Monthly Archives: June 2022

Fig. 3.

MEGAs Tree Explorer ( A ) is a feature-rich, versatile viewer of phylogenies

MEGAs Tree Explorer (A) is a feature-rich, versatile viewer of phylogenies that provides many interactive exploration and customization facilities. In MEGA11, the new side toolbar of Tree Explorer makes formatting, rearrangement, and tree exploration tools more accessible and intuitive. Instead of a thin toolbar with nameless buttons, we have opted for a wide toolbar with text labels identifying each tool. The toolbar can be moved to either side of the window, and it can be toggled in and out of view. To organize related tools by groups and accommodate limited vertical space, collapsible panels are used. With the new toolbar, formatting tools previously displayed in external dialogs are readily accessible, and formats are applied instantly instead of after the user closes the external dialog. In addition to the updated toolbar, there are now options for auto-collapsing of nodes containing clusters of taxa belonging to the same group, user-specified cluster size, or by the branch length difference. For very large trees with many similar sequences, this feature can greatly facilitate the visualization of evolutionary events at a glance. An option has been added to export pairwise patristic distances between taxa to a text file for phylogenies and timetrees. For maximum likelihood and maximum parsimony trees where ancestral sequences are present, an option has been added to navigate through sites where a change in the estimated ancestral state differs between the parent and child on the currently selected branch. The tree information box (B) has been updated for timetrees to show branch- and node-specific information, such as earliest and latest sample times in the currently selected subtree, days elapsed between the divergence time for a selected node and the latest sample time, the nearest and furthest tip from a selected node, clade size and clade taxa, and spatiotemporal information if available.

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MEGA11: Molecular Evolutionary Genetics Analysis Version 11

F ig . 2.

( A ) Timetree inferred in MEGA6 and shown in the Tree Explorer

(A) Timetree inferred in MEGA6 and shown in the Tree Explorer, where it is displayed with divergence times and their respective 95% confidence intervals. A scale bar for absolute divergence times is shown. (B) An information panel that can be made visible by pressing the icon marked with an i. When focused on a tree node (left side), it shows the internal node identifier, and absolute or relative divergence time as appropriate; when focused on a branch (right side), it displays the local clock rate as well as the relative branch length. (C) A timetable exported using the displayed timetree, which shows the ancestordescendant relationship along with relative node times, relative branch rates, absolute divergence times, and confidence intervals. Users can display internal node identifiers in the Tree Explorer as well as internal node names, which can be provided in the input topology file. On pressing the Caption in the Tree Explorer menu bar, MEGA produces the following text to inform the user about the methods, choices, and data used. Caption: The timetree shown was generated using the RelTime method. Divergence times for all branching points in the user-supplied topology were calculated using the Maximum Likelihood method based on the General Time Reversible model. Relative times were optimized and converted to absolute divergence times (shown next to branching points) based on user-supplied calibration constraints. Bars around each node represent 95% confidence intervals which were computed using the method described in Tamura et al. (2013). The estimated log likelihood value of the topology shown is 247671.60. A discrete Gamma distribution was used to model evolutionary rate differences among sites (4 categories, +G, parameter = 38.07). The tree is drawn to scale, with branch lengths measured in the relative number of substitutions per site. The analysis involved 446 nucleotide sequences. All positions with less than 95% site coverage were eliminated. That is, fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position. There were a total of 1,048 positions in the final data set. Evolutionary analyses were conducted in MEGA6 (Tamura et al. 2013).

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MEGA6: Molecular Evolutionary Genetics Analysis version 6.0

The American Society for Biochemistry and Molecular Biology announced today the winners of its annual awards. Colleagues and other leaders in the field nominated the winners for making significant contributions to biochemistry and molecular biology and to the training of emerging scientists.

The recipients will give talks about their work at the societys2023 annual meeting, Discover BMB, slated for March 2528 in Seattle.

In addition to cash prizes ranging from $500 to $35,000, each ASBMB award consists of a plaque and transportation expenses to the ASBMB annual meeting.

Learn more about the ASBMB awards.

Regina Stevens-Truss

Recognizes an individual who encourages effective teaching and learning of biochemistry and molecular biology.

