Results for “Bioinformatics” — Page 5

NASA NTRSDate not supplied

Spaceflight Biospecimen Sharing in Support of Science Discovery and Exploration

For decades, NASA and international partners have flown non-human biological experiments in space to understand the effects of spaceflight and address potential biological hazards. Sending organisms into space is a costly endeavor which makes space-flown biological specimens a valuable resource. To enable maximum scientific return, samples not required by the Principal Investigators are harvested and collected mostly by NASA’s Space Biology Biospecimen Sharing Program. These specimens are collected according to well-established SOPs that maintain quality and integrity. The specimens are then preserved, archived, and made available to the international scientific community through NASA’s Institutional Scientific Collection (ISC) at Ames Research Center (ARC). The ISC-ARC biospecimens and descriptive metadata are findable and accessible for request through the Life Sciences Data Archive (LSDA). The NASA ISC-ARC currently stores over 32,000 specimens from Shuttle, International Space Station, and ground-based investigations (spaceflight analog experiments involving either hindlimb unloading, centrifugation, or partial weight-bearing study designs). Tissues are predominantly from mice and rats, though samples are also available from bacteria and quail. The specimens include tissues from many physiological systems including musculoskeletal, neurosensory, reproductive, respiratory, circulatory, and digestive. Tissues are stored at -80°C, -20°C, +4°C, or ambient and preserved in various fixatives. Descriptive metadata is available for all samples. Historically, these tissues have been used for a wide range of analyses, including histology, genomics, and transcriptomics. Plans are underway to expand the ISC-ARC beyond the mostly-rodent contents, to include a space-relevant microbial culture collection including bacteria, fungi, and yeast. This expansion of the ISC-ARC will now involve identifying and standardizing best practices for microbial curations. To ensure safe long-term storage of microbial isolates, a microbiology laboratory will be dedicated for identification, cell culture, and lyophilization. Awarding of tissue to public science investigators has resulted in 33 publications since 2011, with 48 requests being submitted since 2016. Of note, NASA GeneLab has been awarded ISC-ARC biospecimens in the past few years. GeneLab processes the biospecimens to generate various levels of ‘omics’ data, which are published on GeneLab’s open access online platform for bioinformatics analysis and visualization. This has helped a systems biology community grow around the processed-biospecimens’ datasets, resulting in many new publications and insights. Websites: https://www.nasa.gov/ames/research/space-biosciences/isc-bsp ; https://lsda.jsc.nasa.gov/Biospecimen

Ryan T. Scott↗

NASA NTRSDate not supplied

GL4U: GeneLab for Colleges and Universities

GeneLab for Colleges and Universities (GL4U) will provide space biology-relevant training in bioinformatics to the next generation of scientists through direct and indirect approaches. The GeneLab (GL) team will host two annual data processing bootcamps, one for college-level students (direct) and one for college educators (indirect – Training of Trainers), in which participants learn to analyze space-relevant omics data hosted on GL. The first bootcamp took place in early June 2021 with about 30 SJSU undergraduate students and covered space biology-specific lectures and hands-on instruction using Jupyter Notebooks (JNs) for RNA sequence (RNAseq) data analysis. All training materials including the enclosed files listed below will be made publicly available on GitHub. RNAseq Bootcamp Lectures (attached in combined file): Introduction to NASA, Space Biology, GeneLab, and the Command Line: NASA_GL_CL_Intro_FINAL.pdf - DRAFT from initial submission NASA_SB_GL_CL_Intro_FULL.pdf - FINAL version presented during the bootcamp - only minor edits from the draft version RNAseq and Data Processing Overview: RNAseq_Overview_FINAL.pdf - DRAFT from initial submission RNAseq_Overview_FULL.pdf - FINAL version presented during the bootcamp - only minor edits from the draft version Overview of the Statistics Used for RNAseq Data Analysis: SJSU_Statistics_Intro_Lecture_FINAL.pdf - DRAFT from initial submission Statistics_Overview_FULL.pdf - FINAL version presented during the bootcamp - only minor edits from the draft version Completed JNs in HTML format (attached in combined file): Unix_Intro_JN_06-2021_completed.html R_Intro_JN_06-2021_completed.html RNAseq_fastq_to_counts_JN_06-2021_completed.html RNAseq_DGE_JN_06-2021_completed.html RNAseq Bootcamp Recordings (attached): GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day1_Part_1_of_5.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day1_Part_2_of_5.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day1_Part_3_of_5.mp4 *There were issues with the part 4 recording so that is not available GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day1_Part_5_of_5.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day2_Part_1_of_3.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day2_Part_2_of_3.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day2_Part_3_of_3.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day3_Part_1_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day3_Part_2_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day3_Part_3_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day3_Part_4_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day4_Part_1_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day4_Part_2_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day4_Part_3_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day4_Part_4_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day5_Part_1_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day5_Part_2_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day5_Part_3_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day5_Part_4_of_4.mp4

