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Category Archives: Human Genetics

Bionano Genomics Announces ESHG Lineup Featuring 11 Customer Presentations of OGM Data Spanning Three Major Clinical Research Areas of Application…

Posted: August 31, 2021 at 2:17 am

SAN DIEGO, Aug. 26, 2021 (GLOBE NEWSWIRE) -- Bionano Genomics, Inc. (Nasdaq: BNGO) today announced the European Society of Human Genetics (ESHG) conference lineup featuring 11 customer presentations of optical genome mapping (OGM) data spanning three major clinical areas of application from 10 institutions and six countries. The clinical application areas represented below cover hematological malignancies, inherited genetic disorders and solid tumor analysis. The presentations are expected to cover the clinical utility of OGM across these application areas, along with the unique capabilities of Bionanos Saphyr system to detect all classes of structural variants, across the genome, at a superior resolution relative to traditional techniques. The ESHG conference is being held virtually starting this Saturday from August 28 - 31, 2021.

More than 3,400 participants are registered for this years ESHG meeting, which provides a platform for the dissemination of the most exciting advancements in the field of human genetics. The upcoming customer presentations featuring OGM data are listed below along with the associated clinical areas of application:

OGM Application Area

Presenter

Affiliation

Presentation/Poster Title

Hematological Malignancies

Dr. Anna Puiggros

Hospital del Mar, Barcelona, Spain

Analysis of genomic complexity in patients with chronic lymphocytic leukemia (CLL) using optical genome mapping

Dr. Jonathan L. Lhmann

Hannover Medical School, Hannover, Germany

The clinical utility of optical genome mapping for the assessment of genomic aberrations in acute lymphoblastic leukemia

Inherited Genetic Disorders

Dr. Caroline Schluth-Bolard

Universite Hospital de Lyon, France

What is the best solution to manage failures of chromosomal structural variations detection by short-read strategy?

Dr. Kornelia Neveling

Radboud University Medical Centre, Netherlands

Long-read technologies identify a hidden inverted duplication in a family with choroideremia

Dr. Valrie Race

Univ. Hosp. of Leuven, Leuven, Belgium

Bionano optical genome mapping and southern blot analysis for FSHD detection

Dr. Romain Nicolle

Hospital Necker-Enfants Malades, Paris, France

16p13.11p11.2 triplication syndrome: a new recognizable genomic disorder characterized by Bionano optical genome mapping and WGS

Dr. Jenny Schiller

MVZ Martinsried, Martinsried, Germany

Characterization of breakpoint regions of apparently balanced translocations by optical genome mapping

Dr. Viola Alesi

Bambino Ges Children's Hospital, Rome, Italy,

Optical Genome Mapping: where molecular techniques give up

Dr. Valeria Orlando

Bambino Ges Children's Hospital, Rome, Italy

Optical genome mapping: a cytogenetic revolution

Solid Tumor Analysis

Dr. Florentine Scharf

Medical Genetics Center Munich, Germany

Germline chromothripsis of the APC locus in a patient with adenomatous polyposis

Dr. Mariangela Sabatella

Princess Maxima Center for Pediatric Oncology, Utrecht, Netherlands

Optical Genome Mapping Identifies Germline Retrotransportation Insertion in SMARCB1 in Two Siblings with Atypical Teratoid Rhabdoid Tumor

We believe our progress in Europe, with the increased awareness of OGM and the development of the market there, has been outstanding, commented Erik Holmlin, PhD, CEO of Bionano Genomics. Thanks to key sites like Radboud, Leuven and Cochin, the OGM footprint has now expanded in Germany, Spain and Italy. With the growing installed base of Saphyr in Europe, we have seen these institutions and their research teams conduct ground-breaking research to help demonstrate the potential utility of OGM as an alternative to traditional cytogenetics methods for the identification of genome structural variations that can be more sensitive, give a faster time to results and be less expensive to implement when compared to traditional methods. We believe the momentum of research that has been building will continue as more supporting data, like the data that we expect the researchers to show this week at ESHG, are released from around the world.

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For more details and to register for this online event please go to https://vmx.m-anage.com/home/release/eshg2021/en-GB

About Bionano Genomics

Bionano is a genome analysis company providing tools and services based on its Saphyr system to scientists and clinicians conducting genetic research and patient testing, and providing diagnostic testing for those with autism spectrum disorder (ASD) and other neurodevelopmental disabilities through its Lineagen business. Bionanos Saphyr system is a research use only platform for ultra-sensitive and ultra-specific structural variation detection that enables researchers and clinicians to accelerate the search for new diagnostics and therapeutic targets and to streamline the study of changes in chromosomes, which is known as cytogenetics. The Saphyr system is comprised of an instrument, chip consumables, reagents and a suite of data analysis tools. Bionano provides genome analysis services to provide access to data generated by the Saphyr system for researchers who prefer not to adopt the Saphyr system in their labs. Lineagen has been providing genetic testing services to families and their healthcare providers for over nine years and has performed over 65,000 tests for those with neurodevelopmental concerns. For more information, visit http://www.bionanogenomics.com or http://www.lineagen.com.

