Project description:We have studied protein expression in mouse embryonic stem (mES) cells- R1-9 and identified the largest complement of proteins reported thus far for mES cells, using on-line LC-MS/MS analysis. With support from a transcriptome profile of the same mES cell line, we arrived at an integrated dataset of 9,370 protein expressions that may be useful to understand the stem cell dynamics. 6,278 protein identifications (IDs) were based on two or more peptide signatures and 3,092 with single peptide signatures. These single peptide-based protein IDs were also supported by transcriptome data. The proteomic analysis demonstrated the expression of 1,369 genes (among 9,370) that were not seen in RNA transcripts. Pathway analysis of the protein IDs in our dataset, using KEGG and BioCarta and their gene ontology classification, revealed high representation of the proteins belonging to many regulatory pathways and showed enrichment for protein IDs involved in transcription regulation, signal transduction, cell-cycle, and differentiation. Interestingly, the data support the expression of 1,299 putative open reading frames. In silico domain comparisons of some of these sequences matched with regulatory proteins such as transcription factors or signal transduction molecules. Over 60% of the transcript complement is represented in our protein dataset implying a corresponding richness of the dynamic network of proteins in a pluripotent mES cells.have thus arrived at a dataset of 10428 expressed proteins with high confidence which was also verified by microarray analysis of the expressed mRNAs R1-9 ES cells. Pathway analysis of these expressed proteins was carried out using KEGG, IPA and their gene ontology classification revealed the presence of large number of transcription regulators, signal transducers, cell cycle and differentiation molecules along with other general classes of proteins belonging to a number of regulatory pathways. The database also includes IDs of proteins corresponding to many still unidentified / unannotated ORFs from the mouse genome and with putative regulatory functions. Our study thus represents the largest database of expressed proteins in mouse ES cells that would be a valuable molecular resource for experimental designs in targeted proteomics investigations using mES cell lines.
Project description:Despite the expanding interest in bacterial viruses (bacteriophages), insights into the intracellular development of bacteriophage and its impact on bacterial physiology are still scarce. Here we investigate during lytic infection the whole-genome transcription of the giant phage vB_YecM_?R1-37 (?R1-37) and its host, the gastroenteritis causing bacterium Yersinia enterocolitica. RNA sequencing reveals that the gene expression of ?R1-37 does not follow a pattern typical observed in other lytic bacteriophages, as only selected genes could be classified as typically early, middle or late genes. The majority of the genes appear to be expressed constitutively throughout infection. Additionally, our study demonstrates that transcription occurs mainly from the positive strand, while the negative strand encodes only genes with low to medium expression levels. Interestingly, we also detected the presence of antisense RNA species, as well as one non-coding intragenic RNA species. Gene expression in the phage-infected cell is characterized by the broad replacement of host transcripts with phage transcripts. However, the host response in the late phase of infection was also characterized by up-regulation of several specific bacterial gene products known to be involved in stress response and membrane stability, including the Cpx pathway regulators, ATP-binding cassette (ABC) transporters, phage- and cold-shock proteins.
Project description:Notoginsenoside R1 (NR1) is the main bioactive component in panaxnotoginseng, an old herb medicine widely used in Asian countries in the treatment of microcirculatory diseases. However, little is known about the effect of NR1 on antihypertension and the underlying mechanisms are still not clear. This study is aim to investigate the effect and elicit the mechanism of NR1 in antihypertension. Firstly, to assess the ability of NR1 in antihypertension, NR1 was injected in spontaneously hypertensive rats (SHR) via the vena caudalis. Then we examined the rats systolic blood pressure and inducible nitric oxide synthase (iNOS) activation in rats thoracoabdominal aortic. To further investigate the molecular mechanism of NR1 reduce blood pressure, primary SHR and WYK rat vascular endothelial cells (RVECs) were used for next study. LncRNAs related to hypertension were gained from bioinformatics analysis. The role of LncRNAs was finally characterized in RVECs by siRNA. Our results showed that NR1 significantly reduce blood pressure in SHR and induce nitric oxide (NO) generation through increasing the phosphorylation of iNOS. Through bioinformatics analysis and knockdown LncRNA AK094457 in RVECs, we also found LncRNA AK094457 promoted iNOS expression and NO concentration. Thus, we conclude that NR1 reduces the caudal blood pressure of SHR through induction of iNOS regulated by long non-coding RNA AK094457. These findings may have important implications for understanding the mechanisms of NR1 regulation blood pressure.