Circulating miRNA and cancer diagnosis

miRNAs are a class of small RNA molecules with regulatory function, and play an important role in tumor development and progression. It has been demonstrated that tumor-derived miRNAs exist in the circulating nucleic acids of cancer patients. This phenomenon implies that detection of the circulating miRNA may be an effective method for non-invasive diagnosis of cancer. In this review, we summarize the applications of the circulating miRNA as biomarkers in cancer diagnosis, as well as the latest research progress in this area.     

Highly conserved glycine 86 and arginine 87 residues contribute differently to the structure and activity of the mature HIV‐1 protease

The structural and functional role of conserved residue G86 in HIV‐1 protease (PR) was investigated by NMR and crystallographic analyses of substitution mutations of glycine to alanine and serine (PR_G86A and PR_G86S). While PR_G86S had undetectable catalytic activity, PR_G86A exhibited ～6000‐fold lower catalytic activity than PR. ¹H‐¹⁵N NMR correlation spectra revealed that PR_G86A and PR_G86S are dimeric, exhibiting dimer dissociation constants (K_d) of ～0.5 and ～3.2 μM, respectively, which are significantly lower than that seen for PR with R87K mutation (K_d > 1 mM). Thus, the G86 mutants, despite being partially dimeric under the assay conditions, are defective in catalyzing substrate hydrolysis. NMR spectra revealed no changes in the chemical shifts even in the presence of excess substrate, indicating very poor binding of the substrate. Both NMR chemical shift data and crystal structures of PR_G86A and PR_G86S in the presence of active‐site inhibitors indicated high structural similarity to previously described PR/inhibitor complexes, except for specific perturbations within the active site loop and around the mutation site. The crystal structures in the presence of the inhibitor showed that the region around residue 86 was connected to the active site by a conserved network of hydrogen bonds, and the two regions moved further apart in the mutants. Overall, in contrast to the role of R87 in contributing significantly to the dimer stability of PR, G86 is likely to play an important role in maintaining the correct geometry of the active site loop in the PR dimer for substrate binding and hydrolysis. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

A distinct subset of podoplanin (gp38) expressing F4/80+ macrophages mediate phagocytosis and are induced following zymosan peritonitis

Macrophages are important tissue resident cells that regulate the dynamics of inflammation. However, they are strikingly heterogeneous. During studies looking at podoplanin (gp38) expression on stromal cells in the murine spleen and peritoneal cavity we unexpectedly discovered that podoplanin was expressed on a subset of F4/80⁺ macrophages; a subset which we have termed fibroblastic macrophages (FM). These cells function as phagocytes in vitro as measured by bead mediated phagocytosis assays. FM also exist at high frequency in the peritoneal cavity and in zymosan induced peritonitis in vivo. These FM represent a unique subgroup of F4/80⁺ macrophages and their presence in the inflamed peritoneum suggests that they play a role in zymosan induced peritonitis.     

Optimized medium improves expression and secretion of extremely thermostable bacterial xylanase, XynB, in Kluyveromyces lactis

An extremely thermostable xylanase gene, xynB, from hyperthermophilic bacterium Thermotoga maritima MSB8 was successful expressed in Kluyveromyces lactis. Response surface methodology (RSM) was applied to optimize medium components for production of XynB secreted by the recombinant K. lactis. Secretion level (102 mg/L) and enzyme activity (49 U/ml) of XynB in the optimized medium (yeast extract, lactose, and urea; YLU) were much higher than those (56 mg/L, 16 U/ml) in original medium (yeast extract, lactose, and peptone; YLP). It was also observed that the secretory efficiency of mature XynB was improved by the YLU medium. mRNA levels of 13 characterized secretion-related genes between K. lactis cultured in YLP and YLU were detected using semi-quantitative RT-PCR method. It was found that unfolded protein response (UPR) related genes such as ero1, hac1, and kar2 were up-regulated in K. lactis cultured in YLU. Therefore, nutrient ingredient, especially nitrogen source had a significant influence on the XynB secretory efficiency in the host K. lactis.     

A systematic investigation of <Emphasis Type="Italic">Escherichia coli</Emphasis> central carbon metabolism in response to superoxide stress

Background  

The cellular responses of bacteria to superoxide stress can be used to model adaptation to severe environmental changes. Superoxide stress promotes the excessive production of reactive oxygen species (ROS) that have detrimental effects on cell metabolic and other physiological activities. To antagonize such effects, the cell needs to regulate a range of metabolic reactions in a coordinated way, so that coherent metabolic responses are generated by the cellular metabolic reaction network as a whole. In the present study, we have used a quantitative metabolic flux analysis approach, together with measurement of gene expression and activity of key enzymes, to investigate changes in central carbon metabolism that occur in Escherichia coli in response to paraquat-induced superoxide stress. The cellular regulatory mechanisms involved in the observed global flux changes are discussed.     

几丁聚糖促进人脐静脉内皮细胞的生长及相关蛋白的表达

目的：研究几丁聚糖对体外培养的人脐静脉内皮细胞生长的影响及相关作用机制。方法：用不同质量浓度的几丁聚糖和雷帕霉素培养液培养内皮细胞48h,以四唑盐比色法测细胞增殖。免疫组化测c-Myc,Bcl-2和Bax蛋白的表达。结果：随着几丁聚糖质量浓度≥0．01mg／ml的增加,内皮细胞数增多（P〈0.05）,同时Bax的表达降低。结论：几丁聚糖通过下调Bax的表达抑制内皮细胞的凋亡,起到增殖的效果。     

BayGO: Bayesian analysis of ontology term enrichment in microarray data

Background  

The search for enriched (aka over-represented or enhanced) ontology terms in a list of genes obtained from microarray experiments is becoming a standard procedure for a system-level analysis. This procedure tries to summarize the information focussing on classification designs such as Gene Ontology, KEGG pathways, and so on, instead of focussing on individual genes. Although it is well known in statistics that association and significance are distinct concepts, only the former approach has been used to deal with the ontology term enrichment problem.