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https://www.readbyqxmd.com/read/27922122/identification-of-critical-paralog-groups-with-indispensable-roles-in-the-regulation-of-signaling-flow
#1
Dezso Modos, Johanne Brooks, David Fazekas, Eszter Ari, Tibor Vellai, Peter Csermely, Tamas Korcsmaros, Katalin Lenti
Extensive cross-talk between signaling pathways is required to integrate the myriad of extracellular signal combinations at the cellular level. Gene duplication events may lead to the emergence of novel functions, leaving groups of similar genes - termed paralogs - in the genome. To distinguish critical paralog groups (CPGs) from other paralogs in human signaling networks, we developed a signaling network-based method using cross-talk annotation and tissue-specific signaling flow analysis. 75 CPGs were found with higher degree, betweenness centrality, closeness, and 'bowtieness' when compared to other paralogs or other proteins in the signaling network...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27920791/extending-a-single-residue-switch-for-abbreviating-catalysis-in-plant-ent-kaurene-synthases
#2
Meirong Jia, Reuben J Peters
Production of ent-kaurene as a precursor for important signaling molecules such as the gibberellins seems to have arisen early in plant evolution, with corresponding cyclase(s) present in all land plants (i.e., embryophyta). The relevant enzymes seem to represent fusion of the class II diterpene cyclase that produces the intermediate ent-copalyl diphosphate (ent-CPP) and the subsequently acting class I diterpene synthase that produces ent-kaurene, although the bifunctionality of the ancestral gene is only retained in certain early diverging plants, with gene duplication and sub-functionalization leading to distinct ent-CPP synthases and ent-kaurene synthases (KSs) generally observed...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27919807/a-cryptic-species-produced-by-autopolyploidy-and-subsequent-introgression-involving-medicago-prostrata-fabaceae
#3
J S Eriksson, J L Blanco-Pastor, F D Sousa, Y J K Bertrand, B E Pfeil
Although hybridisation through genome duplication is well known, hybridisation without genome duplication (homoploid hybrid speciation, HHS) is not. Few well-documented cases have been reported. A possible instance of HHS in Medicago prostrata Jacq. was suggested previously, based on only two genes and one individual. We tested whether this species was formed through HHS by sampling eight nuclear loci and 22 individuals, with additional individuals from related species, using gene capture and Illumina sequencing...
December 2, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/27919067/genome-wide-changes-in-lncrna-splicing-and-regional-gene-expression-patterns-in-autism
#4
Neelroop N Parikshak, Vivek Swarup, T Grant Belgard, Manuel Irimia, Gokul Ramaswami, Michael J Gandal, Christopher Hartl, Virpi Leppa, Luis de la Torre Ubieta, Jerry Huang, Jennifer K Lowe, Benjamin J Blencowe, Steve Horvath, Daniel H Geschwind
Autism spectrum disorder (ASD) involves substantial genetic contributions. These contributions are profoundly heterogeneous but may converge on common pathways that are not yet well understood. Here, through post-mortem genome-wide transcriptome analysis of the largest cohort of samples analysed so far, to our knowledge, we interrogate the noncoding transcriptome, alternative splicing, and upstream molecular regulators to broaden our understanding of molecular convergence in ASD. Our analysis reveals ASD-associated dysregulation of primate-specific long noncoding RNAs (lncRNAs), downregulation of the alternative splicing of activity-dependent neuron-specific exons, and attenuation of normal differences in gene expression between the frontal and temporal lobes...
December 5, 2016: Nature
https://www.readbyqxmd.com/read/27918584/the-ace-1-locus-is-amplified-in-all-resistant-anopheles-gambiae-mosquitoes-fitness-consequences-of-homogeneous-and-heterogeneous-duplications
#5
Benoît S Assogba, Pascal Milesi, Luc S Djogbénou, Arnaud Berthomieu, Patrick Makoundou, Lamine S Baba-Moussa, Anna-Sophie Fiston-Lavier, Khalid Belkhir, Pierrick Labbé, Mylène Weill
Gene copy-number variations are widespread in natural populations, but investigating their phenotypic consequences requires contemporary duplications under selection. Such duplications have been found at the ace-1 locus (encoding the organophosphate and carbamate insecticides' target) in the mosquito Anopheles gambiae (the major malaria vector); recent studies have revealed their intriguing complexity, consistent with the involvement of various numbers and types (susceptible or resistant to insecticide) of copies...
