Category Archives: Molecular Medicine

image:Professor Tuuli Lappalainen, Associate Member of the New York Genome Center and one of the leaders of the study. view more

Credit: NYGC

NEW YORK, NY (August 3, 2022) Research on RNA diversity in human tissues, led by scientists from the New York Genome Center and the Broad Institute, is described in a recent study published in Nature. When the genetic code is transcribed to RNA, one gene typically produces several different forms of RNA molecules, or transcripts, with different functions. While this phenomenon has been known for decades, the catalog of human transcripts has remained incomplete.Equipped with the latest sequencing technology, we were able to read segments of over one thousand nucleotides, compared to less than one hundred with standard approaches, describes Dr. Beryl Cummings, one of the leaders of the project and formerly a postdoctoral fellow at the Broad Institute. Importantly, we were able to do this at scale of over 80 samples from many tissues, which led to discovery of tens of thousands of novel transcripts, she adds.The researchers used their data to characterize how genetic and environmental differences can manifest in differences in the transcriptome. Genetic differences between individuals can affect how genes are regulated. We were able to describe with a finer resolution than before how transcript structures are affected. This helps to understand molecular underpinnings of variants that contribute to disease risk, explains Dr. Dafni Glinos from the New York Genome Center and co-first author of the study.

We believe the discoveries, data, and tools we present pave the way for a new era of transcriptome research. About a decade ago, high-through analysis of small DNA or RNA segments revolutionized genomics. I think were at the cusp of a new revolution with long read sequencing says Professor Tuuli Lappalainenfrom the New York Genome Center andone of the leaders of the study.

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About the New York Genome Center

The New York Genome Center (NYGC)is an independent, nonprofit academic research institution that serves as a multi-institutional hub for collaborative genomic research. Leveraging our strengths in technology development, computational biology, and whole-genome sequencing and analysis, our mission is to advance genomic science, and its application to novel biomedical discoveries. NYGCs areas of focus include the development of computational and experimental genomic methods and disease-focused research to advance the understanding of the genetic basis of cancer, neurodegenerative disease, and neuropsychiatric disease. Since 2020, the NYGC has worked with its hospital and academic partners to advance COVID-19 research, whole genome sequencing over 12,000 viral samples to discover new viral variants and explore the genetic basis of severe disease.

Institutional founding members are: Cold Spring Harbor Laboratory, Columbia University, Albert Einstein College of Medicine, Memorial Sloan Kettering Cancer Center, Icahn School of Medicine at Mount Sinai, New York-Presbyterian Hospital, New York University, Northwell Health, The Rockefeller University, Stony Brook University, and Weill Cornell Medicine. Institutional associate members are: American Museum of Natural History, Hospital for Special Surgery, Georgetown Lombardi Comprehensive Cancer Center, Hackensack Meridian Health, The New York Stem Cell Foundation, Princeton University, Roswell Park Cancer Institute and Rutgers Cancer Institute of New Jersey. For more information on the NYGC, please visit:http://www.nygenome.org

Media Contact:

Madisen Grimaldi, NYGC, Senior Communications Associate

mgrimaldi@nygenome.org

c: (215) 870-1149

Scientist Contacts:

Scientist Contact:

Prof. Tuuli Lappalainen Dr. Dafni Glinos Dr. Beryl Cummings

tlappalainen@nygenome.org dafni.glinos@gmail.com berylbcummings@gmail.com

+1-9177532661 or +46-721940550 +44-7564001951 +19197256320

Imaging analysis

Human tissue samples

3-Aug-2022

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.

Originally posted here:
RNA diversity in human tissues mapped with emerging sequencing technology - EurekAlert

CHICAGO, July 24, 2022 /PRNewswire/ -- At the 2022 AACC Annual Scientific Meeting & Clinical Lab Expo, laboratory medicine experts will present the cutting-edge research and technology that is revolutionizing clinical testing and patient care. From July 24-28 in Chicago, the meeting's 250-plus sessions will deliver insights on a broad range of timely healthcare topics. Highlights include discussions exploring the use of artificial intelligence (AI) in personalized medicine, advances in multiplexed genomic sequencing and imaging, real-life applications of human brain organogenesis, how to build trust with patients, and guiding clinical decisions with mass spectrometry.

(PRNewsfoto/AACC)

AI in Personalized Medicine. Precision medicine involves tailoring treatments to individual patients and, increasingly, clinicians are using AI in their clinical prediction models to do this. In the meeting's opening keynote, Dr. Lucila Ohno-Machado, health associate dean of informatics and technology at the University of California San Diego, will introduce how AI models are developed, tested, and validated as well as performance measures that may help clinicians select these models for routine use.

Multiplexed Genomic Sequencing and Imaging. Thanks to advances in multiplexed genomic sequencing and imaging, we can identify small but crucial differences in DNA, RNA, proteins, and more. These techniques have also undergone a 50-million-fold reduction in cost and comparable improvements in quality since they first emerged. In spite of this, healthcare is just beginning to catch up with the implications of these technologies. Dr. George Church, AACC's 2022 Wallace H. Coulter Lectureship Awardee and founding core faculty and lead at the Synthetic Biology Wyss Institute at Harvard University, will discuss advances and implications of multiplex technologies at this plenary session.

