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Integrative genomics

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https://www.readbyqxmd.com/read/29792903/endogenous-pararetrovirus-sequences-are-widely-present-in-citrinae-genomes
#1
Huiwen Yu, Xia Wang, Zhihao Lu, Yuantao Xu, Xiuxin Deng, Qiang Xu
Endogenous pararetroviruses (EPRVs) are characterized in several plant genomes and their biological effects have been reported. In this study, hundreds of EPRV segments were identified in six Citrinae genomes. A total of 1,034 EPRV segments were identified in the genomes of sweet orange, 2,036 in pummelo, 598 in clementine mandarin, 752 in Ichang papeda, 2,060 in citron and 245 in atalantia. Genomic analysis indicated that EPRV segments tend to cluster as hot spots in the genomes, particularly on chromosome 2 and 5...
May 21, 2018: Virus Research
https://www.readbyqxmd.com/read/29792160/nextsv-a-meta-caller-for-structural-variants-from-low-coverage-long-read-sequencing-data
#2
Li Fang, Jiang Hu, Depeng Wang, Kai Wang
BACKGROUND: Structural variants (SVs) in human genomes are implicated in a variety of human diseases. Long-read sequencing delivers much longer read lengths than short-read sequencing and may greatly improve SV detection. However, due to the relatively high cost of long-read sequencing, it is unclear what coverage is needed and how to optimally use the aligners and SV callers. RESULTS: In this study, we developed NextSV, a meta-caller to perform SV calling from low coverage long-read sequencing data...
May 23, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29792157/long-term-health-and-germline-transmission-in-transgenic-cattle-following-transposon-mediated-gene-transfer
#3
Soo-Young Yum, Song-Jeon Lee, Sin-Gi Park, In-Gang Shin, Sang-Eun Hahn, Woo-Jae Choi, Hee-Soo Kim, Hyeong-Jong Kim, Seong-Hun Bae, Je-Hyeong Lee, Joo-Yeong Moon, Woo-Sung Lee, Ji-Hyun Lee, Choong-Il Lee, Seong-Jin Kim, Goo Jang
BACKGROUND: Transposon-mediated, non-viral gene delivery is a powerful tool for generating stable cell lines and transgenic animals. However, as multi-copy insertion is the preferred integration pattern, there is the potential for uncontrolled changes in endogenous gene expression and detrimental effects in cells or animals. Our group has previously reported on the generation of several transgenic cattle by using microinjection of the Sleeping Beauty (SB) and PiggyBac (PB) transposons and seeks to explore the long-term effects of this technology on cattle...
May 23, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29791443/traceability-reproducibility-and-wiki-exploration-for-%C3%A3-la-carte-reconstructions-of-genome-scale-metabolic-models
#4
Méziane Aite, Marie Chevallier, Clémence Frioux, Camille Trottier, Jeanne Got, María Paz Cortés, Sebastián N Mendoza, Grégory Carrier, Olivier Dameron, Nicolas Guillaudeux, Mauricio Latorre, Nicolás Loira, Gabriel V Markov, Alejandro Maass, Anne Siegel
Genome-scale metabolic models have become the tool of choice for the global analysis of microorganism metabolism, and their reconstruction has attained high standards of quality and reliability. Improvements in this area have been accompanied by the development of some major platforms and databases, and an explosion of individual bioinformatics methods. Consequently, many recent models result from "à la carte" pipelines, combining the use of platforms, individual tools and biological expertise to enhance the quality of the reconstruction...
May 23, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29790989/the-galaxy-platform-for-accessible-reproducible-and-collaborative-biomedical-analyses-2018-update
#5
Enis Afgan, Dannon Baker, Bérénice Batut, Marius van den Beek, Dave Bouvier, Martin Cech, John Chilton, Dave Clements, Nate Coraor, Björn A Grüning, Aysam Guerler, Jennifer Hillman-Jackson, Saskia Hiltemann, Vahid Jalili, Helena Rasche, Nicola Soranzo, Jeremy Goecks, James Taylor, Anton Nekrutenko, Daniel Blankenberg
Galaxy (homepage: https://galaxyproject.org, main public server: https://usegalaxy.org) is a web-based scientific analysis platform used by tens of thousands of scientists across the world to analyze large biomedical datasets such as those found in genomics, proteomics, metabolomics and imaging. Started in 2005, Galaxy continues to focus on three key challenges of data-driven biomedical science: making analyses accessible to all researchers, ensuring analyses are completely reproducible, and making it simple to communicate analyses so that they can be reused and extended...