GeneLab↗

NASA NTRSDate not supplied

Enabling Space Biology Knowledge Discovery Through Biospecimen Sharing: The NASA Biological Institutional Scientific Collection and Space Microbial Culture Collection

NASA and international partners have conducted experiments in space to understand the biological impacts and address hazards to health. The resulting basic and applied science is imperative to enabling humanity to venture back to the Moon and then to Mars and beyond. Sending organisms into space is a costly endeavor. All biospecimens not required by spaceflight-relevant Principal Investigators are harvested, preserved, and archived in the NASA Biological Institutional Scientific Collection (NBISC) to maximize the scientific return. The NASA Biological and Physical Sciences (BPS) Division ‘Open Science’ endeavor includes NASA Genelab, the Space Biology Program’s Biospecimen Sharing Program, Physical Sciences Informatics, the Ames Life Sciences Data Archive, and NBISC to integrate extensive data and biospecimen resources from spaceflight and/or ground-based analog experiments. NBISC biospecimens are collected and preserved according to well-established standard operating procedures to maintain scientific quality and are available on-request by the international scientific community. NBISC currently stores over 32,000 biospecimens from Shuttle, International Space Station, and ground-based space analog investigations. Tissue sharing has resulted in at least 33 publications since 2011 and 48 requests since 2016. Many requests for NBISC biospecimen come from first-time investigators who subsequently submit grants as the port-of-entry into the field of space biology. Some NBISC biospecimens have been awarded to NASA Genelab, who then generate various ‘Open Science’ -omics data sets on their platform for bioinformatics. Other NBISC biospecimen awards have led to multiple studies such as fecal microbiome analysis, DNA damage analysis using single-cell DNA sequencing, enzymatic-pathway identification involved in spaceflight muscle atrophy, and characterization of ocular morphological changes. Of note, NBISC has expanded to include a new Space Microbial Culture Collection (SMCC) for the collection, identification, documentation, long-term preservation, and distribution of space-related microbial isolates.

biospecimens↗

NASA NTRSDate not supplied

GL4U: Training the next generation of bioinformaticians, one omics datatype at a time

Spaceflight modifies gene expression in every organism examined to date, including humans. Understanding how these gene expression changes affect physiology is crucial for the development of countermeasures to enable long-duration manned missions. NASA’s GeneLab project provides researchers open access to multi-omics data, including genetic and gene expression data, from spaceflight experiments that can be mined to understand the effects of spaceflight on biological systems. To ensure new knowledge generation through data re-use, it is important to maximize the number of scientists who utilize GeneLab data. Training students on the GeneLab platform is the best way to create long-term adopters of this NASA database and its tools. Turning students into future instructors and advocates will also accelerate the dissemination of these data and tools to the broader scientific community. Therefore, in collaboration with the GeneLab Educational Working Group (EWG), GeneLab has created GeneLab for Colleges and Universities (GL4U). GL4U provides space biology-relevant training in bioinformatics to the next generation of scientists through direct and indirect approaches. The GeneLab team plans to host two annual data processing bootcamps, one for college-level students (direct) and one for college educators (indirect – training of trainers), in which participants learn to analyze GeneLab’s space-relevant omics data. During the bootcamp, educators will receive materials and training to enable them to run the bootcamp at their home institutions or alternatively to adapt the content to implement within existing courses, thereby extending the reach of this initiative. The GL4U direct training pilot program was conducted in June 2021 in collaboration with USRA and San Jose State University (SJSU). During the pilot, SJSU students participated in a week-long bootcamp consisting of space biology-specific lectures and hands-on instruction using Jupyter Notebooks to analyze RNA sequence data. This pilot demonstrates the capacity of GL4U for training young scientists and encouraging data re-use.

