Mass spectrometric analysis of protein histidine phosphorylation

Summary. Protein histidine phosphorylation is now recognized as an important form of post-translational modification. The acid-lability of phosphohistidine has meant that this phosphorylation has not been as well studied as serine/threonine or tyrosine phosphorylation. We show that phosphohistidine and phosphohistidine-containing phosphopeptides derived from proteolytic digestion of phosphohistone H4 are detectable by ESI-MS. We also demonstrate reverse-phase HPLC separation of these phosphopeptides and their detection by MALDI-TOF-MS.     

Safety zones for a Sclerotinia sclerotiorum-based mycoherbicide: Accounting for regional and yearly variation in climate

Variation in the width of 'safety zones' for sheep and dairy pasture treated with a Sclerotinia sclerotiorum (Lib.) de Bary-based mycoherbicide was quantified using 10 years of climate data from each of five regions in New Zealand. Acceptable and risk-averse zones were defined as the maximum distances in any direction from a treated pasture where 'added:natural' ratios of air-borne S. sclerotiorum spores are 1:1 and 1:10, respectively. The 10-year mean 1:1 safety zone had zero width for sheep pasture at all locations, and was at most, 50 m wide for dairy pasture. The width of the 10-year mean 1:10 zone varied regionally from 314 to 443 m for sheep and from 175 to 280 m for dairy pasture, and the 90th percentile 1:10 zones were up to 41% wider. Linear relationships between safety zone width and mean wind speed were evident and these could be used to derive region-specific safety zones.     

雪豹（Uncia uncia）研究的文献计量评价

通过对1950—2010年SCI收录和1989—2010年CSCD收录的雪豹(Uncia uncia)研究文献分析,从年度文献数量变化、国家/地区分布、主要研究机构、期刊分布、发表文献作者、基金资助机构、刊载文献类型、学科类别和语种分布9个方面,对雪豹研究文献的分布规律和研究现状进行了统计分析。结果表明:在SCI上发表雪豹研究论文的国家排名依次是美(50.6%)、英(16.5%)、印度(12.5%)和中国(5.6%);在文献量机构排名方面,国际雪豹基金会和英国爱丁堡大学并列第一,中国科学院排名第五;中国的主要合作国家中包括了美、英和中亚国家(吉尔吉斯斯坦、蒙古)。无论是分布范围还是数量,中国雪豹资源都居于世界第一,而研究却不相匹配,国内在这方面还仍需努力。     

用cDNA微阵列技术快速筛选粗毛栓菌的表达基因(英)

利用cDNA微阵列技术快速筛选具有较强降解木质纤维素能力的白腐真菌粗毛栓菌(Trametes gallica)的表达基因.利用木质素生物降解模式菌株黄孢原毛平革菌（Phanerochaete chrysosporium）的cDNA制备研究所用微阵列.在含有2 596个cDNA片段的芯片上共检测到172个阳性克隆,其中有165个克隆的荧光信号比值（Cy-5/Cy-3）在0.5和2.0之间,占所检测阳性克隆数的95.9％.对应于在限氮条件下生长５天和12天的粗毛栓菌培养物,分别有３个和４个时序特异性差异表达基因.随机挑取122个克隆进行测序和序列比对,发现所测序列中有118个能够很好地定位于黄孢原毛平革菌的基因组上.结果显示,粗毛栓菌与黄孢原毛平革菌在表达序列上存在较大差异,表明这两种真菌之间存在着较远的亲缘关系.通过同源性比对分析,发现２个令人感兴趣的克隆,一个对应于黄孢原毛平革菌过氧化物酶基因lpoB的部分片段,另一个为编码一种热激蛋白的基因.     