Applications of Human Brain Organoid Technology. The human brain is a very complex biological system and is susceptible to several neurological and neurodegenerative disorders that affect millions of people worldwide. In this plenary session, Dr. Alysson R. Muotri, professor of cellular and molecular medicine at the University of California San Diego School of Medicine, will explore the concept of human brain organogenesis, or how to recreate the human brain in a dish. Several applications of this technology in neurological care will be discussed.

Story continues

Building Trust in Healthcare. The world is having a trust crisis that is affecting healthcare delivery across the globe. Dr. Thomas Lee, chief medical officer of Press Ganey Associates and professor of health policy and management at the Harvard T.H. Chan School of Public Health, will describe the importance of building trust among patients and healthcare workers in this plenary session. He will explore a three-component model for building trust, and the types of interventions most likely to be effective.

Guiding Clinical Decisions with Mass Spectrometry. In this, the meeting's closing keynote, Dr. Livia Schiavinato Eberlin, associate professor of surgery and director of translational and innovations research at Baylor College of Medicine, will discuss the development and application of direct mass spectrometry techniques used in clinical microbiology labs, clinical pathology labs, and the operating room. The presentation will focus on results obtained in ongoing clinical studies employing two direct mass spectrometry techniques, desorption electrospray ionization mass spectrometry imaging and the MasSpec Pen technology.

Additionally, at the Clinical Lab Expo, more than 750 exhibitors will display innovative technologies that are just coming to market in every clinical lab discipline.

"Laboratory medicine's capacity to adapt to changing healthcare circumstances and use the field's scientific insights to improve quality of life is unparalleled. This capacity is constantly growing, with cutting-edge diagnostic technologies emerging every day in areas as diverse as mass spectrometry, artificial intelligence, genomic sequencing, and neurology," said AACC CEO Mark J. Golden. "The 2022 AACC Annual Scientific Meeting will shine a light on the pioneers in laboratory medicine who are mobilizing these new advances to enhance patient care."

Session Information

AACC Annual Scientific Meeting registration is free for members of the media. Reporters can register online here: https://www.xpressreg.net/register/aacc0722/media/landing.asp

AI in Personalized Medicine

Session 11001 Biomedical Informatics Strategies to Enhance Individualized Predictive ModelsSunday, July 245-6:30 p.m.U.S. Central Time

Multiplexed Genomic Sequencing and Imaging

Session 12001 Multiplexed and Exponentially Improving TechnologiesMonday, July 258:45 10:15 a.m.U.S. Central Time

Applications of Human Brain Organoid Technology

Session 13001 Applications of Human Brain Organoid TechnologyTuesday, July 268:45 10:15 a.m.U.S. Central Time

Building Trust in Healthcare

Session 14001 Building Trust in a Time of TurmoilWednesday, July 278:45 10:15 a.m.U.S. Central Time

Guiding Clinical Decisions with Mass Spectrometry

Session 15001 Guiding Clinical Decisions with Molecular Information provided by Direct Mass Spectrometry TechnologiesThursday, July 288:45 10:15 a.m.U.S. Central Time

All sessions will take place in Room S100 of the McCormick Place Convention Center in Chicago.

About the 2022 AACC Annual Scientific Meeting & Clinical Lab ExpoThe AACC Annual Scientific Meeting offers 5 days packed with opportunities to learn about exciting science from July 24-28. Plenary sessions will explore artificial intelligence-based clinical prediction models, advances in multiplex technologies, human brain organogenesis, building trust between the public and healthcare experts, and direct mass spectrometry techniques.

At the AACC Clinical Lab Expo, more than 750 exhibitors will fill the show floor of the McCormick Place Convention Center in Chicago with displays of the latest diagnostic technology, including but not limited to COVID-19 testing, artificial intelligence, mobile health, molecular diagnostics, mass spectrometry, point-of-care, and automation.

About AACCDedicated to achieving better health through laboratory medicine, AACC brings together more than 70,000 clinical laboratory professionals, physicians, research scientists, and business leaders from around the world focused on clinical chemistry, molecular diagnostics, mass spectrometry, translational medicine, lab management, and other areas of progressing laboratory science. Since 1948, AACC has worked to advance the common interests of the field, providing programs that advance scientific collaboration, knowledge, expertise, and innovation. For more information, visit http://www.aacc.org.

Christine DeLongAACCSenior Manager, Communications & PR(p) 202.835.8722cdelong@aacc.org

Molly PolenAACCSenior Director, Communications & PR(p) 202.420.7612(c) 703.598.0472mpolen@aacc.org

Cision

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Artificial Intelligence in Personalized Medicine, Genomic Sequencing Advances, Human Brain Organogenesis, Building Trust with Patients, Guiding...

Faculty Positions in Life Science and Medicine at

National Tsing Hua University (Taiwan)

Location

Hsinchu, Taiwan

DeadlinePlease check the following link for information.

Position description and other specified information

Required Qualifications:PhD in related fields.

Application:All applicants are required to submit aCurriculum Vitae and othersupporting materials.

