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https://www.readbyqxmd.com/read/27926879/in%C3%A2-vitro-derivation-and-propagation-of-spermatogonial-stem-cell-activity-from-mouse-pluripotent-stem-cells
#1
Yukiko Ishikura, Yukihiro Yabuta, Hiroshi Ohta, Katsuhiko Hayashi, Tomonori Nakamura, Ikuhiro Okamoto, Takuya Yamamoto, Kazuki Kurimoto, Kenjiro Shirane, Hiroyuki Sasaki, Mitinori Saitou
The in vitro derivation and propagation of spermatogonial stem cells (SSCs) from pluripotent stem cells (PSCs) is a key goal in reproductive science. We show here that when aggregated with embryonic testicular somatic cells (reconstituted testes), primordial germ cell-like cells (PGCLCs) induced from mouse embryonic stem cells differentiate into spermatogonia-like cells in vitro and are expandable as cells that resemble germline stem cells (GSCs), a primary cell line with SSC activity. Remarkably, GSC-like cells (GSCLCs), but not PGCLCs, colonize adult testes and, albeit less effectively than GSCs, contribute to spermatogenesis and fertile offspring...
December 6, 2016: Cell Reports
https://www.readbyqxmd.com/read/27925618/the-comparative-landscape-of-duplications-in-heliconius-melpomene-and-heliconius-cydno
#2
A Pinharanda, S H Martin, S L Barker, J W Davey, C D Jiggins
Gene duplications can facilitate adaptation and may lead to interpopulation divergence, causing reproductive isolation. We used whole-genome resequencing data from 34 butterflies to detect duplications in two Heliconius species, Heliconius cydno and Heliconius melpomene. Taking advantage of three distinctive signals of duplication in short-read sequencing data, we identified 744 duplicated loci in H. cydno and H. melpomene and evaluated the accuracy of our approach using single-molecule sequencing. We have found that duplications overlap genes significantly less than expected at random in H...
December 7, 2016: Heredity
https://www.readbyqxmd.com/read/27924811/insights-into-the-evolution-of-pathogenicity-of-escherichia-coli-from-genomic-analysis-of-intestinal-e-coli-of-marmota-himalayana-in-qinghai-tibet-plateau-of-china
#3
Shan Lu, Dong Jin, Shusheng Wu, Jing Yang, Ruiting Lan, Xiangning Bai, Sha Liu, Qiong Meng, Xuejiao Yuan, Juan Zhou, Ji Pu, Qiang Chen, Hang Dai, Yuanyuan Hu, Yanwen Xiong, Changyun Ye, Jianguo Xu
Escherichia coli is both of a widespread harmless gut commensal and a versatile pathogen of humans. Domestic animals are a well-known reservoir for pathogenic E. coli. However, studies of E. coli populations from wild animals that have been separated from human activities had been very limited. Here we obtained 580 isolates from intestinal contents of 116 wild Marmot Marmota himalayana from Qinghai-Tibet plateau, China, with five isolates per animal. We selected 125 (hereinafter referred to as strains) from the 580 isolates for genome sequencing, based on unique pulse field gel electrophoresis patterns and at least one isolate per animal...
December 7, 2016: Emerging Microbes & Infections
https://www.readbyqxmd.com/read/27924129/interplay-of-genes-in-plant-pathogen-interactions-in-planta-expression-and-docking-studies-of-a-beta-1-3-glucanase-gene-from-piper-colubrinum-and-a-glucanase-inhibitor-gene-from-phytophthora-capsici
#4
K Johnson George, O Rosana Babu, I P Vijesh Kumar, J Santhosh Eapen, M Anandaraj
Oomycete pathogen, Phytophthora capsici is devastating for black pepper (Piper nigrum L.) and causes foot rot disease at all stages of plant growth. Phytophthora secretes a glucanase inhibitor protein (GIP), which is capable of inhibiting defence proteins like endoglucanases. In this particular study Quantitative PCR analysis, molecular docking studies and analysis of sequences of Glucanase inhibitor protein and beta-1,3 glucanse genes were done mainly depending on the data derived from Phytophthora capsici whole genome sequencing and Piper colubrinum RNA-sequencing (RNA-Seq)...
