中国新疆维吾尔自治区不明原因发热人群中Tahyna病毒感染状况调查

本研究通过对新疆地区不明原因发热人群血清Tahyna病毒抗体进行检测,以了解Tahyna病毒在当地的感染状况及分布特征。通过间接免疫荧光方法对新疆维吾尔自治区南部喀什地区、北部伊犁地区742例不明原因发热患者急性期血清标本进行Tahyna病毒抗体检测,并对IgM抗体阳性标本平行进行Tahyna病毒、Snowshoe hare病毒和Inkoo病毒三种抗原性相似的布尼亚病毒的蚀斑减少中和试验。研究结果显示新疆南部喀什地区采集不明原因发热患者急性期血清中,IgM抗体阳性率5.3%,IgG抗体阳性率18.3%;新疆北部伊犁地区采集的急性期患者血清标本中并未发现TAHV IgM抗体阳性;蚀斑减少中和试验结果显示,TAHV IgM抗体阳性患者血清中Tahyna病毒中和抗体滴度较其它两种布尼亚病毒中和抗体滴度升高明显。本研究证实新疆南部地区不明原因发热人群存在Tahyna病毒的急性感染和既往感染,为相关疾病的进一步监测提供基础。     

Biochemical isolation and purification of ovulation-inducing factor (OIF) in seminal plasma of llamas

Background  

The objective of the present study was to isolate and purify the protein fraction(s) of llama seminal plasma responsible for the ovulation-inducing effect of the ejaculate.     

The regulation index: a new method for assessing the relationship between oxygen consumption and environmental oxygen

Critical oxygen pressure (P(C)) is used in respiratory physiology to measure the response to hypoxia. P(C) defines the partial pressure of oxygen (Po(2)) at which an oxygen regulator switches to a conformer. However, not all animals show such clear patterns in oxygen consumption rate (Mo2), and there are many methods for determining P(C). This study assesses two methods that determine regulatory ability and four that calculate P(C). A new method, the regulation index (RI), assigns to an animal a relative measure of regulatory ability by calculating the area under the Mo2 versus Po(2) curve that is greater than a linear trend. The six methods are applied to developmental Mo2 data of two amphibians, Pseudophryne bibronii and Crinia georgiana. The four methods used to determine P(C) produced similar results but failed to identify the increase in regulation on hatching in C. georgiana or the greater regulation in larval C. georgiana compared with P. bibronii. Of the two methods that evaluated regulation, only the RI satisfactorily represented the entire range of Po(2). The RI is advantageous because it has clearly defined limits and does not constrain data to fit any single pattern. The RI can be used in concert with P(C), which can be easily calculated during the RI analysis, to provide a clearer definition of the Mo2 response to environmental Po(2).     

UBE4B,a ubiquitin chain assembly factor,is required for MDM2-mediated p53 polyubiquitination and degradation

Although MDM2 is known to be a critical negative regulator of p53, MDM2 only catalyzes p53 mono- or multiple monoubiquitination in vitro and in vivo, which is insufficient for the initiation of proteasomal degradation. MDM2 does not polyubiquitinate p53 in vitro, however, which indicates that the activity of other ubiquitin ligase(s) or cofactor(s) is required for MDM2-mediated p53 polyubiquitination and degradation. In our recent study, we demonstrated that UBE4B, an E3 and E4 ubiquitin ligase with a U-box domain, interacts physically with both p53 and MDM2. Our findings revealed that UBE4B negatively regulates the level of p53 and inhibits p53-dependent transactivation and apoptosis. We propose that inhibition of MDM2 binding to UBE4B may provide another approach to inhibit MDM2 E3 ligase activity for tumor suppressor p53. It could lead to novel anticancer therapies, with the possibility of reducing the public health burden from cancer.Key words: ubiquitination, MDM2, UBE4B, p53, degradation     

