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https://www.readbyqxmd.com/read/29333587/genetic-characterization-and-modification-of-a-bioethanol-producing-yeast-strain
#1
Ke Zhang, Ya-Nan Di, Lei Qi, Yang Sui, Ting-Yu Wang, Li Fan, Zhen-Mei Lv, Xue-Chang Wu, Pin-Mei Wang, Dao-Qiong Zheng
Yeast Saccharomyces cerevisiae strains isolated from different sources generally show extensive genetic and phenotypic diversity. Understanding how genomic variations influence phenotypes is important for developing strategies with improved economic traits. The diploid S. cerevisiae strain NY1308 is used for cellulosic bioethanol production. Whole genome sequencing identified an extensive amount of single nucleotide variations and small insertions/deletions in the genome of NY1308 compared with the S288c genome...
January 15, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29332099/association-between-the-intron-8-vntr-polymorphism-of-the-dat1-gene-and-crack-cocaine-addiction
#2
Anderson R Stolf, Diana Müller, Jaqueline B Schuch, Gláucia C Akutagava-Martins, Luciano S P Guimaraes, Claudia M Szobot, Ricardo Halpern, Felix H P Kessler, Flavio Pechansky, Tatiana Roman
BACKGROUND: This study aims to compare allele and genotype frequencies of a 30-bp variable number of tandem repeats (VNTR) polymorphism of the DAT1 gene, located at intron 8, between adult crack cocaine users and nonaddicted individuals. Due to its involvement in drug addiction, this gene is a good candidate for molecular studies. METHODS: A cross-sectional sample of 239 current adult crack abusers or dependents from in- and outpatient clinics and 211 control individuals was collected in Brazil...
January 12, 2018: Neuropsychobiology
https://www.readbyqxmd.com/read/29331882/association-analysis-of-slc6a4-and-htr2a-genes-with-obsessive-compulsive-disorder-influence-of-the-stin2-polymorphism
#3
Chayenne Karine Ferreira Gomes, Tamiris Vieira-Fonseca, Fernanda Brito Melo-Felippe, Juliana Braga de Salles Andrade, Leonardo F Fontenelle, Fabiana Barzotti Kohlrausch
BACKGROUND: Obsessive-Compulsive Disorder (OCD) is a complex and chronic disorder characterized by recurrent thoughts and/or repetitive behaviors. Given the potent anti-obsessional effects of the so-called serotonin reuptake inhibitors, genes related to serotonergic system may be well implicated in the etiopathogenesis of OCD. The gene encoding the serotonin transporter (SLC6A4), which shows a variable number of tandem repeat (VNTR) polymorphism in intron 2 (STin2), have been previously associated with OCD...
December 16, 2017: Comprehensive Psychiatry
https://www.readbyqxmd.com/read/29330416/virtual-genome-walking-across-the-32%C3%A2-gb-ambystoma-mexicanum-genome-assembling-gene-models-and-intronic-sequence
#4
Teri Evans, Andrew D Johnson, Matthew Loose
Large repeat rich genomes present challenges for assembly using short read technologies. The 32 Gb axolotl genome is estimated to contain ~19 Gb of repetitive DNA making an assembly from short reads alone effectively impossible. Indeed, this model species has been sequenced to 20× coverage but the reads could not be conventionally assembled. Using an alternative strategy, we have assembled subsets of these reads into scaffolds describing over 19,000 gene models. We call this method Virtual Genome Walking as it locally assembles whole genome reads based on a reference transcriptome, identifying exons and iteratively extending them into surrounding genomic sequence...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330282/population-dependent-intron-retention-and-dna-methylation-in-breast-cancer
#5
Dongwook Kim, Manu Shivakumar, Seonggyun Han, Michael S Sinclair, Youngji Lee, Yonglan Zheng, Olufunmilayo I Olopade, Dokyoon Kim, Younghee Lee
Regulation of gene expression by DNA methylation in gene promoter regions is well-studied; however, the effects of methylation in the gene body (exons and introns) on gene expression are comparatively understudied. Recently, hyper-methylation has been implicated in the inclusion of alternatively spliced exons; moreover, exon recognition can be enhanced by recruiting the methyl-CpG-binding protein (MeCP2) to hyper-methylated sites. This study examines if methylation status of an intron is correlated with how frequently the intron is retained during splicing using DNA methylation and RNA sequencing (RNA-seq) data from breast cancer tissue specimens in The Cancer Genome Atlas (TCGA)...
