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https://www.readbyqxmd.com/read/28642229/evolutionary-dynamics-of-the-kinetochore-network-in-eukaryotes-as-revealed-by-comparative-genomics
#1
Jolien Je van Hooff, Eelco Tromer, Leny M van Wijk, Berend Snel, Geert Jpl Kops
During eukaryotic cell division, the sister chromatids of duplicated chromosomes are pulled apart by microtubules, which connect via kinetochores. The kinetochore is a multiprotein structure that links centromeres to microtubules, and that emits molecular signals in order to safeguard the equal distribution of duplicated chromosomes over daughter cells. Although microtubule-mediated chromosome segregation is evolutionary conserved, kinetochore compositions seem to have diverged. To systematically inventory kinetochore diversity and to reconstruct its evolution, we determined orthologs of 70 kinetochore proteins in 90 phylogenetically diverse eukaryotes...
June 22, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28639420/the-pharmacokinetics-of-enalapril-in-relation-to-ces1-genotype-in-healthy-danish-volunteers
#2
Claus Stage, Gesche Jürgens, Louise Schow Guski, Ragnar Thomsen, Ditte Bjerre, Laura Ferrero-Miliani, Yassine Kamal Lyauk, Henrik Berg Rasmussen, Kim Dalhoff
The present study investigated the influence of variations in the carboxylesterase 1 gene (CES1) on the pharmacokinetics of enalapril. Forty-three healthy, Danish, Caucasian volunteers representing different pre-defined genotypes each received 10 mg of enalapril. At specified time points, plasma concentrations of enalapril and the active metabolite enalaprilat were measured. The volunteers were divided into six different groups according to their genetic profile of CES1: Group 1 (controls, n=16) with two CES1 copies without non-synonymous SNPs in the exons; group 2 (n=5) with four copies of CES1; group 3 (n=6) harbouring the G143E polymorphism; group 4 (n=2) with three CES1 copies and increased transcriptional activity of the duplication (CES1A2); group 5 (n=4) harbouring the CES1A1c variant; and group 6 (n=10) with three CES1 copies and the common promoter with low transcriptional activity of the duplication...
June 21, 2017: Basic & Clinical Pharmacology & Toxicology
https://www.readbyqxmd.com/read/28637883/niche-mediated-depletion-of-the-normal-hematopoietic-stem-cell-reservoir-by-flt3-itd-induced-myeloproliferation
#3
Adam J Mead, Wen Hao Neo, Nikolaos Barkas, Sahoko Matsuoka, Alice Giustacchini, Raffaella Facchini, Supat Thongjuea, Lauren Jamieson, Christopher A G Booth, Nicholas Fordham, Cristina Di Genua, Deborah Atkinson, Onima Chowdhury, Emmanouela Repapi, Nicki Gray, Shabnam Kharazi, Sally-Ann Clark, Tiphaine Bouriez, Petter Woll, Toshio Suda, Claus Nerlov, Sten Eirik W Jacobsen
Although previous studies suggested that the expression of FMS-like tyrosine kinase 3 (Flt3) initiates downstream of mouse hematopoietic stem cells (HSCs), FLT3 internal tandem duplications (FLT3 ITDs) have recently been suggested to intrinsically suppress HSCs. Herein, single-cell interrogation found Flt3 mRNA expression to be absent in the large majority of phenotypic HSCs, with a strong negative correlation between Flt3 and HSC-associated gene expression. Flt3-ITD knock-in mice showed reduced numbers of phenotypic HSCs, with an even more severe loss of long-term repopulating HSCs, likely reflecting the presence of non-HSCs within the phenotypic HSC compartment...
