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https://www.readbyqxmd.com/read/29150374/occurrence-of-enterobacter-hormaechei-carrying-blandm-1-and-blakpc-2-in-china
#1
Biwei Yang, Yu Feng, Alan McNally, Zhiyong Zong
Three carbapenem-resistant clinical isolates of the Enterobacter cloacae complex (ECC) were recovered from different patients in a hospital. All 3 isolates carried 2 carbapenemase genes blaKPC-2 and blaNDM-1. A study was performed to characterize their relatedness and to investigate possible links among the patients. Whole genome sequencing revealed that the isolates were Enterobacter hormaechei and belonged to ST177 of the ECC. There were 19-142 single nucleotide polymorphisms (SNPs) between the isolates, suggesting that the isolates were likely from a central reservoir, which might have existed for some time...
October 19, 2017: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/29149916/whole-exome-sequencing-in-amyotrophic-lateral-sclerosis-suggests-nek1-is-a-risk-gene-in-chinese
#2
Jacob Gratten, Qiongyi Zhao, Beben Benyamin, Fleur Garton, Ji He, Paul J Leo, Marie Mangelsdorf, Lisa Anderson, Zong-Hong Zhang, Lu Chen, Xiang-Ding Chen, Katie Cremin, Hong-Weng Deng, Janette Edson, Ying-Ying Han, Jessica Harris, Anjali K Henders, Zi-Bing Jin, Zhongshan Li, Yong Lin, Xiaolu Liu, Mhairi Marshall, Bryan J Mowry, Shu Ran, David C Reutens, Sharon Song, Li-Jun Tan, Lu Tang, Robyn H Wallace, Lawrie Wheeler, Jinyu Wu, Jian Yang, Huji Xu, Peter M Visscher, Perry F Bartlett, Matthew A Brown, Naomi R Wray, Dongsheng Fan
BACKGROUND: Amyotrophic lateral sclerosis (ALS) is a progressive neurological disease characterised by the degeneration of motor neurons, which are responsible for voluntary movement. There remains limited understanding of disease aetiology, with median survival of ALS of three years and no effective treatment. Identifying genes that contribute to ALS susceptibility is an important step towards understanding aetiology. The vast majority of published human genetic studies, including for ALS, have used samples of European ancestry...
November 17, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29149504/mybl1-rearrangements-and-myb-amplification-in-breast-adenoid-cystic-carcinomas-lacking-the-myb-nfib-fusion-gene
#3
Jisun Kim, Felipe C Geyer, Luciano G Martelotto, Charlotte K Y Ng, Raymond S Lim, Pier Selenica, Anqi Li, Fresia Pareja, Nicola Fusco, Marcia Edelweiss, Rahul Kumar, Rodrigo Gularte-Merida, Andre N Forbes, Ekta Khurana, Odette Mariani, Sunil Badve, Anne Vincent-Salomon, Larry Norton, Jorge S Reis-Filho, Britta Weigelt
Breast adenoid cystic carcinoma (AdCC), a rare type of triple-negative breast cancer (TNBC), has been shown to be driven by MYB pathway activation, most often underpinned by the MYB-NFIB fusion gene. Alternative genetic mechanisms, such as MYBL1 rearrangements, have been reported in MYB-NFIB-negative salivary gland AdCCs. Here we report on the molecular characterization by massively parallel sequencing of four breast AdCCs lacking the MYB-NFIB fusion gene. In two cases, we identified MYBL1 rearrangements (MYBL1-ACTN1 and MYBL1-NFIB), which were associated with MYBL1 overexpression...
November 17, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/29149287/genomic-and-epigenomic-immunity-in-common-bean-the-unusual-features-of-nb-lrr-gene-family
#4
Manon M S Richard, Ariane Gratias, Vincent Thareau, Kyung Do Kim, Sandrine Balzergue, Johann Joets, Scott A Jackson, Valérie Geffroy
In plants, a key class of genes comprising most of disease resistance (R) genes encodes Nucleotide-binding leucine-rich repeat (NL) proteins. Access to common bean (Phaseolus vulgaris) genome sequence provides unparalleled insight into the organization and evolution of this large gene family (∼400 NL) in this important crop. As observed in other plant species, most common bean NL are organized in cluster of genes. However, a particularity of common bean is that these clusters are often located in subtelomeric regions close to terminal knobs containing the satellite DNA khipu...
