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https://www.readbyqxmd.com/read/29666432/genetic-validation-of-bipolar-disorder-identified-by-automated-phenotyping-using-electronic-health-records
#1
Chia-Yen Chen, Phil H Lee, Victor M Castro, Jessica Minnier, Alexander W Charney, Eli A Stahl, Douglas M Ruderfer, Shawn N Murphy, Vivian Gainer, Tianxi Cai, Ian Jones, Carlos N Pato, Michele T Pato, Mikael Landén, Pamela Sklar, Roy H Perlis, Jordan W Smoller
Bipolar disorder (BD) is a heritable mood disorder characterized by episodes of mania and depression. Although genomewide association studies (GWAS) have successfully identified genetic loci contributing to BD risk, sample size has become a rate-limiting obstacle to genetic discovery. Electronic health records (EHRs) represent a vast but relatively untapped resource for high-throughput phenotyping. As part of the International Cohort Collection for Bipolar Disorder (ICCBD), we previously validated automated EHR-based phenotyping algorithms for BD against in-person diagnostic interviews (Castro et al...
April 18, 2018: Translational Psychiatry
https://www.readbyqxmd.com/read/29666333/a-novel-alu-mediated-microdeletion-in-the-runx2-gene-in-a-chinese-patient-with-cleidocranial-dysplasia
#2
Yunzhu Qian, Yingying Zhang, Bin Wei, Mengshu Zhang, Jianxin Yang, Cuihua Leng, Zili Ge, Xingshun Xu, Miao Sun
Cleidocranial dysplasia (CCD; OMIM: 119600) is a rare autosomal dominant skeletal dysplasia caused by RUNX2 gene mutations. The present study described a sporadic case with CCD. The clinical data of the proband with CCD was reported and genetic analysis was performed. The proband presented with typical CCD features including supernumerary impacted teeth, bilateral clavicle dysplasia, delayed closure of cranial sutures, and short stature; while his hands were normal. Sequencing analysis of the entire coding region of the RUNX2 gene revealed no pathogenic changes; however, copy-number analysis with the Affymetrix HD array found ~500 kb genomicmicrodeletion...
March 2018: Journal of Genetics
https://www.readbyqxmd.com/read/29666259/shared-epitope-aryl-hydrocarbon-receptor-crosstalk-underlies-the-mechanism-of-gene-environment-interaction-in-autoimmune-arthritis
#3
Jiaqi Fu, Sarah V Nogueira, Vincent van Drongelen, Patrick Coit, Song Ling, Edward F Rosloniec, Amr H Sawalha, Joseph Holoshitz
The susceptibility to autoimmune diseases is affected by genetic and environmental factors. In rheumatoid arthritis (RA), the shared epitope (SE), a five-amino acid sequence motif encoded by RA-associated HLA-DRB1 alleles, is the single most significant genetic risk factor. The risk conferred by the SE is increased in a multiplicative way by exposure to various environmental pollutants, such as cigarette smoke. The mechanism of this synergistic interaction is unknown. It is worth noting that the SE has recently been found to act as a signal transduction ligand that facilitates differentiation of Th17 cells and osteoclasts in vitro and in vivo...
April 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29666196/whole-genome-sequence-of-an-edible-and-potential-medicinal-fungus-cordyceps-guangdongensis
#4
Chenghua Zhang, Wangqiu Deng, Wenjuan Yan, Taihui Li
Cordyceps guangdongensis is an edible fungus which was approved as a novel food by the Chinese Ministry of Public Health in 2013. It also has a broad prospect of application in pharmaceutical industries, with many medicinal activities. In this study, the whole genome of C. guangdongensis GD15, a single spore isolate from a wild strain, was sequenced and assembled with Illumina and PacBio sequencing technology. The generated genome is 29.05 Mb in size, comprising nine scaffolds with an average GC content of 57...
