AWG 2019 Annual Report – NASA Science

RESEARCH IN REVIEW YEAR 2

The NASA GeneLab mission established GeneLab Analysis Working Groups (AWGs) in 2018 for the only function of optimizing the processing of uncooked spaceflight and ground-related omics knowledge from the GeneLab repository, maximizing the technology of latest information from these uncommon and complicated datasets, and bettering the effectiveness of the GeneLab Data System (GLDS) by means of in depth utilization of analytics. The teams characterize 4 mannequin organism areas of experience: vegetation, multi-omics/programs biology, microbes, and animals (mammals, non-mammals).

AWG members are comprised of researchers, principal investigators, professors and college students, all who be part of on a volunteer foundation. The major exercise of every AWG is to ascertain analytical processes to generate higher-order knowledge from knowledge housed within the GeneLab Data System with relevance to a number of particular utility areas. For instance, the mammalian AWG analyzes all knowledge related to mammalian programs (human, mouse, rat, and so forth.).

By collaborating in a GeneLab Analysis Working Group, investigators be part of a gaggle of scientific excellence and should have the chance to co-author a landmark paper. They innovate new knowledge and evaluation requirements for the group and develop relationships that might result in extra collaborations.

DEMONSTRATING SCIENTIFIC PROGRESS

In 2019, the GeneLab AWGs consisted of 4 teams comprising greater than 120 volunteer members from world wide. In this 2019 annual report, the AWGs amply demonstrated their efforts to advance omics evaluation of spaceflight and ground-related knowledge from experiments performed aboard the International Space Station and shuttle and deal with vital questions in house life sciences. All teams participated within the second AWG workshop and by way of teleconferences all through 2019. A abstract of every AWG’s 2019 accomplishments, objectives, and new management follows.

AWG Major Milestones

AWG workshop: The second annual AWG workshop and showcase was held in Denver, CO, on November 19, 2019, a day earlier than the ASGSR’s annual convention formally started. During the closed morning session AWG members gave standing stories, mentioned processing pipelines and supplied enter on 12 roundtable subjects. The afternoon session, the AWG Showcase, was open to all ASGSR convention attendees. It featured talks by every of the 4 AWG teams, and demonstrated tasks, instruments, and papers in improvement. Workshop contributors comprised over 50 AWG members and included scientists in any respect ranges (PIs, post-docs, college students) from 3 NASA facilities, in addition to universities and institutes within the U.S. and internationally. Members reached consensus on the next:

• Analysis pipelines will probably be used to course of uncooked knowledge in GeneLab’s repository into high-order knowledge.
• Requirements for visualization and implementation methods.
• The want for processed knowledge and each intermediate knowledge product.
• Use Galaxy as a working and educating software.
• Identify new datasets to be added to the info repository.

Manuscripts: AWG investigators revealed six manuscripts utilizing knowledge in GeneLab.

Interns: GeneLab summer season interns labored with the AWGs on creating computational pipelines for the evaluation of organic knowledge within the GeneLab knowledge repository. The output of those pipelines can be found on GeneLab, enabling anybody to make discoveries about how organic programs react to spaceflight.

Plant Biology

Leads: Richard Barker, UW Madison; Colin Kruse, Los Alamos National Lab

Accomplishments 2019

The Plant Analysis Working Group is comprised of worldwide analysis scientists and professors that meets frequently to share and focus on the newest developments in AstroBotany – the self-discipline of botany involved with interactions between plant biology and house setting. The group’s meta-analysis analysis centered on the transcriptional response of Arabidopsis to spaceflight and the mixing of epigenetics, proteomics, and glycomic datasets to make predictions and information future analysis into the metabolic response of crops in orbit. 

New worldwide collaboration with the European Bioinformatics Institute’s Expression Atlas Team: Collaborators of the European Bioinformatics Institute’s Expression Atlas Team generated the NASA GeneLab Expression Atlas to include experimental knowledge. Upon examination of the meta-data from all of the research, the choice was made to include solely these samples that match the staff’s standards (e.g., 3 organic repeats) as outlined in Barker et al., (2020) beneath.