November 15, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29149280/whole-genome-re-sequencing-of-two-italian-tomato-landraces-reveals-sequence-variations-in-genes-associated-with-stress-tolerance-fruit-quality-and-long-shelf-life-traits
#5
Valentina Tranchida-Lombardo, Riccardo Aiese Cigliano, Irantzu Anzar, Simone Landi, Samuela Palombieri, Chiara Colantuono, Hamed Bostan, Pasquale Termolino, Riccardo Aversano, Giorgia Batelli, Maria Cammareri, Domenico Carputo, Maria Luisa Chiusano, Clara Conicella, Federica Consiglio, Nunzio D'Agostino, Monica De Palma, Antonio Di Matteo, Silvana Grandillo, Walter Sanseverino, Marina Tucci, Stefania Grillo
Tomato is a high value crop and the primary model for fleshy fruit development and ripening. Breeding priorities include increased fruit quality, shelf life and tolerance to stresses. To contribute towards this goal, we re-sequenced the genomes of Corbarino (COR) and Lucariello (LUC) landraces, which both possess the traits of plant adaptation to water deficit, prolonged fruit shelf-life and good fruit quality. Through the newly developed pipeline Reconstructor, we generated the genome sequences of COR and LUC using datasets of 65...
November 14, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29148541/integrated-genomic-analysis-identifies-deregulated-jak-stat-myc-biosynthesis-axis-in-aggressive-nk-cell-leukemia
#6
Liang Huang, Dan Liu, Na Wang, Shaoping Ling, Yuting Tang, Jun Wu, Lingtong Hao, Hui Luo, Xuelian Hu, Lingshuang Sheng, Lijun Zhu, Di Wang, Yi Luo, Zhen Shang, Min Xiao, Xia Mao, Kuangguo Zhou, Lihua Cao, Lili Dong, Xinchang Zheng, Pinpin Sui, Jianlin He, Shanlan Mo, Jin Yan, Qilin Ao, Lugui Qiu, Hongsheng Zhou, Qifa Liu, Hongyu Zhang, Jianyong Li, Jie Jin, Li Fu, Weili Zhao, Jieping Chen, Xin Du, Guoliang Qing, Hudan Liu, Xin Liu, Gang Huang, Ding Ma, Jianfeng Zhou, Qian-Fei Wang
Aggressive NK-cell leukemia (ANKL) is a rare form of NK cell neoplasm that is more prevalent among people from Asia and Central and South America. Patients usually die within days to months, even after receiving prompt therapeutic management. Here we performed the first comprehensive study of ANKL by integrating whole genome, transcriptome and targeted sequencing, cytokine array as well as functional assays. Mutations in the JAK-STAT pathway were identified in 48% (14/29) of ANKL patients, while the extracellular STAT3 stimulator IL10 was elevated by an average of 56-fold (P < 0...
November 17, 2017: Cell Research
https://www.readbyqxmd.com/read/29148374/pathogenic-elizabethkingia-miricola-infection-in-cultured-black-spotted-frogs-china-2016
#7
Ruixue Hu, Junfa Yuan, Yin Meng, Zhe Wang, Zemao Gu
Multiregional outbreaks of meningitis-like disease caused by Elizabethkingia miricola were confirmed in black-spotted frog farms in China in 2016. Whole-genome sequencing revealed that this amphibian E. miricola strain is closely related to human clinical isolates. Our findings indicate that E. miricola can be epizootic and may pose a threat to humans.
December 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/29148362/pseudomonas-floridensis-sp-nov-a-bacterial-pathogen-isolated-from-tomato
#8
Sujan Timilsina, Gerald V Minsavage, James Preston, Eric A Newberry, Matthews L Paret, Erica M Goss, Jeffrey B Jones, Gary E Vallad
An unusual fluorescent pseudomonad was isolated from tomato exhibiting leaf spot symptoms similar to bacterial speck. Strains were fluorescent, oxidase- and arginine-dihydrolase-negative, elicited a hypersensitive reaction on tobacco and produced a soft rot on potato slices. However, the strains produced an unusual yellow, mucoid growth on media containing 5 % sucrose that is not typical of levan. Based on multilocus sequence analysis using 16S rRNA, gap1, gltA, gyrB and rpoD, these strains formed a distinct phylogenetic group in the genus Pseudomonas and were most closely related to Pseudomonas viridiflava within the Pseudomonassyringae complex...
