Daily Archives: January 21, 2021

On the most recent episode of A Second Opinion podcast, I asked Dr. Francis Collins if we were going to be prepared for the next pandemic.

Senator, I sure hope so! This has been the worst pandemic in 102 years, and if we are not able to learn from this and plan for what inevitably will be down the road, then we only have ourselves to blame. We dont have a great track record there.

Francis Collins and I have a long professional friendship. We worked closely together from 1998 to 2003 when I was in the United States Senate and he was leading the Human Genome Project, and I have found him to be not only one of the nations top scientific minds, but also an exceptional communicator.

US President George W. Bush (R) presents the 2007 Presidential Medal of Freedom to Human Genome ... [+] Project leader Francis Collins 05 November 2007 in the East Room of the White House in Washington, DC. The award is the highest civilian honour given by the president in recognition of meritorious contribution to the US and to world peace. MANDEL NGAN/AFP via Getty Images

Today, as the director of the National Institutes of Health, Collins has a birds eye view of the pandemic, our national response, and how the iterative nature of science brought us to be able to respond as well as we have.

The Human Genome Project, an international effort to sequence the human genome, is the only government initiative that I recall coming in early and under budget. While the United States contributed a bit more than half of the budget and the manpower, it was an international effort also involving scientists from the United Kingdom, France, Germany, Japan and China. It was a monstrous effort and Collins served as the project lead, ensuring that all worked together and the genome was completed in 2003two years ahead of schedule.

That had never really been tried at that scale before. It was crossing into this territory of Big Science for biology and medicine, but it worked, Collins told me. The project also launched an era of data release and openness, with all of the human DNA information delivered into the public domain daily. The idea, Collins explained, was that DNA is our shared inheritance and all of us should be able to learn from it.

That mindsetthat biomedical research happens faster with collaboration and sharing of datais responsible for any success weve had with the COVID-19 pandemic. While there have been missteps, the technological advances of genomic sequencing and the international data sharing expectations sped our response by months if not years.

You can draw a direct line from the success of the Genome Project to the fact that we learned so quickly about SARS-CoV-2: what kind of virus this was, what kind of approach might be necessary to go after it, Collins said. After the Chinese lab released the sequence of the virus in January 2020a process that takes a good lab just an hour or two nowresearchers around the world could begin researching the virus without needing a sample. That made it possible within 24 hours for the first vaccine design to get started! Collins said.

The investments the American people made in the Human Genome ProjectCollins told me they spent about $3 billion on the project, $400 million of which was on the sequencing itselfhave repaid us hundreds of times over in biomedical, technology, computing, and economic advances.

Yet, one year ago, we still were not prepared for a global pandemic. Even though many of the scientific foundations were there, we have still spent 2020 learning hard lessons in funding, logistics, distribution, and more.

We have this complacency problem, and we need not slip into that, Collins told me.

I warned about this complacency in a series of 2005 speeches, noting that, rapid, voluminous, and essential travel and trade; the decline of staffed hospital beds; and a now heavily urbanized and suburbanized American population dependent as never before upon just in time but easily-disrupted networks of services and supply, had left us unprepared to respond to the unknown, deadly pathogens that would inevitably come.

And come, they have.

Collins had kind words to say about my warnings 15 years ago, but, unfortunately, those speeches didnt save us from our current reality. Some listened, maybe some didnt. Other pressures came along that seemed more urgent for that days needs and we kind of forgot about the difference between the important and the urgent, he observed. We better not do that this time.

WASHINGTON, DC - JULY 2: Dr. Francis Collins, Director of the National Institutes of Health (NIH), ... [+] holds up a model of COVID-19, known as coronavirus, during a US Senate Appropriations subcommittee hearing on the plan to research, manufacture and distribute a coronavirus vaccine, known as Operation Warp Speed, July 2, 2020 on Capitol Hill in Washington, DC. (Photo by Saul Loeb-Pool/Getty Images)

Instead, he highlighted what we have learned in the past 12 months that should serve us well in the future. We have developed new types of public-private partnerships and set up new funding models to more quickly enable urgent research. But there is more work to do. Collins called for active pathogen surveillance and platforms to quickly spin up development of vaccines, therapeutics, monoclonal antibodies, and diagnosticsat scale.