Forward-Looking Statements

This press release contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. Words such as may, will, expect, plan, anticipate, estimate, intend and similar expressions (as well as other words or expressions referencing future events, conditions or circumstances) convey uncertainty of future events or outcomes and are intended to identify these forward-looking statements. Forward-looking statements include statements regarding our intentions, beliefs, projections, outlook, analyses or current expectations concerning, among other things: the timing, content and significance of the presentations identified in this press release; our assessments regarding our progress in the European market, including our expectations with respect to the continued adoption of OGM throughout Europe; the benefits of OGM relative to traditional cytogenetic testing methods and its potential to replace traditional cytogenetic methods; our assessments regarding current and future research by the institutions identified in this press release; and the execution of Bionanos strategy. Each of these forward-looking statements involves risks and uncertainties. Actual results or developments may differ materially from those projected or implied in these forward-looking statements. Factors that may cause such a difference include the risks and uncertainties associated with: potential inaccuracies in presentations given at the ESHG Conference or subsequently published data that may minimize the impact of OGM in human genetics; the impact of the COVID-19 pandemic on our business and the global economy; general market conditions; changes in the competitive landscape and the introduction of competitive products; changes in our strategic and commercial plans; our ability to obtain sufficient financing to fund our strategic plans and commercialization efforts; the ability of medical and research institutions to obtain funding to support adoption or continued use of our technologies; the loss of key members of management and our commercial team; and the risks and uncertainties associated with our business and financial condition in general, including the risks and uncertainties described in our filings with the Securities and Exchange Commission, including, without limitation, our Annual Report on Form 10-K for the year ended December 31, 2020 and in other filings subsequently made by us with the Securities and Exchange Commission. All forward-looking statements contained in this press release speak only as of the date on which they were made and are based on management's assumptions and estimates as of such date. We do not undertake any obligation to publicly update any forward-looking statements, whether as a result of the receipt of new information, the occurrence of future events or otherwise.

CONTACTSCompany Contact:Erik Holmlin, CEOBionano Genomics, Inc.+1 (858) 888-7610eholmlin@bionanogenomics.com

Investor Relations and Media Contact:Amy ConradJuniper Point+1 (858) 366-3243amy@juniper-point.com

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Bionano Genomics Announces ESHG Lineup Featuring 11 Customer Presentations of OGM Data Spanning Three Major Clinical Research Areas of Application...

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Investing in the Power of Pathology and Genomics – Tufts Now

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A $2 million grant from the Mass Life Sciences Center has helped launch the Comparative Pathology and Genomics Shared Resource at Cummings School of Veterinary Medicine, a shared resource with state-of-the-art equipment that fills newly renovated laboratory space. For Cheryl London, a veterinary oncologist and Associate Dean for Research and Graduate Education, it represents a long-time vision becoming reality.

Understanding the pathology of infectious diseases is more critical than ever, said London, who added that the resource will lead to improvements in the treatment and prevention of diseases in humans through detailed genetic characterization of model systems and the associated pathology across species.

London tapped two Cummings School faculty members to lead the effort: assistant professorAmanda Martinot, a veterinary pathologistwho focuses on infectious diseases such as SARS CoV-2 and tuberculosis, and assistant research professor Heather Gardner, GBS20, a veterinary oncologist and geneticist.

Cummings School has been investing in this goal for quite some time. In 2020, the 7,500-square-foot Peabody Pavilion was renovated into modern, flexible lab space designed to support multidisciplinary teams. In addition, the resource will leverage Tufts resources such as the New England Regional Biosafety Laboratory (RBL).

When fully operational, this resource will offer advanced capacities for credentialling and analyzing animal models of disease that will help to grow collaborative opportunities among regional academic and industry entities; provide training opportunities for students, fellows, scientists and clinicians; and ultimately support job growth through expansion of the research enterprise in Central Massachusetts, said London.

Martinots research has focused on tuberculosis (TB). When the Martinot Lab and her collaboratorsCummings School associate professor Gillian Beamer, Tufts University School of Medicineassociate professor Bree Aldridge, and Harvard University professor Peter Sorger, head of the Harvard Program in Therapeutic Sciencesidentified some rare lung biopsies and archived lung specimens from tuberculosis patients that were taken during autopsies many years ago, Martinot thought they were a natural pilot project for the Comparative Pathology and Genomics Shared Resource.

We're trying to understand the biology of tuberculosis in human tissue, what helps the body clear TB, and what fuels TB progression, said Martinot. We use a lot of animal models to try to understand these processes, but there's no animal model that perfectly mimics human TB disease.

The resources new technology can extract meaningful genetic information from the immune cells surrounding and within granulomas, a hallmark pathologic feature of tuberculosissomething they haven't been able to do before. This technology also will allow them to obtain similar information from a variety of pathology samples.

Another pilot project aims to advance research by London and Gardner in canine osteosarcoma, an aggressive bone cancer that affects more than 25,000 dogs each year. In 2019, they published findingsof a study that detailed the landscape of genetic mutations in canine osteosarcoma, and more recently completed a clinical trial to test a new immunotherapy treatment on dogs diagnosed with this type of cancer. TheClinical Trials Officeat Cummings School has treated a number of canine osteosarcoma patients, allowing banking of associated biologic samples for further investigation. With these tissue samples, investigators can ask questions about the molecular and genomic features of cancer over time and identify clinical and pathologic correlates.

Animals get a lot of the same diseases that people do, and the information we learn from animals with these diseases can inform investigation of novel research opportunities across species, said Gardner.

We can start to interrogate the combination of pathology with genetics and follow how the cancer is mutating, Martinot said. And we can look at where these cancer cells live to try to understand how the microenvironment might be supporting the progression of the cancer. That information could lead to potential treatment options.

Paul Mathew, anoncologist at Tufts Medical Center and an associate professor at Tufts School of Medicine, is interested in using the resources technology to ask similar questions about prostate cancer using biopsies from human patients. He wants to understand the tumor and how the microenvironment changes over time in prostate cancer patients. The School of Medicineis one of many potential users of the resourceothers include UMass Medical School and Medical Center, which has plans for a new Veterans Administration outpatient clinic and Institute for Human Genetics.

The resource is home to cutting edge new technology that integrates pathology and genomics, said Martinot. With the help of this grant, we can do whole genome sequencing for genetic analysis of pathogens, tumors, and anything imaginable where the DNA sequence might make a difference.

The goal is to help drive discovery, adds Gardner. We have equipment to support next generation sequencing projects, such as a liquid handler robot to help automate sample processing and an Illumina sequencer. We also have a suite of NanoString equipment, which is a platform that will allow increased use of samples historically considered difficult to work with, including formalin-fixed samples, which are often very degraded.

The new technology that will power this effort falls into two main categories:

Everyone involved with the shared resource is excited about its future potential and the opportunity to see it grow. As Gardner said, The opportunities to impact research, in all areas, are limited by the investigators imagination.

