keyword
MENU ▼
Read by QxMD icon Read
search

Gene Mapping

keyword
https://www.readbyqxmd.com/read/28427179/comprehensive-mapping-of-the-effects-of-azacitidine-on-dna-methylation-repressive-permissive-histone-marks-and-gene-expression-in-primary-cells-from-patients-with-mds-and-mds-related-disease
#1
Magnus Tobiasson, Hani Abdulkadir, Andreas Lennartsson, Shintaro Katayama, Francesco Marabita, Ayla De Paepe, Mohsen Karimi, Kaarel Krjutskov, Elisabet Einarsdottir, Michael Grövdal, Monika Jansson, Asmaa Ben Azenkoud, Lina Corddedu, Sören Lehmann, Karl Ekwall, Juha Kere, Eva Hellström-Lindberg, Johanna Ungerstedt
Azacitidine (Aza) is first-line treatment for patients with high-risk myelodysplastic syndromes (MDS), although its precise mechanism of action is unknown. We performed the first study to globally evaluate the epigenetic effects of Aza on MDS bone marrow progenitor cells assessing gene expression (RNA seq), DNA methylation (Illumina 450k) and the histone modifications H3K18ac and H3K9me3 (ChIP seq). Aza induced a general increase in gene expression with 924 significantly upregulated genes but this increase showed no correlation with changes in DNA methylation or H3K18ac, and only a weak association with changes in H3K9me3...
February 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28426969/chemogenetic-interrogation-of-a-brain-wide-fear-memory-network-in-mice
#2
Gisella Vetere, Justin W Kenney, Lina M Tran, Frances Xia, Patrick E Steadman, John Parkinson, Sheena A Josselyn, Paul W Frankland
Behavior depends on coordinated activity across multiple brain regions. Within such networks, highly connected hub regions are assumed to disproportionately influence behavioral output, although this hypothesis has not been systematically evaluated. Previously, by mapping brain-wide expression of the activity-regulated gene c-fos, we identified a network of brain regions co-activated by fear memory. To test the hypothesis that hub regions are more important for network function, here, we simulated node deletion in silico in this behaviorally defined functional network...
April 19, 2017: Neuron
https://www.readbyqxmd.com/read/28425466/crystal-structures-of-the-no-sensor-nsrr-reveal-how-its-iron-sulfur-cluster-modulates-dna-binding
#3
Anne Volbeda, Erin L Dodd, Claudine Darnault, Jason C Crack, Oriane Renoux, Matthew I Hutchings, Nick E Le Brun, Juan C Fontecilla-Camps
NsrR from Streptomyces coelicolor (Sc) regulates the expression of three genes through the progressive degradation of its [4Fe-4S] cluster on nitric oxide (NO) exposure. We report the 1.95 Å resolution crystal structure of dimeric holo-ScNsrR and show that the cluster is coordinated by the three invariant Cys residues from one monomer and, unexpectedly, Asp8 from the other. A cavity map suggests that NO displaces Asp8 as a cluster ligand and, while D8A and D8C variants remain NO sensitive, DNA binding is affected...
April 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28424708/quantitative-trait-locus-mapping-for-verticillium-wilt-resistance-in-an-upland-cotton-recombinant-inbred-line-using-snp-based-high-density-genetic-map
#4
Koffi Kibalou Palanga, Muhammad Jamshed, Md Harun Or Rashid, Juwu Gong, Junwen Li, Muhammad Sajid Iqbal, Aiying Liu, Haihong Shang, Yuzhen Shi, Tingting Chen, Qun Ge, Zhen Zhang, Tussipkan Dilnur, Weijie Li, Pengtao Li, Wankui Gong, Youlu Yuan
Verticillium wilt (VW) caused by Verticillium dahlia Kleb is one of the most destructive diseases of cotton. Numerous efforts have been made to improve the resistance of upland cotton against VW, with little progress achieved due to the paucity of upland cotton breeding germplasms with high level of resistance to VW. Gossypium barbadense was regarded as more resistant compared to upland cotton; however, it is difficult to apply the resistance from G. barbadense to upland cotton improvement because of the hybrid breakdown and the difficulty to fix resistant phenotype in their interspecific filial...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28424525/genome-wide-detection-of-copy-number-variation-in-chinese-indigenous-sheep-using-an-ovine-high-density-600%C3%A2-k-snp-array
#5
Qing Ma, Xuexue Liu, Jianfei Pan, Lina Ma, Yuehui Ma, Xiaohong He, Qianjun Zhao, Yabin Pu, Yingkang Li, Lin Jiang
Copy number variants (CNVs) represent a form of genomic structural variation underlying phenotypic diversity. In this study, we used the Illumina Ovine SNP 600 K BeadChip array for genome-wide detection of CNVs in 48 Chinese Tan sheep. A total of 1,296 CNV regions (CNVRs), ranging from 1.2 kb to 2.3 Mb in length, were detected, representing approximately 4.7% of the entire ovine genome (Oar_v3.1). We combined our findings with five existing CNVR reports to generate a composite genome-wide dataset of 4,321 CNVRs, which revealed 556 (43%) novel CNVRs...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28424497/the-glycogen-synthase-kinase-mogsk1-regulated-by-mps1-map-kinase-is-required-for-fungal-development-and-pathogenicity-in-magnaporthe-oryzae
