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DOE OSTI2025

Editorial: Transcriptional and epigenetic landscapes of abiotic stress response in plants

In nature, plants constantly face various biotic and abiotic stresses that impact their growth, development, and productivity. Among these, abiotic stresses often have a more severe impact than biotic stresses. For instance, drought has been reported to cause greater yield losses than the combined impact of all plant pathogens (Gupta et al., 2020). Abiotic stresses are the immediate outcome of climate change, and the magnitude of these stresses has gradually increased every year with the rise in global temperatures. Thus, it has become imperative to study the impact of these stresses on plants and how plants respond to them at different levels to show resilient traits. This includes analysing the plants at morpho-physiological, biochemical, and molecular levels. Researchers often compare stressed plants to control (non-stressed) plants or evaluate contrasting genotypes, such as tolerant and sensitive lines, to elucidate the mechanisms underlying stress responses. While these studies have provided some insights, a comprehensive understanding of the intricate mechanisms governing plant responses to abiotic stress remains largely unknown. Recent advances in next-generation tools and technologies have enabled researchers to dissect the molecular basis of plant stress responses at genomic, transcriptomic, proteomic, metabolomic, epigenetic and epigenomic levels. Among these, knowledge of the transcriptional/epigenomic landscape of the trait-associated variations is limited. Given the importance of transcriptional changes and histone modifications in abiotic stress responses, this Research Topic was edited to collage the knowledge available on transcriptional and epigenetic landscapes of abiotic stress response in plants. The Research Topic features eight original research articles and one review, covering various aspects of transcriptome and epigenetic reprogramming in plants during abiotic stresses. Four of the research articles employ transcriptomics integrated with other omics approaches to explore transcriptome reprogramming, candidate gene identification, and the role of long non-coding RNA during different stresses. Two articles focus on the functional characterization of specific candidate genes involved in stress response, while another provides a genome-wide analysis of a stress-responsive gene family. Additionally, one study investigates genome-wide histone modifications, specifically H3K4me3 and H3K27me3, in response to abiotic stresses.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Bi-fated tendon-to-bone attachment cells are regulated by shared enhancers and KLF transcription factors

The mechanical challenge of attaching elastic tendons to stiff bones is solved by the formation of a unique transitional tissue. Here, we show that murine tendon-to-bone attachment cells are bi-fated, activating a mixture of chondrocyte and tenocyte transcriptomes, under regulation of shared regulatory elements and Krüppel-like factors (KLFs) transcription factors. High-throughput bulk and single-cell RNA sequencing of humeral attachment cells revealed expression of hundreds of chondrogenic and tenogenic genes, which was validated by in situ hybridization and single-molecule ISH. ATAC sequencing showed that attachment cells share accessible intergenic chromatin areas with either tenocytes or chondrocytes. Epigenomic analysis revealed enhancer signatures for most of these regions. Transgenic mouse enhancer reporter assays verified the shared activity of some of these enhancers. Finally, integrative chromatin and motif analyses and transcriptomic data implicated KLFs as regulators of attachment cells. Indeed, blocking expression of both Klf2 and Klf4 in developing limb mesenchyme impaired their differentiation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

A novel bivalent chromatin associates with rapid induction of camalexin biosynthesis genes in response to a pathogen signal in Arabidopsis

Temporal dynamics of gene expression underpin responses to internal and environmental stimuli. In eukaryotes, regulation of gene induction includes changing chromatin states at target genes and recruiting the transcriptional machinery that includes transcription factors. As one of the most potent defense compounds in Arabidopsis thaliana , camalexin can be rapidly induced by bacterial and fungal infections. Though several transcription factors controlling camalexin biosynthesis genes have been characterized, how the rapid activation of genes in this pathway upon a pathogen signal is enabled remains unknown. By combining publicly available epigenomic data with in vivo chromatin modification mapping, we found that camalexin biosynthesis genes are marked with two epigenetic modifications with opposite effects on gene expression, trimethylation of lysine 27 of histone 3 (H3K27me3) (repression) and acetylation of lysine 18 of histone 3 (H3K18ac) (activation), to form a previously uncharacterized type of bivalent chromatin. Mutants with reduced H3K27me3 or H3K18ac suggested that both modifications were required to determine the timing of gene expression and metabolite accumulation at an early stage of the stress response. Our study indicates that the H3K27me3-H3K18ac bivalent chromatin, which we name as kairostat, plays an important role in controlling the timely induction of gene expression upon stress stimuli in plants.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2015

