs. Paraves and Eumaniraptora are generally considered to be synonyms, though a few phylogenetic studies suggest that the two groups have a similar but not identical content; Agnolín and Novas (2011) recovered scansoriopterygids and alvarezsaurids as paravians that were not eumaniraptorans, while Turner, Makovicky and Norell (2012) recovered "Epidexipteryx" as the only known non-eumaniraptoran paravian. A nearly identical definition, "the theropod group that includes all taxa closer to "Passer" than to "Dromaeosaurus"", was used by Agnolín and Novas (2013) for their clade Averaptora.
Since the 1960s, the dromaeosaurids and troodontids have often been classified together in a group or clade named the Deinonychosauria, initially based primarily on the presence of a retractable second toe with sickle-claw (now also known to be present in some avialans). The name Deinonychosauria was coined by Ned Colbert and Dale Russell in 1969, and defined as a clade (all theropods closer to dromaeosaurids than to birds) by Jacques Gauthier in 1986. However, several more recent studies have cast doubt on the hypothesis that dromaeosaurids and troodontids were more closely related to each other than either was to birds, instead finding that troodontids were more closely related to birds than to dromaeosaurids. Because Deinonychosauria was originally defined as all animals closer to dromaeosaurids than to birds without specific reference to troodontids, this would render Deinonychosauria a synonym of Dromaeosauridae.
In 2015 Chatterjee created Tetrapterygidae in the second edition of his book "The Rise of Birds: 225 Million Years of Evolution", where he included "Microraptor", "Xiaotingia", "Aurornis", and "Anchiornis"; together they were proposed to be the sister group of the Avialae. Paraves, Eumaniraptora and Averaptora are generally considered to be synonyms. Deinonychosauria is a synonym of Dromaeosauridae if troodontids are closer to Avialae as now seems likely. Tetrapterygidae is a polyphyletic grouping of four-winged basal paravian genera.
Origin and early evolution.
Paravians diverged from other maniraptorans no later than 160 Mya; some 65 Mya later, the ancestors of modern birds diverged from other paravians at approximately 95 Mya.
Other than the crown group of modern birds, which are direct descendants in the stem lineage of Paraves, there are no extant survivors or genetic material, so their entire phylogeny is inferred only from the fossil record. The prototypical fossil is "Archaeopteryx", of which 11 whole or partial examples have been found.


Triflupromazine

Triflupromazine (Vesprin) is an antipsychotic medication of the phenothiazine class. Among different effects of triflupromazine indication for use of this drug is severe emesis and severe Hiccups. Due to its potential side effects (triflupromazine has higher risk for side effects than many other antipsychotics) it is not gold standard in antiemetic therapy.
Serious side effects of triflupromazine can be akathisia and tardive dyskinesia as well as the rare, but potentially fatal, neuroleptic malignant syndrome.


Tiprenolol

Tiprenolol is a beta adrenergic receptor antagonist.


Phosphoenolpyruvic acid

Phosphoenolpyruvate (2-phosphoenolpyruvate, PEP) is the ester derived from the enol of pyruvate and phosphate. It exists as an anion. PEP is an important intermediate in biochemistry. It has the highest-energy phosphate bond found (−61.9 kJ/mol) in organisms, and is involved in glycolysis and gluconeogenesis. In plants, it is also involved in the biosynthesis of various aromatic compounds, and in carbon fixation; in bacteria, it is also used as the source of energy for the phosphotransferase system.
In glycolysis.
PEP is formed by the action of the enzyme enolase on 2-phosphoglyceric acid. Metabolism of PEP to pyruvic acid by pyruvate kinase (PK) generates adenosine triphosphate (ATP) via substrate-level phosphorylation. ATP is one of the major currencies of chemical energy within cells.

In gluconeogenesis.
PEP is formed from the decarboxylation of oxaloacetate and hydrolysis of one guanosine triphosphate molecule. This reaction is catalyzed by the enzyme phosphoenolpyruvate carboxykinase (PEPCK). This reaction is a rate-limiting step in gluconeogenesis:
In plants.
PEP may be used for the synthesis of chorismate through the shikimate pathway. Chorismate may then be metabolized into the aromatic amino acids (phenylalanine, tryptophan and tyrosine) and other aromatic compounds. The first step is when Phosphoenolpyruvate and erythrose-4-phosphate react to form 3-deoxy-D-arabinoheptulosonate-7-phosphate (DAHP), in a reaction catalyzed by the enzyme DAHP synthase.
In addition, in C4 plants, PEP serves as an important substrate in carbon fixation. The chemical equation, as catalyzed by phosphoenolpyruvate carboxylase (PEP carboxylase), is:


