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https://www.readbyqxmd.com/read/29793152/identification-of-seven-polyamine-oxidase-genes-in-tomato-solanum-lycopersicum-l-and-their-expression-profiles-under-physiological-and-various-stress-conditions
#1
Yanwei Hao, Binbin Huang, Dongyu Jia, Taylor Mann, Xinyi Jiang, Yuxing Qiu, Masaru Niitsu, Thomas Berberich, Tomonobu Kusano, Taibo Liu
Polyamines (PAs) are implicated in developmental processes and stress responses of plants. Polyamine oxidases (PAOs), flavin adenine dinucleotide-dependent enzymes that function in PA catabolism, play a critical role. Even though PAO gene families of Arabidopsis and rice have been intensely characterized and their expression in response to developmental and environmental changes has been investigated, little is known about PAOs in tomato (Solanum lycopersicum). We found seven PAO genes in S. lycopersicum and named them SlPAO1∼7...
May 15, 2018: Journal of Plant Physiology
https://www.readbyqxmd.com/read/29793048/dna-methylation-differences-at-the-glucocorticoid-receptor-gene-in-depression-are-related-to-functional-alterations-in-hypothalamic-pituitary-adrenal-axis-activity-and-to-early-life-emotional-abuse
#2
Chloё Farrell, Kelly Doolin, Niamh O' Leary, Chaitra Jairaj, Darren Roddy, Leonardo Tozzi, Derek Morris, Andrew Harkin, Thomas Frodl, Zsófia Nemoda, Moshe Szyf, Linda Booij, Veronica O'Keane
Depression is associated with alterations in hypothalamic-pituitary-adrenal (HPA) axis activity. A proposed mechanism to explain these alterations are changes in DNA methylation levels, secondary to early life adversity (ELA), at stress-related genes. Two gene regions that have been implicated in the literature, the glucocorticoid receptor gene (NR3C1) exon 1F and the FKBP5 gene intron 7 were examined in 67 individuals (33 depressed patients and 34 controls). We investigated whether cortisol concentrations, evaluated in 25 depressed patients and 20 controls, and measures of ELA were associated with the degree of methylation at these candidate gene regions...
May 8, 2018: Psychiatry Research
https://www.readbyqxmd.com/read/29792951/an-analysis-of-variability-in-genome-organisation-of-intracellular-calcium-release-channels-across-insect-orders
#3
Bartlomiej J Troczka, Ewan Richardson, Rafael Homem, T G Emyr Davies
Using publicly available genomic data, combined with RT-PCR validation, we explore structural genomic variation for two major ion channels across insect classes. We have manually curated Ryanodine receptor (RyR) and inositol 1,4,5-trisphosphate receptor (IP3 R) ORFs and their corresponding genomic structures from 26 different insects covering major insect orders. We found that, despite high protein identity for both RyRs (>75%) and IP3 Rs (~67%), the overall complexity of the gene structure varies greatly between different insect orders with the simplest genes (fewest introns) found in Diptera and the most complex in Lepidoptera...
May 21, 2018: Gene
https://www.readbyqxmd.com/read/29792936/efficient-detection-of-copy-number-mutations-in-pms2-exons-with-close-homologs-detection-of-copy-number-variants-in-3-pms2-exons
#4
Daniel S Herman, Christina Smith, Chang Liu, Cecily P Vaughn, Selvi Palaniappan, Colin C Pritchard, Brian H Shirts
Detection of 3' PMS2 copy number mutations that cause Lynch syndrome is difficult, because of highly homologous pseudogenes. To improve the accuracy and efficiency of clinical screening for these mutations, we developed a new method to analyze standard capture-based, next-generation sequencing data to identify deletions and duplications in PMS2 exons 9 to 15. The approach captures sequence reads using PMS2 targets, maps sequences randomly amongst regions with equal mapping quality, counts reads aligned to homologous exons and introns, and flags read count ratios outside of empirically derived reference ranges...
May 21, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29790987/structural-accommodations-accompanying-splicing-of-a-group-ii-intron-rnp
#5
Xiaolong Dong, Srivathsan Ranganathan, Guosheng Qu, Carol Lyn Piazza, Marlene Belfort
Group II introns, the putative progenitors of spliceosomal introns and retrotransposons, are ribozymes that are capable of self-splicing and DNA invasion. In the cell, group II introns form ribonucleoprotein (RNP) complexes with an intron-encoded protein, which is essential to folding, splicing and retromobility of the intron. To understand the structural accommodations underlying splicing, in preparation for retromobility, we probed the endogenously expressed Lactococcus lactis Ll.LtrB group II intron RNP using SHAPE...
