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https://www.readbyqxmd.com/read/29145633/the-initiation-propagation-and-dynamics-of-crispr-spycas9-r-loop-complex
#1
Yan Zeng, Yang Cui, Yong Zhang, Yanruo Zhang, Meng Liang, Hui Chen, Jie Lan, Guangtao Song, Jizhong Lou
CRISPR-Cas9 system has been widely used for efficient genome editing. Although the structures of Cas9 protein in complex with single-guided RNA (sgRNA) and target DNA have been resolved, the molecular details about the formation of Cas9 endonuclease R-loop structure remain elusive. Here we examine the DNA cleavage activities of Streptococcus pyogenes Cas9 (SpyCas9) and its mutants using various target sequences and study the conformational dynamics of R-loop structure during target binding using single-molecule fluorescence energy transfer (smFRET) technique...
November 14, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29145611/identification-of-novel-potentially-pleiotropic-variants-associated-with-osteoporosis-and-obesity-using-cfdr-method
#2
Yuan Hu, Li-Jun Tan, Xiang-Ding Chen, Zhen Liu, Shi-Shi Min, Qin Zeng, Hui Shen, Hong-Wen Deng
Context: Genome-wide association studies (GWASs) have been successful in identifying loci associated with osteoporosis and obesity. However, the findings just explain a small fraction of the total genetic variance. Objective: The aim of this study was to identify novel pleiotropic genes important in osteoporosis and obesity. Design and Setting: A pleiotropic conditional false discovery rate (cFDR) method was applied to three independent GWAS summary statistics of femoral neck bone mineral density (FN BMD), body mass index (BMI) and waist-hip ratio (WHR)...
November 14, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29145422/missense-mutation-at-cldn8-associated-with-a-high-plasma-interferon-gamma-inducible-protein-10-level-in-methadone-maintained-patients-with-urine-test-positive-for-morphine
#3
Tung-Hsia Liu, Ren-Hua Chung, Sheng-Chang Wang, Chiu-Ping Fang, Hsiao-Hui Tsou, Chia-Lung Shih, Hsiang-Wei Kuo, Yun Wang, Yu-Li Liu
We previously reported a high plasma chemokine interferon gamma-inducible protein 10 (IP-10) level and prolonged electrocardiography QT-interval in methadone maintenance treatment (MMT) patients with HIV or HCV infection. The purpose of this study was to evaluate the genetic association of high plasma IP-10 level in the MMT patients. The gene-based and pathway-based association analyses were conducted using a genome-wide association study dataset in 344 MMT patients for identifying genes and pathways associated with plasma IP-10 level...
2017: PloS One
https://www.readbyqxmd.com/read/29145069/the-sultr-gene-family-in-maize-zea-mays-l-gene-cloning-and-expression-analyses-under-sulfate-starvation-and-abiotic-stress
#4
Qin Huang, Meiping Wang, Zongliang Xia
Sulfur is an essential macronutrient required for plant growth, development and stress responses. The family of sulfate transporters (SULTRs) mediates the uptake and translocation of sulfate in higher plants. However, basic knowledge of the SULTR gene family in maize (Zea mays L.) is scarce. In this study, a genome-wide bioinformatic analysis of SULTR genes in maize was conducted, and the developmental expression patterns of the genes and their responses to sulfate starvation and abiotic stress were further investigated...
November 10, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/29144491/corrigendum-genome-wide-dna-methylation-landscape-defines-specialization-of-regulatory-t-cells-in-tissues
#5
Michael Delacher, Charles D Imbusch, Dieter Weichenhan, Achim Breiling, Agnes Hotz-Wagenblatt, Ulrike Träger, Ann-Cathrin Hofer, Danny Kägebein, Qi Wang, Felix Frauhammer, Jan-Philipp Mallm, Katharina Bauer, Carl Herrmann, Philipp A Lang, Benedikt Brors, Christoph Plass, Markus Feuerer
This corrects the article DOI: 10.1038/ni.3799.