This work needs to be done around the world, not just at home. Collins and I agree wholeheartedly on this point. Now is our teachable moment: Viruses dont need visas and pandemics have no borders. The U.S. has a significant leadership role to play here, but we cant do it alone. Were in a circumstance, right now, where the boundaries between countries and cultures are increasingly porous both to ideas and ethical decisionsand viruses! Collins said.

Accomplishing all of these goals will take purposeful funding, diligence, and consistency. Its going to take strong voices like yours and maybe mine to keep putting this in front of leaders of the country and the world, Collins said. If you want to save the next group of lives from the next pandemicmaybe its influenza, maybe its another coronavirus, maybe its a filovirus, I dont know, but its coming!this set of lessons must not be forgotten.

Francis Collins, MD, PhD joined me on A Second Opinion podcast for Monday, January 11, 2021. For more of Dr. Collins insights on faith and science, the structure of NIH and how other countries have emulated it, science funding, and mRNA vaccines, see Episode 104 of A Second Opinion.

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NIH Director Dr. Francis Collins: Connecting The Dots From The Human Genome Project To The COVID-19 Vaccine - Forbes

We often hear the term "genomic tracing" bandied about in press conferences when a mystery COVID-19 case is linked to a cluster (along with a collective sigh of relief).

But what is genomic tracing, how does it work and where has it been used before?

Even though more people are talking about it than ever, genomic tracing has been used to identify and track down disease transmission routes for years.

It relies on genome sequencing a process that's been around since the 1970s, but has become much cheaper and faster in the past five years.

The Microbiological Diagnostic Unit Public Health Laboratory at Melbourne's Doherty Institute, for instance, started sequencing genomes of microbes in 2015, after drug-resistant bacteria outbreaks in Victorian hospitals.

The laboratory has since kept tabs on and helped identify pockets of community transmission of a whole raft of diseases including tuberculosis, gonorrhoea, listeria and salmonella.

So when the COVID-19 pandemic took off, the laboratory had everything in place to sequence the SARS-CoV-2 virus, says Norelle Sherry, a clinical microbiologist and infectious diseases physician at the Doherty Institute and Austin Health.

"We already had sequencing relationships with other labs and sequencing protocols set up for many different other organisms.

"This was just a new organism for us."

When a throat and nose swab returns a COVID-positive result, that same swab sample is sent to a genome sequencing laboratory, like the one at the Doherty's Public Health Laboratory.

While a diagnostic COVID test also uses the virus's genetic material, it only looks for a very small part of it to ascertain if it's there or not.

Breaking down the latest news and research to understand how the world is living through an epidemic, this is the ABC's Coronacast podcast.

Genomic sequencing, on the other hand, maps out the entire SARS-CoV-2 virus genetic code all 29,903 individual building blocks.

"It is really about looking at the whole picture," Dr Sherry says.

The problem is the virus's genetic material, which is in the form of a long strand of RNA, falls apart easily.

So once the RNA is extracted, it's used as a template to synthesise what's called complementary DNA. DNA is more robust than RNA and easier to work with.

From there, scientists must figure out the exact sequence of building blocks that make up the complementary DNA sequence.

The most common technique is known as short-read sequencing. The viral DNA is broken into 97 fragments that are copied and sequenced, by a machine, to produce short(ish) strings of letters.

Each letter A, T, C and G stands for a DNA building block.

This sequencing part of the process can take anywhere from around four to 36 hours, depending on the technology used, Dr Sherry says. The trade-off for greater speed, though, is lower accuracy.

Those 97 sequenced fragments are then put together, like a jigsaw puzzle, into a continuous string of As, Ts, Cs and Gs.