Quantitative Metaproteomics and Activity-based Protein Profiling of Patient Fecal Microbiome Identifies Host and Microbial Serine-type Endopeptidase Activity Associated With Ulcerative Colitis

The gut microbiota plays an important yet incompletely understood role in the induction and propagation of ulcerative colitis (UC). Organism-level efforts to identify UC-associated microbes have revealed the importance of community structure, but less is known about the molecular effectors of disease. We performed 16S rRNA gene sequencing in parallel with label-free data-dependent LC-MS/MS proteomics to characterize the stool microbiomes of healthy (n = 8) and UC (n = 10) patients. Comparisons of taxonomic composition between techniques revealed major differences in community structure partially attributable to the additional detection of host, fungal, viral, and food peptides by metaproteomics. Differential expression analysis of metaproteomic data identified 176 significantly enriched protein groups between healthy and UC patients. Gene ontology analysis revealed several enriched functions with serine-type endopeptidase activity overrepresented in UC patients. Using a biotinylated fluorophosphonate probe and streptavidin-based enrichment, we show that serine endopeptidases are active in patient fecal samples and that additional putative serine hydrolases are detectable by this approach compared with unenriched profiling. Finally, as metaproteomic databases expand, they are expected to asymptotically approach completeness. Using ComPIL and de novo peptide sequencing, we estimate the size of the probable peptide space unidentified (“dark peptidome”) by our large database approach to establish a rough benchmark for database sufficiency. Despite high variability inherent in patient samples, our analysis yielded a catalog of differentially enriched proteins between healthy and UC fecal proteomes. This catalog provides a clinically relevant jumping-off point for further molecular-level studies aimed at identifying the microbial underpinnings of UC.     

Assessment of variability among morphological and molecular characters in wild populations of mint [Mentha longifolia (L.) L.] germplasm

Mentha longifolia is an important medicinal and aromatic perennial herb that exhibits wide distribution range from sub-tropical to temperate regions. In the present study, agro-morphological traits and genetic differences in 19 different populations of M. longifolia were studied to evaluate the level and extent of its diversity. Analysis of variance (ANOVA) showed that the different phenotypic characters show considerable differences among various populations and was significant at p < 0.05. Molecular diversity analysis performed by using arbitrary amplified eleven ISSR primers generated a total of 121 amplicons that range within the size of 200–2500 base pairs (bp). Each primer on average generated 11 amplicons with percentage polymorphism being 100. The analysis of molecular variance (AMOVA) showed more (64%) among population genetic diversity and less (36%) within the populations. Greater genetic differentiation (Gst = 0.6852) among these populations occurs due to low gene flow (Nm = 0.2297) and greater habitat variability. Geographic and genetic distances were positively correlated according to Mantel’s test. In order to remove any kind of biases, we used R software to perform cluster and redundancy analysis to analyse the extent of relatedness among studied populations. In terms of morphological and molecular aspects, the populations were grouped into four and five clusters respectively based on hierarchical clustering method. The results demonstrated that M. longifolia displays a great degree of morphological and genetic variation and can be utilized in breeding, genetic improvement, and gene bank conservation programmes in future.     

陕西宝鸡发现喜山鼠耳蝠

2011年4和8月及2014年4月在陕西省宝鸡市太白县分别采集到2只、1只和1只共4只蝙蝠个体,标本保存于陕西省动物研究所标本馆(标本编号为TB0001、TB0002、TB0017和TB0042)。其主要形态特征为：体型小,头体长34.59 ~ 43.86 mm(n = 4);耳较小,黑色;耳前缘近凸圆,耳后缘在基部有一浅的缺刻;耳屏细长,约为耳长的一半;后足不及胫长的一半;背部毛基黑色,毛尖为赤褐色;腹部毛基为黑色,毛尖为灰褐色;翼膜起始于后足外趾的基部。以上特征均与喜山鼠耳蝠moupinensis亚种(Myotis muricola moupinensis)相符。结合线粒体Cyt b基因序列,构建其系统发生关系,与基因库中宽吻蝠属未定种(Submyotodon sp.)序列聚为较高支持度的一支。综合形态与系统发育证据,参考目前最新的中国兽类物种分类和分布信息,将采集到的标本初步鉴定为喜山鼠耳蝠moupinensis亚种,此次发现是陕西省境内该物种的首次记录,拓展了对其在我国分布范围的认识。     

