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gene duplication

Muhammad I Naseer, Adeel G Chaudhary, Mahmood Rasool, Gauthaman Kalamegam, Fai T Ashgan, Mourad Assidi, Farid Ahmed, Shakeel A Ansari, Syed Kashif Zaidi, Mohammed M Jan, Mohammad H Al-Qahtani
BACKGROUND: Epilepsy is genetically complex but common brain disorder of the world affecting millions of people with almost of all age groups. Novel Copy number variations (CNVs) are considered as important reason for the numerous neurodevelopmental disorders along with intellectual disability and epilepsy. DNA array based studies contribute to explain a more severe clinical presentation of the disease but interoperation of many detected CNVs are still challenging. RESULTS: In order to study novel CNVs with epilepsy related genes in Saudi family with six affected and two normal individuals with several forms of epileptic seizures, intellectual disability (ID), and minor dysmorphism, we performed the high density whole genome Agilent sure print G3 Hmn CGH 2x 400 K array-CGH chips analysis...
October 17, 2016: BMC Genomics
Mercedes Garcia-Gil, Elisabetta Albi
In the last 20 years it has been widely demonstrated that cell nucleus contains neutral and polar lipids localized in nuclear membranes, nucleoli, nuclear matrix and chromatin. Nuclear lipids may show specific organization forming nuclear lipid microdomains and have both structural and functional roles. Depending on their localization, nuclear lipids play different roles such as the regulation of nuclear membrane and nuclear matrix fluidity but they also can act as platforms for vitamin and hormone function, for active chromatin anchoring, and for the regulation of gene expression, DNA duplication and transcription...
October 20, 2016: Neurochemical Research
Xiao-Jie Xu, Fang Lv, Yi Liu, Jian-Yi Wang, Dou-Dou Ma, Asan, Jia-Wei Wang, Li-Jie Song, Yan Jiang, Ou Wang, Wei-Bo Xia, Xiao-Ping Xing, Mei Li
Osteogenesis imperfecta (OI) is a group of hereditary disorders characterized by decreased bone mass and increased fracture risk. The majority of OI cases have an autosomal dominant pattern of inheritance and are usually caused by mutations in genes encoding type I collagen. OI cases of autosomal recessive inheritance are rare, and OI type XI is attributable to mutation of the FKBP10 gene. Here, we used next-generation sequencing and Sanger sequencing to detect mutations in FKBP10 and to analyze their relation to the phenotypes of OI type XI in three Chinese patients...
August 25, 2016: Journal of Human Genetics
Aleksandra Biedrzycka, Alvaro Sebastian, Magdalena Migalska, Helena Westerdahl, Jacek Radwan
Characterisation of highly duplicated genes, such as genes of the major histocompatibility complex (MHC), where multiple loci often co-amplify, has until recently been hindered by insufficient read depths per amplicon. Here we used ultra-deep Illumina sequencing to resolve genotypes at exon 3 of MHC class I genes in the sedge warbler (Acrocephalus schoenobaenus). We sequenced 24 individuals in two replicates and used this data, as well as a simulated dataset, to test the effect of amplicon coverage (range: 500-20 000 reads per amplicon) on the repeatability of genotyping using four different genotyping approaches...
October 19, 2016: Molecular Ecology Resources
Matthew T Whitehead, Guy Helman, Andrea L Gropman
Xp21.2 duplication syndrome is a rare genetic disorder of undetermined prevalence and clinical relevance. As the use of chromosomal microarray has become first line for the work-up of childhood developmental delay, more gene deletions and duplications have been recognized. To the best of our knowledge, the imaging findings of Xp21.2 duplication syndrome have not been reported. We report a case of a 33 month-old male referred for developmental delay that was found to have an Xp21.2 duplication containing IL1RAPL1 and multiple midline brain malformations...
