AndreaBozzo/ceres-open-data-index huggingface dataset:
Temporal dynamics of the gut microbiota in people sharing a confined environment a 520-day ground-based space simulation MARS500

The MARS500 project the longest ground-based space simulation ever provided us with a unique opportunity to trace the crew microbiota over 520 days of isolated confinement such as that faced by astronauts in real long-term interplanetary space flights and after returning to regular life for a total of 2 years.

Tags: library-construction, nucleic-acid-extraction, nucleic-acid-sequencing, sample-collection, sampling-time, sequence-analysis-data-transformation
Organization: National Aeronautics and Space Administration
International Space Station conditions alter genomics proteomics and metabolomics in Aspergillus nidulans

The first global genomic proteomic and secondary metabolomic characterization of the filamentous fungus Aspergillus nidulans following growth onboard the International Space Station (ISS) is reported. The investigation included the A. nidulans wild-type and three mutant strains two of which were genetically engineered to enhance secondary metabolite production. Whole genome sequencing revealed that ISS conditions altered the A. nidulans genome in specific regions. In strain CW12001 which features overexpression of the secondary metabolite global regulator laeA ISS conditions induced the loss of the laeA stop codon. Differential expression of proteins involved in stress response carbohydrate metabolic processes and secondary metabolite biosynthesis was also observed. ISS conditions significantly decreased prenyl xanthone production in the wild-type strain and increased asperthecin production in LO1362 and CW12001 which are deficient in a major DNA repair mechanism. These data provide valuable insights into the adaptation mechanism of A. nidulans to spacecraft environments.

Tags: growth-time, library-construction, nucleic-acid-extraction, nucleic-acid-sequencing, sample-collection, sample-treatment, spaceflight, strain
Organization: National Aeronautics and Space Administration
Molecular mechanism of flocculation self-recognition in yeast and its role in mating and survival

Saccharomyces cerevisiae flocculation occurs when fermentable sugars are limiting and is therefore considered as a way to enhance the survival chance of Flo-expressing yeast cells. In this paper the role of Flo1p in mating was demonstrated by showing that the mating efficiency which contributes to the increased survival rate as well by generating genetic variability is increased when cells flocculate. This was revealed by liquid growth experiments in a low shear environment and differential transcriptome analysis of FLO1 expressing cells compared to the non-flocculent wild-type cells. The results show that a floc provides a uniquely organized multicellular ultrastructure that provides a suitable microenvironment to induce and perform cell conjugation. S. cerevisiae strains BY4742 WT BY4742::FLO8 and BY4742 [FLO1] were grown in microgravity and 1-g. A transcriptomic analysis was performed and the transcriptome data were integrated with the high quality protein-protein interaction networks. The identified high score sub-networks (qvalue < 0.001) were considered and further evaluated concerning their GO enrichment using a hypogeometric test.

Tags: array-scanning-protocol, growth-protocol, hybridization-protocol, labelling-protocol, microgravity, normalization-data-transformation-protocol, nucleic-acid-extraction-protocol, p-gse64468-1, p-gse64468-2, p-gse64468-3, p-gse64468-4, p-gse64468-5, p-gse64468-6, p-gse64468-7, sample-treatment-protocol, strain-genotype
Organization: National Aeronautics and Space Administration
Merged Sentinel-3A and Sentinel-3B OLCI Regional Binned Inland Waters (ILW) Data, version 4

The Inland Waters dataset (ILW) provides data for lakes and other water bodies across the contiguous United States (CONUS) and Alaska. ILW significantly reduces the processing effort required by end users and is a standardized community resource for lake and reservoir algorithm development and performance assessment.The data is provided for 15,450 CONUS waterbodies with a size of at least one 300 m pixel and over 2,300 resolvable lakes with sizes greater than three 300 m pixels. Alaska has 5,874 lakes resolvable lakes. ILW is a times series containing 10 years of MERIS (2002-2012) and OLCI from both Sentinel-3a (2016-present) and Sentinel-3b (2018-present).