January 12, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29330135/apbb2-is-associated-with-amphetamine-use-and-plasma-beta-amyloids-in-patients-receiving-methadone-maintenance-treatment
#6
Chia-Chen Liu, Chiu-Ping Fang, Tung-Hsia Liu, Hsiang-Wei Kuo, Shu Chi Liu, Sheng-Chang Wang, Andrew C H Chen, Yu-Li Liu
APBB2, amyloid beta (A4) precursor protein-binding family B member 2, has been reported to be associated with opioid dependence. In this study, we reported the first time that the genetic variants in the APBB2 gene were associated with use of amphetamine in opioid dependent patients undergoing methadone maintenance treatment (MMT). 344 heroin-dependent patients undergoing MMT were recruited and assessed for use of amphetamine and opioids by urine toxicology, withdrawal severity, and side effects. DNAs were genome-widely genotyped for all patients...
January 9, 2018: Progress in Neuro-psychopharmacology & Biological Psychiatry
https://www.readbyqxmd.com/read/29329719/regulatory-potential-of-the-rna-processing-machinery-implications-for-human-disease
#7
REVIEW
Kirstyn T Carey, Vihandha O Wickramasinghe
Splicing and nuclear export of mRNA are critical steps in the gene expression pathway. While RNA processing factors can perform general, essential functions for intron removal and bulk export of mRNA, emerging evidence highlights that the core RNA splicing and export machineries also display regulatory potential. Here, we discuss recent insights into how this regulatory potential can selectively alter gene expression and regulate important biological processes. We also highlight the participation of RNA processing pathways in the cellular response to DNA damage at multiple levels...
January 9, 2018: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/29329284/identification-of-an-elaborate-nk-specific-system-regulating-hla-c-expression
#8
Hongchuan Li, Martin A Ivarsson, Victoria E Walker-Sperling, Jeff Subleski, Jenna K Johnson, Paul W Wright, Mary Carrington, Niklas K Björkström, Daniel W McVicar, Stephen K Anderson
The HLA-C gene appears to have evolved in higher primates to serve as a dominant source of ligands for the KIR2D family of inhibitory MHC class I receptors. The expression of NK cell-intrinsic MHC class I has been shown to regulate the murine Ly49 family of MHC class I receptors due to the interaction of these receptors with NK cell MHC in cis. However, cis interactions have not been demonstrated for the human KIR and HLA proteins. We report the discovery of an elaborate NK cell-specific system regulating HLA-C expression, indicating an important role for HLA-C in the development and function of NK cells...
January 12, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29329193/mustn1-a-developmentally-regulated-pan-musculoskeletal-cell-marker-and-regulatory-gene
#9
REVIEW
Michael Hadjiargyrou
The Mustn1 gene encodes a small nuclear protein (~9.6 kDa) that does not belong to any known family. Its genomic organization consists of three exons interspersed by two introns and it is highly homologous across vertebrate species. Promoter analyses revealed that its expression is regulated by the AP family of transcription factors, especially c-Fos, Fra-2 and JunD. Mustn1 is predominantly expressed in the major tissues of the musculoskeletal system: bone, cartilage, skeletal muscle and tendon. Its expression has been associated with normal embryonic development, postnatal growth, exercise, and regeneration of bone and skeletal muscle...
January 12, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29327506/next-generation-sequencing-characterizes-the-extent-of-hla-diversity-in-an-argentinian-registry-population
#10
C K Hurley, L Hou, A Lazaro, J Gerfen, E Enriquez, P Galarza, M Belen Rodriguez Cardozo, M Halagan, M Maiers, D Behm, J Ng
Next generation DNA sequencing is used to determine the HLA-A, -B, -C, -DRB1, and -DQB1 assignments of 1472 unrelated volunteers for the unrelated donor registry in Argentina. The analysis characterized all HLA exons and introns for class I alleles; at least exons 2, 3 for HLA-DRB1; and exons 2-6 for HLA-DQB1. Of the distinct alleles present, there are 330 class I and 98 class II. The majority (~98%) of the cumulative allele frequency at each locus is contributed by alleles that appear at a frequency of at least 1 in 1000...
