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https://www.readbyqxmd.com/read/29054766/rethinking-genotype-phenotype-correlations-in-papillorenal-syndrome-a-case-report-on-an-unusual-congenital-camptodactyly-and-skeletal-deformity-with-a-heterogeneous-pax2-mutation-of-hexanucleotide-duplication
#1
Jiewei Liu, Ping Wang, Juan Huang, Zihua Yu
Papillorenal syndrome (PRS), an autosomal dominant inherited condition, is clinically featured by renal hypoplasia and optic nerve dysplasia. Based on current knowledge of genotype-phenotype correlations in PRS, mutations in the Paired box 2 (PAX2) gene have been recognized as a critical pathogenesis of typical renal and optic disease manifestations. However, little information is currently available on the skeletal abnormalities of PRS and the potential contribution of PAX2 mutations. Here, we present a case of a 10-year-old female PRS patient with the typical features of chronic renal failure and severe myopia, but was unexpectedly discovered camptodactyly of her left middle finger which affects the proximal interphalangeal joint...
October 17, 2017: Gene
https://www.readbyqxmd.com/read/29052098/comparative-transcriptome-analysis-reveals-whole-genome-duplications-and-gene-selection-patterns-in-cultivated-and-wild-chrysanthemum-species
#2
So Youn Won, Soo-Jin Kwon, Tae-Ho Lee, Jae-A Jung, Jung Sun Kim, Sang-Ho Kang, Seong-Han Sohn
Comparative transcriptome analysis of wild and cultivated chrysanthemums provides valuable genomic resources and helps uncover common and divergent patterns of genome and gene evolution in these species. Plants are unique in that they employ polyploidy (or whole-genome duplication, WGD) as a key process for speciation and evolution. The Chrysanthemum genus is closely associated with hybridization and polyploidization, with Chrysanthemum species exhibiting diverse ploidy levels. The commercially important species, C...
October 19, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/29052008/genome-wide-analysis-and-expression-profiling-of-pp2c-clade-d-under-saline-and-alkali-stresses-in-wild-soybean-and-arabidopsis
#3
Chao Chen, Yang Yu, Xiaodong Ding, Beidong Liu, Huizi Duanmu, Dan Zhu, Xiaoli Sun, Lei Cao, Zaib-Un-Nisa, Qiang Li, Yanming Zhu
Protein phosphatase 2Cs (PP2Cs) belong to the largest protein phosphatase family in plants. Some members have been described as being negative modulators of plant growth and development, as well as responses to hormones and environmental stimuli. However, little is known about the members of PP2C clade D, which may be involved in the regulation of signaling pathways, especially in response to saline and alkali stresses. Here, we identified 13 PP2C orthologs from the wild soybean (Glycine soja) genome. We examined the sequence characteristics, chromosome locations and duplications, gene structures, and promoter cis-elements of the PP2C clade D genes in Arabidopsis and wild soybean...
October 19, 2017: Protoplasma
https://www.readbyqxmd.com/read/29051384/taxon-restricted-genes-at-the-origin-of-a-novel-trait-allowing-access-to-a-new-environment
#4
M Emília Santos, Augustin Le Bouquin, Antonin J J Crumière, Abderrahman Khila
Taxon-restricted genes make up a considerable proportion of genomes, yet their contribution to phenotypic evolution is poorly understood. We combined gene expression with functional and behavioral assays to study the origin and adaptive value of an evolutionary innovation exclusive to the water strider genus Rhagovelia: the propelling fan. We discovered that two taxon-restricted genes, which we named geisha and mother-of-geisha, specifically control fan development. geisha originated through a duplication event at the base of the Rhagovelia lineage, and both duplicates acquired a novel expression in a specific cell population prefiguring fan development...