June 21, 2017: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28637758/genome-wide-analysis-of-eighteen-epstein-barr-viruses-isolated-from-primary-nasopharyngeal-carcinoma-biopsies
#4
Chaofeng Tu, Zhaoyang Zeng, Peng Qi, Xiayu Li, Zhengyuan Yu, Can Guo, Fang Xiong, Bo Xiang, Ming Zhou, Zhaojian Gong, Qianjin Liao, Jianjun Yu, Yi He, Wenling Zhang, Xiaoling Li, Yong Li, Guiyuan Li, Wei Xiong
Epstein-Barr virus (EBV) is a ubiquitous gamma-herpesvirus that is highly prevalent in almost all human populations, and is associated with many human cancers such as nasopharyngeal carcinoma (NPC), Hodgkin's disease, and gastric carcinoma. However, in these EBV-associated cancers, only NPC exhibits remarkable ethnic and geographic distribution. We hypothesized that EBV genomic variations might contribute to the pathogenesis of different human cancers in different geographic areas. In this study, we collected 18 NPC biopsies from the Hunan Province in Southern China and de novo assembled 18 NPC biopsy specimen-derived EBV (NPC-EBV) genomes, designated as HN1 to HN18...
June 21, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28637710/the-combined-action-of-duplicated-boron-transporters-is-required-for-maize-growth-in-boron-deficient-conditions
#5
Mithu Chatterjee, Qiujie Liu, Caitlin Menello, Mary Galli, Andrea Gallavotti
The micronutrient boron is essential in maintaining the structure of plant cell walls and is critical for high yields in crop species. Boron can move into plants by diffusion or by active and facilitated transport mechanisms. We recently showed that mutations in the maize boron efflux transporter ROTTEN EAR (RTE) cause severe developmental defects and sterility. RTE is part of a small gene family containing five additional members (RTE2-RTE6) that show tissue specific expression. The close paralogous gene RTE2 encodes a protein with 95% amino acid identity with RTE and is similarly expressed in shoot and root cells surrounding the vasculature...
June 21, 2017: Genetics
https://www.readbyqxmd.com/read/28636881/mitochondrial-genome-of-helice-tientsinensis-brachyura-grapsoidea-varunidae-gene-rearrangements-and-higher-level-phylogeny-of-the-brachyura
#6
Zhao-Zhe Xin, Yu-Liu, Dai-Zhen Zhang, Zheng-Fei Wang, Hua-Bin Zhang, Bo-Ping Tang, Chun-Lin Zhou, Xin-Yue Chai, Qiu-Ning Liu
The mitochondrial genome (mt genome) provides important information for understanding molecular evolution and phylogeny. The further understand the molecular evolution and phylogeny of Helice tientsinensis, the complete mt genome was determined. It is 16,212bp long and includes 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes and a control region. The genome composition of H. tientsinensis was highly A+T biased 69.0% and showed negative AT skew (-0.017) and GC skew (-0.289). One PCG, all rRNAs and 12 of the tRNAs appeared to be rearranged with respect to the pancrustacean ground pattern gene order...
June 18, 2017: Gene
https://www.readbyqxmd.com/read/28636652/integrative-analysis-of-genomic-alterations-in-triple-negative-breast-cancer-in-association-with-homologous-recombination-deficiency
#7
Masahito Kawazu, Shinya Kojima, Toshihide Ueno, Yasushi Totoki, Hiromi Nakamura, Akiko Kunita, Wei Qu, Jun Yoshimura, Manabu Soda, Takahiko Yasuda, Natsuko Hama, Mihoko Saito-Adachi, Kazuhito Sato, Shinji Kohsaka, Eirin Sai, Masako Ikemura, Shigeru Yamamoto, Tomoko Ogawa, Masashi Fukayama, Keiichiro Tada, Yasuyuki Seto, Shinichi Morishita, Shoichi Hazama, Tatsuhiro Shibata, Yoshihiro Yamashita, Hiroyuki Mano
Triple-negative breast cancer (TNBC) cells do not express estrogen receptors, progesterone receptors, or human epidermal growth factor receptor 2. Currently, apart from poly ADP-ribose polymerase inhibitors, there are few effective therapeutic options for this type of cancer. Here, we present comprehensive characterization of the genetic alterations in TNBC performed by high coverage whole genome sequencing together with transcriptome and whole exome sequencing. Silencing of the BRCA1 gene impaired the homologous recombination pathway in a subset of TNBCs, which exhibited similar phenotypes to tumors with BRCA1 mutations; they harbored many structural variations (SVs) with relative enrichment for tandem duplication...
