Project description:Change in gene expression for a wild-type (Nostoc punctiforme ATCC 29133) and hmpD-deletion strain (UCD 543) of Nostoc punctiforme ATCC 29133 over the time course of hormogonium development This study is further descirbed in Risser, D.D. and Meeks, J.C. 2013. Comparative transcriptomics with a motility deficient mutant leads to identification of a novel polysaccharide secretion system in Nostoc punctiforme. Molecular Microbiology
Project description:Change in gene expression for a wild-type (Nostoc punctiforme ATCC 29133) and hmpD-deletion strain (UCD 543) of Nostoc punctiforme ATCC 29133 over the time course of hormogonium development This study is further descirbed in Risser, D.D. and Meeks, J.C. 2013. Comparative transcriptomics with a motility deficient mutant leads to identification of a novel polysaccharide secretion system in Nostoc punctiforme. Molecular Microbiology Total RNA from 3 biological replicates at each time point from 0 to 24 hours after hormogonium induction was converted to cDNA, dye-labled and hybridized to nimblegen 12x135k array slides
Project description:To identify the mechanisms of the adaptation to terrestrial ecosystems, an RNA-seq based transcriptome analysis was conducted on a desiccation resistant cyanobacterium, Nostoc sp. MG11.
Project description:Change in gene expression for wild-type Nostoc punctiforme ATCC 29133, or three derivative strains with sigma factors deleted, over the time course of hormogonium development
Project description:HILIC runs (separate LC-MS) of mixed proteome from closely related cyanobacterium Nostoc punctiforme ATCC 29133 and Nostoc sp. PCC 7120. Quantitative comparisons across species can only be made using orthologous peptides. All other peptides are used to assess biological variation and MS/MS co-elution study.
Project description:To investigate the function of All0854, we constructed the all0854 deletion mutant Mall0854, in which all0854 was knocked out by CRISPER-cpf1. We then performed gene expression profiling analysis using data obtained from RNA-seq of wide type Nostoc sp. PCC 7120 and Mall0854.
Project description:Small extracellular vesicles (sEV) are nano-sized (40-150 nm), membrane-encapsulated vesicles that are released by malignant or pathologic and non-pathologic cells into the extracellular space and function as intercellular signaling vectors through the horizontal transfer of biologic molecules, including microRNA (miRNA) and other small non-coding RNA (ncRNA), that can alter the phenotype of recipient cells. sEV are present in essentially all extracellular biofluids, including serum, urine and saliva, and offer a new avenue for discovery and development of novel biomarkers of various disease states and exposures. The objective of this study was to determine the similarities and differences between sEV ncRNA derived from saliva, serum and urine, as well as cell-free ncRNA from serum. Saliva, urine and serum were concomitantly collected from 4 healthy donors, and sEV were isolated from each respective biofluid, along with cfRNA from serum. sEVs were isolated from the respective biofluids via differential ultracentrifugation. Small RNA-sequencing was performed on each sample, and cluster analysis was performed based on ncRNA profiles. While some similarities existed in terms of sEV ncRNA cargo across biofluids, there are also notable differences in ncRNA class and ncRNA secretion, with each sEVs in each biofluid bearing a unique ncRNA profile. We conclude that sEV ncRNA cargo varies according to biofluid, so thus should be carefully selected and interpreted when designing translational or epidemiological studies.
Project description:Plasma derived extracellular vesicles (EVs) have emerged as critical mediators of complications following traumatic injuries and after exposure to radiation. In response to injury, the cargo of these EVs is altered and can contain potent cargo that can influence cell function, including alterations in miRNA cargo. Here, we utilized NanoString's mouse miRNA panel to compare the alterations in miRNA content following exposure to 2 or 9 Gys of whole-body irradiation isolated 3 days after exposure and compared these changes to sham mice.
Project description:Salivary gland-specific binding assays reveal that CrebA, a bZIP transcription factor, directly binds the vast majority of genes encoding the secretory machinery, including proteins of the signal recognition particle and receptor, proteins involved in co-translational import of cargo into the ER, proteins involved in vesicular transport between the ER and Golgi, as well as the structural proteins and enzymes of these organelles. CrebA does not bind salivary gland-specific cargo genes. Instead, it binds and boosts expression of Sage, which encodes a bHLH transcription factor that upregulates cargo expression. CrebA also directly binds and upregulates Xbp1, which encodes a key factor in the unfolded protein response, and Tudor-SN, which encodes a protein that in other systems increases secretory cargo mRNA levels.