人葡萄膜黑色素瘤组织中差异表达基因及相关代谢通路的分析

背景人葡萄膜黑色素瘤（UM）组织与正常组织中存在差异表达基因，但国外不同文献报道的结果不尽一致，而国内对人UM基因表达的改变及其相关的作用通路的研究较少。目的应用基因芯片技术探讨人UM中差异表达的基因，分析差异基因参与的重要信号通路。方法收集在北京同仁医院因原发性UM行眼球摘除并经组织病理学证实为梭形细胞型UM的组织标本4例，以正常供体葡萄膜组织作为对照组。利用HumanGenomeU133Plus2．0芯片技术筛查2种组织中基因表达的差异，并使用GOEAST富集分析软件对差异基因的重要生物学功能及参与的通路进行分析。结果与正常的葡萄膜组织对比，人UM中有4165个差异基因，占12．50％，其中包含1236个上调基因和2929个下调基因，分别占3．71％和8．79％。人UM组织中上调5倍或以上基因为113个，下调50％的基因为1053个；上调10倍或以上的基因为21个，下调90％或以上的基因为422个；上调50倍或以上的基因为1个，下调98％或以上的基因为33个；上调100倍或以上的基因为1个，下调99％或以上的基因为5个。按功能学分类表明，差异表达基因中包括细胞分化与增生基因、发育相关基因、细胞黏附相关基因、免疫应答基因、调节转录基因、信号转导相关基因、凋亡以及抗凋亡相关基因等；差异表达基因参与的代谢通路涉及血管形成过程的代谢通路、细胞周期相关的蛋白激酶通路以及B淋巴细胞或T淋巴细胞的代谢通路等。结论人UM组织与正常人葡萄膜组织中基因表达谱明显不同，这些差异表达的基因除参与血管生成、激酶通路等已知的UM发育有关的代谢通路外，还涉及免疫系统的变化。人UM的发生和进展是多种基因、多种通路共同作用的结果。

Plant phylogenomics based on genome-partitioning strategies:Progress and prospects

The rapid expansion of next-generation sequencing （NGS） has generated a powerful array of approaches to address fundamental questions in biology. Several genome-partitioning strategies to sequence selected subsets of the genome have emerged in the fields of phylogenomics and evolutionary genomics. In this review, we summarize the applications, advantages and limitations of four NGS-based genome- partitioning approaches in plant phylogenomics： genome skimming, transcriptome sequencing （RNA- seq）, restriction site associated DNA sequencing （RAD-Seq）, and targeted capture （Hyb-seq）. Of these four genome-partitioning approaches, targeted capture （especially Hyb-seq） shows the greatest promise for plant phy^ogenetics over the next fex~ years. This reviex~ wi~ aid ~esea^chers in their selection of appropriate genome-partitioning approaches to address questions of evolutionary scale, where we anticipate continued development and expansion ofwhole-genome sequencing strategies in the fields of plant phylogenomics and evolutionary biology research.

Clinicopathological significance of LRP16 protein in 336 gastric carcinoma patients

AIM： To investigate the expression of leukemia related protein 16 （LRP16）, and the possible relationship between LRP16 expression and clinicopathological indices in 336 gastric carcinoma patients. METHODS： Immunohistochemistry was used to detect LRP16 expression in 336 cases of paraffin-embedded gastric carcinoma tissues and 60 cases of distal normal mucosa. The relationships between LRP16 expression and patients＇ age, tumor size, histological grade, clinical stage, metastatic status and prognosis were analysed. RESULTS： The expression of LRP16 was 58.6% （197/336） in gastric carcinoma and 31.7% （19/60） in distal normal gastric mucosa. The expression of LRP16 in carcinoma was significantly higher than that in normal mucosa tissues （x^2 = 14.929, P = 0.001）. LRP16 protein expression was found in 44.1% （63/143） carcinomas at stage Ⅰ and Ⅱ, and 69.4% （134/193） carcinomas at stage Ⅲ and Ⅳ （Z2 = 21.804, P = 0.001）, and in 56.9% （182/320） of cancers without metastasis but 93.8% （15/16） of those with metastasis （2 = 8.543, P = 0.003）. The expression of LRP16 was correlated with tumor size, infiltrative depth, clinical stage, lymphatic invasion and distant metastasis （all P 〈 0.05）. Follow-up data showed that there was a significant difference in median survival time between cancer patients with expression of LRP16 （27.0 mo） and those without （48.0 mo, Log rank =31.644, P = 0.001）. CONCLUSION： The expression of LRP16 may be associated with invasion, metastasis and prognosis of gastric cancer.

Comparative genomics of Helicobacter pylori

Genomic sequences have been determined for a number of strains of Helicobacter pylori （H pylori） and related bacteria. With the development of microarray analysis and the wide use of subtractive hybridization techniques, comparative studies have been carried out with respect to the interstrain differences between H pylori and inter-species differences in the genome of related bacteria. It was found that the core genome of H pylori constitutes 1111 genes that are determinants of the species properties. A great pool of auxiliary genes are mainly from the categories of cag pathogenicity islands, outer membrane proteins, restriction-modification system and hypothetical proteins of unknown function. Persistence of H pylori in the human stomach leads to the diversification of the genome. Comparative genomics suggest that a host jump has occurs from humans to felines. Candidate genes specific for the development of the gastric diseases were identified. With the aid of proteomics, population genetics and other molecular methods, future comparative genomic studies would dramatically promote our understanding of the evolution, pathogenesis and microbiology of Hpylori.