November 16, 2017: Nature Immunology
https://www.readbyqxmd.com/read/29144465/parallel-palaeogenomic-transects-reveal-complex-genetic-history-of-early-european-farmers
#6
Mark Lipson, Anna Szécsényi-Nagy, Swapan Mallick, Annamária Pósa, Balázs Stégmár, Victoria Keerl, Nadin Rohland, Kristin Stewardson, Matthew Ferry, Megan Michel, Jonas Oppenheimer, Nasreen Broomandkhoshbacht, Eadaoin Harney, Susanne Nordenfelt, Bastien Llamas, Balázs Gusztáv Mende, Kitti Köhler, Krisztián Oross, Mária Bondár, Tibor Marton, Anett Osztás, János Jakucs, Tibor Paluch, Ferenc Horváth, Piroska Csengeri, Judit Koós, Katalin Sebők, Alexandra Anders, Pál Raczky, Judit Regenye, Judit P Barna, Szilvia Fábián, Gábor Serlegi, Zoltán Toldi, Emese Gyöngyvér Nagy, János Dani, Erika Molnár, György Pálfi, László Márk, Béla Melegh, Zsolt Bánfai, László Domboróczki, Javier Fernández-Eraso, José Antonio Mujika-Alustiza, Carmen Alonso Fernández, Javier Jiménez Echevarría, Ruth Bollongino, Jörg Orschiedt, Kerstin Schierhold, Harald Meller, Alan Cooper, Joachim Burger, Eszter Bánffy, Kurt W Alt, Carles Lalueza-Fox, Wolfgang Haak, David Reich
Ancient DNA studies have established that Neolithic European populations were descended from Anatolian migrants who received a limited amount of admixture from resident hunter-gatherers. Many open questions remain, however, about the spatial and temporal dynamics of population interactions and admixture during the Neolithic period. Here we investigate the population dynamics of Neolithization across Europe using a high-resolution genome-wide ancient DNA dataset with a total of 180 samples, of which 130 are newly reported here, from the Neolithic and Chalcolithic periods of Hungary (6000-2900 bc, n = 100), Germany (5500-3000 bc, n = 42) and Spain (5500-2200 bc, n = 38)...
November 16, 2017: Nature
https://www.readbyqxmd.com/read/29144457/a-ubiquitin-dependent-signalling-axis-specific-for-alkbh-mediated-dna-dealkylation-repair
#7
Joshua R Brickner, Jennifer M Soll, Patrick M Lombardi, Cathrine B Vågbø, Miranda C Mudge, Clement Oyeniran, Renana Rabe, Jessica Jackson, Meagan E Sullender, Elyse Blazosky, Andrea K Byrum, Yu Zhao, Mark A Corbett, Jozef Gécz, Michael Field, Alessandro Vindigni, Geir Slupphaug, Cynthia Wolberger, Nima Mosammaparast
DNA repair is essential to prevent the cytotoxic or mutagenic effects of various types of DNA lesions, which are sensed by distinct pathways to recruit repair factors specific to the damage type. Although biochemical mechanisms for repairing several forms of genomic insults are well understood, the upstream signalling pathways that trigger repair are established for only certain types of damage, such as double-stranded breaks and interstrand crosslinks. Understanding the upstream signalling events that mediate recognition and repair of DNA alkylation damage is particularly important, since alkylation chemotherapy is one of the most widely used systemic modalities for cancer treatment and because environmental chemicals may trigger DNA alkylation...
November 16, 2017: Nature
https://www.readbyqxmd.com/read/29144405/genomic-analysis-of-the-asmt-gene-family-in-solanum-lycopersicum
#8
Weicheng Liu, Dake Zhao, Chunfang Zheng, Chen Chen, Xin Peng, Yuan Cheng, Hongjian Wan
Acetylserotonin methyltransferase (ASMT) is the last enzyme of melatonin biosynthesis and may play a rate-limiting role in the melatonin production of plants. In this study, systematic analysis of the ASMT gene family in tomato (Solanum lycopersicum Mill) has been presented by the integration of the structural features, phylogenetic relationships, exon/intron configuration, and expression profile during growth and development, as well as biotic stresses. The results revealed that the tomato genome encoded a minimum of 14 members, containing three probable encoded pseudogenes...
November 16, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29143824/pd-1-is-a-haploinsufficient-suppressor-of-t-cell-lymphomagenesis
#9
Tim Wartewig, Zsuzsanna Kurgyis, Selina Keppler, Konstanze Pechloff, Erik Hameister, Rupert Öllinger, Roman Maresch, Thorsten Buch, Katja Steiger, Christof Winter, Roland Rad, Jürgen Ruland
T cell non-Hodgkin lymphomas are a heterogeneous group of highly aggressive malignancies with poor clinical outcomes. T cell lymphomas originate from peripheral T cells and are frequently characterized by genetic gain-of-function variants in T cell receptor (TCR) signalling molecules. Although these oncogenic alterations are thought to drive TCR pathways to induce chronic proliferation and cell survival programmes, it remains unclear whether T cells contain tumour suppressors that can counteract these events...