May 22, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29790873/diversity-of-genetic-events-associated-with-mlh1-promoter-methylation-in-lynch-syndrome-families-with-heritable-constitutional-epimutation
#6
Julie Leclerc, Cathy Flament, Tonio Lovecchio, Lucie Delattre, Emilie Ait Yahya, Stéphanie Baert-Desurmont, Nelly Burnichon, Myriam Bronner, Odile Cabaret, Sophie Lejeune, Rosine Guimbaud, Gilles Morin, Jacques Mauillon, Philippe Jonveaux, Pierre Laurent-Puig, Thierry Frébourg, Nicole Porchet, Marie-Pierre Buisine
PurposeConstitutional epimutations are an alternative to genetic mutations in the etiology of genetic diseases. Some of these epimutations, termed secondary, correspond to the epigenetic effects of cis-acting genetic defects transmitted to the offspring following a Mendelian inheritance pattern. In Lynch syndrome, a few families with such apparently heritable MLH1 epimutations have been reported so far.MethodsWe designed a long-range polymerase chain reaction next-generation sequencing strategy to screen MLH1 entire gene and applied it to 4 French families with heritable epimutations and 10 additional patients with no proven transmission of their epimutations...
April 12, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29789962/genome-based-identification-and-analysis-of-ionotropic-receptors-in-spodoptera-litura
#7
Jia-Ying Zhu, Zhi-Wen Xu, Xin-Min Zhang, Nai-Yong Liu
The ability to sense and recognize various classes of compounds is of particular importance for survival and reproduction of insects. Ionotropic receptor (IR), a sub-family of the ionotropic glutamate receptor family, has been identified as one of crucial chemoreceptor super-families, which mediates the sensing of odors and/or tastants, and serves as non-chemosensory functions. Yet, little is known about IR characteristics, evolution, and functions in Lepidoptera. Here, we identify the IR gene repertoire from a destructive polyphagous pest, Spodoptera litura...
May 22, 2018: Die Naturwissenschaften
https://www.readbyqxmd.com/read/29789581/intron-retention-and-nuclear-loss-of-sfpq-are-molecular-hallmarks-of-als
#8
Raphaelle Luisier, Giulia E Tyzack, Claire E Hall, Jamie S Mitchell, Helen Devine, Doaa M Taha, Bilal Malik, Ione Meyer, Linda Greensmith, Jia Newcombe, Jernej Ule, Nicholas M Luscombe, Rickie Patani
Mutations causing amyotrophic lateral sclerosis (ALS) strongly implicate ubiquitously expressed regulators of RNA processing. To understand the molecular impact of ALS-causing mutations on neuronal development and disease, we analysed transcriptomes during in vitro differentiation of motor neurons (MNs) from human control and patient-specific VCP mutant induced-pluripotent stem cells (iPSCs). We identify increased intron retention (IR) as a dominant feature of the splicing programme during early neural differentiation...
May 22, 2018: Nature Communications
https://www.readbyqxmd.com/read/29788499/group-i-introns-are-widespread-in-archaea
#9
Eric P Nawrocki, Thomas A Jones, Sean R Eddy
Group I catalytic introns have been found in bacterial, viral, organellar, and some eukaryotic genomes, but not in archaea. All known archaeal introns are bulge-helix-bulge (BHB) introns, with the exception of a few group II introns. It has been proposed that BHB introns arose from extinct group I intron ancestors, much like eukaryotic spliceosomal introns are thought to have descended from group II introns. However, group I introns have little sequence conservation, making them difficult to detect with standard sequence similarity searches...
May 18, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29787928/principle-of-k-na-selectivity-in-the-active-site-of-group-ii-intron-at-various-stages-of-self-splicing-pathway
#10
Abhishek Kumar, Priyadarshi Satpati
Group II introns are ribozymes which can catalyze its own splicing and relegate itself. They share common structural features and are evolutionarily related to eukaryotic spliceosome. Hence, group II introns are an excellent model system for understanding the mechanism of RNA-splicing in gene expression. Recent advancement of structural studies has provided x-ray structures of group II intron at different stages (Pre-hydrolytic, post-hydrolytic and free intron) of splicing pathway and revealed heteronuclear metal ion cluster (two potassium; K1 and K2, two magnesium; M1 and M2) in the active site as common structural feature of group II introns...