Regina StevensTruss is a professor at Kalamazoo College in Michigan who has served in numerous leadership positions at the ASBMB. She has been a member of the societys Education and Professional Development Committee and Minority Affairs Committee (now Maximizing Access Committee). She is a past member of the steering committee that created the concept-driven teaching strategies that laid the foundation for the ASBMBs certification exam. She was the principal investigator in 2012 on a National Science Foundation grant that supported a STEM K-12 outreach initiative by the society called Hands-on Outreach to Promote Engagement in Science (HOPES for short).

Squire Booker

Recognizes outstanding contributions to research in biochemistry and molecular biology.

Squire J. Bookeris an Evan Pugh professor of chemistry and of biochemistry and molecular biology and the Eberly Family distinguished chair in science at The Pennsylvania State University. He is also an investigator of the Howard Hughes Medical Institute. His lab studies catalytic mechanisms of redox enzymes involved in natural product biosynthesis and human health. He is deputy editor of ACS Bio & Med Chem Au, an open-access journal of the American Chemical Society, and an executiveassociate editor of the ACS journal Biochemistry. He becamean inaugural fellowof the ASBMB in 2021. He also won this years Ruth Kirschstein Diversity in Science Award. (See below.)

Russell DeboseBoyd

Recognizes outstanding research contributions in the area of lipids.

Russell DeBoseBoydis the Beatrice and Miguel Elias distinguished chair in biomedical science and professor of molecular genetics at the University of Texas Southwestern Medical Center at Dallas. DeBoseBoyds lab studies regulatory mechanisms governing feedback regulation of HMG-CoA reductase, the rate-limiting enzyme in cholesterol synthesis. He is an associate editor for the Journal of Lipid Research and an editorial board member for the Journal of Biological Chemistry, both ASBMB journals. Readour Q&Awith DeBoseBoyd.

Erica Saphire

Awarded to an established scientist for outstanding accomplishments in basic biomedical research.

Erica Ollmann Saphire is a professor and the president and chief executive officer of the La Jolla Institute for Immunology. Saphires lab has solved structures of key proteins of the Ebola, Marburg, rabies and Lassa viruses and explained how they remodel these structures as they drive themselves into cells, how their proteins suppress immune function and where human antibodies can defeat these viruses. She used this information to galvanize two international consortia of former competitors to advance antibody therapeutics together. Saphire is a two-time ASBMB award winner. In 2015, she won the ASBMB Young Investigator Award.

Eytan Ruppin

Given to a scientist forthemost accessible and innovative development or application of computer technology to enhance researchin the life sciencesat the molecular level.

Eytan Ruppin is a computational biologist and chief of the Cancer and Data Science Laboratory in the Center for Cancer Research at the National Cancer Institute. His lab develops computational approaches for the integration of multiomics data to understand better the pathogenesis and treatment of cancer. His research focuses on basic and translational studies aimed at broadening the scope of precision oncology to the realm of tumor transcriptomics.

Scott Dixon

Awarded to a scientist with 10 years or less of post-postdoctoral experience.

Scott Dixonis an associate professor in the biology department at Stanford University.His labstudies cell death and lipid metabolism using small-molecule screening, biochemical analysis of protein function, and model organism genetics. Dixon is a member of theprogram planning committeefor Discover BMB, the societys annual meeting.

Anne Kenworthy

Recognizes and honors scientists at all stages of their careers who have made substantial advances in understanding biological chemistry using innovative physical approaches.

Anne Kenworthy is a professor of molecular physiology and biological physics at the University of Virginia and the assistant director of its Center for Membrane and Cell Physiology. Her lab studies membrane nanodomains, such as lipid rafts and caveolae, to learn how they assemble and function in health and disease. (Read about her recent high-content analysis of membrane vesicles.)Together with collaborators at the University of Michigan and Vanderbilt University, her group also recently provided the first glimpse into molecular architecture of an essential building block of caveolae oligomeric complexes formed by the membrane protein caveolin-1.

Squire Booker

Honors an outstanding scientist who has shown a strong commitment to the encouragement of scientists from historically marginalized groups.