Angela Nelson can be reached atangela.nelson@tufts.edu.

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Humans are more than just a bag of genes – Commentary Box Sports

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I still see myself sitting on a mattress on the floor of my Amsterdam floor. That was in June 1994, and the book had been published ten years earlier under the title Normal Not in Our Genes: Biology, Ideology, and Human Nature. I read it cover to cover and eagerly took notes.

The authors Richard Leontin, Stephen Rose, and Leon Kamen spoke plain language against biological reductionism, particularly against the then-dominant sociobiology, which explained human behavior from nature. In the book, they dissected a plethora of studies showing crime, intelligence, differences between racial or socioeconomic groups, and of course, gender differences as a result of our brains and genes.

Leontin and colleagues saw a link between the widespread acceptance of social biology and the dominant ideology of the time: neoliberal economic policies combined with an emphasis on conservative and traditional norms and values. Only when social movements (from the arms race to anti-racism, for a better environment, liberation or for the right to work) gained power, mobilization power and vision, was biology adopted to show social groups their natural place. After all, society becomes noticeably less flexible if the social system is fixed in our nature, in our genes.

Evolutionary biologist and geneticist Richard Lewontin, who died last July at the age of 92, has spent his life resisting biological reduction, both in popular science and science publications.

in his book Biology as an ideology. DNA Doctrine (1991), translated into Dutch as From the DNA doctrine, it targets the discourse of the Human Genome Project.

The genetic map has also been referred to as the book of life or the blueprint of life.

As I described two months ago, the Human Genome Project produced the first genetic map of humans, which has proven incredibly important to the life sciences today. It has been described as a major science project to capture the scale, political power, and billions of dollars involved.

The speech Leontin turned against was not kind. To reinforce the projects importance and sell the idea to politicians and policy makers, the scholars have compared their mission to The Search for the Holy Grail. The genetic map has also been referred to as the book of life or the blueprint of life. One of the geneticists involved, Walter Gilbert, took the lead and thought he could finally answer the philosophical question about who we are using a genetic map. Your genetic code on CD, that was his idea. At conferences, Gilbert photographed the promise of this genetic map by repeatedly pulling a CD out of his jacket and presenting it to his audience with the words: Heres a human being; thats me!

The discourse of the Human Genome Project differs from that of sociobiology. Sociobiology focused on social groups with the goal of identifying and explaining social problems in biological terms. The Human Genome Project focuses on the individual: fully in line with the zeitgeist of the neoliberal age, the individual must obey the adage know thyself. And because, according to this logic, this individual is nothing more than a bag of genes, knowing yourself is nothing more than knowing your genes. This reductive and simplistic representation is what Leontin continued to fight.

A prominent geneticist, Richard Leontine was a founder and pioneer of evolutionary and population genetics. He caused a stir in the 1960s with research showing that he and colleague John Hobby showed that genes vary widely and that gene mutations are not rare but rather standard. Mutations are not rare and should be selected quickly because they may lead to disease or other abnormalities. Nothing is normal, the rest is an aberration. The species has much greater genetic diversity than expected.

Richard Leontine was passionate and spent his life tackling misrepresentations and misrepresentations in science.

Leontins most groundbreaking research was the genetic diversity between people. Lewantin argued that while any two people can be genetically different from each other, it becomes more complex when it comes to the difference between groups of people. His research from 1972 showed that differences within groups are much greater (85 percent) than differences between groups (15 percent). These results have since become a standard science. But Leontine also struck a nail in the coffin of ethnic approaches. Because if the differences between groups are smaller than those within groups, then there is no genetic basis for the concept of race.

For Richard Leontine, science was a social act. Science represents reality, we need knowledge to diagnose cancer, for example. But science at the same time is an intervention in this reality, contributing to our vision of who we are and how we relate to each other.

Leontine was passionate and spent his life fomenting misrepresentations in the sciences. There is no controversy or controversy within genetics as Leontin was not a major voice. Thus it served as a guide in my scientific development.

When I started researching forensic DNA evidence, it also turned out that he played an important role in this. In a debate about the uniqueness of the DNA profile and the opportunity to incriminate the wrong person, his knowledge of genetic variation within and between populations has contributed to setting standards for reliable consistent calculations.

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In 1997, she helped organize the International Conference on Molecular Biology and Evolution organized by the Svante Pbo Laboratory. I was working on my PhD research in his lab at the time. During lunch, I got to know the famous geneticist Leonten because I wanted to ask him some questions about the forensic DNA evidence. He spontaneously offered to skip the conference session after lunch to continue our conversation.

Leontin was known as the smartest and fastest. He spoke several languages fluently and played the clarinet daily. As a scientist, he was also politically involved and spoke about climate, social and economic inequalities, racism and sexism.While examining in depth the work of his fellow scholars, he was known to be very generous to students and emerging scholars. A fellow scientific sociologist received a handwritten note from him at her new appointment at Harvard, where he himself was working, inviting her to come and get acquainted. He knew the difficult world she was entering.

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What Is the Most Important Scientific Development of the Last 50 Years? – Gizmodo Australia

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There are people who argue, persuasively, that Hollywood films are worse than they used to be. Or that novels have turned inward, away from the form-breaking gestures of decades past. In fact, almost anything can be slotted into a narrative of decline the planet, most obviously, but also (per our former president) toilets and refrigerators. One of the few arenas immune to this criticism is science: I doubt there are very many people nostalgic for the days before the theory of relativity or the invention of penicillin. Over the centuries, science has just kept racking up the wins. But which of these wins limiting ourselves to the last half-century mattered most? What is the most important scientific development of the last 50 years? For this weeks Giz Asks, we reached out to a number of experts to find out.

Research Assistant, Social Sciences, Humboldt University of Berlin

A bit more than 50 years ago, but I would say the most influential were the related developments of the Journal Impact Factor and the Science Citation Index (precursor of todays Web of Science) by Eugene Garfield and Irving H. Sher between 1955 and 1961.

