Category Archives: Genome

Every week, we update this list with new meetings, awards, scholarships and events to help you advance your career.If youd like us to feature something that youre offering to the bioscience community, email us with the subject line For calendar. ASBMB members offerings take priority, and we do not promote products/services. Learn how to advertise in ASBMB Today.

This in-person meeting will be held Sept. 29 through Oct. 2 in Snowbird, Utah. Sessionswill cover recent advances and new technologies in RNA polymerase II regulation, including the contributions of non-coding RNAs, enhancers and promoters, chromatin structure and post-translational modifications, molecular condensates, and other factors that regulate gene expression. Patrick Cramer of the Max Planck Institute will present the keynote address on the structure and function of transcription regulatory complexes. The deadline for abstracts for talks is now July 21. The early registration deadline ($50 in savings) is Aug. 1. The deadline for poster presentation abstracts is Aug. 18. The regular registration deadline is Aug. 28.Learn more.

The American Society for Investigative Pathology, American Society for Matrix Biology and the histochemical Society have teamed up for a series of webinars about science careers. The next one will be at noon Eastern on July 27 titled "Career Options in Science Industry vs. Academia." It will have four panelists from Genentech, FENIX Group, GE Healthcare and the University of Saskatchewan. Learn more and register.

The National Institutes of Health Office of Research on Women's Health has a free quarterly lecture series titled "Diverse Voices: Intersectionality and the Health of Women." The July 28 event will include presentations from Heather Shattuck-Heidorn of the University of Southern Maine and Stephaun Wallace of the Fred Hutchinson Cancer Research Center. Register.

Most meetings on epigenetics and chromatin focus on transcription, while most meetings on genome integrity include little attention to epigenetics and chromatin. This conference in Seattle will bridge this gap to link researchers who are interested in epigenetic regulations and chromatin with those who are interested in genome integrity. The oral and poster abstract deadline and early registration deadline is Aug. 2. The regular registration deadline is Aug. 29.Learn more.

This five-day conference will be held Aug. 1418 in person in Cambridge, Massachusetts, and online. It will be an international forum for discussion of the remarkable advances in cell and human protein biology revealed by ever-more-innovative and powerful mass spectrometric technologies. The conference will juxtapose sessions about methodological advances with sessions about the roles those advances play in solving problems and seizing opportunities to understand the composition, dynamics and function of cellular machinery in numerous biological contexts. In addition to celebrating these successes, the organizers also intend to articulate urgent, unmet needs and unsolved problems that will drive the field in the future. The registration deadline was July 1, but you have until July 12 to register to participate virtually.Learn more.

For Discover BMB, the ASBMB's annual meeting in March in Seattle, we're seeking two types of proposals:

The American Physiological Society is hosting a free webinar that will cover polycystic ovary syndrome, an endocrine disorder associated with modestly elevated androgens, and hormone therapy for transmen, which elevates androgens greatly to achieve levels similar to those in cisgender men. The event announcement says: "The role that these two different concentrations play in cardiovascular physiology and pathophysiology remains unclear. Gaps and opportunities in basic research and clinical practice will be highlighted." The speaker will be Licy Yanes Cardozo, a physician-scientist at the University of Mississippi Medical Center. Learn more and register.

In May, the Howard Hughes Medical Institute launched a roughly $1.5 billion program to "help build a scientific workforce that more fully reflects our increasingly diverse country." The Freeman Hrabowski Scholars Program will fund 30 scholars every other year, and each appointment can last up to 10 years. That represents up to $8.6 million in total support per scholar. HHMI is accepting applications from researchers "who are strongly committed to advancing diversity, equity, and inclusion in science." Learn more.

Save the date for the ASBMB Career Expo. This virtual event aims to highlight the diversity of career choices available to modern biomedical researchers. No matter your career stage, this expo will provide a plethora of career options for you to explore while simultaneously connecting you with knowledgeable professionals in these careers. Each 60-minute session will focus on a different career path and will feature breakout rooms with professionals in those paths. Attendees can choose to meet in a small group with a single professional for the entire session or move freely between breakout rooms to sample advice from multiple professionals. Sessions will feature the following five sectors: industry, government, science communication, science policy and other. The expo will be held from 11 a.m. to 5 p.m. Eastern on Nov. 2. Stay tuned for a link to register!

The Journal of Science Policy & Governanceand the National Science Policy Network issued a call for papersfor an issue containingpolicy ideas from the next generation of scientists. The submission deadline is Nov. 6. Theyencourage submissions "that highlight policy opportunities and audiences related to the 2022 U.S. midterm elections at the local, stateor national level as well as related foreign policy issues."Read the press release.

The ASBMB provides members with a virtual platform to share scientific research and accomplishments and to discuss emerging topics and technologies with the BMB community.

The ASBMB will manage the technical aspects, market the event to tens of thousands of contacts and present the digital event live to a remote audience. Additional tools such as polling, Q&A, breakout rooms and post event Twitter chats may be used to facilitate maximum engagement.

Seminars are typically one to two hours long. A workshop or conference might be longer and even span several days.

Prospective organizers may submit proposals at any time. Decisions are usually made within four to six weeks.

Propose an event.

If you are a graduate student, postdoc or early-career investigator interested in hosting a #LipidTakeover, fill out this application. You can spend a day tweeting from the Journal of Lipid Research's account (@JLipidRes) about your favorite lipids and your work.

The International Union of Biochemistry and Molecular Biology is offering $500 to graduate students and postdocs displaced from their labs as a result of natural disaster, war or "other events beyond their control that interrupt their training." The money is for travel and settling in. Learn more and spread the word to those who could use assistance.

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Calendar of events, awards and opportunities - ASBMB Today

Engineering | Health and medicine | Science | UW News blog

July 15, 2022

Another beautiful day on the University of Washingtons Seattle campus.University of Washington

Seven professors at the University of Washington are among 25 new members of the Washington State Academy of Sciences, according to a July 15 announcement. Joining the academy is a recognition of their outstanding record of scientific and technical achievement, and their willingness to work on behalf of the Academy to bring the best available science to bear on issues within the State of Washington.

Twenty of the incoming members for 2022 were selected by current WSAS members, while the other five were chosen by virtue of recently joining one of the National Academies.

