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https://www.readbyqxmd.com/read/28822142/-prospects-of-molecular-breeding-in-medical-plants
#1
REVIEW
Xiao-Jun Ma, Chang-Ming Mo
The molecular-assisted breeding, transgenic breeding and molecular designing breeding are three development directions of plant molecular breeding. Base on these three development directions, this paper summarizes developing status and new tendency of research field of genetic linkage mapping, QTL mapping, association mapping, molecular-assisted selections, pollen-mediated transformations, agrobacterium-mediated transformations, particle gun-mediated transformations, genome editing technologies, whole-genome sequencing, transcriptome sequencing, proteome sequencing and varietal molecular designing...
June 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28821934/whole-exome-sequencing-to-identify-the-cause-of-congenital-sensorineural-hearing-loss-in-carriers-of-a-heterozygous-gjb2-mutation
#2
Thomas Parzefall, Alexandra Frohne, Martin Koenighofer, Andreas Kirchnawy, Berthold Streubel, Christian Schoefer, Klemens Frei, Trevor Lucas
Bi-allelic variations in the gap junction protein beta-2 (GJB2) gene cause up to 50% of cases of newborn hearing loss. Heterozygous pathogenic GJB2 variations are also fivefold overrepresented in idiopathic patient groups compared to the normal-hearing population. Whether hearing loss in this group is due to unidentified additional variations within GJB2 or variations in other deafness genes is unknown in most cases. Whole-exome sequencing offers an effective approach in the search for causative variations in patients with Mendelian diseases...
August 18, 2017: European Archives of Oto-rhino-laryngology
https://www.readbyqxmd.com/read/28821798/unconventional-mapk-gsk-3%C3%AE-pathway-behind-atypical-epithelial-mesenchymal-transition-in-hepatocellular-carcinoma
#3
Sana Parveen, Dhiviya Vedagiri, Hitha Gopalan Nair, Haripriya Parthasarathy, Krishnan Harinivas Harshan
We recently reported an atypical epithelial mesenchymal transition (EMT) in human hepatoma cell culture Huh7.5, which was non-responsive to the canonical EMT-transcription factors. Here we characterize major pathways regulating this atypical EMT through whole genome transcriptome profiling and molecular analysis, and identify a unique regulation of EMT by GSK-3β. Our analysis reveals remarkable suppression of several key liver-specific markers in Huh7.5M cells indicating that EMT not only changes the epithelial properties, but alters the characteristics associated with hepatocytes as well...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821725/interplay-between-maternal-slc6a4-mutation-and-prenatal-stress-a-possible-mechanism-for-autistic-behavior-development
#4
Calvin P Sjaarda, Patrick Hecht, Amy J M McNaughton, Audrina Zhou, Melissa L Hudson, Matt J Will, Garth Smith, Muhammad Ayub, Ping Liang, Nansheng Chen, David Beversdorf, Xudong Liu
The low activity allele of the maternal polymorphism, 5HTTLPR, in the serotonin transporter, SLC6A4, coupled with prenatal stress is reported to increase the risk for children to develop autism spectrum disorder (ASD). Similarly, maternal Slc6a4 knock-out and prenatal stress in rodents results in offspring demonstrating ASD-like characteristics. The present study uses an integrative genomics approach to explore mechanistic changes in early brain development in mouse embryos exposed to this maternal gene-environment phenomenon...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821592/global-analysis-of-gene-expression-in-response-to-whole-chromosome-aneuploidy-in-hexaploid-wheat
#5
Ai Zhang, Ning Li, Lei Gong, Xiaowan Gou, Bin Wang, Xin Deng, Changping Li, Qianli Dong, Huakun Zhang, Bao Liu
Aneuploidy, a condition of unbalanced chromosome content, represents a large-effect mutation that bears significant relevancy to human health and microbe adaptation. As such, extensive studies of aneuploidy have been conducted in unicellular model organisms and cancer cells. Aneuploidy also frequently is associated with plant polyploidization, but its impact on gene expression and relevance to polyploid genome evolution/functional innovation remain largely unknown. Here, we used a panel of diverse types of whole-chromosome aneuploidy of hexaploid wheat, all under the common genetic background of cv...