These developments laid the groundwork for current regimes of governance and evaluation in academia. Their influence on the structure of science as we know it can hardly be overestimated: Today, it is difficult to imagine any funding, hiring, or publication decision that does not draw in some way either directly on the JIF or data from the Web of Science, or at least on some other form of quantitative assessment and/or large-scale literature database. Additionally, the way we engage with academic literature and hence how we learn about and build on research results has also fundamentally been shaped by those databases.

As such, they influence which other scientific developments were made possible in the last 50 years. Some groundbreaking discoveries might have only been possible under this regime of evaluation of the JIF and the SCI, because those projects might not have been funded under a different regime but also, its possible that we missed out on some amazing developments because they did not (promise to) perform well in terms of quantitative assessment and were discarded early on. Current debates also highlight the perverse and negative effects of quantitative evaluation regimes that place such a premium on publications: goal displacement, gaming of metrics, and increased pressure to publish for early career researchers, to name just a few. So while those two developments are extremely influential, they are neither the only nor necessarily the best possible option for academic governance.

Professor, History of Science, Stanford University, whose research focuses on 20th century science, technology, and medicine

That would surely be the discovery and proof of global warming. Of course, pieces of that puzzle were figured out more than a century ago: John Tyndall in the 1850s, for example, showed that certain gases trap rays from the sun, keeping our atmosphere in the toasty zone. Svante Arrhenius in 1896 then showed that a hypothetical doubling of CO2, one of the main greenhouse gases, would cause a predictable amount of warming which for him, in Sweden, was a good thing.

It wasnt until the late 1950s, however, that we had good measurements of the rate at which carbon was entering our air. A chemist by the name of Charles Keeling set up a monitoring station atop the Mauna Loa volcano in Hawaii, and soon thereafter noticed a steady annual increase of atmospheric CO2. Keelings first measurements showed 315 parts per million and growing, at about 1.3 parts per million per year. Edward Teller, father of the H-bomb, in 1959 warned oil elites about a future of melting ice caps and Manhattan under water, and in 1979 the secret sect of scientists known as the Jasons confirmed the severity of the warming we could expect. A global scientific consensus on the reality of warming was achieved in 1990, when the Intergovernmental Panel on Climate Change produced its first report.

Today we live with atmospheric CO2 in excess of 420 parts per million, a number that is still surging every year. Ice core and sea sediment studies have shown that we now have more carbon in our air than at any time in the last 4 million years: the last time CO2 was this high, most of Florida was underwater and 24.38 m sharks with 8-inch teeth roamed the oceans.

Coincident with this proof of warming has been the recognition that the history of the earth is a history of upheaval. Weve learned that every few million years Africa rams up against Europe at the Straits of Gibraltar, causing the Mediterranean to desiccate which is why there are canyons under every river feeding that sea. We know that the bursting of great glacial lakes created the Scablands of eastern Washington State, but also the channel that now divides France from Great Britain. We know that the moon was formed when a Mars-sized planet crashed into the earth and that the dinosaurs were killed by an Everest-sized meteor that slammed into the Yucatan some 66 million years ago, pulverizing billions of tons of rock and strewing iridium all over the globe. All of these things have been only recently proven. Science-wise, we are living an era of neo-geocatastrophism.

Two things are different about our current climate crisis, however.

First is the fact that humans are driving the disaster. The burning of fossil fuels is a crime against all life on earth, or at least those parts we care most about. Pine bark beetles now overwinter without freezing, giving rise to yellowed trees of death. Coral reefs dissolve, as the oceans acidify. Biodisasters will multiply as storms rip ever harder, and climate fires burn hotter and for longer. Organisms large and small will migrate to escape the heat, with unknown consequences. The paradox is that all these maladies are entirely preventable: we cannot predict the next gamma-ray burst or solar storm, but we certainly know enough to fix the current climate crisis.

The second novelty is the killer, however. For unlike death-dealing asteroids or gamma rays, there is a cabal of conniving corporations laboring to ensure the continued burning of fossil fuels. Compliant governments are co-conspirators in this crime against the planet along with think tanks like the American Petroleum Institute and a dozen-odd other bill-to-shill institutes. This makes the climate crisis different from most previous catastrophes or epidemics. It is as if the malaria mosquito had lobbyists in Congress, or Covid had an army of attorneys. Welcome to the Anthropocene, the Pyrocene, the Age of Agnotology!

So forget the past fifty years: the discovery of this slow boil from oil could well become the most important scientific discovery in all of human history. What else even comes close?

Professor and Chair, History of Science, The University of Oklahoma

Id say the best candidate is the set of ideas and techniques associated with sequencing genes and mapping genomes.

As with most revolutionary developments in science, the genetic sequencing and mapping revolution wasnt launched by a singular discovery; rather, a cluster of new ideas, tools, and techniques, all related to manipulating and mapping genetic material, emerged around the same time. These new ideas, tools, and techniques supported each other, enabling a cascade of continuing invention and discovery, laying the groundwork for feats such as the mapping of the human genome and the development of the CRISPR technique for genetic manipulation.

Probably the most important of these foundational developments were those associated with recombinant DNA (which allow one to experiment with specific fragments of DNA), with PCR (the polymerase chain reaction, used to duplicate sections of DNA precisely, and in quantity), and with gene sequencing (used to determine the sequences of base pairs in a section of DNA, and thus to identify genes and locate them relative to one another).

While each of these depended upon earlier ideas and techniques, they all took marked steps forward in the 1970s, laying the foundation for rapid growth in the ability to manipulate genetic material and to map genes within the larger genomes of individual organisms. The Human Genome Project, which officially ran from 1990-2003, invested enormous resources into this enterprise, spurring startling growth in the speed and accuracy of gene sequencing.

The ramifications of this cluster of developments, both intellectual and practical, have been enormous. One the practical side, the use of DNA evidence in criminal investigation (or in exonerating the wrongly convicted), is now routine, and the potential for precise, real-time genomic identification (and surveillance) is being realised at a startling pace. While gene therapies are still in their infancy, the potential they offer is tantalising, and genomic medicine is growing rapidly.

