An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates

In October 2020, 62 scientists from nine nations worked together remotely in the Second Baylor College of Medicine & DNAnexus hackathon, focusing on different related topics on Structural Variation, Pan-genomes, and SARS-CoV-2 related research. The overarching focus was to assess the current status of the field and identify the remaining challenges. Furthermore, how to combine the strengths of the different interests to drive research and method development forward. Over the four days, eight groups each designed and developed new open-source methods to improve the identification and analysis of variations among species, including humans and SARS-CoV-2. These included improvements in SV calling, genotyping, annotations and filtering. Together with advancements in benchmarking existing methods. Furthermore, groups focused on the diversity of SARS-CoV-2. Daily discussion summary and methods are available publicly at https://github.com/collaborativebioinformatics provides valuable insights for both participants and the research community.

Preventing the next pandemic and tackling antiscience: an interview with Peter Hotez

This interview was conducted by Atiya Henry, Commissioning Editor of Future Microbiology. Peter J Hotez, MD, PhD is Dean of the National School of Tropical Medicine and Professor of Pediatrics and Molecular Virology & Microbiology at Baylor College of Medicine. He is an internationally-recognized physician-scientist in neglected tropical diseases and vaccine development. As head of the Texas Children’s Center for Vaccine Development, he leads a team and product development partnership for developing new vaccines for hookworm infection, schistosomiasis, leishmaniasis, Chagas disease and SARS/MERS/SARS-2 coronavirus. Dr Hotez has authored more than 500 original papers and is the author of four single-author books. Most recently as both a vaccine scientist and autism parent, he has led national efforts to defend vaccines and to serve as an ardent champion of vaccines going up against a growing national ‘antivax’ threat.

Asprosin neutralizing antibodies as a treatment for metabolic syndrome

Background: Recently, we discovered a new glucogenic and centrally-acting orexigenic hormone – asprosin. Asprosin is elevated in metabolic syndrome (MS) patients, and its genetic loss results in reduced appetite, leanness and blood glucose burden, leading to protection from MS.Methods: We generated three independent monoclonal antibodies (mAbs) that recognize unique asprosin epitopes and investigated their preclinical efficacy and tolerability in the treatment of MS.Results: Anti-asprosin mAbs from three distinct species lowered appetite and body weight, and reduced blood glucose in a dose-dependent and epitope-agnostic fashion in three independent MS mouse models, with an IC50 of ~1.5 mg/kg. The mAbs displayed a half-life of over 3 days in vivo, with equilibrium dissociation-constants in picomolar to low nanomolar range.Conclusions: We demonstrate that anti-asprosin mAbs are dual-effect pharmacologic therapy that targets two key pillars of MS – over-nutrition and hyperglycemia. This evidence paves the way for further development towards an investigational new drug application and subsequent human trials for treatment of MS, a defining physical ailment of our time.Funding: DK118290 and DK125403 (R01; National Institute of Diabetes and Digestive and Kidney Diseases), DK102529 (K08; National Institute of Diabetes and Digestive and Kidney Diseases), Caroline Wiess Law Scholarship (Baylor College of Medicine, Harrington Investigatorship (Harrington Discovery Institute at University Hospitals, Cleveland); Chao Physician Scientists Award (Baylor College of Medicine); RP150551 and RP190561 (Cancer Prevention and Research Institute of Texas; CPRIT)

An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates

In October 2020, 62 scientists from nine nations worked together remotely in the Second Baylor College of Medicine & DNAnexus hackathon, focusing on different related topics on Structural Variation, Pan-genomes, and SARS-CoV-2 related research. The overarching focus was to assess the current status of the field and identify the remaining challenges. Furthermore, how to combine the strengths of the different interests to drive research and method development forward. Over the four days, eight groups each designed and developed new open-source methods to improve the identification and analysis of variations among species, including humans and SARS-CoV-2. These included improvements in SV calling, genotyping, annotations and filtering. Together with advancements in benchmarking existing methods. Furthermore, groups focused on the diversity of SARS-CoV-2. Daily discussion summary and methods are available publicly at https://github.com/collaborativebioinformatics provides valuable insights for both participants and the research community.

First person – Yuki Ogawa

ABSTRACTFirst Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping early-career researchers promote themselves alongside their papers. Yuki Ogawa is first author on ‘Endogenously expressed Ranbp2 is not at the axon initial segment’, published in JCS. Yuki is a postdoc in the lab of Matthew Rasband at the Baylor College of Medicine, Houston, USA, investigating how the cytoskeletal proteins are organized in neurons by using CRISPR/Cas9-based genome engineering.