December 2016: PLoS Biology
https://www.readbyqxmd.com/read/27918582/investigating-conservation-of-the-cell-cycle-regulated-transcriptional-program-in-the-fungal-pathogen-cryptococcus-neoformans
#6
Christina M Kelliher, Adam R Leman, Crystal S Sierra, Steven B Haase
The pathogenic yeast Cryptococcus neoformans causes fungal meningitis in immune-compromised patients. Cell proliferation in the budding yeast form is required for C. neoformans to infect human hosts, and virulence factors such as capsule formation and melanin production are affected by cell-cycle perturbation. Thus, understanding cell-cycle regulation is critical for a full understanding of virulence factors for disease. Our group and others have demonstrated that a large fraction of genes in Saccharomyces cerevisiae is expressed periodically during the cell cycle, and that proper regulation of this transcriptional program is important for proper cell division...
December 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27917949/intravenous-hmscs-ameliorate-acute-pancreatitis-in-mice-via-secretion-of-tumor-necrosis-factor-%C3%AE-stimulated-gene-protein-6
#7
Zhigang He, Jie Hua, Daohai Qian, Jian Gong, Shengping Lin, Chenglei Xu, Ge Wei, Hongbo Meng, Tingsong Yang, Bo Zhou, Zhenshun Song
The administration of mesenchymal stem cells/multipotent mesenchymal stromal cells (MSCs) to enhance tissue repair is currently undergoing clinical trials. Some studies, including our previous work, have also revealed the beneficial effect of MSCs in severe acute pancreatitis (SAP); however, their mechanisms or mode of action remain controversial. In this study, we demonstrated that intravenously (i.v.)-administered human MSCs (hMSCs) remarkably promoted recovery from experimental SAP without significant engraftment of hMSCs in the damaged pancreas...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27917507/evidence-of-a-genomic-insertion-in-intron-2-of-sod1-causing-allelic-drop-out-during-routine-diagnostic-testing-for-canine-degenerative-myelopathy
#8
M E Turba, R Loechel, E Rombolà, G Gandini, F Gentilini
Degenerative myelopathy is a severe and progressive neurodegenerative disease and, in the majority of breeds, is associated with the c.118G>A substitution in exon 2 of the canine superoxide dismutase 1 (SOD1) gene. Our laboratories have been engaged in determining the cause of many discordant findings between the parental and the offspring genotypes found by different laboratories. In both cases, the discordant findings refer to actual heterozygous dogs that had been typed as homozygous for the variant allele...
December 4, 2016: Animal Genetics
https://www.readbyqxmd.com/read/27917185/fire-and-brimstone-molecular-interactions-between-sulfur-and-glucosinolate-biosynthesis-in-model-and-crop-brassicaceae
#9
REVIEW
Priyakshee Borpatragohain, Terry J Rose, Graham J King
Glucosinolates (GSLs) represent one of the most widely studied classes of plant secondary metabolite, and have a wide range of biological activities. Their unique properties also affect livestock and human health, and have been harnessed for food and other end-uses. Since GSLs are sulfur (S)-rich there are many lines of evidence suggesting that plant S status plays a key role in determining plant GSL content. However, there is still a need to establish a detailed knowledge of the distribution and remobilization of S and GSLs throughout the development of Brassica crops, and to represent this in terms of primary and secondary sources and sinks...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27916797/pseudogenes-and-their-genome-wide-prediction-in-plants
#10
REVIEW
Jin Xiao, Manoj Kumar Sekhwal, Pingchuan Li, Raja Ragupathy, Sylvie Cloutier, Xiue Wang, Frank M You
Pseudogenes are paralogs generated from ancestral functional genes (parents) during genome evolution, which contain critical defects in their sequences, such as lacking a promoter, having a premature stop codon or frameshift mutations. Generally, pseudogenes are functionless, but recent evidence demonstrates that some of them have potential roles in regulation. The majority of pseudogenes are generated from functional progenitor genes either by gene duplication (duplicated pseudogenes) or retro-transposition (processed pseudogenes)...
