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https://www.readbyqxmd.com/read/29161772/microarray-analysis-of-gene-expression-in-the-cyclooxygenase-cox-knockout-mice-a-connection-to-autism-spectrum-disorder
#1
Ravneet Rai-Bhogal, Eizaaz Ahmad, Hongyan Li, Dorota A Crawford
The cellular and molecular events that take place during brain development play an important role in governing function of the mature brain. Lipid signalling molecules such as prostaglandin E2 (PGE2 ) play an important role in healthy brain development. Abnormalities along the COX/PGE2 signalling pathway due to genetic or environmental causes have been linked to Autism Spectrum Disorders (ASDs). This study aims to evaluate the effect of altered COX/PGE2 signalling on development and function of the prenatal brain using male mice lacking cyclooxygenase-1 and -2 (COX-1(-/-) and COX-2(-/-) ) as potential model systems of ASD...
November 21, 2017: European Journal of Neuroscience
https://www.readbyqxmd.com/read/29161754/the-sorghum-bicolor-reference-genome-improved-assembly-gene-annotations-a-transcriptome-atlas-and-signatures-of-genome-organization
#2
Ryan F McCormick, Sandra K Truong, Avinash Sreedasyam, Jerry Jenkins, Shengqiang Shu, David Sims, Megan Kennedy, Mojgan Amirebrahimi, Brock D Weers, Brian McKinley, Ashley Mattison, Daryl T Morishige, Jane Grimwood, Jeremy Schmutz, John E Mullet
Sorghum bicolor is a drought tolerant C4 grass used for production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (~800 Mbp), diploid genetics, diverse germplasm, and colinearity with other C4 grass genomes. In this study, deep sequencing, genetic linkage analysis, and transcriptome data were used to produce and annotate a high-quality reference genome sequence. Reference genome sequence order was improved, 29.6 Mbp of additional sequence was incorporated, the number of genes annotated increased 24% to 34,211, average gene length and N50 increased, and error frequency was reduced 10-fold to 1 per 100 kbp...
November 21, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29161666/genetic-variants-and-acute-kidney-injury-a-review-of-the-literature
#3
REVIEW
Daniel B Larach, Milo C Engoren, Ellen M Schmidt, Michael Heung
PURPOSE: Limited data exists on potential genetic contributors to acute kidney injury. This review examines current knowledge of AKI genomics. MATERIALS AND METHODS: 32 studies were selected from PubMed and GWAS Catalog queries for original data studies of human AKI genetics. Hand search of references identified 3 additional manuscripts. RESULTS: 33 of 35 studies were hypothesis-driven investigations of candidate polymorphisms that either did not consistently replicate statistically significant findings, or obtained significant results only in few small-scale studies...
November 13, 2017: Journal of Critical Care
https://www.readbyqxmd.com/read/29161613/molecular-characterization-of-urothelial-carcinoma-of-the-bladder-and-upper-urinary-tract
#4
Ji Yun Lee, Kyung Kim, Hyun Hwan Sung, Hwang Gyun Jeon, Byong Chang Jeong, Seong Il Seo, Seong Soo Jeon, Hyun Moo Lee, Han-Yong Choi, Ghee-Young Kwon, Kyoung-Mee Kim, Jeeyun Lee, Ho Yeong Lim, Se Hoon Park
PURPOSE: A better understanding of the molecular basis of urothelial carcinoma (UC) is needed to refine the clinical decision-making process. METHODS AND MATERIALS: We performed next-generation sequencing to investigate the mutational and transcriptional profiles of commonly mutated genes in UC using Ampliseq v2. Copy number variations (CNVs) were detected with nCounter assay. Genetic alterations between upper tract UC (UTUC) and urinary bladder UC (UBUC) were compared...
November 18, 2017: Translational Oncology
https://www.readbyqxmd.com/read/29161494/species-of-sand-flies-diptera-psychodidae-collected-from-natural-reserves-in-the-pacific-and-darien-regions-of-colombia
#5
Rafael J Vivero, María Angélica Contreras, Juan D Suaza, Iván D Vélez, Charles Porter, Sandra Uribe
INTRODUCTION: The departments of Chocó and Antioquia in Colombia show climatic and vegetation conditions favoring the establishment of vector species of the genus Lutzomyia and the transmission of Leishmania spp. to human populations entering conserved forest environments. OBJECTIVE: To report the species of Phlebotomine sandflies present in three natural reserves in the Darien and Pacific regions of Colombia. MATERIALS AND METHODS: Sand flies were collected specifically in the natural reserves El Aguacate (Acandí, Chocó), Nabugá (Bahía Solano, Chocó) and Tulenapa (Carepa, Antioquia)...
