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https://www.readbyqxmd.com/read/27915479/trends-in-next-generation-sequencing-and-a-new-era-for-whole-genome-sequencing
#1
REVIEW
Sang Tae Park, Jayoung Kim
This article is a mini-review that provides a general overview for next-generation sequencing (NGS) and introduces one of the most popular NGS applications, whole genome sequencing (WGS), developed from the expansion of human genomics. NGS technology has brought massively high throughput sequencing data to bear on research questions, enabling a new era of genomic research. Development of bioinformatic software for NGS has provided more opportunities for researchers to use various applications in genomic fields...
November 2016: International Neurourology Journal
https://www.readbyqxmd.com/read/27914874/transmission-networks-and-risk-of-hiv-infection-in-kwazulu-natal-south-africa-a-community-wide-phylogenetic-study
#2
Tulio de Oliveira, Ayesha B M Kharsany, Tiago Gräf, Cherie Cawood, David Khanyile, Anneke Grobler, Adrian Puren, Savathree Madurai, Cheryl Baxter, Quarraisha Abdool Karim, Salim S Abdool Karim
BACKGROUND: The incidence of HIV infection in young women in Africa is very high. We did a large-scale community-wide phylogenetic study to examine the underlying HIV transmission dynamics and the source and consequences of high rates of HIV infection in young women in South Africa. METHODS: We did a cross-sectional household survey of randomly selected individuals aged 15-49 years in two neighbouring subdistricts (one urban and one rural) with a high burden of HIV infection in KwaZulu-Natal, South Africa...
November 30, 2016: Lancet HIV
https://www.readbyqxmd.com/read/27913616/genetic-contributors-to-intergenerational-cag-repeat-instability-in-huntington-s-disease-knock-in-mice
#3
João Luís Neto, Jong-Min Lee, Ali Afridi, Tammy Gillis, Jolene R Guide, Stephani Dempsey, Brenda Lager, Isabel Alonso, Vanessa C Wheeler, Ricardo Mouro Pinto
Huntington's disease is a neurodegenerative disorder caused by the expansion of a CAG trinucleotide repeat in exon 1 of the HTT gene. Longer repeat sizes are associated with increased disease penetrance and earlier ages of onset. Intergenerationally unstable transmissions are common in Huntington's disease families, partly underlying the genetic anticipation seen in this disorder. Huntington's disease CAG knock-in mouse models also exhibit a propensity for intergenerational repeat size changes. In this work, we examine intergenerational instability of the CAG repeat in over 20,000 transmissions in the largest Huntington's disease knock-in mouse model breeding datasets reported to date...
December 2, 2016: Genetics
https://www.readbyqxmd.com/read/27912842/the-rapid-spread-of-carbapenem-resistant-enterobacteriaceae
#4
REVIEW
Robert F Potter, Alaric W D'Souza, Gautam Dantas
Carbapenems, our one-time silver bullet for multidrug resistant bacterial infections, are now threatened by widespread dissemination of carbapenem-resistant Enterobacteriaceae (CRE). Successful expansion of Enterobacteriaceae clonal groups and frequent horizontal gene transfer of carbapenemase expressing plasmids are causing increasing carbapenem resistance. Recent advances in genetic and phenotypic detection facilitate global surveillance of CRE diversity and prevalence. In particular, whole genome sequencing enabled efficient tracking, annotation, and study of genetic elements colocalized with carbapenemase genes on chromosomes and on plasmids...
November 2016: Drug Resistance Updates: Reviews and Commentaries in Antimicrobial and Anticancer Chemotherapy
https://www.readbyqxmd.com/read/27910249/the-hla-a-b-and-drb1-polymorphism-in-a-large-dataset-of-south-brazil-bone-marrow-donors-from-rio-grande-do-sul
#5
J A Boquett, J M Nunes, S Buhler, M Z de Oliveira, L F Jobim, M Jobim, N J R Fagundes, L Schüler-Faccini, A Sanchez-Mazas
Human leukocyte antigen (HLA) genes are very informative in population genetics studies and their variability has been widely used to reconstruct the history of geographic and/or demographic expansions of human populations. The characterization of HLA diversity at the population level is also fundamental in clinical studies, particularly for bone marrow transplantation programs. In this study, we investigated the HLA molecular variation in Rio Grande do Sul, South Brazil, in order to identify possible regional differences across this state...