Expanded genetic code

An expanded genetic code is an artificially modified genetic code in which one or more specific codons have been re-allocated to encode an amino acid that is not among the 22 common naturally-encoded proteinogenic amino acids.
The key prerequisites to expand the genetic code are:
Expanding the genetic code is an area of research of synthetic biology, an applied biological discipline whose goal is to engineer living systems for useful purposes. The genetic code expansion enriches the repertoire of useful tools available to science.
In May 2019, researchers, in a milestone effort, reported the creation of a new synthetic (possibly artificial) form of viable life, a variant of the bacteria "Escherichia coli", by reducing the natural number of 64 codons in the bacterial genome to 61 codons (eliminating two out of the six codons coding for serine and one out of three stop codons) - of which 59 used to encode 20 amino acids.
Introduction.
It is noteworthy that the genetic code for all organisms is basically the same, so that all living beings use the same ’genetic language’. In general, the introduction of new functional unnatural amino acids into proteins of living cells breaks the universality of the genetic language, which ideally leads to alternative life forms. Proteins are produced thanks to the translational system molecules, which decode the RNA messages into a string of amino acids. The translation of genetic information contained in messenger RNA (mRNA) into a protein is catalysed by ribosomes. Transfer RNAs (tRNA) are used as keys to decode the mRNA into its encoded polypeptide. The tRNA recognizes a specific three nucleotide codon in the mRNA with a complementary sequence called the anticodon on one of its loops. Each three-nucleotide codon is translated into one of twenty naturally occurring amino acids. There is at least one tRNA for any codon, and sometimes multiple codons code for the same amino acid. Many tRNAs are compatible with several codons. An enzyme called an aminoacyl tRNA synthetase covalently attaches the amino acid to the appropriate tRNA. Most cells have a different synthetase for each amino acid (20 or more synthetases). On the other hand, some bacteria have fewer than 20 aminoacyl tRNA synthetases, and introduce the "missing" amino acid(s) by modification of a structurally related amino acid by an aminotransferase enzyme. A feature exploited in the expansion of the genetic code is the fact that the aminoacyl tRNA synthetase often does not recognize the anticodon, but another part of the tRNA, meaning that if the anticodon were to be mutated the encoding of that amino acid would change to a new codon.
In the ribosome, the information in mRNA is translated into a specific amino acid when the mRNA codon matches with the complementary anticodon of a tRNA, and the attached amino acid is added onto a growing polypeptide chain. When it is released from the ribosome, the polypeptide chain folds into a functioning protein.
In order to incorporate a novel amino acid into the genetic code several changes are required. First, for successful translation of a novel amino acid, the codon to which the novel amino acid is assigned cannot already code for one of the 20 natural amino acids. Usually a nonsense codon (stop codon) or a four-base codon are used. Second, a novel pair of tRNA and aminoacyl tRNA synthetase are required, these are called the orthogonal set. The orthogonal set must not crosstalk with the endogenous tRNA and synthetase sets, while still being functionally compatible with the ribosome and other components of the translation apparatus. The active site of the synthetase is modified to accept only the novel amino acid. Most often, a library of mutant synthetases is screened for one which charges the tRNA with the desired amino acid. The synthetase is also modified to recognize only the orthogonal tRNA. The tRNA synthetase pair is often engineered in other bacteria or eukaryotic cells.
In this area of research, the 20 encoded proteinogenic amino acids are referred to as standard amino acids, or alternatively as natural or canonical amino acids, while the added amino acids are called non-standard amino acids (NSAAs), or unnatural amino acids (uAAs; term not used in papers dealing with natural non-proteinogenic amino acids, such as phosphoserine), or non-canonical amino acids.
Non-standard amino acids.
The first element of the system is the amino acid that is added to the genetic code of a certain strain of organism.
Over 71 different NSAAs have been added to different strains of "E. coli", yeast or mammalian cells. Due to technical details (easier chemical synthesis of NSAAs, less crosstalk and easier evolution of the aminoacyl-tRNA synthase), the NSAAs are generally larger than standard amino acids and most often have a phenylalanine core but with a large variety of different substituents. These allow a large repertoire of new functions, such as labeling (see figure), as a fluorescent reporter ("e.g." dansylalanine) or to produce translational proteins in "E. coli" with Eukaryotic post-translational modifications ("e.g." phosphoserine, phosphothreonine, and phosphotyrosine).
Unnatural amino acids incorporated into proteins include heavy atom-containing amino acids to facilitate certain x-ray crystallographic studies; amino acids with novel steric/packing and electronic properties; photocrosslinking amino acids which can be used to probe protein-protein interactions in vitro or in vivo; keto, acetylene, azide, and boronate-containing amino acids which can be used to selectively introduce a large number of biophysical probes, tags, and novel chemical functional groups into proteins "in vitro" or "in vivo"; redox active amino acids to probe and modulate electron transfer; photocaged and photoisomerizable amino acids to photoregulate biological processes; metal binding amino acids for catalysis and metal ion sensing; amino acids that contain fluorescent or infra-red active side chains to probe protein structure and dynamics; α-hydroxy acids and -amino acids as probes of backbone conformation and hydrogen bonding interactions; and sulfated amino acids and mimetics of phosphorylated amino acids as probes of post-translational modifications.
Availability of the non-standard amino acid requires that the organism either import it from the medium or biosynthesize it.