October 2016: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
https://www.readbyqxmd.com/read/27924028/novoplasty-de-novo-assembly-of-organelle-genomes-from-whole-genome-data
#5
Nicolas Dierckxsens, Patrick Mardulyn, Guillaume Smits
The evolution in next-generation sequencing (NGS) technology has led to the development of many different assembly algorithms, but few of them focus on assembling the organelle genomes. These genomes are used in phylogenetic studies, food identification and are the most deposited eukaryotic genomes in GenBank. Producing organelle genome assembly from whole genome sequencing (WGS) data would be the most accurate and least laborious approach, but a tool specifically designed for this task is lacking. We developed a seed-and-extend algorithm that assembles organelle genomes from whole genome sequencing (WGS) data, starting from a related or distant single seed sequence...
October 24, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923837/the-nci-60-methylome-and-its-integration-into-cellminer
#6
William C Reinhold, Sudhir Varma, Margot Sunshine, Vinodh Rajapakse, Augustin Luna, Kurt W Kohn, Holly Stevenson, Yonghong Wang, Holger Heyn, Vanesa Nogales, Sebastian Moran, David J Goldstein, James H Doroshow, Paul S Meltzer, Manel Esteller, Yves Pommier
A unique resource for systems pharmacology and genomic studies is the NCI-60 cancer cell line panel, which provides data for the largest publicly available library of compounds with cytotoxic activity (~21,000 compounds), including 108 FDA-approved and 70 clinical trial drugs as well as genomic data, including whole-exome sequencing, gene and microRNA transcripts, DNA copy number, and protein levels. Here we provide the first readily usable genome-wide DNA methylation database for the NCI-60, including 485,577 probes from the Infinium HumanMethylation450k BeadChip array, which yielded DNA methylation signatures for 17,559 genes integrated into our open access CellMiner version 2...
December 6, 2016: Cancer Research
https://www.readbyqxmd.com/read/27923825/rational-selection-of-syngeneic-preclinical-tumor-models-for-immunotherapeutic-drug-discovery
#7
Suzanne I S Mosely, John E Prime, Richard C A Sainson, Jens-Oliver Koopmann, Dennis Y Q Wang, Danielle M Greenawalt, Miika J Ahdesmaki, Rebecca Leyland, Stefanie Mullins, Luciano Pacelli, Danielle Marcus, Judith Anderton, Amanda Watkins, Jane Coates Ulrichsen, Philip Brohawn, Brandon W Higgs, Matthew McCourt, Hazel Jones, James A Harper, Michelle Morrow, Viia Valge-Archer, Ross Stewart, Simon J Dovedi, Robert W Wilkinson
Murine syngeneic tumor models are critical to novel immuno-based therapy development but the molecular and immunological features of these models are still not clearly defined. The translational relevance of differences between the models is not fully understood, impeding appropriate preclinical model selection for target validation, and ultimately hindering drug development. Across a panel of commonly-used murine syngeneic tumor models, we showed variable responsiveness to immunotherapies. We employed array comparative genomic hybridization, whole-exome sequencing, exon microarray analysis, and flow cytometry to extensively characterize these models, which revealed striking differences that may underlie these contrasting response profiles...
December 6, 2016: Cancer Immunology Research
https://www.readbyqxmd.com/read/27923522/development-of-a-multiplex-taqman-real-time-pcr-assay-for-typing-of-mycoplasma-pneumoniae-based-on-type-specific-indels-identified-through-whole-genome-sequencing
#8
Bernard J Wolff, Alvaro J Benitez, Heta P Desai, Shatavia S Morrison, Maureen H Diaz, Jonas M Winchell
We developed a multiplex real-time PCR assay for simultaneously detecting M. pneumoniae and typing into historically-defined P1 types. Typing was achieved based on the presence of short type-specific indels identified through whole genome sequencing. This assay was 100% specific compared to existing methods and may be useful during epidemiologic investigations.
