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https://www.readbyqxmd.com/read/28728275/-changes-and-differences-of-dna-methylation-in-human-macrophages-infected-with-virulent-and-avirulent-mycobacterium-tuberculosis
#1
L N Lyu, H Y Jia, Z H Li, Z Q Liu, Z D Zhang
Objective: To profile DNA methylation and compare differentially methylated region (DMR) of macrophages infected with virulent and avirulent strains of Mycobacterium tuberculosis (MTB). Methods: PMA(50 ng/ml) treated THP-1 macrophages were left uninfected or infected with the virulent H37Rv(THP-1/Rv) or avirulent H37Ra(THP-1/Ra). The genomic DNA was then extracted and DNA methylation was profiled via Reduced Representation Bisulfite Sequencing (RRBS). The DNA methylation pattern and DMRs between the tested samples were indentified...
July 12, 2017: Chinese Journal of Tuberculosis and Respiratory Diseases
https://www.readbyqxmd.com/read/28727829/functional-differentiation-and-spatial-temporal-co-expression-networks-of-the-nbs-encoding-gene-family-in-jilin-ginseng-panax-ginseng-c-a-meyer
#2
Rui Yin, Mingzhu Zhao, Kangyu Wang, Yanping Lin, Yanfang Wang, Chunyu Sun, Yi Wang, Meiping Zhang
Ginseng, Panax ginseng C.A. Meyer, is one of the most important medicinal plants for human health and medicine. It has been documented that over 80% of genes conferring resistance to bacteria, viruses, fungi and nematodes are contributed by the nucleotide binding site (NBS)-encoding gene family. Therefore, identification and characterization of NBS genes expressed in ginseng are paramount to its genetic improvement and breeding. However, little is known about the NBS-encoding genes in ginseng. Here we report genome-wide identification and systems analysis of the NBS genes actively expressed in ginseng (PgNBS genes)...
2017: PloS One
https://www.readbyqxmd.com/read/28727728/an-integrative-genomics-approach-identifies-novel-pathways-that-influence-candidaemia-susceptibility
#3
Vasiliki Matzaraki, Mark S Gresnigt, Martin Jaeger, Isis Ricaño-Ponce, Melissa D Johnson, Marije Oosting, Lude Franke, Sebo Withoff, John R Perfect, Leo A B Joosten, Bart Jan Kullberg, Frank L van de Veerdonk, Iris Jonkers, Yang Li, Cisca Wijmenga, Mihai G Netea, Vinod Kumar
Candidaemia is a bloodstream infection caused by Candida species that primarily affects specific groups of at-risk patients. Because only small candidaemia patient cohorts are available, classical genome wide association cannot be used to identify Candida susceptibility genes. Therefore, we have applied an integrative genomics approach to identify novel susceptibility genes and pathways for candidaemia. Candida-induced transcriptome changes in human primary leukocytes were assessed by RNA sequencing. Genetic susceptibility to candidaemia was assessed using the Illumina immunochip platform for genotyping of a cohort of 217 patients...
2017: PloS One
https://www.readbyqxmd.com/read/28727040/genome-wide-association-studies-and-meta-analysis-reveal-novel-quantitative-trait-loci-and-pleiotropic-loci-for-swine-head-related-traits
#4
H Chen, T Huang, Z Zhang, B Yang, C Jiang, J Wu, Z Zhou, H Zheng, W Xin, M Huang, M Zhang, C Chen, J Ren, H Ai, L Huang
The pig is an important domestic animal that provides a larger amount of meat and serves as a biomedical animal model for human. Head and facial features are closely linked to identity recognition in mammal communication. To uncover the genetic architecture of swine head and facial features, we constructed 5 experimental pig populations and accurately measured 10 traits related to head and facial features, for which genome-wide association studies and meta-analysis were later carried out. As a result, we identified a total of 24 loci harboring 437 SNP on 8 swine chromosomes (SSC) that surpassed suggestively significant levels, of which 17 loci on 6 chromosomes exceeded the 5% genome-wide significance thresholds...
June 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28727022/triennial-growth-and-development-symposium-genetics-and-breeding-for-intramuscular-fat-and-oleic-acid-content-in-pigs
#5
J Estany, R Ros-Freixedes, M Tor, R N Pena
The intramuscular fat (IMF) and oleic acid (OL) content have been favorably related to pork quality and human health. This influences the purchasing behavior of consumers and, therefore, also shifts the attention of breeding companies toward whether these traits are included into the breeding goal of the lines producing for high-valued markets. Because IMF and OL are unfavorably associated with lean content, a key economic trait, the real challenge for the industry is not simply to increase IMF and OL, but rather to come up with the right trade-off between them and lean content...