May 2016: Journal of Radiology Case Reports
Cristina M Crava, Sukania Ramasamy, Lino Ometto, Gianfranco Anfora, Omar Rota-Stabelli
Chemosensory perception allows insects to interact with the environment by perceiving odorant or tastant molecules; genes encoding chemoreceptors are the molecular interface between the environment and the insect, and play a central role in mediating its chemosensory behavior. Here we explore how the evolution of these genes in the emerging pest Drosophila suzukii correlates with the peculiar ecology of this species. We annotated approximately 130 genes coding for gustatory receptors (GRs) and divergent ionotropic receptors (dIRs) in D...
October 19, 2016: G3: Genes—Genomes—Genetics
Hanne Gro Olsen, Tim Martin Knutsen, Anna M Lewandowska-Sabat, Harald Grove, Torfinn Nome, Morten Svendsen, Mariann Arnyasi, Marte Sodeland, Kristil K Sundsaasen, Sandra Rinne Dahl, Bjørg Heringstad, Hanne H Hansen, Ingrid Olsaker, Matthew Peter Kent, Sigbjørn Lien
BACKGROUND: Clinical mastitis is an inflammation of the mammary gland and causes significant costs to dairy production. It is unfavourably genetically correlated to milk production, and, thus, knowledge of the mechanisms that underlie these traits would be valuable to improve both of them simultaneously through breeding. A quantitative trait locus (QTL) that affects both clinical mastitis and milk production has recently been fine-mapped to around 89 Mb on bovine chromosome 6 (BTA6), but identification of the gene that underlies this QTL was not possible due to the strong linkage disequilibrium between single nucleotide polymorphisms (SNPs) within this region...
October 19, 2016: Genetics, Selection, Evolution: GSE
Jason T Huff, Daniel Zilberman, Scott W Roy
The discovery of introns four decades ago was one of the most unexpected findings in molecular biology. Introns are sequences interrupting genes that must be removed as part of messenger RNA production. Genome sequencing projects have shown that most eukaryotic genes contain at least one intron, and frequently many. Comparison of these genomes reveals a history of long evolutionary periods during which few introns were gained, punctuated by episodes of rapid, extensive gain. However, although several detailed mechanisms for such episodic intron generation have been proposed, none has been empirically supported on a genomic scale...
October 19, 2016: Nature
Vincenzo Sannino, Arun M Kolinjivadi, Giorgio Baldi, Vincenzo Costanzo
The correct duplication of genetic information is essential to maintain genome stability, which is lost in cancer cells. Replication fork integrity is ensured by a number of DNA metabolism proteins that assist replication of chromatin regions difficult to replicate due to their intrinsic DNA sequence composition, coordinate repair of DNA molecules resulting from aberrant replication events or protect replication forks in the presence of lesions impairing their progression. Some DNA metabolism genes involved in DNA repair are essential in higher eukaryotes even in unchallenged conditions, suggesting the existence of biological processes requiring these specialized functions in organisms with complex genomes...
2016: International Journal of Developmental Biology
Anton Suvorov, Nicholas O Jensen, Camilla R Sharkey, M Stanley Fujimoto, Paul Bodily, Haley M Cahill Wightman, T Heath Ogden, Mark J Clement, Seth M Bybee
Gene duplication plays a central role in adaptation to novel environments by providing new genetic material for functional divergence and evolution of biological complexity. Several evolutionary models have been proposed for gene duplication to explain how new gene copies are preserved by natural selection but these models have rarely been tested using empirical data. Opsin proteins, when combined with a chromophore, form a photopigment that is responsible for the absorption of light, the first step in the phototransduction cascade...
October 18, 2016: Molecular Ecology
Jinpeng Wang, Jiaxiang Yu, Pengchuan Sun, Yuxian Li, Ruiyan Xia, Yinzhe Liu, Xuelian Ma, Jigao Yu, Nanshan Yang, Tianyu Lei, Zhenyi Wang, Li Wang, Weina Ge, Xiaoming Song, Xiaojian Liu, Sangrong Sun, Tao Liu, Dianchuan Jin, Yuxin Pan, Xiyin Wang
Rice is one of the most researched model plant, and has a genome structure most resembling that of the grass common ancestor after a grass common tetraploidization ∼100 million years ago. There has been a standing controversy whether there had been five or seven basic chromosomes, before the tetraploidization, which were tackled but could not be well solved for the lacking of a sequenced and assembled outgroup plant to have a conservative genome structure. Recently, the availability of pineapple genome, which has not been subjected to the grass-common tetraploidization, provides a precious opportunity to solve the above controversy and to research into genome changes of rice and other grasses...