European Space Agency/NASA GeneLab Exchange Program Pilot Study: International alternate pupil Alicia Villacampa from Raúl Herranz’s ESA-supported laboratory, visited Simon Gilroy’s “collaboratory” to check a speculation generated utilizing the European Modular Cultivation System’s CoSE SciSpeinner Max. A proposal was submitted to ESA in an try and make this program extra sustainable, with the Expression Atlas Team additionally expressing an curiosity. 

Steady Growth for Plant Analysis Working Group: The Plant Biology group elevated in measurement to incorporate: 

• Marie Dinh – Background in molecular biology and is a part of GeneLab’s Sample Processing Team. Marie’s experience is in mouse, bacterial and plant samples.
• Sreeskandarajan Sutharzan (Sutha) – Expertise in machine studying algorithms and RNAseq evaluation. Sutha used machine studying to investigate psoriasis knowledge and can research GeneLab knowledge to find out whether or not it’s amenable to machine studying.
• Laurence Davin – Intricately concerned in processing spaceflight samples within the Lewis lab.
• Christina Johnson – Studied spaceflight-grown vegetation for over a decade and revealed on the Kiss Lab’s BRIC-16 research. A postdoctoral fellow with Ray Wheeler, Christine developed microgreens as a crop for spaceflight functions in collaboration with researchers on the USDA. She has been lively in manuscript and outreach materials improvement.

Development of New NASA Microgreens Education Program: Protocols developed by Kennedy Space Center’s Christina Johnson will rework Okay-12 science courses right into a NASA analysis program. Analysis of the 2019 check program in collaboration with the University of Washington’s PEOPLE program revealed a 90% approval ranking from college students, with 80% selecting STEM fields for his or her future careers. The enhanced lesson plans will probably be examined in summer season 2020 on the PEOPLE program and on the Suito Kokusai Junior and Senior High School as a part of their new AstroBotany lesson collection.

New Plant Samples for GeneLab Processing Team: Collaboration between GeneLab and PI’s within the spaceflight group recognized potential new tissue sources that will be appropriate and insightful if sequenced by GeneLab. 

• Masson Lab: RNA-seq carried out was carried out on two new Brachypodium distachyon ecotypes that grew on orbit within the VEGGIE development {hardware} to raised perceive the pure variation of vegetation to the spaceflight setting.
• Willey Lab: Arabidopsis vegetation uncovered to multi-generation persistent low doses of ionizing radiation had been recognized and provided by Nicol Caplin on the European Space Research and Technology Centre,the place a 20-slide abstract of radiation and the necessity for brand spanking new plant experiments had been produced.
• Gilroy Lab: Arabidopsis seedlings had been grown in a 3D clinostat, and microgreen seedlings had been grown in sq. petri dishes in a 3D clinostat with diffuse gentle from 360 levels. Phenotype: Root development has a random orientation that resembles vegetation grown in sq. petri dishes the VEGGIE on orbit.

Published Manuscripts: Three manuscripts had been revealed within the Frontiers in Plant Science journal.

Test of Arabidopsis Space Transcriptome: A Discovery Environment to Explore Multiple Plant Biology Spaceflight Experiments. (2020) Barker, R, Lombardino, J., Rasmussen, Okay., Gilroy, S. V11. P147.   

Microbiological and Nutritional Analysis of Lettuce Crops Grown on the International Space Station  (2020). Khodadad, C.L.M., Hummerick, E., Spencer L.E.., Dixit A, R., Richards J. T., Romeyn M. W., Smith Trent M., Wheeler R. M., Massa G. D. V11. P199.   

RNAseq Analysis of the Response of Arabidopsis thaliana to Fractional Gravity Under Blue-Light Stimulation During Spaceflight (2019). Herranz R., Vandenbrink J. P., Villacampa A., Manzano A., Poehlman W. L., Feltus F. A., Kiss J. Z., Medina F. J. V10. P1529.

