A unified sampling approach for multipoint analysis of qualitative and quantitative traits in sib pairs

Recent advances in molecular biology have enhanced the opportunity to conduct multipoint mapping for complex diseases. Concurrently, one sees a growing interest in the use of quantitative traits in linkage studies. Here, we present a multipoint sib-pair approach to locate the map position (tau) of a trait locus that controls the observed phenotype (qualitative or quantitative), along with a measure of statistical uncertainty. This method builds on a parametric representation for the expected identical-by-descent statistic at an arbitrary locus, conditional on an event reflecting the sampling scheme, such as affected sib pairs, for qualitative traits, or extreme discordant (ED) sib pairs, for quantitative traits. Our results suggest that the variance about tau&d4;, the estimator of tau, can be reduced by as much as 60%-70% by reducing the length of intervals between markers by one half. For quantitative traits, we examine the precision gain (measured by the variance reduction in tau&d4;) by genotyping extremely concordant (EC) sib pairs and including them along with ED sib pairs in the statistical analysis. The precision gain depends heavily on the residual correlation of the quantitative trait for sib pairs but considerably less on the allele frequency and exact genetic mechanism. Since complex traits involve multiple loci and, hence, the residual correlation cannot be ignored, our finding strongly suggests that one should incorporate EC sib pairs along with ED sib pairs, in both design and analysis. Finally, we empirically establish a simple linear relationship between the magnitude of precision gain and the ratio of the number of ED pairs to the number of EC pairs. This relationship allows investigators to address issues of cost effectiveness that are due to the need for phenotyping and genotyping subjects.     

Dynamic 1H NMR-based extracellular metabonomic analysis of oligodendroglia cells infected with herpes simplex virus type 1

Herpes simplex virus type 1 (HSV-1) is a large, neurotropic, double-stranded DNA virus that establishes a lifelong latent infection in neurons and glial cells. Previous studies reveal that several metabolic perturbations are associated with HSV-1 infection. However, the extracellular metabolic alterations associated with HSV-1 infection have not been systematically profiled in human cells. Here, a proton nuclear magnetic resonance-based metabonomic approach was applied to differentiate the extracellular metabonomic profiles of HSV-1 infected human oligodendroglia cells (n = 18) and matched control cells (n = 18) at three time points (12, 24, and 36 h post-infection). Resulting spectra were analyzed by chemometric and statistical methods. Metabonomic profiling revealed perturbations in 21 extracellular metabolites. Partial least squares discriminant analysis demonstrated that the whole metabolic patterns enabled statistical discrimination between HSV-1 infected human oligodendroglia cells and control cells. Eight extracellular metabolites, seven of which were amino acids, were primarily responsible for score plot discrimination between HSV-1 infected human oligodendroglia cells and control cells at 36 h post-infection: alanine, glycine, isoleucine, leucine, glutamate, glutamine, histidine, and lactate. HSV-1 infection alters amino acid metabolism in human oligodendroglia cells cultured in vitro. HSV-1 infection may disturb these host cellular pathways to support viral replication. Through elucidating the extracellular metabolic changes incident to HSV-1 infection, this study also provides future directions for investigation into the pathogenic mechanism of HSV-1.     

Induction of multiple cytotoxic T lymphocyte responses in mice by a multiepitope DNA vaccine against dengue virus serotype 1

Dengue virus (DENV) is still a major threat to human health in most tropical and subtropical countries and regions. In the present study, a multi‐epitope DNA vaccine that encodes 15 immunogenic and conserved HLA‐A*0201‐, HLA‐A*1101‐, HLA‐A*2402‐restricted CTL epitopes from DENV serotype 1 (DENV‐1) was constructed based on the eukaryotic expressing plasmid pcDNA^TM3.1/myc‐His(?) A. Immunization of HLA‐A*0201, HLA‐A*1101 and HLA‐A*2402 transgenic mice with the recombinant plasmid pcDNA^TM3.1/myc‐His(?) A‐DENV‐1‐Meg resulted in significantly greater IFN‐γ‐secreting T‐cell responses against most (14/15) CTL epitopes than occurred in mice immunized with the empty plasmid pcDNA^TM3.1/myc‐His(?) A. Additionally, the epitope‐specific T cells directed to some epitopes secreted not only IFN‐γ but also IL‐6 and/or TNF‐α. Finally, the induced epitope‐specific T cells also efficiently lysed epitope‐pulsed splenocytes and DENV‐1‐infected splenic monocytes. The present study confirms the immunogenicity of multi‐epitope DENV vaccine, suggesting that it may contribute to the development of a universal DENV vaccine.