UW faculty selected by current Academy members are:

In addition, Dr. Jay Shendure, UW professor of genome sciences, investigator with the Howard Hughes Medical Institute and faculty member in the Molecular Engineering & Sciences Institute, was selected by virtue of his election to the National Academy of Sciences for pioneering a variety of genome sequencing and analysis methods, including exome sequencing and its earliest applications to gene discovery for Mendelian disorders and autism; cell-free DNA diagnostics for cancer and reproductive medicine; massively parallel reporter assays; saturation genome editing; whole organism lineage tracing; and massively parallel molecular profiling of single cells.

New members to the Washington State Academy of Sciences will be formally inducted in September.

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Seven UW faculty members elected to the Washington State Academy of Sciences - University of Washington

A recent study led by the University of Wisconsin Madison has found that some species of copepods such as Eurytemora affinis tiny crustaceans measuring about a millimeter in length and roaming coastal waters of oceans and estuaries around the world in massive numbers can evolve fast enough to survive in the face of rapid climate change.

This is a dominant coastal species, serving as very abundant and highly nutritious fish food, said study senior author Carol Eunmi Lee, a professor of Integrative Biology at UW Madison. But theyre vulnerable to climate change.

Since ocean salinity is dropping rapidly as ice melts and precipitation patterns change, this saltwater species that evolved over the ages in waters high in salinity, now needs to adapt to much fresher water in their environment.

In order to study how copepods respond to drops in salinity, the scientists kept a population of Eurytemora affinisfrom the Baltic Sea in their laboratory and observed them over a few generations. After splitting the copepods into 14 groups of a few thousands each, they placed four of these groups in environments similar to the Baltic, while exposing the other ten groups to declining salinity levels that simulated the type of pressure caused by climate change. For a total of ten generations, these groups had their water gradually reduced to lower salinity levels.

To track evolutionary changes across the genomes of the tiny crustaceans, the researchers sequenced the genome of each line of copepods at the beginning of the experiment, as well as after six and ten generations.

The analysis revealed that the strongest signals of natural selection where changes were largest and more frequent across the groups exposed to low salinity levels were in areas of the genome that are important in regulating ions, such as sodium transporters.

In saltwater, there are a lot of ions, like sodium, that are essential for survival. But when you get to freshwater, these ions are precious, Professor Lee explained. So, the copepods need to suck them up from the environment and hang on to them, and the ability to do that relies on these ion transporters that we found undergoing natural selection.

At the end of the experiment, the copepods with certain genetic combinations of the ion transporter were more likely to survive, even as the salinity of their water decreased. According to the researchers, the gene variants found in the copepods that managed to survive the salinity decline in the laboratory are also common among copepods living in the fresher regions of the Baltic Sea.

This copepod gives us an idea of what it takes, an idea of what conditions are needed, that enable a population to evolve rapidly in response to climate change. It also shows how important evolution is for understanding our changing planet and how or even whether populations and ecosystems will survive, Professor Lee concluded.

The study is published in the journal Nature Communications.

By Andrei Ionescu, Earth.com Staff Writer

Continued here:
Tiny crustaceans have what it takes to survive climate change - Earth.com

We have long been baffled as to why men live around five years less than women, on average. But now a new study suggests that, beyond the age of 60, the main culprit is a genetic defect: the loss of the Y chromosome, which determines sex at birth.

Its clear that men are more fragile, the question is why, explains Lars Forsberg, a researcher at Uppsala University in Sweden.

For decades it was thought that the male Y chromosomes only function was to generate sperm that determine the sex of a newborn. A boy carries one X chromosome from the mother and one Y from the father, while a girl carries two Xs, one from each parent.

In 1963, a team of scientists discovered that as men age, their blood cells lose the Y chromosome due to a copying error that happens when the mother cell divides to produce a daughter cell. In 2014, Forsberg analyzed the life expectancy of older men based on whether their blood cells had lost the Y chromosome, a mutation called mLOY. The effect recorded was mindblowing, the researcher recalls.

Men with fewer Y chromosomes had a higher risk of cancer and lived five and a half years less than those who retained this part of the genome. Three years later, Forsberg discovered that this mutation makes getting Alzheimers three times as likely. What is most worrying is the enormous prevalence of this defect. Twenty percent of men over the age of 60 have the mutation. The rate rises to 40% in those over 70 and 57% in those over 90, according to Forsbergs previous studies. It is undoubtedly the most common mutation in humans, he says.

Until now, nobody knew whether the gradual disappearance of the Y chromosome in the blood played a pivotal role in diseases associated with aging. In a study just published in the journal Science, Forsberg and scientists from Japan and the US demonstrate for the first time that this mutation increases the risk of heart problems, immune system failure and premature death.

The researchers have created the first animal model without a Y chromosome in their blood stem cells: namely, mice modified with the gene-editing tool CRISPR. The study showed that these rodents develop scarring of the heart in the form of fibrosis, one of the most common cardiovascular ailments in humans, and die earlier than normal mice. The authors then analyzed the life expectancy recorded in nearly 15,700 patients with cardiovascular disease whose data are stored in the UK public biobank. The analysis shows that loss of the Y chromosome in the blood is associated with a 30% increased risk of dying from cardiovascular disease.

This genetic factor can explain more than 75% of the difference in life expectancy between men and women over the age of 60, explains biochemist Kenneth Walsh, a researcher at the University of Virginia in the US and co-author of the study. In other words, this mutation would explain four of the five years lower life expectancy in men. Walshs estimate links to a previous study in which men with a high mLOY load live about four years less than those without it.

It is well known that men die earlier than women because they smoke and drink more and are more prone to recklessness. But, beyond the age of 60, genetics becomes the main culprit in the deterioration of their health: It seems as if men age earlier than women, Walsh points out.

The study reveals the molecular keys to the damage associated with the mLOY mutation. Within the large group of blood cells can be found the immune systems white blood cells responsible for defending the body against viruses and other pathogens. The loss of the Y chromosome triggers aberrant behavior in macrophages, a type of white blood cell, causing them to scar heart tissue, which in turn increases the risk of heart failure. Researchers have shown that the damage can be reversed if they give mice pirfenidone, a drug approved to treat humans with idiopathic pulmonary fibrosis, a condition in which the lungs become scarred and breathing becomes increasingly difficult.

