Proteases in malaria parasites - a phylogenomic perspective

Malaria continues to be one of the most devastating global health problems due to the high morbidity and mortality it causes in endemic regions. The search for new antimalarial targets is of high priority because of the increasing prevalence of drug resistance in malaria parasites. Malarial proteases constitute a class of promising therapeutic targets as they play important roles in the parasite life cycle and it is possible to design and screen for specific protease inhibitors. In this mini-review, we provide a phylogenomic overview of malarial proteases. An evolutionary perspective on the origin and divergence of these proteases will provide insights into the adaptive mechanisms of parasite growth, development, infection, and pathogenesis.B.     

Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering

MOTIVATION: With the advancements of next-generation sequencing technology, it is now possible to study samples directly obtained from the environment. Particularly, 16S rRNA gene sequences have been frequently used to profile the diversity of organisms in a sample. However, such studies are still taxed to determine both the number of operational taxonomic units (OTUs) and their relative abundance in a sample. RESULTS: To address these challenges, we propose an unsupervised Bayesian clustering method termed Clustering 16S rRNA for OTU Prediction (CROP). CROP can find clusters based on the natural organization of data without setting a hard cut-off threshold (3%/5%) as required by hierarchical clustering methods. By applying our method to several datasets, we demonstrate that CROP is robust against sequencing errors and that it produces more accurate results than conventional hierarchical clustering methods. Availability and Implementation: Source code freely available at the following URL: http://code.google.com/p/crop-tingchenlab/, implemented in C++ and supported on Linux and MS Windows.     

Superpredation patterns in four large European raptors

Predatory interactions among top predators, like superpredation or intraguild predation (IGP), can influence community structure. Diurnal raptors occupy high trophic levels in terrestrial food webs, and thus can regulate the presence of mesopredators. We studied superpredation (the killing and eating of another predator) in four large European raptors. We gathered 121 dietary studies, totalling 161,456 prey for the Goshawk Accipiter gentilis L., Golden Eagle Aquila chrysaetos L., Bonelli’s Eagle Aquila fasciata Vieillot, and Eagle Owl Bubo bubo L. Results showed that superpredation: (1) is a widespread interaction in large raptors, but it can vary according to the top predator species; (2) is not an important energetic resource for large raptors, but rather seems mostly related to diet diversification when the main prey decreases; (3) is spatially clustered reflecting habitat heterogeneity, but shows no temporal or large-scale spatial trends; and (4) it is associated with lower breeding success of the top predator species. These findings support the food stress hypothesis as the main driving force behind increases in superpredation and IGP in raptors, with the decrease in breeding performance as a side effect. Superpredation by large raptors deserves future research to understand its effects on mesopredators, because on one hand it might contribute to promote biodiversity, while on the other hand, it can sometimes represent an additional risk for small populations of endangered mesopredators.     

Targeting the hemangioblast with a novel cell type-specific enhancer

Background

Hemangioblasts are known as the common precursors for primitive hematopoietic and endothelial lineages. Their existence has been supported mainly by the observation that both cell types develop in close proximity and by in vitro differentiation and genetic studies. However, more compelling evidence will arise from tracking their cell fates using a lineage-specific marker.

Results

We report the identification of a hemangioblast-specific enhancer (Hb) located in the cis-regulatory region of chick Cerberus gene (cCer) that is able to direct the expression of enhanced green fluorescent protein (eGFP) to the precursors of yolk sac blood and endothelial cells in electroporated chick embryos. Moreover, we present the Hb-eGFP reporter as a powerful live imaging tool for visualizing hemangioblast cell fate and blood island morphogenesis.

Conclusions

We hereby introduce the Hb enhancer as a valuable resource for genetically targeting the hemangioblast population as well as for studying the dynamics of vascular and blood cell development.     

单胎头位初产妇产程图分析

目的：探讨存在难产因素初产妇产程图的临床意义。方法：对2009年6月至2010年6月在济南军区总医院住院分娩的326例单胎头位初产妇的产程图进行回顾性分析。结果：产程图异常组中难产因素的构成比和剖宫产率均高于产程图正常组;存在难产因素的组别（胎方位异常组、宫缩乏力组、巨大儿组）产程中各阶段时限均较正常产妇组长,宫颈扩张速度均较正常组慢,胎头位置均高于正常组,以上差异均有统计学意义（P〈0．05）。结论：在产程中对产程图中各阶段时限、宫颈扩张速度及胎头位置等指标进行监测,来预测和及时发现头位难产因素的存在,及时给予处理,改善母儿预后。     

Phosphoproteome analysis of the pathogenic bacterium Helicobacter pylori reveals over-representation of tyrosine phosphorylation and multiply phosphorylated proteins

Increasing evidence shows that protein phosphorylation on serine (Ser), threonine (Thr) and tyrosine (Tyr) residues is a major regulatory post-translational modification in the bacteria. To reveal the phosphorylation state in the Gram-negative pathogenic bacterium Helicobacter pylori, we carried out a global and site-specific phosphoproteomic analysis based on TiO(2) -phosphopeptide enrichment and high-accuracy LC-MS/MS determination. Eighty-two phosphopeptides from 67 proteins were identified with 126 phosphorylation sites, among which 79 class I sites were determined to have a distribution of 42.8:38.7:18.5% for the Ser/Thr/Tyr phosphorylation, respectively. The H. pylori phosphoproteome is characterized by comparably big size, high ratio of Tyr phosphorylation, high abundance of multiple phosphorylation sites in individual phosphopeptides and over-representation of membrane proteins. An interaction network covering 28 phosphoproteins was constructed with a total of 163 proteins centering on the major H. pylori virulence factor VacA, indicating that protein phosphorylation in H. pylori may be delicately controlled to regulate many aspects of the metabolic pathways and bacterial virulence.     

Changes in proteomics profile during maturation of marrow-derived dendritic cells treated with oxidized low-density lipoprotein

Increasing evidence suggests that dendritic cells (DCs) and oxidized low-density lipoprotein (ox-LDL) participate in atherosclerosis. However, few data on the molecular mechanisms of this process are available. To address this question, we used iTRAQ labeling followed by LC-MS/MS analysis to identify many proteins that changed markedly during the maturation of dendritic cells stimulated with ox-LDL. Among a total of 781 identified proteins, 93 were upregulated and 100 were downregulated. The major and significant changes in upregulated proteins were that ox-LDL not only affected the levels of intracellular cathepsins G, Z, D and S, but also significantly enhanced cathepsin S secretion by the treated cells. Our results may provide clues for a more comprehensive understanding the pathogenesis of atherosclerosis.