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https://www.readbyqxmd.com/read/28938099/plasmid-dna-launches-live-attenuated-japanese-encephalitis-virus-and-elicits-virus-neutralizing-antibodies-in-balb-c-mice
#1
Brian Nickols, Irina Tretyakova, Alexander Tibbens, Elena Klyushnenkova, Peter Pushko
We describe novel plasmid DNA that encodes the full-length Japanese encephalitis virus (JEV) genomic cDNA and launches live-attenuated JEV vaccine in vitro and in vivo. The synthetic cDNA based on the sequence of JEV SA14-14-2 live-attenuated virus was placed under transcriptional control of the cytomegalovirus major immediate-early promoter. The stability and yields of the plasmid in E. coli were optimized by inserting three synthetic introns that disrupted JEV cDNA in the structural and nonstructural genes...
September 19, 2017: Virology
https://www.readbyqxmd.com/read/28936921/osteopontin-c-isoform-levels-are-associated-with-sr-and-hnrnp-differential-expression-in-ovarian-cancer-cell-lines
#2
Durval Santos Marques, Jessica Grativol, Rodrigo Alves da Silva Peres, Aline da Rocha Matos, Etel Rodrigues Pereira Gimba
Osteopontin-c splicing isoform activates ovarian cancer progression features. Imbalanced expression of splicing factors from serine/arginine -rich and heterogeneous ribonucleoproteins families has been correlated with the generation of oncogenic splicing isoforms. Our goal was to investigate whether there is any association between the transcriptional patterns of these splicing factors in ovarian cells and osteopontin-c expression levels. We also aimed to investigate the occurrence of these splicing factors binding sites inside osteopontin exon 4 and adjacent introns...
September 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28936718/identification-of-candidate-genes-for-generalized-tonic-clonic-seizures-in-noda-epileptic-rat
#3
Takashi Kuramoto, Birger Voigt, Satoshi Nakanishi, Kazuhiro Kitada, Tadashi Nakamura, Kaori Wakamatsu, Minako Yoshihara, Mikita Suyama, Risa Uemura, Miyuu Tanaka, Mitsuru Kuwamura, Saki Shimizu, Yukihiro Ohno, Masashi Sasa, Tadao Serikawa
The Noda epileptic rat (NER) exhibits generalized tonic-clonic seizures (GTCS). A genetic linkage analysis identified two GTCS-associated loci, Ner1 on Chr 1 and Ner3 on Chr 5. The wild-type Ner1 and Ner3 alleles suppressed GTCS when combined in double-locus congenic lines, but not when present in single-locus congenic lines. Global expression analysis revealed that cholecystokinin B receptor (Cckbr) and suppressor of tumorigenicity 5 (St5), which map within Ner1, and PHD finger protein 24 (Phf24), which maps within Ner3, were significantly downregulated in NER...
September 21, 2017: Behavior Genetics
https://www.readbyqxmd.com/read/28935704/the-splicing-co-factor-barricade-tat-sf1-is-required-for-cell-cycle-and-lineage-progression-in-drosophila-neural-stem-cells
#4
Monika K Abramczuk, Thomas R Burkard, Vivien Rolland, Victoria Steinmann, Peter Duchek, Yanrui Jiang, Sebastian Wissel, Heinrich Reichert, Juergen A Knoblich
Stem cells need to balance self-renewal and differentiation for correct tissue development and homeostasis. Defects in this balance can lead to developmental defects or tumor formation. In recent years, mRNA splicing has emerged as one important mechanism regulating cell fate decisions. Here we address the role of the evolutionary conserved splicing co-factor Barricade (Barc)/Tat-SF1/CUS2 in Drosophila neural stem cell (neuroblast) lineage formation. We show that Barc is required for the generation of neurons during Drosophila brain development by ensuring correct neural progenitor proliferation and differentiation...
September 21, 2017: Development
https://www.readbyqxmd.com/read/28935584/vih-from-the-mud-crab-is-specifically-expressed-in-the-eyestalk-and-potentially-regulated-by-transactivator-of-sox9-oct4-oct1
#5
Chunyun Liu, Xiwei Jia, Zhihua Zou, Xiaowei Wang, Yilei Wang, Ziping Zhang
Vitellogenesis-inhibiting hormone (VIH) is known to regulate ovarian maturation by suppressing the synthesis of vitellogenin (Vtg) in crustaceans, which belongs to a member of crustacean hyperglycemic hormone (CHH) family synthesized and secreted from the X-organ/sinus gland complex of eyestalks. In this study, the cDNA, genomic DNA (gDNA) and the 5'-upstream regulatory (promoter region) sequences of VIH gene were obtained by conventional PCR, genome walker and tail-PCR techniques according to our transcriptomic database of Scylla paramamosain...