June 21, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28636109/xq26-1-26-3-duplication-including-mospd1-and-gpc3-identified-in-boy-with-short-stature-and-double-outlet-right-ventricle
#8
Yukiko Hirota, Takaomi Minami, Tomoyuki Sato, Akiko Yokomizo, Auimi Matsumoto, Masahide Goto, Eriko Jinbo, Takanori Yamamgata
Xq25q26 duplication syndrome has been reported in individuals with clinical features such as short stature, intellectual disability, syndromic facial appearance, small hands and feet, and genital abnormalities. The symptoms are related to critical chromosome regions including Xq26.1-26.3. In this particular syndrome, no patient with congenital heart disease was previously reported. Here, we report a 6-year-old boy with typical symptoms of Xq25q26 duplication syndrome and double outlet right ventricle (DORV) with pulmonary atresia (PA)...
June 21, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28634279/in-frame-seven-amino-acid-duplication-in-aip-arose-over-the-last-3000-years-disrupts-protein-interaction-stability-and-is-associated-with-gigantism
#9
Roberto Salvatori, Serban Radian, Yoan Diekmann, Donato Iacovazzo, Alessia David, Plamena Grabovska, Giorgia Grassi, Anna-Marie Bussell, Karen Stals, Astrid Weber, Richard Quinton, Elizabeth Crowne, Valentina Corazzini, Louise A Metherell, Tara Kearney, Daniel Du Plessis, Ajay Sinha, Atik Baborie, Anne-LIse Locoq, Philippe Chanson, Olaf Ansorge, Sian Ellard, Peter J Trainer, David Balding, Mark Thomas, Marta Korbonits
OBJECTIVE: Mutations in the aryl hydrocarbon receptor-interacting protein (AIP) gene are associated with pituitary adenoma, acromegaly and gigantism. Identical alleles in unrelated pedigrees could be inherited from a common ancestor or result from recurrent mutation events. DESIGN & METHODS: Observational, inferential and experimental study, including: AIP mutation testing; reconstruction of 14 AIP-region (8.3 Mbp) haplotypes; coalescent-based approximate Bayesian estimation of the time to most recent common ancestor (tMRCA) of the derived allele; forward population simulations to estimate current number of allele carriers; proposal of mutation mechanism; protein structure predictions; co-immunoprecipitation and cycloheximide chase experiments...
June 20, 2017: European Journal of Endocrinology
https://www.readbyqxmd.com/read/28634029/discovery-of-scors-anciently-derived-highly-conserved-gene-associated-repeats-in-stony-corals
#10
Huan Qiu, Ehud Zelzion, Hollie M Putnam, Ruth D Gates, Nicole E Wagner, Diane K Adams, Debashish Bhattacharya
Stony coral (Scleractinia) genomes are still poorly explored and many questions remain about their evolution and contribution to the success and longevity of reefs. We analyzed transcriptome and genome data from Montipora capitata, Acropora digitifera, and transcriptome data from 20 other coral species. To our surprise, we found highly conserved, anciently derived, Scleractinia COral-specific Repeat families (SCORs) that are abundant in all the studied lineages. SCORs form complex secondary structures and are located in untranslated regions and introns, but most abundant in intergenic DNA...