This is the second award this year forSquire J. Booker, a professor and distinguished chair at The Pennsylvania State University. (See the ASBMBMerck Award above.) Booker is a past chair of the ASBMBs Minority Affairs Committee and established the ASBMBgrant-writing workshop, which now is known as the Interactive Mentoring Activities for Grantsmanship Enhancement workshop. He also co-organized the 2016 ASBMB annual meeting. He now serves on the Finance and Nominating committees.

Itay Budin

Recognizes outstanding research contributions in the area of lipids by a young investigator.

Itay Budin is an assistant professor of chemistry and biochemistry at the University of California San Diego. His laboratory uses approachesranging from membrane biophysics to synthetic biology to investigate lipid function. Current areas of focus in his lab include the inner mitochondrial membrane and lipid adaptation for life in extreme conditions. In 2017, Budin received a Journal of Biological Chemistry/Herbert Tabor Young Investigator Award.

Catherine Drennan

Recognizes outstanding contributions to biochemical and molecular biological research and a demonstrated commitment to the training of younger scientists.

Catherine Drennanis a professor at the Massachusetts Institute of Technology and a Howard Hughes Medical Institute investigator.Drennans labstudies the structural biology of metalloenzymes. Her teams targets have included multiple enzymes that depend on metal cofactors, such as ribonucleotide reductase, an early enzyme in DNA biosynthesis. She is a former member of the ASBMB Education and Professional Development Committee. As a postdoctoral fellow, she started the undergraduate poster competition at the ASBMBs annual meeting. Her pedagogical work includes research into best practices for active lectures and the development of resources that help undergraduates appreciate the value of chemical principles in biology and medicine. She was a member of the ASBMBsinaugural classof fellows in 2021.

Gira Bhabha

Recognizes individuals with a strong commitment to advancing the careers of women in biochemistry and molecular biology along with demonstrated excellence in research and/or service.

Gira Bhabhais an assistant professor at the NYU Grossman School of Medicine, where she began her independent career in 2017. The Bhabha lab works closely with the lab of Damian Ekiert; since their inception, the two labs have functioned synergistically as a single group. TheBhabha and Ekiert labsstudy structural mechanisms and cell biology of microbes and their interactions with hosts, using integrative approaches including X-ray crystallography, cryo-electron microscopy, cryo-electron tomography, optical microscopy, biochemistry, microbiology and cell biology techniques.

Kerry-Ann Rye

Recognizes individuals with a strong commitment to advancing the careers of women in biochemistry and molecular biology along with demonstrated excellence in research and/or service.

Kerry-Anne Rye is a professor at the University of New South Wales in Sydney and co-editor-in-chief of the ASBMBs Journal of Lipid Research. Before taking the helm at the JLR in 2020, she had been an associate editor since 2008. She has been a research professor since 2013 at UNSW, where she serves as the deputy head of the School of Medical Sciences and studies atherosclerosis and diabetes. Rye was a member of the inaugural class of ASBMB fellows in 2021. She wrote an essay earlier this year about being a member of the society.

Dyann Wirth

Keith Matthews

Recognizes established investigators who are making seminal contributions to the field of molecular parasitology.

Dyann Wirth is a professor at Harvard Universitys T.H. Chan School of Public Health and the Broad Institute. Her lab studies the Plasmodium genus, members of which commonly infect humans with malaria. Her team is working on methods for molecular genetic manipulation of protozoan parasites to analyze genes important for their virulence and resistance to drugs.

Keith Matthewsis a professor at the University of Edinburgh.His laboratorystudies African trypanosomes, parasites spread by the tsetse fly, and the changes they undergo in the fly, using targeted reverse genetic approaches, global RNA and protein analysis, and other strategies.

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ASBMB names 2023 award winners - ASBMB Today

Shortly before an 18-year-old white supremacist entered a supermarket in a Black neighborhood of Buffalo, N.Y., and shot 13 shoppers and employees with an assault rifle bearing a racist epithet, he posted an online diatribe. Other white nationalist terrorists have done that, but this one was different: It cited a considerable quantity of scientific research to support its authors racist claims and actions.

In the weeks since the mid-May shooting, journalists and scientists have discussed what to make of the Buffalo terrorists references to science. Overwhelmingly, these discussions describe the diatribe as relying on pseudoscience or discredited science and co-opting or misreading mainstream science.