March 29, 2017: Biomédica: Revista del Instituto Nacional de Salud
https://www.readbyqxmd.com/read/29161441/contributions-of-function-altering-variants-in-genes-implicated-in-pubertal-timing-and-body-mass-for-self-limited-delayed-puberty
#6
Sasha R Howard, Leonardo Guasti, Ariel Poliandri, Alessia David, Claudia P Cabrera, Michael R Barnes, Karoliina Wehkalampi, Stephen O'Rahilly, Catherine E Aiken, Anthony P Coll, Marcella Ma, Debra Rimmington, Giles S H Yeo, Leo Dunkel
Context: Self-limited delayed puberty (DP) is often associated with delay in physical maturation, but whilst highly heritable the causal genetic factors remain elusive. Genome-wide association studies of the timing of puberty have identified multiple loci for age of menarche (AAM) in females and voice break in males, particularly in pathways controlling energy balance. Objective/Main outcome measures: We aimed to assess the contribution of rare variants in such genes to the phenotype of familial DP...
November 16, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29161428/arabidopsis-inositol-polyphosphate-multikinase-delays-flowering-time-through-mediating-transcriptional-activation-of-flowering-locus-c
#7
Sihong Sang, Yao Chen, Qiaofeng Yang, Peng Wang
Timely flowering is critical for successful reproduction and seed yield in plants. A diverse range of regulators have been found to control flowering time in response to environmental and endogenous signals. Among these regulators, FLOWERING LOCUS C (FLC) acts as a central repressor of floral transition by blocking the expression of flowering integrator genes. Here, we report that Arabidopsis inositol polyphosphate multikinase (AtIPK2β) functions in flowering time control by mediating transcriptional regulation of FLC at the chromatin level...
November 17, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29161398/role-of-gabaa-receptor-subtypes-in-the-behavioural-effects-of-intravenous-general-anaesthetics
#8
C J Weir, S J Mitchell, J J Lambert
Since the introduction of general anaesthetics into clinical practice, researchers have been mystified as to how these chemically disparate drugs act to produce their dramatic effects on central nervous system function and behaviour. Scientific advances, particularly during the last 25 years, have now begun to reveal the molecular mechanisms underpinning their behavioural effects. For certain i.v. general anaesthetics, such as etomidate and propofol, a persuasive case can now be made that the GABAA receptor, a major inhibitory receptor in the mammalian central nervous system, is an important target...
December 1, 2017: British Journal of Anaesthesia
https://www.readbyqxmd.com/read/29161273/enrichment-of-colorectal-cancer-associations-in-functional-regions-insight-for-using-epigenomics-data-in-the-analysis-of-whole-genome-sequence-imputed-gwas-data
#9
Stephanie A Bien, Paul L Auer, Tabitha A Harrison, Conghui Qu, Charles M Connolly, Peyton G Greenside, Sai Chen, Sonja I Berndt, Stéphane Bézieau, Hyun M Kang, Jeroen Huyghe, Hermann Brenner, Graham Casey, Andrew T Chan, John L Hopper, Barbara L Banbury, Jenny Chang-Claude, Stephen J Chanock, Robert W Haile, Michael Hoffmeister, Christian Fuchsberger, Mark A Jenkins, Suzanne M Leal, Mathieu Lemire, Polly A Newcomb, Steven Gallinger, John D Potter, Robert E Schoen, Martha L Slattery, Joshua D Smith, Loic Le Marchand, Emily White, Brent W Zanke, Goncalo R Abeçasis, Christopher S Carlson, Ulrike Peters, Deborah A Nickerson, Anshul Kundaje, Li Hsu
BACKGROUND: The evaluation of less frequent genetic variants and their effect on complex disease pose new challenges for genomic research. To investigate whether epigenetic data can be used to inform aggregate rare-variant association methods (RVAM), we assessed whether variants more significantly associated with colorectal cancer (CRC) were preferentially located in non-coding regulatory regions, and whether enrichment was specific to colorectal tissues. METHODS: Active regulatory elements (ARE) were mapped using data from 127 tissues and cell-types from NIH Roadmap Epigenomics and Encyclopedia of DNA Elements (ENCODE) projects...
