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3' utr intron

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https://www.readbyqxmd.com/read/28059001/possible-association-of-3-utr-357-a-g-ivs11-nt-93-t-c-c-1311-c-t-polymorphism-with-g6pd-deficiency
#1
Mahmoud M Sirdah, Mohammad E Shubair, Mustafa S Al-Kahlout, Jamal M Al-Tayeb, Josef T Prchal, N Scott Reading
BACKGROUND: Glucose-6-phosphate dehydrogenase (G6PD) deficiency is a common X-linked inherited enzymopathic disorder affecting more than 500 million people worldwide. It has so far been linked to 217 distinct genetic variants in the exons and exon-intron boundaries of the G6PD gene, giving rise to a wide range of biochemical heterogeneity and clinical manifestations. OBJECTIVES: Reports from different settings suggested the association of intronic and other mutations outside the reading frame of the G6PD gene with reduced enzyme activity and presenting clinical symptoms...
January 6, 2017: Hematology (Amsterdam, Netherlands)
https://www.readbyqxmd.com/read/28006787/role-of-mir-215-in-hirschsprung-s-disease-pathogenesis-by-targeting-siglec-8
#2
Hao Lei, Hongxing Li, Hua Xie, Chunxia Du, Yankai Xia, Weibing Tang
BACKGROUND/AIMS: Hirschsprung's disease (HSCR), known as aganglionosis, is an infrequent congenital gut motility disorder characterized by absence of enteric neurons. In this study, we focus on the role of the intronic miR-215 and its host gene isoleucyl-tRNA synthetase 2 (IARS2) in the pathogenesis of HSCR. METHODS: Quantitative real time PCR and Western blot were used to detect the miRNA, mRNAs, and proteins levels. The dual-luciferase reporter gene assay confirmed the direct regulation of the specific mRNA and miRNAs in cell lines...
2016: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28003160/regulatory-factor-x1-depresses-apoe-dependent-a%C3%AE-uptake-by-mirna-124-in-microglial-response-to-oxidative-stress
#3
Chen-Zhuo Feng, Jin-Bo Yin, Jian-Jun Yang, Lin Cao
Decreased proteolytic clearance of soluble amyloid β (Aβ) in microglia affects Aβ accumulation on Alzheimer's disease progression. However, the potential molecular mechanism by which microglial Aβ uptake is regulated remains unclear. In this study, we identified a microRNA, miR-124, that was down-regulated in aging with a function in regulating apolipoprotein E (ApoE)-dependent Aβ uptake by targeting regulatory factor X1 (RFX1) transcripts on BV2 microglia cell. Decreased expression of miRNA-124 in BV2 cells exposed to mild hydrogen peroxide increased RFX1 protein level and decreased the expression of ApoE, a gene which has been suggested to enhance cellular Aβ uptake in microglia...
December 18, 2016: Neuroscience
https://www.readbyqxmd.com/read/27989867/identification-and-functional-characterization-of-a-novel-antistasin-wap-like-serine-protease-inhibitor-from-the-tropical-sea-cucumber-stichopus-monotuberculatus
#4
Aifen Yan, Chunhua Ren, Ting Chen, Xiao Jiang, Hongyan Sun, Chaoqun Hu
A novel antistasin/WAP-like serine protease inhibitor, named as StmAW-SPI, was identified from sea cucumber (Stichopus monotuberculatus) and functionally characterized in this study. The full-length cDNA of StmAW-SPI is 1917 bp in length with a 72 bp 5'-untranslated region (UTR), a 294 bp 3'-UTR and a 1551 bp open reading frame (ORF) encoding a protein of 516 amino acids with a deduced molecular weight of 54.56 kDa. The StmAW-SPI protein has 5-fold internal repeats (IRs) of antistasin domain and 6-fold IRs of WAP domain...
October 27, 2016: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/27928018/expression-of-the-antisense-to-latency-transcript-long-noncoding-rna-in-kaposi-s-sarcoma-associated-herpesvirus
#5
Jason M Schifano, Kathleen Corcoran, Hemant Kelkar, Dirk P Dittmer
: The regulation of latency is central to herpesvirus biology. Recent transcriptome-wide surveys have uncovered evidence for promiscuous transcription across the entirety of the Kaposi sarcoma-associated herpesvirus genome and postulated the existence of multiple viral long noncoding RNAs (lncRNAs). NextGen sequencing studies are highly dependent on the specific experimental approach and particular algorithms of analysis, and therefore benefit from independent confirmation of the results...
