Project description:Background: Microorganisms are the major cause of food spoilage during storage, processing and distribution. Pseudomonas fluorescens is a typical spoilage bacterium that contributes to a large extent to the spoilage process of proteinaceous food. RpoS is considered an important global regulator involved in stress survival and virulence in many pathogens. Our previous work revealed that RpoS contributed to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. Results: RNA-seq transcriptomics analysis combined with quantitative proteomics analysis basing on multiplexed isobaric tandem mass tag (TMT) labeling was performed for the P. fluorescens wild-type strain UK4 and its derivative carrying a rpoS mutation. A total of 375 differentially expressed genes (DEGs) and 212 differentially expressed proteins (DEPs) were identified in these two backgrounds. The DGEs were further verified by qRT-PCR tests, and the genes directly regulated by RpoS were confirmed by 5’-RACE-PCR sequencing. The combining transcriptome and proteome analysis revealed a role of this regulator in several cellular processes, including polysaccharide metabolism, intracellular secretion and extracellular structures, cell well biogenesis, stress responses, ammonia and biogenic amine production, which may contribute to biofilm formation, stress resistance and spoilage activities of P. fluorescens. Moreover, in this work we indeed observed that RpoS contributed to the production of the macrocolony biofilm’s matrix.
Project description:In a previous study, we found that H2S alleviates salinity stress in cucumber by maintaining the Na+/K+ balance and by regulating H2S metabolism and the oxidative stress response. However, little is known about the molecular mechanisms behind H2S-regulated salt-stress tolerance in cucumber. Here, an integrated transcriptomic and proteomic analysis based on RNA-seq and 2-DE was used to investigate the global mechanism underlying H2S-regulated salt-stress tolerance. In total, 11 761 differentially expressed genes (DEGs) and 61 differentially expressed proteins (DEPs) were identified. Analysis of the pathways associated with the DEGs showed that salt stress enriched expression of genes in primary and energy metabolism, such as photosynthesis, carbon metabolism and biosynthesis of amino acids. Application of H2S significantly decreased these DEGs but enriched DEGs related to plant-pathogen interaction, sulfur-containing metabolism, cell defense and signal transduction pathways. Notably, changes related to sulfur-containing metabolism and cell defense were also observed through proteome analysis, such as Cysteine synthase 1, Glutathione S-transferase U25-like, Protein disulfide-isomerase and Peroxidase 2. We present the first global analysis of the mechanism underlying H2S regulation of salt-stress tolerance in cucumber through tracking changes in the expression of specific proteins and genes.
Project description:Over 20% of Earth’s terrestrial surface is underlain by permafrost that represents one of the largest terrestrial carbon pools, with an estimated ~1700 Pg of carbon (C) contained in the upper 3 m of permafrost. Models estimate that C release from thawing permafrost might represent the largest new transfer of C from the biosphere to the atmosphere as the climate warms. Here we investigated microbial community phylogeny, genetic functional potential gene expression, and protein production patterns along a natural thaw gradient, including permafrost, the seasonally thawed active layer and nearby thawed thermokarst bog, using a combination of molecular “omics” approaches: metagenomics (MG), metatranscriptomics (MT) and metaproteomics (MP). Highlights from these analyses reveal energy yielding microbial processes and potential strategies for microbial survival in permafrost soils, and linkages between biogeochemical process rates and –omics measurements. The results provide new knowledge about microbial life and activity potential in permafrost, the potential importance of iron reduction as a survival strategy under frozen conditions in mineral soils, and the importance of methanogenesis following thaw. The multi-omics strategy demonstrated here enables better mechanistic understanding of the ecological strategies utilized by soil microbial communities in response to climate change. Associated metagenomics data available at the EBI Metagenomics portal under the accession number <a href="https://www.ebi.ac.uk/metagenomics/projects/SRP052575">SRP052575</a>.
Project description:Objective To establish whether whole-blood MicroRNA (miRNA) profiles differ between postural tachycardia syndrome (POTS) sufferers and control subjects, and to identify the miRNA that regulate plasma H2S. Study design: High-throughput sequencing was used to obtain whole-blood miRNA expression profiles for five POTS sufferers and five normal children. miRNAs with an adjusted P-value of <0.05 (by DESeq) and with a log2 fold change ≥3 were considered to be differentially expressed (DEmiRNAs). The target genes of the DEmiRNAs were identified using RNAhybrid and miRanda, and only those identified by both were considered. The combined effects of the DEmiRNAs were determined using KEGG pathway analysis. Another 40 POTS and 20 normal patients were used as validation subjects. Plasma H2S was determined with a sulfide electrode, and flow-mediated vasodilation (FMD) was performed with a color Doppler ultrasound system. miRNAs were analyzed using QRT-PCR. Results: Thirteen DEmiRNAs were identified. When P values of 0.01 and 0.05 were used, 198 and 481 genes, respectively, were shown to be targeted by the 13 DEmiRNAs. DEmiRNAs were significantly enriched in 36 pathways (P <.05), in which PI3K/Akt signaling was closely related to vascular function. In the validation subjects, the plasma H2S and FMD was higher in the POTS sufferers, as was the expression level of whole-blood miR-21 (P <.05), which identified POTS patients with a sensitivity of 92.5% and a specificity of 100%. Conclusion: Elevated whole-blood miR-21 levels serve as an indicator for POTS and may explain the increased plasma H2S observed in POTS sufferers.