November 25, 2016: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/27923418/outbreak-of-klebsiella-pneumoniae-carbapenemase-producing-citrobacter-freundii-at-a-tertiary-acute-care-facility-in-miami-florida
#9
Adriana Jiménez, José G Castro, L Silvia Munoz-Price, Dennise de Pascale, Luis Shimose, Mustapha M Mustapha, Caressa N Spychala, Roberta T Mettus, Vaughn S Cooper, Yohei Doi
OBJECTIVE To describe the investigation and control of a rare cluster of Klebsiella pneumoniae carbapenemase-producing Citrobacter freundii in a hospital in southern Florida. METHODS An epidemiologic investigation, review of infection prevention procedures, and molecular studies including whole genome sequencing were conducted. RESULTS An outbreak of K. pneumoniae carbapenemase-3-producing C. freundii was identified at a tertiary hospital in Florida in 2014. Of the 6 cases identified, 3 occurred in the same intensive care unit and were caused by the same clone...
December 7, 2016: Infection Control and Hospital Epidemiology
https://www.readbyqxmd.com/read/27923400/allele-specific-expression-in-the-human-heart-and-its-application-to-postoperative-atrial-fibrillation-and-myocardial-ischemia
#10
Martin I Sigurdsson, Louis Saddic, Mahyar Heydarpour, Tzuu-Wang Chang, Prem Shekar, Sary Aranki, Gregory S Couper, Stanton K Shernan, Jon G Seidman, Simon C Body, Jochen D Muehlschlegel
BACKGROUND: Allele-specific expression (ASE) is differential expression of each of the two chromosomal alleles of an autosomal gene. We assessed ASE patterns in the human left atrium (LA, n = 62) and paired samples from the left ventricle (LV, n = 76) before and after ischemia, and tested the utility of differential ASE to identify genes associated with postoperative atrial fibrillation (poAF) and myocardial ischemia. METHODS: Following genotyping from whole blood and whole-genome sequencing of LA and LV samples, we called ASE using sequences overlapping heterozygous SNPs using rigorous quality control to minimize false ASE calling...
December 6, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27923365/an-inactivated-ge-deleted-pseudorabies-vaccine-provides-complete-clinical-protection-and-reduces-virus-shedding-against-challenge-by-a-chinese-pseudorabies-variant
#11
Jichun Wang, Rongli Guo, Yongfeng Qiao, Mengwei Xu, Zhisheng Wang, Yamei Liu, Yiqi Gu, Chang Liu, Jibo Hou
BACKGROUND: Since the end of 2011 an outbreak of pseudorabies affected Chinese pig herds that had been vaccinated with the commercial vaccine made of Bartha K61 strain. It is now clear that the outbreak was caused by an emergent PRV variant. Even though vaccines made of PRV Bartha K61 strain can confer certain cross protection against PRV variants based on experimental data, less than optimal clinical protection and virus shedding reduction were observed, making the control or eradication of this disease difficult...
December 7, 2016: BMC Veterinary Research
https://www.readbyqxmd.com/read/27923352/genome-survey-of-pistachio-pistacia-vera-l-by-next-generation-sequencing-development-of-novel-ssr-markers-and-genetic-diversity-in-pistacia-species
#12
Elmira Ziya Motalebipour, Salih Kafkas, Mortaza Khodaeiaminjan, Nergiz Çoban, Hatice Gözel
BACKGROUND: Pistachio (Pistacia vera L.) is one of the most important nut crops in the world. There are about 11 wild species in the genus Pistacia, and they have importance as rootstock seed sources for cultivated P. vera and forest trees. Published information on the pistachio genome is limited. Therefore, a genome survey is necessary to obtain knowledge on the genome structure of pistachio by next generation sequencing. Simple sequence repeat (SSR) markers are useful tools for germplasm characterization, genetic diversity analysis, and genetic linkage mapping, and may help to elucidate genetic relationships among pistachio cultivars and species...