The Twins Study: NASA's First Foray into 21st Century Omics Research

The full array of 21st century omics-based research methods should be intelligently employed to reduce the health and performance risks that astronauts will be exposed to during exploration missions beyond low Earth Orbit. In March of 2015, US Astronaut Scott Kelly will launch to the International Space Station for a one year mission while his twin brother, Mark Kelly, a retired US Astronaut, remains on the ground. This situation presents an extremely rare flight opportunity to perform an integrated omics-based demonstration pilot study involving identical twin astronauts. A group of 10 principal investigators has been competitively selected, funded, and teamed together to form the Twins Study. A very broad range of biological function are being examined including the genome, epigenome, transcriptome, proteome, metabolome, gut microbiome, immunological response to vaccinations, indicators of atherosclerosis, physiological fluid shifts, and cognition. The plans for the Twins Study and an overview of initial results will be described as well as the technological and ethical issues raised for such spaceflight studies. An anticipated outcome of the Twins Study is that it will place NASA on a trajectory of using omics-based information to develop precision countermeasures for individual astronauts.

Kundrot, C. E.↗

NASA NTRS2015

Research from the NASA Twins Study and Omics in Support of Mars Missions

The NASA Twins Study, NASA's first foray into integrated omic studies in humans, illustrates how an integrated omics approach can be brought to bear on the challenges to human health and performance on a Mars mission. The NASA Twins Study involves US Astronaut Scott Kelly and his identical twin brother, Mark Kelly, a retired US Astronaut. No other opportunity to study a twin pair for a prolonged period with one subject in space and one on the ground is available for the foreseeable future. A team of 10 principal investigators are conducting the Twins Study, examining a very broad range of biological functions including the genome, epigenome, transcriptome, proteome, metabolome, gut microbiome, immunological response to vaccinations, indicators of atherosclerosis, physiological fluid shifts, and cognition. A novel aspect of the study is the integrated study of molecular, physiological, cognitive, and microbiological properties. Major sample and data collection from both subjects for this study began approximately six months before Scott Kelly's one year mission on the ISS, continue while Scott Kelly is in flight and will conclude approximately six months after his return to Earth. Mark Kelly will remain on Earth during this study, in a lifestyle unconstrained by this study, thereby providing a measure of normal variation in the properties being studied. An overview of initial results and the future plans will be described as well as the technological and ethical issues raised for spaceflight studies involving omics.

Kundrot, C.↗

NASA NTRS2015

Omics Research on the International Space Station

The International Space Station (ISS) is an orbiting laboratory whose goals include advancing science and technology research. Completion of ISS assembly ushered a new era focused on utilization, encompassing multiple disciplines such as Biology and Biotechnology, Physical Sciences, Technology Development and Demonstration, Human Research, Earth and Space Sciences, and Educational Activities. The research complement planned for upcoming ISS Expeditions 45&46 includes several investigations in the new field of omics, which aims to collectively characterize sets of biomolecules (e.g., genomic, epigenomic, transcriptomic, proteomic, and metabolomic products) that translate into organismic structure and function. For example, Multi‐Omics is a JAXA investigation that analyzes human microbial metabolic cross‐talk in the space ecosystem by evaluating data from immune dysregulation biomarkers, metabolic profiles, and microbiota composition. The NASA OsteoOmics investigation studies gravitational regulation of osteoblast genomics and metabolism. Tissue Regeneration uses pan‐omics approaches with cells cultured in bioreactors to characterize factors involved in mammalian bone tissue regeneration in microgravity. Rodent Research‐3 includes an experiment that implements pan‐omics to evaluate therapeutically significant molecular circuits, markers, and biomaterials associated with microgravity wound healing and tissue regeneration in bone defective rodents. The JAXA Mouse Epigenetics investigation examines molecular alterations in organ specific gene expression patterns and epigenetic modifications, and analyzes murine germ cell development during long term spaceflight. Lastly, Twins Study ("Differential effects of homozygous twin astronauts associated with differences in exposure to spaceflight factors"), NASA's first foray into human omics research, applies integrated analyses to assess biomolecular responses to physical, physiological, and environmental stressors associated with spaceflight.

