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https://www.readbyqxmd.com/read/29352511/draft-genome-and-reference-transcriptomic-resources-for-the-urticating-pine-defoliator-thaumetopoea-pityocampa-lepidoptera-notodontidae
#1
B Gschloessl, F Dorkeld, H Berges, G Beydon, O Bouchez, M Branco, A Bretaudeau, C Burban, E Dubois, P Gauthier, E Lhuillier, J Nichols, S Nidelet, S Rocha, L Sauné, R Streiff, M Gautier, C Kerdelhué
The pine processionary moth Thaumetopoea pityocampa (Lepidoptera: Notodontidae) is the main pine defoliator in the Mediterranean region. Its urticating larvae cause severe human and animal health concerns in the invaded areas. This species shows a high phenotypic variability for various traits, such as phenology, fecundity, and tolerance to extreme temperatures. This study presents the construction and analysis of extensive genomic and transcriptomic resources, which are an obligate prerequisite to understand their underlying genetic architecture...
January 20, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29352488/understanding-intratumor-heterogeneity-by-combining-genome-analysis-and-mathematical-modeling
#2
REVIEW
Atsushi Niida, Satoshi Nagayama, Satoru Miyano, Koshi Mimori
Cancer is composed of multiple cell populations with different genomes. Each of the populations is called a clone (or subclone) and this phenomenon is called intratumor heterogeneity (ITH). ITH is observed in various types of cancers and presumed to be a major cause leading to therapeutic resistance. If a tumor harbors a major clone sensitive to a specific anti-cancer treatment, the tumor shrinks within a given period after the treatment. However, in most cases, a minor clone resistant to the chemotherapy exists in the tumor and predominantly regrows in spite of the intensive therapy...
January 20, 2018: Cancer Science
https://www.readbyqxmd.com/read/29352324/efficient-genome-wide-genotyping-strategies-and-data-integration-in-crop-plants
#3
REVIEW
Davoud Torkamaneh, Brian Boyle, François Belzile
Next-generation sequencing (NGS) has revolutionized plant and animal research by providing powerful genotyping methods. This review describes and discusses the advantages, challenges and, most importantly, solutions to facilitate data processing, the handling of missing data, and cross-platform data integration. Next-generation sequencing technologies provide powerful and flexible genotyping methods to plant breeders and researchers. These methods offer a wide range of applications from genome-wide analysis to routine screening with a high level of accuracy and reproducibility...
January 19, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29352323/identification-of-a-molecular-marker-tightly-linked-to-bacterial-wilt-resistance-in-tomato-by-genome-wide-snp-analysis
#4
Boyoung Kim, In Sun Hwang, Hyung Jin Lee, Je Min Lee, Eunyoung Seo, Doil Choi, Chang-Sik Oh
Genotyping of disease resistance to bacterial wilt in tomato by a genome-wide SNP analysis Bacterial wilt caused by Ralstonia pseudosolanacearum is one of the destructive diseases in tomato. The previous studies have identified Bwr-6 (chromosome 6) and Bwr-12 (chromosome 12) loci as the major quantitative trait loci (QTLs) contributing to resistance against bacterial wilt in tomato cultivar 'Hawaii7996'. However, the genetic identities of two QTLs have not been uncovered yet. In this study, using whole-genome resequencing, we analyzed genome-wide single-nucleotide polymorphisms (SNPs) that can distinguish a resistant group, including seven tomato varieties resistant to bacterial wilt, from a susceptible group, including two susceptible to the same disease...
January 19, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29352312/a-role-for-domain-i-of-the-hepatitis-c-virus-ns5a-protein-in-virus-assembly
#5
Chunhong Yin, Niluka Goonawardane, Hazel Stewart, Mark Harris
The NS5A protein of hepatitis C virus (HCV) plays roles in both virus genome replication and assembly. NS5A comprises three domains, of these domain I is believed to be involved exclusively in genome replication. In contrast, domains II and III are required for the production of infectious virus particles and are largely dispensable for genome replication. Domain I is highly conserved between HCV and related hepaciviruses, and is highly structured, exhibiting different dimeric conformations. To investigate the functions of domain I in more detail, we conducted a mutagenic study of 12 absolutely conserved and surface-exposed residues within the context of a JFH-1-derived sub-genomic replicon and infectious virus...
