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Transcription profiling of Arabidopsis seedings exposed to UV-B irradiation

Interaction of COP1 and UVR8 which regulate UV-B-induced photomorphogenesis and stress acclimation in Arabidopsis thaliana.

Proton irradiation augments the reduction in tumor progression observed with advanced age

Proton irradiation is touted for its improved tumor targeting due to the physical advantages of ion beams for radiotherapy. Recent studies from our laboratory have shown that in addition to targeting advantages proton irradiation can inhibit angiogenic and immune factors and thereby modulate tumor progression. High-energy protons also constitute a principal component of the galactic cosmic rays to which astronauts are exposed. Increased understanding of the biological effects of proton exposure would thus contribute to both improved cancer therapy and carcinogenesis risk assessment for space travel. In addition age plays a major role in tumor incidence and is a critical consideration for estimating cancer risk. We investigated the effects of host age and proton exposure on tumor progression. Tumor lag time and growth dynamics were tracked following injection of murine Lewis lung carcinoma (LLC) cells into young (68 day) versus old (736 day) mice with or without coincident irradiation. Tumor progression was suppressed in old compared to young mice. Differences in progression were further modulated by proton irradiation (1GeV) with increased inhibition evident in old mice. Through global transcriptome analysis TGFB1 and TGFB2 were determined to be key players that contributed to the tumor dynamics observed. These findings point to older hosts providing decreased systemic tumor support which can be further inhibited by proton irradiation. Overall design: For genome-wide expression profiling of tumor tissue Mouse WG-6 BeadArray chips (Illumina San Diego CA) were used. Total RNA was amplified with the Ambion Illumina TotalPrep Amplification Kit (Ambion Austin TX) and labeled from all replicate biological samples for each condition. For tumor replicates thirty tumor samples from adolescent and thirty tumor samples from old mice for a total of 60 tumor samples were used. All replicate samples were run individually. For each age group ten tumor samples had received proton irradiation while twenty tumor samples were from unirradiated mice (as described above). Total RNA was isolated and purified using TRIzol (Invitrogen) and quantified using an Agilent Bioanalyzer. Samples were deemed suitable for amplification and hybridization if they had 28s/18s = 2:1 RIN >7. Total RNA of 500ng per sample was amplified using AmbionTotalPrep and 1.5ug of the product was loaded onto the chips. Following hybridization at 55C the chips were washed and then scanned using the Illumina iScan System. The data was checked with GenomeStudio (Illumina) for quality control. In GenomeStudio data was background subtracted and rank invariant normalization was applied. Data was imported into MultiExperiment Viewer MeV for statistical analysis. The statistically significant genes were determined using MeV by applying a one-way ANOVA analysis with standard Bonferroni correction with a FDR <0.05 that resulted in a list of significant genes. Average gene expression signals <10 were filtered out due to signal being

OMI/Aura Surface UV Irradiance 1-orbit L2 Swath 13x24 km V003 (OMUVB) at GES DISC

The Aura Ozone Monitoring Instrument (OMI) Version 003 Surface UV Irradiance Product (OMUVB) is now available from the NASA Goddard Earth Sciences Data and Information Services Center (GES DISC) for the public access. The shortname for this Level-2 OMI Surface UVB product is OMUVB. The algorithm scientists for this product are: Dr. Jari Hovila, Dr. Antii Arola and Dr. Johanna Taminnen. The OMUVB product contains erythemally weighted daily dose and dose rate, and spectral irradiances at 305, 310, 324, and 380 nm. It also contains quality flags, cloud optical depth, Lambertian Equivalent Reflectivity, Total Column Ozone amount, and other ancillary information.The OMUVB files are stored in the version 5 EOS Hierarchical Data Format (HDF-EOS5). Each file contains data from the day lit portion of an orbit (~53 minutes). There are approximately 14 orbits per day. The maximum file size for the OMUVB data product is about 10 Mbytes.

