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https://www.readbyqxmd.com/read/29793052/title-lhp1-interacts-with-atrx-through-plant-specific-domains-at-specific-loci-targeted-by-prc2
#1
Haifeng Wang, Danhua Jiang, Elin Axelsson, Zdravko J Lorković, Sean Montgomery, Sarah Holec, Bas J G E Pieters, Abbas H K Al Temimi, Jasmin Mecinović, Frédéric Berger
Heterochromatin Protein 1 (HP1) is a major regulator of chromatin structure and function. In animals, the network of proteins interacting with HP1 is mainly associated with constitutive heterochromatin marked by H3K9me3. HP1 physically interacts with the putative orthologue of the SNF2 chromatin remodeler ATRX, which controls deposition of the histone variant H3.3 in mammals. In Arabidopsis thaliana, we show that the orthologue of ATRX participates in H3.3 deposition and characterize the function of conserved domains of plant ATRX...
May 21, 2018: Molecular Plant
https://www.readbyqxmd.com/read/29793031/cloning-overexpression-and-purification-of-a-gene-of-unknown-function-of-prophage-loci-from-candidatus-liberibacter-asiaticus-the-destructive-bacterial-pathogen-of-huanglongbing-disease-in-citrus-plants
#2
Duangtip Sudhan, Thamrongjet Puttamuk, Supachai Vuttipongchaikij, Pitak Chuawong
Citrus Huanglongbing (HLB) or citrus greening is one of the most destructive diseases affecting citrus industry worldwide. The causal agent in Asia is a phloem-limited, Gram-negative bacterium, 'Candidatus Liberibacter asiaticus' (CLas). Within the genome of CLas lies prophage regions, classified as Type-A, B, C, and D. In particular, Type-D has been indicated to correlate with the blotchy-mottle symptoms of citrus trees. Here we reported the cloning, overexpression, and purification of the ORF1, an open reading frame from the partial Type-D region of CLas obtained from an infected lime tree (Citrus aurantifolia Swingle)...
May 21, 2018: Protein Expression and Purification
https://www.readbyqxmd.com/read/29792943/the-development-of-a-screening-protocol-for-salmonella-spp-and-enteropathogenic-yersinia-spp-in-samples-from-wild-boar-sus-scrofa-also-generating-mlva-data-for-y-enterocolitica-and-y-pseudotuberculosis
#3
Axel Sannö, Magdalena Jacobson, Sandra Sterner, Susanne Thisted-Lambertz, Anna Aspán
Salmonellosis and yersiniosis are notifiable human diseases that are commonly associated with contaminated food. Domestic pigs as well as wild boars and other wild-life have been identified as reservoirs of these bacteria. Methods for cultivation and molecular epidemiological investigations of Salmonella spp. are well established, however, cultivation of enteropathogenic Yersinia spp. is time- consuming and the commonly used method for molecular epidemiological investigations, pulsed-field gel electrophoresis, lack in discriminatory power...
May 21, 2018: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/29792826/fast-evolving-human-specific-neural-enhancers-are-associated-with-aging-related-diseases
#4
Han Chen, Chunyan Li, Zhicheng Zhou, Han Liang
The antagonistic pleiotropy theory hypothesizes that evolutionary adaptations maximizing the fitness in early age increase disease burden after reproduction. This theory remains largely untested at the molecular level. Here, we analyzed enhancer evolution in primates to investigate the relationships between aging-related diseases and enhancers acquired after the human-chimpanzee divergence. We report a 5-fold increased evolutionary rate of enhancers that are activated in neural tissues, leading to fixation of ∼100 human-specific enhancers potentially under adaptation...
May 23, 2018: Cell Systems
https://www.readbyqxmd.com/read/29792315/genomic-variation-among-and-within-six-juglans-species
#5
Kristian A Stevens, Keith Woeste, Sandeep Chakraborty, Marc W Crepeau, Charles A Leslie, Pedro J Martínez-García, Daniela Puiu, Jeanne Romero-Severson, Mark Coggeshall, Abhaya M Dandekar, Daniel Kluepfel, David B Neale, Steven L Salzberg, Charles H Langley
Genomic analysis in Juglans (walnuts) is expected to transform the breeding and agricultural production of both nuts and lumber. To that end, we report here the determination of reference sequences for six additional relatives of Juglans regia : Juglans sigillata (also from section Dioscaryon ), Juglans nigra , Juglans microcarpa, Juglans hindsii (from section Rhysocaryon ) , Juglans cathayensis (from section Cardiocaryon ), and the closely related Pterocarya stenoptera. While these are 'draft' genomes, ranging in size between 640Mbp and 990Mbp, their contiguities and accuracies can support powerful annotations of genomic variation that are often the foundation of new avenues of research and breeding...
