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https://www.readbyqxmd.com/read/28549128/atad3-gene-cluster-deletions-cause-cerebellar-dysfunction-associated-with-altered-mitochondrial-dna-and-cholesterol-metabolism
#1
Radha Desai, Ann E Frazier, Romina Durigon, Harshil Patel, Aleck W Jones, Ilaria Dalla Rosa, Nicole J Lake, Alison G Compton, Hayley S Mountford, Elena J Tucker, Alice L R Mitchell, Deborah Jackson, Abdul Sesay, Miriam Di Re, Lambert P van den Heuvel, Derek Burke, David Francis, Sebastian Lunke, George McGillivray, Simone Mandelstam, Fanny Mochel, Boris Keren, Claude Jardel, Anne M Turner, P Ian Andrews, Jan Smeitink, Johannes N Spelbrink, Simon J Heales, Masakazu Kohda, Akira Ohtake, Kei Murayama, Yasushi Okazaki, Anne Lombès, Ian J Holt, David R Thorburn, Antonella Spinazzola
Although mitochondrial disorders are clinically heterogeneous, they frequently involve the central nervous system and are among the most common neurogenetic disorders. Identifying the causal genes has benefited enormously from advances in high-throughput sequencing technologies; however, once the defect is known, researchers face the challenge of deciphering the underlying disease mechanism. Here we characterize large biallelic deletions in the region encoding the ATAD3C, ATAD3B and ATAD3A genes. Although high homology complicates genomic analysis of the ATAD3 defects, they can be identified by targeted analysis of standard single nucleotide polymorphism array and whole exome sequencing data...
June 1, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28548627/combined-single-molecule-experimental-and-computational-approaches-for-understanding-the-unfolding-pathway-of-a-viral-translation-enhancer-that-participates-in-a-conformational-switch
#2
My-Tra Le, Wojciech K Kasprzak, Bruce A Shapiro, Anne E Simon
How plus-strand [+]RNA virus genomes transition from translation templates to replication templates is a matter of much speculation. We have previously proposed that, for Turnip crinkle virus, binding of the encoded RNA-dependent RNA polymerase (RdRp) to the 3'UTR of the [+]RNA template promotes a regional wide-spread conformational switch to an alternative structure that disassembles the cap-independent translation element (CITE) in the 3'UTR. The active 3'CITE folds into a tRNA-like T-shaped structure (TSS) that binds to 80S ribosomes and 60S subunits in the P-site...
May 26, 2017: RNA Biology
https://www.readbyqxmd.com/read/28548194/-heritability-and-genetic-comorbidity-of-attention-deficit-disorder-with-hyperactivity
#3
Giannina Puddu, Paula Rothhammer, Ximena Carrasco, Francisco Aboitiz, Francisco Rothhammer
This review aims to summarize information about the genetic etiology of attention deficit disorder with hyperactivity (ADHD), with particular reference to the contributions of our research group. We also discuss the genetic comorbidity estimated from genome-wide single nucleotide polymorphisms (SNP´s) between ADHD and major psychiatric disorders such as schizophrenia (E), major depressive disorder (MDD), bipolar disorder (BD) and autism spectrum disorders (ASD). A high genetic comorbidity was found between E and BD (46%), a moderate comorbidity between MDD and E, MDD and BD and MDD and ADHD (18%, 22% and 10% respectively) and a low comorbidity between E and ASD (2...
March 2017: Revista Médica de Chile
https://www.readbyqxmd.com/read/28547657/compartmentalized-expression-patterns-of-pancreatic-and-gastric-related-genes-in-the-alimentary-canal-of-the-ascidian-ciona-intestinalis-evolutionary-insights-into-the-functional-regionality-of-the-gastrointestinal-tract-in-olfactores
#4
Satoshi Nakayama, Michio Ogasawara
Many heterotrophic animals have a one-way alimentary canal that is essential for their nutrition and sequential steps of the digestive system, namely ingestion, digestion, absorption and elimination, are widely shared among bilaterians. Morphological, functional and molecular knowledge of the alimentary canal has been obtained in particular from mammalian research but the shared features and evolution of these aspects of the highly diverged alimentary canal in the animal kingdom are still unclear. We therefore investigate spatial gene expression patterns of pancreatic- and gastric-related molecules of ascidians (a sister group of vertebrates) with special reference to the functional regionality of the gastrointestinal tract...