November 15, 2017: Nature
https://www.readbyqxmd.com/read/29143708/genome-wide-association-study-for-growth-traits-in-nelore-cattle
#10
A P N Terakado, R B Costa, G M F de Camargo, N Irano, T Bresolin, L Takada, C V D Carvalho, H N Oliveira, R Carvalheiro, F Baldi, L G de Albuquerque
The objective of this study was to investigate the association of single nucleotide polymorphisms (SNPs) with birth weight, weight gain from birth to weaning and from weaning to yearling, yearling height and cow weight in Nelore cattle. Data from 5064 animals participating in the DeltaGen and PAINT breeding programs were used. The animals were genotyped with a panel of 777 962 SNPs (Illumina BovineHD BeadChip) and 412 993 SNPs remained after quality control analysis of the genomic data. A genome-wide association study was performed using a single-step methodology...
November 16, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/29143671/gwas-of-agronomic-traits-in-soybean-collection-included-in-breeding-pool-in-kazakhstan
#11
Alibek Zatybekov, Saule Abugalieva, Svetlana Didorenko, Yelena Gerasimova, Ivan Sidorik, Shynar Anuarbek, Yerlan Turuspekov
BACKGROUND: In recent years soybean is becoming one of the most important oilseed crops in Kazakhstan. Only within the last ten years (2006-2016), the area under soybean is expanded from 45 thousand hectares (ha) in 2006 to 120 thousand ha in 2016. The general trend of soybean expansion is from south-eastern to eastern and northern regions of the country, where average temperatures are lower and growing seasons are shorter. These new soybean growing territories were poorly examined in terms of general effects on productivity level among the diverse sample of soybean accessions...
November 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29143670/genes-to-predict-vo2max-trainability-a-systematic-review
#12
REVIEW
Camilla J Williams, Mark G Williams, Nir Eynon, Kevin J Ashton, Jonathan P Little, Ulrik Wisloff, Jeff S Coombes
BACKGROUND: Cardiorespiratory fitness (VO2max) is an excellent predictor of chronic disease morbidity and mortality risk. Guidelines recommend individuals undertake exercise training to improve VO2max for chronic disease reduction. However, there are large inter-individual differences between exercise training responses. This systematic review is aimed at identifying genetic variants that are associated with VO2max trainability. METHODS: Peer-reviewed research papers published up until October 2016 from four databases were examined...
November 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29143598/gwas-for-plant-growth-stages-and-yield-components-in-spring-wheat-triticum-aestivum-l-harvested-in-three-regions-of-kazakhstan
#13
Yerlan Turuspekov, Aida Baibulatova, Kanat Yermekbayev, Laura Tokhetova, Vladimir Chudinov, Grigoriy Sereda, Martin Ganal, Simon Griffiths, Saule Abugalieva
BACKGROUND: Spring wheat is the largest agricultural crop grown in Kazakhstan with an annual sowing area of 12 million hectares in 2016. Annually, the country harvests around 15 million tons of high quality grain. Despite environmental stress factors it is predicted that the use of new technologies may lead to increases in productivity from current levels of 1.5 to up to 3 tons per hectare. One way of improving wheat productivity is by the application of new genomic oriented approaches in plant breeding projects...
November 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29143489/spatial-variation-in-the-parasite-communities-and-genomic-structure-of-urban-rats-in-new-york-city
#14
L P Angley, M Combs, C Firth, M J Frye, I Lipkin, J L Richardson, J Munshi-South
Brown rats (Rattus norvegicus) are a globally distributed pest. Urban habitats can support large infestations of rats, posing a potential risk to public health from the parasites and pathogens they carry. Despite the potential influence of rodent-borne zoonotic diseases on human health, it is unclear how urban habitats affect the structure and transmission dynamics of ectoparasite and microbial communities (all referred to as "parasites" hereafter) among rat colonies. In this study, we use ecological data on parasites and genomic sequencing of their rat hosts to examine associations between spatial proximity, genetic relatedness and the parasite communities associated with 133 rats at five sites in sections of New York City with persistent rat infestations...
November 16, 2017: Zoonoses and Public Health
https://www.readbyqxmd.com/read/29143315/fetal-haemoglobin-induction-in-sickle-cell-disease
#15
REVIEW
Alireza Paikari, Vivien A Sheehan
Fetal haemoglobin (HbF, α2γ2) induction has long been an area of investigation, as it is known to ameliorate the clinical complications of sickle cell disease (SCD). Progress in identifying novel HbF-inducing strategies has been stymied by limited understanding of gamma (γ)-globin regulation. Genome-wide association studies (GWAS) have identified variants in BCL11A and HBS1L-MYB that are associated with HbF levels. Functional studies have established the roles of BCL11A, MYB, and KLF1 in γ-globin regulation, but this information has not yielded new pharmacological agents...