Pharmaceutical companies now request DNA samples from individual experimental subjects in clinical trials in order to correlate drug efficacy with aspects of their genomes. And, perhaps most important of all, the public health aspects of gene sequencing and mapping are stunning: the genome of the SARS-2 Coronavirus that causes Covid-19 was sequenced by the end of February 2020, within weeks of the realisation that it could pose a serious public health threat, and whole-genome analysis of virus samples from around the world, over time, have enabled public health experts to map its spread and the emergence of variants in ways that would have been unthinkable even a decade ago.

The unique aspects of the virus that make it so infectious were identified with startling speed, and work on an entirely new mode of vaccine development began, leading to the development, testing, and mass production of a new class of vaccines (mRNA vaccines) of remarkable efficacy, in unbelievably short time less than a year from identification of the virus to approval and wide use. It is hard to overstate how amazing this novel form of vaccine development has been, and how large its potential is for future vaccines.

On the intellectual/cultural side, the collection of techniques for manipulating and mapping genetic material is challenging longstanding ideas about what is natural and about what makes us human. Organic, living things now can be plausibly described as technologies, and thats an unsettling thing. Aspects of our individual biological identities that once were givens are increasingly becoming choices, with implications we are just beginning to see.

In addition, these same techniques are being deployed to reconstruct our understanding of evolutionary history, including our own evolution and dispersal across the globe, and perhaps nothing is more significant than changing how we understand ourselves and our history.

Professor, Science and Technology Studies, University College London, who researches the history of modern science and technology

My answer would be PCR Polymerase Chain Reaction. Invented by Kary Mullis at the Cetus Corporation in California in 1985, its as important to modern genetics and molecular biology as the triode and the transistor to modern electronics. Indeed it has the same role: its an amplifier. DNA can be multiplied. Its a DNA photocopier.

Without it, especially once automated, much modern genetics would be extremely time-consuming, laborious handcraft, insanely expensive, and many of its applications would not be feasible. It enables sequencing and genetic fingerprinting, and we have it to thank for COVID tests and vaccine development. Plus, you can turn it into a fantastic song by adapting the lyrics to Sleaford Mods TCR. Singalong now: P! C! R! Polymerase! Chain! Reaction!

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6 Greatest Breakthroughs in Agriculture that Changed the World – Krishi Jagran

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Technology has evolved over the years in many fascinating ways

We live in a world where agricultural practices are very advanced. However, we started with collecting wild grains more than 10,50,00 years ago and then planting them around 11,500 years ago. A lot went between when nascent farmers began gathering seeds and when modern farmers started using ultra-modern technologies to cultivate their lands.

The Atlantic came up with a panel of eminent figures who compiled a list of 50 innovations which have been most important to the agricultural sector. In this blog post, we tell you about 6 of these great breakthroughs in agriculture that changed the world.

The German chemist Fritz Haber, who is also known as the father of chemical weapons, won a Nobel Prize for developing an ammonia synthesis process. This process was used to create fertilizers which ultimately led to the green revolution. This brings us to the second breakthrough.

The fertilizers development in the early twentieth century combined with scientific plant breeding methods led to a huge increase in world's food output. The world remembers this landmark turn as the green revolution. Norman Borlaug, the man behind the green revolution, was an agricultural economist who saved 1 billion people from hunger and starvation.

Gregor Mendel, who is also known as the father of genetics, discovered how plant breeding and human genetics works. It was he who deserves the credit for the development of hundreds of high yielding varieties which were made possible only by his research.

The combine harvester has become very essential to farming. However, what we do not realize is the fact that it wasn't always there. Before its invention, farmers had to perform a number of tasks manually. Its invention ensured that more and more hands were free to do other kinds of work.

We have water pumps today which can give off litres and litres of water in a single minute. The first ever water pump was made by Archimedes. The Greek scientist is said to have designed a rotating corkscrew which could push water up a tube. It completely changed the way irrigation was done and it still remains in use in sewage treatment plants.

Refrigeration changed the way food was stored and used forever. One cannot even imagine the difficulties faced in storing food by people who lived in a world where refrigeration was not yet discovered. Its discovery transformed food transport, food safety, and food preservation.

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Roman Catholics of Goa, Mangalore have early lineages of Brahmin community: Study – NewsMeter

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Hyderabad: A new study has revealed that Roman Catholics of Goa, Kumta, and Mangalore regions are the remnants of very early lineages of the Brahmin community of India, majorly with Indo-European-specific genetic composition.

Conducted by Dr Kumarasamy Thangaraj, Chief Scientist, CSIR-Centre for Cellular and Molecular Biology (CCMB), and Director of Centre for DNA Fingerprinting and Diagnostics, Hyderabad; and Dr Niraj Rai, Senior Scientist, DST-Birbal Sahni Institute of Palaeosciences (BSIP), Lucknow, and the researchers analyzed the DNA of 110 individuals from the Roman Catholic community of Goa, Kumta, and Mangalore.

They compared the genetic information of the Roman Catholic group with previously published DNA data from India and West Eurasia. They put this information alongside archaeological, linguistic, and historical records. All of these helped the researchers fill in many of the key details about the demographic changes and history of the Roman Catholic population of South West of India since the Iron Age (until around 2,500 years ago), and how they relate to the contemporary Indian population.

They concluded that the Roman Catholics of Goa, Kumta and Mangalore regions are the remnants of very early lineages of the Brahmin community of India, majorly with Indo-European-specific genetic composition.

The study found consequences of the Portuguese inquisition in Goa on the population history of Roman Catholics. They also found some indication of the Jewish component. This finding has been published in "Human Genetics" on 23 August 2021.

"Our genetic study revealed that the majority of Roman Catholics is genetically close to an early lineage of the Gaur Saraswat community. More than 40 per cent of their paternally inherited Y chromosomes can be grouped under the R1a haplogroup. Such a genetic signal is prevalent among populations of north India, the Middle East, and Europe and unique to this population in the Konkan region," said Dr. Kumarasamy Thangaraj, senior author of the study.