There are three factors that increase the risk of Y chromosome loss. The first is the inevitable ageing process. The longer one lives, the more cell divisions occur in the body and the greater the likelihood of mutations occurring in the genome copying process. The second is smoking. Smoking causes you to lose the Y chromosome in your blood at an accelerated rate; if you stop smoking, healthy cells once again become the majority, says Walsh. But the third is also inevitable: other inherited genetic mutations can increase the gradual loss of the Y chromosome in the blood by a factor of five, explains Forsberg.

Both Forsberg and Walsh believe that this study opens up an enormous field of research. Still to be studied is whether men with this mutation also have cardiac fibrosis and whether this is behind their heart attacks and other cardiac ailments. We also need to better understand why losing the Y chromosome damages health. For now, we have shown that the Y chromosome is not just there for reproduction, but is is also important for our health, says Forsberg. The next step is to identify which genes are responsible for the phenomenon.

The loss of this chromosome has been detected in all organs and tissues of the body and at all ages, although it is more evident after 60. It is abundant in the blood because this is a tissue that produces millions of new cells every day from blood stem cells. Healthy stem cells produce healthy daughter cells and mutated ones produce daughter cells with mLOY.

A previous study showed that this mutation of the Y chromosome disrupts the function of up to 500 genes located elsewhere in the genome. It has also been shown to damage lymphocytes and natural killer cells, evident in men with prostate cancer and Alzheimers disease, respectively.

There are hardly any tests for mLOY at present. But Forsberg and his colleagues have designed a PCR test that measures the level of this mutation in the blood and could serve to determine which levels of this mutation are harmful to health. Right now, we see people in their 80s with 80% of their blood cells mutated, but we dont know what impact this has on their health, says Walsh.

Another unanswered question is why men lose the genetic mark of the male with age. The evolutionary logic, argue the authors of the paper, is that men are biologically designed to have offspring as soon as possible and to live 40 to 50 years at most. The spectacular increase in life expectancy in the last century has meant that men and women live to an advanced age 80 and 86 years in Spain, respectively which makes the effect of these mutations more evident. Another fact which possibly has some bearing on the issue: the vast majority of people who reach 100 are women.

To transform all these discoveries into treatments, we first need to better understand this phenomenon, says Forsberg. We men are not designed to live forever, but perhaps we can increase our life expectancy by a few more years.

Biochemist Jos Javier Fuster, who studies pathological mutations in blood cells at the National Center for Cardiovascular Research, stresses the importance of the work. Until now it was not clear whether the loss of Y was the cause of cancer, Alzheimers disease and heart failure, he explains. This is the first demonstration in animals that it has a causal role. The human Y chromosome is different from the mouse chromosome, so the priority now is to accumulate more data in humans. This is a great first step in understanding this new mechanism behind aging-linked diseases, he adds.

The cells of the human body group their DNA into 23 pairs of chromosomes that pair up one by one when a cell copies its genome to generate a daughter cell. The Y is the only one that does not have a symmetrical partner to pair up with: instead, it does so with an X chromosome; and the entire Y chromosome is often lost, explains Luis Alberto Prez Jurado from Pompeu Fabra University in Barcelona. For now, six genes have been identified within the Y chromosome that would be responsible for an impact on health, he says. All of them are related to the proper functioning of the immune system. In part, this would also explain the greater vulnerability of males to viral infections, including Covid-19.

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mLOY: The genetic defect that explains why men have shorter lives than woman - EL PAS USA

When Josefin Stiller was growing up in Berlin, she loved reading about Greek gods in an encyclopedia of mythology. She often lost track of their relationships, howevertheir feuds, trysts, and betrayalsas she flipped among the entries. Frustrated, she wrote each name on a card and started to arrange children beneath parents on a desk in her bedroom. As lineages became clear, so did family dramas. Sons killed fathers; uncles kidnapped nieces; siblings fell in love. I wonder if this experience of reconstructing a family tree primed me to appreciate trees and the powerful insights they hold, Stiller told me in a recent e-mail.

Years later, as a graduate student in biology, Stiller worked on an evolutionary tree for seahorses and their relatives, using DNA to understand the ancestry of different species. Then, in 2017, she moved to the University of Copenhagen and joined B10K, a scientific collaboration that aims to sequence the genome of every bird speciesmore than ten thousand in alland to reveal their connections in a comprehensive tree. The amount of data and computing power required for this mission is almost unfathomable, but the final product should be as simple in principle as the diagram Stiller had assembled as a child. Everything in biology has a history, and we can show this history as a bifurcating tree, she said.

Birds are the most diverse vertebrates on land, and they have always been central to ideas about the natural world. In 1837, a taxonomist in London told Charles Darwin that the finches he had shot and carelessly lumped together in the Galpagos Islands were, in fact, many different species. Darwin wondered whether the finches might have shared a common ancestor from mainland South Americawhether all of life might have evolved through a process of descent with modificationand he drew a rudimentary tree in his private notebook, beneath the words I think. The tree showed how a single ancestral population could branch into many species, each with its own evolutionary path. On the Origin of Species, published twenty-two years later, includes only one diagram: an evolutionary tree. The tree of life became for biology what the periodic table was for chemistryboth a foundation and an emblem for the field. Thetime will come I believe, though I shall not live to see it, when we shall have fairly true genealogical treesofeach great kingdomofnature, Darwin wrote to a friend.

The rise of genome sequencing, at the turn of the twenty-first century, seemed to bring Darwins dream within reach. It is now realistic to conceive of reconstructing the entire Tree of Lifeeventually to include all of the living and extinct species, Joel Cracraft, the curator of birds at the American Museum of Natural History, wrote, in 2004. The naturalist E. O. Wilson predicted that such a tree could unify biology. Its value to such fields as agriculture, conservation, and medicine would be incalculable; evolutionary trees have already deepened our understanding of SARS-CoV-2, the virus that causes COVID-19. By mapping a major branch on the tree of life, B10K aims to light the way.

When Stiller joined the project, her colleagues were combing through museums and laboratories to sample three hundred and sixty-three bird species, chosen carefully to represent the diversity of living birds. With help from four supercomputers in three different countries, they began to compare each birds DNA to figure out how they were related. I think there was always this idea that, once we sequence full genomes, we will be able to solve it, Stiller told me. But, early in the process, she encountered an evolutionary enigma called Opisthocomus hoazin. I was completely amazed by this bird, she said.