January 19, 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29352301/crystal-structure-of-a-udp-glcnac-epimerase-for-surface-polysaccharide-biosynthesis-in-acinetobacter-baumannii
#6
Bhumika S Shah, Heather E Ashwood, Stephen J Harrop, Daniel N Farrugia, Ian T Paulsen, Bridget C Mabbutt
With new strains of Acinetobacter baumannii undergoing genomic analysis, it has been possible to define regions of genomic plasticity (RGPs), encoding specific adaptive elements. For a selected RGP from a community-derived isolate of A. baumannii, we outline sequences compatible with biosynthetic machinery of surface polysaccharides, specifically enzymes utilized in the dehydration and conversion of UDP-N-acetyl-D-glucosamine (UDP-D-GlcNAc). We have determined the crystal structure of one of these, the epimerase Ab-WbjB...
2018: PloS One
https://www.readbyqxmd.com/read/29352289/electroacupuncture-at-guanyuan-cv-4-zusanli-st-36-and-baihui-du-20-regulate-the-aging-related-changes-in-gene-expression-profile-of-the-hippocampus-in-sub-acutely-aging-rats
#7
Jianmin Liu, Jing Liu, Guang'an Wang, Guangya Liu, Huanjiao Zhou, Yun Fan, Fengxia Liang, Hua Wang
To investigate the molecular mechanisms of sub-acutely aging and demonstrate the effect of electroacupuncture (EA) at the Guanyuan (CV 4), Zusanli (ST 36) and Baihui (DU 20) acupoint on the sub-acutely aging brain, cDNA microarrays and bioinformatics analyses were carried out. Thirty Sprague-Dawley (SD) male rats were selected and randomly divided into three groups: the control group (C), the sub-acutely aging model group (M) and the electroacupuncture group (M+EA). Sub-acutely aging model rats were obtained by D-galactose s...
2018: PloS One
https://www.readbyqxmd.com/read/29352288/phospholipid-scramblase-1-interacts-with-influenza-a-virus-np-impairing-its-nuclear-import-and-thereby-suppressing-virus-replication
#8
Weiyu Luo, Jie Zhang, Libin Liang, Guangwen Wang, Qibing Li, Pengyang Zhu, Yuan Zhou, Junping Li, Yuhui Zhao, Nan Sun, Shanyu Huang, Chenchen Zhou, Yu Chang, Pengfei Cui, Pucheng Chen, Yongping Jiang, Guohua Deng, Zhigao Bu, Chengjun Li, Li Jiang, Hualan Chen
Transcription and replication of the influenza A virus (IAV) genome occur in the nucleus of infected cells and are carried out by the viral ribonucleoprotein complex (vRNP). As a major component of the vRNP complex, the viral nucleoprotein (NP) mediates the nuclear import of the vRNP complex via its nuclear localization signals (NLSs). Clearly, an effective way for the host to antagonize IAV infection would be by targeting vRNP nuclear import. Here, we identified phospholipid scramblase 1 (PLSCR1) as a binding partner of NP by using a yeast two-hybrid (Y2H) screen...
January 19, 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29352281/differential-dna-methylation-and-transcription-profiles-in-date-palm-roots-exposed-to-salinity
#9
Ibtisam Al-Harrasi, Rashid Al-Yahyai, Mahmoud W Yaish
As a salt-adaptive plant, the date palm (Phoenix dactylifera L.) requires a suitable mechanism to adapt to the stress of saline soils. There is growing evidence that DNA methylation plays an important role in regulating gene expression in response to abiotic stresses, including salinity. Thus, the present study sought to examine the differential methylation status that occurs in the date palm genome when plants are exposed to salinity, and to identify salinity responsive genes that are regulated by DNA methylation...
