Project description:Transcriptomic analysis in a Salmonella enterica Serovar Typhimurium SL 1344 that constitutively expresses stdE and stdF compared with a strain carrying an stdEF deletion A four chip study using total RNA recovered from two separate cultures of Salmonella enterica Serovar Typhimurium SL 1344 constitutively expressing stdE and stdF and two separate cultures of Salmonella enterica Serovar Typhimurium SL 1344 lacking stdE and stdF.
Project description:To identify genes activated under hypoxia (1%O2) and serum-free treatment of a cancer cell line, we performed cDNA microarray analysis with an ovarian cancer cell line, OVSAYO. Cells were cultured under normoxia /hypoxia (1%O2) and serum-plus/serum-minus conditions for 16 hours. Total RNA was isolated for cDNA microarray analysis.
Project description:Cancer relapse after curative treatment is thought to originate from drug-tolerant and invisible cancer cell subpopulations. Using cancer cell colonies emerging in the presence of drugs (drug-tolerant colonies, DTCs), we found that the drug-tolerant properties of DTCs are lost through a reversible mechanism. To examine whether epigenetic regulation is responsible for the phenotypic changes in DTCs, we performed a genome-wide analysis for relative CpG methylation between the DTCs and untreated colonies derived from MKN45 by NimbleGen Human Meth 385K Prom Plus CpG Arrays. Global changes in the methylation levels were evident in a chromosomal location-dependent manner. The methylation status of the upstream regions of the transcription start sites of the pluripotency-inducing genes showed good agreement with the qRT-PCR data. These results suggest that reversible drug-tolerant properties in DTCs are epigenetically regulated and associated with transcriptional regulation, including pluripotency-inducing factors. Comparison of untreated colonies v.s. DTCs derived from MKN45 cells.
Project description:To investigate how dSETDB1 regulated the genome-wide distribution of HP1 proteins, we performed ChIP-chip assay on the third instar larval lysate from the dSETDB1null mutants in comparison to the wild type. Third instar larvae from the wild type and dSETDB1null mutants were collected. Three independent biological replicates of ChIP with anti-HP1 were performed.
Project description:“Stress, survival and virulence: the multi-faceted host/microbial interactions.” Bacteria employ epinephrine and norepinephrine, which converge to distinct bacterial crucial processes, like survival and pathogenicity. A novel stress periplasmic membrane protein belonging to previously described BOF family, protein renamed here SrpP, and together with membrane sensor kinase QseC has an essential role in stress response and virulence of S. Typhimurium. SrpP employs its predicted binding pocket, specifically the SrpPE110 residue, and interacts with lipid A modification enzyme, LpxO dioxygenase. Upon this interaction SrpP in S. Typhimurium finely manages multiple membrane functions to culminate in survival upon stress and pathogenesis in vivo, connecting host-stress chemical signaling to cell stress in bacteria. Comparison of sensor histidine kinase qseC mutant expression levels versus wild type strain.
Project description:sox10:GFP transgenic embryos were used to FACS sort neural crest and microarray analysis was done to compare genes expressed differentially between GFP positive and negative and fold changes were compared to differentially expressed genes in embryos treated with morpholino oligonucleotides to knockdown function of Twist1 A Nimblegen catalog design microarray study done in biological triplicates to analyze expression of genes in neural crest and regulated by Twist1
Project description:Despite sharing much of their genomes, males and females are often highly dimorphic, reflecting at least in part the resolution of sexual conflict in response to sexually antagonistic selection. Sexual dimorphism arises owing to sex differences in gene expression, and steroid hormones are often invoked as a proximate cause of sexual dimorphism. Experimental elevation of androgens can lead to masculinization of behavior, physiology, and gene expression, but knowledge of the role of hormones remains incomplete, including how the sexes differ in their gene expression in response to exposure to hormones. We addressed these questions in a bird species with a long history of behavioral endocrinological and ecological study, the dark-eyed junco (Junco hyemalis), using a species-specific microarray. Focusing on two brain regions involved in sexually dimorphic behavior and regulation of hormone secretion, we identified 1,639 genes that differed in expression by sex in the ventromedial telencephalon and 768 in hypothalamus. In response to experimentally elevated testosterone, females exhibited a more “male-like” expression pattern than control females; unexpectedly, male expression patterns became more “female-like” rather than hyper-masculinized when compared to control males. This sex difference in pattern arose both because testosterone altered regulation of different genes in each sex and because testosterone altered regulation of the same genes differentially, i.e., up in one sex, down in the other. Hormonally regulated gene expression is a key genetic and physiological mechanism underlying sexual dimorphism, and further study should help to explain how it relates to the resolution of sexual conflict. Hypothalamus: 24 samples were analyzed, all were biological (not technical) replicates. 6 from males treated with testosterone [MT], 6 from control males [MC], 6 from females treated with testosterone [FT], and 6 from control females [FC]. All hybridizations were paired, and all treatment groups were compared, but no sample was analyzed more than once. Ventromedial telencephalon: 24 samples were analyzed, all were biological (not technical) replicates. 6 from males treated with testosterone [MT], 6 from control males [MC], 6 from females treated with testosterone [FT], and 6 from control females [FC]. All hybridizations were paired, and all treatment groups were compared, but no sample was analyzed more than once.
Project description:Acetic acid bacteria are obligately aerobic alphaproteobacteria that have a unique ability to incompletely oxidize various alcohols and sugars to organic acids. The ability of these bacteria to incompletely oxidize ethanol to acetate has been historically utilized for vinegar production. The mechanism of switching between incomplete oxidation and assimilatory oxidation and the control of energy and carbon metabolism in acetic acid bacteria are not fully understood. To understand the physiology and molecular biology of acetic acid bacteria better, we determined the draft genome sequence of Acetobacter aceti NBRC 14818, which is the type strain of the genus. Based on this draft genome sequence, the transcriptome profiles in A. aceti cells grown on ethanol, acetate, glucose, or mix of ethanol and glucose was determined by using NimbleGen Prokaryotic Expression array (4x72K). Acetobacter aceti NBRC14818 was cultivated in the medium containing ethanol, acetate, glucose, or mix of ethanol and glucose as carbon sources in Erlenmeyer flask with rotary shaking. Total RNA was extracted when optical density at 600 nm was 0.3-0.4. The experiment was performed in duplicate independent cultures.