Y-SNPs Haplotype Diversity in Four Chinese Cattle Breeds

To investigate the genetic diversity of Chinese cattle, 96 male samples of 4 Chinese native cattle breeds were investigated using 5 single nucleotide polymorphisms specific to the bovine Y chromosome. Two previously described haplotypes (taurine Y2 and indicine Y3) were detected in 74 and 22 animals, respectively. The haplotype frequencies varied amongst the four native breeds. The taurine Y2 haplotype dominated in the Qinchuan, Dabieshan, and Yunba breeds. However, the indicine Y3 haplotype occurred in high frequency in the Enshi breed. Among the four native breeds, Yunba had the highest haplotype diversity (0.4330 ± 0.0750), followed by Qinchuan (0.2899 ± 0.1028) and Enshi (0.2222 ± 0.1662), Dabieshan was the least differentiated (0.1079 ± 0.0680). Compared with some foreign cattle breeds, the low level of haplotype diversity was detected in our breeds (0.2633 ± 0.1030).     

HCV-specific interleukin-21+CD4+ T cells responses associated with viral control through the modulation of HCV-specific CD8+ T cells function in chronic hepatitis C patients

Interleukin-21 (IL-21)+CD4+ T cells are involved in the immune response against hepatitis B virus (HBV) by secreting IL-21. However, the role of IL-21+CD4+ T cells in the immune response against chronic hepatitis C (CHC) virus infection is poorly understood. This study aimed to investigate the role of IL-21+CD4+ T cells in CHC patients and the potential mechanisms. The study subjects included nineteen CHC patients who were grouped by viral load (low, < 10⁶ RNA copies/ml, n = 8; high, > 10⁶ RNA copies/ml, n = 11). The peripheral frequency of HCV-specific IL-21+CD4+ T cells was higher in the low viral load group and was negatively correlated with the serum HCV RNA viral load in all CHC patients. Meanwhile, IL-21+ cells accumulated in the liver in the low viral load group. In vitro, IL-21 treatment increased the expression of proliferation markers and cytolytic molecules on HCV-specific CD8+ T cells. In summary, these findings suggest that HCV-specific IL-21+CD4+ T cells might contribute to HCV control by rescuing HCV-specific CD8+ T cells in CHC patients.     

Periostin Mediates the Increased Pro‐Angiogenic Activity of Gastric Cancer Cells under Hypoxic Conditions

This study was conducted to investigate the biological role of periostin in gastric cancer (GC) under hypoxia. Western blot analysis revealed that along with an upregulation of hypoxia‐inducible factor‐1alpha, there was a time‐dependent induction of periostin in MKN‐45 cells under hypoxia (2% O₂), increasing by eightfold as compared to normoxic cells. Pretreatment with 30 µM PD98059, an inhibitor of ERK1/2, significantly reduced hypoxia‐stimulated periostin expression (P < 0.01). Periostin knockdown in MKN‐45 cells was achieved by specific small interfering RNA (siRNA). The conditioned medium from periostin siRNA‐transfected MKN‐45 cells induced significantly less (P < 0.01) endothelial tube formation than control siRNA‐transfected cells. Additionally, periostin silencing markedly decreased the mRNA expression and secretion of vascular endothelial growth factor (VEGF) in hypoxic MKN‐45 cells. Thus, our data suggest that periostin is a hypoxia‐response gene and mediates a cross talk between GC and endothelial cells under hypoxia, partially through regulation of the VEGF expression. © 2013 Wiley Periodicals, Inc. J BiochemMol Toxicol 27:364‐369, 2013; View this article online at wileyonlinelibrary.com . DOI 10.1002/jbt.21498     

Integrating domain similarity to improve protein complexes identification in TAP-MS data

Background

Detecting protein complexes in protein-protein interaction (PPI) networks plays an important role in improving our understanding of the dynamic of cellular organisation. However, protein interaction data generated by high-throughput experiments such as yeast-two-hybrid (Y2H) and tandem affinity-purification/mass-spectrometry (TAP-MS) are characterised by the presence of a significant number of false positives and false negatives. In recent years there has been a growing trend to incorporate diverse domain knowledge to support large-scale analysis of PPI networks.

Methods

This paper presents a new algorithm, by incorporating Gene Ontology (GO) based semantic similarities, to detect protein complexes from PPI networks generated by TAP-MS. By taking co-complex relations in TAP-MS data into account, TAP-MS PPI networks are modelled as bipartite graph, where bait proteins consist of one set of nodes and prey proteins are on the other. Similarities between pairs of bait proteins are computed by considering both the topological features and GO-driven semantic similarities. Bait proteins are then grouped in to sets of clusters based on their pair-wise similarities to produce a set of 'seed' clusters. An expansion process is applied to each 'seed' cluster to recruit prey proteins which are significantly associated with the same set of bait proteins. Thus, completely identified protein complexes are then obtained.

