<scp>RNA</scp>‐seq analyses of <i>Arabidopsis thaliana</i> seedlings after exposure to blue‐light phototropic stimuli in microgravity

Vandenbrink, Joshua P.; Herranz, Raúl; Poehlman, William L.; Feltus, F. Alex; Villacampa, Alicia; Ciska, Malgorzata; Medina, F. Javier; Kiss, John Z.

doi:10.1002/ajb2.1384

Cited by 54 publications

(54 citation statements)

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“…Experimental containers were uploaded to the ISS and loaded into the EMCS as previously described (Kiss et al, 2014; Vandenbrink and Kiss, 2016; Vandenbrink et al, 2019). Experimental conditions were controlled remotely from the Norwegian User Support and Operations Centre (N-USOC; Trondheim, Norway).…”

Section: Methodsmentioning

confidence: 99%

“…In a previous report, we focused on the effects of microgravity in the transcriptional profile of blue-light photostimulated seedlings (Vandenbrink et al, 2019). Here, we will describe the plant transcriptional response to several partial gravity levels in young blue-light photostimulated A. thaliana seedlings cultivated into the European Module Cultivation System (EMCS) centrifuge on board the International Space Station (ISS).…”

Section: Introductionmentioning

confidence: 99%

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RNAseq Analysis of the Response of Arabidopsis thaliana to Fractional Gravity Under Blue-Light Stimulation During Spaceflight

et al. 2019

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Introduction: Traveling to nearby extraterrestrial objects having a reduced gravity level (partial gravity) compared to Earth’s gravity is becoming a realistic objective for space agencies. The use of plants as part of life support systems will require a better understanding of the interactions among plant growth responses including tropisms, under partial gravity conditions.Materials and Methods: Here, we present results from our latest space experiments on the ISS, in which seeds of Arabidopsis thaliana were germinated, and seedlings grew for six days under different gravity levels, namely micro-g, several intermediate partial-g levels, and 1g, and were subjected to irradiation with blue light for the last 48 h. RNA was extracted from 20 samples for subsequent RNAseq analysis. Transcriptomic analysis was performed using the HISAT2-Stringtie-DESeq pipeline. Differentially expressed genes were further characterized for global responses using the GEDI tool, gene networks and for Gene Ontology (GO) enrichment.Results: Differential gene expression analysis revealed only one differentially expressed gene (AT4G21560, VPS28-1 a vacuolar protein) across all gravity conditions using FDR correction (q < 0.05). However, the same 14 genes appeared differentially expressed when comparing either micro-g, low-g level (< 0.1g) or the Moon g-level with 1g control conditions. Apart from these 14-shared genes, the number of differentially expressed genes was similar in microgravity and the Moon g-level and increased in the intermediate g-level (< 0.1g), but it was then progressively reduced as the difference with the Earth gravity became smaller. The GO groups were differentially affected at each g-level: light and photosynthesis GO under microgravity, genes belonged to general stress, chemical and hormone responses under low-g, and a response related to cell wall and membrane structure and function under the Moon g-level.Discussion: Transcriptional analyses of plants under blue light stimulation suggests that root blue-light phototropism may be enough to reduce the gravitational stress response caused by the lack of gravitropism in microgravity. Competition among tropisms induces an intense perturbation at the micro-g level, which shows an extensive stress response that is progressively attenuated. Our results show a major effect on cell wall/membrane remodeling (detected at the interval from the Moon to Mars gravity), which can be potentially related to graviresistance mechanisms.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

RNAseq Analysis of the Response of Arabidopsis thaliana to Fractional Gravity Under Blue-Light Stimulation During Spaceflight

et al. 2019

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“…Experiments in the Biological Research in Canisters (BRICs) produced darkgrown samples in cassettes (Petri dish fixation units, PDFUs) that are sealed prior to launch [e.g., (Kwon et al, 2015;Basu et al, 2017;Johnson et al, 2017;Zupanska et al, 2017;Choi et al, 2019)]. Light-grown material was produced in the European Modular Cultivation System [EMCS, with variable RGB lighting and atmospheric and temperature control, e.g., (Correll et al, 2013;Herranz et al, 2019;Vandenbrink et al, 2019)], in SIMBOX [Science in Microgravity Box, LED lighting, e.g., (Fengler et al, 2015)], and in Petri dishes under 24 h LED light in the Veggie hardware [e.g., (Beisel et al, 2019)] or in the Advanced Biological Research System [ABRS, LED lighting; (Paul et al, 2013b)]. Both the EMCS and SIMBOX have a centrifuge, providing the capability for an extremely informative on-orbit 1 x g control [and for investigating other fractional g environment, e.g., (Correll et al, 2013;Fengler et al, 2015)].…”