Next is to compare that newly constructed viral genome sequence with other sequences.

In Victoria, every SARS-CoV-2 genome sequence is compared to all other Victorian SARS-CoV-2 sequences.

The Communicable Disease Genetic Network also allows laboratories Australia-wide to compare sequences and identify spread between states.

This is done by lining them up and looking for any differences, no matter how small, between the 29,903-long strings of letters.

If a newly sequenced genome is pretty much identical to those from a known cluster, that's a strong clue that it's linked to those infections.

But it's only part of the tracing process, Dr Sherry says.

"By combining that genomic information with epidemiological information about the case where they've been, who they've had contact with, when they got sick then we can use the information together to work out how the virus was likely transmitted.

"Genomics without epidemiology is not actually all that useful."

This genomic information also feeds into a map of sorts, called a phylogenetic tree, that tells researchers how related each sequence is to every other sequence.

And because Australia has had relatively low numbers of COVID-19 cases, almost every positive test result in the nation has been sequenced.

This gives researchers a comprehensive picture of how the coronavirus spread in Australia.

"It means that we have one of the most complete population-level datasets globally," Dr Sherry says.

But in places like the UK, where positive cases are in the tens of thousands every day, only around a 10 per cent are sequenced.

In the coming months, the Doherty's Public Health Laboratory will also keep an eye out for genetic changes in SARS-CoV-2 that may help it dodge the protective effects of vaccines, she adds, "to make sure that we identify them early in the unlikely event that it happens".

Get all the latest science stories from across the ABC.

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COVID-19: what is genomic tracing and how does it work? - ABC News

If you are a lucky species, you will stumble into random gene mutations that just happen to help you survive better - allowing you and your descendants to keep and build on the helpful traits they encode. As with anything involving luck, the more chances you take, the more chances you have of hitting the jackpot.

That's what seems to have happened with our long-ago ancestors - the ones we share with still living lungfish. They struck enough genetic jackpots to allow them to climb out of the water and access the whole new world of land, around 420 million years ago.

In doing so, they became the ancestors of all land animals with backbones (tetrapods). Having a massive genome, like that found in modern lungfish, may have helped with this.

Researchers just sequenced the entire genome of the endangered Australian lungfish (Neoceratodus forsteri), which has the largest known animal genome. It is 14 times the size of ours.

This required new DNA sequencing techniques and masses of computing power, only now technically possible - to piece together a whopping 43 billion nucleotides ('letters' in the genetic code).

"When you look at it from a genomic perspective, [lungfish are] genomically halfway between a fish and a land-based vertebrate," biologist Siegfried Schloissnig from the Research Institute of Molecular Pathology (IMP) in Austria told New Scientist.

Of six still living species of lungfish, four are African, one South American, and one Australian. They first appeared in the fossil record 400 million years ago.

The Australian species has retained the most ancestral features, and was mistakenly classed as an amphibian when first discovered, due to its bizarre mix of fish and newt features, including its weird, leg-like lobed fins.These strange in-between 'living fossils' can live up to 100 years.

Australian lungfish still appear to closely resemble the fossils of their 100-million-year-old (and now extinct) ancestral species that hauled themselves out of the water, eventually spawning mammals, birds, reptiles, and amphibians.

Its genome confirms that this air-gulping swimmer is our closest living fish relative, beating the other contender, coelacanths - another group of lobed finned fish.

So within the Australian lungfish's giant haystack of genes are clues to how animals made the transition from aquatic to terrestrial.

"This... required a number of evolutionary innovations including airbreathing, limbs, posture, prevention of desiccation, nitrogen excretion, reproduction, and olfaction," the researchers write in their paper.

They identified the same genes responsible for our embryonic lung development already present in the lungfish, as are our familiar ulna and radius arm bones, and the genes that encode them. Tetrapod limb patterning genes like hox-c13 and sal1 had never been seen before in fish.