     

采用蛋白质组学技术筛选大肠癌转移相关蛋白

采用对同一亲本来源、不同转移潜能细胞株SW480和SW620的蛋白质表达谱进行双向凝胶电泳和质谱技术分析,并在蛋白质和mRNA水平进行验证,成功鉴定了10个大肠癌转移相关蛋白,其中SW620细胞株表达上调的蛋白质有磷酸甘油酸变位酶1,磷脂酰乙醇胺结合蛋白和高迁移率族蛋白B-1,而热休克蛋白27,膜联蛋白Ⅰ,甲硫腺苷磷酸化酶,切丝蛋白1和表皮型脂肪酸结合蛋白在SW620中表达下调.大多数差异蛋白质功能涉及肿瘤细胞生长、运动、粘附、凋亡等过程,研究结果为阐明大肠癌转移机制及寻找预测大肠癌转移的潜在标志物提供了理论依据.     

Comparison of bacterial diversity along the human intestinal tract by direct cloning and sequencing of 16S rRNA genes

Bacterial diversity of the mucosal biopsies from human jejunum, distal ileum, ascending colon and rectum were compared by analysis of PCR-amplified 16S rDNA clone libraries. A total of 347 clones from the mucosal biopsies were partially sequenced and assigned to six phylogenetic phyla of the domain Bacteria: Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, Verrucomicrobia, and Actinobacteria. The jejunum sample had least microbial diversity compared to the other samples and a trend towards highest diversity in ascending colon was observed. The clone libraries of distal ileum, ascending colon and rectum were not significantly different from each other (P>0.0043), but they differed significantly from the jejunum library (P=0.001). The population of sequences retrieved from jejunal biopsies was dominated by sequences closely related to Streptococcus (67%), while the population of sequences derived from distal ileum, ascending colon and rectum were dominated by sequences affiliated with Bacteroidetes (27-49%), and Clostridium clusters XIVa (20-34%) and IV (7-13%). The results indicate that the microbial community in jejunum is different from those in distal ileum, ascending colon and rectum, and that the major phylogenetic groups are similar from distal ileum to rectum.     

Aminoacyl-tRNA formation in the extreme thermophile Thermus thermophilus

Thermophilic organisms must be capable of accurate translation at temperatures in which the individual components of the translation machinery and also specific amino acids are particularly sensitive. Thermus thermophilus is a good model organism for studies of thermophilic translation because many of the components in this process have undergone structural and biochemical characterization. We have focused on the pathways of aminoacyl-tRNA synthesis for glutamine, asparagine, proline, and cysteine. We show that the T. thermophilus prolyl-tRNA synthetase (ProRS) exhibits cysteinyl-tRNA synthetase (CysRS) activity although the organism also encodes a canonical CysRS. The ProRS requires tRNA for cysteine activation, as is known for the characterized archaeal prolyl-cysteinyl-tRNA synthetase (ProCysRS) enzymes. The heterotrimeric T. thermophilus aspartyl-tRNA(Asn) amidotransferase can form Gln-tRNA in addition to Asn-tRNA: however, a 13-amino-acid C-terminal truncation of the holoenzyme A subunit is deficient in both activities when assayed with homologous substrates. A survey of codon usage in completed prokaryotic genomes identified a higher Glu:Gln ratio in proteins of thermophiles compared to mesophiles.     

Tissue microarray study for classification of breast tumors

Clinical and pathological heterogeneity of breast cancer hinders selection of appropriate treatment for individual cases. Molecular profiling at gene or protein levels may elucidate the biological variance of tumors and provide a new classification system that correlates better with biological, clinical and prognostic parameters. We studied the immunohistochemical profile of a panel of seven important biomarkers using tumor tissue arrays. The tumor samples were then classified with a monothetic (binary variables) clustering algorithm. Two distinct groups of tumors are characterized by the estrogen receptor (ER) status and tumor grade (p = 0.0026). Four biomarkers, c-erbB2, Cox-2, p53 and VEGF, were significantly overexpressed in tumors with the ER-negative (ER-) phenotype. Eight subsets of tumors were further identified according to the expression status of VEGF, c-erbB2 and p53. The malignant potential of the ER-/VEGF+ subgroup was associated with the strong correlations of Cox-2 and c-erbB2 with VEGF. Our results indicate that this molecular classification system, based on the statistical analysis of immunohistochemical profiling, is a useful approach for tumor grouping. Some of these subgroups have a relative genetic homogeneity that may allow further study of specific genetically-controlled metabolic pathways. This approach may hold great promise in rationalizing the application of different therapeutic strategies for different subgroups of breast tumors.