2016: Frontiers in Genetics
Teng Li, Jie Yang, Yinwan Li, Ying Cui, Qiang Xie, Wenjun Bu, David M Hillis
The Rhyparochromidae, the largest family of Lygaeoidea, encompasses more than 1,850 described species, but no mitochondrial genome has been sequenced to date. Here we describe the first mitochondrial genome for Rhyparochromidae: a complete mitochondrial genome of Panaorus albomaculatus (Scott, 1874). This mitochondrial genome is comprised of 16,345 bp, and contains the expected 37 genes and control region. The majority of the control region is made up of a large tandem-repeat region, which has a novel pattern not previously observed in other insects...
October 19, 2016: Scientific Reports
Liliya Rostomyan, Albert Beckers
Growth hormone (GH) secreting pituitary tumors may be caused by genetic abnormalities in a variety of genes including AIP, MEN1, CDKN1B, and PRKAR1A. These can lead to GH secreting pituitary adenomas as an isolated occurrence (e.g. as aggressive sporadic adenomas or in familial isolated pituitary adenomas (FIPA)) or as part of syndromic conditions such as MEN1 or Carney complex. These tumors have more aggressive features than sporadic acromegaly, including a younger age at disease onset and larger tumor size, and they can be challenging to manage...
October 12, 2016: Growth Hormone & IGF Research
Olga V Popova, Kirill V Mikhailov, Mikhail A Nikitin, Maria D Logacheva, Aleksey A Penin, Maria S Muntyan, Olga S Kedrova, Nikolai B Petrov, Yuri V Panchin, Vladimir V Aleoshin
Many features of mitochondrial genomes of animals, such as patterns of gene arrangement, nucleotide content and substitution rate variation are extensively used in evolutionary and phylogenetic studies. Nearly 6,000 mitochondrial genomes of animals have already been sequenced, covering the majority of animal phyla. One of the groups that escaped mitogenome sequencing is phylum Kinorhyncha-an isolated taxon of microscopic worm-like ecdysozoans. The kinorhynchs are thought to be one of the early-branching lineages of Ecdysozoa, and their mitochondrial genomes may be important for resolving evolutionary relations between major animal taxa...
2016: PloS One
Jose C Jimenez-Lopez, Francisco J Lopez-Valverde, Paula Robles-Bolivar, Elena Lima-Cabello, Emma W Gachomo, Simeon O Kotchoni
Aldehyde dehydrogenases (ALDHs) is a protein superfamily that catalyzes the oxidation of aldehyde molecules into their corresponding non-toxic carboxylic acids, and responding to different environmental stresses, offering promising genetic approaches for improving plant adaptation. The aim of the current study is the functional analysis for systematic identification of S. lycopersicum ALDH gene superfamily. We performed genome-based ALDH genes identification and functional classification, phylogenetic relationship, structure and catalytic domains analysis, and microarray based gene expression...
2016: PloS One
Melania Ester Mercado-Pimentel, Craig Miller, Daniela N Rolph, Edrick F Villalobos, Allison M Dunn, Prithvi M Mohan, Suzu Igarashi, Xiangdang Liu, Macken Yrun-Duffy, Neal K Patel, Cecilia M Read, Ross H Francis, Adelina Isabella Lane, Swaroop Murugesh, Abraham Jacob
HYPOTHESIS: p21-activated kinase (PAK) regulates signaling pathways that promote cell survival and proliferation; therefore, pharmacological inhibition of PAK will induce cell death in vestibular schwannomas (VS) and meningiomas. BACKGROUND: All VS and many meningiomas result from loss of the neurofibromatosis type 2 (NF2) gene product merlin, with ensuing PAK hyperactivation and increased cell proliferation/survival. METHODS: The novel small molecule PAK inhibitors PI-8 and PI-15-tested in schwannoma and meningioma cells-perturb molecular signaling and induce cell death...
