Two new species of Paraclius from China (Diptera,Dolichopodidae)

Thirty-one species of Paraclius Loew were known to occur in China. In this paper, two species are described as new to science: Paraclius ventralis sp. nov. and Paraclius wutongshanus sp. nov. A key to the Chinese species of Paraclius is provided.www.zoobank.org/urn:lsid:zoobank.org:pub:3E803E27-5E44-4A55-91D5-DA088F986485.     

Identifying and quantifying metabolites by scoring peaks of GC-MS data

Background

Metabolomics is one of most recent omics technologies. It has been applied on fields such as food science, nutrition, drug discovery and systems biology. For this, gas chromatography-mass spectrometry (GC-MS) has been largely applied and many computational tools have been developed to support the analysis of metabolomics data. Among them, AMDIS is perhaps the most used tool for identifying and quantifying metabolites. However, AMDIS generates a high number of false-positives and does not have an interface amenable for high-throughput data analysis. Although additional computational tools have been developed for processing AMDIS results and to perform normalisations and statistical analysis of metabolomics data, there is not yet a single free software or package able to reliably identify and quantify metabolites analysed by GC-MS.

Results

Here we introduce a new algorithm, PScore, able to score peaks according to their likelihood of representing metabolites defined in a mass spectral library. We implemented PScore in a R package called MetaBox and evaluated the applicability and potential of MetaBox by comparing its performance against AMDIS results when analysing volatile organic compounds (VOC) from standard mixtures of metabolites and from female and male mice faecal samples. MetaBox reported lower percentages of false positives and false negatives, and was able to report a higher number of potential biomarkers associated to the metabolism of female and male mice.

Conclusions

Identification and quantification of metabolites is among the most critical and time-consuming steps in GC-MS metabolome analysis. Here we present an algorithm implemented in a R package, which allows users to construct flexible pipelines and analyse metabolomics data in a high-throughput manner.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0374-2) contains supplementary material, which is available to authorized users.     

高寒草地珠芽蓼内生拮抗固氮菌Z19的鉴定及其固氮功能

【目的】从东祁连山高寒草地珠芽蓼内生细菌中筛选和鉴定具有固氮能力和拮抗能力的内生细菌。【方法】采用16S rRNA基因序列同源性分析和生理生化指标测定方法对该菌株进行鉴定。【结果】从珠芽蓼中分离获得的21株内生细菌中6株内生菌具有固氮能力,76.2%具有抑菌能力,其中5株内生细菌对5种以上的病原菌有抑制作用;菌株Z19具有较强固氮能力和分解纤维素的能力,其纤维素溶解圈直径与菌落直径比达3.33,产生的纤维素酶活性为0.31 U,且对辣椒立枯丝核病菌(Rhizoctonia solani)、油菜菌核病菌(Sclerotinia sclerotiorum)、番茄灰霉病菌(Botrytis cinerea)、小麦根腐病菌(Bipolaris sorokiniana)和番茄早疫病菌(Alternaria solani)具有较强拮抗能力;经PCR扩增和测序,获得了菌株Z19的固氮基因(nifH)序列和16S rRNA基因序列,在GenBank中的登录号分别为EU693340和EU236746;菌株Z19呈革兰氏阳性,杆状,产芽孢。【结论】结合生理生化特征及16S rRNA基因序列同源性比较,鉴定其为枯草芽孢杆菌(Bacillus subtilis)。     

Re-evaluation of Japanese Phytophthora isolates based on molecular phylogenetic analyses

Over the past 40 years in Japan, Phytophthora isolates have been collected from various diseased host tissues and infested soils and identified using morphological characters. In order to develop a molecular method for the characterization of Japanese Phytophthora species, we obtained nuclear ribosomal ITS and LSU and mitochondrial coxI DNA sequences from 151 isolates representing 21 known species and 10 unidentified isolates. These were compared with similar sequences from representative isolates of known species. Of these, 124 isolates were found to have been correctly identified. Among the remaining 37 isolates, 19 showed high homology with other described species. The remaining 18 isolates showed only low levels of homology with any known species, and generated monophyletic sub-clades in a phylogenetic tree based on the ITS and nLSU regions and the coxI gene. Therefore, these isolates are candidates for new species, falling into six groups. Together, the Japanese isolates were found to represent phylogenetically diverse groups of species. In a sequence variation analysis, the ITS regions and the coxI genes were found to be more variable than the nLSU sequences, suggesting that they will be more useful for Phytophthora identification.     

Characterization of a new electrochemically active bacterium,Lysinibacillus sphaericus D-8, isolated with a WO3 nanocluster probe

Microorganisms capable of extracellular electron transfer play important roles in biogeochemical redox processes and have been of great interest in the fields of energy recovery, waste treatment, and environmental remediation. In this study, a new electrochemically active bacterium was identified with a high-throughput method using WO₃ nanoclusters as probes. The 16S rRNA gene sequence designated the strain as Lysinibacillus sphaericus D-8, a Gram-positive bacterium. Its electrochemical activity was characterized in a two-chamber microbial fuel cell and a three-electrode electrochemical cell. Strain D-8 produced 92 mW/m² of power using lactate as the electron donor. The electrochemical impedance spectroscopy results confirmed the electrochemical activity of this strain. Cyclic voltammetry analysis indicated that the presence of soluble redox active compounds might play an important role in the extracellular electron transfer by L. sphaericus D-8. This work might be the first report that demonstrates the electrochemical activity of Lysinibacillus species.     