Aberrant methylation of the 3q25 tumor suppressor gene PTX3 in human esophageal squamous cell carcinoma

AIM:To identify the novel methylation-silenced gene pentraxin 3(PTX3) in esophageal squamous cell carcinoma(ESCC).METHODS:PTX3 mRNA expression was examined in six human ESCC cell lines,one human immortalized normal esophageal epithelial cell line,primary ESCC tumor tissue,and paired adjacent nontumor tissue using reverse transcription polymerase chain reaction(RTPCR).Semi-quantitative immunohistochemistry was used to examine cellular localisation and protein levels.Methylation specific PCR and bisulphite genomic sequencing were employed to investigate the methylation of the candidate gene.RESULTS:In the majority of ESCC cell lines,we found that PTX3 expression was down-regulated due to gene promoter hypermethylation,which was further confirmed by bisulphite genomic sequencing.Demethylation treatment with 5-aza-2'-deoxycytidine restored PTX3 mRNA expression in ESCC cell lines.Methylation was more common in tumor tissues(85%) than in adjacent nontumor tissues(25%)(P < 0.01).CONCLUSION:PTX3 is down-regulated through promoter hypermethylation in ESCC,and could potentially serve as a biomarker of ESCC.

Variations in Laboratory-Scale Actinomycete Communities Exposed to Cadmium as Assessed by Denaturing Gradient Gel Electrophoresis Profiles

The actinomycete populations and functions in cadmium （Cd） contaminated soil were investigated by the cultivation- independent molecular methods. The genomic DNA was extracted and purified from soil adulterated with various con- centrations of Cd in the laboratory. The partial 16S rDNA genes were amplified by polymerase chain reaction （PCR） using specific primers bound to evolutionarily conserved regions within these actinomycete genes. The diversity in PCR- amplified products, as measured by denaturing gradient gel electrophoresis （EGGE）, was used as a genetic fingerprint of the population. Principle component analysis and Shannon-Weaver diversity index （H） analyses were used to analyze the DGGE results. Results showed that the two principal components accounted for only a low level of the total variance. The value H in contaminated soil was lower than that in the control at later stages of cultivation, whereas at earlier stages it was higher. Among the six sampling time points, the first, fifth and sixth weeks had the highest values of H. Significantly negative correlations between bioavallable Cd concentration and H values existed in the samples from weeks 2 （R = 0.929, P 〈 0.05） and 4 （R = 0.909, P 〈 0.05）. These results may shed light on the effect of Cd on the soil environment and the chemical behavior and toxicity of Cd to actinomycetes.

Navigating the currents of seascape genomics： how spatial analyses can augment population genomic studies

Population genomic approaches are making rapid inroads in the study of non-model organisms, including marine taxa. To date, these marine studies have predominantly focused on rudimentary metrics describing the spatial and environmental context of their study region （e.g., geographical distance, average sea surface temperature, average salinity）. We contend that a more nuanced and considered approach to quantifying seascape dynamics and patterns can strengthen population genomic investigations and help identify spatial, temporal, and environmental factors associated with differing selective regimes or demographic histories. Nevertheless, approaches for quantifying marine landscapes are complicated. Characteristic features of the marine environment, including pelagic living in flowing water （experienced by most marine taxa at some point in their life cycle）, require a well-designed spatial-temporal sampling strategy and analysis. Many genetic summary statistics used to describe populations may be inappropriate for marine species with large population sizes, large species ranges, stochastic recruitment, and asymmetrical gene flow. Finally, statistical approaches for testing associations between seascapes and population genomic patterns are still maturing with no single approach able to capture all relevant considerations. None of these issues are completely unique to marine systems and therefore similar issues and solutions will be shared for many organisms regardless of habitat. Here, we outline goals and spatial approaches for land- scape genomics with an emphasis on marine systems and review the growing empirical literature on seascape genomics. We review established tools and approaches and highlight promising new strategies to overcome select issues including a strategy to spatially optimize sampling. Despite the many challenges, we argue that marine systems may be especially well suited for identifying candidate genomic regions under environmentally mediated selection and that seascape genomic approaches are especially useful for identifying robust locus-by-environment associations.

Sequence assembly using next generation sequencing data —challenges and solutions

Sequence assembling is an important step for bioinformatics study.With the help of next generation sequencing(NGS)technology,high throughput DNA fragment(reads)can be randomly sampled from DNA or RNA molecular sequence.However,as the positions of reads being sampled are unknown,assembling process is required for combining overlapped reads to reconstruct the original DNA or RNA sequence.Compared with traditional Sanger sequencing methods,although the throughput of NGS reads increases,the read length is shorter and the error rate is higher.It introduces several problems in assembling.Moreover,paired-end reads instead of single-end reads can be sampled which contain more information.The existing assemblers cannot fully utilize this information and fails to assemble longer contigs.In this article,we will revisit the major problems of assembling NGS reads on genomic,transcriptomic,metagenomic and metatranscriptomic data.We will also describe our IDBA package for solving these problems.IDBA package has adopted several novel ideas in assembling,including using multiple k,local assembling and progressive depth removal.Compared with existence assemblers,IDBA has better performance on many simulated and real sequencing datasets.

Review:Advances in methodology of DNA methylation assay

DNA methylation is one of the most signaficant epigenetic events which greatly influence gene activation, gene imprinting, chromatin stability, and so on. The level of methylation in genome and certain regions should be in a normal range, because any variation would cause physiological dysfunction. In account of essential roles of DNA methylation in the living system, the detection of methylation in both overall genome and specific positions has drawn great interest. So far many biological and chemical methods have been developed to detect DNA methylation. Herein, we summerize some novel methods mainly based on chemical modification and analytic methods in DNA detection.