About NTHU (Please find more in company)

At National Tsing Hua University (NTHU), we believe that everyone deserves the opportunity to explore and realize their unique potential. In everything we do, NTHU will continue to uphold our core values of inclusivity, equality, and inclusivity in safeguarding academic freedom and shared governance.NTHU is widely recognized as a foremost incubator of future leaders in industry and academia. NTHUs consistent record of excellence is exemplified by the outstanding achievement of our faculty and alumni, among whom are two Nobel laureates in physics, one Nobel laureate in chemistry, and one Wolf Prize winner in mathematics.

Salary

1.Statutory Salary:

The statutory salary for a full-time facultymember includes Base SalaryandAdditional Academic Research Pay.

(Please refer to https://yushan.site.nthu.edu.tw/p/412-1518-17613.php?Lang=en)

2. Non-statutory (Additional) Salary:

(1) Yushan Fellows and Yushan Young Fellows: If approved by the Ministry of Education as a Yushan Scholar or Yushan Young Scholar, theMOE willprovide the subsidyfor the non-statutory (additional) salary:

(Please refer tohttps://yushan.moe.gov.tw/TopTalent/EN/Intro)

(2) Flexible Salary Reward: If not approved by the MOE Yushan Fellow Program, NTHU may provide a Flexible Salary Reward if it conforms to the regulations of the NTHU Newly-Recruited Faculties Flexible Salary Reward.

(Please refer to https://yushan.site.nthu.edu.tw/p/412-1518-18110.php?Lang=en)

(3) Newly appointed foreigner (non-Taiwanese) faculty members are eligible to apply for an extra compensation of 25,000 NTD/month till 2027.

Taiwan is ranked 19th in global purchasing power parity (PPP) indicating high standard of living with stable and low cost of living.

(Please refer to https://en.wikipedia.org/wiki/List_of_countries_by_GDP_(PPP)#cite_note-:0-1)

We also provide

1. Subsidy for NTHU Newly-Recruited Faculty Academic Research (start-up subsidy)

2. Subsidy for Guest House and Accommodation

3. Education of children

About College of Life Science(https://cls.site.nthu.edu.tw/app/index.php?Lang=en)

Established in 1991 as the very first Department of Life Science in Taiwan, the Department of Life Science allows students to explore various areas of life science in an integrated yet diverse program built upon a solid foundation of chemistry, physics, mathematics and biology. In 2022, the College of Life Science was reorganized and is now comprised of the Department of Life Science, the Department of Medical Science, the Interdisciplinary Program of Life Science, the School of Medicine and five Institutes, the Institute of Molecular and Cell Biology, the Institute of Bioinformatics and Structural Biology, the Institute of Molecular Medicine, the Institute of Biotechnology, and Institute of Systems Neuroscience. The Department of Life Science, Medical Science and Interdisciplinary Program offer undergraduateBachelor of Science(B.Sc.) programs in Biology and Medical Science whereas the five Institutes offer graduate programs in a variety of research areas. The School of Medicine offers Doctor of Medicine.

Five educational goals of the College of Life Science (ERIGS):

1. Education: Excellence in education and learning in the fields of life science

2. Research: Innovative research and research training at the highest international level in the fields of life science

3. Internal Mobilization: Supporting the development of students and colleagues

4. Globalization: Widening global worldview and providing international environment for the studies of life science

5. Social Responsibility: Model for sharing common wealth from life science research

We strive to train our young life scientists as prophetic leaders of future generations with a passion for science, and compassion for life and a desire to transform the world.

Chronology

1973 Institute of Molecular Biology (IMB) established

1974 Masters program for IMB established

1984 Ph.D. program for IMB established

1985 Re-organized as Institute of Life Science

1987 Life Science Building I completed

1991 Institute of Biomedicine and Department of Life Science established

1992 College of Life Science established

1995 All institutes merged into Department of Life Science

1997 Institute of Biotechnology established

1998 Institute of Radiation Biology merged with the College

2002 Reorganized into four institutes and Department of Life Science

2004 Brain Research Center established

2008 Interdisciplinary Program of Life Science and Institute of Systems Neuroscience established

2010 Department of Medical Science established

2013 Interdisciplinary Neuroscience Ph.D. Degree Program established

2016 Ph.D. Program in Bioindustrial Technology established

2022 School of Medicine established

2022 Reorganized into five institutes, three departments and one interdisciplinary program

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Faculty Positions in Life Science and Medicine at National Tsing Hua University (Taiwan) job with National Tsing Hua University | 37287332 - The...

Singapore-based diagnostics developer INEX Innovate brings The Chinese University of Hong Kong together to further research work on LEXI, INEX's fetal cell based non-invasive pre-natal diagnostics technology.

SINGAPORE, July 26, 2022 /PRNewswire/ -- Singapore-based diagnostics developer and medical laboratory operator, INEX Innovate has contributed an undisclosed sum to leading Hong Kong university The Chinese University of Hong Kong (CUHK), to collaborate and further research in the field of maternal fetal medicine.

INEX's Dr. Chia-Pin Chang with Prof. Richard Choy of The Chinese University of Hong Kong

The CUHK Department of Obstetrics & Gynaecology (O&G) is world-renowned for its many prominent contributions and high-impact publications in the scientific community, attributed to its pursuit towards advancing the frontiers of knowledge in O&G through clinical, scientific and translational research. This initiative will tap on the research expertise of CUHK to further advance LEXI, a novel fetal cell isolation technology developed by INEX Innovate.