Jonathan Matthew Galazka↗

NASA NTRSDate not supplied

Overview of the Translational Radiation Research and Countermeasures (TRRaC) Project in Space Radiation

The Translational Radiation Research and Countermeasures (TRRaC) Project was initiated by the Space Radiation (SR) Element within NASA’s Human Research Program (HRP) to support the SR mission to understand and characterize the space radiation environment, understand and quantify radiation-associated risks, and mitigate the impacts of radiation-induced adverse health outcomes to enable human space exploration. TRRaC’s mission is to translate radiation research results from experimental studies and epidemiological data to humans and astronauts using bioinformatics and computational modeling. TRRaC will leverage existing datasets such as those available from NASA’s GeneLab repository and human medical radiation exposure registries, along with relevant data generated from ground-based research at molecular, cellular, tissue, and system levels, to: (1) refine the radiation dose rate effectiveness factor, (2) characterize radiation quality effects to improve estimates of the risk of exposure-induced death (REID) from space-relevant radiation exposures, and (3) identify pathways and biomarkers for cancer, cardiovascular disease, and central nervous system changes that are impacted by space radiation exposure.

Parastou Eslami↗

NASA NTRSDate not supplied

Enabling Space Biology Knowledge Discovery Through Biospecimen Sharing: The NASA Biological Institutional Scientific Collection

NASA and international partners have conducted experiments in space to understand the biological impacts and address hazards to health. The resulting basic and applied science is imperative to enabling humanity to venture back to the Moon and then to Mars and beyond. Sending organisms into space is a costly endeavor. All biospecimens not required by spaceflight-relevant Principal Investigators are harvested, preserved, and archived in the NASA Biological Institutional Scientific Collection (NBISC) to maximize the scientific return. The NASA Biological and Physical Sciences (BPS) Division has an ‘Open Science’ endeavor which includes NASA Genelab, the Space Biology Program’s Biospecimen Sharing Program, Physical Sciences Informatics, the Ames Life Sciences Data Archive, and NBISC. Its purpose is to integrate extensive data and biospecimen resources from spaceflight and/or ground-based analog experiments. NBISC biospecimens are collected and preserved according to well-established standard operating procedures to maintain scientific quality and are available on-request by the international scientific community. NBISC currently stores over 32,000 biospecimens from Shuttle, International Space Station, and ground-based space analog investigations. Tissue sharing has resulted in at least 33 publications since 2011 and 48 requests since 2016. Many requests for NBISC biospecimen come from first-time investigators who subsequently submit grants as the port-of-entry into the field of space biology. Some NBISC biospecimens have been awarded to NASA Genelab, who then generate various ‘Open Science’ -omics data sets on their platform for bioinformatics. Other NBISC biospecimen awards have led to multiple studies such as fecal microbiome analysis, DNA damage analysis using single-cell DNA sequencing, enzymatic-pathway identification involved in spaceflight muscle atrophy, and characterization of ocular morphological changes. Of note, NBISC has expanded to include a new Space Microbial Culture Collection (SMCC) for the collection, identification, documentation, long-term preservation, and distribution of space-related microbial isolates.

Ryan T. Scott↗

NASA NTRSDate not supplied

Working at NASA as a (Molecular) Biologist...

Trained as a biologist, I landed my first job at NASA as a mission scientist on the Rodent Research project. As a mission scientist, I led science activities associated with development, flight, and post-flight analysis of rodent research missions on the ISS in consultation with project engineers, operational specialists, mission PI(s), and mission Implementation Partner(s). I also assessed the feasibility of scientific experiments as a technical and scientific expert in rodent research on the ISS. Eager to learn more about the molecular changes that occur as a result of spaceflight exposure, I transitioned to the NASA GeneLab project where I eventually became the data processing lead. NASA’s GeneLab helps scientists understand how the fundamental building blocks of life – DNA, RNA, proteins, and metabolites – change from exposure to the space environment including microgravity and cosmic radiation exposure. GeneLab does so by providing fully coordinated epigenomics, genomics, transcriptomics, proteomics, and metabolomics data (collectively known as omics data) alongside essential metadata describing each spaceflight and space-relevant experiment. In order to maximize the intelligibility of these data, particularly for users with limited bioinformatics knowledge, GeneLab has started processing and analyzing these datasets to generate differential gene expression data and identify biological and physiological pathways that are dysregulated as a result of spaceflight. The user interface was designed to be accessible to a broad variety of users, including high school and college students who can use it to learn about omics data analysis and space biology. During the CA Space Grant NASA Panel event, I will provide an overview of my work at NASA on both the Rodent Research and GeneLab projects and will conclude by providing resources for opportunities to work with GeneLab and NASA at large.