Tags: aquatic-sciences, bacteria-archaea, biological-classification, biosphere, coastal-processes, earth-science, earth-science-services, ecosystems, environmental-advisories, environmental-governance-management, human-dimensions, hydrological-advisories, marine-environment-monitoring, ocean-optics, oceans, surface-water, terrestrial-hydrosphere, water-quality-water-chemistry
Organization: National Aeronautics and Space Administration
Effect of acute muscle unloading on soleus and gastrocnemius muscle gene expression

Gene expression changes induced by acute skeletal muscle unloading which leads to physiological changes including muscle atrophy fibre-type switching and loss of ability to transition between lipid and glucose as energy source (metabolic inflexibility) was investigated by hind-limb suspension (HLS) treatment of Male ICR mice (28 x9632 g body wt; Harlan Indianapolis IN). Agilent Whole Mouse Genome Oligo Microarrays were utilised to examine the effects of HLS on mRNA expression profiles of the soleus muscle and the gastrocnemius muscle in the hindlimbs of freely ambulating control and 24h HLS treated mice.

Tags: data-collection, data-transformation, growth-protocol, hindlimb-unloading, labeling, normalization-data-transformation, nucleic-acid-hybridization, rna-extraction, tissue, treatment-protocol
Organization: National Aeronautics and Space Administration
Pyrocumulonimbus Events over British Columbia in August 2017: Results from the NASA GEOS Earth System Model

Model data associated with the manuscript submitted in Atmospheric Chemistry and Physics Journal, titled, " Pyrocumulonimbus Events over British Columbia in 2017: The Long-term Transport and Radiative Impacts of Smoke Aerosols in the Stratosphere".

Abstract. Interactions of meteorology with wildfires in British Columbia, Canada during August 2017 led to three major pyrocumulonimbus (pyroCb) events that resulted in the injection of large amounts of smoke aerosols and other combustion products at the local upper troposphere and lower stratosphere (UTLS). These plumes of UTLS smoke with elevated values of aerosol extinction and backscatter compared to the background state were readily tracked by multiple satellite-based instruments as they spread across the Northern Hemisphere (NH). The plumes resided in the lower stratosphere for about 8-10 months following the fire injections. To investigate the radiative impacts of these events on the Earth system, we performed a number of simulations with the Goddard Earth Observing System (GEOS) atmospheric general circulation model (AGCM). Observations from multiple remote-sensing instruments were used to calibrate the injection parameters (location, amount, composition, and heights) and optical properties of the smoke aerosols in the model. The resulting simulations of three-dimensional smoke transport were evaluated for a year from the day of injections using daily observations from OMPS-LP (Ozone Mapping Profiler Suite Limb Profiler). The model simulated rate of ascent, hemispheric spread, and residence time of the smoke aerosols in the stratosphere are in close agreement with OMPS-LP observations. We found that both aerosol self-lofting and the large-scale atmospheric motion play important roles in lifting the smoke plumes from near the tropopause altitudes (~12 km) to about 22-23 km into the atmosphere. Further, our estimations of the radiative impacts of the pyroCb-emitted smoke aerosols showed that the smoke caused additional warming of the atmosphere by about 0.6-1 W/m2 (zonal mean) that persisted for about 2-3 months after the injections in regions north of 40oN. The surface experienced a comparable magnitude of cooling. The atmospheric warming is mainly located in the stratosphere, coincident with the location of the smoke plumes, leading to an increase in zonal mean shortwave (SW) heating rates of 0.02-0.04 K/day during September 2017.

Tags: aerosols, global-model, pyrocb-event-2017, wildfires
Organization: National Aeronautics and Space Administration
Effects of 21 days of bedrest on human skeletal muscle gene expression

The present study concerns the effects of 21 days of sustained recumbence (bedrest) on skeletal muscle gene expression. 14 male subjects participated in normoxic bedrest (NBR) with muscle unloading for 21 days this is a substudy of tha PlanHab-study which apart from normoxic bedrest also involved hypoxic bedrest and hypoxic ambulation. Throughout both bedrest interventions each subject remained in a horizontal position at all times. He was allowed one pillow for the head and to occasionally lean on an elbow while eating or being transferred to a gurney. Muscular exercise was prohibited. During the HAMB confinement each subject was allowed to move freely within the hypoxic area. To mimic a normal level of physical activity subjects performed 30 minutes of low-to-moderate-intensity exercise twice daily. Muscle samples from Vastus lateralis.