May 22, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29790939/nextstrain-real-time-tracking-of-pathogen-evolution
#6
James Hadfield, Colin Megill, Sidney M Bell, John Huddleston, Barney Potter, Charlton Callender, Pavel Sagulenko, Trevor Bedford, Richard A Neher
Summary: Understanding the spread and evolution of pathogens is important for effective public health measures and surveillance. Nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualisation platform. Together these present a real-time view into the evolution and spread of a range of viral pathogens of high public health importance. The visualization integrates sequence data with other data types such as geographic information, serology, or host species...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29790460/establishment-of-the-european-meningococcal-strain-collection-genome-library-emsc-gl-for-the-2011-to-2012-epidemiological-year
#7
Holly B Bratcher, Carina Brehony, Sigrid Heuberger, Despo Pieridou-Bagatzouni, Pavla Křížová, Steen Hoffmann, Maija Toropainen, Muhamed-Kheir Taha, Heike Claus, Georgina Tzanakaki, Tímea Erdôsi, Jelena Galajeva, Arie van der Ende, Anna Skoczyńska, Marina Pana, Alena Vaculíková, Metka Paragi, Martin Cj Maiden, Dominique A Caugant
Invasive meningococcal disease surveillance in Europe combines isolate characterisation and epidemiological data to support public health intervention. A representative European Meningococcal Strain Collection (EMSC) of IMD isolates was obtained, and whole genome sequenced to characterise 799 EMSC isolates from the epidemiological year July 2011-June 2012. To establish a genome library (GL), the isolate information was deposited in the pubMLST.org/neisseria database. Genomes were curated and annotated at 2,429 meningococcal loci, including those defining clonal complex, capsule, antigens, and antimicrobial resistance...
May 2018: Euro Surveillance: Bulletin Européen sur les Maladies Transmissibles, European Communicable Disease Bulletin
https://www.readbyqxmd.com/read/29790107/the-role-of-pharmacogenomics-in-bipolar-disorder-moving-towards-precision-medicine
#8
REVIEW
Claudia Pisanu, Urs Heilbronner, Alessio Squassina
Bipolar disorder (BD) is a common and disabling psychiatric condition with a severe socioeconomic impact. BD is treated with mood stabilizers, among which lithium represents the first-line treatment. Lithium alone or in combination is effective in 60% of chronically treated patients, but response remains heterogenous and a large number of patients require a change in therapy after several weeks or months. Many studies have so far tried to identify molecular and genetic markers that could help us to predict response to mood stabilizers or the risk for adverse drug reactions...
May 22, 2018: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/29789800/-lra-i-from-lactococcus-raffinolactis-bgtrk10-1-an-isoschizomer-of-eco-ri-exhibits-ion-concentration-dependent-specific-star-activity
#9
Marija Miljkovic, Milka Malesevic, Brankica Filipic, Goran Vukotic, Milan Kojic
Restriction enzymes are the main defence system against foreign DNA, in charge of preserving genome integrity. Lactococcus raffinolactis BGTRK10-1 expresses Lra I Type II restriction-modification enzyme, whose activity is similar to that shown for Eco RI; Lra I methyltransferase protects DNA from Eco RI cleavage. The gene encoding Lra I endonuclease was cloned and overexpressed in E. coli . Purified enzyme showed the highest specific activity at lower temperatures (between 13°C and 37°C) and was stable after storage at -20°C in 50% glycerol...
2018: BioMed Research International
https://www.readbyqxmd.com/read/29789543/rapid-pathway-prototyping-and-engineering-using-in-vitro-and-in-vivo-synthetic-genome-scramble-in-methods
#10
Wei Liu, Zhouqing Luo, Yun Wang, Nhan T Pham, Laura Tuck, Irene Pérez-Pi, Longying Liu, Yue Shen, Chris French, Manfred Auer, Jon Marles-Wright, Junbiao Dai, Yizhi Cai
Exogenous pathway optimization and chassis engineering are two crucial methods for heterologous pathway expression. The two methods are normally carried out step-wise and in a trial-and-error manner. Here we report a recombinase-based combinatorial method (termed "SCRaMbLE-in") to tackle both challenges simultaneously. SCRaMbLE-in includes an in vitro recombinase toolkit to rapidly prototype and diversify gene expression at the pathway level and an in vivo genome reshuffling system to integrate assembled pathways into the synthetic yeast genome while combinatorially causing massive genome rearrangements in the host chassis...
