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https://www.readbyqxmd.com/read/28096531/the-first-imported-case-of-rift-valley-fever-in-china-reveals-a-genetic-reassortment-of-different-viral-lineages
#1
Jingyuan Liu, Yulan Sun, Weifeng Shi, Shuguang Tan, Yang Pan, Shujuan Cui, Qingchao Zhang, Xiangfeng Dou, Yanning Lv, Xinyu Li, Xitai Li, Lijuan Chen, Chuansong Quan, Qianli Wang, Yingze Zhao, Qiang Lv, Wenhao Hua, Hui Zeng, Zhihai Chen, Haofeng Xiong, Chengyu Jiang, Xinghuo Pang, Fujie Zhang, Mifang Liang, Guizhen Wu, George F Gao, William J Liu, Ang Li, Quanyi Wang
We report the first imported case of Rift Valley fever (RVF) in China. The patient returned from Angola, a non-epidemic country, with an infection of a new reassortant from different lineages of Rift Valley fever viruses (RVFVs). The patient developed multiorgan dysfunction and gradually recovered with continuous renal replacement therapy and a short regimen of methylprednisolone treatment. The disordered cytokines and chemokines in the plasma of the patient revealed hypercytokinemia, but the levels of protective cytokines were low upon admission and fluctuated as the disease improved...
January 18, 2017: Emerging Microbes & Infections
https://www.readbyqxmd.com/read/28096303/down-regulation-of-epas1-transcription-and-genetic-adaptation-of-tibetans-to-high-altitude-hypoxia
#2
Yi Peng, Chaoying Cui, Yaoxi He, Ouzhuluobu, Hui Zhang, Deying Yang, Qu Zhang, Bianbazhuoma, Lixin Yang, Yibo He, Kun Xiang, Xiaoming Zhang, Sushil Bhandari, Peng Shi, Yangla, Dejiquzong, Baimakangzhuo, Duojizhuoma, Yongyue Pan, Cirenyangji, Baimayangji, Gonggalanzi, Caijuan Bai, Bianba, Basang, Ciwangsangbu, Shuhua Xu, Hua Chen, Shimin Liu, Tianyi Wu, Xuebin Qi, Bing Su
Tibetans are well adapted to the hypoxic environments at high altitude, yet the molecular mechanism of this adaptation remains elusive. We reported comprehensive genetic and functional analyses of EPAS1, a gene encoding hypoxia inducible factor 2α (HIF-2α) with the strongest signal of selection in previous genome-wide scans of Tibetans. We showed that the Tibetan-enriched EPAS1 variants down-regulate expression in human umbilical endothelial cells and placentas. Heterozygous EPAS1 knockout mice display blunted physiological responses to chronic hypoxia, mirroring the situation in Tibetans...
January 17, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28096159/genome-analysis-of-the-carbapenem-and-colistin-resistant-escherichia-coli-isolate-nrz14408-reveal-horizontal-gene-transfer-pathways-towards-pan-resistance-and-enhanced-virulence
#3
Linda Falgenhauer, Hiren Ghosh, Swapnil Doijad, Yancheng Yao, Boyke Bunk, Cathrin Spröer, Martin Kaase, Rolf Hilker, Jörg Overmann, Can Imirzalioglu, Trinad Chakraborty
Colistin is used as a last-resort antibiotic for treating infections caused by multidrug-resistant Enterobacteriaceae, in particular for carbapenem-resistant isolates.….
January 17, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28095667/sequence-analysis-of-mitochondrial-genome-of-toxascaris-leonina-from-a-south-china-tiger
#4
Kangxin Li, Fang Yang, A Y Abdullahi, Meiran Song, Xianli Shi, Minwei Wang, Yeqi Fu, Weida Pan, Fang Shan, Wu Chen, Guoqing Li
Toxascaris leonina is a common parasitic nematode of wild mammals and has significant impacts on the protection of rare wild animals. To analyze population genetic characteristics of T. leonina from South China tiger, its mitochondrial (mt) genome was sequenced. Its complete circular mt genome was 14,277 bp in length, including 12 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 non-coding regions. The nucleotide composition was biased toward A and T. The most common start codon and stop codon were TTG and TAG, and 4 genes ended with an incomplete stop codon...
