Newsletter No. 22: April 2020

Greetings from GeneLab!

Just Published: Three New GeneLab Papers

The GeneLab Project recently published three new papers. The first, entitled “Visualizing Omics Data from Spaceflight Samples using the NASA GeneLab Platform,” was published in the Proceedings of the 12th International Conference on Bioinformatics and Computational Biology. It describes how GeneLab's database and visualization tools have been used to generate novel science insights including potential impacts of spaceflight on the risk of liver disease.

“MicroRNAs (miRNAs), the Final Frontier: The Hidden Master Regulators Impacting Biological Response in All Organisms Due to Spaceflight,” is the second paper. It was published in THREE (The Health Risks for Extraterrestrial Environments) and provides a comprehensive review of miRNA history, biological processes, and relation to space biology.

The third paper, “NASA GeneLab Platform Utilized for Biological Response to Space Radiation in Animal Models”, summarizes how GeneLab’s rich database of omics experiments with animal models can be used to generate novel hypotheses to better understand human health risks from GCR exposures. This paper was published in MDPI, a scholarly open-access journal.

Click on the links above to read the full papers.

Calling all PI’s: Submit Your ISS Data to GeneLab

Dr. Christina Khodadad from Kennedy Space Center recently submitted three new Vegetable Production System (VEGGIE) datasets to the GeneLab Data Repository. Lettuce crops were grown in the Veggie payload aboard ISS, harvested and returned for chemical, microbiological and molecular analyze. Download the data here:

GLDS-267: Microbiological and nutritional analysis of lettuce crops grown on the International Space Station-VEG01A

GLDS-268: Microbiological and nutritional analysis of lettuce crops grown on the International Space Station-VEG01B

GLDS-269: Microbiological and nutritional analysis of lettuce crops grown on the International Space Station-VEG03A


Veggie payload containing a crop of mature red romaine lettuce in Veggie pillows aboard the ISS with the light panel off (left) and red light panel on (right). Bellows are in the up position.

GLDS-265: Selecting for Chlamydomonas reinhardtii fitness in the KSC Veggie Unit

The first algae dataset was recently added to the GeneLab repository. Since nearly the inception of international space programs, microalgae have been proposed to be part of the biological regenerative support systems for long-duration spaceflight. A simple protocol has been developed for batch liquid cultures using commercial breathable plastic bags by Junya Zhang, Barbara S.F. Muller, Kevin N. Type, Fang Baie, Ying Hu, Marcio F.R. Resende Jr., Bala Rathinasabapathi and A. Mark Settles. They also established and tested a genetic selection experiment to identify genes required for the model algae, Chlamydomonas reinhardtii, to grow in the plastic bag cultures in the Veggie plant growth chamber. These ground-based verification experiments show that selected for improved microalgae productivity in space is feasible.  
 
Submit your spaceflight omics data to GeneLab now! https://genelab.nasa.gov/submit

Many New Omics Dataset Released

In addition to the four new datasets listed above, there are 16 new studies and 17 studies with processed data recently released.  Check out over 230 datasets in the GeneLab Data Repository ranging from rodents, plants, microbes, algae, and fruit fly to human cell lines. Download differential gene expression tables under “Study Files” or navigate through the visualization portal to learn more about the changes in gene expression. To get you started here are a few more newly released studies with processed data:

GLDS-208: Comparative gene expression analysis in the Arabidopsis thaliana root apex using RNA-seq and microarray transcriptome profiles

GLDS-14: Response of Pseudomonas aeruginosa PAO1 to low shear modeled microgravity

GLDS-125: mRNA expression profile in DLD-1 and MOLT-4 cancer cell lines cultured under microgravity

GeneLab Leverages New NASA System to Uniquely Identify Space Biology Data

Data and metadata should be Findable, Accessible, Interoperable, and Reusable (FAIR). Following the FAIR guidelines, GeneLab has integrated a digital object identifier (DOI) with every dataset making it findable, accessible and reusable. Read more…

GeneLab Analysis Working Group Collaborates to Release Four Open Science Datasets

The NASA GeneLab Analysis Working Group has collaboratively generated four complementary datasets to interrogate changes to the gut microbiome of mice due to spaceflight. The four datasets use different technical approaches to determine which microbes and microbial genes are present within feces isolated from space-flown mice and corresponding ground controls. While one of these datasets was generated by the GeneLab sample processing team, the rest were generated in collaboration with Dr. Stefan Green and Kevin Kuntsman at the University of Illinois Chicago and the GeneLab Microbial Analysis Working Group. In future work, the GeneLab Analysis Working Group will analyze this data to understand how gut microbiome may change during spaceflight as well as the relative value of each assay utilized. This will inform future data generation issues. Datasets are available at: https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-249/

Good Health to All,

The GeneLab Team