Amanda M Saravia-Butler↗

NASA NTRSDate not supplied

Method Development for In-situ Detection of Latent Herpesvirus DNA from Saliva using Nanopore Sequencing

Research toward latent herpesvirus reactivation has been intensively addressed through Space Shuttle and International Space Station (ISS) investigations. This work has provided the understanding that persistent reactivation of herpesviruses from asymptomatic crew can be detected through viral shedding in saliva, urine, and blood. Occasionally, viral reactivation from the latency stage can pose a threat to crew health (clinical manifestation) before, during, and after flight missions. Furthermore, previous work detailing correlations with immunity indicate that monitoring viral reactivation could be implemented to assess potential immune dysfunction. While in-flight monitoring is desirable, there is no well-established procedure or method for real-time evaluations, and research to date has relied on postflight, ground-based analysis. The development of portable molecular technologies like the miniPCR™ (miniPCR Bio) thermal cycler and the MinION™ sequencer (Oxford Nanopore Technologies) have confirmed that real-time monitoring is possible in extreme and low resource environments. These devices, combined with simple sample preparation methods, have been used to demonstrate bacterial identification onboard the ISS, as well as rapid viral detection in remote locations on Earth. The work here builds upon previous molecular advancements onboard the ISS toward the development and validation of a spaceflight-compatible method for viral detection from crew samples. Several herpesviruses can be detected in saliva, which provides a non-invasive means to collect samples for monitoring. While the basis for this method lies in previous spaceflight investigations, key points for method optimization include DNA extraction from saliva, viral primer selection, and bioinformatic processes for data analysis. To increase viral yield, numerous DNA extraction methods have been evaluated and will be discussed in detail. For initial development and testing, varicella-zoster virus (VZV) is being targeted though open reading frame 51 and 63 (ORF51, ORF63), as the replication origin-binding protein is highly expressed during latency. Optimization of the thermal cycling parameters has resulted in the ability to test the entire process. The full method has been tested with both viral VZV DNA standards and saliva spiked with varying concentrations of VZV. Viral sequence data were mapped to the reference sequence using minimap2. Prior to mapping, DNA sequencing reads were filtered for length and quality, barcodes were removed, and alignment identity calculated. Following further assessments, statistics were compared across multiple sequencing experiments and are being used to determine the success of the protocols. Forward work will include the incorporation of herpes simplex virus 1 (HSV-1) and Epstein-Barr virus (EBV) primers as well as the validation of results to the terrestrial qPCR standard assay. Upon full validation of the developed method, saliva will be collected from 20 healthy subjects and spiked with viral DNA. These samples will be split and assayed with the MinION and standard qPCR assay.

Hang N Nguyen↗

NASA NTRSDate not supplied

Expanding Repository Data Available For Sharing and Knowledge Discovery

Some of the hardest space biology and space health challenges require data-intensive, bioinformatic, meta-analytical, and computer-assisted research approaches. These challenges include examining interdisciplinary space life science research across experiments and across interacting spaceflight hazards (radiation, altered gravity, confinement, hostile-closed environments, distance-duration from Earth). The approaches to confront these challenges involve mining multiple datasets simultaneously from various hierarchical organizations of biological complexity, all while concurrently evaluating how experimental design factors affect endpoints of standard assays. To enable this field, it is essential that principal investigators (PIs) submit data in a structure so it can be maximally re-used. The purpose of the NASA Ames Life Sciences Data Archive (ALSDA) is to collect, curate, and make publicly available all non-human space-relevant biological data. ALSDA must also ensure data are open-access, and maximally findable, accessible, interoperable, and reusable (FAIR). The scope of ALSDA data collected and submitted by PIs include subject and study design metadata, assay metadata parameters, raw and processed assay data, assay imagery/video, and subject-experienced mission data telemetry (radiation, temperature, humidity, acoustics, vibrations, etc.). ALSDA recently integrated into a collaborative group of Open Science projects to facilitate a suite of new tools and workflows that will improve data submission, accessibility, and reusability by implementing digital data submission agreements, and adopting the data management system originally developed by NASA GeneLab. ALSDA intends to bring current biological repository data and all future collected data into this new scientific data reuse reality. This new suite of tools will enable ALSDA to deploy a science curation system using scientific assay configurations for the data submission portal. It will capture essential assay parameters according to established standards in each sub-field within biology. The submission portal expedites data collection by enhancing ease of PI data submission, providing a user interface and specificity for which data is to be submitted. Data submissions can be brought into cutting-edge informatic analysis portals to enable mining of physiological, behavioral, biochemical, and imaging datasets in conjunction with ‘omics-level datasets. As ALSDA datasets are submitted, curated, and published (e.g., micro-computed tomography, histology, pulse oximetry, serum metabolites, magnetic resonance imaging, intraocular pressure, novel object recognition, etc.), the merging together of spaceflight data along this multi-hierarchical complexity of biology will enable informatics and data-intensive approaches resulting in knowledge discoveries across missions, space hazards, and biological disciplines.

