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Group II intron

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https://www.readbyqxmd.com/read/29738868/bsmi-single-nucleotide-polymorphism-in-vitamin-d-receptor-gene-is-associated-with-decreased-circulatory-levels-of-serum-25-hydroxyvitamin-d-among-micro-and-macrovascular-complications-of-type-2-diabetes-mellitus
#1
Krishnamoorthy Ezhilarasi, Umapathy Dhamodharan, Viswanathan Vijay
Vitamin D Receptor (VDR) gene single nucleotide polymorphism (SNP) in the intron 8 is a well characterized SNP which has previously been linked to various diseases including Type 2 Diabetes Mellitus (T2DM). However, the association of this SNP with micro and macrovascular complications of T2DM remains poorly studied. Hence, the present study was designed to investigate the association of VDR gene SNP with complications of T2DM (disease phenotype) and correlated it with the serum levels of (25[OH]D) (intermediate phenotype) along with other clinical risk factors of T2DM...
May 5, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29709636/genomic-structure-expression-pattern-and-polymorphisms-of-gilt-in-golden-pompano-trachinotus-ovatus-linnaeus-1758
#2
Kecheng Zhu, Wenbo Yu, Huayang Guo, Nan Zhang, Liang Guo, Baosuo Liu, Shigui Jiang, Dianchang Zhang
The interferon-g-inducible lysosomal thiol reductase (GILT) plays a significant character in the processing and presentation of MHC class II restricted antigen (Ag) by catalyzing disulfide bond reduction in mammals. To explore the function of GILT in the immune system of fish, we cloned a GILT gene homologue from Trachinotus ovatus, the full-length cDNA of GILT, which consisted of 2, 747 bp with a 771 bp open reading frame, encoding a protein of 256 amino acids. Moreover, similar to other species GILT gene, 7 exons and 6 introns were identified in T...
April 27, 2018: Gene
https://www.readbyqxmd.com/read/29703781/simultaneous-sequencing-of-coding-and-non-coding-rna-reveals-a-human-transcriptome-dominated-by-a-small-number-of-highly-expressed-non-coding-genes
#3
Vincent Boivin, Gabrielle Deschamps-Francoeur, Sonia Couture, Ryan Nottingham, Philia Bouchard-Bourelle, Alan M Lambowitz, Michelle S Scott, Sherif Abou Elela
Comparing the abundance of one RNA molecule to another is crucial for understanding cellular functions but most sequencing techniques can target only specific subsets of RNA. In this study, we used a new fragmented ribodepleted TGIRT sequencing method that employs a thermostable group II intron reverse transcriptase (TGIRT) to generate a portrait of the human transcriptome depicting the quantitative relationship of all classes of non-ribosomal RNA longer than sixty nucleotides. Comparison between different sequencing methods indicated that FRT is more accurate in ranking both mRNA and non-coding RNA than viral reverse transcriptase-based sequencing methods even those that specifically target these species...
April 27, 2018: RNA
https://www.readbyqxmd.com/read/29696033/redidb-3-0-a-comprehensive-collection-of-rna-editing-events-in-plant-organellar-genomes
#4
Claudio Lo Giudice, Graziano Pesole, Ernesto Picardi
RNA editing is an important epigenetic mechanism by which genome-encoded transcripts are modified by substitutions, insertions and/or deletions. It was first discovered in kinetoplastid protozoa followed by its reporting in a wide range of organisms. In plants, RNA editing occurs mostly by cytidine (C) to uridine (U) conversion in translated regions of organelle mRNAs and tends to modify affected codons restoring evolutionary conserved aminoacid residues. RNA editing has also been described in non-protein coding regions such as group II introns and structural RNAs...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29678149/comparative-mitochondrial-genomics-of-cryptophyte-algae-gene-shuffling-and-dynamic-mobile-genetic-elements
#5
Jong Im Kim, Hwan Su Yoon, Gangman Yi, Woongghi Shin, John M Archibald
BACKGROUND: Cryptophytes are an ecologically important group of algae comprised of phototrophic, heterotrophic and osmotrophic species. This lineage is of great interest to evolutionary biologists because their plastids are of red algal secondary endosymbiotic origin. Cryptophytes have a clear phylogenetic affinity to heterotrophic eukaryotes and possess four genomes: host-derived nuclear and mitochondrial genomes, and plastid and nucleomorph genomes of endosymbiotic origin. RESULTS: To gain insight into cryptophyte mitochondrial genome evolution, we sequenced the mitochondrial DNAs of five species and performed a comparative analysis of seven genomes from the following cryptophyte genera: Chroomonas, Cryptomonas, Hemiselmis, Proteomonas, Rhodomonas, Storeatula and Teleaulax...