Dr. Niraj Rai, the co-corresponding author, said this study strongly suggests profound cultural transformations in the ancient South West of India. "This has mostly happened due to continuous migration and mixing events since last 2500 years", he said.

Lomous Kumar, first author of the paper, said the origins of many population groups in India like the Jews and Parsis are not well-understood.

"These are gradually unfolding with advances in the modern and ancient population genetics. Roman Catholics are one of them with much-debated history of the origin based on inferences of anthropologists and historians", he said

Dr Vinay K Nandikoori, Director, Centre for Cellular and Molecular Biology, Hyderabad, said this multi-disciplinary study using history, anthropology and genetics information have helped them in understanding the population history of Roman Catholics from one of the most diverse and multicultural region of our country.

The other institutes involved in this study are Mangalore University, Canadian Institute for Jewish Research, and Institute of Advanced Materials, Sweden.

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Animal Expert Shares 5 Things That Will Help Your Dog Live a Longer, Healthier Life – ScienceAlert

Posted: at 2:17 am

As anyone who has ever lived with a dog will know, it often feels like we don't get enough time with our furry friends. Most dogs only live around ten to 14 years on average though some may naturally live longer, while others may be predisposed to certain diseases that can limit their lifespan.

But what many people don't know is that humans and dogs share many genetic similarities including a predisposition to age-related cancer. This means that many of the things humans can do to be healthier and longer lived may also work for dogs.

Here are just a few ways that you might help your dog live a longer, healthier life.

One factor that's repeatedly linked with longevity across a range of species is maintaining a healthy bodyweight. That means ensuring dogs aren't carrying excess weight, and managing their calorie intake carefully.

Not only will a lean, healthy bodyweight be better for your dog in the long term, it can also help to limit the impact of certain health conditions, such as osteoarthritis.

Carefully monitor and manage your dog's bodyweight through regular weighing or body condition scoring where you look at your dog's physical shape and "score" them on a scale to check whether they're overweight, or at a healthy weight. Using both of these methods together will allow you to identify weight changes and alter their diet as needed.

Use feeding guidelines as a starting point for how much to feed your dog, but you might need to change food type or the amount you feed to maintain a healthy weight as your dog gets older, or depending on how much activity they get.

Knowing exactly how much you are feeding your dog is also a crucial weight-management tool so weigh their food rather than scooping it in by eye.

More generally, good nutrition can be linked to a healthy ageing process, suggesting that what you feed can be as important as how much you feed. "Good" nutrition will vary for each dog, but be sure to look for foods that are safe, tasty and provide all the nutrients your dog needs.

Exercise has many physiological and psychological benefits, both for our dogs (and us). Physical activity can help to manage a dog's bodyweight, and is also associated with anti-ageing effects in other genetically similar species.

While exercise alone won't increase your dog's lifespan, it might help protect you both from carrying excess bodyweight. And indeed, research suggests that "happy" dog walks lead to both happy dogs and people.

Ageing isn't just physical. Keeping your dog's mind active is also helpful. Contrary to the popular adage, you can teach old dogs new tricks and you might just keep their brain and body younger as a result.

Even when physical activity might be limited, explore alternative low-impact games and pursuits, such as scentwork that you and your dog can do together. Using their nose is an inherently rewarding and fun thing for dogs to do, so training dogs to find items by scent will exercise them both mentally and physically.

Other exercise such as hydrotherapy a type of swimming exercise might be a good option especially for dogs who have conditions which affect their ability to exercise as normal.

Like many companion animals, dogs develop a clear attachment to their caregivers. The human-dog bond likely provides companionship and often, dog lovers describe them as a family member.

A stable caregiver-dog bond can help maintain a happy and mutually beneficial partnership between you and your dog. It can also help you recognize subtle changes in your dog's behavior or movement that might signal potential concerns.

Where there is compatibility between caregiver and dog, this leads to a better relationship and even benefits for owners, too, including stress relief and exercise. Sharing positive, fun experiences with your dog, including playing with them, are great for cementing your bond.

Modern veterinary medicine has seen substantial improvements in preventing and managing health concerns in dogs. Successful vaccination and parasite management programs have effectively reduced the incidence of disease in both dogs and humans including toxocariasis, which can be transmitted from dog feces to humans, and rabies, which can be transmitted dog-to-dog or dog-to-human.

Having a good relationship with your vet will allow you to tailor treatments and discuss your dog's needs. Regular health checks can also be useful in identifying any potential problems at a treatable stage such as dental issues or osteoarthritis which can cause pain and negatively impact the dog's wellbeing.

At the end of the day, it's a combination of our dog's genetics and the environment they live in that impacts their longevity. So while we can't change their genetics, there are many things we can do to improve their health that may just help them live a longer, healthier life.

Jacqueline Boyd, Senior Lecturer in Animal Science, Nottingham Trent University.

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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The Poop About Your Gut Health and Personalized Nutrition – WIRED

Posted: at 2:17 am

Changing your diet to improve your health is nothing newpeople with diabetes, obesity, Crohns disease, celiac disease, food allergies, and a host of other conditions have long done so as part of their treatment. But new and sophisticated knowledge about biochemistry, nutrition, and artificial intelligence has given people more tools to figure out what to eat for good health, leading to a boom in the field of personalized nutrition.

Personalized nutrition, often used interchangeably with the terms precision nutrition or individualized nutrition is an emerging branch of science that uses machine learning and omics technologies (genomics, proteomics, and metabolomics) to analyze what people eat and predict how they respond to it. Scientists, nutritionists, and health care professionals take the data, analyze it, and use it for a variety of purposes, including identifying diet and lifestyle interventions to treat disease, promote health, and enhance performance in elite athletes.

Increasingly, its being adopted by businesses to sell products and services such as nutritional supplements, apps that use machine learning to provide a nutritional analysis of a meal based on a photograph, and stool-sample tests whose results are used to create customized dietary advice that promises to fight bloat, brain fog, and a myriad of other maladies.