May 25, 2017: Cell and Tissue Research
https://www.readbyqxmd.com/read/28546995/the-cost-and-cost-trajectory-of-whole-genome-analysis-guiding-treatment-of-patients-with-advanced-cancers
#5
Deirdre Weymann, Janessa Laskin, Robyn Roscoe, Kasmintan A Schrader, Stephen Chia, Stephen Yip, Winson Y Cheung, Karen A Gelmon, Aly Karsan, Daniel J Renouf, Marco Marra, Dean A Regier
BACKGROUND: Limited data exist on the real-world costs of applying whole-genome analysis (WGA) in a clinical setting. We estimated the costs of applying WGA to guide treatments for patients with advanced cancers and characterized how costs evolve over time. METHODS: The setting is the British Columbia Cancer Agency Personalized OncoGenomics (POG) program in British Columbia, Canada. Cost data were obtained for patients who enrolled in the program from 2012 to 2015...
May 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28546746/genetic-polymorphism-and-chronic-obstructive-pulmonary-disease
#6
REVIEW
Cunhua Yuan, De Chang, Guangming Lu, Xiaowei Deng
Chronic obstructive pulmonary disease (COPD) is a common chronic disease, and its morbidity and mortality are increasing. There are many studies that have tried to explain the pathogenesis of COPD from genetic susceptibility, to identify the susceptibility of COPD factors, which play a role in early prevention, early detection and the early treatment. However, it is well known that COPD is an inflammatory disease characterized by incomplete reversible airflow limitation in which genes interact with the environment...
2017: International Journal of Chronic Obstructive Pulmonary Disease
https://www.readbyqxmd.com/read/28545995/systematic-studies-on-ciliates-alveolata-ciliophora-in-china-progress-and-achievements-based-on-molecular-information
#7
REVIEW
Feng Gao, Jie Huang, Yan Zhao, Lifang Li, Weiwei Liu, Miao Miao, Qianqian Zhang, Jiamei Li, Zhenzhen Yi, Hamed A El-Serehy, Alan Warren, Weibo Song
Due to complex morphological and convergent morphogenetic characters, the systematics of ciliates has long been ambiguous. Since 1990, the Laboratory of Protozoology, Ocean University of China, in collaboration with other research groups worldwide, has carried out a series of integrative investigations on ciliate systematics. To date, genomic DNA has been extracted from about 1700 ciliate strains, and phylogenetic analyses have been performed for two-thirds of orders. Main findings are: (1) Classifications of about 50 hypotrichous species have been resolved, although the monophylies of three hypotrichous orders remain unconfirmed; (2) Euplotia and two orders and all seven families within them are monophyletic assemblages; (3) Lynnella represents an order-level taxon, and is separated from two sister monophyletic subclasses Oligotrichia and Choreotrichia; (4) the peritrich families Zoothamniidae and Vorticellidae are separated from each other, and Zoothamnium exhibits a high genetic diversity; (5) the scuticociliate order Philasterida is monophyletic and separated from loxocephalids, and the thigmotrichids is a suborder within Pleuronematida; (6) 14 classes were recovered including one new class Protocruziea, and Mesodiniea is basal to subphyla Intramacronucleata and Postciliodesmatophora; (7) mitochondrial cytochrome c oxidase subunit I heteroplasmy was reported in ciliates for the first time, and candidate barcoding genes for Frontonia species identification were identified...
May 6, 2017: European Journal of Protistology
https://www.readbyqxmd.com/read/28545823/novel-molecular-subgroups-for-clinical-classification-and-outcome-prediction-in-childhood-medulloblastoma-a-cohort-study
#8
Edward C Schwalbe, Janet C Lindsey, Sirintra Nakjang, Stephen Crosier, Amanda J Smith, Debbie Hicks, Gholamreza Rafiee, Rebecca M Hill, Alice Iliasova, Thomas Stone, Barry Pizer, Antony Michalski, Abhijit Joshi, Stephen B Wharton, Thomas S Jacques, Simon Bailey, Daniel Williamson, Steven C Clifford
BACKGROUND: International consensus recognises four medulloblastoma molecular subgroups: WNT (MBWNT), SHH (MBSHH), group 3 (MBGrp3), and group 4 (MBGrp4), each defined by their characteristic genome-wide transcriptomic and DNA methylomic profiles. These subgroups have distinct clinicopathological and molecular features, and underpin current disease subclassification and initial subgroup-directed therapies that are underway in clinical trials. However, substantial biological heterogeneity and differences in survival are apparent within each subgroup, which remain to be resolved...
May 22, 2017: Lancet Oncology
https://www.readbyqxmd.com/read/28545448/limitations-of-a-metabolic-network-based-reverse-ecology-method-for-inferring-host-pathogen-interactions
#9
Kazuhiro Takemoto, Kazuki Aie
BACKGROUND: Host-pathogen interactions are important in a wide range of research fields. Given the importance of metabolic crosstalk between hosts and pathogens, a metabolic network-based reverse ecology method was proposed to infer these interactions. However, the validity of this method remains unclear because of the various explanations presented and the influence of potentially confounding factors that have thus far been neglected. RESULTS: We re-evaluated the importance of the reverse ecology method for evaluating host-pathogen interactions while statistically controlling for confounding effects using oxygen requirement, genome, metabolic network, and phylogeny data...
