The NASA Task Book

Responsible Center: NASA KSC Grant Monitor: O'Rourke, Aubrie Center Contact: aubrie.e.orourke@nasa.gov Unique ID: 14984	Solicitation / Funding Source: 2020 Space Biology NNH20ZDA001N-SB E.12. Flight/Ground Research Grant/Contract No.: 80NSSC22K0855 Project Type: Ground Flight Program:	No. of Post Docs: 2 No. of PhD Candidates: 0 No. of Master's Candidates: 0 No. of Bachelor's Candidates: 1	No. of PhD Degrees: 2 No. of Master's Degrees: 1 No. of Bachelor's Degrees: 2

Space Biology Element:	(1) Plant Biology

Space Biology Cross-Element Discipline:	None

Space Biology Special Category:	None

Flight Assignment/Project Notes:	NOTE: End date changed to 03/31/2024 per NSSC information (Ed., 2/23/23)

Task Description:	The space flight transcriptome studies collected by the NASA GeneLab and analyzed by its Plant Analysis Working Group (PlantAWG) have facilitated analysis and tool development around profiling the differentially expressed genes (DEG), enrichment of pathways, and Gene Ontology-based (GO-based) functional annotation. To explore additional novel molecular events from the same GeneLab studies, we will (1) analyze the alternatively spliced (AS) forms of transcripts (RNA molecules) identified from the ground control (GC) and the space flight (FLT) samples; (2) identify mutations (if any) gained due to cosmic radiation in the transcribed regions of the genome; and (3) diagnose the AS and somatic mutation consequences on the structure and function of the genes. Our data analysis and collaborative work will extend the current functionality of the NASA GeneLab data by adding alternative splicing, novel transcribed regions and genes, and any functional significance, thus providing researchers insights into the modulated transcriptome's structural and functional consequences in response to space flight. The project workflows will help improve the reference genome annotation of Arabidopsis and set up a platform for analyzing current and future data from non-plant eukaryotes like humans, mice, yeast, and other models. In order to develop a deeper understanding of the causal effects of alternative splicing (AS) in the model plant Arabidopsis thaliana and other space travel-bound plant species, we propose to build an AS Atlas for plants in response to microgravity. The AS atlas will analyze the core set of NASA GeneLab plant studies and put forth a plan to build and extend resources for current and future studies on plants and other eukaryotes, including humans and mouse models. Our data analysis and collaborative work will extend the differential gene expression tools and functional enrichment analysis tools currently provided by the GeneLab data. The identification of novel AS sites and genes is anticipated to provide candidate genes to target for developing smart crops and synthetic biology-based approaches to improve adaptation to microgravity. The project-specific aims include: 1. Develop an alternative splicing atlas of Arabidopsis genes 2. Identify novel genetic mutations gained in the transcribed regions of the genome during space flight (FLT) 3. Validate alternative splicing events, subject to the availability of biological material sampled from the existing GeneLab studies.

Research Impact/Earth Benefits:	This project explores the identification of novel alternative spliced isoforms of Arabidopsis thaliana genes, mutations acquired, and downstream effects on the structure and function of the genes transcribed in response to space flight and microgravity. By analyzing the data from the GeneLab data portal, the project will extend the functionality limited by the existing differential gene expression and Gene Ontology enrichment analysis. The analyzed data will provide researchers additional insights into the modulated transcriptome's structural and functional consequences in response to space flight, hardware and growth conditions. The identification of novel AS sites and genes is anticipated to provide candidate genes to target for developing smart crops and synthetic biology-based approaches to improve adaptation to microgravity. The proposed development of methodologies and data analytics workflows may also help analyze the current and future data from plant and non-plant eukaryotes like humans, mice, yeast, and other models.