The history of neurosurgery at Baylor College of Medicine

The development of neurosurgery at Baylor College of Medicine began with the medical school’s relocation to the new Texas Medical Center in Houston in 1943. An academic service was organized in 1949 as a section of neurosurgery within Baylor’s Department of Surgery. Soon the practice, led by Dr. George Ehni, evolved to include clinical services at Methodist, Jefferson Davis (forerunner of Ben Taub), Texas Children’s, the Veterans Affairs, and the University of Texas MD Anderson Cancer Center hospitals. A neurosurgery residency program was established in 1954. As the clinical practice expanded, neurosurgery was upgraded from a section to a division and then to a department. It has been led by four chiefs/chairs over the past 60 years—Dr. George Ehni (1959–1979), Dr. Robert Grossman (1980–2004), Dr. Raymond Sawaya (2005–2014), and Dr. Daniel Yoshor (2015–2020). Since the 1950s, the department has drawn strength from its robust residency program, its research base in the medical school, and its five major hospital affiliates, which have largely remained unchanged (with the exception of Baylor St. Luke’s Medical Center replacing Methodist in 2004). The recent expansion of the residency program to 25 accredited positions and the growing strength of relationships with the “Baylor five” hospitals affiliated with Baylor College of Medicine portend a bright future.

Microbiome: Living Well and Thriving With Your Bacteria

This symposium aims to invite speakers who are the leading experts in the field of microbiome and longevity, and select short talks from abstracts submitted by young investigators, postdoctoral fellows and graduate students. We will discuss new progress in this exciting research area and raise new questions for future studies. Confirmed speakers include Evgeny Nudler from NYU, Will Ludington from Carnegie, Paul O’Toole from University College Cork, Ireland, and Meng Wang from Baylor College of Medicine.

Third Annual Summer Research Summit on Health Equity Organized by the Center of Excellence in Health Equity, Training and Research, Baylor College of Medicine, Houston, Texas 77030, USA on June 9, 2020

This year’s summit was unique given the COVID-19 pandemic: a major global outbreak that has imposed severe restrictions in all aspects of our life. At the outset, we were faced with three mutually exclusive options. First option was to cancel the summit in its entirety: this was the easiest and most obvious choice once the COVID-19 pandemic forced a near total lockdown all over the country with unprecedented disruptions of normal daily activities as the disease announced its thunderous touchdown on United States (US) soil. It was also the most-logical response faced with uncertainty regarding summit logistics and expected poor attendance due to the raging pandemic. Second option was to conduct a digital summit restricted to local audiences at Baylor College of Medicine: this option entailed implementing a virtual summit with attendance restricted to participants from our institution only. It sounded like a reasonable choice but that would impede the presence of diversity of topics, perspectives, insights and experiential learning opportunities, which are what render the summit exciting and worth attending. And finally, the last option was to conduct a digital unrestricted summit open to all interested audiences throughout the US. The conduct of a virtual summit open to all participants from around the country was initially considered daunting given the likelihood of amplified technical problems associated with an array of internet access differentials around the country, which would require a strong Information Technology (IT) presence throughout the sessions. Nonetheless, the attractiveness of going national with a virtual summit, despite the pandemic and logistical challenges, slowly gained converts and became the dominant choice. The response and level of participation in this first virtual summit showed an unanticipated surge despite the increase in registration fees to cover IT costs. This year, we had attendees from all regions of the US as well as from the United Kingdom. The range of topics was quite diverse encompassing health disparities in relation to cancers, nutrition, musculo-skeletal disorders, amputation rates, vaccination uptakes and COVID-19 infections. Various solutions were passionately presented to address these disparities including novel health technologies, community engagement and partnerships, improvement in health literacy and alternative therapeutics. There were no hitches despite the complex breakout sessions, and above all, attendees were satisfied and offered outstanding evaluation scores. This was definitely a summit that metamorphosed from pessimism to a triumphant success! Copyright © 2020 Salihu et al. Published by Global Health and Education Projects, Inc. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0)which permits unre-stricted use, distribution, and reproduction in any medium, provided the original work, first published in this journal, is properly cited.

Methods developed during the first National Center for Biotechnology Information Structural Variation Codeathon at Baylor College of Medicine

In October 2019, 46 scientists from around the world participated in the first National Center for Biotechnology Information (NCBI) Structural Variation (SV) Codeathon at Baylor College of Medicine. The charge of this first annual working session was to identify ongoing challenges around the topics of SV and graph genomes, and in response to design reliable methods to facilitate their study. Over three days, seven working groups each designed and developed new open-sourced methods to improve the bioinformatic analysis of genomic SVs represented in next-generation sequencing (NGS) data. The groups’ approaches addressed a wide range of problems in SV detection and analysis, including quality control (QC) assessments of metagenome assemblies and population-scale VCF files, de novo copy number variation (CNV) detection based on continuous long sequence reads, the representation of sequence variation using graph genomes, and the development of an SV annotation pipeline. A summary of the questions and developments that arose during the daily discussions between groups is outlined. The new methods are publicly available at https://github.com/NCBI-Codeathons/, and demonstrate that a codeathon devoted to SV analysis can produce valuable new insights both for participants and for the broader research community.