SNP genotyping through the melting analysis of unlabelled oligonucleotide applied on dilute PCR amplicon

Adaptation of DNA melting analysis for polymorphic single nucleotides (SNPs) genotyping using an unlabeled oligonucleotide probe for polymorphic DNAs under the presence of fluorescent DNA binding dye necessitates a reaction condition where the probe efficiently associates with a target strand that is PCR amplified. We present experimental evidence that application of an unlabeled probe to a dilute PCR amplicon provides a condition such that the fluorescent signals gained subsequently by probe melting are sufficient to discriminate allelic identities. This approach is best exploited by adapting the multiplexing PCR technique in order to cover multiple SNPs for given samples. 3′-end modification of the probe is unnecessary as the amplicon dilution step provides a way of inactivating the polymerase through divalent cation chelation. With the use of low-cost reagents and ordinary laboratory equipment, this method offers a rapid, simple and cost-efficient way of SNP genotyping.     

Absence of morningness alleles in non-European populations

ABSTRACT

In spite of suspected circadian differences between different ancestral groups, most human studies have used individuals of European descent. This also applies to three recent genome-wide association studies (GWAS), which pinpointed a number of chronotype loci. We investigated the distribution of these hits in different 1000 Genomes populations. We found 6 out of the 41 alleles previously identified by GWAS in European participants (in the genes RGS16, PER2 and AK5 and between the genes APH1A and CA14) to be absent from some non-European population groups. This highlights the need for ancestral diversity in circadian research and may reflect differences affecting the phenotype of individuals of East Asian ancestry.     

土壤稳定性有机碳组分与优势细菌门类陆向分布及相关性

【目的】为了探究土壤稳定性有机碳组分和优势细菌门类的陆向分布特征及相关性。【方法】本文选择锡林河流域沿着由水及陆的方向依次采集长期性水流、季节性水流、长期性无水流的湿地及旱地土壤,基于国际腐殖物质协会推荐的方法和16SrRNA基因高通量测序技术分别检测土壤稳定性有机碳组分(富里酸、胡敏酸、胡敏素)含量和优势细菌门类的相对丰度,结合Pearson相关性及冗余分析和结构方程模型研究两者的相关性。【结果】三类稳定性有机碳及酸杆菌门、放线菌门、芽单胞菌门呈大致升高的陆向分布趋势,在长期性无水流的旱地土壤中达到峰值;拟杆菌门则呈现降低的陆向分布趋势。结果显示,芽单胞菌门、酸杆菌门和放线菌门作为长期性无水流旱地土壤的优势细菌门类与胡敏酸、胡敏素含量存在显著(P<0.05)或极显著(P<0.01)正相关关系;拟杆菌门作为长期和季节性水流湿地土壤的优势菌门与富里酸、胡敏酸、胡敏素的含量均呈极显著(P<0.01)负相关关系。结构方程模型结果显示,稳定性有机碳组分与优势细菌门类间存在直接和间接作用。【结论】锡林河流域土壤稳定性有机碳组分及优势细菌门类存在陆向分布特征,稳定性有机碳的升高与...     

Molecular dynamics simulation approach for the prediction of transmembrane helix–helix heterodimers assembly

Computational methods are useful to identify favorable structures of transmembrane (TM) helix oligomers when experimental data are not available or when they cannot help to interpret helix-helix association. We report here a global search method using molecular dynamics (MD) simulations to predict the structures of transmembrane homo and heterodimers. The present approach is based only on sequence information without any experimental data and is first applied to glycophorin A to validate the protocol and to the HER2-HER3 heterodimer receptor. The method successfully reproduces the experimental structures of the TM domain of glycophorin A (GpA(TM)) with a root mean square deviation of 1.5 A. The search protocol identifies three energetically stable models of the TM domain of HER2-HER3 receptor with favorable helix-helix arrangement, including right-handed and left-handed coiled-coils. The predicted TM structures exhibit the GxxxG-like motif at the dimer interface which is presumed to drive receptor oligomerization. We demonstrate that native structures of TM domain can be predicted without quantitative experimental data. This search protocol could help to predict structures of the TM domain of HER heterodimer family.     

Microautoradiographic studies on host-parasite interactions II. The exchange of 3H-lysine between Uromyces phaseoli and Phaseolus vulgaris

A new species of anaerobic bacterium that degrades the even-numbered carbon fatty acids, butyrate, caproate and caprylate, to acetate and H₂ and the odd-numbered carbon fatty acids, valerate and heptanoate, to acetate, propionate and H₂ was obtained in coculture with either an H₂-utilizing methanogen or H₂-utilizing desulfovibrio. The organism could be grown only in syntrophic association with the H₂-utilizer and no other energy sources or combination of electron donor and acceptors were utilized. It was a Gram-negative helical rod with 2 to 8 flagella, about 20 nm in diameter, inserted in a linear fashion about 130 nm or more apart along the concave side of the cell. It grew with a generation time of 84 h in co-culture with Methanospirillum hungatii and was present in numbers of at least 4.5×10^-6 per g of anaerobic digestor sludge.     