Task Progress & Bibliography Information FY2024

Task Progress:

We analyzed the transcriptome data available from NASA GeneLab studies OSD-37, OSD-38, OSD-120, OSD-251, OSD-314. The analysis included (1) exploring the alternative splicing events in the ground control and flight samples of plants used in these experimental studies for the protein coding genes, and (2) identifying Single Nucleotide Polymorphism (SNP) mutations found in these samples that may be a result of the respective growth condition exposures. We found about 6600 protein coding genes that undergo splicing and show differential gene expression. These genes are enriched in functions such as DNA repair, response to radiation, response to light stimulus, cellular responses to stress. Flight samples in almost all the studies show more number of unique SNP mutations gained in the microgravity environment of the space. The data sets are getting ready for publication. We have published four peer-reviewed articles, given ten talks, presented three posters, and submitted one white paper. Our project team member was also selected for NASA GeneLab Plant Analysis Working Group (AWG) member spotlight.

Bibliography:

Description: (Last Updated: 09/02/2024)

Show Cumulative Bibliography


Articles in Peer-reviewed Journals	Gupta P, Elser J, Hooks E, D’Eustachio P, Jaiswal P, Naithani S. "Plant Reactome Knowledgebase: empowering plant pathway exploration and OMICS data analysis." Nucleic Acids Research. 2024 Jan 5;52(D1):D1538-47. https://doi.org/10.1093/nar/gkad1052 ; PMID: 37986220, PMCID: PMC10767815 , Jan-2024

Articles in Peer-reviewed Journals	Naithani S, Mohanty B, Elser J, D’Eustachio P, Jaiswal P. "Biocuration of a transcription factors network involved in submergence tolerance during seed germination and coleoptile elongation in rice (Oryza sativa)." Plants. 2023 May 29;12(11):2146. https://doi.org/10.3390/plants12112146 ; PMID: 37299125; PMCID: PMC10255735 , May-2023

Articles in Peer-reviewed Journals	Barker R, Kruse CPS, Johnson C, Saravia-Butler A, Fogle H, Chang H-S, Trane RM, Kinscherf N, Villacampa A, Manzano A, Herranz R, Davin LB, Lewis NG, Perera I, Wolverton C, Gupta P, Jaiswal P, Reinsch SS, Wyatt S, Gilroy S. "Meta-analysis of the space flight and microgravity response of the Arabidopsis plant transcriptome." npj Microgravity. 2023 Mar 20;9(1):21. https://doi.org/10.1038/s41526-023-00247-6 ; PMID: 36941263 ; PMCID: PMC10027818 , Mar-2023

Articles in Peer-reviewed Journals	Naithani S, Deng CH, Sahu SK, Jaiswal P. "Exploring pan-genomes: an overview of resources and tools for unraveling structure, function, and evolution of crop genes and genomes." Biomolecules. 2023 Sep 17;13(9):1403. https://doi.org/10.3390/biom13091403 ; PMID: 37759803 ; PMCID: PMC10527062 , Sep-2023

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Project Title: Alternative Splicing and Transcriptome Modulation Under Space Flight Response in Plants

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Fiscal Year: FY 2023
Division: Space Biology
Research Discipline/Element:
Space Biology: Plant Biology

Start Date: 04/01/2022
End Date: 03/31/2024
Task Last Updated: 02/12/2023

Download Task Book report in PDF pdf

Principal Investigator/Affiliation: Jaiswal, Pankaj Ph.D. / Oregon State University

Address:

Department of Botany and Plant Pathology
2082 Cordley Hall, 1500 SW Jefferson Street
Corvallis , OR 97331

Email: jaiswalp@oregonstate.edu
Phone: 541-737-8471
Congressional District: 4
Web:

Organization Type: UNIVERSITY
Organization Name: Oregon State University
Joint Agency:
Comments:


Key Personnel Changes / Previous PI:	None

Project Information: Grant/Contract No. 80NSSC22K0855

Responsible Center: NASA KSC Grant Monitor: O'Rourke, Aubrie Center Contact: aubrie.e.orourke@nasa.gov Unique ID: 14984	Solicitation / Funding Source: 2020 Space Biology NNH20ZDA001N-SB E.12. Flight/Ground Research Grant/Contract No.: 80NSSC22K0855 Project Type: Ground Flight Program:	No. of Post Docs: 2 No. of PhD Candidates: 0 No. of Master's Candidates: 0 No. of Bachelor's Candidates: 1	No. of PhD Degrees: 2 No. of Master's Degrees: 1 No. of Bachelor's Degrees: 2