Biology↗

NASA NTRSDate not supplied

My Journey to NASA and role as a (Molecular) Biologist…

My journey to NASA started in undergrad, where I performed microbiology research and became hooked in the STEM fields. From there I earned a Ph.D. in Biochemistry and Molecular Biology from Mayo Graduate school where I performed Pancreatic Cancer research and then went on to perform postdoctoral research in Developmental Biology at the University of Miami. Trained as a biologist, I landed my first job at NASA as a mission scientist on the Rodent Research project. As a mission scientist, I led science activities associated with development, flight, and post-flight analysis of rodent research missions on the ISS in consultation with project engineers, operational specialists, mission PI(s), and mission Implementation Partner(s). I also assessed the feasibility of scientific experiments as a technical and scientific expert in rodent research on the ISS. Eager to learn more about the molecular changes that occur as a result of spaceflight exposure, I transitioned to the NASA GeneLab project where I eventually became the data processing lead. NASA’s GeneLab helps scientists understand how the fundamental building blocks of life – DNA, RNA, proteins, and metabolites – change from exposure to the space environment including microgravity and cosmic radiation exposure. GeneLab does so by providing fully coordinated epigenomics, genomics, transcriptomics, proteomics, and metabolomics data (collectively known as omics data) alongside essential metadata describing each spaceflight and space-relevant experiment. To maximize the intelligibility of these data, particularly for users with limited bioinformatics knowledge, GeneLab has started processing and analyzing these datasets to generate differential gene expression data and identify biological and physiological pathways that are dysregulated as a result of spaceflight. The user interface was designed to be accessible to a broad variety of users, including high school and college students who can use it to learn about omics data analysis and space biology. During the CA Space Grant Women in STEM Panel event, I will provide an overview of my journey to NASA including my work at NASA on both the Rodent Research and GeneLab projects. I will conclude by providing resources for opportunities to work with GeneLab and NASA at large followed by links to programs designed specifically to engage women in STEM fields.

Amanda M Saravia-Butler↗

NASA NTRSDate not supplied

My Journey to NASA and Role as a (Molecular) Biologist…

My journey to NASA started in undergrad, where I performed microbiology research and became hooked in the STEM fields. From there I earned a Ph.D. in Biochemistry and Molecular Biology from Mayo Graduate school where I performed Pancreatic Cancer research and then went on to perform postdoctoral research in Developmental Biology at the University of Miami. Trained as a biologist, I landed my first job at NASA as a mission scientist on the Rodent Research project. As a mission scientist, I led science activities associated with development, flight, and post-flight analysis of rodent research missions on the ISS in consultation with project engineers, operational specialists, mission PI(s), and mission Implementation Partner(s). I also assessed the feasibility of scientific experiments as a technical and scientific expert in rodent research on the ISS. Eager to learn more about the molecular changes that occur as a result of spaceflight exposure, I transitioned to the NASA GeneLab project where I eventually became the data processing lead. NASA’s GeneLab helps scientists understand how the fundamental building blocks of life – DNA, RNA, proteins, and metabolites – change from exposure to the space environment including microgravity and cosmic radiation exposure. GeneLab does so by providing fully coordinated epigenomics, genomics, transcriptomics, proteomics, and metabolomics data (collectively known as omics data) alongside essential metadata describing each spaceflight and space-relevant experiment. To maximize the intelligibility of these data, particularly for users with limited bioinformatics knowledge, GeneLab has started processing and analyzing these datasets to generate differential gene expression data and identify biological and physiological pathways that are dysregulated as a result of spaceflight. The user interface was designed to be accessible to a broad variety of users, including high school and college students who can use it to learn about omics data analysis and space biology. During the NASA Ames ECN at Lincoln HS Virtual Panel event, I will provide an overview of my journey to NASA including my work at NASA on both the Rodent Research and GeneLab projects. I will conclude by providing resources for opportunities to work with GeneLab and NASA at large followed by links to programs designed specifically to engage women in STEM fields.

