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GeneLab’s Analysis Working Groups’ 2018 Annual Report

In 2018, the NASA GeneLab project established Analysis Working Groups with the goal of maximizing the generation of new knowledge from rare and complex spaceflight-relevant omics datasets within the GeneLab Data System (GLDS).

The Analysis Working Groups (AWGs) represent four model organism areas of expertise: plants, multi-omics/systems biology, microbes, and animals (mammals, non-mammals). The purpose of these groups is to optimize the processing of raw omics data from the GeneLab repository and assess and improve the effectiveness of the GLDS through extensive utilization of analytics.

2018 in Review

Key accomplishments of the AWGs in year one include:

  1. The first AWG workshop in Orlando, FL, April 23-24, 2018. Workshop participants comprised 65 of the 114 AWG members and included scientists at all levels (PIs, post-docs, students) from three NASA centers, as well as universities and institutes in the U.S. and internationally. Members reached consensus on the following:
    1. analysis pipelines to process raw data in GeneLab’s repository into high-order data
    2. visualization requirements and implementation strategies
    3. the need for processed data and every intermediate data product
    4. using Galaxy as a working and teaching tool
    5. identification of new datasets to be added to the data repository
  2. AWG investigators began work on several manuscripts using data in GeneLab
  3. Ten GeneLab summer interns worked with the AWGs to develop computational pipelines for the analysis of biological data in the GeneLab data repository. The output of these pipelines are available on GeneLab, allowing anyone to make discoveries about how biological systems react to spaceflight.

Milestones

The primary activity of the AWGs was to establish analytical processes to generate higher-order data from data housed in the GLDS, with relevance to one or more specific application areas. All groups participated in the first AWG workshop and via teleconferences throughout 2018. A summary of each AWG’s 2018 accomplishments, goals for 2019, and new leadership follows.

Plants

Lead: Matt Geniza, NASA Ames Research Center
Accomplishments 2018
Plant AWG members contributed to analysis pipelines, provided input on standardizing plant metadata terms, beta tested the GeneLab Analysis Platform, and initiated planning for a potential Plant AWG manuscript utilizing GeneLab omics data. Overall, members provided valuable feedback on how the GeneLab team could better serve the broader research community. Plant AWG members shared their knowledge of ongoing astrobotany projects with GeneLab’s summer interns – investing time with the next generation of scientists.

Goals 2019
The primary goal of the Plant AWG in 2019 is developing a central document exploring the metadata and scientific findings from spaceflight and ground-based experiments now available through GeneLab. This working group is striving to enhance the visibility and utility of GeneLab and spur new collaborations to develop the fundamental and applied knowledge to enable long-term spaceflight and ground-based advances to agriculture.

New co-leads
Richard Barker is a UW-Madison researcher investigating plant responses to spaceflight using custom imaging platforms and cloud-based data analysis. Barker is currently is a co-investigator on three NASA grants and has been involved in the planning and launch of multiple AstroBotany experiments to the International Space Station. As part of GeneLab project, he built the TOAST (Test of Arabidopsis Space Transcriptome) database to support the goal of democratizing space life science research. He was selected as a representative of the American Academy of Science at the Future Leaders in Space Science Congress in Beijing in 2017. Barker is excited to work with the GeneLab AWG to develop new bioinformatic tools that make predictions that can be tested in the laboratory.

Colin Kruse is a PhD candidate studying gravity signaling under the advice of Sarah Wyatt, both of Ohio State University. Kruse first began analyzing big biological data as a member of the BRIC-20 research team and has since expanded his skill set in bioinformatics beyond RNAseq to include genome assembly, ChIP-seq, microbiome sequencing analyses, and several other specialized analyses. Beyond plant space biology, Kruse works in endocrine biology specializing in growth hormone and its impact on cancer development. 

Multi-omics/Systems Biology

Co-leads: Afshin Beheshti, Dan Berrios, NASA Ames Research Center
Accomplishments 2018
Multi-omics/Systems Biology AWG members determined a basic pipeline for transcriptomics, proteomics, and methylation and shared R-scripts for these pipelines. The group developed cross-omics analysis through a network-based tool, and started visualization capabilities and participation with the GeneLab Visualization Working Group.

