Copy number variants in locally raised Chinese chicken genomes determined using array comparative genomic hybridization

BACKGROUND: Copy number variants contribute to genetic variation in birds. Analyses of copy number variants in chicken breeds had focused primarily on those from commercial varieties with nothing known about the occurrence and diversity of copy number variants in locally raised Chinese chicken breeds. To address this deficiency, we characterized copy number variants in 11 chicken breeds and compared the variation among these breeds. RESULTS: We presented a detailed analysis of the copy number variants in locally raised Chinese chicken breeds identified using a customized comparative genomic hybridization array. We identified 833 copy number variants contained within 308 copy number variant regions. The median and mean sizes of the copy number variant regions were 14.6 kb and 35.1 kb, respectively. Of the copy number variant regions, 138 (45%) involved gain of DNA, 159 (52%) involved loss of DNA, and 11 (3%) involved both gain and loss of DNA. Principal component analysis and agglomerative hierarchical clustering revealed the close relatedness of the four locally raised chicken breeds, Shek-Ki, Langshan, Qingyuan partridge, and Wenchang. Biological process enrichment analysis of the copy number variant regions confirmed the greater variation among the four aforementioned varieties than among the seven other breeds studied. CONCLUSION: Our description of the distribution of the copy number variants and comparison of the differences among the copy number variant regions of the 11 chicken breeds supplemented the information available concerning the copy number variants of other Chinese chicken breeds. In addition to its relevance for functional analysis, our results provided the first insight into how chicken breeds can be clustered on the basis of their genomic copy number variation

Antioxidant and Preventive Effects of Extract from Nymphaea candida Flower on In Vitro Immunological Liver Injury of Rat Primary Hepatocyte Cultures

Nymphaea candida is traditional Uighur medicine that is commonly used to treat head pains, cough, hepatitis and hypertension in Xinjiang of China. In this article, the extract of N. candida was measured for antioxidant activity, using 1,1-diphenyl-2-picrylhydrazyl (DPPH) radicals scavenging assay and reducing power determination, and compared with those of the positive controls of butylated hydroxytoluene (BHT) and gallic acid (GA). The active extract was further purified by liquid-liquid partition to afford four fractions, of which the ethyl acetate-soluble (EA) fraction (NCE) exhibited the strongest antioxidant capacity with IC50 value of 12.6 μg/mL for DPPH. Thirteen phenolic compounds were isolated from this fraction, and they all showed significant antioxidant activities in DPPH model system. Furthermore, NCE showed potent antioxidant capacity with IC50 value of 59.32 μg/mL, 24.48 μg/mL and 86.85 μg/mL, for O2−, ·OH and H2O2 radicals, respectively. Moreover, NCE on BCG plus LPS-induced immunological liver injury was evaluated using primary cultured rat hepatocytes. NCE produced significant hepatoprotective effects as evidenced by decreased supernatant enzyme activities (AST—aspartate transaminase, P <  .01; ALT—alanine transferase, P <  .01) and nitric oxide (NO, P <  .01) production. These results revealed the in vitro antioxidant and hepatoprotective activities of NCE against immunological liver injury. Further investigations are necessary to verify these activities in vivo

tRNASer(CGA) differentially regulates expression of wild-type and codon-modified papillomavirus L1 genes

Exogenous transfer RNAs (tRNAs) favor translation of bovine papillomavirus 1 wild-type (wt) L1 mRNA in in vitro translation systems (Zhou et al. 1999, J. Virol., 73, 4972-4982). We, therefore, investigated whether papillomavirus (PV) wt L1 protein expression could be enhanced in eukaryotic cells following exogenous tRNA supplementation. Both Chinese hamster ovary (CHO) and Cos1 cells, transfected with PV1 wt L1 genes, effectively transcribed the genes but did not translate them. However, L1 protein translation was demonstrated following co-transfection with the L1 gene and a gene expressing tRNA(Ser)(CGA). Cell lines, stably transfected with a bovine papillomavirus 1 (BPV1) wt L1 expression construct, produced L1 protein after the transfection of the tRNA(Ser)(CGA) gene, but not following the transfection with basal vectors, suggesting that tRNA(Ser)(CGA) gene enhanced wt L1 translation as a result of endogenous tRNA alterations and phosphorylation of translation initiation factors elF4E and elF2alpha in the tRNA(Ser)(CGA) transfected L1 cell lines. The tRNA(Ser)(CGA) gene expression significantly reduced translation of L1 proteins expressed from codon-modified (HB) PV L1 genes utilizing mammalian preferred codons, but had variable effects on translation of green fluorescent proteins (GFPs) expressed from six serine GFP variants. The changes of tRNA pools appear to match the codon composition of PV wt and HB L1 genes and serine GFP variants to regulate translation of their mRNAs. These findings demonstrate for the first time in eukaryotic cells that translation of the target genes can be differentially influenced by the provision of a single tRNA expression construct