December 2016: Korean Journal of Parasitology
https://www.readbyqxmd.com/read/28094170/common-developmental-genome-deprogramming-in-schizophrenia-role-of-integrative-nuclear-fgfr1-signaling-infs
#5
S T Narla, Y-W Lee, C A Benson, P Sarder, K J Brennand, E K Stachowiak, M K Stachowiak
The watershed-hypothesis of schizophrenia asserts that over 200 different mutations dysregulate distinct pathways that converge on an unspecified common mechanism(s) that controls disease ontogeny. Consistent with this hypothesis, our RNA-sequencing of neuron committed cells (NCCs) differentiated from established iPSCs of 4 schizophrenia patients and 4 control subjects uncovered a dysregulated transcriptome of 1349 mRNAs common to all patients. Data reveals a global dysregulation of developmental genome, deconstruction of coordinated mRNA networks, and the formation of aberrant, new coordinated mRNA networks indicating a concerted action of the responsible factor(s)...
January 13, 2017: Schizophrenia Research
https://www.readbyqxmd.com/read/28092672/bpgap1-spatially-integrates-jnk-erk-signaling-crosstalk-in-oncogenesis
#6
T Jiang, C Q Pan, B C Low
Simultaneous hyperactivation of stress-activated protein kinase/c-Jun N-terminal protein kinase (SAPK/JNK) and mitogen-activated protein kinase kinase/extracellular signal-regulated kinase (MEK/ERK) signaling cascades has been reported in carcinogenesis. However, how they are integrated to promote oncogenesis remains unknown. By analyzing breast invasive carcinoma database (The Cancer Genome Altas), we found that the mRNA expression levels of both JNK1 and ERK2 are positively correlated with the mRNA level of EEA1, an endosome associated protein, indicating the potential JNK/ERK crosstalk at endosome...
January 16, 2017: Oncogene
https://www.readbyqxmd.com/read/28092569/discovery-of-micrornas-and-transcription-factors-co-regulatory-modules-by-integrating-multiple-types-of-genomic-data
#7
Jiawei Luo, Gen Xiang, Chu Pan
It is well known that regulators known as microRNA (miRNA) and transcription factor (TF) have been found to play an important role in gene regulation. However, there are few researches of collaborative regulatory (co-regulatory) mechanism between miRNA and TF on system level (function level). Meanwhile, recent advances in high-throughput genomic technologies have enabled researchers to collect diverse large-scale genomic data, which can be used to study the co-regulatory mechanism between miRNA and TF. In this paper, we propose a novel method called SNCoNMF (Sparse Network regularized non-negative matrix factorization for Co-regulatory modules identification) which adopts multiple non-negative matrix factorization framework to identify co-regulatory modules including miRNAs, TFs and genes...
January 9, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28087842/novel-determinants-of-mammalian-primary-microrna-processing-revealed-by-systematic-evaluation-of-hairpin-containing-transcripts-and-human-genetic-variation
#8
Christine Anne Roden, Jonathan Gaillard, Shaveta Kanoria, William Rennie, Syndi Barish, Jijun Cheng, Wen Pan, Jun Liu, Chris Cotsapas, Ye Ding, Jun Lu
Mature microRNAs (miRNAs) are processed from hairpin-containing primary miRNAs (pri-miRNAs). However, rules that distinguish pri-miRNAs from other hairpin-containing transcripts in the genome are incompletely understood. By developing a computational pipeline to systematically evaluate 30 structural and sequence features of mammalian RNA hairpins, we report several new rules that are preferentially utilized in miRNA hairpins and govern efficient pri-miRNA processing. We propose that a hairpin stem length of 36+/-3nt is optimal for pri-miRNA processing...
January 13, 2017: Genome Research
https://www.readbyqxmd.com/read/28087780/oncogenes-without-a-neighboring-tumor-suppressor-gene-are-more-prone-to-amplification
#9
William K K Wu, Xiangchun Li, Xiansong Wang, Rudin Z W Dai, Alfred S L Cheng, Maggie H T Wang, Thomas Kwong, Tai C Chow, Jun Yu, Matthew T V Chan, Sunny H Wong
Focal copy number gains or losses are important genomic hallmarks of cancer. The genomic distribution of oncogenes and tumor-suppressor genes (TSG) in relation to focal copy number aberrations is unclear. Our analysis revealed that the mean distance of TSGs from oncogenes was significantly shorter than that of non-cancer genes, suggesting that oncogenes and TSGs tend to be in close physical proximity in the human genome. Such relationship was conserved in mouse and drosophila. Pan-cancer analysis using data from The Cancer Genome Atlas indicated that oncogenes without a nearby TSG are more prone to amplification...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28086747/microrna-based-pan-cancer-diagnosis-and-treatment-recommendation
#10
Nikhil Cheerla, Olivier Gevaert
BACKGROUND: The current state-of-the-art in cancer diagnosis and treatment is not ideal; diagnostic tests are accurate but invasive, and treatments are "one-size fits-all" instead of being personalized. Recently, miRNA's have garnered significant attention as cancer biomarkers, owing to their ease of access (circulating miRNA in the blood) and stability. There have been many studies showing the effectiveness of miRNA data in diagnosing specific cancer types, but few studies explore the role of miRNA in predicting treatment outcome...