August 18, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28821546/a-supervised-statistical-learning-approach-for-accurate-legionella-pneumophila-source-attribution-during-outbreaks
#6
Andrew H Buultjens, Kyra Y L Chua, Sarah L Baines, Jason Kwong, Wei Gao, Zoe Cutcher, Stuart Adcock, Susan Ballard, Mark B Schultz, Takehiro Tomita, Nela Subasinghe, Glen P Carter, Sacha J Pidot, Lucinda Franklin, Torsten Seemann, Anders Gonçalves Da Silva, Benjamin P Howden, Timothy P Stinear
Public health agencies are increasingly relying on genomics during Legionnaires' disease investigations. However, the causative bacterium (Legionella pneumophila) has an unusual population structure with extreme temporal and spatial genome sequence conservation. Furthermore, Legionnaires' disease outbreaks can be caused by multiple L. pneumophila genotypes in a single source. These factors can confound cluster identification using standard phylogenomic methods. Here, we show that a statistical learning approach based onL...
August 18, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28821181/conservation-genetics-of-the-cheetah-lessons-learned-and-new-opportunities
#7
Stephen J O'Brien, Warren E Johnson, Carlos A Driscoll, Pavel Dobrynin, Laurie Marker
The dwindling wildlife species of our planet have become a cause célèbre for conservation groups, governments, and concerned citizens throughout the world. The application of powerful new genetic technologies to surviving populations of threatened mammals has revolutionized our ability to recognize hidden perils that afflict them. We have learned new lessons of survival, adaptation, and evolution from viewing the natural history of genomes in hundreds of detailed studies. A single case history of one species, the African cheetah, Acinonyx jubatus, is here reviewed to reveal a long-term story of conservation challenges and action informed by genetic discoveries and insights...
September 1, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28821014/efficient-and-accurate-causal-inference-with-hidden-confounders-from-genome-transcriptome-variation-data
#8
Lingfei Wang, Tom Michoel
Mapping gene expression as a quantitative trait using whole genome-sequencing and transcriptome analysis allows to discover the functional consequences of genetic variation. We developed a novel method and ultra-fast software Findr for higly accurate causal inference between gene expression traits using cis-regulatory DNA variations as causal anchors, which improves current methods by taking into consideration hidden confounders and weak regulations. Findr outperformed existing methods on the DREAM5 Systems Genetics challenge and on the prediction of microRNA and transcription factor targets in human lymphoblastoid cells, while being nearly a million times faster...
August 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28820946/proteogenomic-investigation-of-strain-variation-in-clinical-mycobacterium-tuberculosis-isolates
#9
Tiaan Heunis, Anzaan Dippenaar, Robin M Warren, Paul D van Helden, Ruben G van der Merwe, Nicolaas C Gey van Pittius, Arnab Pain, Samantha L Sampson, David L Tabb
Mycobacterium tuberculosis consists of a large number of different strains that display unique virulence characteristics. Whole-genome sequencing has revealed substantial genetic diversity among clinical M. tuberculosis isolates, and elucidating the phenotypic variation encoded by this genetic diversity will be of utmost importance to fully understand M. tuberculosis biology and pathogenicity. In this study we integrated whole-genome sequencing and mass spectrometry (GeLC-MS/MS) to reveal strain-specific characteristics in the proteomes of two clinical M...
August 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28820917/whole-exome-sequencing-of-lacrimal-gland-adenoid-cystic-carcinoma
#10
David W Sant, Wensi Tao, Matthew G Field, Daniel Pelaez, Ke Jin, Anthony Capobianco, Sander R Dubovy, David T Tse, Gaofeng Wang
Purpose: To identify genomic mutations in lacrimal gland adenoid cystic carcinoma (LGACC) samples from patients. Methods: Genomic DNA was extracted from LGACC specimens. Whole exome sequencing (exome-seq) was conducted to screen for mutations. Capillary sequencing was performed to verify mutations in genes shared by multiple samples. Luciferase assays were used to evaluate functional consequences of NOTCH1 mutations. Results: The mutation profile of LGACC was complicated...