April 20, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29670598/contribution-of-mobile-group-ii-introns-to-sinorhizobium-meliloti-genome-evolution
#6
REVIEW
Nicolás Toro, Francisco Martínez-Abarca, María D Molina-Sánchez, Fernando M García-Rodríguez, Rafael Nisa-Martínez
Mobile group II introns are ribozymes and retroelements that probably originate from bacteria. Sinorhizobium meliloti , the nitrogen-fixing endosymbiont of legumes of genus Medicago , harbors a large number of these retroelements. One of these elements, RmInt1, has been particularly successful at colonizing this multipartite genome. Many studies have improved our understanding of RmInt1 and phylogenetically related group II introns, their mobility mechanisms, spread and dynamics within S. meliloti and closely related species...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29660854/the-butanol-producing-microbe-clostridium-beijerinckii-ncimb-14988-manipulated-using-forward-and-reverse-genetic-tools
#7
Gareth T Little, Benjamin J Willson, John T Heap, Klaus Winzer, Nigel P Minton
The solventogenic anaerobe Clostridium beijerinckii has potential for use in the sustainable bioconversion of plant-derived carbohydrates into solvents, such as butanol or acetone. However, relatively few strains have been extensively characterised either at the genomic level or through exemplification of a complete genetic toolkit. To remedy this situation, a new strain of C. beijerinckii, NCIMB 14988, was selected from amongst a total of 55 new clostridial isolates capable of growth on hexose and pentose sugars...
April 16, 2018: Biotechnology Journal
https://www.readbyqxmd.com/read/29596349/genome-wide-analyses-of-the-nac-transcription-factor-gene-family-in-pepper-capsicum-annuum-l-chromosome-location-phylogeny-structure-expression-patterns-cis-elements-in-the-promoter-and-interaction-network
#8
Weiping Diao, John C Snyder, Shubin Wang, Jinbing Liu, Baogui Pan, Guangjun Guo, Wei Ge, Mohammad Hasan Salman Ali Dawood
The NAM, ATAF1/2, and CUC2 (NAC) transcription factors form a large plant-specific gene family, which is involved in the regulation of tissue development in response to biotic and abiotic stress. To date, there have been no comprehensive studies investigating chromosomal location, gene structure, gene phylogeny, conserved motifs, or gene expression of NAC in pepper ( Capsicum annuum L.). The recent release of the complete genome sequence of pepper allowed us to perform a genome-wide investigation of Capsicum annuum L...
March 29, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29580682/dose-dependent-prevention-of-metabolic-and-neurologic-disease-in-murine-mps-ii-by-zfn-mediated-in-vivo-genome-editing
#9
Kanut Laoharawee, Russell C DeKelver, Kelly M Podetz-Pedersen, Michelle Rohde, Scott Sproul, Hoang-Oanh Nguyen, Tam Nguyen, Susan J St Martin, Li Ou, Susan Tom, Robert Radeke, Kathleen E Meyer, Michael C Holmes, Chester B Whitley, Thomas Wechsler, R Scott McIvor
Mucopolysaccharidosis type II (MPS II) is an X-linked recessive lysosomal disorder caused by deficiency of iduronate 2-sulfatase (IDS), leading to accumulation of glycosaminoglycans (GAGs) in tissues of affected individuals, progressive disease, and shortened lifespan. Currently available enzyme replacement therapy (ERT) requires lifelong infusions and does not provide neurologic benefit. We utilized a zinc finger nuclease (ZFN)-targeting system to mediate genome editing for insertion of the human IDS (hIDS) coding sequence into a "safe harbor" site, intron 1 of the albumin locus in hepatocytes of an MPS II mouse model...
March 10, 2018: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/29575277/association-study-of-functional-polymorphisms-of-dopaminergic-pathway-in-epilepsy-related-factors-of-temporal-lobe-epilepsy-in-brazilian-population
#10
Juliana A Alcantara, Silvia Vincentiisa, Daniel S Kerr, Bernardo Dos Santos, Ruda Alessi, Helio van der Linden, Tiffany Chaim, Maurício H Serpa, Geraldo Busatto, Wagner F Gattaz, Renata Demarque, Kette Dr Valente
BACKGROUND: There is scarce data about the role of neurotransmission modulated by dopamine (DA) in epilepsy, especially temporal lobe epilepsy. This is the first study that aimed to analyze the dopaminergic polymorphisms in an etiologically homogeneous group of patients with temporal lobe epilepsy determined by hippocampal sclerosis (TLE-HS). Selected polymorphisms were: (i) the most expressed receptors in the limbic system D2-like (DRD2/ANKK1 TAQ-1A, D4_VNTR, and D4_rs1800955); (ii) the dopamine transporter DAT - 3 'untranslated region (3'UTR) and Intron 8; (iii) two degrading enzymes regulating the synaptic activity - the main metabolizer of dopamine Catechol-O-methyltransferase (COMT) and monoamine oxidase A (MAOA)...