Hoatzins, which live along oxbow lakes in tropical South America, have blood-red eyes, blue cheeks, and crests of spiky auburn feathers. Their chicks have primitive claws on their tiny wings and respond to danger by plunging into water and then clawing their way back to their nestsa trait that inspired some ornithologists to link them to dinosaurs. Other taxonomists argued that the hoatzin is closely related to pheasants, cuckoos, pigeons, and a group of African birds called turacos. Alejandro Grajal, the director of Seattles Woodland Park Zoo, said that the bird looks like a punk-rock chicken, and smells like manure because it digests leaves through bacterial fermentation, similar to a cow.

DNA research has not solved the mysteries of the hoatzin; it has deepened them. One 2014 analysis suggested that the birds closest living relatives are cranes and shorebirds such as gulls and plovers. Another, in 2020, concluded that this clumsy flier is a sister species to a group that includes tiny, hovering hummingbirds and high-speed swifts. Frankly, there is no one in the world who knows what hoatzins are, Cracraft, who is now a member of B10K, said. The hoatzin may be more than a missing piece of the evolutionary puzzle. It may be a sphinx with a riddle that many biologists are reluctant to consider: What if the pattern of evolution is not actually a tree?

Fossils that resemble hoatzins have been found in Europe and Africa, but today the birds can be found only in the river basins of the Amazon and Orinoco of South America. I live in Germany, so I visited them in Berlins Museum of Natural History, where cabinets are filled with thousands of stuffed birds. Sylke Frahnert, the bird curator, kept two taxidermy hoatzins on a shelf near the cuckoos and turacos, which seems as good a place as any. Over the years, there have been so many conflicting trees of birds, she told me. You would have been crazy to change the collection with every one. One of the museums hoatzins was shot in Brazil more than two centuries ago, and the years have drained the color from its face. I had heard that even the specimens smell like manure, but Frahnert warned me not to sniff them, since birds were once preserved with arsenic.

In the eighteenth century, natural-history museums started using anatomical similarities to classify plants and animals into increasingly specific categories: class, order, family, genus, species. Darwin realized that species share traits because their ancestors were one and the same. Fish, amphibians, reptiles, birds, and mammals all have spines, but not because God had given them to each creature separately; rather, the spine suggested a common parent living long ago. The construction of evolutionary trees was dubbed phylogeny, literally meaning the generation of species, by the zoologist Ernst Haeckel. The more traits two species shared, the theory went, the more recently they had shared a common ancestor. Human beings and other great apes evolved from a common ancestor millions of years ago, but even human beings and bacteria have a common ancestorthe first known living organisms, which date to three and a half billion years ago.

Hoatzinsin some respects the most aberrant of birds, according to one Victorian ornithologistwere a problem from the beginning. Early European naturalists described them as pheasants, and the first major tree for birds, published in 1888 by Max Frbringer, placed them on the fowl branch. But, by the early nineteen-hundreds, some scientists were comparing hoatzins and cuckoos on the basis of traits such as jaws and feathers, and others were noting similarities between hoatzins and turacos, pigeons, barn owls, and rails. Even the hoatzins parasites defied classification: they hosted feather lice found on no other birds.

One crucial problem in phylogeny was convergent evolution. Sometimes natural selection nudges two organisms toward the same trait. Birds and bats independently evolved the ability to fly. Swifts and swallows each evolved into aerodynamic insectivores with nearly identical silhouettes, but traits such as their vocal organs and foot bones reveal that they are only distantly related. Because taxonomists often disagreed about things such as how to distinguish common ancestry from convergent evolution, the literature grew thick with conflicting trees, to the point that some twentieth-century biologists seemed ready to give up. The construction of phylogenetic trees has opened the door to a wave of uninhibited speculation, one wrote in 1959. Science ends where comparative morphology, comparative physiology, comparative ethology have failed us.

Phylogeny made a comeback in the seventies and eighties, after the German entomologist Willi Hennig developed more rigorous criteria for identifying common ancestry and drawing evolutionary trees. These innovations laid a foundation for a new wave of research that did not rely solely on physical specimens but, rather, on the emerging science of DNA. Organisms are related to one another by the degree to which they share genetic information, two ornithologists wrote in the early nineties, adding that genetics could reveal a different view of the process of evolution and its effects. The typical bird genome is a string of more than a billion base pairs that mutate randomly over time. Scientists can compare the same parts of the genome across multiple species to estimate their evolutionary closeness. Typically, species that share mutations have a more recent common ancestor, and species that do not are more distantly related.

Early sequencing was expensive and tedious, but, by the beginning of the twenty-first century, a signal was emerging from the noise. The journal Nature published an article about the promise of a single unified tree of life. But its author also identified a complication: each genome contains many different genes, and each one could generate a different evolutionary tree.

In 2001, a paper in the Proceedings of the Royal Society identified a pair of bird siblings as unlikely as Arnold Schwarzenegger and Danny DeVito: the flamingos closest relative was a little diving bird called a grebe. That was probably the single most astounding result that anybodys ever gotten, Peter Houde, an avian biologist from New Mexico State University, told me. Ornithologists had always reasoned that grebes were closely related to short-legged loons, whereas tall wading birds such as flamingos, storks, and herons probably had a long-legged common ancestor.

That was the first domino to fall. In 2008, Science published a new avian tree based on DNA. Research led by Shannon Hackett, Rebecca Kimball, and Sushma Reddy, scientists affiliated with the Field Museum and the University of Florida, examined nineteen parts of the genomes of a hundred and sixty-nine avian species. The root of their tree resembled trees based on physical specimens: large, flightless birds such as ostriches, emus, and kiwisknown collectively as ratiteswere first to diverge from all the others, followed by land fowl and waterfowl. The remaining ninety-five per cent of living birds, from parrots to penguins and pigeons, are known as modern birds and descended from a common ancestor, probably around the time that an asteroid hit the earth, sixty-six million years ago, and the dinosaurs went extinct. The youngest orderpasserines, which include all songbirdsbranched out into a staggering six thousand species in the span of tens of millions of years. The genetic tree for modern birds was decked with relationships that few, if any, taxonomists had guessed from anatomy; key groups such as parrots, owls, woodpeckers, vultures, and cranes shifted places.

