Comparative Genomics of Helicobacter pylori Strains of China Associated with Different Clinical Outcome

In this study, a whole-genome CombiMatrix Custom oligonucleotide tiling microarray with 90000 probes covering six sequenced Helicobacter pylori (H. pylori) genomes was designed. This microarray was used to compare the genomic profiles of eight unsequenced strains isolated from patients with different gastroduodenal diseases in Heilongjiang province of China. Since significant genomic variation was found among these strains, an additional 76 H. pylori strains associated with different clinical outcomes were isolated from various provinces of China. These strains were tested by polymerase chain reaction to demonstrate this distinction. We identified several highly variable regions in strains associated with gastritis, gastric ulceration, and gastric cancer. These regions are associated with genes involved in the bacterial type I, type II, and type III R-M systems. They were also associated with the virB gene, which lies on the well-studied cag pathogenic island. While previous studies have reported on the diverse genetic characterization of this pathogenic island, in this study, we find that it is conserved in all strains tested by microarray. Moreover, a number of genes involved in the type IV secretion system, which is related to horizontal DNA transfer between H. pylori strains, were identified in the comparative analysis of the strain-specific genes. These findings may provide insight into new biomarkers for the prediction of gastric diseases

Drugs and herbs given to prevent hepatotoxicity of tuberculosis therapy: systematic review of ingredients and evaluation studies

Background: Drugs to protect the liver are frequently prescribed in some countries as part of treatment for tuberculosis. The biological rationale is not clear, they are expensive and may do harm. We conducted a systematic review to a) describe the ingredients of "liver protection drugs"; and b) compare the evidence base for the policy against international standards. Methods: We searched international medical databases (MEDLINE, EMBASE, LILACS, CINAHL, Cochrane Central Register of Controlled Trials, and the specialised register of the Cochrane Infectious Diseases Group) and Chinese language databases (CNKI, VIP and WanFang) to April 2007. Our inclusion criteria were research papers that reported evaluating any liver protection drug or drugs for preventing liver damage in people taking anti-tuberculosis treatment. Two authors independently categorised and extracted data, and appraised the stated methods of evaluating their effectiveness. Results: Eighty five research articles met our inclusion criteria, carried out in China (77), India (2), Russia (4), Ukraine (2). These articles evaluated 30 distinct types of liver protection compounds categorised as herbal preparations, manufactured herbal products, combinations of vitamins and other non-herbal substances and manufactured pharmaceutical preparations. Critical appraisal of these articles showed that all were small, poorly conducted studies, measuring intermediate outcomes. Four trials that were described as randomised controlled trials were small, had short follow up, and did not meet international standards. Conclusion: There is no reliable evidence to support prescription of drugs or herbs to prevent liver damage in people on tuberculosis treatment

Comparative mRNA and microRNA Expression Profiling of Three Genitourinary Cancers Reveals Common Hallmarks and Cancer-Specific Molecular Events

Genome-wide gene expression profile using deep sequencing technologies can drive the discovery of cancer biomarkers and therapeutic targets. Such efforts are often limited to profiling the expression signature of either mRNA or microRNA (miRNA) in a single type of cancer.Here we provided an integrated analysis of the genome-wide mRNA and miRNA expression profiles of three different genitourinary cancers: carcinomas of the bladder, kidney and testis.Our results highlight the general or cancer-specific roles of several genes and miRNAs that may serve as candidate oncogenes or suppressors of tumor development. Further comparative analyses at the systems level revealed that significant aberrations of the cell adhesion process, p53 signaling, calcium signaling, the ECM-receptor and cell cycle pathways, the DNA repair and replication processes and the immune and inflammatory response processes were the common hallmarks of human cancers. Gene sets showing testicular cancer-specific deregulation patterns were mainly implicated in processes related to male reproductive function, and general disruptions of multiple metabolic pathways and processes related to cell migration were the characteristic molecular events for renal and bladder cancer, respectively. Furthermore, we also demonstrated that tumors with the same histological origins and genes with similar functions tended to group together in a clustering analysis. By assessing the correlation between the expression of each miRNA and its targets, we determined that deregulation of 'key' miRNAs may result in the global aberration of one or more pathways or processes as a whole.This systematic analysis deciphered the molecular phenotypes of three genitourinary cancers and investigated their variations at the miRNA level simultaneously. Our results provided a valuable source for future studies and highlighted some promising genes, miRNAs, pathways and processes that may be useful for diagnostic or therapeutic applications

Digital gene expression tag profiling of bat digits provides robust candidates contributing to wing formation