May 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28820899/two-disjunct-pleistocene-populations-and-anisotropic-postglacial-expansion-shaped-the-current-genetic-structure-of-the-relict-plant-amborella-trichopoda
#11
Rémi Tournebize, Stéphanie Manel, Yves Vigouroux, François Munoz, Alexandre de Kochko, Valérie Poncet
Past climate fluctuations shaped the population dynamics of organisms in space and time, and have impacted their present intra-specific genetic structure. Demo-genetic modelling allows inferring the way past demographic and migration dynamics have determined this structure. Amborella trichopoda is an emblematic relict plant endemic to New Caledonia, widely distributed in the understory of non-ultramafic rainforests. We assessed the influence of the last glacial climates on the demographic history and the paleo-distribution of 12 Amborella populations covering the whole current distribution...
2017: PloS One
https://www.readbyqxmd.com/read/28820700/rapid-detection-of-plasmodium-knowlesi-by-isothermal-recombinase-polymerase-amplification-assay
#12
Meng-Yee Lai, Choo-Huck Ooi, Yee-Ling Lau
In this study, we developed a recombinase polymerase amplification (RPA) assay for specific diagnosis of Plasmodium knowlesi. Genomic DNA was extracted from whole blood samples using a commercial kit. With incubation at 37°C, the samples were successfully amplified within 20 minutes. The end product of RPA was further examined by loading onto agarose gel and a specific band was observed with a size of 128 bp. The RPA assay exhibited high sensitivity with limits of detection down to one copy of the plasmid...
August 14, 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/28820138/processes-underlying-rabies-virus-incursions-across-us-canada-border-as-revealed-by-whole-genome-phylogeography
#13
Hannah Trewby, Susan A Nadin-Davis, Leslie A Real, Roman Biek
Disease control programs aim to constrain and reduce the spread of infection. Human disease interventions such as wildlife vaccination play a major role in determining the limits of a pathogen's spatial distribution. Over the past few decades, a raccoon-specific variant of rabies virus (RRV) has invaded large areas of eastern North America. Although expansion into Canada has been largely prevented through vaccination along the US border, several outbreaks have occurred in Canada. Applying phylogeographic approaches to 289 RRV whole-genome sequences derived from isolates collected in Canada and adjacent US states, we examined the processes underlying these outbreaks...
September 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28820135/bioinformatic-analyses-of-whole-genome-sequence-data-in-a-public-health-laboratory
#14
Kelly F Oakeson, Jennifer Marie Wagner, Michelle Mendenhall, Andreas Rohrwasser, Robyn Atkinson-Dunn
The ability to generate high-quality sequence data in a public health laboratory enables the identification of pathogenic strains, the determination of relatedness among outbreak strains, and the analysis of genetic information regarding virulence and antimicrobial-resistance genes. However, the analysis of whole-genome sequence data depends on bioinformatic analysis tools and processes. Many public health laboratories do not have the bioinformatic capabilities to analyze the data generated from sequencing and therefore are unable to take full advantage of the power of whole-genome sequencing...
September 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28820104/nocardia-cavernae-sp-nov-a-novel-actinobacterium-isolated-from-a-karst-cave-sample
#15
Qing-Qing Li, Ming-Xian Han, Bao-Zhu Fang, Jian-Yu Jiao, Lan Liu, Zi-Wen Yang, Wan-Qin Zhang, Da-Qiao Wei, Wen-Jun Li
A novel actinobacterial strain, designated YIM A1135T, was isolated from a soil sample collected from a karst cave in Xingyi county, Guizhou province, south-western China. The taxonomic position of the strain was investigated using a polyphasic approach. Cells of the strain were aerobic, Gram-stain-positive and partially acid-alcohol-fast. Strain YIM A1135T shared 98.3 % 16S rRNA gene sequence similarity with Nocardia jejuensis NBRC 103114T and 97.6 % with Nocardia alba YIM 30243T. DNA-DNA hybridization values between strain YIM A1135T and related type strains of the genus Nocardia were less than 70 %...