Amanda M Saravia-Butler↗

NASA NTRSDate not supplied

Development of Computational Environmental Microbiome Workflows for the Laboratory and the International Space Station

Identification of microorganisms in the spaceflight environment is critical for crew health risk assessment on the International Space Station (ISS). Since 2017, nanopore sequencing technology has been used to support thein situ identification of microbial species during spaceflight. Beginning in 2018, a culture-independent, swab-to-sequencer method was implemented onboard the ISS to provide a more thorough insight of the ISS microbiome. Eliminating microbial culture enables identification of difficult-to-culture organisms, reduces risks associated with potentially pathogenic cultures, and could significantly reduce the time from sample-to-answer. However, this molecular-based approach generates large metagenomic datasets that require substantial computational resources for analysis. To process nanopore-generated sequencing data, the JSC Microbiology Laboratory established a bioinformatics workflow on Amazon EC2 under the security guidance of the NASA Science Managed Cloud Environment (SMCE).This resource allows for the development, testing, and accessing of computational tools for processing large and complex datasets. The work described here will address the downlinking of data from the ISS, the automated pipeline developed to identify targeted bacterial and fungal organisms, and the time from sampling onboard to microbial identification. The pipelines have been enhanced to address high and low biomass samples using optimization based on sample source (air, water, or surface) and type of collection (filter, colony, or swab).The resulting microbiome data can be assessed beyond microbial identifications to gain understanding toward population changes over time, potential selective environmental pressures, and evaluating correlations with a wide range of additional data sets. Metagenome analysis pipelines in development could allow for simultaneous identification of microbial species, gene function, and gene pathways present in the environment. Beyond the ground processing, the developed analysis pipeline is currently deployed onboard the ISS to allow for near real-time assessments of the ISS microbiome. This study serves as a critical foundation for exploration missions, where rapid microbiome analyses will be required.

G. Marie Sharp↗

NASA NTRSDate not supplied

Expanding Repository Data Available For Sharing And Knowledge Discovery

Some of the hardest space biology and space health challenges require data-intensive, bioinformatic, meta-analytical, and computer-assisted research approaches. These challenges include examining interdisciplinary space life science research across experiments and across interacting spaceflight hazards (radiation, altered gravity, confinement, hostile-closed environments, distance-duration from Earth). The approaches to confront these challenges involve mining multiple datasets simultaneously from various hierarchical organizations of biological complexity, all while concurrently evaluating how experimental design factors affect endpoints of standard assays. To enable this field, it is essential that principal investigators (PIs) submit data in a structure so it can be maximally re-used. The purpose of the NASA Ames Life Sciences Data Archive (ALSDA) is to collect, curate, and make publicly available all non-human space-relevant biological data. ALSDA must also ensure data are open-access, and maximally findable, accessible, interoperable, and reusable (FAIR). The scope of ALSDA data collected and submitted by PIs include subject and study design metadata, assay metadata parameters, raw and processed assay data, assay imagery/video, and subject-experienced mission data telemetry (radiation, temperature, humidity, acoustics, vibrations, etc.). ALSDA recently integrated into a collaborative group of Open Science projects to facilitate a suite of new tools and workflows that will improve data submission, accessibility, and reusability by implementing digital data submission agreements, and adopting the data management system originally developed by NASA GeneLab. ALSDA intends to bring current biological repository data and all future collected data into this new scientific data reuse reality. This new suite of tools will enable ALSDA to deploy a science curation system using scientific assay configurations for the data submission portal. It will capture essential assay parameters according to established standards in each sub-field within biology. The submission portal expedites data collection by enhancing ease of PI data submission, providing a user interface and specificity for which data is to be submitted. Data submissions can be brought into cutting-edge informatic analysis portals to enable mining of physiological, behavioral, biochemical, and imaging datasets in conjunction with ‘omics-level datasets. As ALSDA datasets are submitted, curated, and published (e.g., micro-computed tomography, histology, pulse oximetry, serum metabolites, magnetic resonance imaging, intraocular pressure, novel object recognition, etc.), the merging together of spaceflight data along this multi-hierarchical complexity of biology will enable informatics and data-intensive approaches resulting in knowledge discoveries across missions, space hazards, and biological disciplines.

life science↗

NASA NTRSDate not supplied

Transcriptomic Changes in Seedlings from Seeds Exposed to Simulated Space Radiation