Results

The proposed algorithm has been applied to real TAP-MS PPI networks. Fifteen quality measures have been employed to evaluate the quality of generated protein complexes. Experimental results show that the proposed algorithm has greatly improved the accuracy of identifying complexes and outperformed several state-of-the-art clustering algorithms. Moreover, by incorporating semantic similarity, the proposed algorithm is more robust to noises in the networks.

     

Large enhancement of oscillating chemiluminescence with [Ru(bpy)3]2+‐catalyzed Belousov–Zhabotinsky reaction in the presence of tri‐n‐propylamine

Oscillating chemiluminescence enhanced by the addition of tri‐n‐propylamine (TPrA) to the typical Belousov–Zhabotinsky (BZ) reaction system catalyzed by ruthenium(II)tris(2.2'‐bipyridine)(Ru(bpy)₃²⁺) was investigated using a luminometry method. The [Ru(bpy)₃]²⁺/TPrA system was first used as the catalyst for a BZ oscillator in a closed system, which exhibited a shorter induction period, higher amplitude and much more stable chemiluminescence (CL) oscillation. The effects of various concentrations of TPrA, oxygen and nitrogen flow rate on the oscillating behavior of this system were examined. In addition, the CL intensity of the [Ru(bpy)₃]²⁺/TPrA–BZ system was found to be inhibited by phenol, thus providing a way for use of the BZ system in the determination of phenolic compounds. Moreover, the possible mechanism of the oscillating CL reaction catalyzed by [Ru(bpy)₃]²⁺/TPrA and the inhibition effects of oxygen and phenol on this oscillating CL system were considered. Copyright © 2012 John Wiley & Sons, Ltd.     

A new species of Austrodecus Hodgson, 1907 (Arthropoda,Pycnogonida, Austrodecidae) from?the?Southwest Indian Ridge

A new species of pycnogonid collected by the Chinese research vessel R/V Dayangyihao during cruises to the Southwest Indian Ridge in 2008 and 2009 is recorded. The new species, Austrodecus bamberi, is placed into the tristanense-section by the characters of 4-articled ovigers and present auxiliary claws and is distinguished from other species in this section by the number and length of tubercles on the first coxae.     

Phylogenetic position of Jaoa,a green algal genus endemic to China

Jaoa prasina, a freshwater green alga endemic to China, was collected from a stream in Hubei province, China. Unialgal cultivation, morphological observation, and phylogenetic analyses of small subunit ribosomal DNA and RuBisCO large subunit sequences were performed. When cultured on agar medium, the alga was irregularly filamentous, similar to marine species of Acrochaete. Aplanospores were observed on solid medium. A vesicular‐like thallus without rhizoids developed in liquid medium, similar to specimen development in natural habitats. Molecular phylogenetic analyses revealed that Jaoa was closely related to the marine genera Acrochaete Pringsheim and Ulvella Crouan & Crouan. The results suggested the genus Jaoa is a member of the family Ulvellaceae (Ulvophyceae), which contains mostly marine algae. The family name Jaoaceae should be abandoned. We speculate that Jaoa may have evolved from a marine Ulvellaceae ancestor.     

Development of rapid and highly sensitive HSPA1A promoter-driven luciferase reporter system for assessing oxidative stress associated with low-dose photodynamic therapy

Photodynamic therapy (PDT) is a regulatory-approved modality for treating a variety of malignant tumors. It induces tumor tissue damage via photosensitizer-mediated oxidative cytotoxicity. The heat shock protein 70 (HSP70-1) is a stress protein encoded by the HSPA1A gene and is significantly induced by oxidative stress associated with PDT. The aim of this study was to identify the functional region of the HSPA1A promoter that responds to PDT-induced oxidative stress and uses the stress responsiveness of HSPA1A expression to establish a rapid and cost-effective photocytotoxic assessment bioassay to evaluate the photodynamic potential of photosensitizers. By constructing luciferase vectors with a variety of hspa1a promoter fractions and examining their relative luciferase activity, we demonstrated that the DNA sequence from −218 to +87 of the HSPA1A gene could be used as a functional promoter to detect the PDT-induced oxidative stress. The maximal relative luciferase activity level of HSPA1A (HSP70-1) induced by hypericin-PDT was nearly nine times that of the control. Our results suggest that the novel reporter gene assay using a functional region of the HSP70A1A promoter has significant advantages for the detection of photoactivity in terms of both speed and sensitivity, when compared with a cell viability test based on ATP quantification and ROS levels. Furthermore, phthalocyanine zinc and methylene blue both induced significantly elevated levels of relative luciferase activity in a dose-dependent manner.