Bone loss is one of the major health problems for astronauts during long-term spaceflight and for patients during prolonged bed rest or paralysis. Growing evidence suggests that osteocytes, the most abundant cells in the mineralized bone matrix, play a key role in sensing mechanical forces applied to the skeleton and in transducing them into subcellular biochemical signals to modulate bone homeostasis. However, the precise molecular mechanisms underlying both mechanosensation and mechanotransduction in osteocytes under the real microgravity (µG) condition are poorly understood. To unravel the mechanisms by which osteocyte, sense and responds to mechanical unloading, we exposed murine osteocytic cell line, Ocy454, seeded on a highly porous polystyrene 3D scaffold, to 2, 4, or 6 days of µG on board the International Space Station (ISS) and compared their gene expression with cells at 1G on Earth. Bioinformatics analysis of cells exposed to µG revealed several pathways differentially regulated upon exposure to microgravity.

The root apex is an important section of the plant root involved in environmental sensing and cellular development. Analyzing the gene profile of root apex in diverse environments is important and challenging especially when the samples are limiting and precious such as in spaceflight. The feasibility of using tiny root sections for transcriptome analysis was examined in this study. To understand the gene expression profiles of the root apex Arabidopsis thaliana Col-0 roots were sectioned into Zone-I (0.5 mm root cap and meristematic zone) and Zone-II (1.5 mm transition elongation and growth terminating zone). Gene expression was analyzed using microarray and RNA seq. Both the techniques arrays and RNA-Seq identified 4180 common genes as differentially expressed (with > two-fold changes) between the zones. In addition 771 unique genes and 19 novel TARs were identified by RNA-Seq as differentially expressed which were not detected in the arrays. Single root tip zones can be used for full transcriptome analysis; further the root apex zones are functionally very distinct from each other. RNA-Seq provided novel information about the transcripts compared to the arrays. These data will help optimize transcriptome techniques for dealing with small rare samples.

The Heat Shock Factor A2 (HsfA2) as a part of the HSF network is essential to the plant s response to almost any environmental stress and to the cellular homeostatic control mechanisms. Plant cell cultures disabled in HsfA2 function were grown aboard the International Space Station (ISS) in order to ascertain whether or not they use the same terrestrially effective systems to adapt to the novel environment of spaceflight. Cultured lines of Arabidopsis thaliana derived from wild type (WT) cultivar Col-0 and from a knock-out line deficient in the gene encoding HSFA2 (HSFA2 KO) were launched to the ISS on SpaceX-2 as part of the Cellular Expression Logic (CEL) experiment of the BRIC17 spaceflight mission and were fixed in-flight after 10 days on orbit. Microarray gene expression data were analyzed using a two-part comparative approach. First differentially expressed genes were identified between the environments (spaceflight to ground) within cells of the same genotype which represented physiological adaptation to the spaceflight environment. Second gene expression profiles were identified between the genotypes (HSFA2 KO to WT) within the same environment defining genes uniquely required by the two genotypes in the ground and spaceflight adapted states. The physiological state of the cells as a result of disabling a gene has tremendous control over the mechanisms induced to adapt to the environment of spaceflight. The HsfA2 demonstrated a role in the physiological adaptation to the spaceflight environment since the cells disabled in the HsfA2 gene used substantially different genes to achieve the spaceflight adapted state than the WT cells. The endoplasmic reticulum (ER) stress and unfolded protein response (UPR) define the HSFA2 KO cells physiological state regardless of the environment and likely result from the deficiency in the chaperone-mediated protein folding machinery. HsfA2 seems to have a universal stress response role but also specific roles in the physiological adaptation to spaceflight through cell wall remodeling signal perception and transduction and starch biosynthesis. Implementation of knock-out cells identified a set of genes with a required expression level in order for a cell to achieve a spaceflight-adapted state. The HSFA2 KO cells helped to unravel the HsfA2-dependent genes of the adaption of wild type cells to the environment of spaceflight.