October 20, 2017: Science
https://www.readbyqxmd.com/read/29050398/delineating-sptan1-associated-phenotypes-from-isolated-epilepsy-to-encephalopathy-with-progressive-brain-atrophy
#5
Steffen Syrbe, Frederike L Harms, Elena Parrini, Martino Montomoli, Ulrike Mütze, Katherine L Helbig, Tilman Polster, Beate Albrecht, Ulrich Bernbeck, Ellen van Binsbergen, Saskia Biskup, Lydie Burglen, Jonas Denecke, Bénédicte Heron, Henrike O Heyne, Georg F Hoffmann, Frauke Hornemann, Takeshi Matsushige, Ryuki Matsuura, Mitsuhiro Kato, G Christoph Korenke, Alma Kuechler, Constanze Lämmer, Andreas Merkenschlager, Cyril Mignot, Susanne Ruf, Mitsuko Nakashima, Hirotomo Saitsu, Hannah Stamberger, Tiziana Pisano, Jun Tohyama, Sarah Weckhuysen, Wendy Werckx, Julia Wickert, Francesco Mari, Nienke E Verbeek, Rikke S Møller, Bobby Koeleman, Naomichi Matsumoto, William B Dobyns, Domenica Battaglia, Johannes R Lemke, Kerstin Kutsche, Renzo Guerrini
De novo in-frame deletions and duplications in the SPTAN1 gene, encoding the non-erythrocyte αII spectrin, have been associated with severe West syndrome with hypomyelination and pontocerebellar atrophy. We aimed at comprehensively delineating the phenotypic spectrum associated with SPTAN1 mutations. Using different molecular genetic techniques, we identified 20 patients with a pathogenic or likely pathogenic SPTAN1 variant and reviewed their clinical, genetic and imaging data. SPTAN1 de novo alterations included seven unique missense variants and nine in-frame deletions/duplications of which 12 were novel...
September 1, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/29050366/the-resistance-mechanisms-and-treatment-strategies-for-egfr-mutant-advanced-non-small-cell-lung-cancer
#6
REVIEW
Wen-Zhao Zhong, Qing Zhou, Yi-Long Wu
Epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKI) have been established as the standard therapy for EGFR-sensitizing mutant advanced non-small-cell lung cancer (NSCLC). However, patients ultimately develop resistance to these drugs. There are several mechanisms of both primary and secondary resistance to EGFR-TKIs. The primary resistance mechanisms include point mutations in exon 18, deletions or insertions in exon 19, insertions, duplications and point mutations in exon 20 and point mutation in exon 21 of EGFR gene...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29049312/impact-of-annotation-error-in-%C3%AE-globin-genes-on-molecular-diagnosis
#7
J Francis Borgio
BACKGROUND: Recent studies on the variants in duplicated human alpha globin genes (HBA2 and HBA1) actively target the α-globin gene as molecular modulators for the treatment of β-thalassemia major. Identification of the exact position of variant in HBA1, HBA2 or its patchworks is mandatory to support the therapeutic aims in β-thalassemia major, by identifying specific modulators for the reactivation of fetal hemoglobin production. Hence, accurate identification of the variants in α-globin genes is crucial for the proper diagnosis, treatment and genetic counseling...
2017: PloS One
https://www.readbyqxmd.com/read/29048530/population-genomic-analysis-of-a-pitviper-reveals-microevolutionary-forces-underlying-venom-chemistry
#8
Steven D Aird, Jigyasa Arora, Agneesh Barua, Lijun Qiu, Kouki Terada, Alexander S Mikheyev
Venoms are among the most biologically active secretions known, and are commonly believed to evolve under extreme positive selection. Many venom gene families, however, have undergone duplication, and are often deployed in doses vastly exceeding the LD50 for most prey species, which should reduce the strength of positive selection. Here, we contrast these selective regimes using snake venoms, which consist of rapidly evolving protein formulations. Though decades of extensive studies have found that snake venom proteins are subject to strong positive selection, the greater action of drift has been hypothesized, but never tested...
October 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29048480/panax-ginseng-genome-examination-for-ginsenoside-biosynthesis
#9
Xu Jiang, Chu Yang, Liao Baosheng, Xiao Shuiming, Yin Qinggang, Bai Rui, Su He, Dong Linlin, Li Xiwen, Qian Jun, Zhang Jingjing, Zhang Yujun, Zhang Xiaoyan, Wu Mingli, Zhang Jie, Li Guozheng, Zhang Lei, Chang Zhenzhan, Zhang Yuebin, Jia Zhengwei, Liu Zhixiang, Daniel Afreh, Ruth Nahurira, Zhang Lianjuan, Cheng Ruiyang, Zhu Yingjie, Zhu Guangwei, Rao Wei, Zhou Chao, Qiao Lirui, Huang Zhihai, Cheng Yung-Chi, Chen Shilin
Background: Ginseng, which contain ginsenosides as bioactive compounds, has been regarded as an important traditional medicine for several millennia. However, the genetic background of ginseng remains poorly understood partly because of the plant's large and complex genome composition. Results: We report the entire genome sequence of Panax ginseng using next-generation sequencing. The 3.5Gb nucleotide sequence contained more than 60% repeats and encoded 42,006 predicted genes...