In the first case, the unnatural amino acid is first synthesized chemically in its optically pure -form. It is then added to the growth medium of the cell. A library of compounds is usually tested for use in incorporation of the new amino acid, but this is not always necessary, for example, various transport systems can handle unnatural amino acids with apolar side-chains.
In the second case, a biosynthetic pathway needs to be engineered, for example, an "E. coli" strain that biosynthesizes a novel amino acid (p-aminophenylalanine) from basic carbon sources and includes it in its genetic code. Another example: the production of phosphoserine, a natural metabolite, and consequently required alteration of its pathway flux to increase its production.
Codon assignment.
Another element of the system is a codon to allocate to the new amino acid.
A major problem for the genetic code expansion is that there are no free codons. The genetic code has a non-random layout that shows tell-tale signs of various phases of primordial evolution, however, it has since frozen into place and is near-universally conserved. Nevertheless, some codons are rarer than others. In fact, in "E. coli" (and all organisms) the codon usage is not equal, but presents several rare codons (see table), the rarest being the amber stop codon (UAG).
Amber codon suppression.
The possibility of reassigning codons was realized by Normanly "et al." in 1990, when a viable mutant strain of "E. coli" read through the UAG ("amber") stop codon.
This was possible thanks to the rarity of this codon and the fact that release factor 1 alone makes the amber codon terminate translation. Later, in the Schultz lab, the tRNATyr/tyrosyl-tRNA synthetase (TyrRS) from "Methanococcus jannaschii", an archaebacterium, was used to introduce a tyrosine instead of STOP, the default value of the amber codon. This was possible because of the differences between the endogenous bacterial synthases and the orthologous archaeal synthase, which do not recognize each other. Subsequently, the group evolved the orthologonal tRNA/synthase pair to utilise the non-standard amino acid "O"-methyltyrosine. This was followed by the larger naphthylalanine and the photocrosslinking benzoylphenylalanine, which proved the potential utility of the system.
The amber codon is the least used codon in "Escherichia coli", but hijacking it results in a substantial loss of fitness. One study in fact found that there were at least 83 peptides majorly affected by the readthrough Additionally, the labelling was incomplete. As a consequence, several strains have been made to reduce the fitness cost, including the removal of all amber codons from the genome.
In most "E. coli" K-12 strains (viz. "Escherichia coli" (molecular biology) for strain pedigrees) there are 314 UAG stop codons. Consequently, a gargantuan amount of work has gone into the replacement of these. One approach pioneered by the group of Prof. George Church from Harvard, was dubbed MAGE in CAGE: this relied on a multiplex transformation and subsequent strain recombination to remove all UAG codons—the latter part presented a halting point in a first paper, but was overcome. This resulted in the "E. coli" strain C321.ΔA, which lacks all UAG codons and RF1. This allowed an experiment to be done with this strain to make it "addicted" to the amino acid biphenylalanine by evolving several key enzymes to require it structurally, therefore putting its expanded genetic code under positive selection.
Rare sense codon reassignment.
In addition to the amber codon, rare sense codons have also been considered for use. The AGG codon codes for arginine, but a strain has been successfully modified to make it code for 6-"N"-allyloxycarbonyl-lysine.
Another candidate is the AUA codon, which is unusual in that its respective tRNA has to differentiate against AUG that codes for methionine (primordially, isoleucine, hence its location). In order to do this, the AUA tRNA has a special base, lysidine. The deletion of the synthase ("tilS") was possible thanks to the replacement of the native tRNA with that of "Mycoplasma mobile" (no lysidine). The reduced fitness is a first step towards pressuring the strain to loose all instances of AUA, allowing it to be used for genetic code expansion.
Four base codons.
Other approaches include the addition of extra base pairing or the use of orthologous ribosomes that accept in addition to the regular triplet genetic code, tRNAs with quadruple code. This allowed the simultaneous usage of two unnatural amino acids, "p"-azidophenylalanine (pAzF) and N6-[(2-propynyloxy)carbonyl]lysine (CAK), which cross-link with each other by Huisgen cycloaddition.
tRNA/synthetase pair.
Another key element is the tRNA/synthetase pair.
The orthologous set of synthetase and tRNA can be mutated and screened through directed evolution to charge the tRNA with a different, even novel, amino acid. Mutations to the plasmid containing the pair can be introduced by error-prone PCR or through degenerate primers for the synthetase's active site.
Selection involves multiple rounds of a two-step process, where the plasmid is transferred into cells expressing chloramphenicol acetyl transferase with a premature amber codon. In the presence of toxic chloramphenicol and the non-natural amino acid, the surviving cells will have overridden the amber codon using the orthogonal tRNA aminoacylated with either the standard amino acids or the non-natural one. To remove the former, the plasmid is inserted into cells with a barnase gene (toxic) with a premature amber codon but without the non-natural amino acid, removing all the orthogonal synthases that do not specifically recognize the non-natural amino acid.
In addition to the recoding of the tRNA to a different codon, they can be mutated to recognize a four-base codon, allowing additional free coding options.
The non-natural amino acid, as a result, introduces diverse physicochemical and biological properties in order to be used as a tool to explore protein structure and function or to create novel or enhanced protein for practical purposes.
Orthogonal sets in model organisms.
The orthogonal pairs of synthetase and tRNA that work for one organism may not work for another, as the synthetase may mis-aminoacylate endogenous tRNAs or the tRNA be mis-aminoacylated itself by an endogenous synthetase. As a result, the sets created to date differ between organisms.
In 2017 a mouse engineered with an extended genetic code that can produce proteins with unnatural amino acids was reported.