Scientists had long assumed, for example, that daytime hunters such as hawks, eagles, and falcons all descended from a single bird of prey. But, in the genetic tree, hawks and eagles shared a branch with vultures, yet falcons turned out to be closer relatives of passerines and parrots. This meant that the peregrine falcon is more closely related to colorful macaws and tiny sparrows than to any hawk or eagle. The traditional explanation for flightlessness in ratitesthat a common ancestor diverged into ostriches, emus, rheas, cassowaries, and kiwis after the southern continents split apartalso collapsed. DNA showed that the ratites also included flying birds called tinamous, suggesting that the group evolved flightlessness at least three separate times. That study revolutionized our understanding of how the major groups of living birds are related to each other, Daniel J. Field, an avian paleontologist at the University of Cambridge, said. Bird-watching guides had to reorganize their contents to reflect the new relationships.

Excerpt from:
The Bizarre Bird Thats Breaking the Tree of Life - The New Yorker

NEWARK, Calif., July 12, 2022 /PRNewswire/ --Ultima Genomics, Inc. (the Company) has signed an agreement with Regeneron Pharmaceuticals, Inc. (Nasdaq: REGN) to further advance Ultima Genomics' sequencing architecture. Under the terms of the agreement, Regeneron will collaborate with Ultima on the development and testing of Ultima's second-generation sequencing platform, which will build upon the advances of the Company's first instrument, the UG100anticipated to launch in 2023. In conjunction with the agreement, Regeneron, who is currently part of the early access program for the UG100, will also become an investor in Ultima. The primary objective of the collaboration between Ultima and Regeneron is to enable affordable high-throughput sequencing for large-scale genomic analysis and to accelerate insights and discoveries that will profoundly impact life sciences research around the world.

"Regeneron and Ultima share a common goal of using science to improve human health," said John Overton, Ph.D., Vice President and Chief of Sequencing and Lab Operations at the Regeneron Genetics Center (RGC). "With more than 120 active research collaborations and one of the largest whole exome sequencing reference libraries in the world, we at the RGC are keenly interested in the development of technologies that streamline the drug discovery and development process. The high cost of next-generation sequencing constrains the production of genomic information a significant bottleneck for life sciences research. With this agreement, we hope to contribute to an affordable and scalable solution that enables the rapid advance of genomic sciences, and in turn, important medicines for patients in need."

"We founded Ultima Genomics with the mission to continuously drive the scale of genomic information," said Gilad Almogy, Ultima Genomics' founder and Chief Executive Officer."While we will soon be launching our first instrument platform, the UG100, we are already hard at work developing our second platform to provide even lower cost and greater scale. We are excited to collaborate with Regeneron on this project and look forward to providing tools with the ever-increasing capability to our customers. Throughout our development, we have relied on, and are grateful for, the support, trust, and relationship with collaborators such as Regeneron, all of which are among the leading sequencers in the world."

Over the last five years, Ultima Genomics has developed a fundamentally new sequencing architecture designed to scale beyond conventional approaches and enable sequencing at a fraction of the cost of other commercially available technologies. The new architecture includes completely different approaches to flow cell engineering, sequencing chemistry, and machine learning.Ultima is currently in an early access program for the UG100, its first high throughput NGS instrument using the new technology architecture. The second-generation instrument will further increase the scale of genomic data and reduce sequencing costs beyond the first instrument. The timing of development and commercial availability of the Company's second instrument is not yet disclosed.

About Ultima Genomics

Ultima Genomics is unleashing the power of genomics at scale. The Company's mission is to continuously drive the scale of genomic information to enable unprecedented advances in biology and improvements in human health. With humanity on the cusp of a biological revolution, there is a virtually endless need for more genomic information to address biology's complexity and dynamic change and a further need to challenge conventional next-generation sequencing technologies. Ultima's revolutionary new sequencing architecture drives down the costs of sequencing to help overcome the tradeoffs that scientists and clinicians are forced to make between the breadth, depth, and frequency with which they use genomic information. The new sequencing architecture was designed to scale far beyond conventional sequencing technologies, lower the cost of genomic information and catalyze the next phase of genomics in the 21st century. To learn more, visit http://www.ultimagenomics.com

Media inquiries: [emailprotected]

SOURCE Ultima Genomics

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Ultima Genomics signs development agreement with Regeneron aimed at driving the scale of genomic information for drug discovery and development - PR...

SkyQuest Technology Consulting Pvt. Ltd.

Global next generation sequencing market was valued at $10.28 billion in 2021, and it is expected to reach a value of $33.73 billion by 2028, at a CAGR of 18.50% over the forecast period (20222028).

Westford, USA, July 13, 2022 (GLOBE NEWSWIRE) -- Next generation sequencing (NGS) is a game-changing technology that is revolutionizing how we study and understand biology. NGS allows us to sequence vast amounts of DNA or RNA much faster and more cheaply than ever before, making it possible to generate unprecedented amounts of data about the genomes of organisms. The demand for NGS services in the global next generation sequencing market has been growing rapidly in recent years, as the technology has become more affordable and accessible. A wide variety of scientific disciplines are now using NGS, including human genomics, cancer research, microbiology, evolutionary biology, agriculture, and many others. The number of publications featuring NGS data has also been increasing rapidly in recent years.

One of the key factors driving the growth of the next generation sequencing market is the ongoing need for better methods for diagnosing and treating diseases. For example, NGS can be used to detect genetic variations that may be associated with disease risk. It can also be used to identify novel drug targets and develop personalized medicines. In addition, NGS is playing an increasingly important role in basic research as scientists strive to understand the complexities of genome function.

Next Generation Sequencing: A Magic Wand for Early Diagnosis of Cancer

The global prevalence of cancer is alarmingly high, with an estimated 17 million new cases and 10 million deaths in 2020 alone. The World Health Organization (WHO) predicts that these figures will rise to 27 million new cases and 16.3 million deaths by 2040 if current trends continue. Early detection of cancer through screening programs is one of the most effective ways to reduce the burden of this disease, as it can lead to earlier diagnosis and treatment, which can improve survival rates significantly. Apart from this, more than 400,000 children develop cancer every year.