May 23, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29792231/high-burden-of-birthweight-lowering-genetic-variants-in-africans-and-asians
#6
Fasil Tekola-Ayele, Tsegaselassie Workalemahu, Azmeraw T Amare
BACKGROUND: Birthweight is an important predictor of infant morbidity and mortality, and is associated with cardiovascular diseases, obesity, and diabetes in childhood and adulthood. Birthweight and fetal growth show regional and population variations even under similar maternal conditions, and a large proportion of these differences are not explained by environmental factors. Whether and to what extent population genetic variations at key birthweight-associated loci account for the residual birthweight disparities not explained by environmental determinants is unknown...
May 24, 2018: BMC Medicine
https://www.readbyqxmd.com/read/29791872/gene-expression-in-cord-blood-links-genetic-risk-for-neurodevelopmental-disorders-with-maternal-psychological-distress-and-adverse-childhood-outcomes
#7
Michael S Breen, Aliza P Wingo, Nastassja Koen, Kirsten A Donald, Mark Nicol, Heather J Zar, Kerry J Ressler, Joseph D Buxbaum, Dan J Stein
Prenatal exposure to maternal stress and depression has been identified as a risk factor for adverse behavioral and neurodevelopmental outcomes in early childhood. However, the molecular mechanisms through which maternal psychopathology shapes offspring development remain poorly understood. We applied transcriptome-wide screens to 149 umbilical cord blood samples from neonates born to mothers with posttraumatic stress disorder (PTSD; n=20), depression (n=31) and PTSD with comorbid depression (n=13), compared to carefully matched trauma exposed controls (n=23) and healthy mothers (n=62)...
May 20, 2018: Brain, Behavior, and Immunity
https://www.readbyqxmd.com/read/29791844/regulation-of-pathogenic-t-helper-17-cell-differentiation-by-steroid-receptor-coactivator-3
#8
Kentaro Tanaka, Gustavo J Martinez, Xiaowei Yan, Weiwen Long, Kenji Ichiyama, Xinxin Chi, Byung-Seok Kim, Joseph M Reynolds, Yeonseok Chung, Shinya Tanaka, Lan Liao, Yoichi Nakanishi, Akihiko Yoshimura, Pan Zheng, Xiaohu Wang, Qiang Tian, Jianming Xu, Bert W O'Malley, Chen Dong
T helper 17 (Th17) cell development is programmed by the orphan nuclear receptor RORγt, but the underlying mechanism is not well understood. Nuclear receptor-mediated transcriptional activation depends on coactivators. Here, we show that steroid receptor coactivator-3 (SRC-3) critically regulates Th17 cell differentiation. Reduced incidence of experimental autoimmune encephalitis (EAE) associated with decreased Th17 cell generation in vivo was observed in mice with SRC-3 deletion specifically in T cells...
May 22, 2018: Cell Reports
https://www.readbyqxmd.com/read/29791785/expressed-exome-capture-sequencing-eecseq-a-method-for-cost-effective-exome-sequencing-for-all-organisms
#9
Jonathan B Puritz, Katie E Lotterhos
Exome capture is an effective tool for surveying the genome for loci under selection. However, traditional methods require annotated genomic resources. Here, we present a method for creating cDNA probes from expressed mRNA, which are then used to enrich and capture genomic DNA for exon regions. This approach, called "EecSeq", eliminates the need for costly probe design and synthesis. We tested EecSeq in the eastern oyster, Crassostrea virginica, using a controlled exposure experiment. Four adult oysters were heat shocked at 36° C for 1 hour along with four control oysters kept at 14° C...
May 23, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29791438/identity-by-descent-analyses-for-measuring-population-dynamics-and-selection-in-recombining-pathogens
#10
Lyndal Henden, Stuart Lee, Ivo Mueller, Alyssa Barry, Melanie Bahlo
Identification of genomic regions that are identical by descent (IBD) has proven useful for human genetic studies where analyses have led to the discovery of familial relatedness and fine-mapping of disease critical regions. Unfortunately however, IBD analyses have been underutilized in analysis of other organisms, including human pathogens. This is in part due to the lack of statistical methodologies for non-diploid genomes in addition to the added complexity of multiclonal infections. As such, we have developed an IBD methodology, called isoRelate, for analysis of haploid recombining microorganisms in the presence of multiclonal infections...