Efficient Identification of Multiple Pathways: RNA-Seq Analysis of Livers from 56Fe Ion Irradiated Mice

Background: mRNA interactions with each other and other signaling molecules define different biological pathways and functions. Researchers have been investigating various tools to analyze these types of interactions. In particular gene co-expression network methods have proved useful in finding and analyzing these molecular interactions. Many different analytical pipelines to identify these interactions networks have been proposed with the aim of identifying an optimal partition of the network where the individual modules are neither too small to make any general inference or too large to be biologically interpretable. Results: In this study we propose a new pipeline to perform gene co-expression network analysis. The proposed pipeline uses WGCNA a widely used software to perform different aspects of gene co-expression network analysis and modularity maximization algorithm to analyze novel RNA-Seq data to understand the effects of low-dose 56Fe ion irradiation on the formation of hepatocellular carcinoma in mice. The network results along with experimental validation show that using WGCNA combined with Modularity provide a more biologically interpretable network in our dataset. Our pipeline showed better performance than the existing clustering algorithm in WGCNA in finding modules and identified a module with mitochondrial subunits that are supported by mitochondrial complex assay. Conclusions: We present a pipeline that can reduce the problem of parameter selection with the existing algorithm in WGCNA for comparable RNA-Seq datasets which may assist in future research to discover novel mRNA interactions and their downstream molecular effects. C57BL16 males were placed into 2 treatment groups and received the following irradiation treatments at Brookhaven National Laboratories (Long Island NY): 600 MeV/n 56Fe (0.2 Gy) and no irradiation. Left liver lobes were collected at 30 60 120 270 and 360 days post-irradiation flash frozen and stored at -80 xc2 xb0C until they could be processed for RNA-Seq. Livers were sampled by taking two 40-micron thick slices using a cryotome at -20 xc2 xb0C. This allowed multiple sampling of the tissue without the tissue going through multiple freeze/thaw cycles. Total RNA was isolated from the liver slices using RNAqueousTM Total RNA Isolation Kit (ThermoFisher Scientific Waltham MA) and rRNA was removed via Ribo-ZeroTM rRNA Removal Kit (Illumina San Diego CA) prior to library preparation with the Illumina TruSeq RNA Library kit. Samples were sequenced in a paired-end 50 base format on an Illumina HiSeq 1500. Reads were aligned to the mouse GRCm38 reference genome using the STAR alignment program version 2.5.3a with the recommended ENCODE options. The -quantMode GeneCounts option was used to obtain read counts per gene based on the Gencode release M14 annotation file. Total number of reads used in analysis varies between 23-35 millions of reads.

LBA-ECO TG-03 Solar Surface Irradiance and PAR, Brazilian Amazon: 1999-2004

This data set includes solar surface irradiance from Kipp and Zonen CM-21 pyranometers, both total unfiltered and filtered (RG695), and photosynthetically active radiation (PAR) from Skye-Probetech SKE-510 PAR sensors. Measurements were made at six sites acrosss the Brazilian Amazon during the period from 1999 to 2004. These sites were co-located with AERONET (AErosol RObotic NETwork) program sites. There are 17 comma-delimited data files (.csv) with this data set. The AERONET program is an inclusive federation of ground-based remote sensing aerosol networks established by AERONET and the PHOtometrie pour le Traitement Operationnel de Normalisation Satellitaire (PHOTONS) and greatly expanded by AEROCAN (the Canadian sunphotometer network) and other agency, institute and university partners. The goal is to assess aerosol optical properties and validate satellite retrievals of those properties. The network imposes standardization of instruments, calibration, and processing.

TOMS Nimbus-7 Total Ozone Aerosol Index UV-Reflectivity UV-B Erythemal Irradiances Daily L3 Global 1 deg x 1.25 deg V008 (TOMSN7L3) at GES DISC

The Nimbus-7 Total Ozone Mapping Spectrometer (TOMS) version 8 daily global gridded data product contains total column ozone, UV aerosol index, Lambertian effective surface reflectivity (Rayleigh corrected), and UV-B erythemal local noon irradiances. The data are mapped to a global grid of size 180 x 288 with a lat-long resolution of 1.00 x 1.25 degrees. These data are stored in the EOS Hierarchical Data Format (HDF-EOS).The TOMS data were produced by the Laboratory for Atmospheres at NASA Goddard Space Flight Center (Code 614).