May 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28726602/maguari-virus-associated-with-human-disease
#6
Allison Groseth, Veronica Vine, Carla Weisend, Carolina Guevara, Douglas Watts, Brandy Russell, Robert B Tesh, Hideki Ebihara
Despite the lack of evidence for symptomatic human infection with Maguari virus (MAGV), its close relation to Cache Valley virus (CVV), which does infect humans, remains a concern. We sequenced the complete genome of a MAGV-like isolate (OBS6657) obtained from a febrile patient in Pucallpa, Ucayali, Peru, in 1998. To facilitate its classification, we generated additional full-length sequences for the MAGV prototype strain, 3 additional MAGV-like isolates, and the closely related CVV (7 strains), Tlacotalpan (1 strain), Playas (3 strains), and Fort Sherman (1 strain) viruses...
August 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28726394/human-cst-prefers-g-rich-but-not-necessarily-telomeric-sequences
#7
Robert A Hom, Deborah Sharon Wuttke
The human CST (CTC1-STN1-TEN1) heterotrimeric complex plays roles in both telomere maintenance and DNA replication through its ability to interact with ssDNA of a variety of sequences. The precise sequence specificity required to execute these functions is unknown. Telomere-binding proteins have been shown to specifically recognize key telomeric sequence motifs within ssDNA while accommodating non-specifically recognized sequences through conformationally plastic interfaces. To better understand the role CST plays in these processes, we have produced highly purified heterotrimer and elucidated the sequence requirements for CST recognition of ssDNA in vitro...
July 20, 2017: Biochemistry
https://www.readbyqxmd.com/read/28725948/genomics-and-epigenomics-in-rheumatic-diseases-what-do-they-provide-in-terms-of-diagnosis-and-disease-management
#8
Patricia Castro-Santos, Roberto Díaz-Peña
Most rheumatic diseases are complex or multifactorial entities with pathogeneses that interact with both multiple genetic factors and a high number of diverse environmental factors. Knowledge of the human genome sequence and its diversity among populations has provided a crucial step forward in our understanding of genetic diseases, identifying many genetic loci or genes associated with diverse phenotypes. In general, susceptibility to autoimmunity is associated with multiple risk factors, but the mechanism of the environmental component influence is poorly understood...
July 20, 2017: Clinical Rheumatology
https://www.readbyqxmd.com/read/28725363/bridging-two-scholarly-islands-enriches-both-coi-dna-barcodes-for-species-identification-versus-human-mitochondrial-variation-for-the-study-of-migrations-and-pathologies
#9
David S Thaler, Mark Y Stoeckle
DNA barcodes for species identification and the analysis of human mitochondrial variation have developed as independent fields even though both are based on sequences from animal mitochondria. This study finds questions within each field that can be addressed by reference to the other. DNA barcodes are based on a 648-bp segment of the mitochondrially encoded cytochrome oxidase I. From most species, this segment is the only sequence available. It is impossible to know whether it fairly represents overall mitochondrial variation...
