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    Submitter

    Congratulations to Dr. Xiaole Shirley Liu of the Dana-Farber Cancer Institute for receiving the 2020 Benjamin Franklin Award!

    Laureate presentation: www.youtube.com/watch?v=NcHBlYUmS0g

    Comparative metabolomics is aiming to find the biological meaningful common metabolites (biomarkers) from large-scale, high throughout metabolomics profiling data. Thus, approaches and tools towards detecting and aligning the potential same known and unknown metabolites across different samples, different biological experiments and even different instrument runs are desired.

    Inspired by the aims in LC/MS based comparative metabolomics, a series of approaches are developed and two tools entitled as MET-COFEA (bioinfo.noble.org/manu[...]ofea/) and MET-XAlign (bioinfo.noble.org/manu[...]lign/) are implemented.

    MET-COFEA, being an analysis tool, can be used to extract and annotate each meaningful metabolite' associated chromatograph features from each LC-MS sample. For the extracted metabolite compound group with multiple fragment peaks, the neutral molecular mass can be deduced and the compound's representative retention time can be estimated, which can be considered as the common thing for the same metabolite across different samples and different experiment configurations, although the fragmentation pattern can vary from sample to sample, from experiment to experiment. MET-COFEA has already been successfully implemented as a pipeline tool with visualization.

    MET-XAlign, being as an alignment tool, has been dedicatedly developed based on the analysis results from MET-COFEA. It mainly includes an algorithm core and user interface. The identified compounds from MET-COFEA are characterized by compound retention time and neural molecular mass deduced by multiple associated fragments' m/z value, which are represented as its unique Compound_ID.

    Adopting this approach that combined MET-COFEA and MET-XAlign, the LC-MS based comparative metabolomics analysis including metabolite feature extraction and annotation for each sample and alignment across samples can be separated. Our previous experimental results show that the strategy combing MET-COFEA and MET-XAlign can efficiently realize the aim to find the biological meaningful biomarkers from LC/MS based comparative metabolomics data.

    The central dogma of biology is that the genome, transcriptome, proteome, and metabolome are cascading and connected to the end phenome. Recently, high-throughput sequencing technology, particularly the NGS (Next Generation Sequencing), made it capable to discover or measure million-scale genetic variants (such as SNPs) or expressed genes (such as transcripts). High performance mass spectrometry technology makes it possible to detect and measure a broad range of metabolites at a very high sensitivity. All these omics data are complex in nature due to the heterogeneous information and huge data size, but generally biologically correlated. Therefore, it's challenging yet necessary to develop efficient methods and tools to systematically interpret the biological insights behind multiple omics data.

    In classical GWAS (Genome Wide Association Studies), the genetic marker variants and the phenotypic traits can be connected through the canonical LMM (Linear Mixed Model). We extended the concept of genome-wide association into a broader 'ome'-wide association. Briefly, we proposed a novel LMM and developed an online tool named PATOWAS (bioinfo.noble.org/PATOWAS/), by which we can address not only GWAS, but also TWAS (Transcriptome wide association studies), and MWAS (Metabolome wide association studies) in one unified platform. To explain more the phenotypic variation and address the missing heritability, we also proposed another new LMM and developed another association tool named PEPIS (bioinfo.noble.org/PolyGenic_QTL/), by which the polygenic effect and epistasis from marker pairs can be accounted for. Using these tools, two-dimensional (2D) GWAS that accounts for epistatic genetic effects can be mapped, which are complementary to the one-dimensional (1D) GWAS mapping, and can provide more genetic information.

    In short, the combination of 2D GWAS analysis and multi-omics data integration can well address the challenging questions as GXG, GXE, which together can efficiently characterize the complex trait, such as crop yield.
    Education: Coronavirus spike protein and membrane fusion
    Submitted by Eric Martz; posted on Thursday, August 27, 2020

    Submitter

    Two new tutorials are available animating the latest findings about coronavirus spike protein:

    proteopedia.org/w/SA[...]furin
    proteopedia.org/w/SA[...]ation

    Each includes interactive morph animations, and downloadable Powerpoint-ready animations. These are based on recent cryo-EM structures of multiple conformations.