A Comprehensive Survey on Deep Graph Representation Learning

Graph representation learning aims to effectively encode high-dimensional sparse graph-structured data into low-dimensional dense vectors, which is a fundamental task that has been widely studied in a range of fields, including machine learning and data mining. Classic graph embedding methods follow the basic idea that the embedding vectors of interconnected nodes in the graph can still maintain a relatively close distance, thereby preserving the structural information between the nodes in the graph. However, this is sub-optimal due to: (i) traditional methods have limited model capacity which limits the learning performance; (ii) existing techniques typically rely on unsupervised learning strategies and fail to couple with the latest learning paradigms; (iii) representation learning and downstream tasks are dependent on each other which should be jointly enhanced. With the remarkable success of deep learning, deep graph representation learning has shown great potential and advantages over shallow (traditional) methods, there exist a large number of deep graph representation learning techniques have been proposed in the past decade, especially graph neural networks. In this survey, we conduct a comprehensive survey on current deep graph representation learning algorithms by proposing a new taxonomy of existing state-of-the-art literature. Specifically, we systematically summarize the essential components of graph representation learning and categorize existing approaches by the ways of graph neural network architectures and the most recent advanced learning paradigms. Moreover, this survey also provides the practical and promising applications of deep graph representation learning. Last but not least, we state new perspectives and suggest challenging directions which deserve further investigations in the future

Distinct enhancement of sub-bandgap photoresponse through intermediate band in high dose implanted ZnTe:O alloys

The demand for high efficiency intermediate band (IB) solar cells is driving efforts in producing high quality IB photovoltaic materials. Here, we demonstrate ZnTe:O highly mismatched alloys synthesized by high dose ion implantation and pulsed laser melting exhibiting optically active IB states and efficient sub-gap photoresponse, as well as investigate the effect of pulsed laser melting on the structural and optical recovery in detail. The structural evolution and vibrational dynamics indicates a significant structural recovery of ZnTe:O alloys by liquid phase epitaxy during pulsed laser melting process, but laser irradiation also aggravates the segregation of Te in ZnTe:O alloys. A distinct intermediate band located at 1.8 eV above valence band is optically activated as evidenced by photoluminescence, absorption and photoresponse characteristics. The carrier dynamics indicates that carriers in the IB electronic states have a relatively long lifetime, which is beneficial for the fast separation of carriers excited by photons with sub-gap energy and thus the improved overall conversion efficiency. The reproducible capability of implantation and laser annealing at selective area enable the realization of high efficient lateral junction solar cells, which can ensure extreme light trapping and efficient charge separationThis research was supported by National Natural Science Foundation of China (Nos 61274058, 61271077, 61504057, 61574075 and 61322403), the Natural Science Foundation of Jiangsu Province (Nos BK2011437 and BK20130013), the Six Talent Peaks Project in Jiangsu Province (2014XXRJ001), the Priority Academic Program Development of Jiangsu Higher Education Institutions, and the Australian Research Council

Bradyrhizobium diazoefficiens USDA 110–glycine max interactome provides candidate proteins associated with symbiosis

Although the legume−rhizobium symbiosis is a most-important biological process, there is a limited knowledge about the protein interaction network between host and symbiont. Using interolog- and domain-based approaches, we constructed an interspecies protein interactome containing 5115 protein−protein interactions between 2291 Glycine max and 290 Bradyrhizobium diazoefficiens USDA 110 proteins. The interactome was further validated by the expression pattern analysis in nodules, gene ontology term semantic similarity, co-expression analysis, and luciferase complementation image assay. In the G. max−B. diazoefficiens interactome, bacterial proteins are mainly ion channel and transporters of carbohydrates and cations, while G. max proteins are mainly involved in the processes of metabolism, signal transduction, and transport. We also identified the top 10 highly interacting proteins (hubs) for each species. Kyoto Encyclopedia of Genes and Genomes pathway analysis for each hub showed that a pair of 14-3-3 proteins (SGF14g and SGF14k) and 5 heat shock proteins in G. max are possibly involved in symbiosis, and 10 hubs in B. diazoefficiens may be important symbiotic effectors. Subnetwork analysis showed that 18 symbiosis-related soluble N-ethylmaleimide sensitive factor attachment protein receptor proteins may play roles in regulating bacterial ion channels, and SGF14g and SGF14k possibly regulate the rhizobium dicarboxylate transport protein DctA. The predicted interactome provide a valuable basis for understanding the molecular mechanism of nodulation in soybean