November 28, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27913546/diagnosing-von-willebrand-disease-genetic-analysis
#11
Anne Goodeve
Investigation of a patient with possible von Willebrand disease (VWD) includes a range of phenotypic analyses. Often, this is sufficient to discern disease type, and this will suggest relevant treatment. However, for some patients, phenotypic analysis does not sufficiently explain the patient's disorder, and for this group, genetic analysis can aid diagnosis of disease type. Polymerase chain reaction and Sanger sequencing have been mainstays of genetic analysis for several years. More recently, next-generation sequencing has become available, with the advantage that several genes can be simultaneously analyzed where necessary, eg, for discrimination of possible type 2N VWD or mild hemophilia A...
December 2, 2016: Hematology—the Education Program of the American Society of Hematology
https://www.readbyqxmd.com/read/27913274/two-grass-carp-ctenopharyngodon-idella-insulin-like-growth-factor-binding-protein-5-genes-exhibit-different-yet-conserved-functions-in-development-and-growth
#12
Guo-Dong Zheng, Chun-Xue Zhou, Si-Tong Lin, Jie Chen, Xia-Yun Jiang, Shu-Ming Zou
Insulin-like growth factor binding-protein 5 (igfbp5), the most conserved member of the IGFBP family in vertebrates, plays a critical role in controlling cell survival, growth, differentiation, and apoptosis. Here, we characterized the expression patterns of igfbp5a and igfbp5b in grass carp (Ctenopharyngodon idella), which are retained in many fish species, likely from the teleost-specific whole-genome duplication. Both igfbp5a and igfbp5b encode 268- and 263-aa peptides, respectively, which share a sequence identity of 71%...
November 29, 2016: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
https://www.readbyqxmd.com/read/27911792/transcriptomics-and-neuroanatomy-of-the-clonal-raider-ant-implicate-an-expanded-clade-of-odorant-receptors-in-chemical-communication
#13
Sean K McKenzie, Ingrid Fetter-Pruneda, Vanessa Ruta, Daniel J C Kronauer
A major aim of sociogenomic research is to uncover common principles in the molecular evolution of sociality. This endeavor has been hampered by the small number of specific genes currently known to function in social behavior. Here we provide several lines of evidence suggesting that ants have evolved a large and novel clade of odorant receptor (OR) genes to perceive hydrocarbon-based pheromones, arguably the most important signals in ant communication. This genomic expansion is also mirrored in the ant brain via a corresponding expansion of a specific cluster of glomeruli in the antennal lobe...
November 22, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27910910/genome-wide-characterisation-and-expression-profile-of-the-grapevine-atl-ubiquitin-ligase-family-reveal-biotic-and-abiotic-stress-responsive-and-development-related-members
#14
Pietro Ariani, Alice Regaiolo, Arianna Lovato, Alejandro Giorgetti, Andrea Porceddu, Salvatore Camiolo, Darren Wong, Simone Castellarin, Elodie Vandelle, Annalisa Polverari
The Arabidopsis Tóxicos en Levadura (ATL) protein family is a class of E3 ubiquitin ligases with a characteristic RING-H2 Zn-finger structure that mediates diverse physiological processes and stress responses in plants. We carried out a genome-wide survey of grapevine (Vitis vinifera L.) ATL genes and retrieved 96 sequences containing the canonical ATL RING-H2 domain. We analysed their genomic organisation, gene structure and evolution, protein domains and phylogenetic relationships. Clustering revealed several clades, as already reported in Arabidopsis thaliana and rice (Oryza sativa), with an expanded subgroup of grapevine-specific genes...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27910763/il10-a-tale-of-an-evolutionarily-conserved-cytokine-across-vertebrates
#15
M Carla Piazzon, George Lutfalla, Maria Forlenza
IL10 was discovered in 1989, and since then it has been the subject of intense investigation, which has revealed its potent anti-inflammatory and regulatory activities in most immune processes during infection and disease. In 2003, the first non-mammalian IL10 sequence was identified in teleost fish, followed in 2004 by the chicken IL10 sequence. In this review, we summarize the work performed in non-mammalian vertebrates in which the IL10, IL10 receptors (IL10Rs), and their signaling components have been identified...
2016: Critical Reviews in Immunology
https://www.readbyqxmd.com/read/27909301/genetic-architecture-and-evolution-of-the-s-locus-supergene-in-primula-vulgaris
#16
Jinhong Li, Jonathan M Cocker, Jonathan Wright, Margaret A Webster, Mark McMullan, Sarah Dyer, David Swarbreck, Mario Caccamo, Cock van Oosterhout, Philip M Gilmartin
Darwin's studies on heterostyly in Primula described two floral morphs, pin and thrum, with reciprocal anther and stigma heights that promote insect-mediated cross-pollination. This key innovation evolved independently in several angiosperm families. Subsequent studies on heterostyly in Primula contributed to the foundation of modern genetic theory and the neo-Darwinian synthesis. The established genetic model for Primula heterostyly involves a diallelic S locus comprising several genes, with rare recombination events that result in self-fertile homostyle flowers with anthers and stigma at the same height...