January 12, 2018: HLA
https://www.readbyqxmd.com/read/29326799/molecular-heterogeneity-in-acute-promyelocytic-leukemia-a-single-center-experience-from-india
#11
Nikhil Rabade, Goutham Raval, Shruti Chaudhary, P G Subramanian, Rohan Kodgule, Swapnali Joshi, Prashant Tembhare, Syed K Hasan, Hasmukh Jain, Manju Sengar, Gaurav Narula, Shripad Banavali, Pratibha Amare Kadam, Dhanalaxmi Shetty, Sumeet Gujral, Nikhil Patkar
Atypical breakpoints and variant APL cases involving alternative chromosomal aberrations are seen in a small subset of acute promyelocytic leukemia (APL) patients. Over seven different partner genes for RARA have been described. Although rare, these variants prove to be a diagnostic challenge and require a combination of advanced cytogenetic and molecular techniques for accurate characterization. Heterogeneity occurs not only at the molecular level but also at clinico-pathological level influencing treatment response and outcome...
2018: Mediterranean Journal of Hematology and Infectious Diseases
https://www.readbyqxmd.com/read/29325903/gata4-loss-of-function-mutation-and-the-congenitally-bicuspid-aortic-valve
#12
Ruo-Gu Li, Ying-Jia Xu, Juan Wang, Xing-Yuan Liu, Fang Yuan, Ri-Tai Huang, Song Xue, Li Li, Hua Liu, Yan-Jie Li, Xin-Kai Qu, Hong-Yu Shi, Min Zhang, Xing-Biao Qiu, Yi-Qing Yang
Aggregating evidence suggests that genetic determinants play a pivotal role in the pathogenesis of the congenitally bicuspid aortic valve (BAV). BAV is of pronounced genetic heterogeneity, and the genetic components underlying BAV in an overwhelming majority of patients remain elusive. In the current study, the whole coding exons and adjacent introns, as well as 5' and 3' untranslated regions of the GATA4 gene, which codes for a zinc-finger transcription factor crucial for the normal development of the aortic valve, were screened by direct sequencing in 150 index patients with congenital BAV...
November 23, 2017: American Journal of Cardiology
https://www.readbyqxmd.com/read/29325035/amplicon-based-next-generation-sequencing-of-plasma-cell-free-dna-for-detection-of-driver-and-resistance-mutations-in-advanced-non-small-cell-lung-cancer
#13
N Guibert, Y Hu, N Feeney, Y Kuang, V Plagnol, G Jones, K Howarth, J F Beeler, C P Paweletz, G R Oxnard
Background: Genomic analysis of plasma cell-free DNA is transforming lung cancer care, however available assays are limited by cost, turnaround time, and imperfect accuracy. Here we study amplicon-based plasma next-generation sequencing (NGS), rather than hybrid-capture-based plasma NGS, hypothesizing this would allow sensitive detection and monitoring of driver and resistance mutations in advanced non-small cell lung cancer (NSCLC). Methods: Plasma samples from patients with NSCLC and a known targetable genotype (EGFR, ALK/ROS1 and other rare genotypes) were collected while on therapy and analyzed, blinded to tumor genotype...
January 9, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29325031/use-of-deep-whole-genome-sequencing-data-to-identify-structure-risk-variants-in-breast-cancer-susceptibility-genes
#14
Xingyi Guo, Jiajun Shi, Qiuyin Cai, Xiao-Ou Shu, Jing He, Wanqing Wen, Jamie Allen, Paul Pharoah, Alison Dunning, David J Hunter, Peter Kraft, Douglas F Easton, Wei Zheng, Jirong Long
Functional disruptions of susceptibility genes by large genomic structure variant (SV) deletions in germlines are known to be associated with cancer risk. However, few studies have been conducted to systematically search for SV deletions in breast cancer susceptibility genes. We analyzed deep (> 30x) whole genome sequencing (WGS) data generated in blood samples from 128 breast cancer patients of Asian and European descent with either a strong family history of breast cancer or early cancer onset disease...
January 8, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29325021/oligonucleotides-targeting-tcf4-triplet-repeat-expansion-inhibit-rna-foci-and-mis-splicing-in-fuchs-dystrophy
#15
Jiaxin Hu, Ziye Rong, Xin Gong, Zhengyang Zhou, Vivek K Sharma, Chao Xing, Jonathan K Watts, David R Corey, V Vinod Mootha
Fuchs' endothelial corneal dystrophy (FECD) is the most common repeat expansion disorder. FECD impacts 4% of United States population and is the leading indication for corneal transplantation. Most cases are caused by an expanded intronic CUG tract in the TCF4 gene that forms nuclear foci, sequesters splicing factors, and impairs splicing. We investigated the sense and antisense RNA landscape at the FECD gene and find that the sense expanded repeat transcript is the predominant species in patient corneas. In patient tissue, sense foci number were negatively correlated with age and showed no correlation with sex...