SAFARI 2000 Surface Irradiance Measurements, Mongu Tower Site, Zambia, 2000-2002

This data set contains the top-of-canopy irradiance in the shortwave (0.3-2.8 micron) and photosynthetically active radiation (PAR; 0.4-0.7 micron) wavebands collected with an Eppley Precision Spectral Pyranometer (PSP) and a Skye SKE510 pyranometer, respectively. The instruments were deployed at the top of the 30-m tower in the Kataba Local Forest approximately 20 km south of Mongu in Western Province, Zambia. The data include the hourly mean and maximum values from 0500-1600 GMT (7 a.m. - 6 p.m. local time) and cover the period from September 4, 2000 to December 31, 2002. The data were obtained primarily for EOS validation and energy budget modeling.The Skye SKE510 uses a blue enhanced planar diffused silicon detector and has a fairly even response from 400 to 700 nm. The Eppley PSP is a World Meteorological Organization First Class Radiometer designed for the measurement of sun and sky radiation, totally or in defined broad wavelength bands. It comprises a circular multi-junction wire-wound thermopile. A data logger sampled the sensors at 60-second intervals and recorded the maximum and mean values every 60 minutes throughout the day.The data are contained within a single ASCII text file, in comma-separated-value format, with associated date, time, and QA information.

SAFARI 2000 AERONET-derived Diffuse Spectral Irradiance for Eight Core Sites

This data set contains monthly mean values of diffuse irradiance fraction [f(Ediff), or ratio of diffuse-to-total irradiance] at ground level for a 30-degree solar zenith angle and in seven spectral bands (MODIS bands 1-7) as well broadband visible (400-700 nm), near-infrared (700-3000 nm) and shortwave (400-3000 nm). Values are provided for eight SAFARI 2000 core sites, including Ghanzi/Okwa River Crossing, Maun (Main and Floodplain Towers), Pandamatenga, and Tshane, Botswana; Skukuza, South Africa; Etosha National Park, Namibia; and Mongu, Zambia. The fractions were estimated with the 6S radiative transfer model, given the mean aerosol optical depth (AOT) values from AERONET sunphotometer measurements. Where sunphotometers were not deployed at a SAFARI 2000 core site, the nearest neighbor sunphotometer data were used. A rough estimate of the likely spatial extrapolation error is provided. These data can be used to estimate typical surface albedo (blue sky conditions) from the theoretical black-sky and white-sky albedo values provided in the MODIS albedo product (MOD43), as well as in other applications.Data for all eight sites are contained in one ASCII file, in csv format. The data file provides the ratio of diffuse (atmospherically-scattered) irradiance to total irradiance, both at ground level, for the eight sites in southern Africa. Mean values are provided for each of 12 months in 10 spectral bands between 0.4 and 4.0 microns, computed for a 30-degree solar zenith angle. The native resolution of the AERONET sunphotometer data varies, but is typically less than 1 hour. Information about the site location, IGBP classification, and nearest AERONET sunphotometer site is also provided.

Low dose (0.04 Gy) irradiation (LDR) and hindlimb unloading (HLU) microgravity in mice: brain transcriptomic and epigenomic data

The purpose of the present study was to evaluate damage in brain and eye in a ground-based model for spaceflight which includes prolonged unloading and low-dose radiation. Low-dose/Low-dose-rate (LDR) gamma-radiation using 57Co plates (0.04 Gy) was delivered whole-body to mature 6-month old female C57BL/6 mice to simulate the radiation component. Anti-orthostatic tail suspension was used to model the unloading fluid shift and physiological stress aspects of the microgravity component. Mice were hindlimb suspended and/or irradiated for 21 days. Tissues were collected at 7 days 1 4 and 9 months following simulated microgravity. Herein we proposed to use omics-based molecular phenotyping approach for identification and characterization of genomic signatures in multiple organ system associated with low-dose radiation and simulated microgravity.