LEXI is a Non Invasive Prenatal Diagnostic (NIPD) technology that isolates fetal cells from the unborn baby, contained in the pregnant mother's blood for the definitive analysis of in excess of 7000 potential rare fetal genetic conditions.

Currently, expectant mothers whose prenatal screening results show signs of fetal anomaly are often recommended to undergo prenatal diagnostic tests for a definitive diagnosis of fetal genetic abnormalities, as this allows for early medical treatment of these conditions. However, prevailing diagnostic procedures such as amniocentesis are invasive and carry a risk of pregnancy loss of up to approximately 5 per cent[1].

Developed by INEX's Chief Technology Officer, Dr. Chia-Pin Chang, The LEXI cell isolation and enrichment is a process that isolates, identifies, and extracts target cells such as fetal cells from blood samples. The LEXI microfluidic chip enables its microfabricated filter to successfully deplete most of non-target cells in a blood sample and effectively capture fetal cells. Clinicians will need to draw one tube of blood from an expectant mother to generate results of the health condition of the fetus.

Chief Executive of INEX Innovate, Kane Black remarked, "We're thrilled to support and further the research of LEXI withProfessor Richard Choy and his team at The Chinese University of Hong Kong (CUHK), the pioneer centre of scientific excellence that focus on translating research advances into clinical impact both locally and internationally.

Mr. Black further commented fetalcellsinmaternalbloodrepresentthe Holy Grail of prenatal diagnosis. The major challenge has been isolation of these cell from maternal blood owing to their rarity, we look forward to working on this potentially cutting edge medical breakthrough with CUHK."

"We are looking forward to developing a potentially important breakthrough technology in the field of maternal fetal medicine," said Prof. Choy, Department of Obstetrics & Gynaecology at The Chinese University of Hong Kong.

[1] Cynthia L. Anderson, MD, and Charles E. L. Brown, MD, MBA, "Fetal Chromosomal Abnormalities: Antenatal Screening and Diagnosis, American Family Physician, 2009 Jan 15;79(2):117-123.

About INEX Innovate:

INEX Innovate is one of Asia's fastest growing molecular diagnostics developers and medical laboratory operators.

Founded by veteran maternalfoetalmedicine specialists, INEX is uniquely positioned to identify and address clinically unmet needs within the fetal health and women'soncology landscape, with a broad commercial portfolio of validated tests and 48 key patents.

Through our wholly owned subsidiary iGene Laboratory Pte Ltd, INEX operates a state of the art Next Generation Sequencing Laboratory that provides diagnostic testing, clinical research (CRO) and COVID-19 testing services.

The company has been recognised globally with a number of accolades and awards including from Frost & Sullivan, the World Intellectual Property Organisation (WIPO), The Straits Times Singapore's Fastest Growing Companies and the Financial Times ranking of 500 of Asia Pacific's Fastest Growing Companies.

For more information please visit: http://www.inex.sg

About The Chinese University of Hong Kong (CUHK):

Founded in 1963, CUHK is a leading comprehensive research university with a global reputation. Located in the heart of Asia, CUHK has a vision and a mission to combine tradition with modernity, and to bring together China and the West. Under the University's unique collegiate system, the programmes and activities offered by its nine colleges complement the formal curricula by delivering whole-person education and pastoral care. The University has eight faculties: Arts, Business Administration, Education, Engineering, Law, Medicine, Science, and Social Science. Together with the Graduate School, the University offers over 300 undergraduate and postgraduate programmes. All faculties are actively engaged in research in a wide range of disciplines, with an array of research institutes and research centres specialising in interdisciplinary research of the highest quality.

The University currently has more than 1,400 granted patents in different jurisdictions worldwide. Some of these patents have been licensed to relevant industries that help bring these innovations to the market to benefit society. In academic year 2020-21, CUHK has received 226 granted patents and filed 386 patent applications for inventions developed in the areas of medical technology, biotechnology, information technology, telecommunications, and materials science.

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Molecular Diagnostics Developer INEX Innovate Announces Funding for New Research with The Chinese University of Hong Kong - PR Newswire APAC - PR...

Colorized scanning electron micrograph of a cell (pink) infected with a variant strain of SARS-CoV-2 virus particles (UK B.1.1.7; gold), isolated from a patient sample. Courtesy NIAID

UC San Diego researchers have found that a post-COVID lung disease shares origins with other scarring lung diseases, which may offer a path to effective therapies, according to a study released Wednesday.

Although most people recover relatively quickly from COVID-19, around one-third of survivors experience symptoms weeks and months after the initial infection. However, in the study published in Wednesdays online issue of eBioMedicine, UCSD scientists studied interstitial lung disease, a form of long COVID that consists of a group of chronic pulmonary disorders characterized by inflammation and scarring of the lung.

The researchers said little is currently known about ILD which can be fatal without a lung transplant in its most severe form. But they found insights into the causes and paths the disease may take.