May 23, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29790996/dna-methylation-and-inflammation-marker-profiles-associated-with-a-history-of-depression
#11
Bethany Crawford, Zoe Craig, Georgina Mansell, Isobel White, Adam Smith, Steve Spaull, Jennifer Imm, Eilis Hannon, Andrew Wood, Hanieh Yaghootkar, Yingjie Ji, Niamh Mullins, Cathryn M Lewis, Jonathan Mill, Therese M Murphy
Depression is a common and disabling disorder, representing a major social and economic health issue. Moreover, depression is associated with the progression of diseases with an inflammatory etiology including many inflammatory-related disorders. At the molecular level, the mechanisms by which depression might promote the onset of these diseases and associated immune-dysfunction are not well understood. In this study we assessed genome-wide patterns of DNA methylation in whole blood-derived DNA obtained from individuals with a self-reported history of depression (n = 100) and individuals without a history of depression (n = 100) using the Illumina 450K microarray...
May 22, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29790871/phenotypic-expansion-illuminates-multilocus-pathogenic-variation
#12
Ender Karaca, Jennifer E Posey, Zeynep Coban Akdemir, Davut Pehlivan, Tamar Harel, Shalini N Jhangiani, Yavuz Bayram, Xiaofei Song, Vahid Bahrambeigi, Ozge Ozalp Yuregir, Sevcan Bozdogan, Gozde Yesil, Sedat Isikay, Donna Muzny, Richard A Gibbs, James R Lupski
PurposeMultilocus variation-pathogenic variants in two or more disease genes-can potentially explain the underlying genetic basis for apparent phenotypic expansion in cases for which the observed clinical features extend beyond those reported in association with a "known" disease gene.MethodsAnalyses focused on 106 patients, 19 for whom apparent phenotypic expansion was previously attributed to variation at known disease genes. We performed a retrospective computational reanalysis of whole-exome sequencing data using stringent Variant Call File filtering criteria to determine whether molecular diagnoses involving additional disease loci might explain the observed expanded phenotypes...
April 26, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29790644/crispr-cas9-assisted-multiplex-genome-editing-technique-in-escherichia-coli
#13
Xu Feng, Dongdong Zhao, Xueli Zhang, Xiang Ding, Changhao Bi
Genome editing for site-specific chromosome modification is one of the most significant techniques in biological research. While conventional techniques usually deal with one genomic locus at a time, multiple genomic targets are often required to be modified to develop microbial cell factories. Thus, it is necessary to develop techniques for simultaneous editing of multiple loci. In this work, we developed a CRISPR/Cas9 assisted multiplex genome editing (CMGE) technique in Escherichia coli. With this editing method, all functional parts were assembled into replicable plasmids, and stringent inducible expression systems were used to control Cas9 gene expression, which was to decouple transformation from editing process to increase editing efficiency...
May 23, 2018: Biotechnology Journal
https://www.readbyqxmd.com/read/29790460/establishment-of-the-european-meningococcal-strain-collection-genome-library-emsc-gl-for-the-2011-to-2012-epidemiological-year
#14
Holly B Bratcher, Carina Brehony, Sigrid Heuberger, Despo Pieridou-Bagatzouni, Pavla Křížová, Steen Hoffmann, Maija Toropainen, Muhamed-Kheir Taha, Heike Claus, Georgina Tzanakaki, Tímea Erdôsi, Jelena Galajeva, Arie van der Ende, Anna Skoczyńska, Marina Pana, Alena Vaculíková, Metka Paragi, Martin Cj Maiden, Dominique A Caugant
Invasive meningococcal disease surveillance in Europe combines isolate characterisation and epidemiological data to support public health intervention. A representative European Meningococcal Strain Collection (EMSC) of IMD isolates was obtained, and whole genome sequenced to characterise 799 EMSC isolates from the epidemiological year July 2011-June 2012. To establish a genome library (GL), the isolate information was deposited in the pubMLST.org/neisseria database. Genomes were curated and annotated at 2,429 meningococcal loci, including those defining clonal complex, capsule, antigens, and antimicrobial resistance...
May 2018: Euro Surveillance: Bulletin Européen sur les Maladies Transmissibles, European Communicable Disease Bulletin
https://www.readbyqxmd.com/read/29790059/characteristics-of-distribution-of-mycobacterium-tuberculosis-lineages-in-china
#15
Haixia Chen, Li He, Chao Cai, Jingyi Liu, Junnan Jia, Liang Ma, Hairong Huang, Lixia Wang, Xumin Ni, Jimin Gao, Weimin Li
The genotyping methods of Mycobacterium tuberculosis would dramatically improve our understanding of the molecular epidemiology of tuberculosis. 3,929 isolates, from a National Survey of Drug-Resistant Tuberculosis in 2007 in China, were successfully genotyped by large sequence polymorphisms and 15 loci variable number tandem repeats. We found that 2,905 (2,905/3,929, 73.9%) cases belonged to Lineage 2, dominated in the east and central regions, 975 cases (975/3,929, 24.8%) were Lineage 4, highly prevailed in the west regions, and 36 and 13 cases were Lineage 3 and Lineage 1, respectively...