November 17, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29146900/the-genomic-landscape-of-pediatric-myelodysplastic-syndromes
#9
Jason R Schwartz, Jing Ma, Tamara Lamprecht, Michael Walsh, Shuoguo Wang, Victoria Bryant, Guangchun Song, Gang Wu, John Easton, Chimene Kesserwan, Kim E Nichols, Charles G Mullighan, Raul C Ribeiro, Jeffery M Klco
Myelodysplastic syndromes (MDS) are uncommon in children and have a poor prognosis. In contrast to adult MDS, little is known about the genomic landscape of pediatric MDS. Here, we describe the somatic and germline changes of pediatric MDS using whole exome sequencing, targeted amplicon sequencing, and/or RNA-sequencing of 46 pediatric primary MDS patients. Our data show that, in contrast to adult MDS, Ras/MAPK pathway mutations are common in pediatric MDS (45% of primary cohort), while mutations in RNA splicing genes are rare (2% of primary cohort)...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29146883/a-landscape-of-germline-mutations-in-a-cohort-of-inherited-bone-marrow-failure-patients
#10
Olivier Bluteau, Marie Sebert, Thierry Leblanc, Régis Peffault de Latour, Samuel Quentin, Elodie Lainey, Lucie Hernandez, Jean-Hugues Dalle, Flore Sicre de Fontbrune, Etienne Lengline, Raphael Itzykson, Emmanuelle Clappier, Nicolas Boissel, Naddia Vasquez, Mélanie Da Costa, Julien Masliah-Planchon, Wendy Cuccuini, Anna Raimbault, Louis De Jaegere, Lionel Adès, Pierre Fenaux, Sébastien Maury, Claudine Schmitt, Marc Muller, Carine Domenech, Nicolas Blin, Bénédicte Bruno, Isabelle Pellier, Mathilde Hunault, Stéphane Blanche, Arnaud Petit, Guy Leverger, Gérard Michel, Yves Bertrand, André Baruchel, Gérard Socié, Jean Soulier
Bone marrow failure (BMF) in children and young adults is often suspected to be inherited, but in many cases diagnosis remains uncertain. We studied a cohort of 179 patients (from 173 families) with BMF of suspected inherited origin but unresolved diagnosis after medical evaluation and Fanconi anemia exclusion. All patients had cytopenias, and 12.0% presented ≥5% bone marrow blast cells. Median age at genetic evaluation was 11 years; 20.7% of patients were aged ≤2 years and 36.9% were ≥18 years. We analyzed genomic DNA from skin fibroblasts using whole-exome sequencing, and were able to assign a causal or likely causal germline mutation in 86 patients (48...
November 16, 2017: Blood
https://www.readbyqxmd.com/read/29146861/whole-genome-sequence-of-pantoea-americana-strain-vs1-an-extended-spectrum-%C3%AE-lactamase-producing-epibiont-isolated-from-magnolia-grandiflora
#11
Pushpa Lata, Subramaniam S Govindarajan, Feng Qi, Jian-Liang Li, Santosh K Maurya, Malaya K Sahoo
Pantoea americana strain VS1, an extended-spectrum β-lactamase-producing epibiont, was isolated from Magnolia grandiflora in central Florida, USA. Here, we report the de novo whole-genome sequence of this strain, which consists of a total of 191 contigs spanning 5,412,831 bp, with a GC content of 57.3% and comprising 4,836 predicted coding sequences.
November 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29146858/whole-genome-shotgun-sequences-of-three-multidrug-resistant-mycobacterium-tuberculosis-strains-isolated-from-morocco
#12
Lamiaa Lahlou, Nadia El Mrimar, Meriem Laamarti, Tarek Alouane, Mohammed A Bendahou, Fatna Bssaibis, Yassine Ben Lahlou, Adil Zegmout, N El Hafidi, Rachid ElJaoudi, Mohammed Frikh, Abdelhay Lemnouar, Mostafa Elouennass, Azeddine Ibrahimi
Tuberculosis is a contagious disease that usually attacks the lungs but sometimes attacks other parts of the body, such as the kidneys, glands, and bones. It is an endemic and major public health problem in Morocco. Tuberculosis is transmitted through the airways via the inhalation of microdroplets containing Mycobacterium tuberculosis We present here the whole-genome shotgun sequences of three multidrug-resistant M. tuberculosis strains isolated from Morocco.
November 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29146857/whole-genome-sequence-of-salmonella-enterica-subsp-enterica-serovar-typhimurium-strain-upm-260-isolated-from-a-broiler-chicken-in-perak-malaysia
#13
Najwa Syahirah Roslan, Shagufta Jabeen, Nurulfiza Mat Isa, Abdul Rahman Omar, Mohd Hair Bejo, Aini Ideris
Salmonella enterica subsp. enterica serovar Typhimurium is one of several well-categorized Salmonella serotypes recognized globally. Here, we report the whole-genome sequence of S Typhimurium strain UPM 260, isolated from a broiler chicken.
November 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29146851/draft-whole-genome-sequences-of-periodontal-pathobionts-porphyromonas-gingivalis-prevotella-intermedia-and-tannerella-forsythia-contain-phase-variable-restriction-modification-systems
#14
Richard D Haigh, Liam A Crawford, Joseph D Ralph, Joseph J Wanford, Sonia R Vartoukian, Karolin Hijazi, William Wade, Marco R Oggioni
Periodontal disease comprises mild to severe inflammatory host responses to oral bacteria that can cause destruction of the tooth-supporting tissue. We report genome sequences for 18 clinical isolates of Porphyromonas gingivalis, Prevotella intermedia, and Tannerella forsythia, Gram-negative obligate anaerobes that play a role in the periodontal disease process.