But this framing doesnt do enough to hold scientists and the institutions of science accountable for the societal consequences of racist science and scientific racism.

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The term pseudoscience, as used in media descriptions of the Buffalo terrorists diatribe, obscures more than it reveals. Historian of science Michael Gordin has explained that pseudoscience is not a real thing. Rather, the term is a negative category, always ascribed to somebody elses beliefs, not to characterize a doctrine one holds dear oneself. The invocation of pseudoscience in reports about the Buffalo shooting serves mainly to distance science from this horrific massacre, producing the false impression that real science cant be racist.

But real science can be racist. A century ago, racist science was the norm rather than the exception, and the legacy of scientific racism continues to reverberate through the institutions of science. To be sure, some of the research cited by the Buffalo terrorist is outdated and has been discredited, meaning that it is no longer widely accepted as valid. The key words here are no longer this research was once regular, acceptable science until other scientists began to question and critique it.

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The discredited science from the Buffalo terrorists diatribe that is referenced most frequently in the press was produced by J. Philippe Rushton and Richard Lynn, psychologists whose research was heavily supported by the openly racist Pioneer Fund. From the 1980s to the 2010s, these men produced a raft of scientific articles and books that supposedly demonstrated the biological inferiority of people of African descent, purporting to show that they are innately less intelligent and more prone to crime and sexual promiscuity than people of European or Asian descent.

Its important to note that Rushton and Lynn werent pseudoscientists working in pseudoscience labs or institutions. They were tenured professors, Rushton at the University of Western Ontario until his death in 2012 and Lynn at Ulster University until he was finally stripped of his title in 2018. They published in reputable journals, such as the International Journal of Neuroscience and Psychological Science, though they also published in shadier outlets, such as Mankind Quarterly and Personality and Individual Differences. Lynn was a member of the editorial board of the journal Intelligence until 2018. Rushton was a fellow of the Canadian Psychological Association and the John Simon Guggenheim Memorial Foundation. His work was praised and defended by Edward O. Wilson, one of the most celebrated biologists of the late 20th and early 21st centuries.

Although much of Rushton and Lynns research is now widely recognized as racist garbage, it is still available through the journals in which they originally published, in print and online, and does not come with any kind of warning label. An unwitting student searching Google Scholar for race and intelligence could easily stumble upon their work, or a wide variety of similar research, and get no indication it is not to be trusted: It looks like science because it was and in many cases still is science.

Rushton and Lynn are just the most visible edge of a much larger phenomenon, the majority of which hasnt come under the same scrutiny as these men and their work. Racist science is still regularly published in seemingly reputable scientific venues. A case in point is Michael Woodley, a scientist whose affiliation with the Vrije Universiteit Brussel was suspended only after a reference to one of his many racist publications appeared in the Buffalo terrorists diatribe, inspiring a petition by an international group of genetics researchers.

Openly racist research is not the only problem. The Buffalo terrorist also cited cutting-edge research in molecular genetics that is not explicitly racist. Most notable is a 2018 meta-analysis published in Nature Genetics that identifies genomic correlates of educational attainment in white people of European genetic ancestry. UCLAs Daniel Benjamin, a co-founder of the Social Science Genetic Association Consortium, which coordinated the study, described himself as horrified by how the Buffalo terrorist used his groups research. Indeed, their study says little about race other than that the genetic variants that predict educational attainment in white Americans do not predict educational attainment in Black Americans.

To suggest that this study shows any kind of systematic genetic difference between white and Black Americans that makes the former innately more intelligent than the latter is absolutely a misreading that was not intended by the studys authors. Such misreading, however, does not occur only in online white nationalist cesspools. Research in behavior genetics has been consistently misread in this way by scientists since the birth of the field in the 1960s. These scientists include Arthur Jensen, Richard Herrnstein, Charles Murray, Glayde Whitney, and Bo Winegard, all of whom have advanced this misinterpretation dubbed Jensenism in a deluge of popular and scientific books and articles that continue to be published in reputable outlets.

For these scientists, Jensenism appears to be justified by the research. If there are genetic variants that make people smarter (the fundamental tenet of behavior genetics), and if genetic variants are distributed differently in different populations (the fundamental tenet of population genetics), then differences between racial groups in intelligence or educational attainment must be rooted in genetic differences.