Nutrition is the single most powerful lever for our health, says Mike Stroka, CEO of the American Nutrition Association, the professional organization whose mandate includes certifying nutritionists and educating the public about science-based nutrition for health care practice. Personalized nutrition will be even bigger.

In 2019, according to ResearchandMarkets.Com, personalized nutrition was a $3.7 billion industry. By 2027, it is expected to be worth $16.6 billion. Among the factors driving that growth are consumer demand, the falling cost of new technologies, a greater ability to provide information, and the increasing body of evidence that there is no such thing as a one-size-fits-all diet.

The sequencing of the human genome, which started in 1990 and concluded 13 years later, paved the way for scientists to more easily and accurately find connections between diet and genetics.

When the term personalized nutrition first appeared in the scientific literature, in 1999, the focus was on using computers to help educate people about their dietary needs. It wasnt until 2004 that scientists began to think about the way genes affect how and what we eat, and how our bodies respond. Take coffee, for instance: Some people metabolize caffeine and the other nutrients in coffee in a productive, healthy way. Others dont. Which camp you fall into depends on a host of factors including your genetics, age, environment, gender, and lifestyle.

More recently, researchers have been studying connections between the health of the gut microbiome and conditions including Alzheimers, Parkinsons, and depression. The gut microbiome, the bodys least well-known organ, consists of more than 1000 species of bacteria and other microbes. Weighing in at almost a pound, it produces hormones, digests food that the stomach cant, and sends thousands of different diet-derived chemicals coursing through our bodies every day. In many respects the microbiome is key to understanding nutrition and is the basis of the growth in personalized nutrition.

Blood, urine, DNA, and stool tests are part of the personalized nutrition toolkit that researchers, nutritionists, and health care professionals use to measure the gut microbiome and the chemicals (known as metabolites) it produces. They use that data, sometimes in conjunction with self-reported data collected via surveys or interviews, as the basis for nutrition advice.

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Latest Research Strengthens Link Between Genetics and Suicidal Behaviors – University of Utah Health Care

Posted: July 21, 2021 at 2:34 am

Jul 13, 2021 11:00 AM

Author: Doug M Dollemore

Suicide isnt just about a bad day, week, month, or year. Its not just about sadness or feeling hopeless. Nor is it just the predictable end result of schizophrenia, post-traumatic stress, or other mental disorders. In truth, death by suicide can be attributed to any or all of these things, plus a multitude of other factors that, in combination, can lead someone to end their own life.

Among the least understood of these factors is genetics. Research, much of it conducted at University of Utah Health, strongly suggests that risk for suicide death is partially inheritable and tracks in families independent of the effects of a shared environment. Identifying these genetic risk factors, scientists say, could lead to better ways to predict who might be at risk of suicide and new strategies for preventing the worst from happening.

Understanding the underlying factors involved in suicidal behaviors is key, says Eric Monson, M.D. Ph.D., a chief resident psychiatrist at U of U Health. Suicide is inherently preventable, indicating that the more we know about its risks, the more potential lives that could be saved.

To address this growing interest, University of Utah Health scientists are collaborating on an investigation called the Utah Suicide Genetic Risk Study (USGRS). The researchers, in cooperation with the state Office of the Medical Examiner, has collected nearly 8,000 DNA samples from Utahans who died by suicide, one of the largest DNA collections from suicide victims in the world.

This DNA resource is linked to the Utah Population Database (UPDB), which contains medical, demographic, and genealogic information, then de-identified for the research team. Together, these databases are helping U of U Health researchers identify specific gene variants, or SNPs (pronounced snips), and other genetic mutations that could contribute to suicide risk.

Among their latest findings are:

Variants in nerve signaling gene may play a role in risk of death by suicide

A pair of newly discovered variants in a gene that plays a key role in the transmission of nerve signals in the brain could help explain why death by suicide is more prevalent in some families, according to a study published in Molecular Psychiatry and led by U of U Health scientists.

Neurexin-1 (NRXN1) is a gene that helps regulate synapse activity in the brain. Synapses, also known as neuronal junctions, are where electronic signals pass from one nerve cell to another. In a previous genome-wide study of Utah families spanning several generations, NRXN1 was identified as a gene that could potentially elevate the risk of death by suicide. Other research suggests that NRXN1 is also associated with schizophrenia, autism, and other psychiatric disorders. These disorders may be linked to increased suicide risk.

In this new study, the researchers conducted laboratory experiments comparing the effects of normalNRXN1to variant NRXN1. They discovered that NRXN1 variant synapses were twice as active as normal ones, suggesting that genetic alterations in this synapse pathway may play a role in increasing risk of suicide.

This result gives us a clue about one of likely many gene pathways that may lead to increased risk, says Hilary Coon, Ph.D., senior author of the study and a research professor in the Department of Psychiatry. However, more study will be needed to understand how these changes might interact with environmental risk factors and additional genetic risks that are yet to be discovered.

Prior trauma and a genetic predisposition for PTSD among those with bipolar disorder may increase risk of death by suicide

Individuals with bipolar disorder who are genetically predisposed to develop post-traumatic stress disorder following distressing events in their lives could be at greater risk of death by suicide than others who attempt it, according to a study in Translational Psychiatry led by U of U Heath scientists. The researchers say the finding could lead to better screening measures to detect prior trauma among bipolar disorder patients and identify those who are at greatest risk of suicide death.

The study, the largest combined clinical and genetic effort to investigate risk factors for death by suicide in bipolar disorder, is among the first to find differing risk factors for suicide attempts and death, according to Eric Monson, M.D., Ph.D., lead author of the study.

Rates of death by suicide are 10 to 30 times higher for people with bipolar disorder than for the general population, Monson says. What we found in this study is that a combination of prior trauma, a genetic predisposition for PTSD, and a diagnosis of bipolar disorder is almost a perfect storm that puts an individual at greater risk of death by suicide.