Love, John↗

NASA NTRS2016

Biomolecular Analysis Capability for Cellular and Omics Research on the International Space Station

International Space Station (ISS) assembly complete ushered a new era focused on utilization of this state-of-the-art orbiting laboratory to advance science and technology research in a wide array of disciplines, with benefits to Earth and space exploration. ISS enabling capability for research in cellular and molecular biology includes equipment for in situ, on-orbit analysis of biomolecules. Applications of this growing capability range from biomedicine and biotechnology to the emerging field of Omics. For example, Biomolecule Sequencer is a space-based miniature DNA sequencer that provides nucleotide sequence data for entire samples, which may be used for purposes such as microorganism identification and astrobiology. It complements the use of WetLab-2 SmartCycler"TradeMark", which extracts RNA and provides real-time quantitative gene expression data analysis from biospecimens sampled or cultured onboard the ISS, for downlink to ground investigators, with applications ranging from clinical tissue evaluation to multigenerational assessment of organismal alterations. And the Genes in Space-1 investigation, aimed at examining epigenetic changes, employs polymerase chain reaction to detect immune system alterations. In addition, an increasing assortment of tools to visualize the subcellular distribution of tagged macromolecules is becoming available onboard the ISS. For instance, the NASA LMM (Light Microscopy Module) is a flexible light microscopy imaging facility that enables imaging of physical and biological microscopic phenomena in microgravity. Another light microscopy system modified for use in space to image life sciences payloads is initially used by the Heart Cells investigation ("Effects of Microgravity on Stem Cell-Derived Cardiomyocytes for Human Cardiovascular Disease Modeling and Drug Discovery"). Also, the JAXA Microscope system can perform remotely controllable light, phase-contrast, and fluorescent observations. And upcoming confocal microscopy capability will allow for optical sectioning of biological tissues to determine microanatomical localization of biomarkers. Furthermore, NASA's geneLAB effort addresses integration of genomic, epigenomic, transcriptomic, proteomic and metabolomic datasets, by applying an innovative open source science platform for multi-investigator high throughput utilization of the ISS. In sum, the expanding ISS capability for analysis of biomolecules is enabling innovative research in a broad spectrum of areas such as cellular and molecular biology, biotechnology, tissue engineering, biomedicine, and Omics, providing manifold benefits for humanity.