Using an artificial intelligence approach, we found that lung fibrosis caused by COVID-19 resembles idiopathic pulmonary fibrosis, the most common and the deadliest form of ILD, said co-senior study author Dr. Pradipta Ghosh, professor in the departments of Medicine and Cellular and Molecular Medicine at UCSD School of Medicine. At a fundamental level, both conditions display similar gene expression patterns in the lungs and blood, and dysfunctional processes within alveolar type II cells.

Those AT2 cells play several roles in pulmonary function, including the production of lung surfactant that keeps lung cells from collapsing after exhalation and regeneration of lung cells after injury.

The findings are insightful because AT2 cells are known to contain an elegant quality control network that responds to stress, internal or external, Ghosh said. Failure of quality control leads to broader organ dysfunction and, in this case, fibrotic remodeling of the lung.

To conduct the study, Ghosh collaborated with co-author Debashis Sahoo, associate professor in the departments of Computer Science, Engineering and Pediatrics at UCSD for the AI assisted analysis among other aspects.

Ghosh and Sahoo said the approach would help them stay unbiased in navigating the unknowns of an emerging, post-pandemic disease. They analyzed more than 1,000 human lung datasets associated with various lung conditions, specifically looking for gene expression patterns, inflammation signaling and cellular changes. The disease with the closest match: IPF.

IPF affects around 100,000 people in the United States, with 30,000 to 40,000 new cases annually. The condition has a poor prognosis, with an estimated mean survival of 2 to 5 years from time of diagnosis.

City News Service contributed to this article.

Continued here:
UCSD Post-COVID Lung Disease Study May Unlock Path to Therapies - Times of San Diego

Scientists have developed artificial intelligence software that can create proteins that may be useful as vaccines, cancer treatments, or even tools for pulling carbon pollution out of the air.

This research, reported today in the journal Science, was led by the University of Washington School of Medicine and Harvard University. The article is titled"Scaffolding protein functional sites using deep learning."

The proteins we find in nature are amazing molecules, but designed proteins can do so much more, said senior author David Baker, an HHMI Investigator and professor of biochemistry at UW Medicine. In this work, we show that machine learning can be used to design proteins with a wide variety of functions.

For decades, scientists have used computers to try to engineer proteins. Some proteins, such as antibodies and synthetic binding proteins, have been adapted into medicines to combat COVID-19. Others, such as enzymes, aid in industrial manufacturing. But a single protein molecule often contains thousands of bonded atoms; even with specialized scientific software, they are difficult to study and engineer.

Inspired by how machine learning algorithms can generate stories or even images from prompts, the team set out to build similar software for designing new proteins. The idea is the same: neural networks can be trained to see patterns in data. Once trained, you can give it a prompt and see if it can generate an elegant solution. Often the results are compelling or even beautiful, said lead author Joseph Watson, a postdoctoral scholar at UW Medicine.

The team trained multiple neural networks using information from the Protein Data Bank, which is a public repository of hundreds of thousands of protein structures from across all kingdoms of life. The neural networks that resulted have surprised even the scientists who created them.

The team developed two approaches for designing proteins with new functions. The first, dubbed hallucination is akin to DALL-E or other generative A.I. tools that produce new output based on simple prompts. The second, dubbed inpainting, is analogous to the autocomplete feature found in modern search bars and email clients.

Most people can come up with new images of cats or write a paragraph from a prompt if asked, but with protein design, the human brain cannot do what computers now can, said lead author Jue Wang, a postdoctoral scholar at UW Medicine. Humans just cannot imagine what the solution might look like, but we have set up machines that do.

To explain how the neural networks hallucinate a new protein, the team compares it to how it might write a book: You start with a random assortment of words total gibberish. Then you impose a requirement such as that in the opening paragraph, it needs to be a dark and stormy night. Then the computer will change the words one at a time and ask itself Does this make my story make more sense? If it does, it keeps the changes until a complete story is written, explains Wang.

Both books and proteins can be understood as long sequences of letters. In the case of proteins, each letter corresponds to a chemical building block called an amino acid. Beginning with a random chain of amino acids, the software mutates the sequence over and over until a final sequence that encodes the desired function is generated. These final amino acid sequences encode proteins that can then be manufactured and studied in the laboratory.

The team also showed that neural networks can fill in missing pieces of a protein structure in only a few seconds. Such software could aid in the development of new medicines.

With autocomplete, or Protein Inpainting, we start with the key features we want to see in a new protein, then let the software come up with the rest. Those features can be known binding motifs or even enzyme active sites, explains Watson.

Laboratory testing revealed that many proteins generated through hallucination and inpainting functioned as intended. This included novel proteins that can bind metals as well as those that bind the anti-cancer receptor PD-1.

The new neural networks can generate several different kinds of proteins in as little as one second. Some include potential vaccines for the deadly respiratory syncytial virus,orRSV.

All vaccines work by presenting a piece of a pathogen to the immune system. Scientists often know which piece would work best, but creating a vaccine that achieves a desired molecular shape can be challenging. Using the new neural networks, the team prompted a computer to create new proteins that included the necessary pathogen fragment as part of their final structure. The software was free to create any supporting structures around the key fragment, yielding several potential vaccines with diverse molecular shapes.