贵州六盘水发现东阳江麝鼩

在贵州省六盘水市杨梅乡慕尼克村,利用陷阱法捕捉到3号麝鼩属(Crocidura)标本。本次采集标本的体形较小,头体长(49.0 ± 0.8)mm,尾长[(41.8 ± 4.2)mm]略短于头体长(尾长/头体长为85%)。背毛呈浅灰褐色,腹毛颜色浅于背毛,呈灰色。尾部双色,背侧黑褐色,腹侧淡于背侧。前足背部白色,后足则为淡灰色。尾近乎裸露,尾基约1/3着生稀疏白色长毛。颅全长(15.92 ± 0.55)mm,脑颅高(4.75 ± 0.18)mm。上门齿1枚,有一长而大的前尖和一小而矮的后尖。上单尖齿3枚,第1单尖齿最大,第2单尖齿略大于第3单尖齿,1枚第四前臼齿(P4),3枚臼齿。上述特征与东阳江麝鼩(C. dongyangjiangensis)模式标本的描述和鉴定特征基本一致,因此将3号采集标本鉴定为东阳江麝鼩。基于Cyt b基因进行分子系统发育分析,采集标本与麝鼩属物种中的东阳江麝鼩遗传距离最近,在0.004 ~ 0.027之间。系统发生树显示,3号标本与东阳江麝鼩构成一个单系进化分支,进一步证实本次采集的3号标本是东阳江麝鼩,为贵州省分布新记录种。     

陆地棉品种抗黄萎病反应规律的研究

对我国自育的108个陆地棉品种的抗黄萎病性进行了研究。在黄萎病发病期内,对黄萎病发病情况进行连续调查,测定产量、考查产量因素并检测纤维品质。利用因子分析法对陆地棉抗黄萎病反应规律进行分析,得出不同时期的黄萎病病指主要与前后3～5个阶段抗病性有关。病情发展主要由4个主因子决定,且第1、2主因子具有较大的方差贡献率。第1主因子(F1)主要与品种7月26日至8月9日的黄萎病病指有关,第2主因子(F2)主要与品种8月20日至9月4日的黄萎病病指有关。利用因子分析结果将108个品种划分为4个类型,前期抗病性较好而后期发病较快的第Ⅰ类品种,其产量较低,单株结铃数、单铃重、衣分均低于其他3类;纤维品质均较差,纤维长度、整齐度、比强度和马克隆值均较其他3类差。前期和后期病指均较低、发病缓慢的第Ⅱ类则小区产量最高,纤维品质处于平均水平。第Ⅲ类品种前期发病较慢,中期发病较快,具有较高的小区产量,单铃重最高;纤维整齐度、比强度和伸长率好于其他3类品种;前期发病较快,中期发病平缓,后期仍具有较高病指的为第Ⅳ类品种,小区产量较低,单株产量、单株结铃数和衣分较高;其他性状处于中等水平。但研究表明,某一阶段具有的抗病性并不能完全代表品种的抗病性。     

Habitat associations and communities of breeding birds in the highlands of south-west Jordan

Abstract

Habitat associations and communities of breeding birds were studied for the first time in a semi-arid region in the southern highlands of Jordan. Birds were censused and habitat variables estimated in different habitat types, ranging from steppe to open, Mediterranean-type woodland. The variation of abundance of several species was explained adequately with multiple regressions of up to five habitat variables. A distinct bird community was identified by using principal component analysis on the highland plateau (e.g. Short-toed Lark, Isabelline Wheatear), in steppe habitats modified by dry farming methods. The plateau was identified as a transition zone of Palaeoxeric/Turkestanian and Mediterranean faunal types. The remainding cluster included species of diverse origins (Palaearctic, Mediterranean, Saharo-Sindian, Afrotropical and others). It was subdivided into three bird assemblages with preferences for following habitat types: Mediterranean-type open woodlands (e.g. Syrian Serin), dwarf shrub formations of higher altitudes (e.g. Spectacled Warbler), dwarf shrub formations, including clearings and the edge of woodlands at lower altitudes (e.g. Scrub Warbler).