December 2, 2016: HLA
https://www.readbyqxmd.com/read/27908616/spinocerebellar-ataxia-15-a-phenotypic-review-and-expansion
#6
REVIEW
Philip W Tipton, Kimberly Guthrie, Audrey Strongosky, Ronald Reimer, Zbigniew K Wszolek
Spinocerebellar ataxia 15 (SCA15) is a clinically heterogeneous movement disorder characterized by the adult onset of slowly progressive cerebellar ataxia. ITPR1 is the SCA15 causative gene. However, despite numerous reports of genetically-confirmed SCA15, phenotypic uncertainty persists. We reviewed the phenotypes of 60 patients for whom SCA15 was confirmed by the presence of a genetic deletion involving ITPR1. The most prevalent symptoms were gait ataxia (88.3%), dysarthria (75.0%), nystagmus (73.3%), and limb ataxia (71...
November 10, 2016: Neurologia i Neurochirurgia Polska
https://www.readbyqxmd.com/read/27907027/assessment-of-soybean-flowering-and-seed-maturation-time-in-different-latitude-regions-of-kazakhstan
#7
Saule Abugalieva, Svetlana Didorenko, Shynar Anuarbek, Lubov Volkova, Yelena Gerasimova, Ivan Sidorik, Yerlan Turuspekov
Soybean is still a minor crop in Kazakhstan despite an increase in planting area from 4,500 to 11,400 km2 between 2006 and 2014. However, the Government's recently accepted crop diversification policy projects the expansion of soybean cultivation area to more than 40,000 km2 by 2020. The policy is targeting significant expansion of soybean production in South-eastern, Eastern, and Northern regions of Kazakhstan. Successful realization of this policy requires a comprehensive characterization of plant growth parameters to identify optimal genotypes with appropriate adaptive phenotypic traits...
2016: PloS One
https://www.readbyqxmd.com/read/27905065/spatial-measures-of-genetic-heterogeneity-during-carcinogenesis
#8
K Storey, M D Ryser, K Leder, J Foo
In this work we explore the temporal dynamics of spatial heterogeneity during the process of tumorigenesis from healthy tissue. We utilize a spatial stochastic model of mutation accumulation and clonal expansion in a structured tissue to describe this process. Under a two-step tumorigenesis model, we first derive estimates of a non-spatial measure of diversity: Simpson's Index, which is the probability that two individuals sampled at random from the population are identical, in the premalignant population. We next analyze two new measures of spatial population heterogeneity...
November 30, 2016: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/27904820/the-neurobiology-of-the-prader-willi-phenotype-of-fragile-x-syndrome
#9
REVIEW
Zukhrofi Muzar, Reymundo Lozano, Alexander Kolevzon, Randi J Hagerman
Fragile X syndrome (FXS) is the most common inherited cause of intellectual disability and autism, caused by a CGG expansion to greater than 200 repeats in the promoter region of FMR1 on the bottom of the X chromosome. A subgroup of individuals with FXS experience hyperphagia, lack of satiation after meals and severe obesity, this subgroup is referred to have the Prader-Willi phenotype of FXS. Prader-Willi syndrome is one of the most common genetic severe obesity disorders known and it is caused by the lack of the paternal 15q11-13 region...
November 2016: Intractable & Rare Diseases Research
https://www.readbyqxmd.com/read/27903825/synthetic-biology-routes-to-bio-artificial-intelligence
#10
REVIEW
Darren N Nesbeth, Alexey Zaikin, Yasushi Saka, M Carmen Romano, Claudiu V Giuraniuc, Oleg Kanakov, Tetyana Laptyeva
The design of synthetic gene networks (SGNs) has advanced to the extent that novel genetic circuits are now being tested for their ability to recapitulate archetypal learning behaviours first defined in the fields of machine and animal learning. Here, we discuss the biological implementation of a perceptron algorithm for linear classification of input data. An expansion of this biological design that encompasses cellular 'teachers' and 'students' is also examined. We also discuss implementation of Pavlovian associative learning using SGNs and present an example of such a scheme and in silico simulation of its performance...