2017: PloS One
https://www.readbyqxmd.com/read/29161261/mrna-processing-in-mutant-zebrafish-lines-generated-by-chemical-and-crispr-mediated-mutagenesis-produces-unexpected-transcripts-that-escape-nonsense-mediated-decay
#10
Jennifer L Anderson, Timothy S Mulligan, Meng-Chieh Shen, Hui Wang, Catherine M Scahill, Frederick J Tan, Shao J Du, Elisabeth M Busch-Nentwich, Steven A Farber
As model organism-based research shifts from forward to reverse genetics approaches, largely due to the ease of genome editing technology, a low frequency of abnormal phenotypes is being observed in lines with mutations predicted to lead to deleterious effects on the encoded protein. In zebrafish, this low frequency is in part explained by compensation by genes of redundant or similar function, often resulting from the additional round of teleost-specific whole genome duplication within vertebrates. Here we offer additional explanations for the low frequency of mutant phenotypes...
November 21, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29161206/a-hypersensitivity-like-response-to-meloidogyne-graminicola-in-rice-oryza-sativa-l
#11
Ngan Thi Phan, Dirk De Waele, Mathias Lorieux, Lizhong Xiong, Stephane Bellafiore
Meloidogyne graminicola (M. graminicola) is a major plant-parasitic nematode affecting rice cultivation in Asia. Resistance to this nematode was found in the African rice genotypes Oryza glaberrima and O. longistaminata, however, due to interspecific hybrid sterility, the introgression of resistance genes in the widely consumed O. sativa varieties remains challenging. Recently, resistance was found in O. sativa and here we report for the first time the histological and genetic characterization of the resistance to M...
November 21, 2017: Phytopathology
https://www.readbyqxmd.com/read/29161159/unilateral-coats-like-disease-and-an-intragenic-deletion-in-the-terc-gene-a-case-report
#12
G Peene, E Smets, E Legius, C Cassiman
We report a case of a 25-year-old woman with unilateral Coats'-like disease. Her brother was previously diagnosed with an autosomal dominant form of dyskeratosis congenita. Genetic testing was performed by screening the TERC gene for mutations and identified heterozygosity for the n.68_124del mutation. Our case demonstrates that the exudative retinopathy seen in Coats'-like disease can be caused by mutations in a telomere-capping gene TERC as a part of the dyskeratosis congenita spectrum without other systemic involvement...
November 21, 2017: Ophthalmic Genetics
https://www.readbyqxmd.com/read/29161034/dynamic-glycosylation-governs-the-vertebrate-copii-protein-trafficking-pathway
#13
Nathan J Cox, Gokhan Unlu, Brittany J Bisnett, Thomas R Meister, Brett Condon, Peter M Luo, Tim J Smith, Michael Hanna, Abhishek Chhetri, Erik J Soderblom, Anjon Audhya, Ela W Knapik, Michael Boyce
The COPII coat complex, which mediates secretory cargo trafficking from the endoplasmic reticulum, is a key control point for subcellular protein targeting. Because misdirected proteins cannot function, protein sorting by COPII is critical for establishing and maintaining normal cell and tissue homeostasis. Indeed, mutations in COPII genes cause a range of human pathologies, including cranio-lenticulo-sutural dysplasia (CLSD), which is characterized by collagen trafficking defects, craniofacial abnormalities and skeletal dysmorphology...
November 21, 2017: Biochemistry
https://www.readbyqxmd.com/read/29161028/exploring-the-active-centre-of-lsd1-corest-complex-by-molecular-dynamics-simulation-utilizing-its-co-crystallized-cofactor-tetrahydrofolate-as-a-probe
#14
Waleed A A Zalloum, Hiba M Zalloum
Epigenetic targeting of cancer is a recent era to manipulate the gene without destroying the genetic material. Lysine-specific demethylase 1 (LSD1) is one of the enzymes associated with the chromatin for post-translational modifications, where it demethylates lysine amino acid in the chromatin H3 tail. Many studies showed that inhibiting LSD1 could potentially be used to treat cancer epigenetically. LSD1 is associated with its corepressor protein CoREST, and uses tetrahydrofolate as a cofactor to accept CH2 from the demethylation process...
November 21, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29161012/top-down-proteomics-ready-for-prime-time
#15
Bifan Chen, Kyle A Brown, Ziqing Lin, Ying Ge
In the post-genomics era, the study of proteins is critical for understanding cellular functions at the molecular level.1-5 Beyond the genetic code, the human proteome is greatly diversified by various genetic variations, alternative splicing of RNA transcripts, and post-translational modifi-cations (PTMs).6,7 In 2013, the term "proteoform" was designated to describe "all of the different molecular forms in which the protein product of a single gene can be found",6 clearing up the confusion in nomenclature and joining research efforts to develop methodologies for pro-teoform characterization...
