A novel protein structural classes prediction method based on predicted secondary structure

Knowledge of structural classes plays an important role in understanding protein folding patterns. In this paper, features based on the predicted secondary structure sequence and the corresponding E–H sequence are extracted. Then, an 11-dimensional feature vector is selected based on a wrapper feature selection algorithm and a support vector machine (SVM). Among the 11 selected features, 4 novel features are newly designed to model the differences between α/β class and α + β class, and other 7 rational features are proposed by previous researchers. To examine the performance of our method, a total of 5 datasets are used to design and test the proposed method. The results show that competitive prediction accuracies can be achieved by the proposed method compared to existing methods (SCPRED, RKS-PPSC and MODAS), and 4 new features are demonstrated essential to differentiate α/β and α + β classes. Standalone version of the proposed method is written in JAVA language and it can be downloaded from http://web.xidian.edu.cn/slzhang/paper.html.     

Association of Genetic Variants in the Adiponectin Gene with Metabolic Syndrome: A Case-Control Study and a Systematic Meta-Analysis in the Chinese Population

Background

The prevalence of metabolic syndrome has been rising worldwide, including in China, but knowledge on specific genetic determinants of metabolic syndrome is very limited. A number of studies have reported that polymorphisms in the ADIPOQ gene are associated with metabolic syndrome in Chinese Han populations. However, data is still conflicting. The objective of this study was to examine the associations of the adiponectin genetic variants with metabolic syndrome by a case-control study and meta-analyses in Chinese.

Methods

We first investigated the association of ADIPOQ rs2241766 (+45T>G in exon 2), rs266729 (−11377C>G in promoter) and rs1501299 (+276G>T in intron 2) polymorphisms with metabolic syndrome in a Hubei Han Chinese population with 322 metabolic syndrome patients and 161 normal controls recruited from the Yichang, Hubei. Then we comprehensively reviewed the association between ADIPOQ rs2241766/rs266729/rs1501299 and metabolic syndrome in the Chinese populations via a meta-analysis. The strength of association was assessed by odds ratios (ORs) with 95% confidence intervals (CI).

Results

The G allele frequency of rs2241766 in metabolic syndrome patients was significantly higher than those of controls group (29.8% vs 23.3%, OR = 1.40, P = 0.033). The logistic regression analysis adjusted by gender and age showed a nominally significant association for rs2241766 GG+GT genotype (P = 0.065, OR = 1.55) and rs1501299 GG genotype in recessive model (OR = 1.54, P = 0.066). However, no association was observed for rs266729 in our sample. We identified thirteen studies for rs2241766 (2,684 metabolic syndrome patients and 2,864 controls), three studies for rs266729, and eleven studies for rs1501299 (2,889 metabolic syndrome patients and 3,304 controls) in Chinese. Meta-analysis indicated significant associations for the rs2241766 G allele (OR = 1.14, 95%CI = 1.05–1.24, P = 0.003), rs266729 GG+GT genotypes (OR = 0.80, 95%CI = 0.68–0.92, P = 0.003) and rs1501299 GG+TG genotypes (OR = 1.42, 95%CI 1.16–1.75, P = 0.001).

Conclusions

Our results demonstrated ADIPOQ as a pleiotropic locus for metabolic syndrome and its components in the Han Chinese population.     

“雄茭”、灰茭形成规律的初步研究

茭白栽培过程中,常会出现“雄茭”和灰茭分蘖。根据对茭白的形态学观察,认识到:“雄茭”分蘖的产生是分蘖期母茎中茭白黑粉菌菌丝未能入侵新生分蘖腋芽而导致的结果;灰茭分蘖是因其菌丝的潜育期比正常茭短,故在苗端的膨大部分较早地产生了不同程度的黑粉孢子堆。     

Multimeric BLM is dissociated upon ATP hydrolysis and functions as monomers in resolving DNA structures

Bloom (BLM) syndrome is an autosomal recessive disorder characterized by an increased risk for many types of cancers. Previous studies have shown that BLM protein forms a hexameric ring structure, but its oligomeric form in DNA unwinding is still not well clarified. In this work, we have used dynamic light scattering and various stopped-flow assays to study the active form and kinetic mechanism of BLM in DNA unwinding. It was found that BLM multimers were dissociated upon ATP hydrolysis. Steady-state and single-turnover kinetic studies revealed that BLM helicase always unwound duplex DNA in the monomeric form under conditions of varying enzyme and ATP concentrations as well as 3′-ssDNA tail lengths, with no sign of oligomerization being discerned. Measurements of ATPase activity further indicated that BLM helicase might still function as monomers in resolving highly structured DNAs such as Holliday junctions and D-loops. These results shed new light on the underlying mechanism of BLM-mediated DNA unwinding and on the molecular and functional basis for the phenotype of heterozygous carriers of BLM syndrome.     

Genome Sequence of Staphylococcus capitis QN1, Which Causes Infective Endocarditis

Staphylococcus capitis is a subtype of coagulase-negative staphylococci (CoNS) which could emerge as a significant pathogen causing infective endocarditis, prosthetic valve endocarditis, and late-onset sepsis. We isolated S. capitis strain QN1 from the skin swab sample of a female. Here we prepared a genome sequence for this strain consisting of 30 contigs totaling 2,430,101 bases and a GC content of 32.76%.     

尿激酶胸腔注入治疗结核包囊性胸腔积液

目的寻求治疗结核包囊性胸腔积液的新方法。方法胸膜活检确诊为结核性胸腔积液并经Ｂ超或胸部Ｘ线证实有粘连包囊的病人１５例,经胸腔内注入尿激酶每次１０万单位,用６０ｍｌ生理盐水稀释,每８～１２ｈ重复,连续５次,每次记录抽取胸水总量,并复查Ｂ超观察粘连包囊情况。对照组为单纯用抗结核治疗及间断抽胸水１５例。结果实验组１３例有效,总有效率８６．７％。对照组２例有效,有效率１３．３％,疗效明显优于对照组（Ｐ＜０．０５）。结论尿激酶胸腔内注入是治疗结核性粘连包囊性胸腔积液的一种安全可靠的新方法。     

人Ⅳ型胶原的提纯及其抗血清制备

采用胃蛋白酶限制性消化,NaCl分级盐析,还原和烷基化反应,纤维素离子交换层析从人胎盘组织分离纯化Ⅳ型胶原.经SDS-PAGE电泳鉴定符合Ⅳ型胶原α肽链电泳带.用纯化的Ⅳ型胶原免疫兔制备出高效价的特异抗血清.