Orthogonal ribosomes.
Similarly to orthogonal tRNAs and aminoacyl tRNA synthetases (aaRSs), orthogonal ribosomes have been engineered to work in parallel to the natural ribosomes. Orthogonal ribosomes ideally use different mRNA transcripts than their natural counterparts and ultimately should draw on a separate pool of tRNA as well. This should alleviate some of the loss of fitness which currently still arises from techniques such as Amber codon suppression. Additionally, orthogonal ribosomes can be mutated and optimized for particular tasks, like the recognition of quadruplet codons. Such an optimization is not possible, or highly disadvantageous for natural ribosomes.
o-Ribosome.
In 2005 three sets of ribosomes were published, which did not recognize natural mRNA, but instead translated a separate pool of orthogonal mRNA (o-mRNA). This was achieved by changing the recognition sequence of the mRNA, the Shine-Dalgarno sequence, and the corresponding recognition sequence in the 16S rRNA of ribosomes, the so-called Anti-Shine-Darlgarno-Sequence. This way the base pairing, which is usually lost if either sequence is mutated, stays available. However the mutations in the 16S rRNA were not limited to the obviously base-pairing nucleotides of the classical Anti-Shine-Darlgarno sequence.
Ribo-X.
In 2007 the group of Jason W. Chin presented an orthogonal ribosome, which was optimized for Amber codon suppression. The 16S rRNA was mutated in such a way that it bound the release factor RF1 less strongly than the natural ribosome does. This ribosome did not eliminate the problem of lowered cell fitness caused by suppressed stop codons in natural proteins. However through the improved specificity it raised the yields of correctly synthesized target protein significantly (from ~20% to >60% percent for one amber codon to be suppressed and form <1% to >20% for two amber codons).
Ribo-Q.
In 2010 the group of Jason W. Chin presented a further optimized version of the orthogonal ribosome. The Ribo-Q is a 16S rRNA optimized to recognize tRNAs, which have quadruplet anti-codons to recognize quadruplet codons, instead of the natural triplet codons. With this approach the number of possible codons rises from 64 to 256. Even accounting for a variety of stop codons, more than 200 different amino acids could potentially be encoded this way.
Ribosome stapling.
The orthogonal ribosomes described above all focus on optimizing the 16S rRNA. Thus far, this optimized 16S rRNA was combined with natural large-subunits to form orthogonal ribosomes. If the 23S rRNA, the main RNA-component of the large ribosomal subunit, is to be optimized as well, it had to be assured, that there was no crosstalk in the assembly of orthogonal and natural ribosomes (see figureX B). To ensure that optimized 23S rRNA would only form into ribosomes with the optimized 16S rRNA, the two rRNAs were combined into one transcript. By inserting the sequence for the 23S rRNA into a loop-region of the 16S rRNA sequence, both subunits still adopt functioning folds. Since the two rRNAs are linked and thus in constant proximity, they preferably bind each other, not other free floating ribosomal subunits.
Engineered peptidyl transferase center.
In 2014 it was shown that by altering the peptidyl transferase center of the 23S rRNA, ribosomes could be created which draw on orthogonal pools of tRNA. The 3’ end of tRNAs is universally conserved to be CCA. The two cytidines base pair with two guanines the 23S rRNA to bind the tRNA to the ribosome. This interaction is required for translational fidelity. However, by co-mutating the binding nucleotides in such a way, that they can still base pair, the translational fidelity can be conserved. The 3’-end of the tRNA is mutated from CCA to CGA, while two cytidine nucleotides in the ribosomes A- and P-sites are mutated to guanidine. This leads to ribosomes which do not accept naturally occurring tRNAs as substrates and to tRNAs, which cannot be used as substrate by natural ribosomes.
To use such tRNAs effectively, they would have to be aminoacylated by specific, orthogonal aaRSs. Most naturally occurring aaRSs recognize the 3’-end of their corresponding tRNA. aaRSs for these 3’-mutated tRNAs are not available yet. Thus far, this system has only been shown to work in an in-vitro translation setting where the aminoacylation of the orthogonal tRNA was achieved using so called “flexizymes”. Flexizymes are ribozymes with tRNA-amino-aclylation activity.
Applications.
With an expanded genetic code, the unnatural amino acid can be genetically directed to any chosen site in the protein of interest. The high efficiency and fidelity of this process allows a better control of the placement of the modification compared to modifying the protein post-translationally, which, in general, will target all amino acids of the same type, such as the thiol group of cysteine and the amino group of lysine. Also, an expanded genetic code allows modifications to be carried out "in vivo".
The ability to site-specifically direct lab-synthesized chemical moieties into proteins allows many types of studies that would otherwise be extremely difficult, such as:
Future.
The expansion of the genetic code is still in its infancy. Current methodology uses only one non-standard amino acid at the time, whereas ideally multiple could be used.
Recoded synthetic genome.
One way to achieve the encoding of multiple unnatural amino acids is by synthesising a rewritten genome. In 2010, at the cost of $40 million an organism, "Mycoplasma laboratorium", was constructed that was controlled by a synthetic, but not recoded, genome. In 2019, "Eschericia coli" Syn61 was created, with a 4 megabase recoded genome consisting of only 61 codons instead of the natural 64.
In addition to the elimination of the usage of rare codons, the specificity of the system needs to be increased as many tRNA recognise several codons
Expanded genetic alphabet.
Another approach is to expand the number of nucleobases to increase the coding capacity.