Rare genetic variants could help scientist pinpoint genes linked to suicide risk

Five newly discovered rare but potent genetic variants could help scientists identify specific genes and genetic pathways associated with suicide death, according to a study published in the American Journal of Medical Genetics Part B. The study, led by Emily DiBlasi, Ph.D., a research instructor in the Department of Psychiatry, is among the first comprehensive examinations of rare genetic variations linked to suicide death.

Rare variants represent less than 1% of the genetic variations in humans. Unlike more common variants, which usually are found near or adjacent to generalized regions of the human genome, rare variants are found within specific genes. These variants can alter proteins and adversely affect how a gene functions; ultimately, they may have a powerful and damaging influence on the risk of death by suicide.

Rare variants are a compelling source of the unaccounted genetic variation in suicide risk, DiBlasi says. Identifying these risk markers within specific genes could help us better understand some of the more puzzling aspects of the complex role that genetics might have in suicide death.

However, while evidence for the role that genetics might play in suicidal behaviors is growing, DiBlasi and her U of U Health colleagues emphasize it shouldnt be mistaken for destiny.

Were really in the early stages of genetic discovery, DiBlasi says. But based on what we know so far, its important to keep in mind that even if an individual has all of the variants that weve identified, it doesnt mean they are going to die by suicide. It just means that their risk might, and I must stress might, be elevated.

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Mixed-ancestry genetic research shows a bit of Native American DNA could reduce risk of Alzheimer’s disease – The Conversation US

Posted: at 2:34 am

Since the human genome was first mapped, scientists have discovered hundreds of genes influencing illnesses like breast cancer, heart disease and Alzheimers disease. Unfortunately, Black people, Indigenous people and other people of color are underrepresented in most genetic studies. This has resulted in a skewed and incomplete understanding of the genetics of many diseases.

We are two researchers who have been working to find genes that affect peoples risk for various diseases. Our team recently found a genetic region that appears to be protective against Alzheimers disease. To do this, we used a method called admixture mapping that uses data from people with mixed ancestry to find genetic causes of disease.

In 2005, researchers first used a groundbreaking method called a genomewide association study. Such studies comb through huge datasets of genomes and medical histories to see if people with certain diseases tend to share the same version of DNA called a genetic marker at specific spots.

Using this approach, researchers have identified many genes involved in Alzheimers disease. But this method can find genetic markers only for diseases that are common in the genomes of the study participants. If, for example, 90% of participants in an Alzheimers disease study have European ancestry and 10% have Asian ancestry, a genome-wide association study isnt likely to detect genetic risks for Alzheimers disease that are present only in individuals with Asian ancestry.

All peoples genetics reflect where their ancestors came from. But ancestry manifests as both genetic variation and social and cultural experiences. All of these factors can influence risk for certain diseases, and this can create problems. When socially caused disparities in disease prevalence appear across racial groups, the genetic markers of ancestry can be mistaken for genetic markers of disease.

African Americans, for example, are up to twice as likely as white Americans to develop Alzheimers disease. Research shows that much of this disparity is likely due to structural racism causing differences in nutrition, socioeconomic status and other social risk factors. A genome-wide association study looking for genes associated with Alzheimers might mistake genetic variations associated with African descent for genetic causes of the disease.

While researchers can use a number of statistical methods to avoid such mistakes, these methods can miss important findings because they are often unable to overcome the overall lack of diversity in genetic datasets.

Disentangling race, ancestry and health disparities can be a challenge in genome-wide association studies. Admixture mapping, on the other hand, is able to make better use of even relatively small datasets of underrepresented people. This method specifically gets its power from studying people who have mixed ancestry.

Admixture mapping relies on a quirk of human genetics you inherit DNA in chunks, not in a smooth blend. So if you have ancestors from different parts of the world, your genome is made of chunks of DNA from different ancestries. This process of chunked inheritance is called admixture.

Imagine color-coding a genome by ancestry. A person who has mixed European, Native American and African ancestry might have striped chromosomes that alternate among green, blue and red, with each color representing a certain region. A different person with similar ancestry would also have a genome of green, blue and red chunks, but the order and size of the stripes would be different.

Even two biological siblings will have locations in their genomes where their DNA comes from different ancestries. These ancestry stripes are how companies like Ancestry.com and 23andMe generate ancestry reports.

Because genome-wide association studies have to compare huge numbers of tiny individual genetic markers, it is much harder to find rare genetic markers for a disease. In contrast, admixture mapping tests whether the color of a certain ancestry chunk is associated with disease risk.

The statistics are fairly complicated, but essentially, because there are a smaller number of much larger ancestral chunks, it is easier to separate the signal from the noise. Admixture mapping is more sensitive, but it does sacrifice specificity, as it cant point to the individual genetic marker associated with disease risk.

Another important aspect of admixture mapping is that it looks at individuals with mixed ancestry. Since two people who have similar socioeconomic experiences can have different ancestry at certain parts of their genomes, admixture mapping can look at the association between this ancestry chunk and disease without mistaking social causes of disease for genetic causes.

Researchers estimate that 58% to 79% of Alzheimers disease risk is caused by genetic difference, but only about a third of these genetic differences have been discovered. Few studies have looked for genetic links to Alzheimers risk among people with mixed ancestry.

Our team applied admixture mapping to a genetic dataset of Caribbean Hispanic people who have a mix of European, Native American and African ancestry. We found a part of the genome where Native American ancestry made people less likely to have Alzheimers disease. Essentially, we found that if you have the color blue in this certain part of your genome, you are less likely to develop Alzheimers disease. We believe that with further research we can find the specific gene responsible within the blue chunk and have already identified possible candidates.

One important note is that the genetic diversity that plays a role in disease risk is not visible to the naked eye. Anyone with Native American ancestry at this particular spot in the genome not just a person who identifies as or looks Native American may have some protection against Alzheimers disease.

Our paper illustrates that gaining a more complete understanding of Alzheimers disease risk requires using methods that can make better use of the limited datasets that exist for people of non-European ancestry. There is still a lot to learn about Alzheimers disease, but every new gene linked to this disease is a step toward better understanding its causes and finding potential treatments.

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