Project description:Full-Length cDNA transcriptome (Iso-Seq) data sequenced on the PacBio Sequel system using 2.1 chemistry. Multiplexed cDNA library of 12 samples (3 tissues x 4 strains). Tissues: root, embryo, endosperm. Strains: B73, Ki11, B73xKi11, Ki11xB73.
Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of DNA methylations in Burkholderia pseudomallei. SMRTbell™ sequencing
Project description:Saccharina japonica is one of the most important marine economic crops worldwide. Blue light usually plays a significant role in the lives of Saccharina that may be beneficial to the culture system. Here we applied high-throughput paired-end RNA-sequencing (RNA-Seq) to the transcriptome of Saccharina japonica with blue light and dark exposure respectively. Comparative analysis of gene expression was conducted to understand the underlying molecular mechanisms. RNA-seq analysis yielded 70,497 non-redundant unigenes. 25,924 unigenes of them had good comparability with known gene sequences in existing species. Based on the values of RPKM, 11,660 differentially expressed unigenes were detected in expression profiles between blue light and dark exposed samples. Our results provide clues to potential genes identification in the species and lay the foundation for future functional genomics study. mRNA expression of Saccharina japonica with 2 different treatment (sample exposed to Dark condition, and sample exposed to blue light respectively) was determined by method of RNA-Seq
Project description:Deep sequencing of mRNA from Chinese tree shrew; Chinese tree shrew (Tupaia belangeri chinensis) is placed in Order Scandentia and embraces many unique features for a good experimental animal model. Currently, there are many attempts to employ tree shrew to establish model for a variety of human disorders such as social stress, myopia, HCV and HBV infection, and hepatocellular carcinoma .We present here a publicly available annotated genome sequence for Chinese tree shrew. Phylogenomic analysis of tree shrew and other mammalians highly supported its close affinity to primates. Characterization of key factors and signaling pathways of the nervous and immune systems in tree shrews showed that this animal had common and unique features, and had essential genetic basis for being a promising model for biomedical researches. Analysis of ploy(A)+ RNA of different specimens:kidney, pancreas, heart, liver, brain, testis and ovary form Chinese tree shrew
Project description:Understanding human regulatory T cells (Tregs) heterogeneity may identify markers of disease pathogenesis and facilitate the development of optimized cellular therapeutics. To better elucidate human Treg subsets, we conducted direct transcriptional profiling of CD4+FOXP3+Helios+ thymic-derived Treg (tTreg) and CD4+FOXP3+Helios- peripherally-induced Treg (pTreg), followed by comparison to CD4+FOXP3-Helios- T conventional (Tconv) cells. This analysis revealed that the coinhibitory receptor T-cell immunoglobulin and immunoreceptor tyrosine-based inhibitory motif domain (TIGIT) was highly expressed on tTreg. In this study CD4 T cells were stained for the Treg-associated transcription factors FOXP3 and Helios, and subsequently FACS sorted to yield three populations: tTreg (CD4+FOXP3+Helios+), pTreg (CD4+FOXP3+Helios–) and the reference population Tconv (CD4+FOXP3–Helios–). A direct transcriptional profile was obtained from the recovered RNA from the populations defined as tTreg, pTreg, and Tconv.
Project description:Next generation sequencing of 28 thymic epithelial tumors (TETs) revealed a high frequency of GTF2I missense mutation (chr7:74146970T/A) in A thymomas, a relatively indolent subtype. The GTF2I mutation was confirmed in 82% of A and 74% of AB thymomas in a series of 274 TETs but was rare in aggressive subtypes, where recurrent mutations of known cancer genes were identified. Therefore, GTF2I mutation correlated with a better survival. GTF2I Beta and Delta isoforms were expressed in TETs and both mutant isoforms were able to stimulate cell proliferation in vitro. Thymic carcinomas presented a higher number of mutations than thymomas (average 43.5 and 18.4, respectively). Recurrent mutations of known cancer genes, including TP53, CYLD, CDKN2A, BAP1 and PBRM1 were identified in thymic carcinomas. These findings will complement the diagnostic work up of these rare tumors, and also help the development of a molecular classification, and assessment of prognosis and treatment strategies. Tumor samples of 286 patients were collected from 4 different institutions: National Cancer Institute (Bethesda MD), Pisa University Hospital (Pisa, Italy), Padua University Hospital (Padua, Italy) and IRCCS Istituto Clinico Humanitas (Rozzano, Italy).