May 25, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28545258/marker-assisted-molecular-profiling-deletion-mutant-analysis-and-rna-seq-reveal-a-disease-resistance-cluster-associated-with-uromyces-appendiculatus-infection-in-common-bean-phaseolus-vulgaris-l
#10
Antonette R Todd, Nicole Donofrio, Venkateswara R Sripathi, Phillip E McClean, Rian K Lee, Marcial Pastor-Corrales, Venu Kal Kalavacharla
Common bean (Phaseolus vulgaris L.) is an important legume, useful for its high protein and dietary fiber. The fungal pathogen Uromyces appendiculatus (Pers.) Unger can cause major loss in susceptible varieties of the common bean. The Ur-3 locus provides race specific resistance to virulent strains or races of the bean rust pathogen along with Crg, (Complements resistance gene), which is required for Ur-3-mediated rust resistance. In this study, we inoculated two common bean genotypes (resistant "Sierra" and susceptible crg) with rust race 53 of U...
May 23, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28544650/diverse-application-of-mri-for-mouse-phenotyping
#11
REVIEW
Yijen L Wu, Cecilia W Lo
Small animal models, particularly mouse models, of human diseases are becoming an indispensable tool for biomedical research. Studies in animal models have provided important insights into the etiology of diseases and accelerated the development of therapeutic strategies. Detailed phenotypic characterization is essential, both for the development of such animal models and mechanistic studies into disease pathogenesis and testing the efficacy of experimental therapeutics. MRI is a versatile and noninvasive imaging modality with excellent penetration depth, tissue coverage, and soft tissue contrast...
May 22, 2017: Birth Defects Res
https://www.readbyqxmd.com/read/28544620/phenotyping-cardiac-and-structural-birth-defects-in-fetal-and-newborn-mice
#12
REVIEW
Xiaoqin Liu, Andrew J Kim, William Reynolds, Yijen Wu, Cecilia W Lo
Mouse models are invaluable for investigating the developmental etiology and molecular pathogenesis of structural birth defects. While this has been deployed for studying a wide spectrum of birth defects, mice are particularly valuable for modeling congenital heart disease, given they have the same four-chamber cardiac anatomy as in humans. We have developed the use of noninvasive fetal ultrasound together with micro-computed tomography (micro-CT) imaging for high throughput phenotyping of mice for congenital heart defects (CHD) and other developmental anomalies...
May 22, 2017: Birth Defects Res
https://www.readbyqxmd.com/read/28544481/matching-phenotypes-to-whole-genomes-lessons-learned-from-four-iterations-of-the-personal-genome-project-community-challenges
#13
Binghuang Cai, Biao Li, Nikki Kiga, Janita Thusberg, Timothy Bergquist, Yun-Ching Chen, Noushin Niknafs, Hannah Carter, Collin Tokheim, Violeta Beleva-Guthrie, Christopher Douville, Rohit Bhattacharya, Hui Ting Grace Yeo, Jean Fan, Sohini Sengupta, Dewey Kim, Melissa Cline, Tychele Turner, Mark Diekhans, Jan Zaucha, Lipika R Pal, Chen Cao, Chen-Hsin Yu, Yizhou Yin, Marco Carraro, Manuel Giollo, Carlo Ferrari, Emanuela Leonardi, Silvio C E Tosatto, Jason Bobe, Madeleine Ball, Roger Hoskins, Susanna Repo, George Church, Steven E Brenner, John Moult, Julian Gough, Mario Stanke, Rachel Karchin, Sean D Mooney
The advent of next generation sequencing has dramatically decreased the cost for whole genome sequencing and increased the viability for its application in research and clinical care. The Personal Genome Project (PGP) provides unrestricted access to genomes of individuals and their associated phenotypes. This resource enabled the Critical Assessment of Genome Interpretation (CAGI) to create a community challenge to assess the bioinformatics community's ability to predict traits from whole genomes. In CAGI PGP challenge, researchers were asked to predict whether an individual had a particular trait or profile based on their whole genome...
May 23, 2017: Human Mutation
https://www.readbyqxmd.com/read/28544285/salmonella-typhi-genomics-envisaging-the-future-of-typhoid-eradication
#14
REVIEW
Kien-Pong Yap, Kwai Lin Thong
Next-generation whole genome sequencing has revolutionized the study of infectious diseases in recent years. The availability of genome sequences and its understanding have transformed the field of molecular microbiology, epidemiology, infection treatments and vaccine developments. We review the key findings of the publicly accessible genomes of Salmonella enterica serovar Typhi since the first complete genome to the most recent release of thousands of S. typhi genomes, which remarkably shape the genomic research of S...