Tags: labeling, normalization-data-transformation, nucleic-acid-hybridization, rna-extraction, sample-collection, sampling-time, scan-protocol, treatment-protocol
Organization: National Aeronautics and Space Administration
Exposure of zebrafish larvae to relative microgravity between 5-6 days post-fertilization

The general objective of the study was to determine modulation of gene expression by environmental factors with a special emphasis on bone formation. For this reason the specific period of treatment was chosen between 5-6 days post-fertilization (dpf) when bone formation and calcification are taking place. This experiment was designed as a new type of gravitational experiment which we like to call relative microgravity referring to the fact that the larvae first grow in hyper gravity for 5 days and are then returned to 1g normal gravity for 1 day. Zebrafish embryos were placed on a Large Diameter Centrifuge at 3 hpf brought to a gravitational force of 3 g until 5 dpf. Reference embryos were kept in parallel at 1g (Inc). At 5dpf one batch was left at 3g (3g) one batch was returned to 1g (3g>1g) while a third batch was returned to 1g but left on the axis of the centrifuge (Axe; 3g>Axe). The experiment was repeated 4 times each time with 4 batches of 60 larvae.

Tags: array-scanning-and-feature-extraction-protocol, growth-protocol, hypergravity, normalization-data-transformation-protocol, nucleic-acid-extraction-protocol, nucleic-acid-hybridization-to-array-protocol, nucleic-acid-labeling-protocol, p-mtab-43163, p-mtab-43164, p-mtab-43165, p-mtab-43166, p-mtab-43167, p-mtab-43168, p-mtab-43169, treatment-protocol
Organization: National Aeronautics and Space Administration
MESSAGE 2 space experiment with Rhodospirillum rubrum S1H

R. rubrum S1H inoculated on solid agar rich media was sent to the ISS in October 2003 (MESSAGE-part 2 experiment). After 10 days flight R. rubrum cultures returned back to Earth. These cultures were then subjected to both transcriptomic and proteomic analysis and compared with the corresponding ground control. Whole-genome oligonucleotide microarray and high throughput proteomics which offer the possibility to survey respectively the global transcriptional and translational response of an organism were used to test the effect of space flight. Moreover in an effort to identify a specific stress response of R. rubrum to space flight ground simulation of space ionizing radiation and space gravity were performed under identical culture setup and growth conditions encountered during the actual space journey. This study is unique in combining the results from an actual space experiment with the corresponding space ionizing radiation and modeled microgravity ground simulations which lead to a more solid dissection of the different factors contribution acting in space flight conditions. Total RNA was extracted from R. rubrum S1H grown after 10 days in space flight or after 10 days in simulated ionizing radiation or simulated microgravity. Each microarray slide contained 3 technical repeats.

Tags: bioassay_data_transformation, feature_extraction, gravitation, grow, hybridization, image_aquisition, labeling, nucleic_acid_extraction, p-gse14239-1, p-gse14239-10, p-gse14239-11, p-gse14239-2, p-gse14239-3, p-gse14239-5, p-gse14239-7, p-gse14239-8, p-gse14239-9
Organization: National Aeronautics and Space Administration
High Energy Astrophysics Science Archive Research Center

The High Energy Astrophysics Science Archive Research Center (HEASARC) is the primary archive for NASA missions dealing with extremely energetic phenomena, from black holes to the Big Bang.

Tags: act, ariel-v, asca, astronomy, astrophysics, bbxrt, beppo-sax, cgro, chandra, controlled-vocabulary, cosmology, denis, dxs, einstein-heao-2, euve, exosat, fermi, gamma-ray, geochemistry, ginga, heao-1, heao-3, hete-ii, integral, lambda, lunar-samples, oso-8, rosat, rxte, sas-2, sas-3, space-science, suzaku, swift, taxonomy, thesaurus, vela-5b, wmap, xmm-newton
Organization: National Aeronautics and Space Administration
During development the Sku5 mutant roots engage different genes than wild type WS roots either on the ground or in spaceflight.