October 2016: Ecology and Evolution
https://www.readbyqxmd.com/read/28725233/g-quadruplex-in-plants-a-ubiquitous-regulatory-element-and-its-biological-relevance
#10
REVIEW
Vikas Yadav, Hemansi, Nayun Kim, Narendra Tuteja, Puja Yadav
G quadruplexes (G4) are higher-order DNA and RNA secondary structures formed by G-rich sequences that are built around tetrads of hydrogen-bonded guanine bases. Potential G4 quadruplex sequences have been identified in G-rich eukaryotic non-telomeric and telomeric genomic regions. Upon function, G4 formation is known to involve in chromatin remodeling, gene regulation and has been associated with genomic instability, genetic diseases and cancer progression. The natural role and biological validation of G4 structures is starting to be explored, and is of particular interest for the therapeutic interventions for human diseases...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28725045/genomic-epidemiology-of-global-klebsiella-pneumoniae-carbapenemase-kpc-producing-escherichia-coli
#11
N Stoesser, A E Sheppard, G Peirano, L W Anson, L Pankhurst, R Sebra, H T T Phan, A Kasarskis, A J Mathers, T E A Peto, P Bradford, M R Motyl, A S Walker, D W Crook, J D Pitout
The dissemination of carbapenem resistance in Escherichia coli has major implications for the management of common infections. bla KPC, encoding a transmissible carbapenemase (KPC), has historically largely been associated with Klebsiella pneumoniae, a predominant plasmid (pKpQIL), and a specific transposable element (Tn4401, ~10 kb). Here we characterize the genetic features of bla KPC emergence in global E. coli, 2008-2013, using both long- and short-read whole-genome sequencing. Amongst 43/45 successfully sequenced bla KPC-E...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28724920/interleukin-36%C3%AE-provides-protection-against-hsv-1-infection-but-does-not-modulate-initiation-of-adaptive-immune-responses
#12
Katelynn A Milora, Siva R Uppalapati, Julio C Sanmiguel, Wei Zou, Liselotte E Jensen
Interleukin-36 (IL-36) represents three cytokines, IL-36α, IL-36β and IL-36γ, which bind to the same receptor, IL-1RL2; however, their physiological function(s) remain poorly understood. Here, the role of IL-36 in immunity against HSV-1 was examined using the flank skin infection mouse model. Expression analyses revealed increased levels of IL-36α and IL-36β mRNA in infected skin, while constitutive IL-36γ levels remained largely unchanged. In human keratinocytes, IL-36α mRNA was induced by HSV-1, while IL-1β and TNFα increased all three IL-36 mRNAs...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28724769/stlv-1-infection-of-papio-anubis-tax-sequence-heterogeneity-and-t-cell-recognition
#13
James M Termini, Diogo M Magnani, Helen S Maxwell, William Lauer, Iris Castro, Jerilyn Pecotte, Glen N Barber, David I Watkins, Ronald C Desrosiers
Natural infection of baboons with simian T lymphotropic virus (STLV) is a potentially useful model system for study of vaccination against the human virus HTLV. Here we expand the number of available full-length STLV-1 baboon sequences from one to three and relate T cell responses that recognize the immunodominant Tax protein to the tax sequences present in two individual baboons. Continuously growing T cell lines were established from two baboons, 12141 and 12752. Next-generation sequencing (NGS) of complete STLV genome sequences from these lines revealed them to be closely related but distinct from each other and from the STLV-1 baboon sequence in the NCBI sequence database...
July 19, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28724751/tomo-seq-identifies-sox9-as-a-key-regulator-of-cardiac-fibrosis-during-ischemic-injury
#14
Grégory P A Lacraz, Jan Philipp Junker, Monika M Gladka, Bas Molenaar, Koen T Scholman, Marta Vigil-Garcia, Danielle Versteeg, Hesther de Ruiter, Marit W Vermunt, Menno P Creyghton, Manon M H Huibers, Nicolaas de Jonge, Alexander van Oudenaarden, Eva van Rooij
Background -Cardiac ischemic injury induces a pathological remodeling response, which can ultimately lead to heart failure. Detailed mechanistic insights into molecular signaling pathways relevant for different aspects of cardiac remodeling will support the identification of novel therapeutic targets. Methods -While genome-wide transcriptome analysis on diseased tissues has greatly advanced our understanding of the regulatory networks that drive pathological changes in the heart, this approach has been disadvantaged by the fact that the signals are derived from tissue homogenates...
July 19, 2017: Circulation
https://www.readbyqxmd.com/read/28724549/identification-of-new-tumor-suppressor-genes-in-triple-negative-breast-cancer
#15
Roberto Rangel, Liliana Guzman-Rojas, Takahiro Kodama, Michiko Kodama, Justin Y Newberg, Neal G Copeland, Nancy A Jenkins
Although genomic sequencing has provided a better understating of the genetic landmarks in triple-negative breast cancer (TNBC), functional validation of candidate cancer genes (CCG) remains unsolved. In this study, we used a transposon mutagenesis strategy based on a two-step Sleeping Beauty (SB) forward genetic screen to identify and validate new tumor suppressors (TS) in this disease. We generated 120 siRNAs targeting 40 SB-identified candidate breast cancer TS genes and used them to downregulate expression of these genes in four human TNBC cell lines...
July 19, 2017: Cancer Research
https://www.readbyqxmd.com/read/28724479/holocene-selection-for-variants-associated-with-general-cognitive-ability-comparing-ancient-and-modern-genomes
#16
Michael A Woodley, Shameem Younuskunju, Bipin Balan, Davide Piffer
Human populations living during the Holocene underwent considerable microevolutionary change. It has been theorized that the transition of Holocene populations into agrarianism and urbanization brought about culture-gene co-evolution that favored via directional selection genetic variants associated with higher general cognitive ability (GCA). To examine whether GCA might have risen during the Holocene, we compare a sample of 99 ancient Eurasian genomes (ranging from 4.56 to 1.21 kyr BP) with a sample of 503 modern European genomes (Fst = 0...