Section: Overview Of the Plant Rnaseq And Microarray Data Within Toasmentioning

confidence: 99%

“…These studies are now generating extensive characterizations of the responses of diverse plant species to spaceflight. As part of the output from this research, there is an ever-increasing set of genome-scale analyses that range from transcriptomics [e.g., (Kwon et al, 2015;Johnson et al, 2017;Paul et al, 2017;Choi et al, 2019;Herranz et al, 2019;Vandenbrink et al, 2019)] and proteomics [e.g., (Mazars et al, 2014;Ferl et al, 2015;Basu et al, 2017)] to epigenomics [e.g., (Zhou et al, 2019)]. These datasets help catalog the plant response to growing in space.…”

Section: Introductionmentioning

confidence: 99%

Test of Arabidopsis Space Transcriptome: A Discovery Environment to Explore Multiple Plant Biology Spaceflight Experiments

et al. 2020

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Recent advances in the routine access to space along with increasing opportunities to perform plant growth experiments on board the International Space Station have led to an ever-increasing body of transcriptomic, proteomic, and epigenomic data from plants experiencing spaceflight. These datasets hold great promise to help understand how plant biology reacts to this unique environment. However, analyses that mine across such expanses of data are often complex to implement, being impeded by the sheer number of potential comparisons that are possible. Complexities in how the output of these multiple parallel analyses can be presented to the researcher in an accessible and intuitive form provides further barriers to such research. Recent developments in computational systems biology have led to rapid advances in interactive data visualization environments designed to perform just such tasks. However, to date none of these tools have been tailored to the analysis of the broad-ranging plant biology spaceflight data. We have therefore developed the Test Of Arabidopsis Space Transcriptome (TOAST) database (https://astrobiology. botany.wisc.edu/astrobotany-toast) to address this gap in our capabilities. TOAST is a relational database that uses the Qlik database management software to link plant biology, spaceflight-related omics datasets, and their associated metadata. This environment helps visualize relationships across multiple levels of experiments in an easy to use gene-centric platform. TOAST draws on data from The US National Aeronautics and Space Administration's (NASA's) GeneLab and other data repositories and also connects results to a suite of web-based analytical tools to facilitate further investigation of responses to spaceflight and related stresses. The TOAST graphical user interface allows for quick comparisons between plant spaceflight experiments using real-time, gene-specific queries, or by using functional gene ontology, Kyoto Encyclopedia of Genes and Genomes pathway, or other filtering systems to explore genetic networks of interest. Testing of the database shows that TOAST confirms patterns of gene expression already highlighted in the literature, such as revealing the modulation of oxidative stressrelated responses across multiple plant spaceflight experiments. However, this data

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“…Thus, we tested the effects of storage of seeds on germination and growth as well as cold storage procedures following the termination of the experiment (Kiss et al, 2009). In some of our later EMCS experiments, we improved the lighting and imaging by using infrared illumination to provide highquality images of the seedlings (Vandenbrink et al, 2019), and ground-based studies were important in identifying and optimizing these parameters (Kiss et al, 2014). Thus, in the present study, we continued using this general approach to Figure 5.…”

Section: Importance Of Optimization Of Spaceflight Experimentsmentioning

confidence: 99%

Growth and Development of Ecotypes of Arabidopsis thaliana: Preliminary Experiments to Prepare for a Moon Lander Mission

Shymanovich

Kiss

2020

Gravitational and Space Research

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NASA is planning to launch robotic landers to the Moon as part of the Artemis lunar program. We have proposed sending a greenhouse housed in a 1U CubeSat as part of one of these robotic missions. A major issue with these small landers is the limited power resources that do not allow for a narrow temperature range that we had on previous spaceflight missions with plants. Thus, the goal of this project was to extend this temperature range, allowing for greater flexibility in terms of hardware development for growing plants on the Moon. Our working hypothesis was that a mixture of ecotypes of Arabidopsis thaliana from colder and warmer climates would allow us to have successful growth of seedlings. However, our results did not support this hypothesis as a single genotype, Columbia (Col-0), had the best seed germination, growth, and development at the widest temperature range (11–25 °C). Based on results to date, we plan on using the Columbia ecotype, which will allow engineers greater flexibility in designing a thermal system. We plan to establish the parameters of growing plants in the lunar environment, and this goal is important for using plants in a bioregenerative life support system needed for human exploration on the Moon.

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RNA‐seq analyses of Arabidopsis thaliana seedlings after exposure to blue‐light phototropic stimuli in microgravity

Cited by 54 publications

References 63 publications

RNAseq Analysis of the Response of Arabidopsis thaliana to Fractional Gravity Under Blue-Light Stimulation During Spaceflight

RNAseq Analysis of the Response of Arabidopsis thaliana to Fractional Gravity Under Blue-Light Stimulation During Spaceflight

Test of Arabidopsis Space Transcriptome: A Discovery Environment to Explore Multiple Plant Biology Spaceflight Experiments

Growth and Development of Ecotypes of Arabidopsis thaliana: Preliminary Experiments to Prepare for a Moon Lander Mission

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