October 12, 2016: Otology & Neurotology
Shimpei Baba, Takashi Saito, Yasukazu Yamada, Eri Takeshita, Noriko Nomura, Kenichiro Yamada, Nobuaki Wakamatsu, Masayuki Sasaki
Lesch-Nyhan disease (LND) is a rare X-linked recessive disorder caused by deficiency of the purine salvage enzyme hypoxanthine-guanine phosphoribosyltransferase (HPRT), encoded by the HPRT1. To date, nearly all types of mutations have been reported in the whole gene; however, duplication mutations are rare. We here report the case of a 9-month-old boy with LND. He showed developmental delay, athetosis, and dystonic posture from early infancy, but no self-injurious behaviors. Hyperuricemia was detected, and his HPRT enzyme activity in erythrocytes was completely deficient...
October 18, 2016: Nucleosides, Nucleotides & Nucleic Acids
Y M Zheng, W Z Li, Z X Wang, W Zhang, H Lv, J X Xiao, Y Yuan
OBJECTIVE: To report thigh muscle magnetic resonance imaging (MRI) tests of four Chinese patients with dystrophinopathy with edema changes in adductor longus muscles that mimics adductor enthesopathy. METHODS: Four boys, who were from four unrelated families and aged from 5 to 11 years, were investigated because of the clinical manifestations including myalgia or muscle weakness or the incidental findings of elevated serum creatine kinase levels, and were diagnosed with dystrophinopathy by gene test of Duchenne muscular dystrophy (DMD)...
October 18, 2016: Beijing da Xue Xue Bao. Yi Xue Ban, Journal of Peking University. Health Sciences
Jingzi Zhong, Tiantian Xu, Gang Chen, Haixia Liao, Jiapeng Zhang, Dan Lan
Introduction Duchenne and Becker muscular dystrophies (DMD and BMD) are X-linked myopathies caused by mutations of the dystrophin gene. Methods Multiplex ligation-dependent probe amplification (MLPA) combined with next-generation sequencing (NGS) of the exons of the dystrophin gene were performed in 92 suspected DMD/BMD patients. Patients with negative results were subjected to additional muscle diseases panel tests. Results DNA rearrangements were detected in 65(70.65%) patients using MLPA. The deletions primarily clustered at exons 45-55, followed by exons 2-19...
October 17, 2016: Muscle & Nerve
Jonathan J Lyons, Xiaomin Yu, Jason D Hughes, Quang T Le, Ali Jamil, Yun Bai, Nancy Ho, Ming Zhao, Yihui Liu, Michael P O'Connell, Neil N Trivedi, Celeste Nelson, Thomas DiMaggio, Nina Jones, Helen Matthews, Katie L Lewis, Andrew J Oler, Ryan J Carlson, Peter D Arkwright, Celine Hong, Sherene Agama, Todd M Wilson, Sofie Tucker, Yu Zhang, Joshua J McElwee, Maryland Pao, Sarah C Glover, Marc E Rothenberg, Robert J Hohman, Kelly D Stone, George H Caughey, Theo Heller, Dean D Metcalfe, Leslie G Biesecker, Lawrence B Schwartz, Joshua D Milner
Elevated basal serum tryptase levels are present in 4-6% of the general population, but the cause and relevance of such increases are unknown. Previously, we described subjects with dominantly inherited elevated basal serum tryptase levels associated with multisystem complaints including cutaneous flushing and pruritus, dysautonomia, functional gastrointestinal symptoms, chronic pain, and connective tissue abnormalities, including joint hypermobility. Here we report the identification of germline duplications and triplications in the TPSAB1 gene encoding α-tryptase that segregate with inherited increases in basal serum tryptase levels in 35 families presenting with associated multisystem complaints...
October 17, 2016: Nature Genetics
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