The PathoChip,a functional gene array for assessing pathogenic properties of diverse microbial communities

Pathogens present in the environment pose a serious threat to human, plant and animal health as evidenced by recent outbreaks. As many pathogens can survive and proliferate in the environment, it is important to understand their population dynamics and pathogenic potential in the environment. To assess pathogenic potential in diverse habitats, we developed a functional gene array, the PathoChip, constructed with key virulence genes related to major virulence factors, such as adherence, colonization, motility, invasion, toxin, immune evasion and iron uptake. A total of 3715 best probes were selected from 13 virulence factors, covering 7417 coding sequences from 1397 microbial species (2336 strains). The specificity of the PathoChip was computationally verified, and approximately 98% of the probes provided specificity at or below the species level, proving its excellent capability for the detection of target sequences with high discrimination power. We applied this array to community samples from soil, seawater and human saliva to assess the occurrence of virulence genes in natural environments. Both the abundance and diversity of virulence genes increased in stressed conditions compared with their corresponding controls, indicating a possible increase in abundance of pathogenic bacteria under environmental perturbations such as warming or oil spills. Statistical analyses showed that microbial communities harboring virulence genes were responsive to environmental perturbations, which drove changes in abundance and distribution of virulence genes. The PathoChip provides a useful tool to identify virulence genes in microbial populations, examine the dynamics of virulence genes in response to environmental perturbations and determine the pathogenic potential of microbial communities.     

RBRDetector: Improved prediction of binding residues on RNA‐binding protein structures using complementary feature‐ and template‐based strategies

Computational prediction of RNA‐binding residues is helpful in uncovering the mechanisms underlying protein‐RNA interactions. Traditional algorithms individually applied feature‐ or template‐based prediction strategy to recognize these crucial residues, which could restrict their predictive power. To improve RNA‐binding residue prediction, herein we propose the first integrative algorithm termed RBRDetector (RNA‐Binding Residue Detector) by combining these two strategies. We developed a feature‐based approach that is an ensemble learning predictor comprising multiple structure‐based classifiers, in which well‐defined evolutionary and structural features in conjunction with sequential or structural microenvironment were used as the inputs of support vector machines. Meanwhile, we constructed a template‐based predictor to recognize the putative RNA‐binding regions by structurally aligning the query protein to the RNA‐binding proteins with known structures. The final RBRDetector algorithm is an ingenious fusion of our feature‐ and template‐based approaches based on a piecewise function. By validating our predictors with diverse types of structural data, including bound and unbound structures, native and simulated structures, and protein structures binding to different RNA functional groups, we consistently demonstrated that RBRDetector not only had clear advantages over its component methods, but also significantly outperformed the current state‐of‐the‐art algorithms. Nevertheless, the major limitation of our algorithm is that it performed relatively well on DNA‐binding proteins and thus incorrectly predicted the DNA‐binding regions as RNA‐binding interfaces. Finally, we implemented the RBRDetector algorithm as a user‐friendly web server, which is freely accessible at http://ibi.hzau.edu.cn/rbrdetector . Proteins 2014; 82:2455–2471. © 2014 Wiley Periodicals, Inc.     

Resistin induces monocyte-endothelial cell adhesion by increasing ICAM-1 and VCAM-1 expression in endothelial cells via p38MAPK-dependent pathway

Resistin, firstly reported as an adipocyte-specific hormone, is suggested to be an important link between obesity and diabetes. Recent studies have suggested an association between resistin and atherogenic processes. The adhesion of circulating monocytes to endothelial cells is a critical step in the early stages of atherosclerosis. The purpose of the present study was to investigate the effect of resistin on the adhesion of THP-1 monocytes to human umbilical vein endothelial cells (HUVECs) and the underlying mechanism. Our results showed that resistin caused a significant increase in monocyte adhesion. In exploring the underlying mechanisms of resistin action, we found that resistin-induced monocyte adhesion was blocked by inhibition of p38MAPK activation using SB203580 and SB202190. Furthermore, resistin increased the expression of intercellular adhesion molecule-1 (ICAM-1) and vascular cell adhesion molecule-1 (VCAM-1) by HUVECs and these effects were also p38MAPK-dependent. Resistin-induced monocyte adhesion was also blocked by monoclonal antibodies against ICAM-1 and VCAM-1. Taken together, these results show that resistin increases both the expression of ICAM-1 and VCAM-1 by endothelial cells and monocyte adhesion to HUVECs via p38MAPK-dependent pathways.     