June 17, 2017: Genomics
https://www.readbyqxmd.com/read/28633406/in-saccharomyces-cerevisiae-gene-targeting-fidelity-depends-on-a-transformation-method-and-proportion-of-the-overall-length-of-the-transforming-and-targeted-dna
#11
Anamarija Štafa, Marina Svetec Miklenic, Antonio Zandona, Bojan Žunar, Neža Cadež, Hrvoje Petkovic, Ivan Krešimir Svetec
Gene replacement is one of the most essential approaches in construction of the genetically modified yeast strains. However, the fidelity of gene targeting and the effort needed for construction of a particular strain can vary significantly. We investigated the influence of two important factors-the choice of the transformation method and the design of the transforming DNA fragment, which can vary in overall length (including flanking regions and selectable marker) compared to the length of the targeted region in the genome...
June 15, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28633361/evolution-of-mirna-tailing-by-3-terminal-uridylyl-transferases-in-metazoa
#12
Vengamanaidu Modepalli, Yehu Moran
In bilaterian animals the 3' ends of microRNAs (miRNAs) are frequently modified by tailing and trimming. These modifications affect miRNA-mediated gene regulation by modulating miRNA stability. Here we analyzed data from three non-bilaterian animals: two cnidarians (Nematostella vectensis and Hydra magnipapillata) and one poriferan (Amphimedon queenslandica). Our analysis revealed that non-bilaterian miRNAs frequently undergo modifications like the bilaterian counterparts: the majority are expressed as different length isoforms and frequent modifications of the 3' end by mono U or mono A tailing are observed...
June 14, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28633360/expression-properties-exhibit-correlated-patterns-with-the-fate-of-duplicated-genes-their-divergence-and-transcriptional-plasticity-in-saccharomycotina
#13
Florian Mattenberger, Beatriz Sabater-Muñoz, Christina Toft, Gaurav Sablok, Mario A Fares
Gene duplication is an important source of novelties and genome complexity. What genes are preserved as duplicated through long evolutionary times can shape the evolution of innovations. Identifying factors that influence gene duplicability is therefore an important aim in evolutionary biology. Here, we show that in the yeast Saccharomyces cerevisiae the levels of gene expression correlate with gene duplicability, its divergence, and transcriptional plasticity. Genes that were highly expressed before duplication are more likely to be preserved as duplicates for longer evolutionary times and wider phylogenetic ranges than genes that were lowly expressed...
June 15, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28633043/de-novo-12q22-q23-3-duplication-associated-with-temporal-lobe-epilepsy
#14
Maria Stella Vari, Monica Traverso, Tommaso Bellini, Francesca Madia, Francesca Pinto, Carlo Minetti, Pasquale Striano, Federico Zara
PURPOSE: Temporal lobe epilepsy (TLE) is the most common form of focal epilepsy and may be associated with acquired central nervous system lesions or could be genetic. Various susceptibility genes and environmental factors are believed to be involved in the aetiology of TLE, which is considered to be a heterogeneous, polygenic, and complex disorder. Rare point mutations in LGI1, DEPDC5, and RELN as well as some copy number variations (CNVs) have been reported in families with TLE patients...
June 15, 2017: Seizure: the Journal of the British Epilepsy Association
https://www.readbyqxmd.com/read/28630945/the-icr96-exon-cnv-validation-series-a-resource-for-orthogonal-assessment-of-exon-cnv-calling-in-ngs-data
#15
Shazia Mahamdallie, Elise Ruark, Shawn Yost, Emma Ramsay, Imran Uddin, Harriett Wylie, Anna Elliott, Ann Strydom, Anthony Renwick, Sheila Seal, Nazneen Rahman
Detection of deletions and duplications of whole exons (exon CNVs) is a key requirement of genetic testing. Accurate detection of this variant type has proved very challenging in targeted next-generation sequencing (NGS) data, particularly if only a single exon is involved. Many different NGS exon CNV calling methods have been developed over the last five years. Such methods are usually evaluated using simulated and/or in-house data due to a lack of publicly-available datasets with orthogonally generated results...