May 22, 2018: Nature Communications
https://www.readbyqxmd.com/read/29789391/mst2-kinase-suppresses-rdna-transcription-in-response-to-dna-damage-by-phosphorylating-nucleolar-histone-h2b
#11
Dafni Eleftheria Pefani, Maria Laura Tognoli, Deniz Pirincci Ercan, Vassilis Gorgoulis, Eric O'Neill
The heavily transcribed rDNA repeats that give rise to the ribosomal RNA are clustered in a unique chromatin structure, the nucleolus. Due to its highly repetitive nature and transcriptional activity, the nucleolus is considered a hotspot of genomic instability. Breaks in rDNA induce a transient transcriptional shut down to conserve energy and promote rDNA repair; however, how nucleolar chromatin is modified and impacts on rDNA repair is unknown. Here, we uncover that phosphorylation of serine 14 on histone H2B marks transcriptionally inactive nucleolar chromatin in response to DNA damage...
May 22, 2018: EMBO Journal
https://www.readbyqxmd.com/read/29788909/whole-genome-analysis-reveals-the-diversity-and-evolutionary-relationships-between-necrotic-enteritis-causing-strains-of-clostridium-perfringens
#12
Jake A Lacey, Theodore R Allnutt, Ben Vezina, Thi Thu Hao Van, Thomas Stent, Xiaoyan Han, Julian I Rood, Ben Wade, Anthony L Keyburn, Torsten Seemann, Honglei Chen, Volker Haring, Priscilla A Johanesen, Dena Lyras, Robert J Moore
BACKGROUND: Clostridium perfringens causes a range of diseases in animals and humans including necrotic enteritis in chickens and food poisoning and gas gangrene in humans. Necrotic enteritis is of concern in commercial chicken production due to the cost of the implementation of infection control measures and to productivity losses. This study has focused on the genomic analysis of a range of chicken-derived C. perfringens isolates, from around the world and from different years. The genomes were sequenced and compared with 20 genomes available from public databases, which were from a diverse collection of isolates from chickens, other animals, and humans...
May 22, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29788735/hpv-status-and-its-genomic-integration-affect-survival-of-patients-with-cervical-cancer
#13
M Ibragimova, M Tsyganov, O Shpileva, O Churuksaeva, V Bychkov, L Kolomiets, N Litviakov
To evaluate the relapse-free and overall survival of HPV-positive patients with regard to the physical status of type 16 HPV and of HPV-negative patients with primary CC. As a main result of the study the predictive value of the physical status of type 16 HPV was determined for relapse-free and overall survival of patients with CC. Episomal form of the virus is a favorable predictive factor. Integrated form of the virus is a severely unfavorable predictive factor and survival of such patients is significantly lower, than for HPV- patients and patients with mixed form of the virus...
March 14, 2018: Neoplasma
https://www.readbyqxmd.com/read/29788479/repeated-cis-regulatory-tuning-of-a-metabolic-bottleneck-gene-during-evolution
#14
Meihua Christina Kuang, Jacek Kominek, William G Alexander, Jan-Fang Cheng, Russell L Wrobel, Chris Todd Hittinger
Repeated evolutionary events imply underlying genetic constraints that can make evolutionary mechanisms predictable. Morphological traits are thought to evolve frequently through cis-regulatory changes because these mechanisms bypass constraints in pleiotropic genes that are reused during development. In contrast, the constraints acting on metabolic traits during evolution are less well studied. Here we show how a metabolic bottleneck gene has repeatedly adopted similar cis-regulatory solutions during evolution, likely due to its pleiotropic role integrating flux from multiple metabolic pathways...
May 21, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29788473/enhancing-psychosis-spectrum-nosology-through-an-international-data-sharing-initiative
#15
Anna R Docherty, Eduardo Fonseca-Pedrero, Martin Debbané, Raymond C K Chan, Richard J Linscott, Katherine G Jonas, David C Cicero, Melissa J Green, Leonard J Simms, Oliver Mason, David Watson, Ulrich Ettinger, Monika Waszczuk, Alexander Rapp, Phillip Grant, Roman Kotov, Colin G DeYoung, Camilo J Ruggero, Nicolas R Eaton, Robert F Krueger, Christopher Patrick, Christopher Hopwood, F Anthony O'Neill, David H Zald, Christopher C Conway, Daniel E Adkins, Irwin D Waldman, Jim van Os, Patrick F Sullivan, John S Anderson, Andrey A Shabalin, Scott R Sponheim, Stephan F Taylor, Rachel G Grazioplene, Silviu A Bacanu, Tim B Bigdeli, Corinna Haenschel, Dolores Malaspina, Diane C Gooding, Kristin Nicodemus, Frauke Schultze-Lutter, Neus Barrantes-Vidal, Christine Mohr, William T Carpenter, Alex S Cohen
The latent structure of schizotypy and psychosis-spectrum symptoms remains poorly understood. Furthermore, molecular genetic substrates are poorly defined, largely due to the substantial resources required to collect rich phenotypic data across diverse populations. Sample sizes of phenotypic studies are often insufficient for advanced structural equation modeling approaches. In the last 50 years, efforts in both psychiatry and psychological science have moved toward (1) a dimensional model of psychopathology (eg, the current Hierarchical Taxonomy of Psychopathology [HiTOP] initiative), (2) an integration of methods and measures across traits and units of analysis (eg, the RDoC initiative), and (3) powerful, impactful study designs maximizing sample size to detect subtle genomic variation relating to complex traits (the Psychiatric Genomics Consortium [PGC])...