Human deep space and planetary travel is limited by uncertainties regarding the health risks associated with exposure to galactic cosmic radiation (GCR) and in particular the high linear energy transfer (LET) heavy ion component. Here we assessed the impact of two high-LET ions 56Fe and 28Si and low-LET X rays on genome-wide methylation patterns in human bronchial epithelial cells. We found that all three radiation types induced rapid and stable changes in DNA methylation but at distinct subsets of CpG sites affecting different chromatin compartments. The 56Fe ions induced mostly hypermethylation and primarily affected sites in open chromatin regions including enhancers promoters and edges ( shores ) of CpG islands. The 28Si ion-exposure had mixed effects inducing both hyper and hypomethylation and affecting sites in more repressed heterochromatic environments whereas X rays induced mostly hypomethylation primarily at sites in gene bodies and intergenic regions. Significantly the methylation status of 56Fe ion irradiation sensitive sites but not those affected by X ray or 28Si ions could discriminate tumor from normal tissue for human lung adenocarcinomas and squamous cell carcinomas. Thus high LET radiation exposure leaves a lasting imprint on the epigenome and affects sites relevant to human lung cancer. The 56Fe ion signature may prove useful in monitoring the cumulative biological impact and associated cancer risks encountered by astronauts in deep space. Genome wide DNA methylation profiling of normal human bronchial epithelial cells irradiated with varying doses of 28Si-ion radiation ( 300 MeV/u at 0 0.3 1.0 Gy) 56Fe-ion radiation (600 MeV/u at 0 0.1 0.3 1.0 Gy) or X rays (320 kV at 0 1.0 Gy). Triplicate control and irradiated samples were incubated and sampled at 4 timepoints between 2 and 62 days. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across >485,000 CpGs from collected samples. Samples include: 56Fe ions 4 doses x 4 time points x 3 replicates (4 removed in QC) = 44 samples; 28Si ions = 3 doses x 4 time points x 3 replicates = 36 samples; X ray 2 doses x 4 time points x 3 replicates (2 removed in QC)= 22 samples. Overall design: Bisulphite converted DNA from the 102 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip.

We investigated differentially regulated genes in human myelomonocytic U937 cells in 20s and 5min microgravity and in hypergravity and compared expression profiles to identify potential gravity-regulated genes and adaptation processes. Overall design: Human myelomonocytic U937 cells were exposed to altered gravity during a parabolic flight.

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.

We investigated differentially regulated genes in human myelomonocytic U937 cells in 20s and 5min microgravity and in hypergravity and compared expression profiles to identify potential gravity-regulated genes and adaptation processes. Overall design: Human myelomonocytic U937 cells were exposed to altered gravity during a sounding rocket mission.

Analysis of effect of hindlimb suspension and reloading on C57Bl/6 mouse soleus muscle. Experimental groups examined: -Control mice 14 days -Hindlimb suspension for 7 days -Hindlimb suspension for 7 days and subsequent reloading for 1 day -Hindlimb suspension for 7 days and subsequent reloading for 7 days

Anoxia induces several heat shock proteins and a heat pre-treatment can acclimatize Arabidopsis seedlings to a subsequent anoxic treatment. In this work we analyzed the response of Arabidopsis seedlings to anoxia heat and a combined heat+anoxia stress. A significant overlapping between the anoxic and heat shock responses has been observed by whole-genome microarray analysis. Overall design: We treated Arabidopsis seedling 4-days old dark germinated with: Control (23C dark liquid Murashige-Skoog medium containing 30mM sucrose). Heat-treated (38C for 90 minutes dark liquid Murashige-Skoog medium containing 30mM sucrose). Anoxia-treated (23C under anoxia for 6h dark liquid Murashige-Skoog medium containing 30mM sucrose). Combined heat+Anoxia-treatment (23C treated at 38C for 90 min and thereafter under anoxia for 6h dark liquid Murashige-Skoog medium containing 30mM sucrose). Two biological replicates for each condition.

To investigate gene expression patterns in rat mammary carcinomas induced by ionizing radiation. Gene expression patterns were analyzed in radiation-induced rat mammary carcinomas and normal mammary gland tissues.