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The next generation of sequencing technology is often heralded as a magic wand for the early diagnosis of cancer. This is because it has the potential to provide rapid and accurate identification of tumors at an early stage, when they are most treatable. Next generation sequencing (NGS) technology intervenes at the level of DNA, providing information on genetic variation within a tumor. This can be used to detect early-stage cancers that may not yet have developed symptoms or detectable changes at the cellular level. The Global next generation sequencing market is also gaining demand for monitoring the progression of a cancer, and to assess how well treatments are working.

There are several reasons why NGS is seen as such a powerful tool in cancer diagnosis and treatment. First, it is extremely sensitive and can detect very small amounts of DNA from a tumor. Second, it can rapidly generate large amounts of data, which can be used to identify even rare mutations that may be associated with cancer. Finally, NGS is relatively simple and inexpensive to perform, making it widely accessible across the global next generation sequencing market from almost all strata of society, especially in developed market like the US, the UK, and Germany, among others. Despite all these advantages, there are still some challenges associated with the use of NGS in cancer diagnosis and treatment. While NGS can identify DNA alterations that may be associated with cancer.

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Next Generation Sequencing is Becoming Popular among Parents to Check Inborn Errors

As more and more parents learn about the benefits of next generation sequencing (NGS), its popularity is growing as a tool to check for inborn errors. NGS can provide a more comprehensive picture of a child's health, allowing parents to catch potential problems early and get their children the treatment they need. While NGS is not yet perfect, it is becoming more reliable and affordable as technology improves. As more parents learn about its potential, next generation sequencing market is likely to become even more popular as a way to keep children healthy and catch problems early.

As the technology for DNA sequencing gets cheaper and more sophisticated, an increasing number of parents are opting to have their child's genome sequenced at birth. This is especially true for parents who have a family history of genetic diseases. Sequencing the genome of a newborn is becoming more popular as the technology gets cheaper and more sophisticated. Inborn errors of metabolism are a group of rare genetic disorders that can cause serious health problems. Many of these disorders in the global next generation sequencing market are difficult to diagnose, and they often go undetected until something goes wrong.

According to the National Institutes of Health, about 25% of all live births in the United States each year are affected by at least one hereditary disease. However, the prevalence of these disorders varies widely, depending on the specific condition. For example, conditions like cystic fibrosis and sickle cell disease are relatively common, while others like Huntingtons disease are much rarer.

There are many different types of hereditary diseases, and they can affect any organ or system in the body. Some of the more common conditions include heart defects, respiratory problems, mental retardation, metabolic disorders, and cancer. Many of these disorders are life-threatening or cause significant disability, so it is important to be aware if any family members who have been affected by them. As a result, people are increasingly focusing getting their genome sequenced to know if they are carrying any gene that can lead to cancer.

With advancement in the next generation sequencing market, parents can now choose to have their child's genome sequenced at birth. This gives them the ability to catch these disorders early and start treatment immediately. It also allows them to make informed decisions about their child's future health. Although the cost of sequencing a genome is still relatively high, it is dropping rapidly. And as the technology continues to improve, it is expected that more parents will choose to have their child's genome sequenced at birth.

Food Industry to Offer Lucrative Opportunity for Next Generation Sequencing Market as Safety Concern Rises

The application of next generation sequencing in food safety and quality is an area of great interest and promise. The use of next generation sequencing technologies has the potential to revolutionize how we monitor food safety and quality. By providing rapid and high-throughput sequence data, next generation sequencing can be used to detect pathogens and other microorganisms in food more quickly and accurately than ever before. Additionally, the application of next generation sequencing can help us to better understand the genetic basis of food spoilage and contamination.

Growing concern about food safety has led to stricter quality control measures in the food industry. In particular, there is a greater focus on ensuring that food products are free from contaminants and meet safety standards, which is offering a lucrative opportunity for the players active in the next generation sequencing market to make most out of it. To this end, food manufacturers are increasingly adopting quality management systems such as Hazard Analysis and Critical Control Points (HACCP). These systems help to identify and control potential hazards at all stages of the food production process, from raw materials to finished products.

There are many different applications of next generation sequencing market in food safety and quality. One example is the use of next generation sequencing for pathogen detection. Pathogens are a major cause of foodborne illness, and traditional methods for detecting them often have low sensitivity or take too long to provide results. However, next generation sequencing can be used to rapidly detect pathogens in food samples with high accuracy. This information can then be used to taking steps to prevent outbreaks before they occur. In addition to pathogen detection, another important application of next generation sequencing is monitoring antibiotic resistance in bacteria present in food items. Antibiotic resistance is a growing public health concern, as it makes infections harder to treat and increases the risk of potentially deadly superbugs infection.

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AI and Accelerated Computing to Bring Down the Cost of Next Generation Sequencing to Less Than $300

AI and accelerated computing are already enabling a wide range of new applications in genomics. One such application is next generation sequencing (NGS), which is used to determine the order of nucleotides in DNA. NGS is currently used for a variety of purposes, including diagnosing genetic diseases, determining ancestry, and predicting drug response in the global next generation sequencing market. The cost of NGS has fallen dramatically in recent years, from $5.6 billion per genome in 2001 to less than $1,000 today. However, there is still room for further improvement.

AI and accelerated computing can help bring down the cost of NGS by making it more efficient. For example, AI can be used to streamline the process of sequence alignment, which is often the most time-consuming and computationally intensive step in NGS. In addition, accelerated computing can be used to speed up other parts of the NGS process, such as variant calling and read mapping. The combination of AI and accelerated computing has the potential to reduce the cost of NGS even further, to less than $300 per genome. This would make it affordable for many more people to access this important technology.

Top 10 Biologics Companies in the US Raised Over 1.65 billion in 2021, but Ultima Genomics took the Larger Piece of Pie

These companies in the global next generation sequencing market are working on developing new treatments and cures for a variety of diseases and conditions. Some of the diseases that they are targeting include cancer, Alzheimers disease, Parkinsons disease, and multiple sclerosis. The amount of money that these companies have raised shows how important it is to find new treatments for these diseases. The hope is that with this additional funding, these companies will be able to make even more progress in developing new therapies and cures. In May 2022, the company managed to raise $600 million through private equity. The company is planning to use this funding to bring down the NGS to $100 in the years to come. Apart from this, Kriya Therapeutics, Moma Therapeutics, and Aspen Neuroscience raised around $270 million, and 150 million, $147.5 million, respectively. All three of these companies are working on cutting-edge therapies that have the potential to change the lives of patients suffering from these devastating diseases. Apart from this, these company are holding major market share as they have established themselves in the market.

