Intrinsically disordered regions of human plasma membrane proteins preferentially occur in the cytoplasmic segment

A systematic survey of intrinsically disordered (ID) regions was carried out in 2109 human plasma membrane proteins with full assignment of the transmembrane topology with respect to the lipid bilayer. ID regions with 30 consecutive residues or more were detected in 41.0% of the human proteins, a much higher percentage than the corresponding figure (4.7%) for inner membrane proteins of Escherichia coli. The domain organization of each of the membrane protein in terms of transmembrane helices, structural domains, ID, and unassigned regions as well as the distinction of inside or outside of the cell was determined. Long ID regions constitute 13.3 and 3.5% of the human plasma membrane proteins on the inside and outside of the cell, respectively, showing that they preferentially occur on the cytoplasmic side. We interpret this phenomenon as a reflection of the general scarcity of ID regions on the extracellular side and their relative abundance on the cytoplasmic side in multicellular eukaryotic organisms.     

Comparison of the VIDAS system, FTA filter-based PCR and culture on SM ID for detecting Salmonella in Dermanyssus gallinae

AIMS: To compare different analytical methods for detecting Salmonella in Dermanyssus gallinae. METHODS AND RESULTS: The detection limit of three Salmonella detection methods [Vitek immunodiagnostic assay (VIDAS) Salmonella immuno-concentration/immunoassay, FTA filter-based PCR, and Salmonella detection and identification medium (SM ID) preceded by a pre-enrichment step] was evaluated by crushing mites in serial dilutions of pure cultures of Salmonella enterica ssp. Enterica serotype Enteritidis. Each method was then compared for its ability to detect Salmonella in artificially contaminated mites. In 105 mites artificially engorged with Salm. Enteritidis-contaminated blood, Salmonella was isolated from 68 samples of the samples cultured on SM ID and tests were positive for Salmonella using FTA filter-based PCR and VIDAS in 77 and 65 samples, respectively. Using SM ID as our reference method, specificities and sensitivities were 97% and 94% and 73% and 98.5% for VIDAS and PCR, respectively. CONCLUSIONS: Each method allowed the detection of Salmonella in contaminated mites and is usable for screening mites. PCR is more sensitive but less specific than VIDAS for detecting Salmonella. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first time that the VIDAS has been used to detect pathogens in vectors. The development of analytical methods for Salmonella detection in mites is a necessary step in the study of the role of D. gallinae as a vector of salmonellae and to check the contamination of D. gallinae in poultry facilities.     

Genetic identification of endangered North African ungulates using noninvasive sampling

North African ungulates include several threatened and emblematic species, yet are poorly studied mainly due to their remoteness and elusiveness. Noninvasive sampling provides a useful approach to obtain ecological and genetic information essential to guide conservation actions. The very first and most important step in conservation planning is to accurately identify species, and molecular genetics has been proved to be a useful tool. Several molecular genetics protocols are available for species identification, even for samples with poor quality DNA, such as faeces, hairs or bones. Most of these protocols use mitochondrial DNA for barcoding despite this marker being especially prone to problems, including mtDNA introgression, nuclear insert copies, high intraspecific diversity or heteroplasmy. In this work, we developed a molecular method based on polymorphisms in small fragments of the mitochondrial cytochrome b (cytb, mtDNA) and the nuclear kappa casein genes (KCAS, nDNA) for identifying endangered North African ungulates. These fragments revealed polymorphisms, including species‐specific variation, which allowed species identification of nine ungulate species that co‐occur in North Africa. The method was validated across more than 400 samples, including different types of noninvasive samples collected in the field. The simplicity, high reliability and relative low cost of the described method make it a promising tool to improve ecological studies of the North African ungulates and consequently, the implementation of more efficient management and conservation plans for these endangered ungulates.     

Genetic fingerprinting proves cross‐correlated automatic photo‐identification of individuals as highly efficient in large capture–mark–recapture studies

Capture–mark–recapture (CMR) approaches are the backbone of many studies in population ecology to gain insight on the life cycle, migration, habitat use, and demography of target species. The reliable and repeatable recognition of an individual throughout its lifetime is the basic requirement of a CMR study. Although invasive techniques are available to mark individuals permanently, noninvasive methods for individual recognition mainly rest on photographic identification of external body markings, which are unique at the individual level. The re‐identification of an individual based on comparing shape patterns of photographs by eye is commonly used. Automated processes for photographic re‐identification have been recently established, but their performance in large datasets (i.e., > 1000 individuals) has rarely been tested thoroughly. Here, we evaluated the performance of the program AMPHIDENT, an automatic algorithm to identify individuals on the basis of ventral spot patterns in the great crested newt (Triturus cristatus) versus the genotypic fingerprint of individuals based on highly polymorphic microsatellite loci using GENECAP. Between 2008 and 2010, we captured, sampled and photographed adult newts and calculated for 1648 samples/photographs recapture rates for both approaches. Recapture rates differed slightly with 8.34% for GENECAP and 9.83% for AMPHIDENT. With an estimated rate of 2% false rejections (FRR) and 0.00% false acceptances (FAR), AMPHIDENT proved to be a highly reliable algorithm for CMR studies of large datasets. We conclude that the application of automatic recognition software of individual photographs can be a rather powerful and reliable tool in noninvasive CMR studies for a large number of individuals. Because the cross‐correlation of standardized shape patterns is generally applicable to any pattern that provides enough information, this algorithm is capable of becoming a single application with broad use in CMR studies for many species.     