Space Biology Element:	(1) Plant Biology

Space Biology Cross-Element Discipline:	None

Space Biology Special Category:	None

Flight Assignment/Project Notes:	NOTE: End date changed to 03/31/2024 per NSSC information (Ed., 2/23/23)

Task Description:	The space flight transcriptome studies collected by the NASA GeneLab and analyzed by its Plant Analysis Working Group (PlantAWG) have facilitated analysis and tool development around profiling the differentially expressed genes (DEG), enrichment of pathways, and Gene Ontology-based (GO-based) functional annotation. To explore additional novel molecular events from the same GeneLab studies, we will (1) analyze the alternatively spliced (AS) forms of transcripts (RNA molecules) identified from the ground control (GC) and the space flight (FLT) samples; (2) identify mutations (if any) gained due to cosmic radiation in the transcribed regions of the genome; and (3) diagnose the AS and somatic mutation consequences on the structure and function of the genes. Our data analysis and collaborative work will extend the current functionality of the NASA GeneLab data by adding alternative splicing, novel transcribed regions and genes, and any functional significance, thus providing researchers insights into the modulated transcriptome's structural and functional consequences in response to space flight. The project workflows will help improve the reference genome annotation of Arabidopsis and set up a platform for analyzing current and future data from non-plant eukaryotes like humans, mice, yeast, and other models. In order to develop a deeper understanding of the causal effects of alternative splicing (AS) in the model plant Arabidopsis thaliana and other space travel-bound plant species, we propose to build an AS Atlas for plants in response to microgravity. The AS atlas will analyze the core set of NASA GeneLab plant studies and put forth a plan to build and extend resources for current and future studies on plants and other eukaryotes, including humans and mouse models. Our data analysis and collaborative work will extend the differential gene expression tools and functional enrichment analysis tools currently provided by the GeneLab data. The identification of novel AS sites and genes is anticipated to provide candidate genes to target for developing smart crops and synthetic biology-based approaches to improve adaptation to microgravity. The project-specific aims include: 1. Develop an alternative splicing atlas of Arabidopsis genes 2. Identify novel genetic mutations gained in the transcribed regions of the genome during space flight (FLT) 3. Validate alternative splicing events, subject to the availability of biological material sampled from the existing GeneLab studies.

Research Impact/Earth Benefits:	This project explores the identification of novel alternative spliced isoforms of Arabidopsis thaliana genes, mutations acquired, and downstream effects on the structure and function of the genes transcribed in response to space flight and microgravity. By analyzing the data from the GeneLab data portal, the project will extend the functionality limited by the existing differential gene expression and Gene Ontology enrichment analysis. The analyzed data will provide researchers additional insights into the modulated transcriptome's structural and functional consequences in response to space flight, hardware and growth conditions. The identification of novel AS sites and genes is anticipated to provide candidate genes to target for developing smart crops and synthetic biology-based approaches to improve adaptation to microgravity. The proposed development of methodologies and data analytics workflows may also help analyze the current and future data from plant and non-plant eukaryotes like humans, mice, yeast, and other models.

Task Progress & Bibliography Information FY2023

Task Progress:

We targeted the following five NASA GeneLab studies for analyzing data in our project. - GLDS-37 - GLDS-38 - GLDS-120 - GLDS-208 - GLDS-210 - GLDS-218

Alternative splicing and Single Nucleotide Polymorphism (SNP) scoring methods were standardized.

Alternative splicing data analysis completed on the Ground Control (GC) and Flight (FLT) transcriptomes from GLDS-37 and 38. A four way comparison of columbia-0 genotype data across two studies and 2 treatments revealed that they share ~8000 genes in common from both studies and treatments. Anywhere between 550-1800 genes show unique splicing patterns from the two studies. Early analysis of the genes encoding for auxin transporters, cell wall biosynthesis, and oxidative stress response show alternate splicing events between the two treatments.

SNP identification from the columbia-0 genotype from the GC and FLT transcriptomes completed from GLDS-37 and 38. Detailed analysis is underway.

The project continues to make progress on analyzing the rest of the above mentioned GLDS studies.