These basic premises, however, are false. Scientists have not identified any genetic variants that promote intelligence or education, and racial categories do not represent biological populations. To their credit, some behavior geneticists have publicly denounced the drawing of racist conclusions from their findings. Nonetheless, scientific articles and the books scientists write to popularize their findings too often oversell the research in ways that invite racist misreading, which other scientists are only too willing to provide.

Science is a vitally important social activity, contributing positively to all areas of life. Yet scientists are not always right and their work is not always beneficial. If scientists and the institutions of science are to maintain their credibility, they need to do a better job of confronting and addressing their own racism and the press needs to hold them to higher standards.

Emily Klancher Merchant is an assistant professor of science and technology studies at University of California, Davis and the author of Building the Population Bomb (Oxford University Press, 2021).

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Hold science to higher standards on racism - STAT

Dr. John H. Krystal, world-leading expert in alcoholism and depression, will serve on scientific advisory board

VANCOUVER, June 21, 2022 (GLOBE NEWSWIRE) -- Clearmind Medicine Inc. (CSE: CMND, OTC Pink: CMNDF, FSE: CWY0) (Clearmind or the "Company"), a biotech company focused on discovery and development of novel psychedelic-derived therapeutics to solve major undertreated health problems, today announced the appointment to its Scientific Advisory Board of John Krystal, Chair of the Psychiatry Department at Yale Universitys School of Medicine.

A leading expert on alcoholism, post-traumatic stress disorder, schizophrenia, and depression, Dr. Krystals work links psychopharmacology, neuroimaging, molecular genetics, and computational neuroscience to study the neurobiology and treatment of these disorders. He is best known for leading the discovery of the rapid antidepressant effects of ketamine.

"We are truly honored to add Dr. Krystal, one of the worlds most recognized experts in alcoholism, to our Scientific Advisory Board, said Dr. Adi Zuloff-Shani, Clearmind's Chief Executive Officer. Clearmind has emphasized collaboration with scientists and clinicians at the very best academic, medical and research institutions in the world, helping us bring innovative expertise to bear on some of the most pressing global health needs.

Dr. Krystal is a Professor of Translational Research; Psychiatry, Neuroscience, and Psychology; he chairs the Department of Psychiatry at Yale University; and he is Chief of Psychiatry and Behavioral Health at Yale-New Haven Hospital. He is a graduate of the University of Chicago and the Yale University School of Medicine

Among many other positions he holds or has held, Dr. Krystal is the Director of the NIAAA Center for the Translational Neuroscience of Alcoholism and the Clinical Neuroscience Division of the VA National Center for PTSD, co-director of the Neuroscience Forum of the U.S. National Academies of Sciences, Engineering, and Medicine; and editor of Biological Psychiatry (IF=12.1). He is a member of the U.S. National Academy of Medicine and a Fellow of the American Association for the Advancement of Science.

We believe that the scientists on our Scientific Advisory Board, working closely with us to challenge, validate and guide our scientific agenda for developing breakthrough therapies that improve human mental-health at scale, increase access to care, reduce suffering and improve health outcomes around the world, said Zuloff-Shani.

About Clearmind Inc. (CSE: CMND), (OTC: CMNDF), (FSE:CWY0)

Clearmind is a new biotech company focused on the discovery and development of safe and novel psychedelic-derived therapeutics to treat alcohol use disorder and other pressing health challenges.

The Israeli Canadian company holds several patents for the non-hallucinogenic compound MEAI (5-methoxy-2-aminoindane, a novel psychoactive substance). The company intends to seek additional patents for its compounds whenever warranted and will remain opportunistic regarding the acquisition of additional intellectual property to build its portfolio.

Clearmind has established a research collaboration with the Hebrew University of Jerusalem and Bar Ilan University. The partnerships aim to expand its R&D capabilities and discover new candidate treatments for other mental health issues.

For further information, please contact:

Investor Relations

invest@clearmindmedicine.com

Telephone: (604) 260-1566

General Inquiries

Info@Clearmindmedicine.com

http://www.Clearmindmedicine.com

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Yale's Department of Psychiatry Chair to Join Clearmind Medicine - The Bakersfield Californian