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．     

免疫组织化学反应抗原恢复新法在临床病理诊断中的应用

应用蒸馏水在ｐＨ６２, 加热煮沸后能够较好的恢复组织中被封闭的抗原。经２８０４ 张组织切片在进行免疫组织化学反应之前, 用现配ｐＨ６２ 的蒸馏水加热煮沸后微火保温１０ 分钟, 然后再按常规免疫组化染色。经此法恢复抗原处理后, 并显示强度和阳性率与微波辅助盐溶液方法相比结果基本相似, 两者与未抗原恢复处理相比有显著性差异（Ｐ＜ ００１）。经彩色图像分析结果同样有显著性差异（Ｐ＜ ００５）。本法恢复抗原与微波技术相比, 同样能使组织内抗原得以充分的暴露, 提高抗原的检出率, 证明了蒸馏水在ｐＨ６２ 时,可作为一种新的暴露抗原的方法, 且操作简单, 抗原恢复均匀, 很适合各种实验室的应用     

流域生态学——新学科,新思想,新途径

在评述流域生态学定义、来源及有关认识的基础上,论述了流域生态学作为一门学科的意义和主要研究内容．文章认为流域生态学的研究与应用是流域社会、经济可持续发展的有效途径,有必要尽快地系统开展相关研究     

Establishment of La-tPA/G-CSF dual transgenic mice and expression in their mammary gland

Expression vectors of human granulocyte colony stimulating factor (G-CSG) and long acting tissue plasminogen activator (La-tPA) in mammary gland were constructed using promoters of mouse whey acid protein gene (WAP) and sheep β-lactoglobulin gene (BLG) with sizes of 2.6 and 5 kb respectively. Two kinds of transgenic mice of G-CSF and La-tPA were produced with microinjection. The expression of G-CSF and La-tPA was achieved in mammary glands of transgenic mice, respectively. In order to establish dual transgenic mice of La-tPA /G-CSF, transgenic mice carrying G-CSF and La-tPA gene characterized with specific expression in mammary gland were mated. La-tPA/G-CSF dual transgenic mice were screened out from the hybrid offspring by Once-PCR. The co-expression of La-tPA and G-CSF in mammary gland of the dual transgenic mice was confirmed by the milk assayed and Northern blot analysis. Some parameters about the dual transgenic mice indicated that there were fewer litters than that of normal mice. The ratio of dual transgenes was 46.1% in F1 generation, and offspring’s sex ratio was normal. Hence a dual transgenic mouse model was established for the study of co-expression foreign proteins in mammary gland.     

Circular RNA circABCC4 as the ceRNA of miR‐1182 facilitates prostate cancer progression by promoting FOXP4 expression

In recent years, circular RNAs (circRNAs) have been identified to be essential regulators of various human cancers. However, knowledge of the functions of circRNAs in prostate cancer remains very limited. The correlation between circABCC4 and human cancer is largely unknown. This study aims to investigate the biological functions of circABCC4 in prostate cancer progression and illustrate the underlying mechanism. We found that circABCC4 was remarkably up‐regulated in prostate cancer tissues and cell lines and promoted FOXP4 expression by sponging miR‐1182 in prostate cancer cells. CircABCC4 knockdown markedly suppressed prostate cancer cell proliferation, cell‐cycle progression, migration and invasion in vitro. Furthermore, silencing of the circRNA also delayed tumor growth in vivo. Taken together, our findings indicated that circABCC4 facilitates the malignant behaviour of prostate cancer by promoting FOXP4 expression through sponging of miR‐1182. The circABCC4–miR‐1182‐FOXP4 regulatory loop may be a promising therapeutic target for prostate cancer intervention.     

Human DNA ligases I and III, but not ligase IV, are required for microhomology-mediated end joining of DNA double-strand breaks

DNA nonhomologous end-joining (NHEJ) and homologous recombination are two distinct pathways of DNA double-strand break repair in mammalian cells. Biochemical and genetic studies showed that DNA ends can also be joined via microhomology-mediated end joining (MHEJ), especially when proteins responsible for NHEJ, such as Ku, are reduced or absent. While it has been known that Ku-dependent NHEJ requires DNA ligase IV, it is unclear which DNA ligase(s) is required for Ku-independent MHEJ. In this study, we used a cell-free assay to determine the roles of DNA ligases I, III and IV in MHEJ and NHEJ. We found that siRNA mediated down-regulation of DNA ligase I or ligase III in human HTD114 cells led to impaired end joining that was mediated by 2-, 3- or 10-bp microhomology. In addition, nuclear extract from human fibroblasts harboring a mutation in DNA ligase I displayed reduced MHEJ activity. Furthermore, treatment of HTD114 nuclear extracts with an antibody against DNA ligase I or III also significantly reduced MHEJ. These data indicate that DNA ligases I and III are required in MHEJ. DNA ligase IV, on the contrary, is not required in MHEJ but facilitates Ku-dependent NHEJ. Therefore, MHEJ and NHEJ require different DNA ligases.     

Fluorescent labeling for clonal selection of Marc 145 cells secreting high levels of recombinant protein PBD-1

Despite the powerful impact gene expression markers like the green fluorescent protein (GFP) or enhanced GFP (EGFP) exert on linking the expression of recombinant protein for selection of high producers in recent years, there is still a strong incentive to develop more economical and efficient methods for isolating mammalian cell clones secreting high levels of recombinant proteins. Here we present a new method based on the co-expression of EGFP that allows clonal selection in standard 96-well cell culture plates. The genes encoding the EGFP protein and the related protein are linked by an internal ribosome entry site and thus are transcribed into the same mRNA in an independent translation process. Since both proteins arise from a common mRNA, the EGFP expression level correlates with the expression level of the therapeutic protein in each clone. By expressing recombinant porcine β-defensin 1 in Marc 145 cells, we demonstrate the robustness and performance of this technique. The method can be served as an alternative to identify high-producer clones with various cell sorting methods.