December 7, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27913194/genetic-screening-of-thap1-in-primary-dystonia-patients-of-india
#6
Subhajit Giri, Tufan Naiya, Zaffar Equbal, Charulata Savant Sankhla, Shyamal Kumar Das, Kunal Ray, Jharna Ray
BACKGROUND: Primary Dystonia is a common movement disorder manifested by dystonic symptoms only. DYT6, a major genetic factor, plays a significant role in primary pure dystonia pathogenesis. In this study we analyzed THAP1 (DYT 6) gene in primary pure dystonia patients, which has been widely studied in other populations but not in Indians. METHODS: The study cohort contained 227 index primary pure dystonia patients with the involvement of cervical region and 254 neurologically control individuals collected from East Indian population...
January 10, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/27899424/genetic-architecture-of-sporadic-frontotemporal-dementia-and-overlap-with-alzheimer-s-and-parkinson-s-diseases
#7
Raffaele Ferrari, Yunpeng Wang, Jana Vandrovcova, Sebastian Guelfi, Aree Witeolar, Celeste M Karch, Andrew J Schork, Chun C Fan, James B Brewer, Parastoo Momeni, Gerard S Schellenberg, William P Dillon, Leo P Sugrue, Christopher P Hess, Jennifer S Yokoyama, Luke W Bonham, Gil D Rabinovici, Bruce L Miller, Ole A Andreassen, Anders M Dale, John Hardy, Rahul S Desikan
BACKGROUND: Clinical, pathological and genetic overlap between sporadic frontotemporal dementia (FTD), Alzheimer's disease (AD) and Parkinson's disease (PD) has been suggested; however, the relationship between these disorders is still not well understood. Here we evaluated genetic overlap between FTD, AD and PD to assess shared pathobiology and identify novel genetic variants associated with increased risk for FTD. METHODS: Summary statistics were obtained from the International FTD Genomics Consortium, International PD Genetics Consortium and International Genomics of AD Project (n>75 000 cases and controls)...
February 2017: Journal of Neurology, Neurosurgery, and Psychiatry
https://www.readbyqxmd.com/read/27864472/transcriptome-wide-identification-of-nmd-targeted-human-mrnas-reveals-extensive-redundancy-between-smg6-and-smg7-mediated-degradation-pathways
#8
Martino Colombo, Evangelos D Karousis, Joël Bourquin, Rémy Bruggmann, Oliver Mühlemann
Besides degrading aberrant mRNAs that harbor a premature translation termination codon (PTC), nonsense-mediated mRNA decay (NMD) also targets many seemingly "normal" mRNAs that encode for full-length proteins. To identify a bona fide set of such endogenous NMD targets in human cells, we applied a meta-analysis approach in which we combined transcriptome profiling of knockdowns and rescues of the three NMD factors UPF1, SMG6 and SMG7. We provide evidence that this combinatorial approach identifies NMD-targeted transcripts more reliably than previous attempts that focused on inactivation of single NMD factors...
November 18, 2016: RNA
https://www.readbyqxmd.com/read/27851806/5-hydroxymethylcytosine-precedes-loss-of-cpg-methylation-in-enhancers-and-genes-undergoing-activation-in-cardiomyocyte-maturation
#9
David K Kranzhöfer, Ralf Gilsbach, Björn A Grüning, Rolf Backofen, Thomas G Nührenberg, Lutz Hein
BACKGROUND: Cardiomyocytes undergo major changes in DNA methylation during maturation and transition to a non-proliferative state after birth. 5'-hydroxylation of methylated cytosines (5hmC) is not only involved in DNA loss of CpG methylation but is also thought to be an epigenetic mark with unique distribution and functions. Here, we sought to get insight into the dynamics of 5'-hydroxymethylcytosine in newborn and adult cardiomyocytes. METHODS: Cardiomyocyte nuclei from newborn and adult C57BL/6 mice were purified by flow cytometric sorting...
2016: PloS One
https://www.readbyqxmd.com/read/27814995/tmem230-mutation-analysis-in-parkinson-s-disease-in-a-chinese-population
#10
Weiqian Yan, Beisha Tang, Xiaoxia Zhou, Lifang Lei, Kai Li, Qiying Sun, Qian Xu, Xinxiang Yan, Jifeng Guo, Zhenhua Liu
Mutations in TMEM230 were identified as a genetic factor for Parkinson's disease (PD) with typical clinical symptoms and Lewy bodies in a North American population, and a highly prevalent TMEM230 mutation, c.550_552delTAGinsCCCGGG (p.*184ProGlyext*5), was found in 7 Chinese families. In the present study, we investigated the prevalence of TMEM230 mutations in a large cohort of Chinese PD patients and healthy controls individuals from mainland China. We sequenced all exons and exon-intron boundaries of TMEM230 in Chinese Han population including 1235 patients with PD and 1252 healthy control individuals...