March 21, 2018: Science China. Life Sciences
https://www.readbyqxmd.com/read/29789923/the-haf2-protein-shapes-histone-acetylation-levels-of-prr5-and-lux-loci-in-arabidopsis
#16
Kyounghee Lee, Pil Joon Seo
The histone acetyltransferase HAF2 facilitates H3 acetylation deposition at the PRR5 and LUX promoters to contribute to robust circadian oscillation. The circadian clock ensures synchronization of endogenous rhythmic processes with environmental cycles. Multi-layered regulation underlies precise circadian oscillation, and epigenetic regulation is emerging as a crucial scheme for robust circadian maintenance. Here, we report that HISTONE ACETYLTRANSFERASE OF THE TAFII250 FAMILY 2 (HAF2) is involved in circadian homeostasis...
May 22, 2018: Planta
https://www.readbyqxmd.com/read/29789882/rapid-development-of-stable-transgene-cho-cell-lines-by-crispr-cas9-mediated-site-specific-integration-into-c12orf35
#17
Menglin Zhao, Jiaxian Wang, Manyu Luo, Han Luo, Meiqi Zhao, Lei Han, Mengxiao Zhang, Hui Yang, Yueqing Xie, Hua Jiang, Lei Feng, Huili Lu, Jianwei Zhu
Chinese hamster ovary (CHO) cells are the most widely used mammalian hosts for recombinant protein production. However, by conventional random integration strategy, development of a high-expressing and stable recombinant CHO cell line has always been a difficult task due to the heterogenic insertion and its caused requirement of multiple rounds of selection. Site-specific integration of transgenes into CHO hot spots is an ideal strategy to overcome these challenges since it can generate isogenic cell lines with consistent productivity and stability...
May 22, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29789573/high-throughput-screening-of-prostate-cancer-risk-loci-by-single-nucleotide-polymorphisms-sequencing
#18
Peng Zhang, Ji-Han Xia, Jing Zhu, Ping Gao, Yi-Jun Tian, Meijun Du, Yong-Chen Guo, Sufyan Suleman, Qin Zhang, Manish Kohli, Lori S Tillmans, Stephen N Thibodeau, Amy J French, James R Cerhan, Li-Dong Wang, Gong-Hong Wei, Liang Wang
Functional characterization of disease-causing variants at risk loci has been a significant challenge. Here we report a high-throughput single-nucleotide polymorphisms sequencing (SNPs-seq) technology to simultaneously screen hundreds to thousands of SNPs for their allele-dependent protein-binding differences. This technology takes advantage of higher retention rate of protein-bound DNA oligos in protein purification column to quantitatively sequence these SNP-containing oligos. We apply this technology to test prostate cancer-risk loci and observe differential allelic protein binding in a significant number of selected SNPs...
May 22, 2018: Nature Communications
https://www.readbyqxmd.com/read/29789437/dynamics-of-reca-mediated-repair-of-replication-dependent-dna-breaks
#19
Vincent Amarh, Martin A White, David R F Leach
Chromosomal replication is the major source of spontaneous DNA double-strand breaks (DSBs) in living cells. Repair of these DSBs is essential for cell viability, and accuracy of repair is critical to avoid chromosomal rearrangements. Repair of replication-dependent DSBs occurs primarily by homologous recombination with a sister chromosome. However, this reaction has never been visualized at a defined chromosomal locus, so little is known about its spatial or temporal dynamics. Repair of a replication-independent DSB generated in Escherichia coli by a rare-cutting endonuclease leads to the formation of a bundle of RecA filaments...
May 22, 2018: Journal of Cell Biology
https://www.readbyqxmd.com/read/29789399/ebf1-gene-polymorphism-and-its-interaction-with-smoking-and-drinking-on-the-risk-of-coronary-artery-disease-for-chinese-patients
#20
Yongjun Ying, Yuxuan Luo, Hui Peng
Objective : Early B cell factor 1 (EBF1) is a transcription factor that is expressed in early B cells, adipocytes, and olfactory neurons, and is essential for the maturation of early B lymphocytes. This study analyzes the influence of EBF1 gene polymorphism and its interaction with smoking and drinking on the risk of coronary artery disease (CAD). Methods: In this study, 243 CAD cases were enrolled as the CAD group and 215 non-CAD patients as the control group by case-control study. We analyzed their genotypes of the rs987401919, rs36071027, and rs1056065671 loci of the EBF1 gene by Sanger sequencing, and detected their content of HDL-C, LDL-C, and TG...
May 22, 2018: Bioscience Reports
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