Tandem duplications of a degenerated GTP-binding domain at the origin of GTPase receptors Toc159 and thylakoidal SRP

The evolutionary origin of some nuclear encoded proteins that translocate proteins across the chloroplast envelope remains unknown. Therefore, sequences of GTPase proteins constituting the Arabidopsis thaliana translocon at the outer membrane of chloroplast (atToc) complexes were analyzed by means of HCA. In particular, atToc159 and related proteins (atToc132, atToc120, and atToc90) do not have proven homologues of prokaryotic or eukaryotic ancestry. We established that the three domains commonly referred to as A, G, and M originate from the GTPase G domain, tandemly repeated, and probably evolving toward an unstructured conformation in the case of the A domain. It resulted from this study a putative common ancestor for these proteins and a new domain definition, in particular the splitting of A into three domains (A1, A2, and A3), has been proposed. The family of Toc159, previously containing A. thaliana and Pisum sativum, has been extended to Medicago truncatula and Populus trichocarpa and it has been revised for Oryza sativa. They have also been compared to GTPase subunits involved in the cpSRP system. A distant homology has been revealed among Toc and cpSRP GTP-hydrolyzing proteins of A. thaliana, and repetitions of a GTPase domain were also found in cpSRP protein receptors, by means of HCA analysis.     

Utility of albicans ID plate for rapid identification of Candida albicans in clinical samples

Albicans ID (bioMérieux, Marcy l'Etoile, France) is a ready-to-use medium that contains a chromogenic substrate that allows rapid detection and specific identification of Candida albicans. We have evaluated its clinical performance by culturing 846 clinical specimens from pregnant women and neonates. A 99.2% sensitivity and a 100% specificity were observed in the identification of C. albicans isolates from primary culture.     

基于引物“随机组合”构建观赏桃SSR指纹图谱

近年来,我国观赏桃新品种日渐繁多、名称混乱、市场难以监管,同时用以区分品种的SSR指纹图谱的构建方法在研究界无统一的科学标准,尤其是构成最终引物组合的核心引物的确定,具体操作流程层出不穷、五花八门。为探索筛选SSR指纹图谱核心引物的科学方法,同时构建观赏桃SSR指纹图谱,该研究选用35对已报道的SSR引物对22份观赏桃种质进行试验。结果表明:通过PCR扩增与分析,多态性较高的8对引物——候选引物总共扩增出31个多态性条带,变幅为3~5个,PIC值变幅为0.458~0.668,MI值变幅为1.374~3.340。采用"随机组合"法对8对引物进行C_8~1、C_8~2、C_8~3…依次分析,得到区分能力最强的3种不同的最少引物组合方式——候选组合,并能区分出18份种质,从中发现区分能力最强的3种引物组合方式并不都是由引物PIC值、alleles数量或MI值等多态性指标最高的引物组成,而是由互补性最强的引物组成。选用组合内各引物多态性条带总数最多的组合方式"4-3"(BPPCT001+BPPCT015a+BPPCT017+BPPCT025)为22份观赏桃种质构建了指纹图谱。基于此,通过常规多态性指标筛选候选引物可以确定出单对引物鉴别能力最强的少量引物;通过"随机组合"筛选候选组合可以进一步确定出引物之间互补性最强的几种组合方式;根据组合内各引物的多态性条带总数确定最终核心引物可以确定出可扩容性最大的引物组合。该研究最终建立了候选引物——候选组合——核心引物组合"三步法"确定SSR指纹图谱核心引物组合的科学方法,不仅为22份供试观赏桃种质构建了SSR指纹图谱,也为其它作物SSR指纹图谱的构建提供了新的思路。     

电子微芯片皮下注射技术在猎隼繁殖及迁徙研究中的应用快报

采用电子微芯片皮下注射技术在新疆北部对13只猎隼幼鸟进行微芯片注射.微芯片的编号代表了大量生物学信息.微芯片注射技术是研究鸟类迁徙及获取繁殖生物学的重要手段.希望回收到ID信息者及时与中国猎隼研究小组（新疆）联系.     

Assessment of genetic differentiation in the large yellow croaker, Pseudosciaena crocea Richardson,and its first hybrid filial generations with AFLP markers

The genetic diversity (the digital characteristics) of four populations (120 individuals) of breeding large yellow croakers, Pseudosciaena crocea Richardson, was analyzed with amplified fragment length polymorphism (AFLP) markers. Ten primer combinations amplified 248 bands, of which 39.52% were polymorphic. Shannon's information index of the Daiqv (DQ) population was higher than that of the Minyu (MY) population, at 0.2167 and 0.2074, respectively. Additionally, the Shannon's information index value for the minus-hybrid (DQ population♂ × MY population♀) first hybrid generation was higher than the value for the plus-hybrid (MY population♂ × DQ population♀) first hybrid generation at 0.1687 and 0.1613, respectively. The F_ST of the parental generation was lower than that of the filial generation at 0.0329 and 0.0891, respectively. Gene flow was very high according to F_st values in both parental and filial generations. The UPGMA clustering analysis based on genetic similarity organized the four populations into three groups. The minus-hybrid stock was the most distinct as compared to the other populations.