It is clear that biologics research is an area where there is a lot of interest and investment is coming in the global next generation sequencing market. This is good news for patients who are waiting for new treatments and cures. With more funding available, these top companies should be able to make even more progress in finding new ways to treat.

Ultima Genomics is a new biotech company that is working on cutting the cost of sequencing the human genome. Theyve created a powerful technology called named Triple X that adjusts itself by integrating new data and machine learning to bring down the cost. The first use for this companys pitch will be whole-genome sequencing, which can also be applied to other approaches like single-cell and methylation sequencing.

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Key Vendors in Next Generation Sequencing Market

PerkinElmer Inc. (US)

BGI Group (China)

Agilent Technologies Inc. (US)

Eurofins Scientific SE (Luxembourg)

Pacific Biosciences of California Inc. (US)

Oxford Nanopore Technologies (UK)

QIAGEN NV (Netherlands)

F. Hoffmann-La Roche AG (Switzerland)

GENEWIZ Inc. (US)

Psomagen, Inc. (South Korea)

10x Genomics Inc. (US)

Takara Bio (Japan)

Zymo Research (US)

NuGen Technologies (US)

Hamilton Company (US)

Beckman Coulter (US)

Becton, Dickinson, and Company (US)

Lucigen Corporation (US)

Novogene Co., Ltd. (China)

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Next Generation Sequencing Market to Reach $33.73 billion By 2028 Thanks to Increased Attention Early Disease Diagnosis and High Prevalence of Cancer...

Global Whole Genome Amplification Market Forecast 2022-2028, key research on the industry condition of the Whole Genome Amplification is presented together with the best content, definition, expert opinion, SWOT analysis, meaning, and newest development around the world. The Whole Genome Amplification research includes information on industry size, sales, price, revenue, market share, gross margin, growth rate, and cross structure. The study examines the profit made from the sale of this report and technologies across a number of segments, as well as provides a comprehensive table of contents on the Market.

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Segmentation based on Key players

Sigma-Aldrich QIAGEN NV GE Healthcare LGC Group

Segmentation based on Type

Single Cell WGA Kit Complete WGA Kit WGA Reamplification Kit WGA & Chip DNA Kit Others

Segmentation based on Application

Drug Discovery & Development Disease Diagnosis Agriculture & Veterinary Research Forensics Others

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The research examines the Whole Genome Amplification market in-depth, focusing on several factors such as drivers, restraints, opportunities, and threats. Before investing, stakeholders can use this information to make informed judgments. It also enables you to conduct useful competitive research in order to generate marketing ideas for your products. When it comes to customer happiness, its critical to have a clear understanding of whats going on in the market. The general market scenario is accurately described in this research.

Impact Of Covid-19 on Whole Genome Amplification :

COVID-19 is an unprecedented global public health crisis that has impacted practically every business, and its long-term repercussions are expected to have an influence on industry growth during the forecast period. Our continuous study is enhancing our research approach to guarantee that fundamental COVID-19 concerns and potential solutions are included. The research examines COVID-19 in light of changes in consumer behavior and demand, purchasing patterns, supply chain re-routing, market dynamics, and government involvement. The updated study considers the impact of COVID-19 on the market and provides insights, analysis, projections, and forecasts.

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The following geographic segments are covered in the report:

The Whole Genome Amplification report provides information on the market area, which is divided into sub-regions and countries/regions. In addition to the market share in each country and sub-region, this chapter in this report also contains information on profit opportunities. This chapter of the report mentions the market share and growth rate for each region, country, and sub-region during the estimated period.

North America includes the United States, Canada, and Mexico

Europe includes Germany, France, UK, Italy, Spain

South America includes Colombia, Argentina, Nigeria, and Chile

The Asia Pacific includes Japan, China, Korea, India, Saudi Arabia, and Southeast Asia

When analyzing the key market participants, what aspects are taken into account?

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Whole Genome Amplification Market Report: One Research Solution Reveal Everything You Need to Know About Key Players: Sigma-Aldrich, QIAGEN NV, GE...

The discoveries show that ancient DNA can be recovered from Pompeiian human bones, providing new insight into this historic communitys genetic history and lifestyles.

Research that was recently published in Scientific Reports presents the first human genome that has been successfully sequenced from a person who passed away in Pompeii, Italy, after Mount Vesuvius explosion in the year 79 CE. Only little segments of mitochondrial DNA from Pompeiian human and animal remains have been sequenced up to this point.

The DNA of two peoples bones that were discovered in Pompeiis House of the Craftsman was studied and extracted by Gabriele Scorrano and colleagues. The bones length, form, and structure revealed that one pair belonged to a male who was between 35 and 40 years old when he passed away, while the other set belonged to a femalewho was over 50. The authors were able to extract and sequence ancient DNA from both people, but since the sequences from the females bones had gaps in them, they could only sequence the entire genome from the males remains.

The male subjects DNA was compared to 1,030 ancient and 471 current western Eurasian subjects, and it was found that the male subjects DNA was most comparable to that of modern central Italians and other people who resided in Italy during the Roman Imperial era. However, studies of the males Y chromosome and mitochondrial DNA revealed sets of genes that are often prevalent in Sardinian people but not in other people who resided in Italy during the Roman Imperial era. This shows that the Italian Peninsula may have seen high levels of genetic diversity at the time.

Additional analyses of the male individuals skeleton and DNA identified lesions in one of the vertebrae and DNA sequences that are commonly found in Mycobacterium, the group of bacteria that the tuberculosis-causing bacteria Mycobacterium tuberculosis belongs to. This suggests that the individual may have been affected by tuberculosis prior to his death.

The authors speculate that it may have been possible to successfully recover ancient DNA from the male individuals remains as pyroclastic materials released during the eruption may have provided protection from DNA-degrading environmental factors, such as atmospheric oxygen. The findings demonstrate the possibility to retrieve ancient DNA from Pompeiian human remains and provide further insight into the genetic history and lives of this population, they add.