April 17, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29665944/-current-status-and-challenges-of-car-t-immunotherapy-in-hematologic-malignancies-review
#5
Xin Cheng, Ya-Jie Wang, Shuai Feng, Ya-Yun Wu, Tong-Hua Yang, Xun Lai
The chimeric antigen receptor (CAR) T cell therapy has gradually became a new trend in the treatment of refractory and relapsed hematologic malignancies by developing for 30 years. With the exciting development of genetic engineering, CAR-T technology has subjected to 4 generations of innovation. Structure of CAR-T started from a single signal molecule to 2 or more than 2 co-stimulatory molecules, and then coding the CAR gene or promoter. CAR-T can specifically recognize tumor antigens, and does not be restricted by major histocompatibility complex (MHC), thus making a breakthrough in clinical treatment...
April 2018: Zhongguo Shi Yan Xue Ye Xue za Zhi
https://www.readbyqxmd.com/read/29663588/from-transects-to-transcripts-teasing-apart-the-architecture-of-reproductive-isolation
#6
Jill A Hamilton, Joshua M Miller
Understanding the processes underlying speciation has long been a challenge to evolutionary biologists. This spurs from difficulties teasing apart the various mechanisms that contribute to the evolution of barriers to reproduction. The study by Rafati et al. () in this issue of Molecular Ecology combines spatially explicit whole-genome resequencing with evaluation of differential gene expression across individuals with mixed ancestry to associate the genomic architecture of reproductive barriers with expression of reproductive incompatibilities...
March 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29662059/genome-wide-association-study-of-depression-phenotypes-in-uk-biobank-identifies-variants-in-excitatory-synaptic-pathways
#7
David M Howard, Mark J Adams, Masoud Shirali, Toni-Kim Clarke, Riccardo E Marioni, Gail Davies, Jonathan R I Coleman, Clara Alloza, Xueyi Shen, Miruna C Barbu, Eleanor M Wigmore, Jude Gibson, Saskia P Hagenaars, Cathryn M Lewis, Joey Ward, Daniel J Smith, Patrick F Sullivan, Chris S Haley, Gerome Breen, Ian J Deary, Andrew M McIntosh
Depression is a polygenic trait that causes extensive periods of disability. Previous genetic studies have identified common risk variants which have progressively increased in number with increasing sample sizes of the respective studies. Here, we conduct a genome-wide association study in 322,580 UK Biobank participants for three depression-related phenotypes: broad depression, probable major depressive disorder (MDD), and International Classification of Diseases (ICD, version 9 or 10)-coded MDD. We identify 17 independent loci that are significantly associated (P < 5 × 10-8 ) across the three phenotypes...
April 16, 2018: Nature Communications
https://www.readbyqxmd.com/read/29661558/genetic-assessment-and-folate-receptor-autoantibodies-in-infantile-onset-cerebral-folate-deficiency-cfd-syndrome
#8
V Th Ramaekers, K Segers, J M Sequeira, M Koenig, L Van Maldergem, V Bours, U Kornak, E V Quadros
INTRODUCTION: Cerebral folate deficiency (CFD) syndromes are defined as neuro-psychiatric conditions with low CSF folate and attributed to different causes such as autoantibodies against the folate receptor-alpha (FR) protein that can block folate transport across the choroid plexus, FOLR1 gene mutations or mitochondrial disorders. High-dose folinic acid treatment restores many neurologic deficits. STUDY AIMS AND METHODS: Among 36 patients from 33 families the infantile-onset CFD syndrome was diagnosed based on typical clinical features and low CSF folate...
March 3, 2018: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/29661182/women-s-perspectives-on-the-ethical-implications-of-non-invasive-prenatal-testing-a-qualitative-analysis-to-inform-health-policy-decisions
#9
Meredith Vanstone, Alexandra Cernat, Jeff Nisker, Lisa Schwartz
BACKGROUND: Non-Invasive Prenatal Testing (NIPT) is a technology which provides information about fetal genetic characteristics (including sex) very early in pregnancy by examining fetal DNA obtained from a sample of maternal blood. NIPT is a morally complex technology that has advanced quickly to market with a strong push from industry developers, leaving many areas of uncertainty still to be resolved, and creating a strong need for health policy that reflects women's social and ethical values...