Goals 2020:

New Tools and Resources: Integrate the microbiome knowledge from Khodadad et al., (2020), into the MANGO database to extend accessibility and ease of comparability with the microbiome of the International Space Station.

New Plant AWG/GeneLab Manuscript: The meta-analysis of the “AWG minimal” collection of GeneLab processed evaluation will probably be analyzed utilizing customized R-scripts (produces PCA and MDS plots that ought to reveal if the {hardware}, tissues samples, presence of sunshine or darkish or the absence of gravity has the best impact on gene expression). These knowledge will then be parsed to the PI staff who frequently attends AWG conferences for interpretation, dialogue and manuscript completion. A literature assessment and metadata meta-analysis will probably be carried out to create a tough draft.

Regular Members: Laurence Davin, Marie Dinh, Simon Gilroy, Raul Herranz, Kim Hixon, Christina Johnson, Norm Lewis, Imara Perera, Sigrid Reinsch, Sreeskandarajan Sutharzan (Sutha), Alicia Villacampa, and Sarah Wyatt.

Multi-omics/Systems Biology

Lead: Afshin Beheshti, NASA Ames Research Center

Accomplishments 2019

The Multi-omics/Systems Biology Analysis Working Group (AWG) is setup for figuring out the very best pipelines and evaluation that may be achieved to narrate completely different omics platforms that embrace transcriptomics, proteomics, metabolomics and methylation knowledge. In this course of the group labored the next tasks in 2019, which can proceed ahead.

Multi-omics Analysis Reveals Mitochondrial Stress: One massive consortium mission of 23 Multi-omics AWG members and 6 scientists exterior the AWG, utilized multi-omics evaluation to disclose mitochondrial stress driving spaceflight well being dangers. This work utilized NASA’s GeneLab platform and analyzed the huge omics knowledge obtainable in GeneLab’s repository and decided extraordinarily novel findings on key drivers accountable for well being dangers as a result of house setting. This massive consortium mission utilized transcriptomic, proteomic, epigenetic, and metabolomics to find out {that a} systemic mitochondrial-driven response is accountable for growing potential well being dangers as a result of house setting. In addition, each astronaut physiological knowledge from blood and urine and in addition qPCR outcomes on mitochondrial genes from the Twin Study verify these thrilling outcomes. Lastly, that is the primary research to incorporate the biggest cohort of physiological astronaut knowledge spanning over 30 years. The manuscript for this mission will probably be submitted for publication in 2020.

Health Risks Associated with Space Radiation: This mission was pushed by 11 multi-omics AWG members who centered on figuring out potential well being dangers related to house radiation. For this work the group utilized 30 transcriptomic datasets particularly related to house radiation from each in vivo and in vitrosamples that had been both flown to house and uncovered to direct house radiation, or simulated house radiation experiments that had been carried out on the NASA Space Radiation Laboratory at Brookhaven National Laboratory.

From these datasets, house radiation doses beginning at 1 mGy to 1000 mGy had been used. Utilizing an unbiased novel programs biology strategy, we predicted particular tissue unbiased organic pathways as a operate of house radiation dose that may contribute to elevated well being dangers. Specifically, we decided key oncogenic pathways that may both be activated or inhibited with growing publicity to house radiation and can contribute to elevated threat of most cancers induction. We additionally demonstrated a novel strategy to make the most of RNA-sequencing knowledge for particular evaluation associated to RNA-specific error charges and base substitutions that may happen with house radiation publicity. This novel evaluation revealed that A > G and C > T substitutions are occurring as a consequence of house radiation, which has beforehand been unreported. This work has resulted in an accepted publication, NASA GeneLab Platform Utilized for Biological Response to Space Radiation in Animal Models. This paper additionally demonstrated that the AWG can produce a novel paper from GeneLab knowledge inside 5 weeks from begin to end.