September 18, 2017: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/28934927/evolution-and-expression-analysis-reveal-the-potential-role-of-the-hd-zip-gene-family-in-regulation-of-embryo-abortion-in-grapes-vitis-vinifera-l
#6
Zhiqian Li, Chen Zhang, Yurui Guo, Weili Niu, Yuejin Wang, Yan Xu
BACKGROUND: The HD-Zip family has a diversity of functions during plant development. In this study, we identify 33 HD-Zip transcription factors in grape and detect their expressions in ovules and somatic embryos, as well as in various vegetative organs. RESULTS: A genome-wide survey for HD-Zip transcription factors in Vitis was conducted based on the 12 X grape genome (V. vinifera L.). A total of 33 members were identified and classified into four subfamilies (I-IV) based on phylogeny analysis with Arabidopsis, rice and maize...
September 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28934905/talen-mediated-targeted-editing-of-the-gde5-gene-suppresses-fibroblastic-cell-proliferation
#7
Minako Nakamura, Thanutchaporn Kumrungsee, Tetsushi Sakuma, Takashi Yamamoto, Noriyuki Yanaka
In this study, we investigated the physiological function of glycerophosphodiesterase 5 (GDE5) in the proliferation of NIH3T3 fibroblasts. We used transcription activator-like effector nuclease (TALEN) in NIH3T3 cells with an intron targeting-mediated GDE5 gene knockout. The heterozygously GDE5-targeted NIH3T3 fibroblasts were isolated and showed decreased cell proliferation and up-regulation of EGFR mRNA expression, indicating that GDE5 modulates fibroblastic cell proliferation.
September 22, 2017: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/28934498/widespread-intra-dependencies-in-the-removal-of-introns-from-human-transcripts
#8
Seong Won Kim, Allison J Taggart, Claire Heintzelman, Kamil J Cygan, Caitlin G Hull, Jing Wang, Barsha Shrestha, William G Fairbrother
Research into the problem of splice site selection has followed a reductionist approach focused on how individual splice sites are recognized. Early applications of information theory uncovered an inconsistency. Human splice signals do not contain enough information to explain the observed fidelity of splicing. Here, we conclude that introns do not necessarily contain 'missing' information but rather may require definition from neighboring processing events. For example, there are known cases where an intronic mutation disrupts the splicing of not only the local intron but also adjacent introns...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934495/a-germline-limited-piggybac-transposase-gene-is-required-for-precise-excision-in-tetrahymena-genome-rearrangement
#9
Lifang Feng, Guangying Wang, Eileen P Hamilton, Jie Xiong, Guanxiong Yan, Kai Chen, Xiao Chen, Wen Dui, Amber Plemens, Lara Khadr, Arjune Dhanekula, Mina Juma, Hung Quang Dang, Geoffrey M Kapler, Eduardo Orias, Wei Miao, Yifan Liu
Developmentally programmed genome rearrangement accompanies differentiation of the silent germline micronucleus into the transcriptionally active somatic macronucleus in the ciliated protozoan Tetrahymena thermophila. Internal eliminated sequences (IES) are excised, followed by rejoining of MAC-destined sequences, while fragmentation occurs at conserved chromosome breakage sequences, generating macronuclear chromosomes. Some macronuclear chromosomes, referred to as non-maintained chromosomes (NMC), are lost soon after differentiation...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934396/evaluation-of-shared-genetic-aetiology-between-osteoarthritis-and-bone-mineral-density-identifies-smad3-as-a-novel-osteoarthritis-risk-locus
#10
Sophie Hackinger, Katerina Trajanoska, Unnur Styrkarsdottir, Eleni Zengini, Julia Steinberg, Graham R S Ritchie, Konstantinos Hatzikotoulas, Arthur Gilly, Evangelos Evangelou, John P Kemp, David Evans, Thorvaldur Ingvarsson, Helgi Jonsson, Unnur Thorsteinsdottir, Kari Stefansson, Andrew W McCaskie, Roger A Brooks, Jeremy M Wilkinson, Fernando Rivadeneira, Eleftheria Zeggini
Osteoarthritis (OA) is a common complex disease with high public health burden and no curative therapy. High bone mineral density (BMD) is associated with an increased risk of developing OA, suggesting a shared underlying biology. Here, we performed the first systematic overlap analysis of OA and BMD on a genome wide scale. We used summary statistics from the GEFOS consortium for lumbar spine (n = 31,800) and femoral neck (n = 32,961) BMD, and from the arcOGEN consortium for three OA phenotypes (hip, ncases=3,498; knee, ncases=3,266; hip and/or knee, ncases=7,410; ncontrols=11,009)...