August 18, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28819851/rarecyte-%C3%A2-ctc-analysis-step-3-using-the-cytepicker-%C3%A2-module-for-individual-cell-retrieval-and-subsequent-whole-genome-amplification-of-circulating-tumor-cells-for-genomic-analysis
#16
Jackie L Stilwell, Paulina Varshavskaya, Jeffrey L Werbin, Joshua J Nordberg, Arturo B Ramirez, Steve Quarre, Jay Tzucker, Jennifer Chow, Brennan Enright, Eric P Kaldjian
The CytePicker module built into the RareCyte CyteFinder instrument allows researchers to easily retrieve individual cells from microscope slides for genomic analyses, including array CGH, targeted sequencing, and next-generation sequencing. Here, we describe the semiautomated retrieval of CTCs from the blood processed by AccuCyte (see Chapter 13) and amplification of genomic DNA so that molecular analysis can be performed.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28819847/negative-enrichment-and-isolation-of-circulating-tumor-cells-for-whole-genome-amplification
#17
Nisha Kanwar, Susan J Done
Circulating tumor cells (CTCs) are a rare population of cells found in the peripheral blood of patients with many types of cancer such as breast, prostate, colon, and lung cancers. Higher numbers of these cells in blood are associated with a poorer prognosis of patients. Genomic profiling of CTCs would help characterize markers specific for the identification of these cells in blood, and also define genomic alterations that give these cells a metastatic advantage over other cells in the primary tumor. Here, we describe an immunomagnetic method to enrich CTCs from the blood of patients with breast cancer, followed by single-cell laser capture microdissection to isolate single CTCs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28819830/identification-and-characterization-of-tyrosine-kinases-in-anole-lizard-indicate-the-conserved-tyrosine-kinase-repertoire-in-vertebrates
#18
Ake Liu, Funan He, Xun Gu
The tyrosine kinases (TKs) play principal roles in regulation of multicellular aspects of the organism and are implicated in many cancer types and congenital disorders. The anole lizard has recently been introduced as a model organism for laboratory-based studies of organismal function and field studies of ecology and evolution. However, the TK family of anole lizard has not been systematically identified and characterized yet. In this study, we identified 82 TK-encoding genes in the anole lizard genome and classified them into 28 subfamilies through phylogenetic analysis, with no member from ROS and STYK1 subfamilies identified...
August 17, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28819310/genome-wide-target-enrichment-aided-chip-design-a-66%C3%A2-k-snp-chip-for-cashmere-goat
#19
Xian Qiao, Rui Su, Yang Wang, Ruijun Wang, Ting Yang, Xiaokai Li, Wei Chen, Shiyang He, Yu Jiang, Qiwu Xu, Wenting Wan, Yaolei Zhang, Wenguang Zhang, Jiang Chen, Bin Liu, Xin Liu, Yixing Fan, Duoyuan Chen, Huaizhi Jiang, Dongming Fang, Zhihong Liu, Xiaowen Wang, Yanjun Zhang, Danqing Mao, Zhiying Wang, Ran Di, Qianjun Zhao, Tao Zhong, Huanming Yang, Jian Wang, Wen Wang, Yang Dong, Xiaoli Chen, Xun Xu, Jinquan Li
Compared with the commercially available single nucleotide polymorphism (SNP) chip based on the Bead Chip technology, the solution hybrid selection (SHS)-based target enrichment SNP chip is not only design-flexible, but also cost-effective for genotype sequencing. In this study, we propose to design an animal SNP chip using the SHS-based target enrichment strategy for the first time. As an update to the international collaboration on goat research, a 66 K SNP chip for cashmere goat was created from the whole-genome sequencing data of 73 individuals...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819248/a-portable-microfluidic-platform-for-rapid-molecular-diagnostic-testing-of-patients-with-myeloproliferative-neoplasms
#20
Hua Wang, Xinju Zhang, Xiao Xu, Qunfeng Zhang, Hengliang Wang, Dong Li, Zhihua Kang, Zhiyuan Wu, Yigui Tang, Zhenhua An, Ming Guan
The ability to simultaneously detect JAK2 V617F and MPL W515K/L mutations would substantially improve the early diagnosis of myeloproliferative neoplasms (MPNs) and decrease the risk of arterial thrombosis. The goal of this study is to achieve a point of care testing platform for simultaneous analysis of major genetic alterations in MPN. Here, we report a microfluidic platform including a glass capillary containing polypropylene matrix that extracts genomic DNA from a drop of whole blood, a microchip for simultaneous multi-gene mutation screening, and a handheld battery-powered heating device...
August 17, 2017: Scientific Reports
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