The Impact of Spaceflight on Liver: Four multi-omics AWG members assisted GeneLab with efficiently publishing a manuscript to find out that the liver is tremendously impacted by spaceflight. Previously, the liver has not been one of many organs of concern for NASA or spaceflight-related biology. Through this work it was demonstrated that spaceflight impacts the liver and must be one other organ of concern throughout spaceflight missions. Four separate datasets had been used from completely different rodent spaceflight missions that encompassed unrelated strains of mice and length in house. A programs biology strategy was used that included each transcriptomic and proteomic knowledge to point out that spaceflight elevated the possibilities of fatty liver illness no matter length of flight and completely different strains. In addition, histology knowledge had been utilized to verify the outcomes from the omics evaluation. Overall, it was decided that spaceflight induced elevated lipid accumulation and a number of other organic components (i.e. GCG, insulin, lipid metabolism, and so forth.) that contributes to elevated possibilities of fatty liver illness equivalent to nonalcoholic fatty liver illness. The publication could be discovered right here, Multi-omics analysis of multiple missions to space reveal a theme of lipid dysregulation in mouse liver.

There are a number of ongoing Multi-omics AWG tasks that may end in publications all through 2020, together with the next:

• Determine conserved organic pathways impacted by spaceflight that will probably be conserved between a mess of eukaryotic species. This work led the AWG members concerned to submit a joint grant utility to the NNH18ZTT001N-FG2: Appendix D: Solicitation of Proposals for Flight and Ground Space Biology Research.
• Utilize GeneLab RNA-seq knowledge to check single base substitutions and mismatch charges throughout chromosomes.
• Genomic variations occurring between completely different mouse strains that impression response and final result to spaceflight.
• Assist a NASA PI with novel evaluation on proteomic knowledge associated to floor analog house radiation experiments.
• Correlate knowledge from NASA’s Life Sciences Data Archive with GeneLab omics knowledge to display the potential and methodology of using completely different platforms from NASA to generate novel speculation and evaluation.

Lastly, the Multi-omics AWG has grown to 100 members. The fixed inflow of latest folks has enabled the group to be extraordinarily productive and always generate novel tasks.

Goals 2020:

The objectives for 2020 are the next:

• Submit the multi-omics evaluation to reveals mitochondrial stress driving spaceflight well being dangers mission in high-impact journal.
• Finish the on-going tasks highlighted above and submit the work for publication.
• Submit new grant proposals with the AWG members based mostly on the work/publications that will probably be generated
• Keep recruiting new members
• Start new/novel tasks to proceed pushing the boundaries for using GeneLab to generate hypotheses to help future spaceflight associated work.

Microbes

Leads: Daniela Bezdan, Weill Cornell Medicine; Stefan Green, University of Illinois at Chicago; Michael Strong, National Jewish Health and University of Colorado, Denver

Accomplishments 2019

Team Transitions: The Microbes AWG efficiently transitioned to non-NASA management.

Benchmarking Study: This 12 months the GeneLab Microbes AWG developed a microbiome benchmarking research from Rodent Research-6 feces. In this research, working group members recognized completely different microbiome profiling assays that may very well be utilized in mixture to achieve a extra full understanding of the microbial contents of the mouse intestine and the way this modifications throughout spaceflight. These assays included a number of shotgun approaches (brief learn, lengthy learn, and artificial lengthy learn) and a number of amplicon approaches. These datasets had been generated by means of a collaboration between the GeneLab Sample Processing Lab and dealing group members, Drs. Stefan Green and Samantha Waters. These knowledge had been launched to the general public by means of the GeneLab Data System (http://doi.org/10.26030/h713-bd02).

Consensus processing pipeline: The Microbes AWG additionally helped to ascertain a normal pipeline with which all 16S amplicon metagenome profiling datasets on GeneLab will probably be analyzed. These analyzed knowledge will enable the general public to raised perceive these datasets and permit extra speedy reanalysis and publication.

Goals 2020:

The major objective of the Microbes AWG will probably be to finish evaluation of the RR-6 datasets described above and to report these findings in a publication. The group may even search to ascertain a consensus shotgun metagenomic pipeline to be used by GeneLab.