March 25, 2018: European Journal of Neurology: the Official Journal of the European Federation of Neurological Societies
https://www.readbyqxmd.com/read/29546998/unexpected-diversity-in-the-mobilome-of-a-pseudomonas-aeruginosa-strain-isolated-from-a-dental-unit-waterline-revealed-by-smrt-sequencing
#11
Antony T Vincent, Steve J Charette, Jean Barbeau
The Gram-negative bacterium Pseudomonas aeruginosa is found in several habitats, both natural and human-made, and is particularly known for its recurrent presence as a pathogen in the lungs of patients suffering from cystic fibrosis, a genetic disease. Given its clinical importance, several major studies have investigated the genomic adaptation of P. aeruginosa in lungs and its transition as acute infections become chronic. However, our knowledge about the diversity and adaptation of the P. aeruginosa genome to non-clinical environments is still fragmentary, in part due to the lack of accurate reference genomes of strains from the numerous environments colonized by the bacterium...
March 16, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29527965/comparative-analysis-of-the-mitochondrial-genomes-of-six-newly-sequenced-diatoms-reveals-group-ii-introns-in-the-barcoding-region-of-cox1
#12
Cloe S Pogoda, Kyle G Keepers, Sarah E Hamsher, Joshua G Stepanek, Nolan C Kane, J Patrick Kociolek
Diatoms are the most diverse lineage of algae and at the base of most aquatic food webs, but only 11 of their mitochondrial genomes have been described. Herein, we present the mitochondrial genomes of six diatom species, including: Melosira undulata, Nitzschia alba, Surirella sp., Entomoneis sp., Halamphora coffeaeformis, and Halamphora calidilacuna. Comparison of these six genomes to the 11 currently published diatom mitochondrial genomes revealed a novel ubiquitous feature block consisting of tatC-orf157-rps11...
March 11, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29505122/an-evolutionarily-conserved-p-subfamily-pentatricopeptide-repeat-protein-is-required-to-splice-the-plastid-ndha-transcript-in-the-moss-physcomitrella-patens-and-arabidopsis-thaliana
#13
Ayaka Ito, Chieko Sugita, Mizuho Ichinose, Yoshinobu Kato, Hiroshi Yamamoto, Toshiharu Shikanai, Mamoru Sugita
Pentatricopeptide repeat (PPR) proteins are known to play important roles in post-transcriptional regulation in plant organelles. However, the function of the majority of PPR proteins remains unknown. To examine their functions, Physcomitrella patens PpPPR_66 knockout (KO) mutants were generated and characterized. The KO mosses exhibited a wild-type-like growth phenotype but showed aberrant chlorophyll fluorescence due to defects in chloroplast NADH dehydrogenase-like (NDH) activity. Immunoblot analysis suggested that disruption of PpPPR_66 led to a complete loss of the chloroplast NDH complex...
May 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29497064/author-correction-facile-single-stranded-dna-sequencing-of-human-plasma-dna-via-thermostable-group-ii-intron-reverse-transcriptase-template-switching
#14
Douglas C Wu, Alan M Lambowitz
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
March 1, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29495422/a-genome-wide-association-study-of-idiopathic-dilated-cardiomyopathy-in-african-americans
#15
Huichun Xu, Gerald W Dorn, Amol Shetty, Ankita Parihar, Tushar Dave, Shawn W Robinson, Stephen S Gottlieb, Mark P Donahue, Gordon F Tomaselli, William E Kraus, Braxton D Mitchell, Stephen B Liggett
Idiopathic dilated cardiomyopathy (IDC) is the most common form of non-ischemic chronic heart failure. Despite the higher prevalence of IDC in African Americans, the genetics of IDC have been relatively understudied in this ethnic group. We performed a genome-wide association study to identify susceptibility genes for IDC in African Americans recruited from five sites in the U.S. (662 unrelated cases and 1167 controls). The heritability of IDC was calculated to be 33% (95% confidence interval: 19-47%; p = 6...
