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      Long-Term Effects of Very Low Dose Particle Radiation on Gene Expression in the Heart: Degenerative Disease Risks

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          Abstract

          Compared to low doses of gamma irradiation (γ-IR), high-charge-and-energy (HZE) particle IR may have different biological response thresholds in cardiac tissue at lower doses, and these effects may be IR type and dose dependent. Three- to four-month-old female CB6F1/Hsd mice were exposed once to one of four different doses of the following types of radiation: γ-IR 137Cs (40-160 cGy, 0.662 MeV), 14Si-IR (4-32 cGy, 260 MeV/n), or 22Ti-IR (3-26 cGy, 1 GeV/n). At 16 months post-exposure, animals were sacrificed and hearts were harvested and archived as part of the NASA Space Radiation Tissue Sharing Forum. These heart tissue samples were used in our study for RNA isolation and microarray hybridization. Functional annotation of twofold up/down differentially expressed genes (DEGs) and bioinformatics analyses revealed the following: (i) there were no clear lower IR thresholds for HZE- or γ-IR; (ii) there were 12 common DEGs across all 3 IR types; (iii) these 12 overlapping genes predicted various degrees of cardiovascular, pulmonary, and metabolic diseases, cancer, and aging; and (iv) these 12 genes revealed an exclusive non-linear DEG pattern in 14Si- and 22Ti-IR-exposed hearts, whereas two-thirds of γ-IR-exposed hearts revealed a linear pattern of DEGs. Thus, our study may provide experimental evidence of excess relative risk (ERR) quantification of low/very low doses of full-body space-type IR-associated degenerative disease development.

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          limma powers differential expression analyses for RNA-sequencing and microarray studies

          limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for information borrowing to overcome the problem of small sample sizes. Over the past decade, limma has been a popular choice for gene discovery through differential expression analyses of microarray and high-throughput PCR data. The package contains particularly strong facilities for reading, normalizing and exploring such data. Recently, the capabilities of limma have been significantly expanded in two important directions. First, the package can now perform both differential expression and differential splicing analyses of RNA sequencing (RNA-seq) data. All the downstream analysis tools previously restricted to microarray data are now available for RNA-seq as well. These capabilities allow users to analyse both RNA-seq and microarray data with very similar pipelines. Second, the package is now able to go past the traditional gene-wise expression analyses in a variety of ways, analysing expression profiles in terms of co-regulated sets of genes or in terms of higher-order expression signatures. This provides enhanced possibilities for biological interpretation of gene expression differences. This article reviews the philosophy and design of the limma package, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.
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            Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

            Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gene set libraries available for analysis and download. In total, Enrichr currently contains 180 184 annotated gene sets from 102 gene set libraries. New features have been added to Enrichr including the ability to submit fuzzy sets, upload BED files, improved application programming interface and visualization of the results as clustergrams. Overall, Enrichr is a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries. Enrichr is freely available at: http://amp.pharm.mssm.edu/Enrichr.
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              Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors.

              Differentiated cells can be reprogrammed to an embryonic-like state by transfer of nuclear contents into oocytes or by fusion with embryonic stem (ES) cells. Little is known about factors that induce this reprogramming. Here, we demonstrate induction of pluripotent stem cells from mouse embryonic or adult fibroblasts by introducing four factors, Oct3/4, Sox2, c-Myc, and Klf4, under ES cell culture conditions. Unexpectedly, Nanog was dispensable. These cells, which we designated iPS (induced pluripotent stem) cells, exhibit the morphology and growth properties of ES cells and express ES cell marker genes. Subcutaneous transplantation of iPS cells into nude mice resulted in tumors containing a variety of tissues from all three germ layers. Following injection into blastocysts, iPS cells contributed to mouse embryonic development. These data demonstrate that pluripotent stem cells can be directly generated from fibroblast cultures by the addition of only a few defined factors.
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                Author and article information

                Contributors
                Role: Academic Editor
                Journal
                Cells
                Cells
                cells
                Cells
                MDPI
                2073-4409
                13 February 2021
                February 2021
                : 10
                : 2
                : 387
                Affiliations
                [1 ]Department of Emergency Medicine, Dorothy M Davis Heart and Lung Research Institute, Wexner Medical School, The Ohio State University, Columbus, OH 43210, USA; venkata.garikipati@ 123456osumc.edu
                [2 ]Bioinformatics Group, The Institute of Molecular Biology, The National Academy of Sciences of the Republic of Armenia, Yerevan 0014, Armenia; arakelyanaa@ 123456gmail.com
                [3 ]PathVerse, Yerevan 0014, Armenia
                [4 ]Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; eablakely@ 123456jbl.gov
                [5 ]SRI International, Menlo Park, CA 94025, USA; polly.chang@ 123456sri.com
                [6 ]Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; maycao@ 123456temple.edu (M.M.T.); maria.cimini@ 123456temple.edu (M.C.); tuj39930@ 123456temple.edu (V.M.); nmkbjp18@ 123456gmail.com (A.B.); raj.kishore@ 123456temple.edu (R.K.)
                [7 ]Kimmel Cancer Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA; sankar.addya@ 123456jefferson.edu
                [8 ]Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; malik.bisserier@ 123456mssm.edu (M.B.); agnieszka.brojakowska@ 123456mssm.edu (A.B.); abrisham.eskandari@ 123456icahn.mssm.edu (A.E.); mkhlgatian@ 123456gmail.com (M.K.K.); lahouaria.hadri@ 123456mssm.edu (L.H.); kenneth.fish@ 123456mssm.edu (K.M.F.)
                Author notes
                [* ]Correspondence: david.goukassian@ 123456mssm.edu ; Tel.: +1-212-824-8917
                Author information
                https://orcid.org/0000-0002-6851-1056
                https://orcid.org/0000-0001-8826-4649
                https://orcid.org/0000-0002-7319-9685
                https://orcid.org/0000-0003-4764-6258
                https://orcid.org/0000-0002-8168-3004
                Article
                cells-10-00387
                10.3390/cells10020387
                7917872
                33668521
                49e9aa9a-efbc-4196-8e1f-6023734f1ff4
                © 2021 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 05 January 2021
                : 08 February 2021
                Categories
                Article

                heart,space radiation,gene expression,gamma radiation,nasa,female mice

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