October 1, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28932927/screening-for-germline-mutations-in-mismatch-repair-genes-in-patients-with-lynch-syndrome-by-next-generation-sequencing
#11
Barbara Luísa Soares, Ayslan Castro Brant, Renan Gomes, Tatiane Pastor, Naye Balzan Schneider, Ândrea Ribeiro-Dos-Santos, Paulo Pimentel de Assumpção, Maria Isabel W Achatz, Patrícia Ashton-Prolla, Miguel Angelo Martins Moreira
Lynch syndrome (LS) is an autosomal dominant disorder, with high penetrance that affects approximately 3% of the cases of colorectal cancer. Affected individuals inherit germline mutations in genes responsible for DNA mismatch repair, mainly at MSH2, MLH1, MSH6 and PMS2. The molecular screening of these individuals is frequently costly and time consuming due to the large size of these genes. In addition, PMS2 mutation detection is often a challenge because there are 16 different pseudogenes identified until now...
September 20, 2017: Familial Cancer
https://www.readbyqxmd.com/read/28931690/conformational-changes-in-the-5-end-of-the-hiv-1-genome-dependent-on-the-debranching-enzyme-dbr1-during-early-stages-of-infection
#12
Alvaro E Galvis, Hugh E Fisher, Hung Fan, David Camerini
Previous studies in our laboratory showed that the RNA debranching enzyme (DBR1) is not required for early steps in HIV cDNA formation, but is necessary for synthesis of intermediate and late cDNA products. To further characterize this effect, we evaluated the topology of the 5' end of the HIV-1 RNA genome during early infection with and without inhibition of DBR1 synthesis. Cells were transfected with DBR1 shRNA followed 48 hours later by infection with an HIV-1 derived vector containing an RNase H deficient reverse transcriptase...
September 20, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28931628/type-b-response-regulators-act-as-central-integrators-in-transcriptional-control-of-the-auxin-biosynthesis-enzyme-taa1
#13
Zhenwei Yan, Xin Liu, Karin Ljung, Shuning Li, Wanying Zhao, Fan Yang, Meiling Wang, Yi Tao
During embryogenesis and organ formation, establishing proper gradient is critical for auxin function, which is achieved through coordinated regulation of both auxin metabolism and transport. Expression of auxin biosynthetic genes is often tissue specific and is regulated by environmental signals. However, the underlying regulatory mechanisms remain elusive. Here, we investigated the transcriptional regulation of a key auxin biosynthetic gene, TAA1 (L-Tryptophan aminotransferase of Arabidopsis 1). A canonical and a novel ARR (Arabidopsis response regulators) binding site were identified in the promoter and the second intron of TAA1, which were required for its tissue specific expression...
September 20, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28931431/fasciclin-calcareous-corpuscle-binary-complex-mediated-protein-protein-interactions-in-taenia-solium-metacestode
#14
Chun-Seob Ahn, Jeong-Geun Kim, Young-An Bae, Seon-Hee Kim, Joo-Ho Shin, Yichao Yang, Insug Kang, Yoon Kong
BACKGROUND: Neurocysticercosis (NC) caused by Taenia solium metacestode (TsM) is a serious neurological disease of global concern. Diverse bioactive molecules involved in the long-term survival of TsM might contribute to disease progression. Fasciclin (Fas) is an extracellular protein that mediates adhesion, migration and differentiation of cells by interacting with other molecules. We hypothesized that TsMFas might bind to calcareous corpuscle (CC) through its adhesive property and participate in crucial protein-protein interactions, thus contributing to the creation of a symbiotic interactome network...
September 20, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28928239/the-rna-editing-enzyme-adar-promotes-lung-adenocarcinoma-migration-and-invasion-by-stabilizing-fak
#15
Elianna M Amin, Yuan Liu, Su Deng, Kay See Tan, Neel Chudgar, Marty W Mayo, Francisco Sanchez-Vega, Prasad S Adusumilli, Nikolaus Schultz, David R Jones
Large-scale, genome-wide studies report that RNA binding proteins are altered in cancers, but it is unclear how these proteins control tumor progression. We found that the RNA-editing protein ADAR (adenosine deaminase acting on double-stranded RNA) acted as a facilitator of lung adenocarcinoma (LUAD) progression through its ability to stabilize transcripts encoding focal adhesion kinase (FAK). In samples from 802 stage I LUAD patients, increased abundance of ADAR at both the mRNA and protein level correlated with tumor recurrence...