November 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29146841/draft-whole-genome-sequences-of-18-flavobacterium-spp
#15
Cynthia B Stine, Cong Li, Tina C Crosby, Nicholas R Hasbrouck, Claudia Lam, Daniel A Tadesse
We report here the draft whole-genome sequences for 18 Flavobacterium species type strains that have historically been associated with fish gill disease.
November 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29146838/retraction-for-hong-et-al-whole-genome-de-novo-sequencing-of-the-lignin-degrading-wood-rot-fungus-phanerochaete-chrysosporium-atcc-20696
#16
Chang-Young Hong, Su-Yeon Lee, Sun-Hwa Ryu, Sung-Suk Lee, Myungkil Kim
No abstract text is available yet for this article.
November 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29146476/mutation-screening-of-the-glis3-gene-in-a-cohort-of-592-chinese-patients-with-congenital-hypothyroidism
#17
Chunyun Fu, Shiyu Luo, Xigui Long, Yingfeng Li, Shangyang She, Xuehua Hu, Meizhen Mo, Zhanghong Wang, Yuhua Chen, Chun He, Jiasun Su, Yue Zhang, Fei Lin, Bobo Xie, Qifei Li, Shaoke Chen
OBJECTIVES: Defects in the human GLI-similar 3 (GLIS3) gene are reported to be a rare cause of congenital hypothyroidism (CH) and neonatal diabetes. The aim of this study was to examine the prevalence of GLIS3 mutation among CH patients in the Guangxi Zhuang Autonomous Region of China and to define the relationships between GLIS3 genotypes and clinical phenotypes. METHODS: Blood samples were collected from 592 patients with CH in Guangxi Zhuang Autonomous Region, China, and genomic DNA was extracted from peripheral blood leukocytes...
November 13, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/29145861/hybrid-de-novo-genome-assembly-and-centromere-characterization-of-the-gray-mouse-lemur-microcebus-murinus
#18
Peter A Larsen, R Alan Harris, Yue Liu, Shwetha C Murali, C Ryan Campbell, Adam D Brown, Beth A Sullivan, Jennifer Shelton, Susan J Brown, Muthuswamy Raveendran, Olga Dudchenko, Ido Machol, Neva C Durand, Muhammad S Shamim, Erez Lieberman Aiden, Donna M Muzny, Richard A Gibbs, Anne D Yoder, Jeffrey Rogers, Kim C Worley
BACKGROUND: The de novo assembly of repeat-rich mammalian genomes using only high-throughput short read sequencing data typically results in highly fragmented genome assemblies that limit downstream applications. Here, we present an iterative approach to hybrid de novo genome assembly that incorporates datasets stemming from multiple genomic technologies and methods. We used this approach to improve the gray mouse lemur (Microcebus murinus) genome from early draft status to a near chromosome-scale assembly...
November 16, 2017: BMC Biology
https://www.readbyqxmd.com/read/29145855/generation-of-a-platform-strain-for-ionic-liquid-tolerance-using-adaptive-laboratory-evolution
#19
Elsayed T Mohamed, Shizeng Wang, Rebecca M Lennen, Markus J Herrgård, Blake A Simmons, Steven W Singer, Adam M Feist
BACKGROUND: There is a need to replace petroleum-derived with sustainable feedstocks for chemical production. Certain biomass feedstocks can meet this need as abundant, diverse, and renewable resources. Specific ionic liquids (ILs) can play a role in this process as promising candidates for chemical pretreatment and deconstruction of plant-based biomass feedstocks as they efficiently release carbohydrates which can be fermented. However, the most efficient pretreatment ILs are highly toxic to biological systems, such as microbial fermentations, and hinder subsequent bioprocessing of fermentative sugars obtained from IL-treated biomass...
November 16, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/29145608/medreaders-a-database-for-transcription-factors-that-bind-to-methylated-dna
#20
Guohua Wang, Ximei Luo, Jianan Wang, Jun Wan, Shuli Xia, Heng Zhu, Jiang Qian, Yadong Wang
Understanding the molecular principles governing interactions between transcription factors (TFs) and DNA targets is one of the main subjects for transcriptional regulation. Recently, emerging evidence demonstrated that some TFs could bind to DNA motifs containing highly methylated CpGs both in vitro and in vivo. Identification of such TFs and elucidation of their physiological roles now become an important stepping-stone toward understanding the mechanisms underlying the methylation-mediated biological processes, which have crucial implications for human disease and disease development...
November 14, 2017: Nucleic Acids Research
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