January 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/27798706/application-of-high-throughput-next-generation-sequencing-for-hla-typing-on-buccal-extracted-dna-results-from-over-10-000-donor-recruitment-samples
#11
Yuxin Yin, James H Lan, David Nguyen, Nicole Valenzuela, Ping Takemura, Yung-Tsi Bolon, Brianna Springer, Katsuyuki Saito, Ying Zheng, Tim Hague, Agnes Pasztor, Gyorgy Horvath, Krisztina Rigo, Elaine F Reed, Qiuheng Zhang
BACKGROUND: Unambiguous HLA typing is important in hematopoietic stem cell transplantation (HSCT), HLA disease association studies, and solid organ transplantation. However, current molecular typing methods only interrogate the antigen recognition site (ARS) of HLA genes, resulting in many cis-trans ambiguities that require additional typing methods to resolve. Here we report high-resolution HLA typing of 10,063 National Marrow Donor Program (NMDP) registry donors using long-range PCR by next generation sequencing (NGS) approach on buccal swab DNA...
2016: PloS One
https://www.readbyqxmd.com/read/27788248/dna-methylation-patterns-in-the-hypothalamus-of-female-pubertal-goats
#12
Chen Yang, Jing Ye, Xiumei Li, Xiaoxiao Gao, Kaifa Zhang, Lei Luo, Jianping Ding, Yunhai Zhang, Yunsheng Li, Hongguo Cao, Yinghui Ling, Xiaorong Zhang, Ya Liu, Fugui Fang
Female pubertal development is tightly controlled by complex mechanisms, including neuroendocrine and epigenetic regulatory pathways. Specific gene expression patterns can be influenced by DNA methylation changes in the hypothalamus, which can in turn regulate timing of puberty onset. In order to understand the relationship between DNA methylation changes and gene expression patterns in the hypothalamus of pubertal goats, whole-genome bisulfite sequencing and RNA-sequencing analyses were carried out. There was a decline in DNA methylation levels in the hypothalamus during puberty and 268 differentially methylated regions (DMR) in the genome, with differential patterns in different gene regions...
2016: PloS One
https://www.readbyqxmd.com/read/27760516/the-1-78-kb-insertion-in-the-3-untranslated-region-of-rxfp2-does-not-segregate-with-horn-status-in-sheep-breeds-with-variable-horn-status
#13
Gesine Lühken, Stefan Krebs, Sophie Rothammer, Julia Küpper, Boro Mioč, Ingolf Russ, Ivica Medugorac
BACKGROUND: The mode of inheritance of horn status in sheep is far more complex than a superficial analysis might suggest. Observations, which were mostly based on crossbreeding experiments, indicated that the allele that results in horns is dominant in males and recessive in females, and some authors even speculated about the involvement of more than two alleles. However, all recent genome-wide association analyses point towards a very strong effect of a single autosomal locus on ovine chromosome 10, which was narrowed down to a putatively causal insertion polymorphism in the 3'-untranslated region of the relaxin/insulin-like family peptide receptor 2 gene (RXFP2)...
October 19, 2016: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/27727437/molecular-diagnosis-of-myotonic-dystrophy
#14
Sujata Chakraborty, Matteo Vatta, Linda L Bachinski, Ralf Krahe, Stephen Dlouhy, Shaochun Bai
Myotonic dystrophy types 1 (DM1) and 2 (DM2) are autosomal dominant, microsatellite repeat expansion disorders that affect muscle function. Myotonic dystrophy type 1 is caused by CTG repeat expansion in the 3' UTR region of the DMPK gene. Patients with DM2 have expansion of CCTG repeats in intron 1 of the CNBP gene. In this unit, we review and discuss the clinical phenotypes, genetic mutations causing the diseases, and the molecular diagnostic approaches and tools that are used to determine repeat sizes in DM1/2...
October 11, 2016: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/27659147/dendritic-transport-element-of-human-arc-mrna-confers-rna-degradation-activity-in-a-translation-dependent-manner
#15
Kensuke Ninomiya, Mutsuhito Ohno, Naoyuki Kataoka
Localization of mRNA in neuronal cells is a critical process for spatiotemporal regulation of gene expression. Cytoplasmic localization of mRNA is often conferred by transport elements in 3' untranslated region (UTR). Activity-regulated cytoskeleton-associated protein (arc) mRNA is one of the localizing mRNAs in neuronal cells, and its localization is mediated by dendritic targeting element (DTE). As arc mRNA has introns in its 3' UTR, it was thought that arc mRNA is a natural target of nonsense-mediated mRNA decay (NMD)...