The wild type WS plants and the Sku5 mutant plants in the WS background were germinated on ISS or on the ground and the gene expression profiles in roots at 4 days or 8 days were established. The Sku5 gene (AT4G12420) codes for a multi-copper oxidase-like protein SKU5 protein that is involved in directed root tip growth. The Sku5 protein is glycosylated GPI-anchored and localizes to the plasma membrane and the cell wall. The Sku5 gene is expressed most strongly in expanding tissues. The development of WS and Sku5 plants on orbit differs from that on the ground as demonstrated by the comparison of the gene expression profiles between 4 days old to 8 days old plant in the two environments. However the development of Sku5 mutant plants also differs from WS at either age and in either environment suggesting the role of the genetic background in these developmental decisions. The 4 days old Sku5 roots in orbit engaged substantially more genes than the 4 days old WS roots in orbit but also more than the 4 days old Sku5 roots on the ground. Overall the 4 days old roots differentially expressed more genes in spaceflight relative to ground than the 8 days old roots of either genotype. Finally the 4 days old Sku5 roots in orbit differ in 862 genes from the 8 days Sku5 roots in orbit while on the ground there is merely half of the number of genes differentially expressed between the 4 days and 8 days developmental stages of the Sku5 roots. APEX03-2 (Advanced Plant Experiment 03-2) also identified as TAGES-Isa (Transgenic Arabidopsis Gene Expression System xe2 x80 x94Intracellular Signaling Architecture) was launched on SpaceX mission CRS-5 on 10 January 2015. Dry sterilized Arabidopsis seeds were planted aseptically on the surface of 10-cm2 solid media plates and remained dormant until removed from cold stowage and exposed to light at the initiation of the experiment on the ISS (International Space Station). The plates were grown in the Vegetable Production System (VPS/Veggie) hardware on the Columbus Module of the ISS with the overhead LED lighting of the VPS. At four or for the second experimental set at eight days seedlings were harvested by an astronaut into KFT (Kennedy Fixation Tube) containing RNAlater solutions. Upon return to Earth the harvested material was used to compare the transcriptomes of each genotype and each age using RNAseq technology. The patterns of gene expression was compared between treatments (spaceflight versus ground control) within each genotype of same age or between two ages within same genotype and within same treatment. For 4 day old roots 5-8 roots were combined to serve as one biological replica. For 8 day old roots 2-3 roots were used to form one biological replica. In each case the four biological replicas were used for the transcriptomic analysis.

Tags: age, genotype, growth-protocol, library-construction, nucleic-acid-extraction, nucleic-acid-sequencing, sample-collection, spaceflight, treatment-protocol
Organization: National Aeronautics and Space Administration
Global gene expression analysis highlights microgravity sensitive key genes in longissimus dorsi and tongue of 30 days space-flown mice

Microgravity as well as chronic muscle disuse are two causes of low back pain originated at least in part from paraspinal muscle deconditioning. At present no study investigated the complexity of the molecular changes in human or mouse paraspinal muscles exposed to microgravity. The aim of this study was to evaluate longissimus dorsi and tongue (as a new potential in-flight negative control) adaptation to microgravity at global gene expression level. C57BL/N6 male mice were flown aboard the BION-M1 biosatellite for 30 days (BF) or housed in a replicate flight habitat on ground (BG). Global gene expression analysis identified 89 transcripts differentially regulated in longissimus dorsi of BF vs. BG mice (False Discovery Rrate < 0,05 and fold change < -2 and > +2) while only a small number of genes were found differentially regulated in tongue muscle ( BF vs. BG = 27 genes). Overall Design: C57BL/N6 mice were randomly divided in 3 groups: Bion Flown (BF) mice flown aboard the Bion M1 biosatellite in microgravity environment for 30 days; Bion Ground (BG) mice housed in the same habitat of flown animals but exposed to earth gravity; and Flight Control (FC) mice housed in a standard animal facility.