November 30, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27903804/structural-protein-vp2-of-african-horse-sickness-virus-is-not-essential-for-virus-replication-in-vitro
#11
René G P van Gennip, Sandra G P van de Water, Christiaan A Potgieter, Piet A van Rijn
: The Reoviridae family consists of non-enveloped multi-layered viruses with a double stranded RNA genome consisting of 9 to 12 genome segments. The Orbivirus genus of the Reoviridae family contains African horse sickness virus (AHSV), bluetongue virus and epizootic haemorrhagic disease virus causing notifiable diseases and are spread by biting Culicoides species. Here, we used reverse genetics for AHSV to study the role of outer capsid protein VP2 encoded by genome segment 2 (Seg-2)...
November 30, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27903293/personalized-medicine-approach-confirms-a-milder-case-of-abat-deficiency
#12
A Besse, A K Petersen, J V Hunter, V Appadurai, S R Lalani, P E Bonnen
ABAT deficiency (OMIM 613163) is a rare inborn error of metabolism caused by recessive variants in the gene 4-aminobutyric acid transaminase (ABAT), which is responsible for both the catalysis of GABA and maintenance of nucleoside pools in the mitochondria. To date, only a few patients have been reported worldwide. Their clinical presentation has been remarkably consistent with primary features of severe psychomotor retardation, encephalopathy, hypotonia, and infantile-onset refractory epilepsy. We report a new case of ABAT deficiency that marks an important departure from previous clinical findings...
December 1, 2016: Molecular Brain
https://www.readbyqxmd.com/read/27902788/fertilization-of-grapevine-based-on-gene-expression
#13
Cheng Zhang, Haifeng Jia, Jingjue Zeng, Tariq Perraiz, Zhenqiang Xie, Xudong Zhu, Chen Wang
The application of genetic information in agricultural production is an important issue, which is highly worthy of attention. Gene expression data can accurately reflect the growth and metabolic status of plants, with which we can predict and monitor the nutritional requirements of plants and then derive accurate fertilization strategies. In this study, to verify the feasibility and workability of gene information-based fertilization strategies and to figure out the specific nutritional requirements of grapevine ( L...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27902491/the-adaptation-rate-of-a-quantitative-trait-in-an-environmental-gradient
#14
R Hermsen
The spatial range of a species habitat is generally determined by the ability of the species to cope with biotic and abiotic variables that vary in space. Therefore, the species range is itself an evolvable property. Indeed, environmental gradients permit a mode of evolution in which range expansion and adaptation go hand in hand. This process can contribute to rapid evolution of drug resistant bacteria and viruses, because drug concentrations in humans and livestock treated with antibiotics are far from uniform...
November 30, 2016: Physical Biology
https://www.readbyqxmd.com/read/27899595/panther-version-11-expanded-annotation-data-from-gene-ontology-and-reactome-pathways-and-data-analysis-tool-enhancements
#15
Huaiyu Mi, Xiaosong Huang, Anushya Muruganujan, Haiming Tang, Caitlin Mills, Diane Kang, Paul D Thomas
The PANTHER database (Protein ANalysis THrough Evolutionary Relationships, http://pantherdb.org) contains comprehensive information on the evolution and function of protein-coding genes from 104 completely sequenced genomes. PANTHER software tools allow users to classify new protein sequences, and to analyze gene lists obtained from large-scale genomics experiments. In the past year, major improvements include a large expansion of classification information available in PANTHER, as well as significant enhancements to the analysis tools...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899484/lack-of-cul4b-in-adipocytes-promotes-ppar%C3%AE-mediated-adipose-tissue-expansion-and-insulin-sensitivity
#16
Peishan Li, Yu Song, Wenying Zan, Liping Qin, Shuang Han, Baichun Jiang, Hao Dou, Changshun Shao, Yaoqin Gong
Obesity and obesity-associated diseases are linked to dysregulation of peroxisome proliferator-activated receptor γ (PPARγ) signaling pathway. Identification of the factors that regulate PPARγ expression and activity is crucial for combating obesity. However, the ubiquitin E3 ligases that target PPARγ for proteasomal degradation have been rarely identified and their functions in vivo have not been characterized. Here we report that CUL4B-RING E3 ligase (CRL4B) negatively regulates PPARγ by promoting its polyubiquitination and proteasomal degradation...