Goals 2019 – This group will publish three papers: multi-omics rodent research, External RNA Controls Consortium spike-in data, and a collaboration with University Chicago on relating spaceflight/bedrest studies with anorexia data. In addition, they plan to develop and establish the multi-omics pipeline and tool from University of California San Diego and others from the AWG, and begin development and pipelines for cross-species pipelines.

Co-leads – The current leadership will remain through 2019.

Microbes

Lead, Jon Galazka, NASA Ames Research Center
Accomplishments 2018
The Microbes AWG focuses on analyzing microbial datasets within GeneLab that includes gene-expression, proteomic, metabolomic and environmental metagenomic datasets. In 2018, the Microbes AWG developed draft pipelines for both 16S and whole genome metagenomic data types. These were then utilized by a set of interns to process a number of metagenomic datasets in GeneLab.

Goals 2019
This year, the Microbes AWG is focused on understanding the relative strengths of different assays for establishing a description of microbial communities. This work is important for maximizing the value of data generated from precious spaceflight samples. In addition, the Microbes AWG will focus on finalizing essential pipelines and developing manuscripts describing their analyses.

New co-leads
The GeneLab Microbes AWG took an important step by transferring leadership to three new co-chairs: Daniela Bezdan, Stefan Green and Michael Strong.

Daniela Bezdan is currently holding a position as Research Director of the Mason Laboratory of Integrative Genomics at Weill Cornell Medicine. Her expertise is in technology development for new, cutting-edge Next-Generation Sequencing (NGS) applications using novel experimental and bioinformatics methods. Bezdan is also the Executive Director of the International consortium MetaSUB – Metagenomics & Metadesign of Subways & Urban Biomes with 293 members in 25 countries, and an active member of the Extreme Microbiome Project consortium. Her academic career history includes the EMBL in Heidelberg (Germany), the Max-Planck-Institute in Tübingen (Germany), the UCSD (USA), the University of Kyoto (Japan), the CRG in Barcelona (Spain) and the Weill-Cornell-Med in New York. She studied in organic chemistry, biotechnology, biokinetics, genomics, and bioinformatics. She has published in the fields of systems biology, developmental biology, regulatory genomics, metagenomics, next-generation sequencing technology, and bioinformatics. More recently she has worked on several NASA projects, NASA grants (TRISH) and NASA publications. Bezdan is a member of the NASA Twin Study Team, the Biomolecule Sequencer Team, the Mars rover 2020 project, and others.

Stefan Green is a molecular microbiologist and microbial ecologist with extensive experience in the acquisition and analysis of microbiome sequence data. Over the past 20 years, he has focused his research efforts on the analysis of complex microbial communities in a wide range of natural, contaminated, and human-associated environments. Most recently, he has focused on genetic analysis of individual microbial taxa and has attempted to link observed critical microbial functional capabilities (phenotype) with underlying genetic determinants (genotype).

Currently, Green is director of the Sequencing Core at the University of Illinois at Chicago (UIC), a core facility performing high-throughput RNA and DNA extractions, next-generation sequencing preparations including high-throughput amplicon sequencing, target capture, next-generation sequencing, bioinformatic analyses, and quantitative PCR analyses. Over the past eight years his scientific contributions at UIC have resulted in authorship and co-authorship of over 80 peer-reviewed manuscripts and book chapters. Currently, he is a co-investigator on seven NSF- and NIH-funded projects, and is a co-PI on a NASA-funded project employing NGS to lookat the effects of spaceflight on gut microbiome in mice. Green recently completed a study on the effects of spaceflight on human microbiome as part of the NASA Twins study. In his spare time he also studies factors leading to PCR bias.