When tested in the lab, the team found that known antibodies against RSV stuck to three of their hallucinated proteins. This confirms that the new proteins adopted their intended shapes and suggests they may be viable vaccine candidates that could prompt the body to generate its own highly specific antibodies. Additional testing, including in animals, is still needed.

I started working on the vaccine stuff just as a way to test our new methods, but in the middle of working on the project, my two-year-old son got infected by RSV and spent an evening in the ER to have his lungs cleared. It made me realize that even the test problems we were working on were actually quite meaningful, said Wang.

These are very powerful new approaches, but there is still much room for improvement, said Baker, who was a recipient of the 2021 Breakthrough Prize in Life Sciences. Designing high activity enzymes, for example, is still very challenging. But every month our methods just keep getting better! Deep learning transformed protein structure prediction in the past two years, we are now in the midst of a similar transformation of protein design.

This project was led by Jue Wang, Doug Tischer, and Joseph L. Watson, who are postdoctoral scholars at UW Medicine, as well as Sidney Lisanza and David Juergens, who are graduate students at UW Medicine. Senior authors include Sergey Ovchinnikov, a John Harvard Distinguished Science Fellow at Harvard University, and David Baker, professor of biochemistry at UW Medicine.

Compute resources for this work were donated by Microsoft and Amazon Web Services.

Funding was provided by the Audacious Project at the Institute for Protein Design; Microsoft; Eric and Wendy Schmidt by recommendation of the Schmidt Futures; the DARPA Synergistic Discovery and Design project (HR001117S0003 contract FA8750-17-C-0219); the DARPA Harnessing Enzymatic Activity for Lifesaving Remedies project (HR001120S0052 contract HR0011-21-2-0012); the Washington Research Foundation; the Open Philanthropy Project Improving Protein Design Fund; Amgen; the Human Frontier Science Program Cross Disciplinary Fellowship (LT000395/2020-C) and EMBO Non-Stipendiary Fellowship (ALTF 1047-2019); the EMBO Fellowship (ALTF 191-2021); the European Molecular Biology Organization (ALTF 139-2018); the la Caixa Foundation; the National Institute of Allergy and Infectious Diseases (HHSN272201700059C), the National Institutes ofHealth (DP5OD026389); the National Science Foundation (MCB 2032259); the Howard Hughes Medical Institute, the National Institute on Aging (5U19AG065156); the National Cancer Institute (R01CA240339); the Swiss National Science Foundation; the Swiss National Center of Competence for Molecular Systems Engineering; the Swiss National Center of Competence in Chemical Biology; and the European Research Council(716058).

Written by Ian Haydon, UW Medicine Institute for Protein Design

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Biologists train AI to generate medicines and vaccines - UW Medicine Newsroom

As the latest COVID-19 vaccine, Novavax, jumps the final regulatory hurdle onto the US market, the US Food and Drug Administration has its eyes set on the COVID-19 vaccine plan for this fall and winter, when we're likely to see another wave of cases.

The FDA last month made arecommendationthat vaccine manufacturers should make a booster dose of COVID-19 vaccine that targets the omicron variant -- specifically, theBA.4 and BA.5 subvariants. BA.5, the most contagious version of the virus to date, now makes upthe majorityof COVID-19 cases in the US and seemslikely to leadto another summer surge of COVID-19 cases ahead of the anticipated fall or winter booster rollout.

The current advice for this summer is the same: Get the booster shots you're eligible for. (For everyone 50 and older, that means two boosters.) But the question at hand for health regulators was whether vaccine-makers should continue to use their original primary vaccine formulas (which will probably stay the same for the time being) for boosters, or if they should create a vaccine that targets omicron, which has been dominant worldwide for months and keeps mutating into more-contagious versions of itself.

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While there's still the chance we could be dealing with a whole new variant come fall or winter (you can never underestimate COVID-19), the FDA decided boosters targeting BA.5 should be the way forward.

The US government is expected to roll out vaccine boosters based on need: People most at risk will be eligible for a new booster first. And the vaccines based on earlier strains of the virus that causes COVID-19 (also called "ancestral" strains) are still protective against severe disease and death from omicron -- the most important function of vaccination in general.

While the details are being tested and ironed out, here's what we know about the fall COVID-19 vaccine strategy.

Both BA.4 and BA.5 are considered part of the "original" omicron variant (BA.1) family. They're newer versions of the virus that causes COVID-19. BA.5 quickly overtook the conversation on BA.4/BA.5 because of its extreme contagiousness, and it's now the dominant variant in the US. In a late June post, Dr. Eric Topol, professor of molecular medicine, called BA.5 "the worst version of the virus that we've seen."

While more time and research is needed to see what effect they have in the US (which has already experienced a high number of cases this late spring and summer), BA.5 is thought to whittle away much of the infection protection people got prior sickness, even with other omicron variants.

Omicron caused such a huge number of cases last winter because it was the most contagious variant to date, evading some infection protection from prior illness and effectiveness of the vaccines. The fact that newer versions of omicron are proving to be even more contagious isn't a big surprise, as this is the path COVID-19 has taken over the last two and half years.

Read more abouteverything we know about BA.5.

Specifically, the FDA is asking for abivalent(two-component) vaccine booster, which will include the BA.4/BA.5 spike protein in addition to an older strain. The FDA doesn't make vaccines, so the agency will likely authorize individual vaccine types as companies create and test them, as it did for the original COVID-19 vaccines and booster doses.