August 2017: Twin Research and Human Genetics: the Official Journal of the International Society for Twin Studies
https://www.readbyqxmd.com/read/28724449/novel-promoters-and-coding-first-exons-in-dlg2-linked-to-developmental-disorders-and-intellectual-disability
#17
Claudio Reggiani, Sandra Coppens, Tayeb Sekhara, Ivan Dimov, Bruno Pichon, Nicolas Lufin, Marie-Claude Addor, Elga Fabia Belligni, Maria Cristina Digilio, Flavio Faletra, Giovanni Battista Ferrero, Marion Gerard, Bertrand Isidor, Shelagh Joss, Florence Niel-Bütschi, Maria Dolores Perrone, Florence Petit, Alessandra Renieri, Serge Romana, Alexandra Topa, Joris Robert Vermeesch, Tom Lenaerts, Georges Casimir, Marc Abramowicz, Gianluca Bontempi, Catheline Vilain, Nicolas Deconinck, Guillaume Smits
BACKGROUND: Tissue-specific integrative omics has the potential to reveal new genic elements important for developmental disorders. METHODS: Two pediatric patients with global developmental delay and intellectual disability phenotype underwent array-CGH genetic testing, both showing a partial deletion of the DLG2 gene. From independent human and murine omics datasets, we combined copy number variations, histone modifications, developmental tissue-specific regulation, and protein data to explore the molecular mechanism at play...
July 19, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28724070/marker-trait-association-analysis-of-iron-and-zinc-concentration-in-lentil-lens-culinaris-medik-seeds
#18
Hamid Khazaei, Rajib Podder, Carolyn T Caron, Shudhangshu S Kundu, Marwan Diapari, Albert Vandenberg, Kirstin E Bett
Lentil ( Medik.) seeds are relatively rich in iron (Fe) and zinc (Zn), making lentil a potential crop to aid in the global battle against human micronutrient deficiency. Understanding the genetic basis for uptake of seed Fe and Zn is required to increase sustainable concentrations of these minerals in seeds. The objectives of this study were to characterize genetic variation in seed Fe and Zn concentration and to identify molecular markers associated with these traits across diverse lentil accessions. A set of 138 cultivated lentil accessions from 34 countries were evaluated in four environments (2 sites × 2 yr) in Saskatchewan, Canada...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28723894/cysteine-protease-cathepsin-b-mediates-radiation-induced-bystander-effects
#19
Yu Peng, Man Zhang, Lingjun Zheng, Qian Liang, Hanzeng Li, Jeng-Ting Chen, Hongyan Guo, Sawako Yoshina, Yu-Zen Chen, Xiang Zhao, Xiaoqi Wu, Bin Liu, Shohei Mitani, Jau-Song Yu, Ding Xue
The radiation-induced bystander effect (RIBE) refers to a unique process in which factors released by irradiated cells or tissues exert effects on other parts of the animal not exposed to radiation, causing genomic instability, stress responses and altered apoptosis or cell proliferation. Although RIBEs have important implications for radioprotection, radiation safety and radiotherapy, the molecular identities of RIBE factors and their mechanisms of action remain poorly understood. Here we use Caenorhabditis elegans as a model in which to study RIBEs, and identify the cysteine protease CPR-4, a homologue of human cathepsin B, as the first RIBE factor in nematodes, to our knowledge...
July 19, 2017: Nature
https://www.readbyqxmd.com/read/28723667/resistance-to-ctla-4-checkpoint-inhibition-reversed-through-selective-elimination-of-granulocytic-myeloid-cells
#20
Paul E Clavijo, Ellen C Moore, Jianhong Chen, Ruth J Davis, Jay Friedman, Young Kim, Carter Van Waes, Zhong Chen, Clint T Allen
PURPOSE: Local immunosuppression remains a critical problem that limits clinically meaningful response to checkpoint inhibition in patients with head and neck cancer. Here, we assessed the impact of MDSC elimination on responses to CTLA-4 checkpoint inhibition. EXPERIMENTAL DESIGN: Murine syngeneic carcinoma immune infiltrates were characterized by flow cytometry. Granulocytic MDSCs (gMDSCs) were depleted and T-lymphocyte antigen-specific responses were measured...
June 11, 2017: Oncotarget
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