Michael Strong earned his B.S. in Microbiology at the University of California, Santa Barbara, his Ph.D. in Molecular Biology at the University of California, Los Angeles, and did his postdoctoral work at Harvard Medical School in the field of genomics.  He is currently an Associate Professor at National Jewish Health, a leading respiratory hospital and research center, and is a core faculty member of the Computational Bioscience program at the University of Colorado, Denver.  His work encompasses the fields of microbial genomics, structural informatics, and systems biology, to better understand opportunistic environmental bacteria and respiratory pathogens, including nontuberculous mycobacteria, which can cause serious human disease.  He is funded by the National Science Foundation and the Cystic Fibrosis Foundation. www.stronglab.org

Animals (mammals, non-mammals)

Co-leads: Sylvain Costes, Candice Tahamic, Sigrid Reinsch, NASA Ames Research Center
Accomplishments 2018
The Animal AWG aims to facilitate the use of omics in understanding basic mechanisms by which animals and constituent tissues and cells adapt to the spaceflight environment. Last year, this AWG also provided expertise on the adaptation of best practices for processing omics data in Genelab. To this end, the Animal AWG has contributed to the development of consensus analysis pipelines for generating higher order (processed) omics data. By making processed omics data publicly available, spaceflight omics results will be accessible to a wide range of users of varying skill levels and computational resources, thereby maximizing scientific discovery.

Goals 2019
Current and upcoming activities are geared toward the development of manuscript(s) that demonstrate the power of omics in unraveling the mechanisms and shared molecular responses of animals during adaptation to the spaceflight environment.

New co-leads
The Animal AWG has recently transitioned leadership to Nathaniel Szewczyk and Tejaswini Mishra to better reflect the vision for the AWGs to be a scientific group driven by the greater spaceflight research community.

Nathaniel Szewczyk is a Professor of Space Biology at the University of Nottingham in the UK and an Investigator at the MRC/ARUK Centre for Musculoskeletal Ageing Research, the NIHR Nottingham BRC, and the National Centre for Sport and Exercise Medicine. He received his BS in Biology and Psychology from Carnegie Mellon University, PhD in Molecular, Cellular, and Developmental Biology from the University of Pittsburgh, and did a post-doc in Space Life Sciences at NASA Ames Research Center. His research focuses on muscle health, using a variety of model systems: cells, C. elegans (nematode), rodents and human subjects in order to understand the mechanisms by which genes control health, the mechanisms by which activity and inactivity control muscle health, and to study drugs and nutritional interventions that improve muscle health. His current spaceflight work involves identifying the signaling pathways and transcription factors regulating the C. elegans genomic response to spaceflight as well as drugs that alter the C. elegans genomic response to spaceflight.

Tejaswini Mishra is a postdoctoral research fellow working on personalized medicine in the laboratory of Michael Snyder in the Genetics department of Stanford University School of Medicine in California. Mishra obtained her B.S and M.S degrees in Biotechnology from the University of Mumbai, India, and her Ph.D. from Pennsylvania State University. At Penn State she used sequencing technologies to study regulation of cell fate decisions during blood cell development. She also participated in the NHGRI-funded Mouse ENCODE Project, whose goal was to identify functional elements in the mouse genome. Her current work at Stanford focuses on delineating a personal baseline of health in each individual, using longitudinal multi-omics data collected over time from human subjects. She is currently developing frameworks for integrative analysis of large multi-omics datasets in order to understand human-to-human molecular variation and to predict personal health outcomes and disease trajectories. This work is performed through the Integrative Human Microbiome Project and the NASA Twins Study.

Join an AWG Now

NASA’s GeneLab Project is currently recruiting investigators, bioinformaticians, graduate students, and postdocs to participate in the AWGs, which investigate specific subsets of omics data from experiments conducted onboard the International Space Station, the Space Shuttle, as well as ground-based research with relevance to spaceflight (e.g. radiation or unloading/weightlessness).
If you are interested in participating, and/or if you have students with strong bioinformatics skills who are interested, review the GeneLab Analysis Working Groups Charter and send an email to arc-dl-genelab-awg@mail.nasa.gov with name of the group of interest in the subject line (Plants, Multi-omics/Systems Biology, Microbes, Animals [mammals, non-mammals]). Please submit a capability/qualification statement electronically in PDF format. The response must include the following: 1) Contact: name, affiliation, address, phone, e-mail, and website. 2) Subject area expertise. Provide a concise description of your expertise in terms of omics analyses, including a list of relevant work and publications performed in the past five years. Participation in the AWGs is entirely voluntary and participants are not compensated.

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