Outside the protection of Earth’s magnetic field, living organisms are constantly exposed to space radiation that consists of energetic protons and other heavier charged particles. With the goal of manned Mars exploration, the production of fresh crop during long duration space missions can be beneficial for meeting astronauts’ nutritional and psychological needs. In our study, we not only evaluated plant/fruit morphometrics and edible fresh mass, but also analyzed transcriptomic changes in seedlings from seeds of three plant species (Arabidopsis, mizuna, and tomato) exposed to simulated Galactic Cosmic Rays(GCR) and solar particle events(SPE). The radiation experiments were performed in the NASA Space Radiation Laboratory (NSRL) facility at Brookhaven National Lab (BNL). 10-day Arabidopsis seedlings were exposed acutely (~240 cGy/hr) to simulated GCR scenarios of combined ions including protons, helium, oxygen, titanium, and/or iron ions at 40 or 80 cGy. Seeds of Arabidopsis, mizuna, and tomato were exposed to 40 or 80 cGy simulated GCR (dry seeds) or SPE (imbibed seeds) at lower dose rates(20-26 cGy/hr). Seedlings from control and irradiated seeds were then collected in RNAlater at similar growth stages with true leaves emerged. Total RNA was isolated and analyzed via Illumina whole transcriptome sequencing technology. Plant species-specific bioinformatics revealed transcriptional biomarkers and signaling pathways induced by simulated space radiation that were found to be dose, dose-rate, and species dependent. DNA damage response, stress signaling, and metabolic pathways are among the most significant changes. These data highlight some critical insights on the mechanisms of how plants respond and adapt to the space radiation environment and provide a molecular basis for crop selection and refinement in deep space exploration.

Anirudha Dixit↗

NASA NTRSDate not supplied

Enabling Space Biological Knowledge Discovery Through Image and Video Data Sharing

Increased biomedical risks and challenges associated with deep space missions and experiments (cis-Lunar, Mars transit/surface) require new knowledge discovery and development of novel ecosystems. Supporting distant and long-duration missions and experiments requires biological data (from yeast, microbes, fruit flies, C. elegans, plants, crops, rodents, humans) be findable, accessible, interoperable, reusable (FAIR), and maximally open-access. As data-intensive, bioinformatic, meta-analytical, and computer-assisted approaches continue to be a centerpiece of modern research, the NASA Biological and Physical Sciences division is expanding its Open Science capabilities beyond NASA GeneLab. The NASA Ames Life Sciences Data Archive (ALSDA) is a repository which is responsible for collecting and access to space biological imagery and video, alongside tabular and environmental data. In this presentation, we will discuss strategies dealing with archiving, curating, and accessibility of images from very distinct imaging modalities (e.g., micro-computed tomography, magnetic resonance imaging, photographic images of plants, fluorescence microscopy, behavioral videos, etc.). There are two main challenges: 1. Open-source data storage and 2. Metadata related to the imagery-video. Both have been solved by leveraging two existing open-source systems. For data storage, ALSDA is utilizing components through the Open Microscopy Environment (OME), which can read most imaging proprietary formats and display on a web interface complex multidimensional images (Z stack, multi-channel, temporal, spectral). Most technical metadata from imaging modalities are captured seamlessly. For metadata capturing experimental details, ALSDA (like GeneLab) uses the ISA-Tab specification which relies on the ISA data model to order and classify metadata. The ISA data model uses a tree structure with three files to capture the metadata: The top layer is the Investigations file, the second layer is the Study file(s), and the last layer is the Assay file(s). We believe such an approach may be useful for other types of image research data from other investigators in the AGU community.

imaging↗

NASA NTRS2023

Developing a Hybrid Spacesuit Simulator as a Research Tool for Assessing Extravehicular Activity Relevant Workload