January 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28081126/a-pan-lyssavirus-taqman-real-time-rt-pcr-assay-for-the-detection-of-highly-variable-rabies-virus-and-other-lyssaviruses
#11
Ashutosh Wadhwa, Kimberly Wilkins, Jinxin Gao, Rene Edgar Condori Condori, Crystal M Gigante, Hui Zhao, Xiaoyue Ma, James A Ellison, Lauren Greenberg, Andres Velasco-Villa, Lillian Orciari, Yu Li
Rabies, resulting from infection by Rabies virus (RABV) and related lyssaviruses, is one of the most deadly zoonotic diseases and is responsible for up to 70,000 estimated human deaths worldwide each year. Rapid and accurate laboratory diagnosis of rabies is essential for timely administration of post-exposure prophylaxis in humans and control of the disease in animals. Currently, only the direct fluorescent antibody (DFA) test is recommended for routine rabies diagnosis. Reverse-transcription polymerase chain reaction (RT-PCR) based diagnostic methods have been widely adapted for the diagnosis of other viral pathogens, but there is currently no widely accepted rapid real-time RT-PCR assay for the detection of all lyssaviruses...
January 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28078999/hdacs-and-hdac-inhibitors-in-urothelial-carcinoma-perspectives-for-an-antineoplastic-treatment
#12
Maria Pinkerneil, Michèle J Hoffmann, Wolfgang A Schulz, Günter Niegisch
Histone deacetylases (HDACs) influence diverse cellular processes and may contribute to tumor development and progression by multiple mechanisms. Class I HDACs are often overexpressed in cancers contributing to a genome-wide epigenetic state permitting increased proliferation, and diminished apoptosis and cell differentiation. Class IIA and IIB isoenzymes may likewise contribute to tumorigenesis as components of specific intranuclear repressor complexes or regulators of posttranslational protein modifications...
January 11, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28077636/klebsiella-phage-%C3%AE-k64-1-encodes-multiple-depolymerases-for-multiple-host-capsular-types
#13
Yi-Jiun Pan, Tzu-Lung Lin, Ching-Ching Chen, Yun-Ting Tsai, Yi-Hsiang Cheng, Yi-Yin Chen, Pei-Fang Hsieh, Yi-Tsung Lin, Jin-Town Wang
: The genome of the multi-host bacteriophage ΦK64-1, capable of infecting Klebsiella capsular types K1, K11, K21, K25, K30, K35, K64, and K69, as well as new capsular types KN4 and KN5 was analyzed and revealed that 11 genes (S1-1, S1-2, S1-3, S2-1, S2-2, S2-3, S2-4, S2-5, S2-6, S2-7, and S2-8) encode proteins with amino acid sequence similarity to tail fibers/spikes or lyases. S2-5 previously was shown to encode a K64 capsule depolymerase (K64dep). Specific capsule-degrading activities of an additional 8 putative capsule depolymerases (S2-4 against K1; S1-1 against K11; S1-3 against K21; S2-2 against K25; S2-6 against K30/K69; S2-3 against K35; S1-2 against KN4; S2-1 against KN5) was demonstrated by expression and purification of the recombinant proteins...
January 11, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28073171/pan-cancer-survey-of-epithelial-mesenchymal-transition-markers-across-the-cancer-genome-atlas
#14
Don L Gibbons, Chad J Creighton
BACKGROUND: While epithelial-mesenchymal transition (EMT) can be readily induced experimentally in cancer cells, the EMT process as manifested in human tumors needs to be better understood. Pan-cancer genomic datasets from The Cancer Genome Atlas (TCGA)-representing over 10,000 patients and 32 distinct cancer types-provide a rich resource for examining correlative patterns involving EMT mediators in the setting of human cancers. RESULTS: Here, we surveyed a 16-gene signature of canonical EMT markers in TCGA pan-cancer cohort...