The vaccines currently authorized or approved only use older or "ancestral" strains of the virus. These vaccines still provide good protection against severe disease and death, but the effectiveness against infection is becoming more limited as the virus keeps mutating.

At a White House COVID-19 Response Teambriefing Tuesday, Dr. Ashish Jha said that if the timeline goes accordingly, he expects the first people to be eligible will start getting vaccinated in October, with other people becoming eligible in November or December.

But there is no authorized booster yet, so an exact timeline isn't available right now.

Moderna and Pfizer had both been working on boosters that target the general omicron variant. With the FDA's request to target omicron's newest strains, they will need to switch lanes to meet their target, hopefully in time for fall.

Novavax which justreceived CDC recommendationfor its primary two-dose vaccine also said it'sspeeding up workon a formula specifically targeting the new versions of omicron.

Pfizer announced last month that it struck a deal with the US government to provide more doses including ones that are adapted for omicron, pending FDA authorization.

The information contained in this article is for educational and informational purposes only and is not intended as health or medical advice. Always consult a physician or other qualified health provider regarding any questions you may have about a medical condition or health objectives.

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Here's What We Know About COVID Vaccine Plans for the Fall - CNET

Researchers used data from the American Heart Associations COVID-19 CVD Registry to determine the impact of smoking or vaping among people hospitalized with COVID-19

DALLAS, July 26, 2022 People who reported smoking or vaping prior to their hospitalization for COVID-19 were more likely than their counterparts who did not smoke or vape to experience severe complications, including death, from the SARS-CoV-2 infection. The findings are from a new study based on data from the American Heart Associations COVID-19 CVD Registry and published in PLOS ONE, a peer-reviewed, open access scientific journal published by the Public Library of Science.

Researchers examined data on people over 18 years of age who were hospitalized with COVID-19 in 107 registry-participating hospitals across the nation between January 2020 to March 2021. Smoking status was self-reported and people were classified as smoking if they reported currently using either traditional, combustible cigarettes or e-cigarette products, with no distinction between the two and no information on duration of smoking or former smoking status. For the final analysis, records were selected for 4,086 people with a 1:2 ratio of people who smoked (1,362) to people who did not smoke (2,724), with the two groups matched for no statistically significant difference in age, sex, race, medical history or medication.

The study findings indicate smoking or vaping are associated with more severe COVID-19 independent of age, sex, race or medical history:

In general, people who smoke or vape tend to have a higher prevalence of other health conditions and risk factors that could play a role in how they are impacted by COVID-19. However, the robust and significant increase in the risk of severe COVID-19 seen in our study, independent of medical history and medication use and particularly among young individuals, underscores the urgent need for extensive public health interventions such as anti-smoking campaigns and increased access to cessation therapy, especially in the age of COVID, said the studys senior author, Aruni Bhatnagar, Ph.D., FAHA, a professor of medicine, biochemistry and molecular biology at the University of Louisville in Louisville, Kentucky. These findings provide the clearest evidence to date that people who smoke or vape have a higher risk of developing severe COVID-19 and dying as a result of SARS-CoV-2 infection.

Bhatnagar is co-director of the American Heart Associations Tobacco Center for Regulatory Science which supported the study in part with funding from the U. S. National Institutes of Health and the Food and Drug Administration research grants.

We established the COVID-19 CVD Registry early on in the pandemic to better understand the link between COVID-19 and cardiovascular disease, specifically, to identify increased risk to help inform the diagnosis and care of people who are at highest risk for complications, said Sandeep R. Das, M.D., M.P.H., M.B.A., FAHA, co-chair of the steering committee for the American Heart Association COVID-19 CVD Registry Powered by Get With The Guidelines and director for Quality and Value in the Cardiology Division at UT Southwestern Medical Center in Dallas, Texas. The findings of this study deliver on that goal and provide invaluable information individuals and their health care teams.

The American Heart Association launched the registry in 2020 to gather data specific to all patients hospitalized with COVID-19 as part of the Get With The Guidelines quality improvement program. Registry participation was offered at no cost to all U.S. hospitals caring for adults with active COVID-19 and with the infrastructure to support accurate data collection. More than 160 hospitals provided data on more than 79,000 patient records between 2020 and June 2022.

The American Heart Association receives funding primarily from individuals; foundations and corporations (including pharmaceutical, device manufacturers and other companies) also make donations and fund specific Association programs and events. The Association has strict policies to prevent these relationships from influencing the science content. Revenues from pharmaceutical and biotech companies, device manufacturers and health insurance providers and the Associations overall financial information are available here.

Additional Resources:

About the American Heart Association

The American Heart Association is a relentless force for a world of longer, healthier lives.We are dedicated to ensuring equitable health in all communities.Through collaboration with numerous organizations, and powered by millions of volunteers, we fund innovative research, advocate for the public's health and share lifesaving resources.The Dallas-based organization has been a leading source of health information for nearly a century.Connect with us onheart.org,Facebook,Twitteror by calling 1-800-AHA-USA1.

