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https://www.readbyqxmd.com/read/28525986/the-lspc3-41i-restriction-modification-system-is-the-major-determinant-for-genetic-manipulations-of-lysinibacillus-sphaericus-c3-41
#1
Pan Fu, Yong Ge, Yiming Wu, Ni Zhao, Zhiming Yuan, Xiaomin Hu
BACKGROUND: Lysinibacillus sphaericus has been widely used in integrated mosquito control program and it is one of the minority bacterial species unable to metabolize carbohydrates. In consideration of the high genetic conservation at genomic level and difficulty of genetic horizontal transfer, it is hypothesized that effective restriction-modification (R-M) systems existed in mosquitocidal L. sphaericus. RESULTS: In this study, six type II R-M systems including LspC3-41I were predicted in L...
May 19, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28522810/integrative-analysis-of-genomic-sequencing-data-reveals-higher-prevalence-of-lrp1b-mutations-in-lung-adenocarcinoma-patients-with-copd
#2
Dakai Xiao, Fuqiang Li, Hui Pan, Han Liang, Kui Wu, Jianxing He
Both chronic Obstruction Pulmonary Disease (COPD) and lung cancer are leading causes of death globally. Although COPD and lung cancer coexist frequently, it is unknown whether lung cancer patients with COPD harbor distinct genomic characteristics compared to those without COPD. In this study, we retrospectively analyzed genomic sequencing data from 272 patients with lung adenocarcinoma (LUAD) and compared the genetic alterations in LUAD patients with and without COPD. Integrative analysis of whole-genome and exome sequencing data revealed that COPD and non-COPD groups showed high concordance in mutational burden and spectra...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28515302/transposon-mutagenesis-of-the-zika-virus-genome-highlights-regions-essential-for-rna-replication-and-restricted-for-immune-evasion
#3
Benjamin O Fulton, David Sachs, Megan C Schwarz, Peter Palese, Matthew J Evans
The molecular constraints affecting Zika virus (ZIKV) evolution are not well understood. To investigate ZIKV genetic flexibility, we used transposon mutagenesis to add 15-nucleotide insertions throughout the MR766 ZIKV genome and subsequently deep sequenced the viable mutants. Few ZIKV insertion mutants replicated, which likely reflects a high degree of functional constraints on the genome. The NS1 gene exhibited distinct mutational tolerances at different stages of the screen. This result may define regions of the NS1 protein that are required for the different stages of the viral life cycle...
May 17, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28511652/ing3-promotes-prostate-cancer-growth-by-activating-the-androgen-receptor
#4
Arash Nabbi, Urszula L McClurg, Subhash Thalappilly, Amal Almami, Mahsa Mobahat, Tarek A Bismar, Olivier Binda, Karl T Riabowol
BACKGROUND: The androgen receptor (AR) is a major driver of prostate cancer, and increased AR levels and co-activators of the receptor promote the development of prostate cancer. INhibitor of Growth (ING) proteins target lysine acetyltransferase or lysine deacetylase complexes to the histone H3K4Me3 mark of active transcription, to affect chromatin structure and gene expression. ING3 is a stoichiometric member of the TIP60 lysine acetyltransferase complex implicated in prostate cancer development...
May 16, 2017: BMC Medicine
https://www.readbyqxmd.com/read/28507329/breeding-histories-and-selection-criteria-for-oilseed-rape-in-europe-and-china-identified-by-genome-wide-pedigree-dissection
#5
Xiaohua Wang, Yan Long, Nian Wang, Jun Zou, Guangda Ding, Martin R Broadley, Philip J White, Pan Yuan, Qianwen Zhang, Ziliang Luo, Peifa Liu, Hua Zhao, Ying Zhang, Hongmei Cai, Graham J King, Fangsen Xu, Jinling Meng, Lei Shi
Selection breeding has played a key role in the improvement of seed yield and quality in oilseed rape (Brassica napus L.). We genotyped Tapidor (European), Ningyou7 (Chinese) and their progenitors with the Brassica 60 K Illumina Infinium SNP array and mapped a total of 29,347 SNP markers onto the reference genome of Darmor-bzh. Identity by descent (IBD) refers to a haplotype segment of a chromosome inherited from a shared common ancestor. IBDs identified on the C subgenome were larger than those on the A subgenome within both the Tapidor and Ningyou7 pedigrees...