TOMS Earth Probe UV-B Erythemal Local Noon Irradiance Monthly L3 Global 1 deg x 1.25 deg Lat/Lon Grid V008 (TOMSEPL3mery) at GES DISC

This Earth Probe (EP) Total Ozone Mapping Spectrometer (TOMS) version 8 monthly averaged global gridded data product contains UV-B erythemal local noon irradiance values. The data are mapped to a global grid of size 180 x 288 with a lat-long resolution of 1.00 x 1.25 degrees. These data are stored in an ASCII format.The TOMS data were produced by the Laboratory for Atmospheres at NASA Goddard Space Flight Center (Code 614).

Expression profiling of murine lung 70 days following exposure to fractionated or acute dose of 1.0 Gy 56Fe- particle irradiation

Irradiation of the K-rasLA1 mouse model with a fractionated dose of 1.0Gy 56Fe- particles increases the incidence of invasive carcinoma compared to unirradiated controls or those irradiated with an acute dose. Microarray profiling was perfromed on whole lungs from K-rasLA1 mice in order to determine global expression changes in the lung following radiation exposure. RNA was extracted from K-rasLA1 lungs from unirradiated control animals or those irradiated with a fractionated or acute dose of 1.0Gy 56Fe- particles 70 days post-irradiation when lungs are still histologically indistiguishable and only contain benign lesions. 129S2 K-rasLA1 mice were either irradiated with an acute (1.0Gy x1; n = 15) or fractionated (0.2Gy x5; n=13) dose of 1.0Gy 56Fe- particles or left unirradiated (n=13). Animals were euthanized 70 days post-irradiation and RNA was extracted from the whole left lung of each animal.

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Low dose (0.04 Gy) irradiation (LDR) and hindlimb unloading (HLU) microgravity in mice: retina transcriptomic and epigenomic data

The purpose of the present study was to evaluate damage in brain and eye in a ground-based model for spaceflight which includes prolonged unloading and low-dose radiation. Low-dose/Low-dose-rate (LDR) gamma-radiation using 57Co plates (0.04 Gy) was delivered whole-body to mature 6-month old female C57BL/6 mice to simulate the radiation component. Anti-orthostatic tail suspension was used to model the unloading fluid shift and physiological stress aspects of the microgravity component. Mice were hindlimb suspended and/or irradiated for 21 days. Tissues were collected at 7 days 1 and 4 months following simulated microgravity. Herein we proposed to use omics-based molecular phenotyping approach for identification and characterization of genomic signatures in multiple organ system associated with low-dose radiation and simulated microgravity.

OMI/Aura Surface UVB Irradiance and Erythemal Dose Daily L2 Global Gridded 0.25 degree x 0.25 degree V3 (OMUVBG) at GES DISC

This is Level-2G daily global gridded Aura-OMI Spectral Surface UVB Irradiance and Erythemal Dose product (OMUVBG). The OMUVBG is a special Level-2 Global Gridded type data Product (referred as Level 2G or L2G) where Level-2 or swath pixel data are binned (but not averaged)into 0.25x0.25 degree global grids. It contains the data for all L2 scenes that have observation time between UTC times of 00:00:00 and 23:59:59.9999. All ancillary parameters such as latitude, longitude, time, solar and viewing angles are also saved for each pixel. First two dimensions of each parameter correspond to spatial (Lat/Lon based) Grid ID and third dimension identifies the pixel or observed scene (referred as 'candidates' ID). Scientists can apply a data filtering scheme of their choice, average good quality pixels data in each grid and create their Level-3 products.The OMUVBG files are available in the version 5 EOS Hierarchical Data Format (HDF-EOS5). Each file contains daily data from the day lit portion of the globe. The maximum file size for the OMUVBG data product is about 128 MBytes.