May 24, 2017: Tropical Medicine & International Health: TM & IH
https://www.readbyqxmd.com/read/28543738/crispr-editing-in-biological-and-biomedical-investigation
#15
Xing-Da Ju, Jing Xu, Zhong Sheng Sun
The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas (CRISPR--associated protein) system, a prokaryotic RNA-based adaptive immune system against viral infection, is emerging as a powerful genome editing tool in broad research areas. To further improve and expand its functionality, various CRISPR delivery strategies have been tested and optimized, and key CRISPR system components such as Cas protein have been engineered with different purposes. Benefiting from more in-depth understanding and further development of CRISPR, versatile CRISPR-based platforms for genome editing have been rapidly developed to advance investigations in biology and biomedicine...
May 20, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28543693/somatic-driver-mutations-in-melanoma
#16
REVIEW
Bobby Y Reddy, David M Miller, Hensin Tsao
Melanoma has one of the highest somatic mutational burdens among solid malignancies. Although the rapid progress in genomic research has contributed immensely to our understanding of the pathogenesis of melanoma, the clinical significance of the vast array of genomic alterations discovered by next-generation sequencing is far from being fully characterized. Most mutations prevalent in melanoma are simply neutral "passengers," which accompany functionally significant "drivers" under transforming conditions. The delineation of driver mutations from passenger mutations is critical to the development of targeted therapies...
June 1, 2017: Cancer
https://www.readbyqxmd.com/read/28543182/prognostic-significance-of-promoter-cpg-island-methylation-of-obesity-related-genes-in-patients-with-nonmetastatic-renal-cell-carcinoma
#17
Julia Mendoza-Pérez, Jian Gu, Luis A Herrera, Nizar M Tannir, Shanyu Zhang, Surena Matin, Jose A Karam, Christopher G Wood, Xifeng Wu
BACKGROUND: Greater than 40% of renal cell carcinoma (RCC) cases in the United States are attributed to excessive body weight. Moreover, obesity also may be linked to RCC prognosis. However, the molecular mechanisms underlying these associations are unclear. In the current study, the authors evaluated the role of promoter methylation in obesity-related genes in RCC tumorigenesis and disease recurrence. METHODS: Paired tumors (TU) and normal adjacent (N-Adj) tissues from 240 newly diagnosed and previously untreated white patients with RCC were examined...
May 23, 2017: Cancer
https://www.readbyqxmd.com/read/28542519/characterization-of-the-whole-chloroplast-genome-of-chikusichloa-mutica-and-its-comparison-with-other-rice-tribe-oryzeae-species
#18
Zhiqiang Wu, Cuihua Gu, Luke R Tembrock, Dong Zhang, Song Ge
Chloroplast genomes are a significant genomic resource in plant species and have been used in many research areas. The complete genomic information from wild crop species could supply a valuable genetic reservoir for breeding. Chikusichloa mutica is one of the most important wild distant relatives of cultivated rice. In this study, we sequenced and characterized its complete chloroplast (cp) genome and compared it with other species in the same tribe. The whole cp genome sequence is 136,603 bp in size and exhibits a typical quadripartite structure with large and small single-copy regions (LSC, 82,327 bp; SSC, 12,598 bp) separated by a pair of 20,839-bp inverted repeats (IRA, B)...
2017: PloS One
https://www.readbyqxmd.com/read/28542451/mapping-genes-for-resistance-to-stripe-rust-in-spring-wheat-landrace-pi-480035
#19
Jinita Sthapit Kandel, Vandhana Krishnan, Derick Jiwan, Xianming Chen, Daniel Z Skinner, Deven R See
Stripe rust caused by Puccinia striiformis Westend. f. sp. tritici Erikks. is an economically important disease of wheat (Triticum aestivum L.). Hexaploid spring wheat landrace PI 480035 was highly resistant to stripe rust in the field in Washington during 2011 and 2012. The objective of this research was to identify quantitative trait loci (QTL) for stripe rust resistance in PI 480035. A spring wheat, "Avocet Susceptible" (AvS), was crossed with PI 480035 to develop a biparental population of 110 recombinant inbred lines (RIL)...
2017: PloS One
https://www.readbyqxmd.com/read/28541828/simple-green-production-of-silver-nanoparticles-facilitated-by-bacterial-genomic-dna-and-their-antibacterial-activity
#20
Jiraporn Chumpol, Sineenat Siri
Green synthesis of AgNPs has gained many research interests as a low cost and eco-friendly approach. This work reported on the use of bacterial genomic DNA as the alternative biopolymer for a green production of AgNPs under a neutral pH. Although both ssDNA and dsDNA could function as stabilizing agents during the synthesis process, the ssDNA, generated by pre-heating the dsDNA at 100 °C, was more efficient to produce AgNPs with higher yield as determined by the intensity of the surface plasmon resonance (SPR) peak of silver at 475 nm...
May 25, 2017: Artificial Cells, Nanomedicine, and Biotechnology
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