Guinart-Ramirez, Y.↗

NASA NTRS2016

Epigenetics Research on the International Space Station

The International Space Station (ISS) is a state-of-the orbiting laboratory focused on advancing science and technology research. Experiments being conducted on the ISS include investigations in the emerging field of Epigenetics. Epigenetics refers to stably heritable changes in gene expression or cellular phenotype (the transcriptional potential of a cell) resulting from changes in a chromosome without alterations to the underlying DNA nucleotide sequence (the genetic code), which are caused by external or environmental factors, such as spaceflight microgravity. Molecular mechanisms associated with epigenetic alterations regulating gene expression patterns include covalent chemical modifications of DNA (e.g., methylation) or histone proteins (e.g., acetylation, phorphorylation, or ubiquitination). For example, Epigenetics ("Epigenetics in Spaceflown C. elegans") is a recent JAXA investigation examining whether adaptations to microgravity transmit from one cell generation to another without changing the basic DNA of the organism. Mouse Epigenetics ("Transcriptome Analysis and Germ-Cell Development Analysis of Mice in Space") investigates molecular alterations in organ-specific gene expression patterns and epigenetic modifications, and analyzes murine germ cell development during long term spaceflight, as well as assessing changes in offspring DNA. NASA's first foray into human Omics research, the Twins Study ("Differential effects of homozygous twin astronauts associated with differences in exposure to spaceflight factors"), includes investigations evaluating differential epigenetic effects via comprehensive whole genome analysis, the landscape of DNA and RNA methylation, and biomolecular changes by means of longitudinal integrated multi-omics research. And the inaugural Genes in Space student challenge experiment (Genes in Space-1) is aimed at understanding how epigenetics plays a role in immune system dysregulation by assaying DNA methylation in immune cells directly in space using miniPCR technology. In addition, NASA's geneLAB campaign covers the epigenome as part of the "expressome", by employing an innovative open source science platform for multi-investigator high throughput utilization of the ISS. Earth benefits of Epigenetics research onboard the ISS range from contributions to the fundamental understanding of epigenetic phenomena with applications in countermeasure development for biomedical conditions, to the generation of integrated strategies for personalized medicine based on unique physiological responses.

Love, John↗

NASA NTRS2016

Advances in Rodent Research Missions on the International Space Station

A research platform for rodent experiment on the ISS is a valuable tool for advancing biomedical research in space. Capabilities offered by the Rodent Research project developed at NASA Ames Research Center can support experiments of much longer duration on the ISS than previous experiments performed on the Space Shuttle. NASAs Rodent Research (RR)-1 mission was completed successfully and achieved a number of objectives, including validation of flight hardware, on-orbit operations, and science capabilities as well as support of a CASIS-sponsored experiment (Novartis) on muscle atrophy. Twenty C57BL6J adult female mice were launched on the Space-X (SpX) 4 Dragon vehicle, and thrived for up to 37 days in microgravity. Daily health checks of the mice were performed during the mission via downlinked video; all flight animals were healthy and displayed normal behavior, and higher levels of physical activity compared to ground controls. Behavioral analysis demonstrated that Flight and Ground Control mice exhibited the same range of behaviors, including eating, drinking, exploratory behavior, self- and allo-grooming, and social interactions indicative of healthy animals. The animals were euthanized on-orbit and select tissues were collected from some of the mice on orbit to assess the long-term sample storage capabilities of the ISS. In general, the data obtained from the flight mice were comparable to those from the three groups of control mice (baseline, vivarium and ground controls, which were housed in flight hardware), showing that the ISS has adequate capability to support long-duration rodent experiments. The team recovered 35 tissues from 40 RR-1 frozen carcasses, yielding 3300 aliquots of tissues to distribute to the scientific community in the U.S., including NASAs GeneLab project and scientists via Space Biology's Biospecimen Sharing Program Ames Life Science Data Archive. Tissues also were distributed to Russian research colleagues at the Institute for Biomedical Problems. The expression levels of select genes including albumin, catalase, GAPDH, HMGCoA Reductase, and IGF1 were determined using RNA isolated from the livers by qPCR and no significant differences by one factor ANOVA were found between flight and ground control groups. In addition, some of the liver samples were analyzed for transcriptomic, epigenomic and proteomic profiles; some of the data sets are now available to the scientific community through GeneLabs open science data website. A second long duration mission, Rodent Research-2 (RR-2) was completed on the ISS in 2015; 20 female C57BL6J mice were successfully maintained on the ISS for various durations, with the last group of 5 animals living on-orbit for 54 days. Furthermore, we continue to expand the ISSs capabilities by introducing new on-orbit technologies including blood collection and separation, bone densitometry scanning, muscle grip strength and anesthesia with recovery. In addition, series of ground-based verification testing to fly male mice and increase the total number of mice on-orbit from 20 to 40. Subsequent missions will provide the capability to return live mice from the ISS animals to evaluate recovery on Earth, further expanding operational and science capabilities of the RR project on the ISS.