April 16, 2018: BMC Medical Ethics
https://www.readbyqxmd.com/read/29661147/genotyping-of-plasmodiophora-brassicae-reveals-the-presence-of-distinct-populations
#10
Michael D Holtz, Sheau-Fang Hwang, Stephen E Strelkov
BACKGROUND: Plasmodiophora brassicae is a soilborne pathogen of the family Brassicaceae and the causal agent of clubroot disease. In Canada, P. brassicae is now one of the most important constraints to canola (Brassica napus) production, and is managed mainly by the deployment of resistant cultivars. In recent years, however, new strains of the pathogen have emerged that are capable of overcoming host resistance, posing new challenges for disease management. Despite its economic significance, molecular studies of P...
April 16, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29661130/a-survey-of-functional-genomic-variation-in-domesticated-chickens
#11
Martijn F L Derks, Hendrik-Jan Megens, Mirte Bosse, Jeroen Visscher, Katrijn Peeters, Marco C A M Bink, Addie Vereijken, Christian Gross, Dick de Ridder, Marcel J T Reinders, Martien A M Groenen
BACKGROUND: Deleterious genetic variation can increase in frequency as a result of mutations, genetic drift, and genetic hitchhiking. Although individual effects are often small, the cumulative effect of deleterious genetic variation can impact population fitness substantially. In this study, we examined the genome of commercial purebred chicken lines for deleterious and functional variations, combining genotype and whole-genome sequence data. RESULTS: We analysed over 22,000 animals that were genotyped on a 60 K SNP chip from four purebred lines (two white egg and two brown egg layer lines) and two crossbred lines...
April 16, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29660854/the-butanol-producing-microbe-clostridium-beijerinckii-ncimb-14988-manipulated-using-forward-and-reverse-genetic-tools
#12
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/29660239/the-population-genetic-test-tajima-s-d-identifies-genes-encoding-pathogen-associated-molecular-patterns-and-other-virulence-related-genes-in-ralstonia-solanacearum
#13
Noam Eckshtain-Levi, Alexandra J Weisberg, Boris A Vinatzer
Detection of pathogen-associated molecular patterns (PAMPs) by plant pattern receptors (PRRs) is an essential part of plant immunity. Until recently, elf18, an epitope of elongation factor tu (EF-Tu), was the sole confirmed PAMP of Ralstonia solanacearum, the causal agent of bacterial wilt disease, limiting our understanding of R. solanacearum - plant interactions. Therefore, we set out to identify additional R. solanacearum PAMPs based on the hypothesis that genes encoding PAMPs are under selection to avoid recognition by plant PRRs...
April 16, 2018: Molecular Plant Pathology
https://www.readbyqxmd.com/read/29659827/a-mei1-homozygous-missense-mutation-associated-with-meiotic-arrest-in-a-consanguineous-family
#14
M Ben Khelifa, F Ghieh, R Boudjenah, C Hue, D Fauvert, R Dard, H J Garchon, F Vialard
Although meiotic arrest in males is observed in about 25% of azoospermic patients, pure homogeneous arrest in all seminiferous tubules is less frequent, and may be due to mutation of a single gene. However, given the large number of genes involved in meiosis, this gives rises to extensive genetic heterogeneity. Only two genetic abnormalities have been reported on a regular basis: the X-linked exonic TEX11 deletion, and the AZFb microdeletion on the Y chromosome. Other single gene defects were private and found in consanguineous families...
April 5, 2018: Human Reproduction
https://www.readbyqxmd.com/read/29659813/draft-genome-of-the-protandrous-chinese-black-porgy-acanthopagrus-schlegelii
#15
Zhiyong Zhang, Kai Zhang, Shuyin Chen, Zhiwei Zhang, Jinyong Zhang, Xinxin You, Chao Bian, Jin Xu, Chaofeng Jia, Jun Qiang, Fei Zhu, Hongxia Li, Hailin Liu, Dehua Shen, Zhonghong Ren, Jieming Chen, Jia Li, Tianheng Gao, Ruobo Gu, Junmin Xu, Qiong Shi, Pao Xu
Background: As one of the most popular and valuable commercial marine fishes in China and East Asian countries, the Chinese black porgy (Acanthopagrus schlegelii), also known as the blackhead seabream, has some attractive characteristics such as fast growth rate, good meat quality, resistance to diseases, and excellent adaptability to various environments. Furthermore, the black porgy is a good model for investigating sex changes in fish due to its protandrous hermaphroditism. Here, we obtained a high-quality genome assembly of this interesting teleost species and performed a genomic survey on potential genes associated with the sex-change phenomenon...