First ISCCP Regional Experiment (FIRE) Atlantic Stratocumulus Transition Experiment (ASTEX) Centre Meteorologie Spatiale (CMS) Hourly Solar Irradiance Data

The First ISCCP Regional Experiments have been designed to improve data products and cloud/radiation parameterizations used in general circulation models (GCMs). Specifically, the goals of FIRE are (1) to improve basic understanding of the interaction of physical processes in determining life cycles of cirrus and marine stratocumulus systems and the radiative properties of these clouds during their life cycles and (2) to investigate the interrelationships between the ISCCP data, GCM parameterizations, and higher space and time resolution cloud data.To-date, four intensive field-observation periods were planned and executed: a cirrus IFO (October 13 - November 2, 1986); a marine stratocumulus IFO off the southwestern coast of California (June 29 - July 20, 1987); a second cirrus IFO in southeastern Kansas (November 13 - December 7, 1991); and a second marine stratocumulus IFO in the eastern North Atlantic Ocean (June 1 - June 28, 1992). Each mission combined coordinated satellite, airborne, and surface observations with modeling studies to investigate the cloud properties and physical processes of the cloud systems.These files are calculations of the hourly solar irradiance at the surface, based on observations by the METEOSAT. The file naming convention is: esDDMMYYsxx.fiswhere DDMMYY is the date and xx = slot numberMean time (UT) is obtained from the slot number overthe ASTEX region by the formula: UT = (xx/2) - 0.17These files are: I2 pixels, 376 pixels/row, 326 rows. Each pixel has a spatial resolution of 0.04 degrees.The header of each file claims there are two channels, although the provided documentation states that there is only one channel per file.The units are: flux [tenths of Joule/cm^2]

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Gene-expression profiling of Saccharomyces cerevisiae irradiated by high-LET radiations

Ionizing radiations are categorized by linear energy transfer (LET) into low-LET and high-LET. High-LET is considered to have a higher relative biological effectiveness (RBE) than low-LET radiations. However the details of the effects have not been clearly determined. The aim of this study was to characterize the difference between high-LET and low LET radiations. The global effects of the three types of high-LET radiations (fast neutron heavy ion (C) and thermal neutron) were compared with the low-LET radiation (gamma ray) using yeast DNA microarrays. Highly induced genes by the three types of high-LET radiations were those genes related to oxidative stress. Oxidative stress was one of the common factors associated with the four types of radiations. Oxidative stress induced by high-LET radiations may be more serious than that induced by gamma rays. Additionally genes related to protein synthesis and the ubiquitin and proteasome system were detected. This suggests that more protein damages can be induced by high-LET radiation that denatures the proteins in yeast cells. The genes specifically altered by each type of high-LET radiation were also studied. Overall design: This series contains 4 kinds of irradiation-induced gene expression profiles. Triplicates hybridization was done in each irradiation exposure and each array have high and low power scanned data respectively. All biological samples were collected independently.

OMI/Aura Surface UVB Irradiance and Erythemal Dose Daily L3 Global Gridded 1.0 degree x 1.0 degree V3 (OMUVBd) at GES DISC

This is Level-3 daily global gridded Aura-OMI Spectral Surface UVB Irradiance and Erythemal Dose product (OMUVBd). The OMUVBd product contains global erythemally weighted daily dose and erythemal dose rate at local solar noon at 1.0x1.0 deg grids.The OMUVBd files are available in the version 5 EOS Hierarchical Data Format (HDF-EOS5). Each file contains daily data from the day lit portion of the globe. The maximum file size for the OMUVBd data product is about 5 MBytes.

First ISCCP Regional Experiment (FIRE) Atlantic Stratocumulus Transition Experiment (ASTEX) Centre Meteorologie Spatiale (CMS) Weekly Solar Irradiance Data

The First ISCCP Regional Experiments have been designed to improve data products and cloud/radiation parameterizations used in general circulation models (GCMs). Specifically, the goals of FIRE are (1) to improve basic understanding of the interaction of physical processes in determining life cycles of cirrus and marine stratocumulus systems and the radiative properties of these clouds during their life cycles and (2) to investigate the interrelationships between the ISCCP data, GCM parameterizations, and higher space and time resolution cloud data.To-date, four intensive field-observation periods were planned and executed: a cirrus IFO (October 13 - November 2, 1986); a marine stratocumulus IFO off the southwestern coast of California (June 29 - July 20, 1987); a second cirrus IFO in southeastern Kansas (November 13 - December 7, 1991); and a second marine stratocumulus IFO in the eastern North Atlantic Ocean (June 1 - June 28, 1992). Each mission combined coordinated satellite, airborne, and surface observations with modeling studies to investigate the cloud properties and physical processes of the cloud systems.These files are calculations of the monthly solar irradiance at the surface, based on observations by the METEOSAT. The file naming convention is: esmxx.fis where xx is the month number of 1992.These files are: I2 pixels, 376 pixels/row, 326 rows. Each pixel has a spatial resolution of 0.04 degrees.The header of each file claims there are two channels, although the provided documentation states that there is only one channel per file.The units are: flux [tenths of Joule/cm^2]