2018: PloS One
https://www.readbyqxmd.com/read/29352241/short-tandem-repeat-analysis-after-whole-genome-amplification-of-single-b-lymphoblastoid-cells
#10
Lieselot Deleye, Ann-Sophie Vander Plaetsen, Jana Weymaere, Dieter Deforce, Filip Van Nieuwerburgh
To allow multiple genetic analyses on a single cell, whole genome amplification (WGA) is required. Unfortunately, studies comparing different WGA methods for downstream human identification Short Tandem Repeat (STR) analysis remain absent. Therefore, the aim of this work was to assess the performance of four commercially available WGA kits for downstream human identification STR profiling on a B-lymphoblastoid cell line. The performance was assessed using an input of one or three micromanipulated cells. REPLI-g showed a very low dropout rate, as it was the only WGA method in this study that could provide a complete STR profile in some of its samples...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352173/maize-chlorotic-mottle-virus-exhibits-low-divergence-between-differentiated-regional-sub-populations
#11
Luke Braidwood, Diego F Quito-Avila, Darlene Cabanas, Alberto Bressan, Anne Wangai, David C Baulcombe
Maize chlorotic mottle virus has been rapidly spreading around the globe over the past decade. The interactions of maize chlorotic mottle virus with Potyviridae viruses causes an aggressive synergistic viral condition - maize lethal necrosis, which can cause total yield loss. Maize production in sub-Saharan Africa, where it is the most important cereal, is threatened by the arrival of maize lethal necrosis. We obtained maize chlorotic mottle virus genome sequences from across East Africa and for the first time from Ecuador and Hawaii, and constructed a phylogeny which highlights the similarity of Chinese to African isolates, and Ecuadorian to Hawaiian isolates...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352122/comparative-transcriptomic-and-proteomic-analysis-of-arthrobacter-sp-cgmcc-3584-responding-to-dissolved-oxygen-for-camp-production
#12
Huanqing Niu, Junzhi Wang, Wei Zhuang, Dong Liu, Yong Chen, Chenjie Zhu, Hanjie Ying
Arthrobacter sp. CGMCC 3584 is able to produce high yields of extracellular cyclic adenosine monophosphate (cAMP), which plays a vital role in the field of treatment of disease and animal food, during aerobic fermentation. However, the molecular basis of cAMP production in Arthrobacter species is rarely explored. Here, for the first time, we report the comparative transcriptomic and proteomic study of Arthrobacter cells to elucidate the higher productivity of cAMP under high oxygen supply. We finally obtained 14...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352086/temporal-and-spatial-distribution-of-the-acetic-acid-bacteria-communities-throughout-the-wooden-casks-used-for-the-fermentation-and-maturation-of-lambic-beer-underlines-their-functional-role
#13
J De Roos, M Verce, M Aerts, P Vandamme, L De Vuyst
Few data have been published on the occurrence and functional role of acetic acid bacteria (AAB) in lambic beer production processes, mainly due to their difficult recovery and possibly unknown role. Therefore, a novel aseptic sampling method, spanning both the spatial and temporal distribution of AAB and their substrates and metabolites, was combined with a highly selective medium and matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI TOF MS) as a high-throughput dereplication method followed by comparative gene sequencing for their isolation and identification, respectively...
January 19, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29352080/functional-analysis-of-cancer-associated-dna-polymerase-%C3%AE%C2%B5-variants-in-saccharomyces-cerevisiae
#14
Stephanie R Barbari, Daniel P Kane, Elizabeth A Moore, Polina V Shcherbakova
DNA replication fidelity relies on base selectivity of the replicative DNA polymerases, exonucleolytic proofreading, and post-replicative DNA mismatch repair (MMR). Ultramutated human cancers without MMR defects carry alterations in the exonuclease domain of DNA polymerase ε (Polε). They have been hypothesized to result from defective proofreading. However, modeling in yeast of the most common variant, Polε-P286R, produced an unexpectedly strong mutator effect that exceeded the effect of proofreading deficiency by two orders of magnitude and indicated the involvement of other infidelity factors...
January 19, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29352078/the-highly-divergent-mitochondrial-genomes-indicate-that-the-booklouse-liposcelis-bostrychophila-psocoptera-liposcelididae-is-a-cryptic-species
#15
Shiqian Feng, Qianqian Yang, Hu Li, Fan Song, Václav Stejskal, George P Opit, Wanzhi Cai, Zhihong Li, Renfu Shao
The booklouse, Liposcelis bostrychophila is an important storage pest worldwide. The mt genome of an asexual strain (Beibei, China) of the booklouse, L. bostrychophila, comprises two chromosomes; each chromosome contains approximate half of the 37 genes typically found in animals. The mt genomes of two sexual strains of L. bostrychophila, however, comprise five and seven chromosomes respectively; each chromosome contains one to six genes. To understand mt genome evolution in L. bostrychophila and whether L...