    A protease (typically furin, ample in the lungs) clips spike protein, inducing it to extend a receptor-binding surface to engage the ACE2 receptor on the host cell.

    The mechanism of membrane fusion, which deposits the viral RNA inside the host cell initiating infection, appears similar to that of influenza hemagglutinin. The spike protein "spears" the host cell membrane, capturing it with a "fusion peptide", and pulls the virus membrane very close. Fusion has been seen in molecular dynamics simulations (see Figure 2 in the fusion link). Spike protein has a cavity that is the target of drug screening (see Figure 4 in the fusion link). A cute graphical abstract shows a 3-legged folding stool as an analogy to spike protein, with the drug-target cavity between its legs (see Figure 3 in the fusion link).

    These tutorials have been cataloged at Merlot.Org: www.merlot.org/merl[...]eated

    These and all tutorials at Proteopedia.Org are offered under a Creative Commons Attribution Share Alike 3.0 license.

    Submitter

    Dear colleagues,

    We're writing to invite you to use ObjTables (objtables.org), a free and open-source toolkit, to create and reuse high-quality spreadsheets, such as supplementary tables to articles.

    Comparing and integrating data is essential to science. However, it is difficult to reuse many data sets, including spreadsheets, one of the most common formats. ObjTables makes spreadsheets reusable by combining spreadsheets with schemas, an object-relational mapping system, numerous data types for scientific information, and high-level software tools. First, ObjTables enables authors to use Excel and similar programs to create spreadsheets and use ObjTables to error check spreadsheets. Second, ObjTables extends the impact of sharing data by helping other investigators compare, merge, and translate spreadsheets into data structures that can be analyzed with tools such as Python. ObjTables is available as a web application, a command-line program, a web service, and a Python package.

    We hope that you join this initiative to make supplementary tables more reusable. Please contact us to share feedback or get involved. Together, we believe we can create a robust ecosystem of reusable data for research!

    Regards,

    Jonathan Karr
    Arthur Goldberg
    Icahn School of Medicine at Mount Sinai
    www.karrlab.org

    Wolfram Liebermeister
    INRAE, Université Paris-Saclay
    genome.jouy.inra.fr/~wli[...].html
    Education: Major Histocompatibility Complex Tutorial now on YouTube
    Submitted by Eric Martz; posted on Saturday, July 25, 2020

    Submitter

    A tutorial on Major Histocompatibility Complex (MHC) molecular structure and function has been posted on YouTube (go to MolviZ.Org and click on MHC). It comes with an immediate-feedback quiz, and a set of open-ended questions to provoke discussion. A teachers's guide includes answers to the open-ended questions. The tutorial features 3D atomic-resolution structures, and covers:

    CONTENTS

    • Main functions of MHC classes I and II with CD8 and CD4 T lymphocytes.
    • Cells expressing each class of MHC.
    • Sources of peptides in the proteasome and lysosome.
    • Reduction of MHC I on virus-infected cells inviting Natural Killer Cells.
    • Severe immunodeficiency resulting from genetic absence of MHC II.
    • Structure of MHC class I: Alpha chain and domains, beta-2 microglobulin, peptide in cleft with closed ends, papain cleavage locus, CD8 binding site, secondary structure.
    • Evolutionary conservation of CD8 binding site and residues binding peptide anchor residues and ends. Variability in sequences of lips of the cleft due to alleles needed to accomodate wide range of peptides.
    • Peptide side chains buried (anchor residues) vs. exposed to T cell surveillance.
    • Comparison of two different peptides in MHC I from perspective of T cells.
    • Structure of MHC class II: Alpha and beta chains, peptide in cleft with open ends.

    AUTHORS

    The video is an enhanced screen capture of an interactive tutorial (free and open source) that became unusable in recent years because popular web browsers no longer support Java applets. Eventually, the interactive tutorial may be ported to JSmol, which works in popular browsers. Until then, the video is available, and may also increase awareness due to the popularity of YouTube.