Activation of PI3K/AKT and MAPK Pathway through a PDGFRβ-Dependent Feedback Loop Is Involved in Rapamycin Resistance in Hepatocellular Carcinoma

Background: Rapamycin is an attractive approach for the treatment and prevention of HCC recurrence after liver transplantation. However, the objective response rates of rapamycin achieved with single-agent therapy were modest, supporting that rapamycin resistance is a frequently observed characteristic of many cancers. Some studies have been devoted to understanding the mechanisms of rapamycin resistance, however, the mechanisms are cell-type-dependent and studies on rapamycin resistance in HCC are extremely limited. Methodology/Principal Findings: The anti-tumor sensitivity of rapamycin was modest in vitro and in vivo. In both human and rat HCC cells, rapamycin up-regulated the expression and phosphorylation of PDGFRb in a time and dose-dependent manner as assessed by RT-PCR and western blot analysis. Using siRNA mediated knockdown of PDGFRb, we confirmed that subsequent activation of AKT and ERK was PDGFRb-dependent and compromised the anti-tumor activity of rapamycin. Then, blockade of this PDGFRb-dependent feedback loop by sorafenib enhanced the anti-tumor sensitivity of rapamycin in vitro and in an immunocompetent orthotopic rat model of HCC. Conclusions: Activation of PI3K/AKT and MAPK pathway through a PDGFRb-dependent feedback loop compromises the anti-tumor activity of rapamycin in HCC, and blockade of this feedback loop by sorafenib is an attractive approach t

IL-17 induces AKT-dependent IL-6/JAK2/STAT3 activation and tumor progression in hepatocellular carcinoma

<p>Abstract</p> <p>Background</p> <p>The Th17 subset and IL-17 have been found in increased frequencies within certain tumors. However, their relevance in cancer biology remains controversial. This study aimed to clarify the biological action of IL-17 on hepatocellular carcinoma (HCC).</p> <p>Methods</p> <p>Effects and underlying molecular mechanisms of IL-17 on human HCC were explored <it>in vitro </it>using exogenous IL-17 stimulation and in nude mice by implanting IL-17 overexpressed HCC cells. The clinical significance of IL-17 was investigated in tissue microarrays containing HCC tissues from 323 patients following hepatectomy using immunohistochemistry.</p> <p>Results</p> <p>Although exogenous IL-17 showed no direct effect on the growth rate of HCC cells <it>in vitro</it>, PCR and ELISA showed that IL-17 selectively augmented the secretion of diverse proinvasive factors and transwell showed a direct promotion of invasion of HCC cells by IL-17. Furthermore, transfection of IL-17 into HCC cells significantly promoted neoangiogenesis, neutrophil recruitment and tumor growth <it>in vivo</it>. Using siRNA mediated knockdown of AKT and STAT3, we suggested that the effects of IL-17 were operated through activation of the AKT signaling in HCC, which resulted in IL-6 production. Then, IL-6 in turn activated JAK2/STAT3 signaling and subsequently up-regulated its downstream targets IL-8, MMP2, and VEGF. Supporting these findings, in human HCC tissues, immunostaining indicated that IL-17 expression was significantly and positively associated with STAT3 phosphorylation, neutrophil infiltration and increased tumor vascularity. The clinical significance of IL-17 was authenticated by revealing that the combination of intratumoral IL-17+ cells and phospho-STAT3 served as a better prognosticator for postoperative tumor recurrence than either marker alone.</p> <p>Conclusions</p> <p>IL-17 mediated tumor-promoting role involves a direct effect on HCC cells through IL-6/JAK2/STAT3 induction by activating the AKT pathway.</p

Preservation of Cognitive Function by Lepidium meyenii

Maca has been used as a foodstuff and a traditional medicine in the Andean region for over 2,000 years. Recently the neuroprotective effects of maca also arouse interest of researchers. Decrease in mitochondrial function and decline in autophagy signaling may participate in the process of age-related cognitive decline. This study aimed to investigate if maca could improve cognitive function of middle-aged mice and if this effect was associated with improvement of mitochondrial activity and modulation of autophagy signaling in mouse cortex. Fourteen-month-old male ICR mice received maca powder administered by gavage for five weeks. Maca improved cognitive function, motor coordination, and endurance capacity in middle-aged mice, accompanied by increased mitochondrial respiratory function and upregulation of autophagy-related proteins in cortex. Our findings suggest that maca is a newly defined nutritional plant which can improve mitochondrial function and upregulate autophagy-related proteins and may be an effective functional food for slowing down age-related cognitive decline