May 14, 2018: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29787827/genetic-variants-of-fatty-acid-elongase-6-in-chinese-holstein-cow
#11
Si Chen, Menglin Chai, Chen Tian, Yuzhuang Li, Tian Deng, Hui Wu, Xiaolin Liu
In the dairy industry, genetic variants have contributed to the improvement of milk production traits. Fatty acid elongase 6 (ELOVL6), which elongates saturated fatty acids (SFAs) and monounsaturated fatty acids (MUFAs), plays a distinct role in the balance of long-chain fatty acids composition in animals. ELOVL6 catalyzes the elongation of palmitic acids (C16:0) which is the most common saturated fatty acid found in animals and also an essential precursor to synthesize other long-chain fatty acids. However, the genetic variant research of bovine ELOVL6 on milk quality traits is still unknown...
May 19, 2018: Gene
https://www.readbyqxmd.com/read/29785901/association-of-snp-and-str-polymorphisms-of-insulin-like-growth-factor-2-receptor-igf2r-gene-with-milk-traits-in-holstein-friesian-cows
#12
Marta Dux, Magdalena Muranowicz, Eulalia Siadkowska, Dagmara Robakowska-Hyżorek, Krzysztof Flisikowski, Emilia Bagnicka, Lech Zwierzchowski
The objective of the study reported in this Research Communication was to investigate the association of polymorphisms in the insulin-like growth factor receptor 2 (IGF2R) gene with milk traits in 283 Polish Holstein-Friesian (PHF) cows from the IGAB PAS farm in Jastrzębiec. IGF2R regulates the availability of biologically active IGF2 which is considered as a genetic marker for milk or meat production in farm animals. Two novel genetic polymorphisms were identified in the bovine IGF2R gene: a polymorphic TG-repeat in intron 23 (g...
May 2018: Journal of Dairy Research
https://www.readbyqxmd.com/read/29784571/familial-hypercholesterolemia-with-extensive-coronary-artery-disease-and-tuberous-and-tendinous-xanthomas-a-case-report-and-mutation-analysis
#13
Deniz Agirbasli, Tommy Hyatt, Mehmet Agirbasli
This is a case report of a 38-year-old Syrian refugee male with early-onset extensive atherosclerosis. The physical and laboratory examination were remarkable with severe xanthomas in the upper and lower extremities and with low-density lipoprotein cholesterol (LDL-C) 417 mg/dL, total cholesterol 495 mg/dL, high-density lipoprotein cholesterol 30 mg/dL, and triglycerides 242 mg/dL. LDL-C level responded poorly to the high-dose statin treatment. The genetic analysis indicated that the patient had a large homozygous deletion in LDL receptor gene including the exons 7-14...
April 26, 2018: Journal of Clinical Lipidology
https://www.readbyqxmd.com/read/29782946/delivery-of-the-improved-bmp-2-advanced-plasmid-dna-within-a-gene-activated-scaffold-accelerates-mesenchymal-stem-cell-osteogenesis-and-critical-size-defect-repair
#14
Rosanne M Raftery, Irene Mencía-Castaño, Simon Sperger, Gang Chen, Brenton Cavanagh, Georg Feichtinger, Heinz Redl, Ara Hacobian, Fergal J O'Brien
Gene-activated scaffolds have been shown to induce controlled, sustained release of functional transgene both in vitro and in vivo. Bone morphogenetic proteins (BMPs) are potent mediators of osteogenesis however we found that the delivery of plasmid BMP-2 (pBMP-2) alone was not sufficient to enhance bone formation. Therefore, the aim of this study was to assess if the use of a series of modified BMP-2 plasmids could enhance the functionality of a pBMP-2 gene-activated scaffold and ultimately improve bone regeneration when implanted into a critical sized bone defect in vivo...
May 18, 2018: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/29782841/alternative-splicing-of-gnrh2-and-gnrh2-associated-peptide-plays-roles-in-gonadal-differentiation-of-the-rice-field-eel-monopterus-albus
#15
Ke Feng, Hongrui Luo, Mingxi Hou, Yongming Li, Ji Chen, Zuoyan Zhu, Wei Hu
The rice field eel, Monopterus albus, is a protogynous hermaphrodite fish, in which the gonads are initially female ovaries which then transform into male testes. The exact mechanisms governing sex reversal in the rice field eel are unknown. In this study, a novel alternative splicing variant of GnRH2 (GnRH2-SV), retaining the second intron, was discovered in the gonad of the rice field eel. Compared to GnRH2, GnRH2-SV may give rise to a novel truncated GnRH2-associated peptide (New GAP2). The normal transcript of GnRH2 was primarily expressed in the brain, and could also be detected in the liver, spleen, ovary, and testis...