Choi, S. Y.↗

NASA NTRS2016

The OMICS of Sports & Space: How Genomics is Transforming Both Fields

Join top 10 New York Times Bestseller “The Sports Gene” author David Epstein and NASA Twins Study investigator Christopher E. Mason, Ph.D., in the debate as old as physical competition—nature versus nurture. From personal experience, Epstein tackles the great debate and traces how far science has come in solving this timeless riddle, and how genetics has entered into the field of sports. He’s an investigative science reporter for ProPublica and longtime contributor to Sports Illustrated. Epstein will share insights into performance-enhancing drugs, the lucky genetics that separate a professional athlete from a less talented athlete, and his research into the death of a friend with Hypertrophic Cardiomyopathy (HCM).From an epigenomic viewpoint, Mason examines the benefits and risks for astronauts who face extreme spaceflight conditions and what it means for the future of human space travel. He is an associate professor in the Department of Physiology and Biophysics, The Feil Family Brain and Mind Research Institute (BMRI) & The Institute for Computational Biomedicine at Weill Cornell Medicine. He is also part of the Tri-Institutional Program on Computational Biology and a Medicine Fellow of Genomics, Ethics, and Law in the Information Society Project at Yale Law School.The study of omics shows tremendous potential in prevention, diagnosis and treatment of injuries and diseases but genetic discrimination and molecular privacy concerns are raised in both sports and space.

Reeves, Katherine↗

NASA NTRS2016

GeneLab: Multi-Omics Investigation of Rodent Research-1 Bio-Banked Tissues

NASAs Rodent Research (RR) project is playing a critical role in advancing biomedical research on the physiological effects of space environments. Due to the limited resources for conducting biological experiments aboard the International Space Station (ISS), it is imperative to use crew time efficiently while maximizing high-quality science return. NASAs GeneLab project has as its primary objectives to 1) further increase the value of these experiments using a multi-omics, systems biology-based approach, and 2) disseminate these data without restrictions to the scientific community. The current investigation assessed viability of RNA, DNA, and protein extracted from archived RR-1 tissue samples for epigenomic, transcriptomic, and proteomic assays. During the first RR spaceflight experiment, a variety of tissue types were harvested from subjects, snap-frozen or RNAlater-preserved, and then stored at least a year at -80OC after return to Earth. They were then prioritized for this investigation based on likelihood of significant scientific value for spaceflight research. All tissues were made available to GeneLab through the bio-specimen sharing program managed by the Ames Life Science Data Archive and included mouse adrenal glands, quadriceps, gastrocnemius, tibialis anterior, extensor digitorum longus, soleus, eye, and kidney. We report here protocols for and results of these tissue extractions, and thus, the feasibility and value of these kinds of omics analyses. In addition to providing additional opportunities for investigation of spaceflight effects on the mouse transcriptome and proteome in new kinds of tissues, our results may also be of value to program managers for the prioritization of ISS crew time for rodent research activities. Support from the NASA Space Life and Physical Sciences Division and the International Space Station Program is gratefully acknowledged.

GeneLab↗

NASA NTRS2017

Network Analysis of Rodent Transcriptomes in Spaceflight

Network analysis methods leverage prior knowledge of cellular systems and the statistical and conceptual relationships between analyte measurements to determine gene connectivity. Correlation and conditional metrics are used to infer a network topology and provide a systems-level context for cellular responses. Integration across multiple experimental conditions and omics domains can reveal the regulatory mechanisms that underlie gene expression. GeneLab has assembled rich multi-omic (transcriptomics, proteomics, epigenomics, and epitranscriptomics) datasets for multiple murine tissues from the Rodent Research 1 (RR-1) experiment. RR-1 assesses the impact of 37 days of spaceflight on gene expression across a variety of tissue types, such as adrenal glands, quadriceps, gastrocnemius, tibalius anterior, extensor digitorum longus, soleus, eye, and kidney. Network analysis is particularly useful for RR-1 -omics datasets because it reinforces subtle relationships that may be overlooked in isolated analyses and subdues confounding factors. Our objective is to use network analysis to determine potential target nodes for therapeutic intervention and identify similarities with existing disease models. Multiple network algorithms are used for a higher confidence consensus.