#6
Tengsheng Zhou, Yasin F Dagdas, Xiaohan Zhu, Shiqin Zheng, Liqiong Chen, Zachary Cartwright, Nicholas J Talbot, Zonghua Wang
Magnaporthe oryzae, the causal agent of blast disease, is one of the most destructive plant pathogens, causing significant yield losses on staple crops such as rice and wheat. The fungus infects plants with a specialized cell called an appressorium, whose development is tightly regulated by MAPK signaling pathways following the activation of upstream sensors in response to environmental stimuli. Here, we show the expression of the Glycogen synthase kinase 3 (GSK3) MoGSK1 in M. oryzae is regulated by Mps1 MAP kinase, particularly under the stressed conditions...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28424478/the-prevalence-of-thalassemia-in-mainland-china-evidence-from-epidemiological-surveys
#7
Ketong Lai, Guifeng Huang, Li Su, Yunyan He
Comprehensive data regarding the epidemiology and prevalence of thalassemia in mainland China are lacking. To assess the prevalence of thalassemia, we performed a meta-analysis including 16 articles published from 1981 to 2015. The overall prevalence of α-thalassemia, β-thalassemia and α + β-thalassemia was 7.88%, 2.21% and 0.48%, respectively. Trends in thalassemia prevalence in mainland China were not steady; a prevalence map based on a geographic information system (GIS) showed that the geographic distribution of thalassemia was highest in the south of China and decreased from south to north...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28424372/effects-of-drought-stress-on-global-gene-expression-profile-in-leaf-and-root-samples-of-dongxiang-wild-rice-oryza-rufipogon
#8
Fantao Zhang, Yi Zhou, Meng Zhang, Xiangdong Luo, Jiankun Xie
Drought is a serious constraint to rice production throughout the world, and although Dongxiang wild rice ( Oryza rufipogon , DXWR) possesses a high degree of drought resistance, the underlying mechanisms of this trait remains unclear. In the present study, cDNA libraries were constructed from the leaf and root tissues of drought-stressed and untreated DXWR seedlings, and transcriptome sequencing was performed with the goal of elucidating the molecular mechanisms involved in drought stress response. The results indicated that 11,231 transcripts were differentially expressed in the leaves (4,040 up-regulated and 7,191 down-regulated) and 7,025 transcripts were differentially expressed in the roots (3,097 up-regulated and 3,928 down-regulated)...
April 19, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/28424353/constrained-release-of-lamina-associated-enhancers-and-genes-from-the-nuclear-envelope-during-t-cell-activation-facilitates-their-association-in-chromosome-compartments
#9
Michael I Robson, Jose I de Las Heras, Rafal Czapiewski, Aishwarya Sivakumar, Alastair R W Kerr, Eric Schirmer
The 3D organization of the genome changes concomitantly with expression changes during hematopoiesis and immune activation. Studies have focused either on lamina-associated domains (LADs) or on topologically-associated domains (TADs), defined by preferential local chromatin interactions, and chromosome compartments, defined as higher-order interactions between TADs sharing functionally similar states. However, few studies have investigated how these affect one another. To address this, we mapped LADs using Lamin B1-DamID during Jurkat T-cell activation, finding significant genome re-organization at the nuclear periphery dominated by release of loci frequently important for T-cell function...
April 19, 2017: Genome Research
https://www.readbyqxmd.com/read/28424341/alterations-in-three-dimensional-organization-of-the-cancer-genome-and-epigenome
#10
Joanna Achinger-Kawecka, Phillippa C Taberlay, Susan J Clark
The structural and functional basis of the genome is provided by the three-dimensional (3D) chromatin state. To enable accurate gene regulation, enhancer elements and promoter regions are brought into close spatial proximity to ensure proper, cell type-specific gene expression. In cancer, genetic and epigenetic processes can deregulate the transcriptional program. To investigate whether the 3D chromatin state is also disrupted in cancer we performed Hi-C chromosome conformation sequencing in normal and prostate cancer cells and compared the chromatin interaction maps with changes to the genome and epigenome...