Animals (mammals, non-mammals)

Co-leads: Tejaswini Mishra, Stanford University; Nathaniel Szewczyk, University of Nottingham

Accomplishments 2019

The Animal AWG facilitates using omics in understanding primary mechanisms by which animals and constituent tissues and cells adapt to the spaceflight setting.

Team Transitions: The Animal AWG efficiently transitioned to non-NASA management and recognized publications, grants, and coverage tasks to steer.

First Paper Published: The AWG revealed its first paper, “Mice Exposed to Combined Chronic Low-Dose Irradiation and Modeled Microgravity Develop Long-Term Neurological Sequelae,” within the International Journal of Molecular Sciences.

Several duties had been accomplished by the Animal AWG all year long:

• New pipeline developed for brand spanking new spaceflight knowledge.
• Established new C. elegans and Drosophila flight datasets.
• Facilitated an settlement between GeneLab and the UK’s Molecular Muscle 2 experiment for GeneLab to course of and host knowledge from the UK samples in addition to for the AWG to suggest samples to fly based mostly upon ongoing knowledge evaluation of previous flight samples.
• Facilitated submission of a profitable STEP-1 proposal to fly extra samples as recognized by ongoing cross species evaluation of potential mechanisms controlling gene expression modifications in response to spaceflight.

Professional Development:

• Attended GeneLab workshop on the annual American Society for Gravitational and Space Research convention.
• Participated in worldwide exchanges with the University of Nottingham and NASA Ames Research Center; submitted funding utility to assist the worldwide alternate
• Expanded AWG membership to characterize the Japanese house company, JAXA, whereas persevering with with NASA and ESA scientific communities.
• Sponsored two UK-funded Ph.D college students.

Goals 2020:

Current actions embrace:

• Write manuscripts that display mechanisms and shared molecular responses of animals throughout adaptation to the spaceflight setting
• Submit invited STEP-2 flight proposal
• Identify methods to assist NASA’s Decadal Survey
• Integrate human knowledge into cross-species AWG analyses
• Explore mechanism of monetary assist for ESA scientific group involvement in GeneLab
• Establish future flight proposals to achieve new Drosophila flight datasets.

MAJOR ACCOMPLISHMENTS BY GENELAB AWGS

Plant Biology

• Formed a brand new worldwide collaboration with the European Bioinformatics Institute’s Expression Atlas Team and generated the NASA GeneLab Expression Atlas to include experimental knowledge.
• Developed new NASA Microgreens Education that may rework Okay-12 science courses right into a NASA analysis program.
• Published three manuscripts revealed within the Frontiers in Plant Science.

Multi-omics

Microbes

• Generated 6 datasets from Rodent Research-6 mouse fecal samples to benchmark completely different profiling assays and higher perceive modifications within the intestine microbiome as a consequence of spacflight.
• Established a normal GeneLab pipeline for the evaluation of 16S amplicon microbiome profiling knowledge.

Animals (mammals, non-mammals)

JOIN A GENELAB ANALYSIS WORKING GROUP

NASA’s GeneLab Project is presently recruiting investigators, bioinformaticians, graduate college students, and postdocs to take part within the AWGs, which examine particular subsets of omics knowledge from experiments performed onboard the International Space Station, the Space Shuttle, in addition to ground-based analysis with relevance to spaceflight (e.g. radiation or unloading/weightlessness).

If you have an interest in collaborating, and/or when you’ve got college students with robust bioinformatics abilities who’re , assessment the GeneLab Analysis Working Groups Charter and ship an e-mail to arc-dl-genelab-awg@mail.nasa.gov with title of the group of curiosity within the topic line (Plants, Multi-omics/Systems Biology, Microbes, Animals [mammals, non-mammals]). Please submit a functionality/qualification assertion electronically in PDF format. The response should embrace: 1) Contact: title, affiliation, deal with, cellphone, e-mail, and web site. 2) Subject space experience: present a concise description of your experience when it comes to omics analyses, together with an inventory of related work and publications carried out up to now 5 years. Participation within the AWGs is fully voluntary and contributors will not be compensated.