November 29, 2016: Diabetes
https://www.readbyqxmd.com/read/27899195/the-future-of-clinical-cancer-genomics
#17
Kenneth Offit
The current and future applications of genomics to the practice of preventive oncology are being impacted by a number of challenges. These include rapid advances in genomic science and technology that allow massively parallel sequencing of both tumors and the germline, a diminishing of intellectual property restrictions on diagnostic genetic applications, rapid expansion of access to the internet which includes mobile access to both genomic data and tools to communicate and interpret genetic data in a medical context, the expansion of for-profit diagnostic companies seeking to monetize genetic information, and a simultaneous effort to depict medical professionals as barriers to rather than facilitators of understanding one's genome...
October 2016: Seminars in Oncology
https://www.readbyqxmd.com/read/27895927/expansion-mosaicism-and-interruption-mechanisms-of-the-cag-repeat-mutation-in-spinocerebellar-ataxia-type-1
#18
REVIEW
Cara Kraus-Perrotta, Sarita Lagalwar
Spinocerebellar ataxia type 1 (SCA1) is an autosomal dominant neurodegenerative disorder that primarily affects the cerebellum and brainstem. The genetic mutation is an expansion of CAG trinucleotide repeats within the coding region of the ataxin-1 gene, characterizing SCA1 as a polyglutamine expansion disease like Huntington's. As with most polyglutamine expansion diseases, SCA1 follows the rules of genetic anticipation: the larger the expansion, the earlier and more rapid the symptoms. Unlike the majority of polyglutamine expansion diseases, the presence of histidine interruptions within the polyglutamine tract of ataxin-1 protein can prevent or mitigate disease...
2016: Cerebellum & Ataxias
https://www.readbyqxmd.com/read/27895652/rapid-evolution-of-manifold-crispr-systems-for-plant-genome-editing
#19
REVIEW
Levi Lowder, Aimee Malzahn, Yiping Qi
Advanced CRISPR-Cas9 based technologies first validated in mammalian cell systems are quickly being adapted for use in plants. These new technologies increase CRISPR-Cas9's utility and effectiveness by diversifying cellular capabilities through expression construct system evolution and enzyme orthogonality, as well as enhanced efficiency through delivery and expression mechanisms. Here, we review the current state of advanced CRISPR-Cas9 and Cpf1 capabilities in plants and cover the rapid evolution of these tools from first generation inducers of double strand breaks for basic genetic manipulations to second and third generation multiplexed systems with myriad functionalities, capabilities, and specialized applications...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27895639/netosis-as-source-of-autoantigens-in-rheumatoid-arthritis
#20
REVIEW
Elisa Corsiero, Federico Pratesi, Edoardo Prediletto, Michele Bombardieri, Paola Migliorini
In neutrophils (but also in eosinophils and in mast cells), different inflammatory stimuli induce histone deimination, chromatin decondensation, and NET formation. These web-like structures that trap and kill microbes contain DNA, cationic granule proteins, and antimicrobial peptides, but the most abundant proteins are core histones. Histones contained in NETs have been deiminated, and arginines are converted in citrullines. While deimination is a physiological process amplified in inflammatory conditions, only individuals carrying genetic predisposition to develop rheumatoid arthritis (RA) make antibodies to deiminated proteins...
2016: Frontiers in Immunology
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