A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas

Human blood plasma can be obtained relatively noninvasively and contains proteins from most, if not all, tissues of the body. Therefore, an extensive, quantitative catalog of plasma proteins is an important starting point for the discovery of disease biomarkers. In 2005, we showed that different proteomics measurements using different sample preparation and analysis techniques identify significantly different sets of proteins, and that a comprehensive plasma proteome can be compiled only by combining data from many different experiments. Applying advanced computational methods developed for the analysis and integration of very large and diverse data sets generated by tandem MS measurements of tryptic peptides, we have now compiled a high-confidence human plasma proteome reference set with well over twice the identified proteins of previous high-confidence sets. It includes a hierarchy of protein identifications at different levels of redundancy following a clearly defined scheme, which we propose as a standard that can be applied to any proteomics data set to facilitate cross-proteome analyses. Further, to aid in development of blood-based diagnostics using techniques such as selected reaction monitoring, we provide a rough estimate of protein concentrations using spectral counting. We identified 20,433 distinct peptides, from which we inferred a highly nonredundant set of 1929 protein sequences at a false discovery rate of 1%. We have made this resource available via PeptideAtlas, a large, multiorganism, publicly accessible compendium of peptides identified in tandem MS experiments conducted by laboratories around the world.     

Integrated soil and plant phosphorus management for crop and environment in China. A review

In semi-arid grassland ecosystems, soil biogeochemical processes are controlled by seasonal and inter-annual rainfall variation and temperature, which may override the long-term impact of grazers on N availability and N dynamics. In a three-year (2004?C2006) case study of an Inner Mongolian grassland, we analysed time-integrated (ion-exchange resins) and instantaneous (soil mineral N extractions) inorganic N availability at three sites of varying grazing intensities and combined these data with information on soil water content (SWC), aboveground net primary productivity (ANPP) and plant N uptake. Additionally, the effects of rainfall and grazing on N-form availability (NO ₃ ^? -N, NH ₄ ⁺ -N) were considered. Grazing had less impact on N availability compared to seasonal and annual rainfall distribution. One of the three study years (2004) showed a grazing effect with higher resin-N availability at the ungrazed site compared to the heavily grazed site. Inorganic N availability was low in the driest year (2005) and highest in a year of average rainfall amount and favourable distribution (2004). In general, we found a positive relationship between inorganic N availability and both plant productivity and plant N uptake. Rainfall also controlled the plant available NO ₃ ^? -N and NH ₄ ⁺ -N pools; NH ₄ ⁺ -N dominated the available inorganic N-form in times of low SWC, while the available NO ₃ ^? -N increased with SWC. We observed N availability and plant productivity in a temporal synchronized pattern. Increased rainfall variability and land-use practices affecting SWC will likely alter N availability dynamics (and the relation of N-forms) and, therefore, important processes of semi-arid natural grassland carbon and N cycling.     

Development and validation of a UPLC/MS method for a nutritional metabolomic study of human plasma

In order to study the effect of a diet on metabolites found in body fluids such as plasma, we have developed and validated a UPLC/MS method. While methods using NMR have been well established to analyse different biological tissues, recent studies have described robust untargeted UPLC-MS methods for plasma analysis. One major concern when profiling plasma is the presence of an important quantity of proteins which have to be precipitated without any loss of metabolites prior to LC/MS analysis. The utilization of untargeted approaches in nutritional metabolomics still suffers from the lack of identification of specific biomarkers. We therefore suggest an alternative method still using a global approach but focusing at the same time on metabolites previously described in human plasma in order to detect biomarkers of metabolic dysregulations. Thus, to fulfil our objectives, analytical parameters were tested (i) the anticoagulant type for sample collection, (ii) the protein precipitation method and (iii) UPLC/MS analytical conditions. Three protein precipitation methods and two anticoagulants were tested and compared. The method utilizing blood collection on heparin and methanol precipitation was chosen for giving the most reproducible results while keeping the complexity of the sample. Finally, a validation was proposed to evaluate the stability of this analytical method applied to a large batch of samples for nutritional metabolomic studies.     

CD40 signal expression in gastric cancer tissue and its correlation with prognosis of gastric cancer patients

CD40 signaling plays a critical role in the survival rate of gastric cancer patients. Tumour samples were collected from 73 patients with who were diagnosed as gastric cancer in general surgery department in the 1st affiliated hospital of Suzhou University between September 2002 and July 2003. All patients had not received radiotherapy and chemotherapy before operation. These patients include 46 male and 27 female. Here we show that CD40 is constitutively expressed in the human gastric carcinoma tissues, and CD40 protein and mRNA positive expression in gastric cancer tissues closely correlated with lymph node metastasis and tumour TNM stage. CD40 positive expression in gastric cancer patients with lymph node metastasis was markedly higher than that in gastric cancer patients without lymph node metastasis. CD40 positive expression in stage III-IV gastric cancer patients was markedly higher than that in stage I-II gastric cancer patients. Moreover, CD40 expression closely correlated with prognosis of gastric cancer patients. Therefore, CD40 was taken as grouping variable, and lymph node metastasis and clinical staging were taken as stratification variables, respectively, further analysis showed that prognosis in gastric cancer patients with lymph node metastasis and CD40 positive expression was markedly worse than that in gastric cancer patients without lymph node metastasis and CD40 negative expression (P = 0.0076). These results suggest that CD40 signaling plays a critical role in the survival of gastric cancer patients.     