"Such novelties might have predisposed the [lobe-finned fish]to conquer land demonstrating how the lungfish genome can contribute to better understanding of this major transition during vertebrate evolution," the team write.

The researchers also found huge additions to the lungfish's genes associated with smell - what would have been a new suite of sensors suitable to their ancestors' new environment. These genes code for receptors of airborne odours, while groups of receptors for waterborne scents shrunk.

Many of the excess genes that bulk out their hefty genome arose through copied sections of their DNA. Some of the lungfish's individual chromosomes contain as many nucleotides as our entire human genome.

This form of genome expansion, through copies, is known to be animportant driving force of evolution, with evidence that it helps provide organisms with the ability to rapidly adapt to a changing environment.

The Australian lungfish is an incredible living record of our evolution, and after preserving this genetic history for so long, it's now under threat by human activities altering the freshwater habitats it calls home.

The animal hunts for frogs, worms and snails, as well as munching on plants in the water. It usually relies on gills to breathe, but its single lung allows the lungfish to surface for fresh air when dry conditions reduce their watery environment, making it murky and stagnant.

"There is no doubt that the newly sequenced genome will unveil more of the secrets of this bizarre vertebrate in the future," saidIMP cellular geneticist Elly Tanaka.

"Not only can it teach us things about adaptations to life on land, but it may also explain how certain genomes evolve to be so big."

This research was published in Nature.

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The Massive Genome of The Lungfish May Explain How We Made The Leap to Land - ScienceAlert

America's 46th president wants to use government policy and technology to address social justice, climate change, and economic prosperity.

President Joe Biden has added a science advisor to his Cabinet and wants tech leaders to help solve the country's biggest problems including climate change, the COVID-19 pandemic, and social justice.

Image: Bet_Noire

President Joe Biden is making science part of the decision-making process again by adding the director of the Office of Science and Technology Policy to his Cabinet. Biden asked Eric Lander to lead the OSTP. Lander was one of the leaders of the Human Genome Project and is now the president ofthe Broad Institute of MIT and Harvard. He also was the co-chair of the President's Council of Advisors on Science and Technology for President Barack Obama.

Gary Shapiro, president and CEO of CTA, said he looks forward to working with the new OSTP and providing a forward-thinking approach to how tech can continue to serve as a tool for helping the country.

SEE: Big data's role in COVID-19 (free PDF) (TechRepublic)

"President-elect Biden's decision to elevate the Office of Science and Technology Policy to Cabinet level reflects tech's vital role in solving pressing challengesfrom creating a cleaner environment to conquering the pandemic," he said.

In his nomination letter to Lander, Biden asked the researcher to consider five specific questions and recommend general strategies, specific actions, and new structures that the federal government should adopt to support these priorities. The five questions are:

Tom Wheeler, a former chairman of the FCC and currently a visiting fellow with the Center for Technology Innovation at The Brookings Institution, said that adding the head of the OSTP to the Cabinet sends the message that science and technology are guiding principles again after four years of an administration that took the opposite approach.

The American Association for the Advancement of Science and The National Academies of Sciences, Engineering, and Medicine both applauded Lander's appointment. Lander is known for his scientific accomplishments but also for his combative management style. Colleagues have accused him of rewriting the history of CRISPR and downplaying contributions of the two women who won a Nobel prize in 2020 for their work on the gene-editing technology.

Wheeler also was on the Obama transition team. He said the new government was facing one existential crisis back in early 2008: The economic collapse. He described the five enormous problems the incoming Biden administration faces:

Wheeler said that the new administration should focus on how technology can help provide solutions to these existential crises.

"An easy one to envision is broadband policy: Connecting those who are not connected because they don't have access or or they can't afford it; that one thing hits four of those issues," he said.

Wheeler said it's time for government leaders to start using policy to put guardrails around all forms of technology.

"It's the innovators who always make the rules early on until those rules begin to infringe on the right of others and the public interest," he said. "That time is now."