December 7, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27923066/somatic-genomics-and-clinical-features-of-lung-adenocarcinoma-a-retrospective-study
#13
Jianxin Shi, Xing Hua, Bin Zhu, Sarangan Ravichandran, Mingyi Wang, Cu Nguyen, Seth A Brodie, Alessandro Palleschi, Marco Alloisio, Gianluca Pariscenti, Kristine Jones, Weiyin Zhou, Aaron J Bouk, Joseph Boland, Belynda Hicks, Adam Risch, Hunter Bennett, Brian T Luke, Lei Song, Jubao Duan, Pengyuan Liu, Takashi Kohno, Qingrong Chen, Daoud Meerzaman, Crystal Marconett, Ite Laird-Offringa, Ian Mills, Neil E Caporaso, Mitchell H Gail, Angela C Pesatori, Dario Consonni, Pier Alberto Bertazzi, Stephen J Chanock, Maria Teresa Landi
BACKGROUND: Lung adenocarcinoma (LUAD) is the most common histologic subtype of lung cancer and has a high risk of distant metastasis at every disease stage. We aimed to characterize the genomic landscape of LUAD and identify mutation signatures associated with tumor progression. METHODS AND FINDINGS: We performed an integrative genomic analysis, incorporating whole exome sequencing (WES), determination of DNA copy number and DNA methylation, and transcriptome sequencing for 101 LUAD samples from the Environment And Genetics in Lung cancer Etiology (EAGLE) study...
December 2016: PLoS Medicine
https://www.readbyqxmd.com/read/27923045/tumor-evolution-in-two-patients-with-basal-like-breast-cancer-a-retrospective-genomics-study-of-multiple-metastases
#14
Katherine A Hoadley, Marni B Siegel, Krishna L Kanchi, Christopher A Miller, Li Ding, Wei Zhao, Xiaping He, Joel S Parker, Michael C Wendl, Robert S Fulton, Ryan T Demeter, Richard K Wilson, Lisa A Carey, Charles M Perou, Elaine R Mardis
BACKGROUND: Metastasis is the main cause of cancer patient deaths and remains a poorly characterized process. It is still unclear when in tumor progression the ability to metastasize arises and whether this ability is inherent to the primary tumor or is acquired well after primary tumor formation. Next-generation sequencing and analytical methods to define clonal heterogeneity provide a means for identifying genetic events and the temporal relationships between these events in the primary and metastatic tumors within an individual...
December 2016: PLoS Medicine
https://www.readbyqxmd.com/read/27923043/clonal-evolutionary-analysis-during-her2-blockade-in-her2-positive-inflammatory-breast-cancer-a-phase-ii-open-label-clinical-trial-of-afatinib-vinorelbine
#15
Gerald Goh, Ramona Schmid, Kelly Guiver, Wichit Arpornwirat, Imjai Chitapanarux, Vinod Ganju, Seock-Ah Im, Sung-Bae Kim, Arunee Dechaphunkul, Jedzada Maneechavakajorn, Neil Spector, Thomas Yau, Mehdi Afrit, Slim Ben Ahmed, Stephen R Johnston, Neil Gibson, Martina Uttenreuther-Fischer, Javier Herrero, Charles Swanton
BACKGROUND: Inflammatory breast cancer (IBC) is a rare, aggressive form of breast cancer associated with HER2 amplification, with high risk of metastasis and an estimated median survival of 2.9 y. We performed an open-label, single-arm phase II clinical trial (ClinicalTrials.gov NCT01325428) to investigate the efficacy and safety of afatinib, an irreversible ErbB family inhibitor, alone and in combination with vinorelbine in patients with HER2-positive IBC. This trial included prospectively planned exome analysis before and after afatinib monotherapy...
December 2016: PLoS Medicine
https://www.readbyqxmd.com/read/27922636/dna-methylation-and-substance-use-risk-a-prospective-genome-wide-study-spanning-gestation-to-adolescence
#16
C A M Cecil, E Walton, R G Smith, E Viding, E J McCrory, C L Relton, M Suderman, J-B Pingault, W McArdle, T R Gaunt, J Mill, E D Barker
Epigenetic processes have been implicated in addiction; yet, it remains unclear whether these represent a risk factor and/or a consequence of substance use. Here, we believe we conducted the first genome-wide, longitudinal study to investigate whether DNA methylation patterns in early life prospectively associate with substance use in adolescence. The sample comprised of 244 youth (51% female) from the Avon Longitudinal Study of Parents and Children (ALSPAC), with repeated assessments of DNA methylation (Illumina 450k array; cord blood at birth, whole blood at age 7) and substance use (tobacco, alcohol and cannabis use; age 14-18)...