May 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28502652/comparative-and-evolutionary-analysis-of-an-adapter-molecule-myd88-in-invertebrate-metazoans
#6
Yipeng Ren, Junli Xue, Huanhuan Yang, Baoping Pan, Wenjun Bu
The myeloid differentiation factor 88 (MyD88) is an essential adapter in Toll-like receptor (TLR) signalling pathways, with TLR the first pattern-recognition receptor (PRR) that was discovered in Drosophila. In the present study, a MyD88 gene was identified and characterized from a commercially important shellfish, Scapharca subcrenata, including a DEATH domain and TIR domain conserved within other molluscs. Furthermore, comparative genomic evidence revealed that MyD88 was of different lengths and contained quantitative exon and intron regions, which might be involved in specific mechanisms...
May 11, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28500398/comparative-clinical-utility-of-tumor-genomic-testing-and-cell-free-dna-in-metastatic-breast-cancer
#7
Kara N Maxwell, Danielle Soucier-Ernst, Emin Tahirovic, Andrea B Troxel, Candace Clark, Michael Feldman, Christopher Colameco, Bijal Kakrecha, Melissa Langer, David Lieberman, Jennifer J D Morrissette, Matt R Paul, Tien-Chi Pan, Stephanie Yee, Natalie Shih, Erica Carpenter, Lewis A Chodosh, Angela DeMichele
PURPOSE: Breast cancer metastases differ biologically from primary disease; therefore, metastatic biopsies may assist in treatment decision making. Commercial genomic testing of both tumor and circulating tumor DNA have become available clinically, but utility of these tests in breast cancer management remains unclear. METHODS: Patients undergoing a clinically indicated metastatic tumor biopsy were consented to the ongoing METAMORPH registry. Tumor and blood were collected at the time of disease progression before subsequent therapy, and patients were followed for response on subsequent treatment...
May 12, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28499833/mitochondrial-dysfunction-in-cancer-potential-roles-of-atf5-and-the-mitochondrial-upr
#8
REVIEW
Pan Deng, Cole M Haynes
Mitochondria form a cellular network of organelles, or cellular compartments, that efficiently couple nutrients to energy production in the form of ATP. As cancer cells rely heavily on glycolysis, historically mitochondria and the cellular pathways in place to maintain mitochondrial activities were thought to be more relevant to diseases observed in non-dividing cells such as muscles and neurons. However, more recently it has become clear that cancers rely heavily on mitochondrial activities including lipid, nucleotide and amino acid synthesis, suppression of mitochondria-mediated apoptosis as well as oxidative phosphorylation (OXPHOS) for growth and survival...
May 9, 2017: Seminars in Cancer Biology
https://www.readbyqxmd.com/read/28498781/phase-i-study-and-biomarker-analysis-of-pyrotinib-a-novel-irreversible-pan-erbb-receptor-tyrosine-kinase-inhibitor-in-patients-with-human-epidermal-growth-factor-receptor-2-positive-metastatic-breast-cancer
#9
Fei Ma, Qiao Li, Shanshan Chen, Wenjie Zhu, Ying Fan, Jiayu Wang, Yang Luo, Puyuan Xing, Bo Lan, Meiying Li, Zongbi Yi, Ruigang Cai, Peng Yuan, Pin Zhang, Qing Li, Binghe Xu
Purpose This phase I study assessed the safety, tolerability, pharmacokinetics, antitumor activity, and predictive biomarkers of pyrotinib, an irreversible pan-ErbB inhibitor, in patients with human epidermal growth factor receptor 2 (HER2)-positive metastatic breast cancer. Patients and Methods Pyrotinib was administered continuously, orally, once per day to patients who did not have prior exposure to tyrosine kinase inhibitors of HER2. Planned dose escalation was 80, 160, 240, 320, 400, and 480 mg. For pharmacokinetic analysis, timed blood samples were collected on day 1 and day 28...
May 12, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28496186/an-ancient-selective-sweep-linked-to-reproductive-life-history-evolution-in-sockeye-salmon
#10
Andrew J Veale, Michael A Russello
Study of parallel (or convergent) phenotypic evolution can provide important insights into processes driving sympatric, ecologically-mediated divergence and speciation, as ecotype pairs may provide a biological replicate of the underlying signals and mechanisms. Here, we provide evidence for a selective sweep creating an island of divergence associated with reproductive behavior in sockeye salmon (Oncorhynchus nerka), identifying a series of linked single nucleotide polymorphisms across a ~22,733 basepair region spanning the leucine-rich repeat-containing protein 9 gene exhibiting signatures of divergent selection associated with stream- and shore-spawning in both anadromous and resident forms across their pan-Pacific distribution...