2017: Wellcome Open Research
https://www.readbyqxmd.com/read/28630856/chimeric-genes-in-deletions-and-duplications-associated-with-intellectual-disability
#16
Sonia Mayo, Sandra Monfort, Mónica Roselló, Carmen Orellana, Silvestre Oltra, Alfonso Caro-Llopis, Francisco Martínez
We report on three nonrelated patients with intellectual disability and CNVs that give rise to three new chimeric genes. All the genes forming these fusion transcripts may have an important role in central nervous system development and/or in gene expression regulation, and therefore not only their deletion or duplication but also the resulting chimeric gene may contribute to the phenotype of the patients. Deletions and duplications are usually pathogenic when affecting dose-sensitive genes. Alternatively, a chimeric gene may also be pathogenic by different gain-of-function mechanisms that are not restricted to dose-sensitive genes: the emergence of a new polypeptide that combines functional domains from two different genes, the deregulated expression of any coding sequence by the promoter region of a neighboring gene, and/or a putative dominant-negative effect due to the preservation of functional domains of partially truncated proteins...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28629429/linked-read-sequencing-resolves-complex-genomic-rearrangements-in-gastric-cancer-metastases
#17
Stephanie U Greer, Lincoln D Nadauld, Billy T Lau, Jiamin Chen, Christina Wood-Bouwens, James M Ford, Calvin J Kuo, Hanlee P Ji
BACKGROUND: Genome rearrangements are critical oncogenic driver events in many malignancies. However, the identification and resolution of the structure of cancer genomic rearrangements remain challenging even with whole genome sequencing. METHODS: To identify oncogenic genomic rearrangements and resolve their structure, we analyzed linked read sequencing. This approach relies on a microfluidic droplet technology to produce libraries derived from single, high molecular weight DNA molecules, 50 kb in size or greater...
June 19, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28628658/effects-of-obesogenic-diet-and-estradiol-on-dorsal-raphe-gene-expression-in-old-female-macaques
#18
Cynthia L Bethea, Kevin Mueller, Arubala P Reddy, Steven G Kohama, Henryk F Urbanski
The beneficial effects of bioidentical ovarian steroid hormone therapy (HT) during the perimenopause are gaining recognition. However, the positive effects of estrogen (E) plus or minus progesterone (P) administration to ovariectomized (Ovx) lab animals were recognized in multiple systems for years before clinical trials could adequately duplicate the results. Moreover, very large numbers of women are often needed to find statistically significant results in clinical trials of HT; and there are still opposing results being published, especially in neural and cardiovascular systems...
2017: PloS One
https://www.readbyqxmd.com/read/28627438/genome-wide-identification-phylogeny-and-expression-of-bone-morphogenetic-protein-genes-in-tetraploidized-common-carp-cyprinus-carpio
#19
Lin Chen, Chuanju Dong, Shengnan Kong, Jiangfan Zhang, Xuejun Li, Peng Xu
Bone morphogenetic proteins (Bmps) are a group of signaling molecules known to play important roles during formation and maintenance of various organs, not only bone, but also muscle, blood and so on. Common carp (Cyprinus carpio) is one of the most intensively studied fish due to its economic and environmental importance. Besides, common carp had encountered an additional round of whole genome duplication (WGD) compared with many closely related diploid teleost, which make it one of the most important models for genome evolutionary studies in teleost...
June 13, 2017: Gene
https://www.readbyqxmd.com/read/28626004/sex-chromosome-evolution-heterochiasmy-and-physiological-qtl-in-the-salmonid-brook-charr-salvelinus-fontinalis
#20
Ben J G Sutherland, Ciro Rico, Céline Audet, Louis Bernatchez
Whole genome duplication can have large impacts on genome evolution, and much remains unknown about these impacts. This includes the mechanisms of coping with a duplicated sex determination system and whether this has an impact on increasing the diversity of sex determination mechanisms. Other impacts include sexual conflict, where alleles having different optimums in each sex can result in sequestration of genes into non-recombining sex chromosomes. Sex chromosome development itself may involve sex-specific recombination rate (i...
June 16, 2017: G3: Genes—Genomes—Genetics
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