November 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29160859/the-role-of-rnf213-4810g-a-and-4950g-a-variants-in-patients-with-moyamoya-disease-in-korea
#16
Young Seok Park, Hui Jeong An, Jung Oh Kim, Won Seop Kim, In Bo Han, Ok Joon Kim, Nam Keun Kim, Dong-Seok Kim
Although a founder variant of RNF213 4810G>A is a major genetic risk factor for moyamoya disease (MMD) in East Asians, the frequency and disease susceptibility of RNF213 variants remain largely unknown. This study investigated the mutation analysis of RNF213 (4448, 4810, 4863, and 4950) between Korean MMD and healthy controls. We performed a polymerase chain reaction-restriction fragment length polymorphism analysis. To identify the association between RNF213 gene polymorphisms and MMD disease, we performed statistical analyses such as multivariable logistic regression and Fisher's exact test...
November 21, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29160764/dna-methylation-profile-in-chronic-myelomonocytic-leukemia-associates-with-distinct-clinical-biological-and-genetic-features
#17
Laura Palomo, Roberto Malinverni, Marta Cabezón, Blanca Xicoy, Montserrat Arnan, Rosa Coll, Helena Pomares, Olga García, Francisco Fuster-Tormo, Javier Grau, Evarist Feliu, Francesc Solé, Marcus Buschbeck, Lurdes Zamora
Chromosomal abnormalities are detected in 20-30% of patients with chronic myelomonocytic leukemia (CMML) and correlate with prognosis. On the mutation level, disruptive alterations are particularly frequent in chromatin regulatory genes. However, little is known about the consequential alterations in the epigenetic marking of the genome. Here, we report the analysis of genomic DNA methylation patterns of 64 CMML patients and 10 healthy controls, using a DNA methylation microarray focused on promoter regions...
November 21, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29160746/nucleic-acid-therapies-for-cystic-fibrosis
#18
Shruti Sasaki, Shuling Guo
Nucleic acid therapeutics are an established class of drugs that enable specific targeting of a gene of interest. This diverse family of drugs includes antisense oligonucleotides, siRNAs, and mRNA replacement therapies, which can elicit both gene repression and activation, primarily at the RNA level. Recent advances in medicinal chemistry have increased drug potency and enhanced delivery and distribution to a broad array of tissue and cell types. A key advantage of nucleic acid therapeutics is in their application to monogenic diseases...
November 21, 2017: Nucleic Acid Therapeutics
https://www.readbyqxmd.com/read/29160618/deciphering-the-fine-nucleotide-diversity-of-full-hla-class-i-and-class-ii-genes-in-a-well-documented-population-from-sub-saharan-africa
#19
Thomas Goeury, Lisa Creary, Lydie Brunet, Maxime Galan, Maeva Pasquier, Barbara Kervaire, André Langaney, Jean-Marie Tiercy, Marcelo A Fernández-Viña, José Manuel Nunes, Alicia Sanchez-Mazas
With the aim to understand how NGS improves both our assessment of genetic variation within populations and our knowledge on HLA molecular evolution, we sequenced and analysed 8 HLA loci in a well-documented population from sub-Saharan Africa (Mandenka). The results of full-gene NGS-MiSeq sequencing compared to those obtained by traditional typing techniques or limited sequencing strategies showed that segregating sites located outside exon 2 are crucial to describe not only class I, but also class II population diversity...
November 21, 2017: HLA
https://www.readbyqxmd.com/read/29160564/functional-differences-in-transport-properties-of-natural-hkt1-1-variants-influence-shoot-na-exclusion-in-grapevine-rootstocks
#20
Sam W Henderson, Jake D Dunlevy, Yue Wu, Deidre H Blackmore, Rob R Walker, Everard J Edwards, Matthew Gilliham, Amanda R Walker
Under salinity, Vitis spp. rootstocks can mediate salt (NaCl) exclusion from grafted V. vinifera scions enabling higher grapevine yields and production of superior wines with lower salt content. Until now, the genetic and mechanistic elements controlling sodium (Na(+) ) exclusion in grapevine were unknown. Using a cross between two Vitis interspecific hybrid rootstocks, we mapped a dominant quantitative trait locus (QTL) associated with leaf Na(+) exclusion (NaE) under salinity stress. The NaE locus encodes six high-affinity potassium transporters (HKT)...
November 21, 2017: New Phytologist
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