An unnatural base pair (UBP) is a designed subunit (or nucleobase) of DNA which is created in a laboratory and does not occur in nature. A demonstration of UBPs were achieved "in vitro" by Ichiro Hirao's group at RIKEN institute in Japan. In 2002, they developed an unnatural base pair between 2-amino-8-(2-thienyl)purine (s) and pyridine-2-one (y) that functions "in vitro" in transcription and translation for the site-specific incorporation of non-standard amino acids into proteins. In 2006, they created 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and pyrrole-2-carbaldehyde (Pa) as a third base pair for replication and transcription. Afterward, Ds and 4-[3-(6-aminohexanamido)-1-propynyl]-2-nitropyrrole (Px) was discovered as a high fidelity pair in PCR amplification. In 2013, they applied the Ds-Px pair to DNA aptamer generation by "in vitro" selection (SELEX) and demonstrated the genetic alphabet expansion significantly augment DNA aptamer affinities to target proteins.
In 2012, a group of American scientists led by Floyd Romesberg, a chemical biologist at the Scripps Research Institute in San Diego, California, published that his team designed an unnatural base pair (UBP). The two new artificial nucleotides or "Unnatural Base Pair" (UBP) were named "d5SICS" and "dNaM." More technically, these artificial nucleotides bearing hydrophobic nucleobases, feature two fused aromatic rings that form a (d5SICS–dNaM) complex or base pair in DNA. In 2014 the same team from the Scripps Research Institute reported that they synthesized a stretch of circular DNA known as a plasmid containing natural T-A and C-G base pairs along with the best-performing UBP Romesberg's laboratory had designed, and inserted it into cells of the common bacterium "E. coli" that successfully replicated the unnatural base pairs through multiple generations. This is the first known example of a living organism passing along an expanded genetic code to subsequent generations. This was in part achieved by the addition of a supportive algal gene that expresses a nucleotide triphosphate transporter which efficiently imports the triphosphates of both d5SICSTP and dNaMTP into "E. coli" bacteria. Then, the natural bacterial replication pathways use them to accurately replicate the plasmid containing d5SICS–dNaM.
The successful incorporation of a third base pair into a living micro-organism is a significant breakthrough toward the goal of greatly expanding the number of amino acids which can be encoded by DNA, thereby expanding the potential for living organisms to produce novel proteins. The artificial strings of DNA do not encode for anything yet, but scientists speculate they could be designed to manufacture new proteins which could have industrial or pharmaceutical uses.
In May 2014, researchers announced that they had successfully introduced two new artificial nucleotides into bacterial DNA, and by including individual artificial nucleotides in the culture media, were able to passage the bacteria 24 times; they did not create mRNA or proteins able to use the artificial nucleotides.
Related methods.
Selective pressure incorporation (SPI) method for production of alloproteins.
There have been many studies that have produced protein with non-standard amino acids, but they do not alter the genetic code. These protein, called alloprotein, are made by incubating cells with an unnatural amino acid in the absence of a similar coded amino acid in order for the former to be incorporated into protein in place of the latter, for example -2-aminohexanoic acid (Ahx) for methionine (Met).
These studies rely on the natural promiscuous activity of the aminoacyl tRNA synthetase to add to its target tRNA an unnatural amino acid (i.e. analog) similar to the natural substrate, for example methionyl-tRNA synthase's mistaking isoleucine for methionine. In protein crystallography, for example, the addition of selenomethionine to the media of a culture of a methionine-auxotrophic strain results in proteins containing selenomethionine as opposed to methionine ("viz." Multi-wavelength anomalous dispersion for reason). Another example is that photoleucine and photomethionine are added instead of leucine and methionine to cross-label protein.
Similarly, some tellurium-tolerant fungi can incorporate tellurocysteine and telluromethionine into their protein instead of cysteine and methionine.
The objective of expanding the genetic code is more radical as it does not replace an amino acid, but it adds one or more to the code. On the other hand, proteome-wide replacements are most efficiently performed by global amino acid substitutions. For example, global proteome-wide substitutions of natural amino acids with fluorinated analogs have been attempted in "E. coli" and "B. subtilis". A complete tryptophan substitution with thienopyrrole-alanine in response to 20899 UGG codons in "E. coli" was reported in 2015 by Budisa and Söll. Moreover, many biological phenomena, such as protein folding and stability, are based on synergistic effects at many positions in the protein sequence.
In this context, the SPI method generates recombinant protein variants or alloproteins directly by substitution of natural amino acids with unnatural counterparts. An amino acid auxotrophic expression host is supplemented with an amino acid analog during target protein expression. This approach avoids the pitfalls of suppression-based methods and it is superior to it in terms of efficiency, reproducibility and an extremely simple experimental setup. Numerous studies demonstrated how global substitution of canonical amino acids with various isosteric analogs caused minimal structural perturbations but dramatic changes in thermodynamic, folding, aggregation spectral properties and enzymatic activity.
"in vitro" synthesis.
The genetic code expansion described above is "in vivo". An alternative is the change of coding "in vitro" translation experiments. This requires the depletion of all tRNAs and the selective reintroduction of certain aminoacylated-tRNAs, some chemically aminoacylated.
Chemical synthesis.
There are several techniques to produce peptides chemically, generally it is by solid-phase protection chemistry. This means that any (protected) amino acid can be added into the nascent sequence.
In November 2017, a team from the Scripps Research Institute reported having constructed a semi-synthetic "E. coli" bacteria genome using six different nucleic acids (versus four found in nature). The two extra 'letters' form a third, unnatural base pair. The resulting organisms were able to thrive and synthesize proteins using "unnatural amino acids". The unnatural base pair used is dNaM–dTPT3. This unnatural base pair has been demonstrated previously, but this is the first report of transcription and translation of proteins using an unnatural base pair.