April 19, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28424047/deciphering-mechanisms-underlying-the-genetic-variation-of-general-production-and-liver-quality-traits-in-the-overfed-mule-duck-by-pqtl-analyses
#11
Yoannah François, Alain Vignal, Caroline Molette, Nathalie Marty-Gasset, Stéphane Davail, Laurence Liaubet, Christel Marie-Etancelin
BACKGROUND: The aim of this study was to analyse the mechanisms that underlie phenotypic quantitative trait loci (QTL) in overfed mule ducks by identifying co-localized proteomic QTL (pQTL). The QTL design consisted of three families of common ducks that were progeny-tested by using 294 male mule ducks. This population of common ducks was genotyped using a genetic map that included 334 genetic markers located across 28 APL chromosomes (APL for Anas platyrhynchos). Mule ducks were phenotyped for 49 traits related to growth, metabolism, overfeeding ability and meat and fatty liver quality, and 326 soluble fatty liver proteins were quantified...
April 19, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28423598/next-generation-mapping-reveals-novel-large-genomic-rearrangements-in-prostate-cancer
#12
Weerachai Jaratlerdsiri, Eva K F Chan, Desiree C Petersen, Claire Yang, Peter I Croucher, M S Riana Bornman, Palak Sheth, Vanessa M Hayes
Complex genomic rearrangements are common molecular events driving prostate carcinogenesis. Clinical significance, however, has yet to be fully elucidated. Detecting the full range and subtypes of large structural variants (SVs), greater than one kilobase in length, is challenging using clinically feasible next generation sequencing (NGS) technologies. Next generation mapping (NGM) is a new technology that allows for the interrogation of megabase length DNA molecules outside the detection range of single-base resolution NGS...
April 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423512/kinase-analysis-of-penile-squamous-cell-carcinoma-on-multiple-platforms-to-identify-potential-therapeutic-targets
#13
Eddy S Yang, Christopher D Willey, Amitkumar Mehta, Michael R Crowley, David K Crossman, Dongquan Chen, Joshua C Anderson, Gurudatta Naik, Deborah L Della Manna, Tiffiny S Cooper, Guru Sonpavde
Penile squamous cell carcinoma (PSCC) is an orphan malignancy with poorly understood biology and suboptimal systemic therapy. Given that kinases may be drivers and readily actionable, we performed comprehensive multiplatform analysis of kinases in PSCC tumor and normal tissue. Fresh frozen tumors were collected from 11 patients with PSCC. After macrodissection to demarcate tumor from normal tissue, the samples underwent multiplatform analysis of kinases. Next Generation Sequencing (NGS) of 517 kinase genes was performed using Agilent Kinome capture and run on the Illumina MiSeq at PE150bp...
March 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423013/mapping-the-co-localization-of-the-circadian-proteins-per2-and-bmal1-with-enkephalin-and-substance-p-throughout-the-rodent-forebrain
#14
Ariana Frederick, Jory Goldsmith, Nuria de Zavalia, Shimon Amir
Despite rhythmic expression of clock genes being found throughout the central nervous system, very little is known about their function outside of the suprachiasmatic nucleus. Determining the pattern of clock gene expression across neuronal subpopulations is a key step in understanding their regulation and how they may influence the functions of various brain structures. Using immunofluorescence and confocal microscopy, we quantified the co-expression of the clock proteins BMAL1 and PER2 with two neuropeptides, Substance P (SubP) and Enkephalin (Enk), expressed in distinct neuronal populations throughout the forebrain...
2017: PloS One
https://www.readbyqxmd.com/read/28422981/qtl-analysis-and-dissection-of-panicle-components-in-rice-using-advanced-backcross-populations-derived-from-oryza-sativa-cultivars-hr1128-and-nipponbare
#15
Zhizhong Sun, Xiaoling Yin, Jia Ding, Dong Yu, Miao Hu, Xuewu Sun, Yanning Tan, Xiabing Sheng, Ling Liu, Yi Mo, Ning Ouyang, Beibei Jiang, Guilong Yuan, Meijuan Duan, Dingyang Yuan, Jun Fang
Panicle traits are among the most important agronomic characters which directly relate to yield in rice. Grain number (GN), panicle length (PL), primary branch number (PBN), and secondary branch number (SBN) are the major components of rice panicle structure, and are all controlled by quantitative trait loci (QTLs). In our research, four advanced backcross overlapping populations (BIL152, BIL196a, BIL196b, and BIL196b-156) carrying introgressed segments from chromosome 6 were derived from an indica/japonica cross that used the super-hybrid rice restorer line HR1128 and the international sequenced japonica cultivar 'Nipponbare' as the donor and recurrent parents, respectively...