January 10, 2017: Developmental Dynamics: An Official Publication of the American Association of Anatomists
https://www.readbyqxmd.com/read/28069585/expression-of-hmgb2-indicates-worse-survival-of-patients-and-is-required-for-the-maintenance-of-warburg-effect-in-pancreatic-cancer
#15
Xin Cai, Hongjian Ding, Yanxia Liu, Gaofeng Pan, Qingguo Li, Zhen Yang, Weiyan Liu
High mobility group proteins (HMGs) are the second most abundant chromatin proteins and exert global genomic functions in the establishment of active or inactive chromatin domains. Through interaction with nucleosomes, transcription factors, nucleosome-remodeling machines and histones, the HMGs family proteins contribute to the fine tuning of transcription in response to rapid environmental changes. Mammalian high mobility group Bs (HMGBs) are characterized by two tandem HMG box domains followed by a long acidic tail...
January 9, 2017: Acta Biochimica et Biophysica Sinica
https://www.readbyqxmd.com/read/28061744/comprehensive-evaluation-of-extracellular-small-rna-isolation-methods-from-serum-in-high-throughput-sequencing
#16
Yan Guo, Kasey Vickers, Yanhua Xiong, Shilin Zhao, Quanhu Sheng, Pan Zhang, Wanding Zhou, Charles R Flynn
BACKGROUND: DNA and RNA fractions from whole blood, serum and plasma are increasingly popular analytes that are currently under investigation for their utility in the diagnosis and staging of disease. Small non-coding ribonucleic acids (sRNAs), specifically microRNAs (miRNAs) and their variant isoforms (isomiRs), and transfer RNA (tRNA)-derived small RNAs (tDRs) comprise a repertoire of molecules particularly promising in this regard. RESULTS: In this designed study, we compared the performance of various methods and kits for isolating circulating extracellular sRNAs (ex-sRNAs)...
January 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28060574/the-hcp-proteins-fused-with-diverse-extended-toxin-domains-represent-a-novel-pattern-of-antibacterial-effectors-in-type-vi-secretion-systems
#17
Jiale Ma, Zihao Pan, Jinhu Huang, Min Sun, Chengping Lu, Huochun Yao
The type VI secretion system (T6SS) is a widespread molecular weapon deployed by many bacterial species to target eukaryotic host cells or rival bacteria. Using a dynamic injection mechanism, diverse effectors can be delivered by T6SS directly into recipient cells. Here, we report a new family of T6SS effectors encoded by extended Hcps carrying diverse toxin domains. Bioinformatic analyses revealed that these Hcps with C-terminal extension toxins, designated as Hcp-ET, exist widely in the Enterobacteriaceae...
January 6, 2017: Virulence
https://www.readbyqxmd.com/read/28057934/the-driving-force-of-prophages-and-crispr-cas-system-in-the-evolution-of-cronobacter-sakazakii
#18
Haiyan Zeng, Jumei Zhang, Chensi Li, Tengfei Xie, Na Ling, Qingping Wu, Yingwang Ye
Cronobacter sakazakii is an important foodborne pathogens causing rare but life-threatening diseases in neonates and infants. CRISPR-Cas system is a new prokaryotic defense system that provides adaptive immunity against phages, latter play an vital role on the evolution and pathogenicity of host bacteria. In this study, we found that genome sizes of C. sakazakii strains had a significant positive correlation with total genome sizes of prophages. Prophages contributed to 16.57% of the genetic diversity (pan genome) of C...
January 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28056774/identification-of-coding-and-non-coding-mutational-hotspots-in-cancer-genomes
#19
Scott W Piraino, Simon J Furney
BACKGROUND: The identification of mutations that play a causal role in tumour development, so called "driver" mutations, is of critical importance for understanding how cancers form and how they might be treated. Several large cancer sequencing projects have identified genes that are recurrently mutated in cancer patients, suggesting a role in tumourigenesis. While the landscape of coding drivers has been extensively studied and many of the most prominent driver genes are well characterised, comparatively less is known about the role of mutations in the non-coding regions of the genome in cancer development...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28056099/integrated-analysis-of-genome-wide-copy-number-alterations-and-gene-expression-profiling-of-lung-cancer-in-xuanwei-china
#20
Yanliang Zhang, Qiuyue Xue, Guoqing Pan, Qing H Meng, Xiaoyu Tuo, Xuemei Cai, Zhenghui Chen, Ya Li, Tao Huang, Xincen Duan, Yong Duan
OBJECTIVES: Lung cancer in Xuanwei (LCXW), China, is known throughout the world for its distinctive characteristics, but little is known about its pathogenesis. The purpose of this study was to screen potential novel "driver genes" in LCXW. METHODS: Genome-wide DNA copy number alterations (CNAs) were detected by array-based comparative genomic hybridization and differentially expressed genes (DEGs) by gene expression microarrays in 8 paired LCXW and non-cancerous lung tissues...
2017: PloS One
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