genomics↗

NASA NTRS2018

GeneLab: "Omics" Data Systems for Spaceflight and Simulated Spaceflight Environment

NASA's GeneLab Data System is a repository that hosts multi-omics datasets generated by biological experiments flown onboard the International Space Station. Strategies regarding how GeneLab envisions the involvement of the scientific community and the public at large will be discussed, and current and future capabilities of the system will be described. Information describing how scientists can participate in analyzing the current datasets on plants, microbes, invertebrates or mammals will be provided, and initial findings from the current datasets will be discussed during this presentation. Anyone interested in genomics, transcriptomics, epigenomics and proteomics, and systems biology, or who is curious to understand how space modifies living organisms should attend.

Omics↗

NASA NTRS2019

DNA Damage Response to Low and High-LET in a Large Cohort of Mice and Humans and Latest Advancement in NASA Space Omics

This presentation will first focus on a thorough evaluation of the DNA damage response to both low and high-LET in a cohort of 76 mice primary skin fibroblast derived from 15 different strains or in human blood mononuclear cells derived from 550 healthy donors. In both the human and mice work, we have hypothesized that DNA repair capacity can be used as a marker to evaluate and differentiate individual radiation sensitivity. More specifically, this work is based on the concept that the combined time-dose dependence of radiation-induced foci (RIF) of p53-binding protein 1 (53BP1) following low-LET exposure contains sufficient information to infer sensitivity to any other LET. This work is one of the most extensive studies on the kinetics and possible genetic underpinnings of radiation-induced DNA damage and repair. Results on humans are still preliminary as we are still in the process of collecting and isolating primary blood mononuclear cells from 500 to 800 healthy subjects of European descent, 18-75 years of age, 50/50 male/female distribution. We have analyzed 53BP1+ RIF formation as well as oxidative stress and cell death in primary cells from 192 subjects in response to the same HZE particles as used in mice: 600 MeV/n Fe, 350 MeV/n Ar and 350 MeV/n Si, 1.1 and 3 particles/100m2, 4 and 24 hours after irradiation. The second part of the talk will focus on describing GeneLab: The NASA Systems Biology Platform for Space Omics Repository, Analysis and Visualization. NASA GeneLab is an open-access repository for omics datasets generated by biological experiments conducted in space or experiments relevant to spaceflight (e.g. simulated cosmic radiation, simulated microgravity, bed rest studies). Started as a repository designed to archive precious omics from space experiments, GeneLab has expanded its scope to maximize the intelligibility of the raw data (e.g. RNAseq, microarray, WGBS, metagenome), particularly for users with limited bioinformatics knowledge. As such GeneLab is now providing processed data derived from the raw data covering a large spectrum of omics (genome, epigenome, transcriptome, epitranscriptome, proteome, metabolome), to help users explore important questions: Which genes or proteins are expressed differently in space for various living organisms? What are the consequences arising from these changes? What specifics DNA mutations or epigenetic changes happen in space? What species or genetic features lead to better adaption to such a unique environment? In this presentation, we will report on the current and future objectives for GeneLab, and review recent published studies relating molecular changes observed in various animal models and tissue with microgravity, radiation, circadian rhythm, hydration and carbon dioxide conditions.