December 6, 2016: Translational Psychiatry
https://www.readbyqxmd.com/read/27921396/frequency-and-type-of-inheritable-mutations-induced-by-%C3%AE-rays-in-rice-as-revealed-by-whole-genome-sequencing
#17
Shan Li, Yun-Chao Zheng, Hai-Rui Cui, Hao-Wei Fu, Qing-Yao Shu, Jian-Zhong Huang
Mutation breeding is based on the induction of genetic variations; hence knowledge of the frequency and type of induced mutations is of paramount importance for the design and implementation of a mutation breeding program. Although γ ray irradiation has been widely used since the 1960s in the breeding of about 200 economically important plant species, molecular elucidation of its genetic effects has so far been achieved largely by analysis of target genes or genomic regions. In the present study, the whole genomes of six γ-irradiated M2 rice plants were sequenced; a total of 144-188 million high-quality (Q>20) reads were generated for each M2 plant, resulting in genome coverage of >45 times for each plant...
2016: Journal of Zhejiang University. Science. B
https://www.readbyqxmd.com/read/27920765/novel-pathways-for-ameliorating-the-fitness-cost-of-gentamicin-resistant-small-colony-variants
#18
Martin Vestergaard, Wilhelm Paulander, Bingfeng Leng, Jesper B Nielsen, Henrik T Westh, Hanne Ingmer
Small colony variants (SCVs) of the human pathogen Staphylococcus aureus are associated with persistent infections. Phenotypically, SCVs are characterized by slow growth and they can arise upon interruption of the electron transport chain that consequently reduce membrane potential and thereby limit uptake of aminoglycosides (e.g., gentamicin). In this study, we have examined the pathways by which the fitness cost of SCVs can be ameliorated. Five gentamicin resistant SCVs derived from S. aureus JE2 were independently selected on agar plates supplemented with gentamicin...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27920729/transcriptional-network-architecture-of-breast-cancer-molecular-subtypes
#19
Guillermo de Anda-Jáuregui, Tadeo E Velázquez-Caldelas, Jesús Espinal-Enríquez, Enrique Hernández-Lemus
Breast cancer heterogeneity is evident at the clinical, histological and molecular level. High throughput technologies allowed the identification of intrinsic subtypes that capture transcriptional differences among tumors. A remaining question is whether said differences are associated to a particular transcriptional program which involves different connections between the same molecules. In other words, whether particular transcriptional network architectures can be linked to specific phenotypes. In this work we infer, construct and analyze transcriptional networks from whole-genome gene expression microarrays, by using an information theory approach...
2016: Frontiers in Physiology
https://www.readbyqxmd.com/read/27920554/next-generation-sequence-detects-arap3-as-a-novel-oncogene-in-papillary-thyroid-carcinoma
#20
Qing-Xuan Wang, En-Dong Chen, Ye-Feng Cai, Yi-Li Zhou, Zhou-Ci Zheng, Ying-Hao Wang, Yi-Xiang Jin, Wen-Xu Jin, Xiao-Hua Zhang, Ou-Chen Wang
PURPOSE: Thyroid cancer is the most frequent malignancies of the endocrine system, and it has became the fastest growing type of cancer worldwide. Much still remains unknown about the molecular mechanisms of thyroid cancer. Studies have found that some certain relationship between ARAP3 and human cancer. However, the role of ARAP3 in thyroid cancer has not been well explained. This study aimed to investigate the role of ARAP3 gene in papillary thyroid carcinoma. METHODS: Whole exon sequence and whole genome sequence of primary papillary thyroid carcinoma (PTC) samples and matched adjacent normal thyroid tissue samples were performed and then bioinformatics analysis was carried out...
2016: OncoTargets and Therapy
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