This new approach should apply across the board to everything from artificial intelligence to Section 230 to net neutrality, Wheeler said. He was a chief architect of net neutrality during his five years as FCC chairman.

He also said that government policies and the policy-making process should adopt an agile approach, just as many digital companies do.

The existing government regulatory agencies that we know today were created in response to the Industrial Revolution, he said, which resulted in a rules-based hierarchy and a rigid process.

"That structure is handicapped when it comes to dealing with the need for agile, adaptive oversight to handle a rapidly changing tech and marketplace reality," he said. "How do we bring agile regulation into government? That will be the challenge."

Wheeler said digital companies have been able to make the rules for themselves because only those leaders had the vision to see where the industry was going.

"Big Tech was unfathomable to most Americans as well those who represent them in Congress," he said. "We're getting to the point now that the people are aware that their rights are being abused and therefore their representatives are similarly coming up to speed."

At CES 2021, National Economic Council Director-Designate Brian Deese spoke with CES President Gary Shapiro about Biden's tech and economic priorities. Deese will be part of the Cabinet and will help shape economic policy decisions. Deese said Biden wants to reinvest in manufacturing and research and development.

He said the COVID-19 vaccine is "a testament to technology and science," but added that the operational challenge of "getting the vaccines into people's arms will be one of the most costly and complex issues in our country's history." He said tech companies can help with the public health response.

During the Trump administration, the OSTP focused on quantum computing and artificial intelligence. An administration official attended CES 2020 to talk about new guidelines for artificial intelligence (AI). In August 2020, the White House, the National Science Foundation (NSF), and the Department of Energy (DOE) announced more than $1 billion in funding for 12 new AI and QIS research and development (R&D) institutes nationwide.

Learn the latest news and best practices about data science, big data analytics, and artificial intelligence. Delivered Mondays

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Human genome expert to join the Cabinet as Biden brings science and technology back to the table - TechRepublic

Bridgestone Corporation announced results of its four-year collaboration with genomic big data solutions company NRGene to advance the commercialization of guayule, an alternative to natural rubber, as part of the effort to diversify its sources of raw materials. The combined effort focused on analyzing DNA to allow more efficient use of inherent genetic diversity to breed highly productive varieties of guayule.

Native to the desert regions of the southwestern United States and northern Mexico, guayule is a shrub capable of producing natural rubber and can grow on marginal farmland with minimal fertilizer inputs. Guayule has the physical and genetic characteristics of a desert plant, successfully tolerating arid environments and making its demand for water lower than other commercial crops grown in the region. This is important since dwindling water resources in the Southwest US are demanding that agriculture find ways to reduce water usage and guayule could be a solution.

Utilizing NRGenes DeNovoMAGIC system, scientists at Bridgestone and NRGene have successfully assembled a specific guayule genome. This achievement provided a complete description of the genome sequence and all its genes, allowing for the use of additional genomic diversity in the identification of the genetic basis for important traits such as rubber percentage.

Furthermore, Bridgestone developed mapping populations that allowed NRGene to construct a genetic and physical map by successfully identifying the correct order of DNA fragments. These maps enable Bridgestone to use the information contained in the genetic code to assist in its breeding efforts. The joint work was successful in constructing pseudochromosomes (i.e. molecules that contain most of the information of the chromosomes) using an approach that combines multiple genomes, marking a historic milestone in guayule research.

The collaboration between Bridgestone and NRGene will provide important advances for the future of the automotive and rubber industries. The combination of our previous work with the sequencing and assembly of the hevea genome and our current work with guayule uniquely positions Bridgestone to utilize these resources for comparative genetic analysis of the rubber biosynthetic pathways and become a leader in the genetics and improvement of rubber-producing plants.

William Niaura, director, Innovation, Bridgestone Americas

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Bridgestone collaboration with NRGene achieves new milestones in assembly of multiple guayule genomes; alternative to natural rubber - Green Car...