January 19, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29352063/arabidopsis-thaliana-fancd2-promotes-meiotic-crossover-formation
#16
Marie-Therese Kurzbauer, Monica Pradillo, Claudia Kerzendorfer, Jason Sims, Rene Ladurner, Cecilia Oliver, Michael Peter Janisiw, Magdalena Mosiolek, Dieter Schweizer, Gregory P Copenhaver, Peter Schlogelhofer
Fanconi anemia (FA) is a human autosomal recessive disorder characterized by chromosomal instability, developmental pathologies, predisposition to cancer and reduced fertility. So far, nineteen genes have been implicated in FA, most of them involved in DNA repair. Some are conserved across higher eukaryotes, including plants. The Arabidopsis thaliana genome encodes a homologue of the Fanconi anemia D2 gene (FANCD2) whose function in DNA repair is not yet fully understood. Here we provide evidence that AtFANCD2 is required for meiotic homologous recombination...
January 19, 2018: Plant Cell
https://www.readbyqxmd.com/read/29351920/exceptional-response-to-pembrolizumab-in-a-metastatic-chemotherapy-radiation-resistant-ovarian-cancer-patient-harboring-a-cd274-pd-l1-genetic-rearrangement
#17
Stefania Bellone, Natalia Buza, Jungmin Choi, Luca Zammataro, Laurie Gay, Julia A Elvin, David L Rimm, Yuting Liu, Elena Ratner, Peter E Schwartz, Alessandro D Santin
PURPOSE: Ovarian carcinoma no longer responsive to surgery and chemotherapy remains an incurable disease. Alternative therapeutic options remain desperately needed. EXPERIMENTAL DESIGN: We describe a heavily pretreated ovarian cancer patient with recurrent disease experiencing a remarkable clinical response to treatment with the anti-PD1 immune check-point inhibitor pembrolizumab. The clinical, pathological, and genomic characteristics of this exceptional ovarian cancer responder were carefully investigated using immunohistochemistry (IHC), quantitative multiplex fluorescence methods (ie, automated quantitative analysis, AQUA) and whole exome sequencing (WES) techniques...
January 19, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29351916/pathways-impacted-by-genomic-alterations-in-pulmonary-carcinoid-tumors
#18
Michael K Asiedu, Charles F Thomas, Jie Dong, Sandra C Schulte Tomaszek, Prasidda Khadka, Zhifu Sun, Farhad Kosari, Jin Jen, Julian R Molina, George Vasmatzis, Rui Kuang, Marie Christine Aubry, Ping Yang, Dennis A Wigle
PURPOSE: Pulmonary carcinoid tumors account for up to 5% of all lung malignancies in adults, comprise 30% of all carcinoid malignancies, and are defined histologically as typical carcinoid (TC) and atypical carcinoid (AC) tumors. The role of specific genomic alterations in the pathogenesis of pulmonary carcinoid tumors remains poorly understood. We sought to identify genomic alterations and pathways that are deregulated in these tumors to find novel therapeutic targets for pulmonary carcinoid tumors...
January 19, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29351903/integrative-genomic-analysis-predicts-causative-cis-regulatory-mechanisms-of-the-breast-cancer-associated-genetic-variant-rs4415084
#19
Yi Zhang, Mohith Manjunath, Shilu Zhang, Deborah Chasman, Sushmita Roy, Jun S Song
Previous genome-wide association studies (GWAS) have identified several common genetic variants that may significantly modulate cancer susceptibility. However, the precise molecular mechanisms behind these associations remain largely unknown; it is often not clear whether discovered variants are themselves functional or merely genetically linked to other functional variants. Here we provide an integrated method for identifying functional regulatory variants associated with cancer and their target genes by combining analyses of expression quantitative trait loci (eQTL), a modified version of allele-specific expression (ASE) that systematically utilizes haplotype information, transcription factor (TF) binding preference, and epigenetic information...
January 19, 2018: Cancer Research
https://www.readbyqxmd.com/read/29351892/identification-and-functional-analysis-of-cassava-della-proteins-in-plant-disease-resistance-against-cassava-bacterial-blight
#20
Xiaolin Li, Wen Liu, Bing Li, Guoyin Liu, Yunxie Wei, Chaozu He, Haitao Shi
Gibberellin (GA) is an essential plant hormone in plant growth and development as well as various stress responses. DELLA proteins are important repressors of GA signal pathway. GA and DELLA have been extensively investigated in several model plants. However, the in vivo roles of GA and DELLA in cassava, one of the most important crops and energy crops in the tropical area, are unknown. In this study, systematic genome-wide analysis identified 4 MeDELLAs in cassava, as evidenced by the evolutionary tree, gene structures and motifs analyses...
December 26, 2017: Plant Physiology and Biochemistry: PPB
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