海南霸王岭热带雨林的种间分离

 基于地理信息系统软件绘制了海南岛霸王岭热带雨林1个0.5 hm2永久样地所有DBH≥1 cm树木的分布图,进而借助最近邻体分析扩展模块判定每个个体的最近邻体植株,并得到每个基株最近邻体种对的距离。采用N×N最近邻体列联表的截表法,研究了这个多物种群落的种间分离。结果表明,随机毗邻种对占优势,正分离种对次之,负分离种对最少。多数灌木和一些小乔木（平均胸径<15 cm）彼此呈正分离,少数负分离;灌木和乔木间的分离关系复杂;大乔木种类（平均胸径≥65 cm）间不存在负分离。种间分离存在种间差异。种间分离与分布格局明显相关,聚集分布的物种与其它物种正分离比例远比随机分布、均匀分布大;相反,聚集分布物种与其它物种负分离比例要比随机分布、均匀分布小。聚集 聚集分布的种对最可能出现正分离;聚集 均匀分布的种对以及随机 随机分布的种对则最可能出现负分离。但是,无论物种的分布格局或种对相对分布格局如何,随机毗邻的种对都占优势。与种间联结不同,种间分离反映的是小尺度的物种空间关系。在此基础上,初步阐述了种间分离的可能原因及其生态学涵义。     

Genetic association of the gene encoding RPGRIP1L with susceptibility to vascular dementia

A previous genome-wide association study (GWAS) failed to discover any nucleotide sequence variant associated with susceptibility to vascular dementia (VaD) and remained a problem of false negatives produced by a low statistical power. The current study was conducted to identify such potential false negatives and to provide comprehensive evidence for the most plausible predisposing genetic factor using large-scale Korean cohorts. We identified the gene encoding retinitis pigmentosa GTPase regulator-interacting protein 1-like (RPGRIP1L) with multiple nucleotide variants associated with susceptibility to VaD by a modest significant threshold (P<10(-4)). Genetic associations were intensively examined with its sequence variants using 207 VaD patients and 207 age- and gender-matched control subjects. Genetic association analysis with dense variants in the region associated with VaD revealed 3 variants (P<0.0017) in strong linkage. Further analysis with VaD-related phenotypes using Korean Association REsource (KARE) cohort data showed that the region of the gene was associated with alanine aminotransferase (ALT), aspartate aminotransferase (AST), and blood pressure (BP) (P<7.6×10(-4)). The current study provided the first evidence of the association between RPGRIP1L gene and susceptibility of VaD. Functional studies are needed to understand underlying biological mechanism of the genetic association.     

Species diversity and abundance of small mammals in Nechisar National Park,Ethiopia

Species diversity and abundance of small mammals were studied in Nechisar National Park, Ethiopia, during August 2008 – March 2009. Twenty species of rodents and four species of insectivores were recorded from the study area. Mastomys natalensis (17.37%), Arvicanthis dembeensis (17.09%), Mastomys erythroleucus (8.90%), Stenocephalemys albipes (8.76%), Arvicanthis niloticus (8.19%), Acomys cahirinus (7.34%), Lemniscomys striatus (6.92%), Gerbilliscus nigricauda (6.21%), Grammomys dolichurus (3.67%), Gerbilliscus robusta (2.12%), Mus proconodon (1.98%), Mus mahomet (1.41), Dendromus melanotis (1.27%), Arvicanthis abyssinicus (1.13%), Mus musculus (0.99%), Praomys fumatus (0.85%), Xerus erythropus (0.85%), Lemniscomys barbarus (0.71%), Mus tenellus (0.71%) and Otomys typus (0.28%) were the rodents and their respective relative abundance in the study area. Crocidura olivieri (1.55%), Crocidura fumosa (0.85%), Crocidura bicolor (0.57%) and Elephantulus rufescens (0.28%) were the insectivores recorded with their respective relative abundance. Mastomys natalensis was the most abundant and O. typus and E. rufescens were the least (two each). Diversity of small mammals ranged from 2.299 to 2.625 with an average of 2.412. The highest small mammal diversity was in grasslands and the lowest was in Lake Chamo shore. Small mammal density varied from 5 to 43 ha^?1 and biomass varied from 244 to 2559 g ha^?1 with significant changes in relation to seasons and habitats.     

祁连山红腹牧草蝗雌雄虫空间格局及关联性

应用地统计学的方法,研究了祁连山北坡石羊河上游,6—10月之间红腹牧草蝗Omocestus haemorrhoidalis(Charpentie)雌雄虫的空间分布格局、动态变化及空间相关性。结果表明:红腹牧草蝗雌雄虫的半变异函数为球状模型与高斯模型,二者空间分布类型相同,均呈聚集分布;随时间的变化均呈现"扩散-聚集-扩散-聚集"的动态特征,7—8月之间雌虫的变化强度明显强于雄虫;二者的模糊贴近度指数在0.53～0.71之间,且指数随红腹牧草蝗的生长呈逐渐增加到减少的变化特征,表明雌雄虫在数量与空间上有较强的跟随关系,且跟随关系随红腹牧草蝗的生长发生明显的阶段性变化。     

草海国家级自然保护区水生植物群落的数量分类与排序分析

在群落样方调查的基础之上,采用双向指示种分析法（TW INSPAN）和除趋势对应分析（DCA）对草海国家级自然保护区水生植物群落进行分类和排序。TW INSPAN将50个样方分为17组,根据植被分类的原则划分为17个群丛,论述了各个群丛的群落学特征。50个样方的DCA排序结果反映了植物群落类型与环境梯度之间的关系,表明影响群落分布格局的主导生态因子为水分条件,第一轴反映了各个群落类型所在的水分条件梯度。排序结果与分类结果较吻合,反映出植物群落类型和物种分布随环境因子梯度变化的趋势。