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2 results on '"Julia Stair"'

1. Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation

Author

Jizhong Zhou, Dong Xu, Liyou Wu, Dorothea K. Thompson, Igor B. Rogozin, Amudhan Venkateswaran, Min Zhai, Eugene V. Koonin, Alexander S. Beliaev, Marina V. Omelchenko, Michael J. Daly, Elena K. Gaidamakova, Yongqing Liu, Kira S. Makarova, and Julia Stair

Subjects
DNA Repair, Transcription, Genetic, DNA repair, DNA damage, Molecular Sequence Data, Transcriptome, Radiation, Ionizing, Operon, Deinococcus, Amino Acid Sequence, Gene, Genetics, chemistry.chemical_classification, DNA ligase, Multidisciplinary, biology, Sequence Homology, Amino Acid, DNA replication, Deinococcus radiodurans, Gene Expression Regulation, Bacterial, Biological Sciences, biology.organism_classification, chemistry, Sequence Alignment, Cell Division
Abstract

Deinococcus radiodurans R1 (DEIRA) is a bacterium best known for its extreme resistance to the lethal effects of ionizing radiation, but the molecular mechanisms underlying this phenotype remain poorly understood. To define the repertoire of DEIRA genes responding to acute irradiation (15 kGy), transcriptome dynamics were examined in cells representing early, middle, and late phases of recovery by using DNA microarrays covering ≈94% of its predicted genes. At least at one time point during DEIRA recovery, 832 genes (28% of the genome) were induced and 451 genes (15%) were repressed 2-fold or more. The expression patterns of the majority of the induced genes resemble the previously characterized expression profile of recA after irradiation. DEIRA recA , which is central to genomic restoration after irradiation, is substantially up-regulated on DNA damage (early phase) and down-regulated before the onset of exponential growth (late phase). Many other genes were expressed later in recovery, displaying a growth-related pattern of induction. Genes induced in the early phase of recovery included those involved in DNA replication, repair, and recombination, cell wall metabolism, cellular transport, and many encoding uncharacterized proteins. Collectively, the microarray data suggest that DEIRA cells efficiently coordinate their recovery by a complex network, within which both DNA repair and metabolic functions play critical roles. Components of this network include a predicted distinct ATP-dependent DNA ligase and metabolic pathway switching that could prevent additional genomic damage elicited by metabolism-induced free radicals.

Published
2003

2. Effects of Folate Availability on Expression of Adipocyte Metabolic Genes Via Modulation of DNA Methylation

Author

Gouffon, Julia Stair

Subjects
Epigenetics, DNA Methylation, Adipocytes, Folate, Metabolism, Genomics, Molecular, Genetic, and Biochemical Nutrition, Nutrition
Abstract

Epigenetic modifications serve as a means of intermediate gene expression control and nutritional inputs may modify methylation patterns in regulatory regions of genes. Therefore, we proposed that specific nutrient availability of folate affects adipocyte development and metabolism through impacting the one-carbon cycle and subsequent DNA methylation patterns. Accordingly, we sought to determine if the methylation level of CpG islands could be influenced in adipocytes and if so, how this might affect gene signaling in mature adipocytes. We treated adipocytes with 0 to 0.9 millimolar [mM] folate, the methyl donor S-adenosylmethionine (SAMe) and the methylation inhibitor, 5-aza-2-deoxycitidine (2-DC) both during adipocyte differentiation and the maturation process. Lipogenesis was measured by accumulation of oil red O and lipolysis was quantified by a glycerol release assay. Methylated regions of adipocyte genomic DNA was evaluated using a methylation-specific antibody and hybridized against a Nimblegen whole genome CpG island array to identify targets for expression analysis RNA was obtained and genes involved in adipocyte differentiation, one-carbon metabolism, lipogenesis and lipolysis were quantified using RT-PCR. We found that low folate levels or inhibition by 2-DC decreased CpG methylation, thus increasing gene expression. Surprisingly SAMe performed similarly and decreased global CpG methylation. Low folate increased lipid accretion and subsequent lipolysis. Exposure to folate during the critical differentiation process had a greater impact on lipogenesis and lipolysis than exposure during the maturation.

Published
2012

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