Design and initial characterization of the SC-200 proteomics standard mixture

High-throughput (HTP) proteomics studies generate large amounts of data. Interpretation of these data requires effective approaches to distinguish noise from biological signal, particularly as instrument and computational capacity increase and studies become more complex. Resolving this issue requires validated and reproducible methods and models, which in turn requires complex experimental and computational standards. The absence of appropriate standards and data sets for validating experimental and computational workflows hinders the development of HTP proteomics methods. Most protein standards are simple mixtures of proteins or peptides, or undercharacterized reference standards in which the identity and concentration of the constituent proteins is unknown. The Seattle Children's 200 (SC-200) proposed proteomics standard mixture is the next step toward developing realistic, fully characterized HTP proteomics standards. The SC-200 exhibits a unique modular design to extend its functionality, and consists of 200 proteins of known identities and molar concentrations from 6 microbial genomes, distributed into 10 molar concentration tiers spanning a 1,000-fold range. We describe the SC-200's design, potential uses, and initial characterization. We identified 84% of SC-200 proteins with an LTQ-Orbitrap and 65% with an LTQ-Velos (false discovery rate?=?1% for both). There were obvious trends in success rate, sequence coverage, and spectral counts with protein concentration; however, protein identification, sequence coverage, and spectral counts vary greatly within concentration levels.     

Classifying proteins into functional groups based on all-versus-all BLAST of 10 million proteins

To address the monumental challenge of assigning function to millions of sequenced proteins, we completed the first of a kind all-versus-all sequence alignments using BLAST for 9.9 million proteins in the UniRef100 database. Microsoft Windows Azure produced over 3 billion filtered records in 6 days using 475 eight-core virtual machines. Protein classification into functional groups was then performed using Hive and custom jars implemented on top of Apache Hadoop utilizing the MapReduce paradigm. First, using the Clusters of Orthologous Genes (COG) database, a length normalized bit score (LNBS) was determined to be the best similarity measure for classification of proteins. LNBS achieved sensitivity and specificity of 98% each. Second, out of 5.1 million bacterial proteins, about two-thirds were assigned to significantly extended COG groups, encompassing 30 times more assigned proteins. Third, the remaining proteins were classified into protein functional groups using an innovative implementation of a single-linkage algorithm on an in-house Hadoop compute cluster. This implementation significantly reduces the run time for nonindexed queries and optimizes efficient clustering on a large scale. The performance was also verified on Amazon Elastic MapReduce. This clustering assigned nearly 2 million proteins to approximately half a million different functional groups. A similar approach was applied to classify 2.8 million eukaryotic sequences resulting in over 1 million proteins being assign to existing KOG groups and the remainder clustered into 100,000 functional groups.     

Assessing predicted HIV-1 replicative capacity in a clinical setting

HIV-1 replicative capacity (RC) provides a measure of within-host fitness and is determined in the context of phenotypic drug resistance testing. However it is unclear how these in-vitro measurements relate to in-vivo processes. Here we assess RCs in a clinical setting by combining a previously published machine-learning tool, which predicts RC values from partial pol sequences with genotypic and clinical data from the Swiss HIV Cohort Study. The machine-learning tool is based on a training set consisting of 65000 RC measurements paired with their corresponding partial pol sequences. We find that predicted RC values (pRCs) correlate significantly with the virus load measured in 2073 infected but drug na?ve individuals. Furthermore, we find that, for 53 pairs of sequences, each pair sampled in the same infected individual, the pRC was significantly higher for the sequence sampled later in the infection and that the increase in pRC was also significantly correlated with the increase in plasma viral load and with the length of the time-interval between the sampling points. These findings indicate that selection within a patient favors the evolution of higher replicative capacities and that these in-vitro fitness measures are indicative of in-vivo HIV virus load.     

Substantial genetic structure among stocked and native populations of the European grayling (<Emphasis Type="Italic">Thymallus thymallus</Emphasis>, Salmonidae) in the United Kingdom

While currently in a state of recovery in the United Kingdom (UK), the grayling (Thymallus thymallus) remains of conservation interest due to its historical decline, socio-economic value and the potential impact of hatchery-reared stock fish on the genetic structure and diversity of wild populations. However, little is known about the levels and distribution of genetic diversity among UK grayling populations. To this end, 27 UK populations of grayling were genotyped across 10 microsatellite loci and sequenced at the mtDNA D-Loop. All populations clustered into four higher-level groups: Northern England, Southern England, Wales, and group consisting of a mixture of native and introduced populations. Ten populations showed evidence of bottleneck or founder effects, and the effective population size (Ne) was low in all populations. In most cases, historical stocking records agreed with the genetic relationships revealed in the study. A D-Loop haplotype network supported the groupings observed in the nuclear data, while phylogenetic inference places the UK populations amongst Central European samples. The combined datasets demonstrate that many of the UK populations can be treated as separate Management Units and we recommend that to preserve population specific genetic diversity, that stocking should be an intervention of last resort. However, if stocking is deemed essential, brood stock should originate from the river to be stocked.