Conducting human tests in a pressurized spacesuit is limited by availability, cost, and manpower; however, pressurized spacesuits are not always needed depending on the objectives of testing, including the development and testing of new informatics capabilities. The Human Physiology, Performance, Protection & Operations Laboratory (H-3PO) at NASA is developing a Hybrid Spacesuit Simulator (HS3) to support testing and characterization of human performance during analog planetary exploration extravehicular activities (EVAs). The goal of HS3 is to create a low-cost, modular, and unpressurized spacesuit simulator as a research tool that provides relevant physical and cognitive workload approximations with EVA-like immersion. HS3 consists of a soft outer suit, thermal control, gloves, boots, helmet, and integrated bioinformatics and communications. Baseline HS3 assessments were performed during 3-hour EVA simulations in two different subjects (DEMO1 and DEMO2) that included traverses at variable resistances and geological sampling activities. Liquid cooling garment (LCG) temperature, mean skin temperature, heart rate, motion capture, and metabolic rate were collected during each 3-hour simulated EVA. During DEMO1 and DEMO2, baseline metabolic rates at rest were 836 ± 327 BTU/hr and 869 ± 207 BTU/hr and increased to 2124 ± 548 BTU/hr and 2269 ± 559 BTU/hr, respectively, during 500m traverse. Average inlet LCG temperatures were 29.57 ± 6.62 °C and 25.63 ± 6.48 °C for DEMO1 and DEMO2 with increased outlet LCG temperatures of 33.53 ± 6.62 °C and 29.21 ± 4.79 °C, respectively. Overall, HS3 will enable future studies to characterize EVA tasks, human performance, and test future EVA capabilities in analog test environments without the need for pressurized suited environments.

Monica Hew↗

NASA NTRS2020

Prochlorococcus phage ferredoxin: structural characterization and electron transfer to cyanobacterial sulfite reductases

Marine cyanobacteria are infected by phages whose genomes encode ferredoxin (Fd) electron carriers. These Fds are thought to redirect the energy harvested from light to phage-encoded oxidoreductases that enhance viral fitness, but it is unclear how the biophysical properties and partner specificities of phage Fds relate to those of photosynthetic organisms. Here, results of a bioinformatics analysis using a sequence similarity network revealed that phage Fds are most closely related to cyanobacterial Fds that transfer electrons from photosystems to oxidoreductases involved in nutrient assimilation. Structural analysis of myovirus P-SSM2 Fd (pssm2-Fd), which infects the cyanobacterium Prochlorococcus marinus, revealed high levels of similarity to cyanobacterial Fds (root mean square deviations of ≤0.5 Å). Additionally, pssm2-Fd exhibited a low midpoint reduction potential (–336 mV versus a standard hydrogen electrode), similar to other photosynthetic Fds, although it had lower thermostability (Tm = 28 °C) than did many other Fds. When expressed in an Escherichia coli strain deficient in sulfite assimilation, pssm2-Fd complemented bacterial growth when coexpressed with a P. marinus sulfite reductase, revealing that pssm2-Fd can transfer electrons to a host protein involved in nutrient assimilation. The high levels of structural similarity with cyanobacterial Fds and reactivity with a host sulfite reductase suggest that phage Fds evolved to transfer electrons to cyanobacterially encoded oxidoreductases.

cyanobacteria↗

NASA NTRSDate not supplied

Developing A Hybrid Spacesuit Simulator as A Research Tool for Assessing Extravehicular Activity Relevant Workload

Conducting human tests in a pressurized spacesuit is limited by availability, cost, and manpower; however, pressurized spacesuits are not always needed depending on the objectives of testing, including the development and testing of new informatics capabilities. The Human Physiology, Performance, Protection & Operations Laboratory (H-3PO) at NASA is developing a Hybrid Spacesuit Simulator (HS3) to support testing and characterization of human performance during analog planetary exploration extravehicular activities (EVAs). The goal of HS3 is to create a low-cost, modular, and unpressurized spacesuit simulator as a research tool that provides relevant physical and cognitive workload approximations with EVA-like immersion. HS3 consists of a soft outer suit, thermal control, gloves, boots, helmet, and integrated bioinformatics and communications. Baseline HS3 assessments were performed during 3-hour EVA simulations in two different subjects (DEMO1 and DEMO2) that included traverses at variable resistances and geological sampling activities. Liquid cooling garment (LCG) temperature, mean skin temperature, heart rate, motion capture, and metabolic rate were collected during each 3-hour simulated EVA. During DEMO1 and DEMO2, baseline metabolic rates at rest were 836 ± 327 BTU/hr and 869 ± 207 BTU/hr and increased to 2124 ± 548 BTU/hr and 2269 ± 559 BTU/hr, respectively, during 500m traverse. Average inlet LCG temperatures were 29.57 ± 6.62 °C and 25.63 ± 6.48 °C for DEMO1 and DEMO2 with increased outlet LCG temperatures of 33.53 ± 6.62 °C and 29.21 ± 4.79 °C, respectively. Overall, HS3 will enable future studies to characterize EVA tasks, human performance, and test future EVA capabilities in analog test environments without the need for pressurized suited environments.

Suit simulator↗