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For Media Inquiries: 214-706-1173

Cathy Lewis: cathy.lewis@heart.org; 214-706-1324

Michelle Rosenfeld: michelle.rosenfeld@heart.org; 214-706-1099

For Public Inquiries: 1-800-AHA-USA1 (242-8721)

heart.org and stroke.org

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Smoking, vaping linked to higher risk of severe COVID-19 complications, including death - American Heart Association

In January 2022, the U.S. Food and Drug Administration (FDA) cautioned the public against a peculiar method for testing oneself COVID-19 tests.

"FACT: When it comes to at-home rapid antigen #COVID19 tests, those swabs are for your nose and not your throat," the agency said Friday.

The anti-throat-swabbing warning came amid the first omicron surge in the United States. The reason? Anecdotal reports surfaced about people who were testing positive for COVID-19 only after they swabbed their throats. (A typical COVID-19 at-home test involves swabbing one's nose exclusively.)

Nearly seven months later, as the country faces yet another surge due to omicron subvariant BA.5, the FDA warning has yet to put an end to this off-label collection method. Anecdotal reports continue to surface on social media regarding symptomatic people who received negative results on an at-home test with nasal swabs, followed by a positive test only after they poked the back of their throat with the long swab instead.

Other countries' health agencies do call for testing one's throat for viral residue. Canadian provinces, including Ontario and Nova Scotia, have updated their recommendations for at-home testing to include swabs of both throat and nose.

"To collect a sample for a rapid antigen test (RATs), users should follow the instructions described in the kit insert," Ontario Health, a government health agency, advises in an information sheet updated in February 2022. "In addition to the collection method option approved by Health Canada (as described in the kit insert), users may choose to perform combined oral and nasal sampling as it may increase test sensitivity." The health agency proceeds to instruct people how to properly collect a sample from one's throat.

The collection method of throat swabbing remains a divisive issue among experts in infectious disease.

Despite the FDA's warning, many Americans are apt to wonder who to believe. Is this a collection method that does indeed "increase test sensitivity," as Ontario Health claims?

The answer depends on who's asked as the collection method of throat swabbing remains a divisive issue among experts in infectious disease.

Nathaniel Hafer, an assistant professor in molecular medicine at University of Massachusetts' Chan Medical School who has researched both at-home antigen tests and polymerase chain reaction (PCR) tests, told Salon he believes it is best for people to follow the instructions of their specific test. In other words, if the test calls for throat swabbing, do it; if not, avoid it.

"I come down on the side that people should really do what's indicated in the test kit itself, which for all kits that are authorized in the U.S., the collection should be from the nose only," Hafer. "I think people should be following the instructions in the kits."

Yet Dr. Amesh Adalja, a senior scholar at the Johns Hopkins Center, disagreed. He told Salon via email he's been "recommending this for months" as in, swabbing one's throat when using an at-home tests "especially when sore throat is a prominent symptom."

As for lab-based PCR tests, Dr. Adalja said he doesn't recommend that physicians swab throats unless the instructions call for that method, which some do. For example, the Rheonix COVID-19 test does involve throat swabs. In other parts of the world, it is more common for PCR tests to be performed using throat swabs.

Going off-instructions could lead to some weird gray areas that raise new questions. For instance, say an individual swabs one's throat when doing an at-home test that doesn't call for throat swabbing and then tests positive. Does that imply the result would be inaccurate?

Hafer said there is some "anecdotal evidence" that the location of the tropisms of SARS-CoV-2 have changed over time with different variants.

"People are speculating that there's just more virus in the throat. I mean, that might be true, but the kits have not been tested for that kind of collection method, and so people might be getting actually true results," Hafer said. "But when people don't use the kids according to the instructions, they're opening the door to not get accurate results and that's both in the positive direction and the negative direction."

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William Schaffner, a professor of infectious diseases at the Vanderbilt University Medical Center, told Salon he believes when a person swabs their throat with an at-home antigen test and they're positive, that means definitively that they are indeed positive no question.

"They've been infected with the virus," Schaffner said. He noted that he thinks people should be following the test's instructions, but he's not surprised that people are swabbing their throats and getting positive test results.

"If you swab the throat, which is way in the back and you can consider that the back of the nose also, we call that the nasopharynx, way back there in the throat this is a virus that does cause sore throats, and indeed it gets down into your chest."

Indeed, as Schaffner pointed out, if the virus is lingering in the cavity where the nose and throat meet that is likely why positive results are appearing after throat swabs.

Notably, most of this adviceis based anecdotal reports. There have not been any scientific papers with peer-reviewed evidence that confirm or deny the efficacy of throat swabbing with at-home tests that don't call for it. One study,published on medRxiv by researchers in Cape Town, South Africa, concluded that saliva swabs were the preferred sample-collection method for detecting omicron infections.

In the meantime, everyday people may take it upon themselves to swab their throats when self-testing. If that yields a positive result, it's time to contact a doctor and isolate from people.

In that scenario, "they should obviously contact their healthcare provider, particularly if they're in a high risk group," Schaffner said.

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Experts still torn on whether you should swab your throat when taking COVID tests - Salon

Engineering | Health and medicine | Science | UW News blog

July 15, 2022

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

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

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

UW faculty selected by current Academy members are:

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

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

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