April 1, 2018: GigaScience
https://www.readbyqxmd.com/read/29659762/activation-of-%C3%AF-20-dependent-recombination-and-horizontal-gene-transfer-in-mycoplasma-genitalium
#16
Sergi Torres-Puig, Carlos Martínez-Torró, Ignasi Granero-Moya, Enrique Querol, Jaume Piñol, Oscar Q Pich
In the human pathogen Mycoplasma genitalium, homologous recombination is under the control of σ20, an alternative sigma factor that boosts the generation of genetic and antigenic diversity in the population. Under laboratory growth conditions, σ20 activation is rare and the factors governing its intermittent activity are unknown. Two σ20-regulated genes, rrlA and rrlB, showed to be important for recombination of homologous DNA sequences in this bacterium. Herein, we demonstrate that rrlA and rrlB code for two small proteins that participate in a feed-forward loop essential for σ20 function...
April 11, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29659705/irscope-an-online-program-to-visualize-the-junction-sites-of-chloroplast-genomes
#17
Ali Amiryousefi, Jaakko Hyvönen, Peter Poczai
Motivation: Genome plotting is performed using a wide range of visualizations tools each with emphasis on a different informative dimension of the genome. These tools can provide a deeper insight into the genomic structure of the organism. Results: Here we announce a new visualization tool that is specifically designed for chloroplast genomes. It allows the users to depict the genetic architecture of up to ten chloroplast genomes in the vicinity of the sites connecting the inverted repeats to the short and long single copy regions...
April 5, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29653293/transcriptional-profiling-of-murine-osteoblast-differentiation-based-on-rna-seq-expression-analyses
#18
Layal Abo Khayal, Johannes Grünhagen, Ivo Provazník, Stefan Mundlos, Uwe Kornak, Peter N Robinson, Claus-Eric Ott
Osteoblastic differentiation is a multistep process characterized by osteogenic induction of mesenchymal stem cells, which then differentiate into proliferative pre-osteoblasts that produce copious amounts of extracellular matrix, followed by stiffening of the extracellular matrix, and matrix mineralization by hydroxylapatite deposition. Although these processes have been well characterized biologically, a detailed transcriptional analysis of murine primary calvaria osteoblast differentiation based on RNA sequencing (RNA-seq) analyses has not previously been reported...
April 10, 2018: Bone
https://www.readbyqxmd.com/read/29653232/gata6-loss-of-function-mutation-contributes-to-congenital-bicuspid-aortic-valve
#19
Ying-Jia Xu, Ruo-Min Di, Qi Qiao, Xiu-Mei Li, Ri-Tai Huang, Song Xue, Xing-Yuan Liu, Juan Wang, Yi-Qing Yang
Congenital bicuspid aortic valve (BAV), the most common form of birth defect in humans, is associated with substantial morbidity and mortality. Increasing evidence demonstrates that genetic risk factors play a key role in the pathogenesis of BAV. However, BAV is a genetically heterogeneous disease and the genetic determinants underpinning BAV in an overwhelming majority of patients remain unknown. In the present study, the coding exons and flanking introns of the GATA6 gene, which encodes a zinc-finger transcription factor essential for the normal development of the aortic valves, were sequenced in 152 unrelated patients with congenital BAV...
April 10, 2018: Gene
https://www.readbyqxmd.com/read/29653176/hyperactive-piggybac-transposase-improves-transformation-efficiency-in-diverse-insect-species
#20
Kolja N Eckermann, Hassan M M Ahmed, Mohammad KaramiNejadRanjbar, Stefan Dippel, Christian E Ogaugwu, Peter Kitzmann, Musa D Isah, Ernst A Wimmer
Even in times of advanced site-specific genome editing tools, the improvement of DNA transposases is still on high demand in the field of transgenesis: especially in emerging model systems where evaluated integrase landing sites have not yet been created and more importantly in non-model organisms such as agricultural pests and disease vectors, in which reliable sequence information and genome annotations are still pending. In fact, random insertional mutagenesis is essential to identify new genomic locations that are not influenced by position effects and thus can serve as future stable transgene integration sites...
April 10, 2018: Insect Biochemistry and Molecular Biology
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