September 19, 2017: Science Signaling
https://www.readbyqxmd.com/read/28928128/targeting-a-single-alternative-polyadenylation-site-coordinately-blocks-expression-of-androgen-receptor-mrna-splice-variants-in-prostate-cancer
#16
Jamie L Van Etten, Michael Nyquist, Yingming Li, Rendong Yang, Yeung Ho, Rachel Johnson, Olivia Ondigi, Daniel F Voytas, Christine Henzler, Scott M Dehm
Prostate cancer is the second leading cause of male cancer deaths due to disease progression to castration-resistant prostate cancer (CRPC). Androgen receptor (AR) splice variants including AR-V7 function as constitutively active transcription factors in CRPC cells, thereby promoting resistance to AR-targeted therapies. To date, there are no AR variant-specific treatments for CRPC. Here we report that the splicing of AR variants AR-V7 as well as AR-V1 and AR-V9 is regulated coordinately by a single polyadenylation signal in AR intron 3...
August 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28927745/apolipoprotein-m-gene-single-nucleotide-polymorphisms-discovery-in-patients-with-chronic-obstructive-pulmonary-disease-and-determined-by-the-base-quenched-probe-technique
#17
Yang Yu, Jun Zhang, Yingying Qiao, Lili Pan, Juzhang Li, Huihui Mao, Jiang Wei, Xiaoying Zhang, Ning Xu, Guanghua Luo
BACKGROUND: It has been reported increased serum apoM levels seen in the patients suffered from obstructive sleep apnoea and chronic obstructive pulmonary diseases. In the present, we further examine the prevalence of apoM gene SNPs in COPD patients. And a new method base-quenched probe technique is established. METHODS: In the present study, we first used the Roche 454 GS Junior high-throughput sequencer to analyze 6 COPD samples and 6 control samples, in these samples we found 3 interesting SNPs (rs805264, rs707922 and rs707921) and then we designed primers and probes to establish a simple and quick screening method that is a base-quench probe technique and the genotype was confirmed by melting curves...
September 16, 2017: Gene
https://www.readbyqxmd.com/read/28927534/alternative-rna-splicing-and-gastric-cancer
#18
REVIEW
Ying Li, Yuan Yuan
Alternative splicing (AS) linked to diseases, especially to tumors. Recently, more and more studies focused on the relationship between AS and gastric cancer (GC). This review surveyed the hot topic from four aspects: First, the common types of AS in cancer, including exon skipping, intron retention, mutually exclusive exon, alternative 5 ' or 3' splice site, alternative first or last exon and alternative 3' untranslated regions. Second, basic mechanisms of AS and its relationship with cancer. RNA splicing in eukaryotes follows the GT-AG rule by both cis-elements and trans-acting factors regulatory...
July 2017: Mutation Research
https://www.readbyqxmd.com/read/28926398/association-of-a-3-untranslated-region-polymorphism-in-pcsk9-with-hiv-viral-load-and-cd4-levels-in-hiv-hepatitis-c-virus-co-infected-women
#19
Mark H Kuniholm, Hua Liang, Kathryn Anastos, Deborah Gustafson, Seble Kassaye, Marek Nowicki, Beverly E Sha, Emilia J Pawlowski, Stephen J Gange, Bradley E Aouizerat, Tatiana Pushkarsky, Michael I Bukrinsky, Vinayaka R Prasad
OBJECTIVE: To assess variation in genes that regulate cholesterol metabolism in relation to the natural history of HIV infection. DESIGN: Cross-sectional and longitudinal analysis of the Women's Interagency HIV Study (WIHS). METHODS: We examined 2,050 single nucleotide polymorphisms (SNPs) in 19 genes known to regulate cholesterol metabolism in relation to HIV viral load and CD4 T cell levels in a multiracial cohort of 1,066 antiretroviral therapy (ART) naïve women...
September 18, 2017: AIDS
https://www.readbyqxmd.com/read/28926086/common-variants-in-dlg1-locus-are-associated-with-non-syndromic-cleft-lip-with-or-without-cleft-palate
#20
Adrianna Mostowska, Agnieszka Gaczkowska, Kacper Żukowski, Kerstin U Ludwig, Kamil K Hozyasz, Piotr Wójcicki, Elizabeth Mangold, Anne C Böhmer, Stefanie Heilmann-Heimbach, Michael Knapp, Małgorzata Zadurska, Barbara Biedziak, Margareta Budner, Agnieszka Lasota, Agata Daktera-Micker, Paweł P Jagodziński
Non-syndromic cleft lip with or without cleft palate (nsCL/P) is a common craniofacial anomaly with a complex and heterogeneous etiology. Knowledge regarding specific genetic factors underlying this birth defect is still not well understood. Therefore, we conducted an independent replication analysis for the top-associated variants located within the DLG1 locus at chromosome 3q29, which was identified as a novel cleft-susceptibility locus in our genome-wide association study (GWAS). Mega-analysis of the pooled individual data from the GWAS and replication study confirmed that common DLG1 variants are associated with the risk of nsCL/P...
September 19, 2017: Clinical Genetics
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