Tags: animal-and-tissue-sampling, animal-husbandry, cosmic-radiation, data-collection, data-transformation, genelab-microarray-data-processing-protocol, labeling, mouse-habitation, normalization-data-transformation, nucleic-acid-hybridization, radiation-dosimetry, rna-extraction, sample-collection, spaceflight, tissue
Organization: National Aeronautics and Space Administration
Adaptive response of Arabidopsis seedlings in microgravity and Mars reduced gravity environment is enhanced by red light photostimulation

The response of plants to the spaceflight environment and microgravity is still not well understood although there has been an increased emphasis on this topic. Even less is known about plants  response to partial or reduced gravity levels. In the absence of the directional cues provided by the gravity vector the plant is especially perceptive to other cues such as light. Here we investigate the response of Arabidopsis thaliana 6-day-old seedlings to microgravity and the Mars partial gravity level during spaceflight as well as the effects of red light photostimulation by determining meristematic cell growth and proliferation. These experiments involve microscopic techniques together with transcriptomic studies. We demonstrate that microgravity and partial gravity trigger differential responses. The microgravity environment activates hormonal routes responsible for proliferation/growth and upregulates plastid/mitochondrial-encoded transcripts even in the dark. In contrast the Mars gravity level inhibits these routes and activates responses to stress factors to restore cell growth parameters only when red photostimulation is provided. This response is accompanied by upregulation of numerous transcription factors such as the environmental acclimation-related WRKY family. In the long term these discoveries can be applied in the design of bioregenerative life support systems and space farming.

Tags: spaceflight-altered-gravity-light, treatment-protocol-nucleic-acid-extraction-library-construction-nucleic-acid-sequencing
Organization: National Aeronautics and Space Administration
Rodent Research-1 (RR1) NASA Validation Flight: Mouse adrenal gland transcriptomic proteomic and epigenomic data

NASA  s 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. NASA  s 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 -80C 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.

Tags: animal-and-tissue-sampling, dna-library-construction, labeling, library-construction, mass-spectrometry, microgravity, nucleic-acid-extraction, nucleic-acid-sequencing, protein-extraction, proteomic-labeling, rna-library-construction, sample-collection
Organization: National Aeronautics and Space Administration
Transcriptional analysis of livers from mice preserved with the Rapid Freeze hardware

Data from the NASA Rodent Research-1 (RR-1) mission showed that gene-expression levels in mouse livers are different depending on what tissue preservation protocol is used and that slow freezing is not an effective method for preserving signals in gene-expression data. In response to these and other observations the Rapid Freeze hardware was built for use on the International Space Station. The Rapid Freeze hardware freezes mouse tissues (Glovebox freezer) and whole carcasses (Cryochiller) at rates closely mimicking those attained with immersion in liquid nitrogen. Because this hardware will be used extensively on future rodent research missions it is crucial to understand whether or not it preserves signals in gene expression data in order to maximize the value of these rare and expensive spaceflight experiments. Therefore this study was designed with three goals: 1) To evaluate the temperature profile of the Cryochiller and Glovebox freezer cartridges (Rapid Freeze hardware) over time during mock on-orbit procedures; 2) To determine the freezing profiles of tissues and carcasses using Rapid Freeze hardware at both optimal and sub-optimal temperatures (to mimic on-orbit operations) compared with those frozen in liquid nitrogen (the laboratory gold standard) or frozen at -80 C (the current standard method); 3) To identify gene expression changes in a) tissues that were frozen via the Glovebox freezer and b) tissues dissected from whole or partial carcasses that were frozen via the Cryochiller versus tissues that were frozen via control methods (liquid nitrogen or -80C slow freeze) to assess how the Rapid Freeze hardware compares with laboratory gold standard practices and our current standard methods.

Tags: dissection-condition-preservation-method-order-of-preservation, treatment-protocol-sample-collection-nucleic-acid-extraction-spike-in-protocol-library-construc
Organization: National Aeronautics and Space Administration