February 26, 2018: Journal of Personalized Medicine
https://www.readbyqxmd.com/read/29467729/polymorphism-in-mitochondrial-group-i-introns-among-cryptococcus-neoformans-and-cryptococcus-gattii-genotypes-and-its-association-with-drug-susceptibility
#16
Felipe E E S Gomes, Thales D Arantes, José A L Fernandes, Leonardo C Ferreira, Héctor Romero, Sandra M G Bosco, Maria T B Oliveira, Gilda M B Del Negro, Raquel C Theodoro
Cryptococcosis, one of the most important systemic mycosis in the world, is caused by different genotypes of Cryptococcus neoformans and Cryptococcus gattii , which differ in their ecology, epidemiology, and antifungal susceptibility. Therefore, the search for new molecular markers for genotyping, pathogenicity and drug susceptibility is necessary. Group I introns fulfill the requisites for such task because (i) they are polymorphic sequences; (ii) their self-splicing is inhibited by some drugs; and (iii) their correct splicing under parasitic conditions is indispensable for pathogen survival...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29461868/genome-wide-identification-characterization-and-transcriptional-analysis-of-the-metacaspase-gene-family-in-cucumber-cucumis-sativus
#17
Yong Zhou, Lifang Hu, Lunwei Jiang, Shiqiang Liu
Metacaspase (MC), a family of caspase-like proteins, plays vital roles in regulating programmed cell death (PCD) during development and in response to stresses in plants. In this study, five MC genes (designated as CsMC1 to CsMC5) were identified in the cucumber (Cucumis sativus) genome. Sequence analysis revealed that CsMC1-CsMC3 belong to type I MC proteins, while CsMC4 and CsMC5 are type II MC proteins. Phylogenetic tree and conserved motif analysis of MC proteins indicated that these proteins can be classified into two groups, which are correlated with the types of these MC proteins...
March 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29418041/intrageneric-variability-between-the-chloroplast-genomes-of-trachelomonas-grandis-and-trachelomonas-volvocina-and-phylogenomic-analysis-of-phototrophic-euglenoids
#18
Nadja Dabbagh, Angelika Preisfeld
The latest studies of chloroplast genomes of phototrophic euglenoids yielded different results according to intrageneric variability such as cluster arrangement or diversity of introns. Although the genera Euglena and Monomorphina in those studies show high syntenic arrangements at the intrageneric level, the two investigated Eutreptiella species comprise low synteny. Furthermore Trachelomonas volvocina show low synteny to the chloroplast genomes of the sister genera Monomorphina aenigmatica, M. parapyrum, Cryptoglena skujae, Euglenaria anabaena, Strombomonas acuminata, all of which were highly syntenic...
February 8, 2018: Journal of Eukaryotic Microbiology
https://www.readbyqxmd.com/read/29416663/genetic-variation-in-cdh13-gene-was-associated-with-non-small-cell-lung-cancer-nsclc-a-population-based-case-control-study
#19
Yingfu Li, Chuanyin Li, Qianli Ma, Yu Zhang, Yueting Yao, Shuyuan Liu, Xinwen Zhang, Chao Hong, Fang Tan, Li Shi, Yufeng Yao
Cadherin 13 (CDH13, T-cadherin, H-cadherin) has been identified as an anti-oncogene in various cancers. Recent studies have reported that downregulation of H-cadherin in cancers is associated with CDH13 promoter hypermethylation, which could be affected by the single nucleotide polymorphisms (SNPs) near CpG sites in the CDH13 promoter. In the current study, we investigated and analyzed the association of seven SNPs (rs11646213, rs12596316, rs3865188, rs12444338, rs4783244, rs12051272 and rs7195409) with non-small cell lung cancer (NSCLC) using logistic regression analysis...
January 2, 2018: Oncotarget
https://www.readbyqxmd.com/read/29377672/molecular-mechanism-and-evolution-of-nuclear-pre-mrna-and-group-ii-intron-splicing-insights-from-cryo-electron-microscopy-structures
#20
Wojciech P Galej, Navtej Toor, Andrew J Newman, Kiyoshi Nagai
Nuclear pre-mRNA splicing and group II intron self-splicing both proceed by two-step transesterification reactions via a lariat intron intermediate. Recently determined cryo-electron microscopy (cryo-EM) structures of catalytically active spliceosomes revealed the RNA-based catalytic core and showed how pre-mRNA substrates and reaction products are positioned in the active site. These findings highlight a strong structural similarity to the group II intron active site, strengthening the notion that group II introns and spliceosomes evolved from a common ancestor...
April 25, 2018: Chemical Reviews
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