All the project data and publicly available GeneLab data for the above mentioned studies is being mapped to the A. thaliana genome and development of a Genome Browser instance development is underway.

Bibliography:

Description: (Last Updated: 09/02/2024)

Show Cumulative Bibliography

None in FY 2023

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Project Title: Alternative Splicing and Transcriptome Modulation Under Space Flight Response in Plants

Reduce

Images:

Fiscal Year: FY 2022
Division: Space Biology
Research Discipline/Element:
Space Biology: Plant Biology

Start Date: 04/01/2022
End Date: 03/31/2023
Task Last Updated: 05/13/2022

Download Task Book report in PDF pdf

Principal Investigator/Affiliation: Jaiswal, Pankaj Ph.D. / Oregon State University

Address:

Department of Botany and Plant Pathology
2082 Cordley Hall, 1500 SW Jefferson Street
Corvallis , OR 97331

Email: jaiswalp@oregonstate.edu
Phone: 541-737-8471
Congressional District: 4
Web:

Organization Type: UNIVERSITY
Organization Name: Oregon State University
Joint Agency:
Comments:

Project Information: Grant/Contract No. 80NSSC22K0855

Responsible Center: NASA KSC Grant Monitor: O'Rourke, Aubrie Center Contact: aubrie.e.orourke@nasa.gov Unique ID: 14984	Solicitation / Funding Source: 2020 Space Biology NNH20ZDA001N-SB E.12. Flight/Ground Research Grant/Contract No.: 80NSSC22K0855 Project Type: Ground Flight Program:	No. of Post Docs: No. of PhD Candidates: No. of Master's Candidates: No. of Bachelor's Candidates:	No. of PhD Degrees: No. of Master's Degrees: No. of Bachelor's Degrees:

Space Biology Element:	(1) Plant Biology

Space Biology Cross-Element Discipline:	None

Space Biology Special Category:	None

Task Description:	The space flight transcriptome studies collected by the NASA GeneLab and analyzed by its Plant Analysis Working Group (PlantAWG) have facilitated analysis and tool development around profiling the differentially expressed genes (DEG), enrichment of pathways, and Gene Ontology-based (GO-based) functional annotation. To explore additional novel molecular events from the same GeneLab studies, we will (1) analyze the alternatively spliced (AS) forms of transcripts (RNA molecules) identified from the ground control (GC) and the space flight (FLT) samples; (2) identify mutations (if any) gained due to cosmic radiation in the transcribed regions of the genome; and (3) diagnose the AS and somatic mutation consequences on the structure and function of the genes. Our data analysis and collaborative work will extend the current functionality of the NASA GeneLab data by adding alternative splicing, novel transcribed regions and genes, and any functional significance, thus providing researchers insights into the modulated transcriptome's structural and functional consequences in response to space flight. The project workflows will help improve the reference genome annotation of Arabidopsis and set up a platform for analyzing current and future data from non-plant eukaryotes like humans, mice, yeast, and other models. In order to develop a deeper understanding of the causal effects of alternative splicing (AS) in the model plant Arabidopsis thaliana and other space travel-bound plant species, we propose to build an AS Atlas for plants in response to microgravity. The AS atlas will analyze the core set of NASA GeneLab plant studies and put forth a plan to build and extend resources for current and future studies on plants and other eukaryotes, including humans and mouse models. Our data analysis and collaborative work will extend the differential gene expression tools and functional enrichment analysis tools currently provided by the GeneLab data. The identification of novel AS sites and genes is anticipated to provide candidate genes to target for developing smart crops and synthetic biology-based approaches to improve adaptation to microgravity. The project-specific aims include: 1. Develop an alternative splicing atlas of Arabidopsis genes 2. Identify novel genetic mutations gained in the transcribed regions of the genome during space flight (FLT) 3. Validate alternative splicing events, subject to the availability of biological material sampled from the existing GeneLab studies.

Research Impact/Earth Benefits:

Task Progress & Bibliography Information FY2022

Task Progress:

New project for FY2022.

Bibliography:

Description: (Last Updated: 09/02/2024)

Show Cumulative Bibliography

None in FY 2022

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