DNA repair kinetics↗

NASA NTRS2019

GeneLab: A Systems Biology Platform for Omics Analysis

NASA GeneLab is an open-access repository for omics datasets generated by biological experiments conducted in space or experiments relevant to spaceflight (e.g. simulated cosmic radiation, simulated microgravity, bed rest studies). The GeneLab Data Systems (GLDS) version 4.0 will be available on October 1st 2019, and will provide the latest in terms of professional state-of-the-art bioinformatics platform for the space biology and radiation community to upload their data into an omics data commons, to process their data with vetted standard workflows and to compare to existing analyses. Started in 2015 as a repository designed to archive omics data from space experiments, GeneLab has expanded its scope to all ionizing radiation omics experiments conducted on the ground and has put considerable effort in providing carefully characterized radiation metadata on all dataset. GeneLab is also providing processed data derived from the raw data covering a large spectrum of omics (genome, epigenome, transcriptome, epitranscriptome, proteome, metabolome) to help users explore important questions: 1) Which genes or proteins are expressed differently in space for various living organisms? 2) What specific DNA mutations or epigenetic changes happen in space or after exposure to ionizing radiation? and 3) How does genetics affect these responses? Processed data available on GeneLab are derived by standard data analysis workflows vetted by hundreds of scientists who volunteered to join one of the four GeneLab Analysis Working Groups (Animal AWG, Plant AWG, Microbe AWG, Multi-Omics AWG). In this presentation, we will discuss how to bridge the gap between irradiation studies performed on earth and biological experiments conducted in space since the early 1990's. We will discuss how radiation dosimetry was estimated for datasets derived from samples collected during the Space Shuttle era or on the International Space Station. Finally, we will address future strategies regarding dose monitoring in future missions into space, inter-agency efforts to unify data under one umbrella, and knowledge dissemination across the radiation research community and the space biology community.

open-science↗

NASA NTRS2016

Advances in Rodent Research Missions on the International Space Station

A Research platform for rodent experiment on the ISS is an essential tool for advancing biomedical research in space. The Rodent Research allows for experiments of much longer duration that experiments on the Shuttle. NASA’s Rodent Research (RR)-1 mission was successfully completed, including post-flight analysis and achieved a number of objectives including validation of flight hardware, on-orbit operations, and science capabilities that were developed at the NASA Ames Research Center. Briefly, twenty C57BL/6J adult female mice were launched on the SpX4 Dragon vehicle, which thrived for up to 37 days in microgravity. Daily health checks of the mice were performed during the mission via downlinked video; all animals were healthy and displayed normal behavior without any significant signs of stress. Behavioral analysis demonstrated that Flight and Ground Control mice exhibited the same range of behaviors, including eating, drinking, exploratory behavior, self- and allo-grooming, and social interactions indicative of healthy animals. The animals were euthanized and select tissues were collected from some of the mice on orbit to assess the long-term sample storage capabilities of the ISS. The data obtained from the flight mice were comparable to those from the 3 groups of control mice (baseline, vivarium and ground controls), suggesting that the ISS has adequate capability to support long-duration rodent experimentations. We recovered over 35 tissues from 40 RR1 frozen carcasses, yielded over 3200 aliquots of tissues, and distributed to the scientific community, including NASA’s GeneLab and scientists in the U.S. through Biospecimen Sharing Program via Ames Life Science Data Archive. Tissues were also distributed to Russian research colleagues at the Institute for Biomedical Problems. The expression levels of select genes including albumin, catalase, GAPDH, HMGCoA Reductase, and IGF1 were determined using RNA isolated from the livers by qPCR and no significant differences by one factor ANOVA were found between flight and ground control groups. In addition, some of the liver samples were subject to transcriptomics, epigenomics and proteomics. The data are now available to the scientific community through GeneLab’s open science data website. Since the RR1 mission, another long duration mission (Rodent Research-2) was completed on the ISS in 2015 in which 20 female C57 BL/6J mice were successfully maintained on the ISS for varying time points, with the last group of 5 animals being on-orbit for 54 days. This second Rodent Research flight expanded the program’s capabilities with the introduction of new technologies including blood collection and separation and bone densitometry scanning. Furthermore, we have continued to expand the ISS’s capabilities by running a series of ground-based verification testing using male mice. Our next step is to fly male mice for Rodent Research-4 on SpaceX-10 to study the effects of microgravity on bone healing and regeneration. It will be the first long-duration mission using male mice using Rodent Hardware. In addition, the number of mice will increase from 20 mice (on RR-1 and RR-2) to 40 for RR-4. When samples return to Earth, a number of tissues will be dissected from the frozen carcasses and select tissue samples will become available to the scientific community via BSP. Altogether, we have continued to expand our capabilities for performing long-duration missions on the ISS as emphasized in the National Research Council’s Decadal Survey released in 2011 and to maximize science return from each mission.