Maxygen

Maxygen Inc. was a biopharmaceutical company focused on developing improved versions of protein drugs using DNA shuffling and other protein modification technologies. The company was headquartered in Redwood City, CA. It dissolved in 2013. The Maxygen legacy was revived in 2018 with a focus on Directed Evolution of Proteins using Molecular Breeding. Maxygen LLC is currently headquartered in Sunnyvale, CA.
Clinical Programs.
Maxygen Inc's clinical programs included a novel G-CSF for the treatment of chemotherapy-induced neutropenia, which entered clinical trials in 2006. Maxygen also had a preclinical program, MAXY-4, to develop a novel CTLA4-Ig therapeutic for the treatment of rheumatoid arthritis and other autoimmune diseases.
Technologies.
Maxygen Inc. was established to commercially exploit its proprietary recombination-based technologies for creating genetic diversity, known as its Molecular Breeding directed evolution platform. These technologies allow the generation of millions of variant genes and proteins, which then can be screened to identify those with potential commercial interest. This laboratory process mimics the powerful natural process of evolution. The success of Maxygen's technology was documented in numerous scientific publications and patents.
Other protein engineering and protein modification technologies used by Maxygen include mutagenesis, rational design, PEGylation, glycosylation, and de-immunization.
History.
Maxygen was founded in 1997 by Dr. Alejandro Zaffaroni, a San Francisco Bay Area scientist and entrepreneur, and three co-founders: Dr. Willem P.C. Stemmer, Dr. Russell Howard and Isaac Stein. Dr. Zaffaroni has founded multiple companies including ALZA Corporation, DNAX Research Institute, Affymax, Affymetrix, Symyx Technologies, and Alexza.
Maxygen Inc. has demonstrated that the MolecularBreeding directed evolution platform has commercial potential in a number of areas, including agriculture, veterinary medicine, enzyme/chemical processes, and human therapeutics. To accelerate its development of improved biopharmaceuticals, Maxygen acquired the Danish company Profound Pharma A/S in 2000, created by Christian Karsten Hansen and Jan Møller Mikkelsen in 1999. To facilitate the commercial development of products made with its technologies, in 2002 Maxygen established Codexis to focus on enzyme/chemical applications and MaxyAg to focus on agricultural applications. MaxyAg was later renamed Verdia Inc., and Verdia was sold to DuPont in 2004 for $64 million. In addition, Maxygen established Avidia in 2003 to develop protein subunits as commercial products, including therapeutics. Avidia was purchased by Amgen in 2006 for $290 million.
In 2008, the company sold its MAXY-VII candidate drug, a recombinant form of clotting factor VIIa, to Bayer HealthCare.
2009 saw the formation of a joint venture between Maxygen and Astellas called Perseid Therapeutics, in which Maxygen retained majority ownership. The intention was to work through Perseid to exploit most of Maxygen's proprietary technology and intellectual property. By 2011, Astellas exercised an option to fully acquire Perseid and with it the sole candidate drug in its portfolio, MAXY-4 (which became ASP2408 under Astellas), a CTLA-4-immunoglobulin fusion protein therapeutic, which was positioned to be a direct competitor to Orencia, marketed by Bristol-Myers Squibb.
It was reported in June 2013 that the company's board of directors had chosen to "liquidate and dissolve the struggling protein pharmaceuticals developer", which led to the exit of the company's CEO/CFO James Sulat by the end of June 2013. The company's intention at the time was to seek a buyer for its MAXY-G34 candidate drug, a pegylated, granulocyte colony stimulating factor. Maxygen filed a certificate of dissolution on August 29, 2013. The company has ceased all operations.
Corporate governance.
Chief Scientific Officer - Robert Whalen<br>Director of Molecular Biology - James English
Tassos Gianakakos is a former Director of Business Development for Maxygen.