Reference: Bioarchaeological and palaeogenomic portrait of two Pompeians that died during the eruption of Vesuvius in 79 AD by Gabriele Scorrano, Serena Viva, Thomaz Pinotti, Pier Francesco Fabbri, Olga Rickards, and Fabio Macciardi, 26 May 2022, Scientific Reports.DOI: 10.1038/s41598-022-10899-1

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Scientists Have Sequenced the DNA of a 2000-Year-Old Human From Pompeii - SciTechDaily

Covered in sheep fluids, John Gorzynski climbed the stairs to his Wales apartment, exhausted. It was springtime, 2016, which for a veterinarian in rural areas of the United Kingdom means only one thing: newborn lambs, and a lot of them.

Gorzynski was his town's on-call vet. In one night, he'd performed five cesarean sections on sheep struggling to birth their lambs, and it was now 3 a.m. But before he could reach the door to his flat and have a good shower, his phone rang.

Another lamb in peril -- back to work.

"In that moment, I knew I needed a change," said Gorzynski, DVM, PhD, who is now a postdoctoral scholar at Stanford Medicine. "That lifestyle was just not sustainable for me."

He yearned to return to a research lab, where his work schedule wouldn't hinge on laboring farm animals.

The desire set Gorzynski on a path that, in 2016, brought him to the Stanford Medicine lab of biomedical data scientist and geneticist Euan Ashley, MB ChB, DPhil. During his time at Stanford, he and others have devised record-setting genome sequencing techniques, researched heart disease in great apes and deciphered genetic cardiovascular conundrums in humans.

Gorzynski grew up on a small organic farm in New York, diligently cultivated by his father. The upbringing, he said, fostered his love of animals and the outdoors. "As a kid I'd just sit up in the orchard trees, picking and snacking on cherries, apples and peaches," he said. "It's where my love of nature and animals originated."

Eventually, though, Gorzynski deviated from the family business when he chose a career in medicine. Everything was on track when he was an undergraduate at St John's University in New York -- but then he witnessed his first autopsy. "It totally put me off being a human doctor," he recalled.

His passion for medicine persisted, however, so after graduating in 2007, Gorzynski explored other options. "I hadn't considered veterinary medicine before that -- but it suddenly seemed like a clear choice," he said.

Lured by its metropolitan location and solid research reputation, Gorzynski enrolled at the University of London's Royal Veterinary College for veterinary training and joined the lab of professor of veterinary cardiology Adrian Boswood, VetMB, who researched genetic causes of cardiovascular disease in great apes, a group of primates that include chimpanzees, gorillas and bonobos.

During his time at the lab, two chimpanzees died of sudden cardiac failure at the London Zoo. Both were around 16 or 17 years old, some 35 years shy of the average lifespan of a chimpanzee in captivity. And here was the kicker: They were related. "It made me wonder if there might be a genetic component at play," Gorzynski said.

In investigating the cause of the apes' deaths, Gorzynski and others found anatomical anomalies that resembled a cardiovascular disease in humans: arrhythmogenic right ventricular cardiomyopathy, or ARVC, which interferes with proper heart rhythms. That can lead to insufficient blood supply to organs and, ultimately, sudden death.

In humans, at least 50% of this type of cardiomyopathy is due to a genetic defect. Because humans and chimpanzees share a whopping 98% of their DNA, it stands to reason that whatever we know about humans could apply to chimpanzees, and vice versa.

The disease is believed to arise from a mutation in genes associated with a structure in heart muscle cells. With DNA from the deceased chimpanzees, Gorzynski and others dug more deeply into whether the primates harbored mutations in the key genes known to cause ARVC in humans.

Expanding the research to include the rest of the zoo's chimpanzees, the researchers monitored their heart function and examined their DNA to determine whether any heart abnormalities were genetic. Eventually, using samples from wild chimpanzees from the Jane Goodall Institute, the team also investigated the incidence of ARVC in apes in their natural habitats to compare with those in captivity.

In the end, the research was inconclusive.

"We found genetic differences between captive and wild chimpanzees, but our data wasn't granular enough to see if those variants were actually causative of the disease," Gorzynski said. The technology just wasn't advanced enough. His research hit a standstill.

After his veterinary training wrapped up, Gorzynski practiced animal medicine in Four Crosses, Powys, Wales as a mixed-animal surgeon for the next 2 years.

"I just decided, 'I'm going to live my best James Herriot life,'" he said, referring to the pen name of a veterinary surgeon who chronicled his work in the book All Creatures Great and Small and its sequels. "I saw birds, dogs, cats, ferrets, sheep, cows, horses -- it was great, and fun, but it was exhausting."

After the fateful night of five sheep C-sections, when Gorzynski made up his mind to return to ape research, he began seeking graduate programs. Ashley's work -- everything from studying the biology of endurance athletes to deciphering mystery diseases -- caught Gorzynski's interest. And the intrigue went both ways.

"I remember sending him a note, and Euan responded and said, 'You know, I've been waiting for someone like you -- I have this really interesting project,'" Gorzynski said.

That project focused on Koko, a famed gorilla born in the San Francisco Zoo who wowed the world with her sign language skills. Gorzynski returned to the United States to start research as a Stanford Medicine graduate student working with Ashley, a professor of genetics, of biomedical data science and of cardiovascular medicine.

Stanford's cardiovascular team was monitoring Koko, along with other great apes at a nearby preserve where Koko had lived, for structural heart disease and saw signs of a cardiovascular condition. Powered by new, more advanced genome sequencing, Gorzynski hoped to determine if there were key genes that spurred Koko's heart ailments. Sadly, Koko died in June, 2018 of unrelated causes.

To broaden the research, Gorzynski reconnected with his collaborators at the Jane Goodall Institute to share genomic data and findings. (The specimens Gorzynski sequences are collected after a great ape dies of natural causes in a sanctuary in the Republic of the Congo that the institute supports.)

When that research was paused in 2020 by COVID-19-related travel restrictions, Gorzynski had to find new ways to round out his degree. The detour resulted in him contributing to research that set a new world record: the fastest genome sequencing technique. The process, from sequencing the genome of a patient to providing clinical information, took several hours, a big improvement from the typical timing of a few weeks.

Now that travel restrictions have loosened, Gorzynski has resumed his ape-related studies. "What we learn from our studies could inform heart disease in humans but, honestly, that's not why I'm doing this research," Gorzynski said. "My focus is the health and well-being of the animals, and my hope is that this research can teach us how to better maintain a healthy population of wild great apes."

Photo by Savory

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Unconventional paths: Gorzynski and the great apes - Scope