This article was originally published here

Mol Reprod Dev. 2021 Jan 20. doi: 10.1002/mrd.23449. Online ahead of print.

ABSTRACT

BRDT, a member of the BET family of double bromodomain-containing proteins, is essential for spermatogenesis in the mouse and has been postulated to be a key regulator of transcription in meiotic and post-meiotic cells. To understand the function of BRDT in these processes, we first characterized the genome-wide distribution of the BRDT binding sites, in particular within gene units, by ChIP-Seq analysis of enriched fractions of pachytene spermatocytes and round spermatids. In both cell types, BRDT binding sites were mainly located in promoters, first exons, and introns of genes. BRDT binding sites in promoters overlapped with several histone modifications and histone variants associated with active transcription, and were enriched for consensus sequences for specific transcription factors, including MYB, RFX, ETS, and ELF1 in pachytene spermatocytes, and JunD, c-Jun, CRE, and RFX in round spermatids. Subsequent integration of the ChIP-seq data with available transcriptome data revealed that stage-specific gene expression programs are associated with BRDT binding to their gene promoters, with most of the BDRT-bound genes being upregulated. Gene Ontology analysis further identified unique sets of genes enriched in diverse biological processes essential for meiosis and spermiogenesis between the two cell types, suggesting distinct developmentally stage-specific functions for BRDT. Taken together, our data suggest that BRDT cooperates with different transcription factors at distinctive chromatin regions within gene units to regulate diverse downstream target genes that function in male meiosis and spermiogenesis.

PMID:33469999 | DOI:10.1002/mrd.23449

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Genome-wide chromatin occupancy of BRDT and gene expression analysis suggest transcriptional partners and specific epigenetic landscapes that regulate...

SAN DIEGO, Jan. 18, 2021 (GLOBE NEWSWIRE) -- Bionano Genomics, Inc. (Nasdaq: BNGO) announced that the last day of its five-day Next-Generation Cytogenomics Symposium featured presentations by members of the COVID-19 Host Genome Structural Variant (SV) Consortiumusing the Saphyr system for optical genome mapping (OGM) to analyze the genomes of patients with severe COVID-19 disease. The presentations by scientists and clinicians from leading hospitals and research institutions in Europe and the US showed that Saphyr was able to detect structural variants that may predispose to severe or mild COVID-19 disease, which had not been identified previously by large studies using next-generation sequencing (NGS) or array-based methods to analyze genomic variation.

Dr. Alex Hoischen, Radboud University, discussed his published results on genomic variants found in families with severe COVID-19. In two families with severely ill brothers, mutations were found in the Toll Like Receptor 7 gene (TLR7), which affects the production of interferons, signaling molecules used to control the immune response. Several other studies have since made similar findings in other genes of the TLR family. Dr. Hoischen discussed how individual patients each may carry individually rare variants, that are collectively common and point to important pathways involved in the disease. His interest in the consortium is based on his understanding that larger SVs have a greater chance to be rare and disruptive, and genome-wide studies have lacked so far in their assessment.

Dr. Erich Jarvis, Howard Hughes Medical Institute investigator, professor at The Rockefeller University and head of the Vertebrate Genome Project (VGP),discussed an interesting difference between hospitalized patients and controls where the severely ill show more variation in a part of the Interferon Alpha and Beta Receptor Subunit 1 gene, a key part of the interferon pathway that regulates immune response. Dr. Jarvis is using Saphyr and the pipeline he developed for the VGP to build reference-quality genomes of patients and controls and will compare them with each other and with animal species that are sensitive to infection with SARS-CoV-2 or not, as previously reported.

Dr. Ravindra Kolhe, Vice-Chairman of Pathology at the Medical College of Georgia at Augusta University and founder of the COVID-19 Host Genome SV Consortium explained that he founded the consortium because COVID-19 shows a split mortality where a very large number of people get infected, but only a small percentage of those get sick or die. Mortalities are associated with diabetes, hypertension and a history of heart failure, yet independent of that a seemingly random group of patients get extremely ill. Since other studies looking at host genetics use NGS or single nucleotide polymorphism (SNP) arrays that are ill suited to analyze SVs, the consortium focuses on the use of OGM to detect the larger genomic variants most likely to make the largest impact.