Labile cell

In cellular biology, labile cells are cells that multiply constantly throughout life. The cells are alive for only a short period of time. Due to this, they can end up reproducing new stem cells and replace functional cells. Especially if the cells become injured through a process called necrosis, or even if the cells go through apoptosis. The way these cells regenerate and replace themselves is quite unique. While going through cell division, one of the two daughter cells actually becomes a new stem cell. This occurs so then that daughter cell can end up restoring the population of the stem cells that were lost. The other daughter cell separates itself into a functional cell in order to replace the lost, or injured cells during this process. Labile cells are one type of the cells that are involved in the division of cells. The other two types that are involved include stable cells and permanent cells.
Each of these type of cells respond to injuries of the cells they occupy differently. Cell types that are thought to be cells that are constantly dividing include skin cells, cells in the gastrointestinal tract, and blood cells in the bone marrow. Acting as stem cells for these cell types.
In labile cells, it is not a speed-up in the segments of the cell cycle (i.e. G1 phase, S phase, G2 phase and M phase), but rather a short or absent G0 phase that is responsible for the cells' constant division.
Hazards.
Constantly dividing cells have a higher risk of becoming malignant and develop cancer, dividing uncontrollably. This is why muscle cancer is very rare, even though muscle tissue accounts for ~50% of total body weight, since muscle cells are not constantly dividing cells, and therefore not considered labile.
In addition, cytotoxic drugs, such as alkylating antineoplastic agents, used in treatment of cancer, work by inhibiting the proliferation of dividing cells, with the malignant cells as the desired target. However, this has the adverse effect of also striking against the cells normally dividing in the body, and thus impairing normal body function of hair, skin, GI tract and bone marrow.


Ronald W. Davis

Ronald Wayne "Ron" Davis (born July 17, 1941) is Professor of Biochemistry & Genetics, and Director of the Stanford Genome Technology Center at Stanford University. Davis is a researcher in biotechnology and molecular genetics, particularly active in human and yeast genomics and the development of new technologies in genomics, with over 30 biotechnology patents. In 2013, it was said of Davis that "A substantial number of the major genetic advances of the past 20 years can be traced back to Davis in some way."
Scientific career.
After completing his PhD at Caltech and a postdoctoral fellowship at Harvard University working with Jim Watson, Davis joined the faculty of Stanford's Department of Biochemistry in 1972. He became an Associate Professor in 1980, full Professor in 1980, and joined the Department of Genetics as a professor in 1990. He became director of the Stanford Genome Technology Center in 1994. He was elected a member of the National Academy of Sciences in 1983.
Davis developed the R-loop technique of electron microscopy for mapping coding RNAs which led to the discovery of RNA splicing. With Janet E. Mertz, Davis was the first to demonstrate the use of restriction endonucleases for joining DNA fragments. Davis collaborated in the development of the first DNA microarray for gene expression profiling with Patrick O. Brown, and the gene expression profile of the first complete eukaryotic genome ("Saccharomyces cerevisiae"). Davis, with David Botstein, Mark Skolnick, and Ray White developed the method for constructing a genetic linkage map using restriction fragment length polymorphisms that enabled and led to the Human Genome Project.
He and his colleagues submitted a proposal to NIH to map the human genome in 1979; that proposal was turned down as being too ambitious. The Stanford Genome Technology Center was included in the Human Genome Project that began in 1990 and was completed in 2003.
Recognition and awards.
In 2013 Davis was named, alongside Elon Musk and Jeff Bezos, as one of today’s nine greatest innovators by "The Atlantic": "A substantial number of the major genetic advances of the past 20 years can be traced back to Davis in some way."
He has won recognition for his contributions to genetic research from many groups, as early as 1976 and as recently as 2015, from one of his alumni colleges and from the National Academy of Sciences. Starting from his most recent award, here are awards and recognition Davis has received for his achievements in and contributions to science. In 2015, he received the Precision Medicine World Conference Luminary Award for his development of “R-loop Technique of Electron Microscopy”. In 2013, he received the Warren Alpert Foundation Prize.
He received the Gruber Prize in Genetics in 2011, which noted among other achievements, two landmark papers, one in 1977 concerning genome editing and another in 1980 which "helped launch the field of genomics." In 2007, California Institute of Technology gave him its Distinguished Alumni Award. In 2005, Davis received the Dickson Prize in Medicine. In 2004, he received the Lifetime Achievement Award from the Genetics Society of America. The National Academy of Sciences (NAS) gave him the 1982 NAS Award in Molecular Biology. In 1976, he received the Eli Lilly Award in Microbiology and Immunology.
Open Medicine Foundation.
Dr. Davis is the director of the Scientific Advisory Board at the Open Medicine Foundation, a non-profit 501(c)(3) organization
(EIN# 26-4712664), whose goal is to fund and initiate research into chronic complex diseases. Presently the foundation is invested in The End ME/CFS Project, which aims to fast-track research for a cure for myalgic encephalomyelitis / chronic fatigue syndrome (ME/CFS).
In April 2019, a notable result was reported; a test of blood without red cells (white cells in plasma), identified ME/CFS patients from healthy people with 100% accuracy in a small sample, 20 patients and 20 healthy people. The test used a biotechnological device designed by Davis and his team, which is called the "nanoneedle".
“The small device that Davis and his colleagues created was originally developed to detect changes in electrical signals when cancer cells were exposed to different treatments.”, as described in Stat News. it was used to test cells of ME/CFS patients, and in their first hypothesis, found it to be useful in distinguishing patients from healthy people. People with this disease are described as not using energy well and taking a long time to recover from energy expenditure; “the researchers decided to mimic this by stressing cells from 20 healthy controls and 20 ME/CFS patients by exposing them to increased levels of salt.” Rahim Esfandyarpour, lead author of the paper, said “When they [cells from ME/CFS patients] face this new environment, their reaction is different than the reaction of healthy cells.”
Family.
Davis married Janet Dafoe in July 1969. Their son, Whitney Dafoe was born in 1983, followed by their daughter Ashley Davis. Whitney Dafoe became ill with severe ME/CFS around 2009, declining from active and healthy in his career as a photographer to housebound, and by 2015 bed bound from this disease, unable to tolerate sounds and light, unable to do much at all, and eventually unable to eat, drink or speak. As his endurance decreased, Dafoe moved back home in May 2011. His mother cut her work as a clinical psychologist to five hours a week to spend full time on his daily care as he continued declining in function, while Davis continues his research career and helps with his son’s daily care. Dafoe’s need for treatment is the motivation for Davis to direct his medical and scientific research efforts toward this disease; he dropped all other projects in hand before his son became so ill.