Choi, S.↗

NASA NTRS2019

NASA GeneLab Space Omics Database: Expanding from Space to Ionizing Radiation Data on the Ground

NASA GeneLab is an open-access repository for omics datasets generated by biological experiments conducted in space or ground experiments relevant to spaceflight (e.g. simulated cosmic radiation, simulated microgravity, bed rest studies). The GeneLab Data Systems (GLDS) version 4.0 will be available on October 1st 2019, and will provide a state-of-the-art bioinformatics platform for the space biology and radiation communities to upload their data into an omics data commons, to process their data with vetted standard workflows and to compare with existing analyses. Started in 2015 as a repository designed to archive omics data from space experiments, GeneLab has expanded its scope to all ionizing radiation omics experiments conducted on the ground and has put considerable effort in providing carefully characterized radiation metadata on all datasets. GeneLab is also providing processed data derived from the raw data covering a large spectrum of omics (genome, epigenome, transcriptome, epitranscriptome, proteome, metabolome) to help users explore important questions: 1) Which genes or proteins are expressed differently in space for various living organisms? 2) What specific DNA mutations or epigenetic changes happen in space or after exposure to ionizing radiation? and 3) How does genetics affect these responses? Processed data available on GeneLab are derived by standard data analysis workflows vetted by hundreds of scientists who volunteered to join one of the four GeneLab Analysis Working Groups (Animal AWG, Plant AWG, Microbe AWG, Multi-Omics AWG). In this presentation, we will discuss how to bridge the gap between irradiation studies performed on earth and biological experiments conducted in space since the early 1990's. We will discuss how radiation dosimetry was estimated for datasets derived from samples collected during the Space Shuttle era on the International Space Station and on other orbiting platforms. Finally, we will address future strategies regarding dose monitoring in future missions into space, inter-agency efforts to unify data under one umbrella, and knowledge dissemination across the radiation research community and the space biology community.

open-science↗

NASA NTRS2019

GeneLab: Overview of Challenges and Opportunities

The NASA GeneLab project capitalizes on multi-omic technologies to maximize the return on spaceflight experiments. To do this, GeneLab maintains a publicly accessible database (GLDS) that houses spaceflight and spaceflight relevant multi-omics data, and collaborates with NASA principal investigators and projects to generate additional omics data. GeneLab houses more than 200 transcriptomic, proteomic, metabolomic and epigenomic datasets from plant, animal and microbial experiments, with a growing number of these having been produced by the GeneLab sample processing lab. The GLDS contains rich metadata about each experiment and has recently integrated radiation dosimetery data from experiments flown on the Space Shuttle. GeneLab has also recently implemented an effort to present processed data in the GLDS in addition to the raw omics data. The processed data will enable interpretation of the data by a larger group of students, scientists and the general public. Standard pipelines for the transformation of raw data into visualizations were developed by four GeneLab Analysis Working Groups (animals, plants, microbes, multi-omics) comprised of over 100 scientists from NASA and academia. These pipelines are now being used by a group of bioinformatics interns to provide standard basic analysis of the data for incorporation into GLDS.

Galazka, Jonathan M.↗