Dr. Kolhe presented the previously announced finding from the consortium on 37 ICU-admitted, severely ill COVID-19 patients whose genomes were analyzed using Saphyr.In several severely ill patients Saphyr detected structural variants affecting important immune genes. In another patient Saphyr found a duplication of the STK26 gene, which reduces the production of interferon likelyleading to reduced viral clearance and increasing the disease severity. When other severely ill patients were compared with asymptomatic COVID-19 patients, the sameSTK26gene was found to be significantly more active in all the sick patients, making it a possible biomarker for disease severity. OGM identified many more variants in the severely ill patients affecting genes controlling immunity, airway mucous, and viral replication. Dr. Kolhe stated that his team wants to use structural variants identified with Saphyr to design preventative measures for those people whose genomes show them to be the most vulnerable and develop a biomarker panel that can be run at the time of patient admission, to make sure that appropriate measures are taken based on the genetic makeup and patients get the treatment they need as early as possible. In order to do so, the consortium has announced plans to analyze 1000 genomes with Saphyr allowing them to determine with high confidence which SV are involved in disease susceptibility and severity.

Siavash Raisi, Dr. Vineet Bafnas laboratory at UCSD presented on FaNDOM, an algorithm they developed that is used by the consortium to quickly and efficiently verify the structural variants identified by the Saphyr system. It was able to provide an independent confirmation of all of the variants identified by Saphyr using Bionano Access and Solve software and reported in the consortium publication.

Dr. Silviu-Alin Bacanu, Virginia Commonwealth University described how existing resources and other host genome studies can be used to prioritize genes and structural variants identified with Saphyr.He described several studies including the genome-wide association studies on COVID-19 host genetics and the UK Biobank which has collected genomic data on more than 250,000 individuals. Although these large studies are unable to identify important large variants directly, their data can help prioritize variants detected by OGM based on whether they affect genes or pathways which these larger studies have identified as possible correlated with disease severity and outcome.

Dr. Alan Beggs and Dr. Catherine Brownstein, Boston Childrens Hospital (BCH) discussed their previously announced study on the genomes of patients with Multisystem Inflammatory Syndrome in Children (MIS-C), a severe inflammatory attack of multiple organs weeks after COVID-19 infection in children with an average age of 8 years old. BCH has reported 67 cases of hospitalized MIS-C, and the Childrens Rare Disease Cohort Initiative has banked their specimens. Drs. Beggs and Brownstein are enrolling 50 patients each with MIS-C, severe COVID-19, and asymptomatic or mildly affected patients and will compare their genomes using OGM with Saphyr and with NGS.

Dr. Michael Zody, New York Genome Center (NYGC) presented on the use of NGS on patients also analyzed with Saphyr. The NYGC has an active research project to sequence both the viral and the patient genomes using NGS. Their study is focused on patients with severe COVID-19 without prior high-risk diseases and on MIS-C cases, and in a collaboration with Dr. Jean-Laurent Casanova has found rare defects in immunity that affect the disease severity by altering the interferon response in patients. By combining the NGS data collected by NYGC with the OGM data from the consortium, smaller events and single nucleotide variants detected by NGS and large variants detected by Saphyr can be analyzed together.

Recordings of all the presentations from the symposium can be found at http://bit.ly/3pLPT28

About Bionano GenomicsBionano 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, and 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, visitwww.bionanogenomics.comor http://www.lineagen.com.