2017: PloS One
https://www.readbyqxmd.com/read/28422736/identification-of-map-kinase-pathways-as-therapeutic-targets-in-gallbladder-carcinoma-using-targeted-parallel-sequencing
#16
Mengdan Li, Lihong Chen, Yiping Qu, Fang Sui, Qi Yang, Meiju Ji, Bingyin Shi, Mingwei Chen, Peng Hou
The aim of this study was to profile somatic mutation spectrum in gallbladder cancers (GBCs), and determine the role of MAP kinase pathway in GBC by a series of in vitro and in vivo studies. We performed targeted massively parallel sequencing of DNA isolated from GBCs and matched blood from 14 GBC patients to search for mutations in 504 genes commonly altered in human cancers. We identified recurrent mutations enriched in several major signaling pathways including MAP kinase, Wnt/β-catenin and NF-κB pathways...
March 31, 2017: Oncotarget
https://www.readbyqxmd.com/read/28422143/dissecting-the-genetic-architecture-of-fusarium-verticillioides-seed-rot-resistance-in-maize-by-combining-qtl-mapping-and-genome-wide-association-analysis
#17
Ming Ju, Zijian Zhou, Cong Mu, Xuecai Zhang, Jingyang Gao, Yakun Liang, Jiafa Chen, Yabin Wu, Xiaopeng Li, Shiwei Wang, Jingjing Wen, Luming Yang, Jianyu Wu
Fusarium verticillioides can be transmitted via seeds and cause systemic infection in maize (Zea mays L.); its mycotoxin has harmful effects on animal and human health. We combined QTL mapping in recombinant inbred line (RIL) populations with a genome-wide association study (GWAS) of 217 diverse maize lines using 224,152 single nucleotide polymorphisms (SNPs) under controlled conditions to determine the genetic architecture of F. verticillioides seed rot (FSR) resistance. Our study identified 8 quantitative trait loci (QTLs) and 43 genes associated with 57 SNPs that were correlated with FSR resistance through linkage mapping and GWAS, respectively...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28422050/k-mer-content-correlation-and-position-analysis-of-genome-dna-sequences-for-the-identification-of-function-and-evolutionary-features
#18
Aaron Sievers, Katharina Bosiek, Marc Bisch, Chris Dreessen, Jascha Riedel, Patrick Froß, Michael Hausmann, Georg Hildenbrand
In genome analysis, k-mer-based comparison methods have become standard tools. However, even though they are able to deliver reliable results, other algorithms seem to work better in some cases. To improve k-mer-based DNA sequence analysis and comparison, we successfully checked whether adding positional resolution is beneficial for finding and/or comparing interesting organizational structures. A simple but efficient algorithm for extracting and saving local k-mer spectra (frequency distribution of k-mers) was developed and used...
April 19, 2017: Genes
https://www.readbyqxmd.com/read/28421098/fine-mapping-the-branching-habit-trait-in-cultivated-peanut-by-combining-bulked-segregant-analysis-and-high-throughput-sequencing
#19
Galya Kayam, Yael Brand, Adi Faigenboim-Doron, Abhinandan Patil, Ilan Hedvat, Ran Hovav
The growth habit of lateral shoots (also termed "branching habit") is an important descriptive and agronomic character of peanut. Yet, both the inheritance of branching habit and the genetic mechanism that controls it in this crop remain unclear. In addition, the low degree of polymorphism among cultivated peanut varieties hinders fine-mapping of this and other traits in non-homozygous genetic structures. Here, we combined high-throughput sequencing with a well-defined genetic system to study these issues in peanut...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28421044/comparative-genomics-of-glossina-palpalis-gambiensis-and-g-morsitans-morsitans-to-reveal-gene-orthologs-involved-in-infection-by-trypanosoma-brucei-gambiense
#20
Illiassou Hamidou Soumana, Bernadette Tchicaya, Stéphanie Rialle, Hugues Parrinello, Anne Geiger
Blood-feeding Glossina palpalis gambiense (Gpg) fly transmits the single-celled eukaryotic parasite Trypanosoma brucei gambiense (Tbg), the second Glossina fly African trypanosome pair being Glossina morsitans/T.brucei rhodesiense. Whatever the T. brucei subspecies, whereas the onset of their developmental program in the zoo-anthropophilic blood feeding flies does unfold in the fly midgut, its completion is taking place in the fly salivary gland where does emerge a low size metacyclic trypomastigote population displaying features that account for its establishment in mammals-human individuals included...
2017: Frontiers in Microbiology
keyword
keyword
110605
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"