May 18, 2018: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/29782529/molecular-effect-of-an-optn-common-variant-associated-to-paget-s-disease-of-bone
#16
Iris A L Silva, Natércia Conceição, Édith Gagnon, Jacques P Brown, M Leonor Cancela, Laëtitia Michou
Paget's disease of bone (PDB) is a chronic bone disorder and although genetic factors appear to play an important role in its pathogenesis, to date PDB causing mutations were identified only in the Sequestosome 1 (SQSTM1) gene at the PDB3 locus. PDB6 locus, also previously linked to PDB, contains several candidate genes for metabolic bone diseases. We focused our analysis in the most significantly associated variant with PDB, within the Optineurin (OPTN) gene, i.e. the common variant rs1561570. Although it was previously shown to be strongly associated with PDB in several populations, its contribution to PDB pathogenesis remains unclear...
2018: PloS One
https://www.readbyqxmd.com/read/29782346/claudins-and-nephrolithiasis
#17
Allein Plain, R Todd Alexander
PURPOSE OF REVIEW: The greatest risk factor for kidney stone formation is increased urinary calcium excretion. Most filtered calcium is reabsorbed from the proximal tubule and the thick ascending limb (TAL) of Henle's loop via a paracellular pathway. Claudins are tight junction proteins that confer the permeability properties of an epithelium. We review the contribution of renal claudins to nephron calcium permeability and how perturbations in these pathways cause alterations in tubular calcium transport, hypercalciuria, nephrocalcinosis, or nephrolithiasis...
May 17, 2018: Current Opinion in Nephrology and Hypertension
https://www.readbyqxmd.com/read/29782154/miclip-mapseq-a-substrate-identification-approach-for-radical-sam-rna-methylating-enzymes
#18
Vanja Stojković, Tongyue Chu, Gabriel Therizols, David E Weinberg, Danica Galonić Fujimori
Although present across bacteria, the large family of radical SAM RNA methylating enzymes is largely uncharacterized. Escherichia coli RlmN, the founding member of the family, methylates an adenosine in 23S rRNA and several tRNAs to yield 2-methyladenosine (m2A). However, varied RNA substrate specificity among RlmN enzymes, combined with the ability of certain family members to generate 8-methyladenosine (m8A), makes functional predictions across this family challenging. Here, we present a method for unbiased substrate identification that exploits highly efficient, mechanism-based crosslinking between the enzyme and its RNA substrates...
May 21, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29781058/hammondia-sp-oocysts-shed-by-a-brazilian-fox-lycalopex-vetulus-differ-from-hammondia-heydorni-and-hammondia-triffittae
#19
Luís F P Gondim, Rodrigo M Soares, Silvia C Osaki, Alessandra Snak, Laura R Grillo, Nelson L M Fernandes, Anderson L de Carvalho
A Brazilian fox (Lycalopex vetulus) was rescued from a highway, and 16 days after maintained in captivity, the fox shed oocysts with sizes compatible with Hammondia sp. and Neospora caninum. DNA extracted from oocysts were initially tested in two PCRs targeting the internal transcribed spacer 1 (ITS-1) of the rDNA of Hammondia heydorni and the Nc-5 gene of N. caninum. A 270-bp product was visualized in the PCR for H. heydorni. No amplification was observed for N. caninum PCR. Since ITS-1-based PCR is not sufficient to differentiate Hammondia species derived from canids, oocyst DNA was examined using multilocus sequence analysis of five genetic fragments [intron 1 of the alpha tubulin gene (intron 1), internal transcribed spaces 1 and 2 (ITS-1 and ITS-2) of the rDNA, 28S rRNA gene (D2/D3 domain), and heat shock protein 70 (Hsp70)]...
May 21, 2018: Parasitology Research
https://www.readbyqxmd.com/read/29780401/molecular-characterization-of-squamosa-promoter-binding-protein-like-spl-gene-family-in-betula-luminifera
#20
Xiu-Yun Li, Er-Pei Lin, Hua-Hong Huang, Ming-Yue Niu, Zai-Kang Tong, Jun-Hong Zhang
As a major family of plant-specific transcription factors, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE ( SPL ) genes play vital regulatory roles in plant growth, development and stress responses. In this study, 18 SPL genes were identified and cloned from Betula luminifera . Two zinc finger-like structures and a nuclear location signal (NLS) segments were existed in the SBP domains of all BlSPLs. Phylogenetic analysis showed that these genes were clustered into nine groups (group I-IX). The intron/exon structure and motif composition were highly conserved within the same group...
2018: Frontiers in Plant Science
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