December 2, 2016: Nature Plants
https://www.readbyqxmd.com/read/27908631/confirmation-of-the-gnb4-gene-as-causal-for-charcot-marie-tooth-disease-by-a-novel-de-novo-mutation-in-a-czech-patient
#17
Laššuthová Petra, Šafka Brožková Dana, Neupauerová Jana, Krůtová Marcela, Mazanec Radim, Seeman Pavel
The association of GNB4 with Charcot-Marie-Tooth (CMT) has recently been described in a publication by Soong et al. (Soong, et al., 2013). Here we present a patient with CMT in whom whole exome sequencing identified the mutation p.Lys57Glu in the GNB4 gene (NM_021629.3:c.169A>G). The patient, now 41 years old, is a sporadic case in the family. At the age of 35 he presented with severe disability (CMT neuropathy score 29), profound muscle atrophies, pes cavus and scoliosis. Previously, the patient was tested for PMP22 duplications/deletions and later also with 64 CMT gene panel, with no causal variant found...
September 22, 2016: Neuromuscular Disorders: NMD
https://www.readbyqxmd.com/read/27906638/gene-duplications-and-losses-among-vertebrate-deoxyribonucleoside-kinases-of-the-non-tk1-family
#18
Zeeshan Mutahir, Louise Slot Christiansen, Anders R Clausen, Martin W Berchtold, Zoran Gojkovic, Birgitte Munch-Petersen, Wolfgang Knecht, Jure Piškur
Deoxyribonucleoside kinases (dNKs) salvage deoxyribonucleosides (dNs) and catalyze the rate limiting step of this salvage pathway by converting dNs into corresponding monophosphate forms. These enzymes serve as an excellent model to study duplicated genes and their evolutionary history. So far, among vertebrates only four mammalian dNKs have been studied for their substrate specificity and kinetic properties. However, some vertebrates, such as fish, frogs, and birds, apparently possess a duplicated homolog of deoxycytidine kinase (dCK)...
December 2016: Nucleosides, Nucleotides & Nucleic Acids
https://www.readbyqxmd.com/read/27906199/microduplication-of-the-arid1a-gene-causes-intellectual-disability-with-recognizable-syndromic-features
#19
Marie Bidart, Michèle El Atifi, Sarra Miladi, John Rendu, Véronique Satre, Pierre F Ray, Caroline Bosson, Françoise Devillard, Daphné Lehalle, Valérie Malan, Jeanne Amiel, Maria Antonietta Mencarelli, Margherita Baldassarri, Alessandra Renieri, Jill Clayton-Smith, Gaëlle Vieville, Julien Thevenon, Florence Amblard, François Berger, Pierre-Simon Jouk, Charles Coutton
PURPOSE: To determine whether duplication of the ARID1A gene is responsible for a new recognizable syndrome. METHODS: We describe four patients with a 1p36.11 microduplication involving ARID1A as identified by array-comparative genomic hybridization . We performed comparative transcriptomic analysis of patient-derived fibroblasts using RNA sequencing and evaluated the impact of ARID1A duplication on the cell cycle using fluorescence-activated cell sorting. Functional relationships between differentially expressed genes were investigated with ingenuity pathway analysis (IPA)...
December 1, 2016: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/27904954/the-mathematics-of-xenology-di-cographs-symbolic-ultrametrics-2-structures-and-tree-representable-systems-of-binary-relations
#20
Marc Hellmuth, Peter F Stadler, Nicolas Wieseke
The concepts of orthology, paralogy, and xenology play a key role in molecular evolution. Orthology and paralogy distinguish whether a pair of genes originated by speciation or duplication. The corresponding binary relations on a set of genes form complementary cographs. Allowing more than two types of ancestral event types leads to symmetric symbolic ultrametrics. Horizontal gene transfer, which leads to xenologous gene pairs, however, is inherent asymmetric since one offspring copy "jumps" into another genome, while the other continues to be inherited vertically...
November 30, 2016: Journal of Mathematical Biology
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