May 16, 2018: Schizophrenia Bulletin
https://www.readbyqxmd.com/read/29788229/subtiwiki-in-2018-from-genes-and-proteins-to-functional-network-annotation-of-the-model-organism-bacillus-subtilis
#16
Bingyao Zhu, Jörg Stülke
Living cells are made up of individual parts, i.e. the genome, the proteins, the RNA and lipid molecules as well as the metabolites and ions. However, life depends on the functional interaction among these components which is often organized in networks. Here, we present the recent development of SubtiWiki, the integrated database for the model bacterium Bacillus subtilis (http://subtiwiki.uni-goettingen.de/). SubtiWiki is based on a relational database and provides access to published information about the genes and proteins of B...
January 4, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29788182/global-distribution-of-genetic-traits-gadget-web-server-polygenic-trait-scores-worldwide
#17
Aroon T Chande, Lu Wang, Lavanya Rishishwar, Andrew B Conley, Emily T Norris, Augusto Valderrama-Aguirre, I King Jordan
Human populations from around the world show striking phenotypic variation across a wide variety of traits. Genome-wide association studies (GWAS) are used to uncover genetic variants that influence the expression of heritable human traits; accordingly, population-specific distributions of GWAS-implicated variants may shed light on the genetic basis of human phenotypic diversity. With this in mind, we developed the GlobAl Distribution of GEnetic Traits web server (GADGET http://gadget.biosci.gatech.edu). The GADGET web server provides users with a dynamic visual platform for exploring the relationship between worldwide genetic diversity and the genetic architecture underlying numerous human phenotypes...
May 18, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29787760/in-vivo-gene-correction-with-targeted-sequence-substitution-through-microhomology-mediated-end-joining
#18
Jeong Hong Shin, Soobin Jung, Suresh Ramakrishna, Hyongbum Henry Kim, Junwon Lee
Genome editing technology using programmable nucleases has rapidly evolved in recent years. The primary mechanism to achieve precise integration of a transgene is mainly based on homology-directed repair (HDR). However, an HDR-based genome-editing approach is less efficient than non-homologous end-joining (NHEJ). Recently, a microhomology-mediated end-joining (MMEJ)-based transgene integration approach was developed, showing feasibility both in vitro and in vivo. We expanded this method to achieve targeted sequence substitution (TSS) of mutated sequences with normal sequences using double-guide RNAs (gRNAs), and a donor template flanking the microhomologies and target sequence of the gRNAs in vitro and in vivo...
May 19, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29787443/old-data-new-concepts-integrating-indirect-effects-into-radiation-protection
#19
Carmel Mothersill, Colin Seymour
PURPOSE: To address the following key question, what are the consequences of nontargeted and delayed effects for linear nonthreshold models of radiation risk? This paper considers low-dose "indirect" or nontargeted effects and how they might impact radiation protection, particularly at the level of the environment. Nontargeted effects refer to effects in cells, tissues, or organisms that were not targeted by irradiation and that did not receive direct energy deposition. They include genomic instability and lethal mutations in progeny of irradiated cells and bystander effects in neighboring cells, tissues, or organisms...
July 2018: Health Physics
https://www.readbyqxmd.com/read/29786967/developmental-chromatin-restriction-of-pro-growth-gene-networks-acts-as-an-epigenetic-barrier-to-axon-regeneration-in-cortical-neurons
#20
Ishwariya Venkatesh, Vatsal Mehra, Zimei Wang, Ben Califf, Murray G Blackmore
Axon regeneration in the central nervous system is prevented in part by a developmental decline in the intrinsic regenerative ability of maturing neurons. This loss of axon growth ability likely reflects widespread changes in gene expression, but the mechanisms that drive this shift remain unclear. Chromatin accessibility has emerged as a key regulatory mechanism in other cellular contexts, raising the possibility that chromatin structure may contribute to the age-dependent loss of regenerative potential. Here we establish an integrated bioinformatic pipeline that combines analysis of developmentally dynamic gene networks with transcription factor regulation and genome-wide maps of chromatin accessibility...
May 22, 2018: Developmental Neurobiology
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