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Transcription profiling of atm mutant adm mutant and wild type whole plants and roots of Arabidopsis after gamma ray irradiation in a time series

Whole seedlings of wild type (4d) and atm mutants (4d) have been analyzed after a gamma ray irradiation of 0.75h 1.5h 3h & 5h (time course). Roots of wt (4d) atm (3d) and atr (4d) mutants have been analyzed after a 1h irradiation. Ataxia Telangiectasia Mutated (ATM) encodes a large protein with a phosphatidylinositol 3-kinase (PI3K)-like domain at the C terminus (reviewed by Rotman and Shiloh 1998). PI3K-related proteins make up a large family of Ser-Thr protein kinases numerous members of which are involved in the regulation of cell cycle progression responses to DNA damage and the maintenance of genomic stability (Hoekstra 1997). AtATM plays an essential role in meiosis and in the somatic response to DNA damage in plants similar to the function of ATM in mammals and other eukaryotes. Ataxia telangiectasia-mutated and Rad3-related (ATR) plays a central role in cell-cycle regulation transmitting DNA damage signals to downstream effectors of cell-cycle progression.

Gene expression profiling in human fibroblast after low-LET irradiation

Exposure to radiation provokes cellular responses controlled in part by gene expression networks. MicroRNAs (miRNAs) are small non-coding RNAs which mostly regulate gene expression by degrading the messages or inhibiting translation. Here we investigated changes in miRNA expression patterns after low (0.1 Gy) and high (2.0 Gy) doses of X-ray in human fibroblasts. At early (0.5 h) and late (6 and 24 h) time points irradiation caused qualitative and quantitative differences in the down-regulation of miRNA levels including miR-92b 137 660 and 656. A transient up-regulation of miRNAs was observed after 2 h post-irradiation following high doses of radiation including miR-558 and 662. MicroRNA levels were inversely correlated with targets from mRNA and proteomic profiling after 2.0 Gy of radiation. MicroRNAs miR-579 608 548-3p and 585 are noted for targeting genes involved in radioresponsive mechanisms such as cell cycle checkpoint and apoptosis. We suggest here a model in which miRNAs may act as hub regulators of specific cellular responses immediately down-regulated so as to stimulate DNA repair mechanisms followed by up-regulation involved in suppressing apoptosis for cell survival. Taken together miRNAs may mediate signaling pathways in sequential fashion in response to radiation and may serve as biodosimetric markers of radiation exposure. Overall design: The gene expression patterns in human fibroblasts after 2.0 Gy of low-LET radiation was determined at 2 and 24 hrs post-irradiation time in technical triplicates. Control non-irradiated samples were also prepared in triplicates.

TOMS Earth-Probe Total Ozone (O3) Aerosol Index UV-Reflectivity UV-B Erythemal Irradiances Daily L3 Global 1 deg x 1.25 deg V008 (TOMSEPL3) at GES DISC

The Earth Probe (EP) Total Ozone Mapping Spectrometer (TOMS) version 8 daily global gridded data product contains total column ozone, UV aerosol index, Lambertian effective surface reflectivity (Rayleigh corrected), and UV-B erythemal local noon irradiances. The data are mapped to a global grid of size 180 x 288 with a lat-long resolution of 1.00 x 1.25 degrees. These data are stored in the EOS Hierarchical Data Format (HDF-EOS).The TOMS data were produced by the Laboratory for Atmospheres at NASA Goddard Space Flight Center (Code 614).