November 16, 2017: British Journal of Haematology
https://www.readbyqxmd.com/read/29143212/rhodococcus-psychrotolerans-sp-nov-isolated-from-rhizosphere-of-deschampsia-antarctica
#16
Leonardo Jose Silva, Danilo Tosta Souza, Diego Bonaldo Genuario, Harold Alexander Vargas Hoyos, Suikinai Nobre Santos, Luiz Henrique Rosa, Tiago Domingues Zucchi, Itamar Soares Melo
A novel actinobacterium, designated strain CMAA 1533(T), was isolated from the rhizosphere of Deschampsia antarctica collected at King George Island, Antarctic Peninsula. Strain CMAA 1533(T) was found to grow over a wide range of temperatures (4-28 °C) and pH (4-10). Macroscopically, the colonies were observed to be circular shaped, smooth, brittle and opaque-cream on most of the culture media tested. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CMAA 1533(T) belongs to the family Nocardiaceae and forms a distinct phyletic line within the genus Rhodococcus...
November 15, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29142962/what-genetics-tells-us-about-the-pathogenesis-of-iga-nephropathy-the%C3%A2-role%C3%A2-of-immune-factors-and-infection
#17
REVIEW
Yue-Miao Zhang, Xu-Jie Zhou, Hong Zhang
Immunoglobulin A nephropathy (IgAN) is the most common type of primary glomerulonephritis, which is characterized by IgA1-containing immune-deposits in the glomerular mesangium. The epidemiologic observations of familial clustering as well as ethnic and regional discrepancies indicate a genetic component to IgAN. Large, international, genome-wide association studies have identified several susceptibility genes and loci for IgAN, many of which have been implicated in immune regulation and are shared with other autoimmune diseases...
May 2017: KI Reports
https://www.readbyqxmd.com/read/29142828/metabolic-engineering-of-ustilago-trichophora-tz1-for-improved-malic-acid-production
#18
Thiemo Zambanini, Hamed Hosseinpour Tehrani, Elena Geiser, Christiane K Sonntag, Joerg M Buescher, Guido Meurer, Nick Wierckx, Lars M Blank
Ustilago trichophora RK089 has been found recently as a good natural malic acid producer from glycerol. This strain has previously undergone adaptive laboratory evolution for enhanced substrate uptake rate resulting in the strain U. trichophora TZ1. Medium optimization and investigation of process parameters enabled titers and rates that are able to compete with those of organisms overexpressing major parts of the underlying metabolic pathways. Metabolic engineering can likely further increase the efficiency of malate production by this organism, provided that basic genetic tools and methods can be established for this rarely used and relatively obscure species...
June 2017: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29142311/a-standardized-herbal-extract-mitigates-tumor-inflammation-and-augments-chemotherapy-effect-of-docetaxel-in-prostate-cancer
#19
Chin-Hsien Tsai, Sheue-Fen Tzeng, Shih-Chuan Hsieh, Yu-Chih Yang, Yi-Wen Hsiao, Mong-Hsun Tsai, Pei-Wen Hsiao
Activation of the NFκB pathway is often associated with advanced cancer and has thus been regarded as a rational therapeutic target. Wedelia chinensis is rich in luteolin, apigenin, and wedelolactone that act synergistically to suppress androgen receptor activity in prostate cancer. Interestingly, our evaluation of a standardized Wedelia chinensis herbal extract (WCE) concluded its efficacy on hormone-refractory prostate cancer through systemic mechanisms. Oral administration of WCE significantly attenuated tumor growth and metastasis in orthotopic PC-3 and DU145 xenografts...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29142306/an-exome-sequencing-based-approach-for-genome-wide-association-studies-in-the-dog
#20
Bart J G Broeckx, Thomas Derrien, Stéphanie Mottier, Valentin Wucher, Edouard Cadieu, Benoît Hédan, Céline Le Béguec, Nadine Botherel, Kerstin Lindblad-Toh, Jimmy H Saunders, Dieter Deforce, Catherine André, Luc Peelman, Christophe Hitte
Genome-wide association studies (GWAS) are widely used to identify loci associated with phenotypic traits in the domestic dog that has emerged as a model for Mendelian and complex traits. However, a disadvantage of GWAS is that it always requires subsequent fine-mapping or sequencing to pinpoint causal mutations. Here, we performed whole exome sequencing (WES) and canine high-density (cHD) SNP genotyping of 28 dogs from 3 breeds to compare the SNP and linkage disequilibrium characteristics together with the power and mapping precision of exome-guided GWAS (EG-GWAS) versus cHD-based GWAS...
November 15, 2017: Scientific Reports
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