October 5, 2017: GigaScience
https://www.readbyqxmd.com/read/29046205/-clinical-phenotype-and-genetic-analysis-of-med13l-syndrome
#10
Qing-Jie Meng, Xue-Lian He, Han Xiao, Qian Xia, Bo Bi, Yun Xiang
A boy aged 4 years and 2 months was found to have delayed language and motor development, instability of gait, poor eye contact, stereotyped behavior, and seizure at the age of 3 years. Physical examination showed special facial features, including plagiocephaly, blepharoptosis, wide nasal bridge, down-turned mouth corners at both sides, and low-set ears. There were only two knuckles at the little finger of the left hand. The anteroposterior and lateral films of the spine showed scoliosis; echocardiography showed ventricular septal defect; the Gesell Developmental Scale showed delayed language development and moderate intellectual disability; there were no abnormalities in the karyotype; genome-wide SNP arrays found a duplication in 12q24...
October 2017: Zhongguo Dang Dai Er Ke za Zhi, Chinese Journal of Contemporary Pediatrics
https://www.readbyqxmd.com/read/29045953/-detection-of-large-deletions-in-x-linked-alport-syndrome-using-competitive-multiplex-fluorescence-polymerase-chain-reaction
#11
F Wang, Y Q Zhang, J Ding, L X Yu
OBJECTIVE: To evaluate the ability of multiplex competitive fluorescence polymerase chain reaction in detection of large deletion and duplication genotypes of X-linked Alport syndrome. METHODS: Clinical diagnosis of X-linked Alport syndrome was based on either abnormal staining of type IV collagen α5 chain in the epidermal basement membrane alone or with abnormal staining of type IV collagen α5 chain in the glomerular basement membrane and Bowman's capsule/ultrastructural changes in the glomerular basement membrane typical of Alport syndrome...
October 18, 2017: Beijing da Xue Xue Bao. Yi Xue Ban, Journal of Peking University. Health Sciences
https://www.readbyqxmd.com/read/29044765/a-novel-inborn-error-of-the-coenzyme-q10-biosynthesis-pathway-cerebellar-ataxia-and-static-encephalomyopathy-due-to-coq5-c-methyltransferase-deficiency
#12
May Christine V Malicdan, Thierry Vilboux, Bruria Ben-Zeev, Jennifer Guo, Aviva Eliyahu, Ben Pode-Shakked, Amir Dori, Sravan Kakani, Settara C Chandrasekharappa, Carlos Ferreira, Natalia Shelestovich, Dina Marek-Yagel, Hadass Pri-Chen, Ilan Blatt, John E Niederhuber, Langping He, Camilo Toro, Robert W Taylor, John Deeken, Tal Yardeni, Douglas C Wallace, William A Gahl, Yair Anikster
Primary coenzyme Q10 (CoQ10 ; MIM# 607426) deficiencies are an emerging group of inherited mitochondrial disorders with heterogonous clinical phenotypes. Over a dozen genes are involved in the biosynthesis of CoQ10 , and mutations in several of these are associated with human disease. However, mutations in COQ5 (MIM# 616359), catalyzing the only C-methylation in the CoQ10 synthetic pathway, have not been implicated in human disease. Here, we report three female siblings of Iraqi-Jewish descent, who had varying degrees of cerebellar ataxia, encephalopathy, generalized tonic-clonic seizures and cognitive disability...
October 16, 2017: Human Mutation
https://www.readbyqxmd.com/read/29043379/copy-number-variation-and-disease-resistance-in-plants
#13
REVIEW
Aria Dolatabadian, Dhwani Apurva Patel, David Edwards, Jacqueline Batley
Plant genome diversity varies from single nucleotide polymorphisms to large-scale deletions, insertions, duplications, or re-arrangements. These re-arrangements of sequences resulting from duplication, gains or losses of DNA segments are termed copy number variations (CNVs). During the last decade, numerous studies have emphasized the importance of CNVs as a factor affecting human phenotype; in particular, CNVs have been associated with risks for several severe diseases. In plants, the exploration of the extent and role of CNVs in resistance against pathogens and pests is just beginning...
October 17, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29042476/the-three-dimensional-genome-regulating-gene-expression-during-pluripotency-and-development
#14
REVIEW
Guillaume Andrey, Stefan Mundlos
The precise expression of genes in time and space during embryogenesis is largely influenced by communication between enhancers and promoters, which is propagated and governed by the physical proximity of these elements in the nucleus. Here, we review how chromatin domains organize the genome by guiding enhancers to their target genes thereby preventing non-specific interactions with other neighboring regions. We also discuss the dynamics of chromatin interactions between enhancers and promoters, as well as the consequent changes in gene expression, that occur in pluripotent cells and during development...