    MolviZ.Org also has free, open source interactive tutorials on DNA, Hemoglobin, Antibody (also on YouTube), the Ramachandran Principle (also on YouTube), Lipid Bilayers and Membrane Channels, Collagen, the Lac Repressor, and many more.

    Submitter

    EXCERPT

    Researchers at the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health, have produced the first end-to-end DNA sequence of a human chromosome. The results, published [July 14] in Nature, show that generating a precise, base-by-base sequence of a human chromosome is now possible, and will enable researchers to produce a complete sequence of the human genome.
    Source: www.nih.gov/news[...]uence
    Education: Antibody Tutorial now on YouTube
    Submitted by Eric Martz; posted on Saturday, July 11, 2020

    Submitter

    A tutorial on Antibody molecular structure and function has been posted on YouTube (go to MolviZ.Org and click on Antibody). It comes with an immediate-feedback quiz, and a set of open-ended questions to provoke discussion. A teachers's guide includes answers to the open-ended questions. The tutorial features 3D atomic-resolution structures, and covers
    • What is antibody? What is antigen?
    • Fab, Fc, hinge. Variable and constant domains.
    • Immunoglobulin domains: beta strands, hydrophobic core.
    • Heavy chains, light chains, disulfide bonds, glycosylation.
    • Epitopes and paratopes. CDR's.
    Authors are Eric Martz (Martz.MolviZ.Org) and Frieda Reichsman (MoleculesInMotion.com).

    The video is an enhanced screen capture of an interactive tutorial (free and open source) that became unusable in recent years because popular web browsers no longer support Java applets. Eventually, the interactive tutorial may be ported to JSmol, which works in popular browsers. Until then, the video is available, and may also increase awareness due to the popularity of YouTube.

    MolviZ.Org also has free, open source interactive tutorials on DNA, Hemoglobin, the Ramachandran Principle (also available at YouTube), Lipid Bilayers and Membrane Channels, Collagen, the Lac Repressor, and many more.

    Submitter

    August 10-14, 2020
    Online
    www.transmittingscience.com/cour[...]udio/

    COURSE OVERVIEW

    This course will cover some advanced issues in most statistical computing workflow for Environmental Science. We will cover several aspects of data structure and workspace management, visualization techniques and statistical analysis using the free platforms and programming language R and Rstudio.

    The course is given in four modules covering exploratory data analysis, univariate and multivariate statistical techniques and a final discussion session where students will work and discuss their projects.

    REQUIREMENTS

    Graduate or postgraduate degree in Life Sciences and basic knowledge of Statistics and R.

    All participants must bring their own personal laptop and a good internet connection (Windows, Macintosh, Linux).

    July 14-17, 2020
    National Institutes of Health (ONLINE)
    faes.org/even[...]y2020

    OBJECTIVES

    Participants will get a brief introduction to the programming concepts, followed by hands-on walkthrough for writing scripts using the Unix Shell Programming Language, R, Perl and Python. We will start from reading the data, processing it and all the way until saving the processed data.

    BACKGROUND

    Computer programs are meant to perform repeated, monotonous, fast, reproducible tasks, handling any amount of data. Researchers often come across situations where existing programs don't suit their needs. In the era of BigData, without the ability to quickly put together a program that would solve their problem, researchers face a road block that is not efficiently solvable by a human. This training will walk through participants in writing programs that would help them solve their own problems.

    Simultaneous access to two screens is highly recommended for adequate learning experience. Examples include two laptops, one computer with two screens, one laptop and one tablet, etc.

    HIGHLIGHTS

    • Participants will work in a friendly Linux GUI Desktop environment.
    • Participants will get a copy of all the scripts used in the class.
    • Participants will also receive a cookbook style manual for all the hands-on exercises.
    Hands-on Skills/Tools Taught:
    • Programming concepts using Microbit MakeCode
    • Programming in Unix Shell Language
    • Programming in R using RStudio
    • Programming in Python using Jupyter
    • Programming in Perl
    • GitHub for version control
    • Serverless computing
    • Coding in the cloud
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    Acknowledgments

    We wish to thank the following for their support:

    [Regeneron]
    [Bio-IT World]
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