Forward-Looking StatementsThis 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 and content of the presentations identified in this press release; the effectiveness and utility of Bionanos technology in basic genetic research and clinical settings, and in the contexts and applications contemplated by the presentations identified in this press release; adoption of Saphyr as a standard platform in research and pathology settings; 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: 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 withour 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, 2019 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 Contact:Ashley R. RobinsonLifeSci Advisors, LLC+1 (617) 430-7577arr@lifesciadvisors.com

Media Contact:Darren Opland, PhDLifeSci Communications+1 (617) 733-7668darren@lifescicomms.com

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Day Five of Bionano's Next-Generation Cytogenomics Symposium: Saphyr Identifies Structural Variants that May Predispose to Severe COVID-19 Illness -...

A new study shows that humans express a powerful hormone during exercise and that treating mice with the hormone improves physical performance, capacity and fitness. Researchers say the findings present new possibilities for addressing age-related physical decline.

The research, published on Wednesday inNature Communications, reveals a detailed look at how the mitochondrial genome encodes instructions for regulating physical capacity, performance and metabolism during aging and may be able to increase healthy lifespan.

Mitochondria are known as the cells energy source, but they are also hubs that coordinate and fine-tune metabolism by actively communicating to the rest of the body, saidChanghan David Lee, assistant professor at theUSC Leonard Davis School of Gerontologyand corresponding author of the study. As we age, that communication network seems to break down, but our study suggests you can restore that network or rejuvenate an older mouse so it is as fit as a younger one.

The study looked at the role of MOTS-c, one of several recently identified hormones known to mimic the effects of exercise. However, MOTS-c is unique because it is encoded in the small genome of mitochondria rather than the larger genome in a cells nucleus. This opens up a whole new genome to target for new interventions, says Lee, who, along with Pinchas Cohen, professor of gerontology, medicine and biological sciences and dean of the USC Leonard Davis School, first described the evolutionarily conserved protein and its effects on metabolism in 2015.

Lees subsequent studies showed how mitochondrial-encoded MOTS-c instructs proteins to interact with the nuclear genome and plays important roles inregulating cell metabolism and stress responses.

Even groups of mice that had been fed a high-fat diet showed marked physical improvement after MOTS-c treatment and less weight gain than untreated mice. These findings echo previous research on MOTS-c treatment in mice, which also found that it reversed diet-induced obesity and diet- and age-dependent insulin resistance.

Additionally, treating the oldest mice nearing the end of their lives with MOTS-c resulted in marked physical improvements. This late-life treatment improved grip strength, gait (measured by stride length) and physical performance, which was assessed with a walking test (running was not possible at this age).

The older mice were the human equivalent of 65 and above and once treated, they doubled their running capacity on the treadmill, Lee said. They were even able to outrun their middle-aged, untreated cohorts.

In muscle cells, levels of MOTS-c significantly increased nearly 12-fold after exercise and remained partially elevated after a four-hour rest, while MOTS-c levels in blood plasma also increased by approximately 50% during and after exercise and then returned to baseline after the rest period. The findings suggest that the exercise itself induced the expression of the mitochondrial-encoded regulatory peptides.

The expression of MOTS-c during exercise in humans and the results from the studies in mice lend support to the idea that aging is regulated by genes in both the mitochondrial and nuclear genomes. While further research on MOTS-c is needed, the data indicates that MOTS-c treatment could increase health span, or the portion of the life span spent in good health, and address frailty and other age-related conditions, Lee said.

The results from MOTS-c treatment in mice are extremely promising for future translation into humans, he added, especially the fact that such results were obtained even with treatment starting at older ages.

Indicators of physical decline in humans, such as reduced stride length or walking capacity, are strongly linked to mortality and morbidity, he said. Interventions targeting age-related decline and frailty that are applied later in life would be more translationally feasible compared to lifelong treatments.

Reference: Reynolds JC, Lai RW, Woodhead JST, et al. MOTS-c is an exercise-induced mitochondrial-encoded regulator of age-dependent physical decline and muscle homeostasis. Nat Comms. 2021;12(1):470. doi:10.1038/s41467-020-20790-0.

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Treating Mice With Hormone Improves Physical Performance - Technology Networks