January 8, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29324881/genome-wide-analysis-and-expression-profiles-of-glyoxalase-gene-families-in-chinese-cabbage-brassica-rapa-l
#16
Guixin Yan, Xin Xiao, Nian Wang, Fugui Zhang, Guizhen Gao, Kun Xu, Biyun Chen, Jiangwei Qiao, Xiaoming Wu
The glyoxalase pathway is composed of glyoxalase I (GLYI) and glyoxalase II (GLYII) and is responsible for the detoxification of a cytotoxic metabolite methylglyoxal (MG) into the nontoxic S-D-lactoylglutathione. The two glyoxalase enzymes play a crucial role in stress tolerance in various plant species. Recently, the GLY gene families have well been analyzed in Arabidopsis, rice and soybean, however, little is known about them in Chinese cabbage (Brassica rapa). Here, 16 BrGLYI and 15 BrGLYII genes were identified in the B...
2018: PloS One
https://www.readbyqxmd.com/read/29324689/characterization-of-translationally-controlled-tumour-protein-from-the-sea-anemone-anemonia-viridis-and-transcriptome-wide-identification-of-cnidarian-homologues
#17
Aldo Nicosia, Carmelo Bennici, Girolama Biondo, Salvatore Costa, Marilena Di Natale, Tiziana Masullo, Calogera Monastero, Maria Antonietta Ragusa, Marcello Tagliavia, Angela Cuttitta
Gene family encoding translationally controlled tumour protein (TCTP) is defined as highly conserved among organisms; however, there is limited knowledge of non-bilateria. In this study, the first TCTP homologue from anthozoan was characterised in the Mediterranean Sea anemone, Anemonia viridis. The release of the genome sequence of Acropora digitifera, Exaiptasia pallida, Nematostella vectensis and Hydra vulgaris enabled a comprehensive study of the molecular evolution of TCTP family among cnidarians. A comparison among TCTP members from Cnidaria and Bilateria showed conserved intron exon organization, evolutionary conserved TCTP signatures and 3D protein structure...
January 11, 2018: Genes
https://www.readbyqxmd.com/read/29323256/splicing-of-platelet-resident-pre-mrnas-upon-activation-by-physiological-stimuli-results-in-functionally-relevant-proteome-modifications
#18
Giovanni Nassa, Giorgio Giurato, Giovanni Cimmino, Francesca Rizzo, Maria Ravo, Annamaria Salvati, Tuula A Nyman, Yafeng Zhu, Mattias Vesterlund, Janne Lehtiö, Paolo Golino, Alessandro Weisz, Roberta Tarallo
Platelet activation triggers thrombus formation in physiological and pathological conditions, such as acute coronary syndromes. Current therapies still fail to prevent thrombotic events in numerous patients, indicating that the mechanisms modulating platelet response during activation need to be clarified. The evidence that platelets are capable of de novo protein synthesis in response to stimuli raised the issue of how megakaryocyte-derived mRNAs are regulated in these anucleate cell fragments. Proteogenomics was applied here to investigate this phenomeon in platelets activated in vitro with Collagen or Thrombin Receptor Activating Peptide...
January 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29322449/synthesis-and-engineering-of-circular-rnas
#19
Sonja Petkovic, Sabine Müller
Circular RNAs (circRNAs) have been discovered in all kingdoms of life. They are produced from introns as well as from exons. However, strongest interest is in circRNAs that are transcribed and spliced from exons of protein and noncoding genes in eukaryotic cells including humans. Therefore, synthesis and engineering of circRNAs as models for structure and function studies are strongly required. In vitro, methods for RNA synthesis and circularization are available. Chemical synthesis allows for preparation of RNAs incorporating nonnatural nucleotides in small RNA segments, whereas enzymatic synthesis is advantageous for production of long RNAs, however, without the possibility for site-specific modification...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29321894/development-of-a-genotype-by-sequencing-immunogenetic-assay-as-exemplified-by-screening-for-variation-in-red-fox-with-and-without-endemic-rabies-exposure
#20
Michael E Donaldson, Yessica Rico, Karsten Hueffer, Halie M Rando, Anna V Kukekova, Christopher J Kyle
Pathogens are recognized as major drivers of local adaptation in wildlife systems. By determining which gene variants are favored in local interactions among populations with and without disease, spatially explicit adaptive responses to pathogens can be elucidated. Much of our current understanding of host responses to disease comes from a small number of genes associated with an immune response. High-throughput sequencing (HTS) technologies, such as genotype-by-sequencing (GBS), facilitate expanded explorations of genomic variation among populations...
January 2018: Ecology and Evolution
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