November 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/27624183/exome-genotyping-linkage-disequilibrium-and-population-structure-in-loblolly-pine-pinus-taeda-l
#16
Mengmeng Lu, Konstantin V Krutovsky, C Dana Nelson, Tomasz E Koralewski, Thomas D Byram, Carol A Loopstra
BACKGROUND: Loblolly pine (Pinus taeda L.) is one of the most widely planted and commercially important forest tree species in the USA and worldwide, and is an object of intense genomic research. However, whole genome resequencing in loblolly pine is hampered by its large size and complexity and a lack of a good reference. As a valid and more feasible alternative, entire exome sequencing was hence employed to identify the gene-associated single nucleotide polymorphisms (SNPs) and to genotype the sampled trees...
September 13, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27612015/full-length-nucleotide-sequence-of-ermap-alleles-encoding-scianna-sc-antigens
#17
Kshitij Srivastava, Eunah Lee, Eric Owens, Pairaya Rujirojindakul, Willy A Flegel
BACKGROUND: Scianna (SC) blood group system comprises two antithetical antigens, Sc1 and Sc2, and five additional antigens. The antigens reside on a glycoprotein encoded by the erythroblast membrane-associated protein (ERMAP) gene. For the common ERMAP alleles, we determined the full-length nucleotide sequence that encodes the Scianna glycoprotein. STUDY DESIGN AND METHODS: Blood donor samples from five populations were analyzed including 20 African Americans, 10 Caucasians, 10 Thai, five Asians, and five Hispanics for a total of 100 chromosomes...
December 2016: Transfusion
https://www.readbyqxmd.com/read/27607449/gnai3-another-candidate-gene-to-screen-in-persons-with-ocular-albinism
#18
Alejandra Young, Uma Dandekar, Calvin Pan, Avery Sader, Jie J Zheng, Richard A Lewis, Debora B Farber
Ocular albinism type 1 (OA), caused by mutations in the OA1 gene, encodes a G-protein coupled receptor, OA1, localized in melanosomal membranes of the retinal pigment epithelium (RPE). This disorder is characterized by both RPE macro-melanosomes and abnormal decussation of ganglion cell axons at the brain's optic chiasm. We demonstrated previously that Oa1 specifically activates Gαi3, which also signals in the Oa1 transduction pathway that regulates melanosomal biogenesis. In this study, we screened the human Gαi3 gene, GNAI3, in DNA samples from 26 patients who had all clinical characteristics of OA but in whom a specific mutation in the OA1 gene had not been found, and in 6 normal control individuals...
2016: PloS One
https://www.readbyqxmd.com/read/27561685/short-term-calorie-restriction-ameliorates-genomewide-age-related-alterations-in-dna-methylation
#19
Chul H Kim, Eun K Lee, Yoen J Choi, Hye J An, Hyung O Chung, Dae E Park, Byung C Ghim, Byung P Yu, Jong Bhak, Hae Y Chung
DNA methylation plays major roles in many biological processes, including aging, carcinogenesis, and development. Analyses of DNA methylation using next-generation sequencing offer a new way to profile and compare methylomes across the genome in the context of aging. We explored genomewide DNA methylation and the effects of short-term calorie restriction (CR) on the methylome of aged rat kidney. Whole-genome methylation of kidney in young (6 months old), old (25 months old), and OCR (old with 4-week, short-term CR) rats was analyzed by methylated DNA immunoprecipitation and next-generation sequencing (MeDIP-Seq)...
August 25, 2016: Aging Cell
https://www.readbyqxmd.com/read/27554590/cloning-and-characterization-of-novel-cyclotides-genes-from-south-american-plants
#20
Nicolau Brito da Cunha, Aulus Estevão Anjos de Deus Barbosa, Renato Goulart de Almeida, William Farias Porto, Mariana Rocha Maximiano, Luana Cristina Silva Álvares, Cassia Beatriz Rodrigues Munhoz, Chesterton Ulysses Orlando Eugênio, Antônio Américo Barbosa Viana, Octavio Luiz Franco, Simoni Campos Dias
Cyclotides are multifunctional plant cyclic peptides containing 28-37 amino acid residues and a pattern of three disulfide bridges, forming a motif known as the cyclic cystine knot. Due to their high biotechnological potential, the sequencing and characterization of cyclotide genes are crucial not only for cloning and establishing heterologous expression strategies, but also to understand local plant evolution in the context of host-pathogen relationships. Here, two species from the Brazilian Cerrado, Palicourea rigida (Rubiaceae) and Pombalia lanata (A...
November 2016: Biopolymers
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