Abstract Background As the only truly flying mammals, bats use their unique wing - consisting of four elongated digits (digits II-V) connected by membranes - to power their flight. In addition to the elongated digits II-V, the forelimb contains one shorter digit (digit I) that is morphologically similar to the hindlimb digits. Here, we capitalized on the morphological variation among the bat forelimb digits to investigate the molecular mechanisms underlying digit elongation and wing formation. Using next generation sequencing technology, we performed digital gene expression tag profiling (DGE-tag profiling) of developing digits in a pooled sample of two Myotis ricketti and validated our sequencing results using real-time quantitative PCR (RT-qPCR) of gene expression in the developing digits of two Hipposideros armiger. Results Among hundreds of genes exhibiting significant differences in expression between the short and long digits, we highlight 14 genes most related to digit elongation. These genes include two Tbx genes (Tbx3 and Tbx15), five BMP pathway genes (Bmp3, RGMB, Smad1, Smad4 and Nog), four Homeobox genes (Hoxd8, Hoxd9, Hoxa1 and Satb1), and three other genes (Twist1, Tmeff2 and Enpp2) related to digit malformations or cell proliferation. In addition, our results suggest that Tbx4 and Pitx2 contribute to the morphological similarity and five genes (Acta1, Tnnc2, Atp2a1, Hrc and Myoz1) contribute to the functional similarity between the thumb and hindlimb digits. Conclusions Results of this study not only implicate many developmental genes as robust candidates underlying digit elongation and wing formation in bats, but also provide a better understanding of the genes involved in autopodial development in general

How did the Dabie Orogen collapse? Insights from 3-D magnetotelluric imaging of profile data

The Dabie Orogen is a key part of the Central Orogen of China and is well known because of its exposures to high- and ultrahigh-pressure metamorphic rocks. It has been proposed to have formed by continent-continent collision between the Yangtze and North China blocks in the Middle-to-Late Triassic and to have collapsed in the middle of the Early Cretaceous. However, there are few signatures in the lithospheric architecture that might constrain the scale of the orogenic collapse; as a result there has been a long-term debate on its origin. A 300 km long broadband magnetotelluric transect perpendicular to a major collapsed structure has been completed to find some possible clues to the mechanisms of the orogenic collapse. The inverted resistivity cross section from 3-D inversion of magnetotelluric profile data refines the postcollision lithospheric structure and in particular identifies domains of refertilized and depleted lithospheric mantle and isolated midcrustal low-velocity and high-conductivity zones. A correlation between voluminous surface magmatism in the Early Cretaceous and deep refertilized lithospheric mantle is illuminated by elevated electrical conductivity. We suggest that the lowermost crust was removed by delamination beneath the eastern Dabie during the orogenic collapse, while beneath the Tongbai-Xinyang Terrain residual cratonic crust is underlain by depleted lithospheric mantle with relatively high resistivity. The isolated low-velocity and high-conductivity zones in the middle crust have been ascribed to shear-promoted graphitic films which were destroyed by local granitic intrusions around 134 to 125 Ma. This lithospheric process can be attributed to far-field effects, such as refertilization in the lower lithospheric mantle, promoted by upwelling of the asthenosphere and related fluids, during Paleo-Pacific subduction beneath the Euro-Asian continent.17 page(s

Ultrasound‐Assisted Liquid‐Phase Synthesis and Mechanical Properties of Aluminum Matrix Nanocomposites Incorporating Boride Nanocrystals

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Archean mantle contributes to the genesis of chromitite in the Palaeozoic Sartohay ophiolite, Asiatic Orogenic Belt, northwestern China

Podiform chromitites in ophiolite usually are interpreted as the crystallization products of mafic magmas, contemporaneous with the generation of the ophiolite at mid-oceanic ridges or back-arc spreading centres. However, the real ages of the chromitites can rarely be determined directly, because their chemistry provides few opportunities for geochronology. Here we employ the ¹⁸⁷Re-Os¹⁸⁸ decay system (N-TIMS) to date the chromitite and a cross-cutting troctolite in the Sartohay ophiolite, northwestern China, and we have dated zircons separated from the troctolite by SHRIMP U-Pb methods. Inherited zircons from the troctolite yield a lower intercept age of 0.48 ± 0.08 Ga and an upper intercept age of 2.28 ± 0.11 Ga; two concordant grains give ages >2.4 Ga. Whole-rock Re-Os data for the troctolites and chromites plot between 2.45 Ga and 0.43 Ga reference isochrons. Plots of T-MA VS ¹⁸⁷Os/¹⁸⁸Os suggest mixing between ultra-depleted chromitite and suprachondritic troctolite, mainly affecting the ¹⁸⁷Os/¹⁸⁸Os of the troctolites; subsets of troctolite samples scatter around reference isochrons with ages of 0.4-0.5 Ga. The zircon data and the Re/Os data are consistent with published Sm-Nd evidence that the troctolites, and hence the Sartohay ophiolite, were formed in Palaeozoic time. However, the ¹⁸⁷Os/¹⁸⁸Os compositions of the chromites (0.1109 ± 4 to 0.1249 ± 5), give Neo-Proterozoic to Paleo-Archean model ages (T-MA = 0.8-3.5 Ga), indicating extraction from the primitive mantle as early as 3.5 Ga, some 3 Ga before the formation of the Sartohay ophiolite. A Re-Os apparent isochron age (2.45 Ga), the old T-MA model ages and the ancient zircon ages (>2.4 Ga) all are consistent with part formation of the Sartohay chromitite in Archean time, and then reworked in the Palaeozoic time. We suggest that a volume of early Archean depleted mantle remained within the Siberian lithospheric mantle for 2.5-3.0 Ga; it later became portions of the mantle wedge above the Paleozoic subduction zone of the Paleo-Asian Ocean, and ultimately was incorporated into the overthrust ophiolite.8 page(s