October 15, 2017: Development
https://www.readbyqxmd.com/read/29040752/expansion-of-the-dehydrin-gene-family-in-the-pinaceae-is-associated-with-considerable-structural-diversity-and-drought-responsive-expression
#15
Juliana Stival Sena, Isabelle Giguère, Philippe Rigault, Jean Bousquet, John Mackay
Temperatures are expected to increase over the next century in all terrestrial biomes and particularly in boreal forests, where drought-induced mortality has been predicted to rise. Genomics research is helping to develop hypotheses regarding the molecular basis of drought tolerance and recent work proposed that the osmo-protecting dehydrin proteins have undergone a clade-specific expansion in the Pinaceae, a major group of conifer trees. The objectives of this study were to identify all of the putative members of the gene family, trace their evolutionary origin, examine their structural diversity and test for drought-responsive expression...
October 13, 2017: Tree Physiology
https://www.readbyqxmd.com/read/29040588/glyphosate-resistance-and-epsps-gene-duplication-convergent-evolution-in-multiple-plant-species
#16
Eric L Patterson, Dean J Pettinga, Karl Ravet, Paul Neve, Todd A Gaines
One of the increasingly widespread mechanisms of resistance to the herbicide glyphosate is copy number variation (CNV) of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene. EPSPS gene duplication has been reported in eight weed species, ranging from 3-5 extra copies to more than 150 extra copies. In the case of Palmer amaranth (Amaranthus palmeri), a section of >300 kb containing EPSPS and many other genes has been replicated and inserted at new loci throughout the genome, resulting in significant increase in total genome size...
October 10, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29039010/identification-of-pseudogenes-in-brachypodium-distachyon-chromosomes
#17
Salvatore Camiolo, Andrea Porceddu
Pseudogenes are gene copies that have lost the capability to encode a functional protein. Based on their structure, pseudogenes are classified in two types. Processed pseudogenes arise by a process of retrotranscription from a spliced mRNA and subsequent integration into the genome. Nonprocessed (or duplicated) pseudogenes are generated by genomic duplication and subsequent mutations that disable their functionality so that they cannot longer encode a functional protein. Differently from processed pseudogenes, duplicated pseudogenes are expected to conserve the exon-intron structure of their functional paralogs...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29038757/complete-mitochondrial-genome-sequences-of-the-northern-spotted-owl-strix-occidentalis-caurina-and-the-barred-owl-strix-varia-aves-strigiformes-strigidae-confirm-the-presence-of-a-duplicated-control-region
#18
Zachary R Hanna, James B Henderson, Anna B Sellas, Jérôme Fuchs, Rauri C K Bowie, John P Dumbacher
We report here the successful assembly of the complete mitochondrial genomes of the northern spotted owl (Strix occidentalis caurina) and the barred owl (S. varia). We utilized sequence data from two sequencing methodologies, Illumina paired-end sequence data with insert lengths ranging from approximately 250 nucleotides (nt) to 9,600 nt and read lengths from 100-375 nt and Sanger-derived sequences. We employed multiple assemblers and alignment methods to generate the final assemblies. The circular genomes of S...
2017: PeerJ
https://www.readbyqxmd.com/read/29038452/involvement-of-ubiquitin-conjugating-enzyme-e2-gene-family-in-ripening-process-and-response-to-cold-and-heat-stress-of-vitis-vinifera
#19
Yingying Gao, Yi Wang, Haiping Xin, Shaohua Li, Zhenchang Liang
Ubiquitin-conjugating (UBC) E2 enzyme plays crucial roles in plant growth and development. Limited information can describe the function of UBC enzyme E2 in grapes. A total of 43 UBC enzyme E2 genes with conserved UBC domain were identified in grapes. These genes were divided into five groups based on phylogenetic tree with tomatoes. Sequence analyses indicated that VvUBCs in the same group possessed similar gene structures and conserved motifs. Gene distribution in chromosomes was uneven, and gene duplication existed in 36 VvUBCs...
October 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29038443/phylogenetic-analysis-of-the-metazoan-carotenoid-oxygenase-superfamily-a-new-ancestral-gene-assemblage-of-bco-like-bcol-proteins
#20
Eugenia Poliakov, Joseph Soucy, Susan Gentleman, Igor B Rogozin, T Michael Redmond
Here we describe a new family of carotenoid cleavage oxygenases (CCOs) in metazoans, the BCO2-like (BCOL) clade, which contains lancelet, nematode, and molluscan carotenoid oxygenase sequences. Phylogenetic analysis of CCOs in all kingdoms of life confirmed that the BCOL enzymes are an independent clade of ancient origin. One of the predicted lancelet BCOL proteins, cloned and analyzed for carotenoid cleavage activity in a bacterial carotenoid expression system, had activity similar to lancelet BCO2 proteins, although with a preference for cis isomers...
October 16, 2017: Scientific Reports
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