人结合珠蛋白cDNA克隆及其在大肠杆菌中的表达和鉴定

目的：克隆人结合珠蛋白（haptoglobin,Hp）cDNA,并在大肠杆菌中表达和鉴定。方法：从Hela细胞中分离总RNA,采用RT-PCR方法获得人Hp cDNA,分别克隆至原核表达载体pET-32a和PGEX-4T-1,转化至大肠杆菌BL21,IPTG诱导表达,并进行SDS—PAGE及Western blot鉴定。结果：成功构建了高效原核表达质粒PET-32a-Hp和PGEX-4T1-Hp;Western印迹结果表明,经IPTG诱导,在大肠杆菌中表达了分子量约30kD和37kD的目的蛋白;表达产物经Ni2^＋-NTA离子交换树脂纯化,纯度〉90％。结论：在E．coli成功表达和纯化了人Hp融合蛋白,为进一步开发人Hp诊断试剂打下基础。     

人结合珠蛋白cDNA 克隆及其在大肠杆菌中的表达和鉴定

目的：克隆人结合珠蛋白（haptoglobin,Hp）cDNA ,并在大肠杆菌中表达和鉴定。方法：从Hela 细胞中分离总RNA,采用RT-PCR 方法获得人Hp cDNA,分别克隆至原核表达载体pET-32a和PGEX-4T-1,转化至大肠杆菌BL21,IPTG 诱导表达,并进行SDS-PAGE 及Western blot 鉴定。结果: 成功构建了高效原核表达质粒PET-32a-Hp 和PGEX-4T1-Hp;Western 印迹结果表明,经IPTG 诱导,在大肠杆菌中表达了分子量约30 kD和37 kD 的目的蛋白;表达产物经Ni2+-NTA 离子交换树脂纯化, 纯度>90%。结 论：在E.coli成功表达和纯化了人Hp 融合蛋白,为进一步开发人Hp 诊断试剂打下基础。     

华癸中生根瘤菌质粒复制基因repC的克隆与鉴定

摘要：【目的】repC为质粒复制必需的起始蛋白基因。本研究旨在对华癸中生根瘤菌菌株HN3015及其质粒消除突变株进行repC基因的克隆和鉴定。【方法】采用通用引物RC1和RC3进行repC基因的PCR扩增,扩增产物克隆到载体pMD-18T,然后测序。利用Southern 杂交对repC基因定位。利用在线软件分析基因的序列特征,BLAST 工具进行同源性搜索;ExPASy推断其氨基酸的序列;ClustalW进行同源核苷酸和氨基酸序列的多重比较分析;PredictProtein 进行蛋白二级结构分析。【结果】     

红麻(Hibiscus cannabinus L.)种质资源的鉴定与分类研究

对300份野生红麻和337份栽培红麻的形态学鉴定发现,红麻的茎、叶、花、果等植物学性状的类型多样,差异明显,遗传多样性十分丰富。野生红麻和栽培红麻一样,染色体数为2n=36,同属红麻种（Hibiscus cannabinus L．）;核型有2n=36=32M＋2SM＋2M（SAT）、2n=36=34M＋2M（SAT）和2n=36=32M＋2ST＋2M（SAT）等;综合形态学研究结果,将野生红麻分为普通、多毛、螺旋花和扁圆果4种类型,其中普通型又可分为3个亚类,普通型与栽培红麻亲缘关系最近,并发现红麻存在亚种。栽培红麻可分为9个变种17个类型,其中4个为新发现变种,7个为新发现类型。     

渗透胁迫下水稻种子萌发特性及抗旱性鉴定指标研究

用聚乙二醇（PEG）-6000作为渗透剂模拟干旱胁迫,探讨在4种不同浓度的渗透胁迫下水稻种子的萌发特性,并确立间接评价水稻苗期抗旱性的萌发期鉴定指标。结果表明,高浓度渗透液对种子萌发的抑制作用明显大于低浓度,萌发率的干旱胁迫反应指数随渗透液浓度的降低和萌发进程而增加。在不同浓度的渗透胁迫处理中,20％浓度下萌发6d后的萌发率表现较大的变异幅度和变异系数以及较均衡的品种频率分布,较好地反映了水稻种质对渗透胁迫的不同反应,认为20％／6d条件较适合作为萌发率鉴定的渗透液模拟干旱胁迫;经反复干旱后的幼苗存活率与萌发胁迫指数和20％胁迫浓度下萌发8d后芽鞘长的干旱胁迫反应指数（DRI）表现极显著或显著正相关,认为萌发胁迫指数和芽鞘长的DRI可作为评价水稻苗期抗旱性的间接鉴定指标。