不同覆盖方式对底泥内源营养盐释放的控制效果

通过底泥内源营养盐释放控制室内模拟试验,考察了塑料包被、斜发沸石、方解石、石英砂和硝酸钙5种覆盖材料对底泥氮磷释放效率的影响,系统分析了各自优劣程度,为实际环境中不同污染背景水体选择适宜的控制技术提供科学依据.结果表明: 不同覆盖材料对底泥总磷释放的控制效果依次为:塑料包被>硝酸钙>斜发沸石>方解石>石英砂;不同覆盖材料对底泥总氮释放的控制效果依次为:斜发沸石>塑料包被>方解石>石英砂>硝酸钙;不同覆盖材料对底泥硝态氮释放的控制效果依次为:塑料包被>斜发沸石>方解石>石英砂>硝酸钙;不同覆盖材料对底泥铵态氮释放的控制效果依次为:硝酸钙>石英砂>斜发沸石>方解石>塑料包被;温度和底泥内源营养盐释放有对应关系,水样中总磷、总氮和硝态氮浓度会随着温度上升而增加,而铵态氮浓度呈下降趋势.     

Nucleotide Binding Domain Interactions During the Mechanochemical Reaction Cycle of ATP-Binding Cassette Transporters

ATP-binding cassette (ABC) transporters serve as importers and exporters for a wide variety of solutes in both prokaryotes and eukaryotes, and are implicated in microbial drug resistance and a number of significant human genetic disorders. Initial crystal structures of the soluble nucleotide binding domains (NBDs) of ABC transporters, while a significant step towards understanding the coupling of ATP binding and hydrolysis to transport, presented researchers with important questions surrounding the role of the signature sequence residues, the composition of the nucleotide binding sites, and the mode of NBD dimerization during the transport reaction cycle. Recent studies have begun to address these concerns. This mini-review summarizes the biochemical and structural characterizations of two archaebacterial NBDs from Methanocaldococcus jannaschii, MJ0796 and MJ1267, and offers current perspectives on the functional mechanism of ABC transporters.     

大型绿藻浒苔转化表达系统选择标记的筛选

主要研究了条浒苔对抗生素氯霉素和除草剂Basta的敏感性,以确定适合的阳性选择标记基因。应用不同浓度氯霉素(0、25、50、75、100、125μg/ml)和Basta(0、5、12.5、25、37.5、50μg/ml)对不同发育时期条浒苔细胞存活率影响进行了测定。实验结果表明:不同发育时期条浒苔对氯霉素和Basta的敏感性不同。其中最大浓度125μg/ml浓度的氯霉素在15d内对条浒苔孢子和小苗两个不同发育时期的细胞均难以达到全部杀死效果,相对存活率仍分别为1%和20%;而Basta对条浒苔孢子和小苗均具有很强的杀生作用,其中5μg/ml浓度的Basta在3d内可将条浒苔孢子全部杀死,12.5μg/ml浓度下约一周时间可以将浒苔小苗全部致死。本实验结果提示bar基因有可能成为浒苔基因工程较理想的选择标记基因。     

模糊C－均值聚类和TWINSPAN分类的比较研究

以英国威尔士北部Ｓｎｏｗｄｏｎｉａ山地Ａｂｅｒ山谷植被为例,对模糊ｃ－均值聚类和ＴＷＩＮＳＰＡＮ分类进行了应用和比较研究。两种方法的结果一致。模糊ｃ－均值聚类结果给出样地和植被类型间的隶属程度,在一定程度上优于ＴＷＩＮＳＰＡＮ。     

杉木连栽土壤对其幼树生长的影响

在会同林区采用３种不同连栽杉木次数的土壤,进行杉木幼树盆栽试验．结果表明,杉木连栽不利其幼树生长．连裁使幼树高生长下降３７—４０％,基径下降１９—２８％,冠幅下降２１—２９％,总生物量减少４５—５０％．杉木连栽还造成土壤养分递减,即腐殖质减少７—２８％,速效养分下降２３—２８％,土壤微生物数量和活性也大大降低．因此,杉木纯林连栽经营方式应尽快改变．     

Changes to the rumen bacterial population of sheep with the addition of 2,4,6-trinitrotoluene to their diet

Previous work has shown that bacterial isolates from the sheep rumen are capable of detoxifying 2,4,6-trinitrotoluene (TNT) into polar constituents. In this study, the dietary effects of TNT on the sheep rumen microbial community were evaluated using molecular microbiology ecology tools. Rumen samples were collected from sheep fed with and without TNT added to their diet, genomic DNA was extracted, and the 16S rRNA-V3 gene marker was used to quantify changes in the microbial population in the rumen. Control and treatment samples yielded 533 sequences. Phylogenetic analyses were performed to determine the microbial changes between the two conditions. Results indicated the predominant bacterial populations present in the rumen were comprised of the phyla Firmicutes and Bacteroidetes, irrespective of presence/absence of TNT in the diet. Significant differences (P < 0.001) were found between the community structure of the bacteria under TNT (−) and TNT (+) diets. Examination of the TNT (+) diet showed an increase in the clones belonging to family Ruminococcaceae, which have previously been shown to degrade TNT in pure culture experiments.