May 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28495757/complete-genome-sequence-of-a-novel-multidrug-resistant-klebsiella-pneumoniae-phage-vb_kpn_ime260
#11
Shaozhen Xing, Xiangchun Pan, Qiang Sun, Guangqian Pei, Xiaoping An, Zhiqiang Mi, Yong Huang, Baohua Zhao, Yigang Tong
Klebsiella pneumoniae is the most common clinically important opportunistic bacterial pathogen and its infection is often iatrogenic. Its drug resistance poses a grave threat to public health. The genomic data reported here comprise an important resource for research on phage therapy in the control of drug-resistant bacteria.
May 11, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28490487/bifidobacterium-bacteremia-clinical-characteristics-and-a-genomic-approach-to-assess-pathogenicity
#12
Eirin Esaiassen, Erik Hjerde, Jorunn Pauline Cavanagh, Gunnar Skov Simonsen, Claus Klingenberg
Bifidobacteria are commensals that colonize the orogastrointestinal tract, and rarely cause invasive human infections. However, an increasing number of bifidobacterial blood culture isolates has lately been observed in Norway. In order to investigate the pathogenicity of Bifidobacterium species responsible for bacteremia, we studied Bifidobacterium isolates from 15 patients with a positive blood culture obtained during 2013 to 2015. We collected clinical data and analyzed phenotypic and genotypic antibiotic susceptibility...
May 10, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28489509/akt-inhibition-in-solid-tumors-with-akt1-mutations
#13
David M Hyman, Lillian M Smyth, Mark T A Donoghue, Shannon N Westin, Philippe L Bedard, Emma J Dean, Hideaki Bando, Anthony B El-Khoueiry, José A Pérez-Fidalgo, Alain Mita, Jan H M Schellens, Matthew T Chang, Jonathan B Reichel, Nancy Bouvier, S Duygu Selcuklu, Tara E Soumerai, Jean Torrisi, Joseph P Erinjeri, Helen Ambrose, J Carl Barrett, Brian Dougherty, Andrew Foxley, Justin P O Lindemann, Robert McEwen, Martin Pass, Gaia Schiavon, Michael F Berger, Sarat Chandarlapaty, David B Solit, Udai Banerji, José Baselga, Barry S Taylor
Purpose AKT1 E17K mutations are oncogenic and occur in many cancers at a low prevalence. We performed a multihistology basket study of AZD5363, an ATP-competitive pan-AKT kinase inhibitor, to determine the preliminary activity of AKT inhibition in AKT-mutant cancers. Patients and Methods Fifty-eight patients with advanced solid tumors were treated. The primary end point was safety; secondary end points were progression-free survival (PFS) and response according to Response Evaluation Criteria in Solid Tumors (RECIST)...
May 10, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28484671/genome-wide-analysis-of-wrky-transcription-factors-in-wheat-triticum-aestivum-l-and-differential-expression-under-water-deficit-condition
#14
Pan Ning, Congcong Liu, Jingquan Kang, Jinyin Lv
BACKGROUND: WRKY proteins, which comprise one of the largest transcription factor (TF) families in the plant kingdom, play crucial roles in plant development and stress responses. Despite several studies on WRKYs in wheat (Triticum aestivum L.), functional annotation information about wheat WRKYs is limited. RESULTS: Here, 171 TaWRKY TFs were identified from the whole wheat genome and compared with proteins from 19 other species representing nine major plant lineages...
2017: PeerJ
https://www.readbyqxmd.com/read/28481120/molecular-epidemiology-of-wu-polyomavirus-in-hospitalized-children-with-acute-respiratory-tract-infection-in-china
#15
Teng Zhu, Qing-Bin Lu, Shu-Yan Zhang, Ying Wo, Lu Zhuang, Pan-He Zhang, Xiao-Ai Zhang, Wei Wei, Wei Liu
AIM: To explore the molecular epidemiology and clinical characteristics of Washington University polyomavirus (WUPyV) infection in pediatric patients with acute respiratory tract infections in China. MATERIALS & METHODS: A laboratory surveillance was performed to recruit pediatric patients with acute respiratory tract infections. WUPyV was detected using real-time PCR and complete genome was sequenced for randomly selected positive nasopharyngeal aspirate. RESULTS: Altogether 122 (7...
