Evaluation of next-generation sequencing software in mapping and assembly

Next-generation high-throughput DNA sequencing technologies have advanced progressively in sequence-based genomic research and novel biological applications with the promise of sequencing DNA at unprecedented speed. These new non-Sanger-based technologies feature several advantages when compared with traditional sequencing methods in terms of higher sequencing speed, lower per run cost and higher accuracy. However, reads from next-generation sequencing (NGS) platforms, such as 454/Roche, ABI/SOLiD and Illumina/Solexa, are usually short, thereby restricting the applications of NGS platforms in genome assembly and annotation. We presented an overview of the challenges that these novel technologies meet and particularly illustrated various bioinformatics attempts on mapping and assembly for problem solving. We then compared the performance of several programs in these two fields, and further provided advices on selecting suitable tools for specific biological applications.published_or_final_versio

Gut microbiome is associated with metabolic syndrome accompanied by elevated gamma-glutamyl transpeptidase in men

It is predicted that by 2035, metabolic syndrome (MS) will be found in nearly more than half of our adult population, seriously affecting the health of our body. MS is usually accompanied by the occurrence of abnormal liver enzymes, such as elevated gamma-glutamyl transpeptidase (GGT). More and more studies have shown that the gut microbiota is involved in MS; however, the correlation between gut microbiota and MS with elevated GGT has not been studied comprehensively. Especially, there are few reports about its role in the physical examination of the population of men with MS and elevated GGT. By using the whole-genome shotgun sequencing technology, we conducted a genome-wide association study of the gut microbiome in 66 participants diagnosed as having MS accompanied by high levels of GGT (case group) and 66 participants with only MS and normal GGT level (control group). We found that the number of gut microbial species was reduced in participants in the case group compared to that of the control group. The overall microbial composition between the two groups is of significant difference. The gut microbiota in the case group is characterized by increased levels of “harmful bacteria” such as Megamonas hypermegale, Megamonas funiformis, Megamonas unclassified, Klebsiella pneumoniae, and Fusobacterium mortiferum and decreased levels of “beneficial bacteria” such as Faecalibacterium prausnitzii, Eubacterium eligens, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bacteroides dorei, and Alistipes putredinis. Moreover, the pathways of POLYAMSYN-PWY, ARG+POLYAMINE-SYN, PWY-6305, and GOLPDLCAT-PWY were also increased in the case group, which may play a role in the elevation of GGT by producing amine, polyamine, putrescine, and endogenous alcohol. Taken together, there are apparent changes in the composition of the gut microbiome in men with MS and abnormal GGT levels, and it is high time to discover specific gut microbiome as a potential therapeutic target in that population. More in-depth studies of relevant mechanism could offer some new methods for the treatment of MS with elevated GGT

A First Generation Microsatellite- and SNP-Based Linkage Map of Jatropha

Jatropha curcas is a potential plant species for biodiesel production. However, its seed yield is too low for profitable production of biodiesel. To improve the productivity, genetic improvement through breeding is essential. A linkage map is an important component in molecular breeding. We established a first-generation linkage map using a mapping panel containing two backcross populations with 93 progeny. We mapped 506 markers (216 microsatellites and 290 SNPs from ESTs) onto 11 linkage groups. The total length of the map was 1440.9 cM with an average marker space of 2.8 cM. Blasting of 222 Jatropha ESTs containing polymorphic SSR or SNP markers against EST-databases revealed that 91.0%, 86.5% and 79.2% of Jatropha ESTs were homologous to counterparts in castor bean, poplar and Arabidopsis respectively. Mapping 192 orthologous markers to the assembled whole genome sequence of Arabidopsis thaliana identified 38 syntenic blocks and revealed that small linkage blocks were well conserved, but often shuffled. The first generation linkage map and the data of comparative mapping could lay a solid foundation for QTL mapping of agronomic traits, marker-assisted breeding and cloning genes responsible for phenotypic variation

論《周禮》“以為民極”開展的民本思想

從《尚書》已可見禹繼承堯、舜以來傳賢的概念，提出“民惟邦本，本固邦寧”的政治概念，正式開啟民本思想之先聲，也成為後代施政規劃所取法的核心。《周禮》即借用《尚書‧洪範》“建用皇極”的概念，在“惟王建國，辨方正位，體國經野，設官分職，以為民極”的全書宗旨中，將“以為民極”的民本概念視為施政者努力開創全民福祉的核心。由於以民為本的思想，主要藉由養民、教民、治民三大方面體現之，因而本文再分別從此三大方面體現其所開展的民本思想。最後，總結《周禮》以發展民生經濟奠定王朝的根基，再以德禮之教締造講求道德的社會團體，並以“五刑”輔助治理邦國，共同促成理想社會的達成。 Chinese people-oriented thought originated with the abdication stories of Yao (堯), Shun (舜) and Yu (禹). The political concept that “people are the basis of the state and the state will be tranquil if the basis is firm” in Shangshu (尚書, The Book of Ancient Documents), evolved into the central policy of s government of ancient China. Taking the concept of Jianyonghuangji (建用皇極) from Hongfan (洪範) in The Book of Ancient Documents, Zhouli developed the idea of Yiweiminji which meant that the rulers should devote themselves to the welfare of all people. This paper will shed light on people-oriented thought through the three main aspects of Yiweiminji in Zhouli: nurturing the people, educating the people and governing the people. According to these ideas, rulers should make the livelihood and benefit of all people as the foundation of the state, should improve moral standards by the teachings of virtue and rituals, and promote social order through Wuxing (五刑, five punishments) to create an ideal society