Hassan Naim

Hassan Naim is a Lebanese-Swiss biochemist. He currently holds the position of Director of the "Institut für Physiologische Chemie" (Institute for Physiological Chemistry/Biochemistry) at the University of Veterinary Medicine Hanover, while collaborating regularly with the University of Hannover.
Scientific career.
Hassan Naim received his Ph.D. degree in Biochemistry from the University of Bern, Switzerland. Following appointments at the Biochemistry Department, University of Lausanne (membrane transport in T cells) and the University Children’s Hospital Bern (structure and function of brush border membrane proteins) he moved in 1989 to the Biochemistry Department, University of Texas Southwestern Medical Center at Dallas, USA to continue his work on structure-function relationships of brush border proteins. In 1991 he was recruited as a group leader and Faculty member at the University of Düsseldorf, Germany. In 1997 he was appointed as a Professor and Chair of the Department of Biochemistry at the University of Veterinary Medicine in Hannover, Germany.
Current Research Interests.
Current research interests in the Naim laboratory focus on the molecular mechanisms underlying protein trafficking, particularly polarized protein sorting in epithelial cells, in health and disease.
Publications.
Some of Naim's recent publications include (but are not limited to):


Marinobacter maritimus

Marinobacter maritimus is a Gram-negative, psychrotolerant and motile bacterium from the genus of Marinobacter which has been isolated from sea water near the Kerguelen islands.


Colwellia

Colwellia is a genus of deep-sea psychrophilic, piezophilic, and facultative anaerobic bacteria from the family Colwelliaceae. "Colwellia" grows at a temperature at −20 °C by producing cryoprotective polymeric substances.


Luz Oliveros-Belardo

Luz Oliveros-Belardo (3 November 1906 – 12 December 1999) was a Filipina pharmaceutical chemist, honored with the National Scientist of the Philippines award by the Philippine government in 1987.
Early life.
Luz Oliveros was born in Navotas, Rizal, the daughter of Aurelio Oliveros and Elisa Belarmino. She held undergraduate and master's degrees in chemistry from the University of the Philippines in Manila. In 1957 she earned a PhD in pharmaceutical chemistry at the University of Connecticut, with a dissertation involving molecular refraction in terpenes.
Career.
Luz Oliveros-Belardo was director of the Natural Sciences Research Center at the Philippine Women's University. She became Dean of the College of Pharmacy in 1947. Her research focused on extracting essential oils and other chemicals from native Philippine plants for pharmaceuticals, food production, scents, and other applications. For example, she developed an experimental formulation based on apitong ("Dipterocarpus grandiflorus") oleoresin that was suitable for motor fuel.
In 1965-1966, she was named an AAUW fellow by the American Association of University Women to pursue her research at Stanford University. In 1974, the Philippine Association of University Women recognized her with their Achievement Award in Natural Science. She received the National Scientist Award in 1987.
Dr. Luz Oliveros-Belardo extracted 33 new Philippine essential oils from native plants and studied their chemical and physical properties. Her first research was on the chemical and pharmacological properties of Tanglad Tagalog ("Cymbopogon ciratus") and found that its chemicals, such as potassium citrate that is an effective diuretic compound capable of resisting increased blood pressure. She was one of the first Southeast Asians that conducted studies on Chichirica ("Vinca rosea") leaves and found that it is rich in alkaloids, glycosides, terpenoids, sterols, fatty acids, and volatile oil.
Personal life.
Luz Oliveros married a dentist, Ricardo A. Belardo. They had two daughters. She died in 1999, aged 93 years. Her remains were buried at Libingan ng mga Bayani in Fort Bonifacio, Taguig.