May 8, 2017: Future Microbiology
https://www.readbyqxmd.com/read/28474344/differential-expression-of-duplicated-binary-toxin-genes-bina-binb-in-lysinibacillus-sphaericus-c3-41
#16
Pan Fu, Xingchen Xiang, Yong Ge, Zhiming Yuan, Xiaomin Hu
Due to the self-produced binary toxins BinA/BinB, some Lysinibacillus sphaericus isolates exhibit high toxicity against mosquito larvae and are utilized in mosquito control programs. Previous whole genome sequencing revealed the presence of a large plasmid pBsph in L. sphaericus C3-41, which contains a 30.5-kb duplication of the genome including the binary toxin genes binA/binB. This was confirmed by Southern blot and qPCR experiments in this study. Mutants of L. sphaericus C3-41, bearing disruptions of the chromosomal-bin (C3-41ΔCab ) or the plasmid-bin (C3-41ΔPab ) and a plasmid cured strain G725, were generated...
May 5, 2017: Letters in Applied Microbiology
https://www.readbyqxmd.com/read/28473198/subcellular-distribution-of-rad23b-controls-xpc-degradation-and-dna-damage-repair-in-response-to-chemotherapy-drugs
#17
Xue You, Weiwei Guo, Lin Wang, Yongfan Hou, Huanhuan Zhang, Yi Pan, Ruomei Han, Meiqin Huang, Lujian Liao, Yan Chen
The RAD23B-XPC complex in the nucleus plays a key role in the initial damage recognition during global genome nucleotide excision repair (NER). Within the complex, XPC, a product of Xeroderma pigmentosum C, recognizes and interacts with the unpaired bases in the undamaged DNA strand, while RAD23B stabilizes XPC. However, how RAD23B is regulated by other factors is not well known. We report here a mode of spatial regulation of RAD23B that controls XPC stability and DNA damage repair. We first identified that RAD23B was able to directly associate with PAQR3, a newly-discovered tumor suppressor implicated in many types of human cancers...
May 1, 2017: Cellular Signalling
https://www.readbyqxmd.com/read/28472932/chromosome-microarray-analysis-in-the-investigation-of-children-with-congenital-heart-disease
#18
Xiao-Li Wu, Ru Li, Fang Fu, Min Pan, Jin Han, Xin Yang, Yong-Ling Zhang, Fa-Tao Li, Can Liao
BACKGROUND: Our study was aimed to explore the clinical implication of chromosome microarray analysis (CMA) in genetically etiological diagnosis of children with congenital heart disease (CHD). METHODS: A total of 104 children with CHD with or without multiple congenital anomalies (MCA) or intellectual disabilities/developmental delay (ID/DD) but normal karyotype were investigated using Affymetrix CytoScan HD array. RESULT: Pathogenic copy number variations (PCNVs) were identified in 29 children (27...
May 4, 2017: BMC Pediatrics
https://www.readbyqxmd.com/read/28468311/tubacin-an-hdac6-selective-inhibitor-reduces-the-replication-of-the-japanese-encephalitis-virus-via-the-decrease-of-viral-rna-synthesis
#19
Chien-Yi Lu, Yi-Chih Chang, Chun-Hung Hua, Chieh Chuang, Su-Hua Huang, Szu-Hao Kung, Mann-Jen Hour, Cheng-Wen Lin
Japanese encephalitis virus (JEV), a neurotropic flavivirus, annually causes over 30,000 Japanese Encephalitis (JE) cases in East and Southeast Asia. Histone deacetylases (HDACs) modulate lysine acetylation of histones and non-histone proteins, regulating many processes including inflammation and antiviral immune response. This study investigated antiviral activity of pan- and selective-HDAC inhibitors as host-targeting agents against JEV. Among HDAC inhibitors, selective HDAC6 inhibitors (tubastatin-A (TBSA) and tubacin) concentration-dependently inhibited JEV-induced cytopathic effect and apoptosis, as well as reduced virus yield in human cerebellar medulloblastoma cells...
May 1, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28468258/pan-cancer-mutational-and-transcriptional-analysis-of-the-integrator-complex
#20
Antonio Federico, Monica Rienzo, Ciro Abbondanza, Valerio Costa, Alfredo Ciccodicola, Amelia Casamassimi
The integrator complex has been recently identified as a key regulator of RNA Polymerase II-mediated transcription, with many functions including the processing of small nuclear RNAs, the pause-release and elongation of polymerase during the transcription of protein coding genes, and the biogenesis of enhancer derived transcripts. Moreover, some of its components also play a role in genome maintenance. Thus, it is reasonable to hypothesize that their functional impairment or altered expression can contribute to malignancies...
April 29, 2017: International Journal of Molecular Sciences
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