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Whole-genome sequencing

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https://www.readbyqxmd.com/read/29331684/reprogramming-neurodegeneration-in-the-big-data-era
#1
REVIEW
Lujia Zhou, Patrik Verstreken
Recent genome-wide association studies (GWAS) have identified numerous genetic risk variants for late-onset Alzheimer's disease (AD) and Parkinson's disease (PD). However, deciphering the functional consequences of GWAS data is challenging due to a lack of reliable model systems to study the genetic variants that are often of low penetrance and non-coding identities. Pluripotent stem cell (PSC) technologies offer unprecedented opportunities for molecular phenotyping of GWAS variants in human neurons and microglia...
January 10, 2018: Current Opinion in Neurobiology
https://www.readbyqxmd.com/read/29331671/the-molecular-characteristics-of-avian-influenza-viruses-h9n2-derived-from-air-samples-in-live-poultry-markets
#2
Yanheng Wu, Jinsi Lin, Shuhuan Yang, Ying Xie, Man Wang, Xueqin Chen, Yayang Zhu, Le Luo, Wuyang Shi
OBJECTIVE: To study the molecular characteristics of H9N2-subtype avian influenza viruses (AIVs) isolated from air samples collected in live poultry markets (LPMs) and explore their sequence identities with AIVs that caused human infection. METHODS: Weekly surveillance of H9N2-subtype AIVs in the air of LPMs was conducted from 2015 to 2016. H9-positive samples were isolated from chicken embryos. Whole genome sequences of the isolated AIVs were obtained through high-throughput sequencing...
January 10, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29331642/protein-adaptations-in-extremophiles-an-insight-into-extremophilic-connection-of-mycobacterial-proteome
#3
REVIEW
Ashutosh Kumar, Anwar Alam, Deeksha Tripathi, Mamta Rani, Hafeeza Khatoon, Saurabh Pandey, Nasreen Z Ehtesham, Seyed E Hasnain
The biological paradox about how extremophiles persist at extreme ecological conditions throws a fascinating picture of the enormous potential of a single cell to adapt to homeostatic conditions in order to propagate. Unicellular organisms face challenges from both environmental factors and the ecological niche provided by the host tissue. Although the existence of extremophiles and their physiological properties were known for a long time, availability of whole genome sequence has catapulted the study on mechanisms of adaptation and the underlying principles that have enabled these unique organisms to withstand evolutionary and environmental pressures...
January 10, 2018: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/29330875/performance-of-the-early-access-ampliseq%C3%A2-mitochondrial-panel-with-degraded-dna-samples-using-the-ion-torrent%C3%A2-platform
#4
Ka Tak Wai, Mark Barash, Peter Gunn
The Early Access AmpliSeq™ Mitochondrial Panel amplifies whole mitochondrial genomes for phylogenetic and kinship identifications, using Ion Torrent™ technology. There is currently limited information on its performance with degraded DNA, a common occurrence in forensic samples. This study evaluated the performance of the Panel with DNA samples degraded in vitro, to mimic conditions commonly found in forensic investigations. Purified DNA from five individuals was heat-treated at five time points each (125°C for 0, 30, 60, 120 and 240 minutes; total n = 25)...
January 13, 2018: Electrophoresis
https://www.readbyqxmd.com/read/29330721/transcriptomic-analysis-and-discovery-of-genes-in-the-response-of-arachis-hypogaea-to-drought-stress
#5
Xiaobo Zhao, Chunjuan Li, Shubo Wan, Tingting Zhang, Caixia Yan, Shihua Shan
The peanut (Arachis hypogaea) is an important crop species that is threatened by drought stress. The genome sequences of peanut, which was officially released in 2016, may help explain the molecular mechanisms that underlie drought tolerance in this species. We report here a gene expression profiling of A. hypogaea to gain a global view of its drought resistance. Using whole-transcriptome sequencing, we analysed differential gene expression in response to drought stress in the drought-resistant peanut cultivar J11...
January 12, 2018: Molecular Biology Reports
https://www.readbyqxmd.com/read/29330416/virtual-genome-walking-across-the-32%C3%A2-gb-ambystoma-mexicanum-genome-assembling-gene-models-and-intronic-sequence
#6
Teri Evans, Andrew D Johnson, Matthew Loose
Large repeat rich genomes present challenges for assembly using short read technologies. The 32 Gb axolotl genome is estimated to contain ~19 Gb of repetitive DNA making an assembly from short reads alone effectively impossible. Indeed, this model species has been sequenced to 20× coverage but the reads could not be conventionally assembled. Using an alternative strategy, we have assembled subsets of these reads into scaffolds describing over 19,000 gene models. We call this method Virtual Genome Walking as it locally assembles whole genome reads based on a reference transcriptome, identifying exons and iteratively extending them into surrounding genomic sequence...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330370/a-rna-sequencing-approach-for-the-identification-of-novel-long-non-coding-rna-biomarkers-in-colorectal-cancer
#7
Atsushi Yamada, Pingjian Yu, Wei Lin, Yoshinaga Okugawa, C Richard Boland, Ajay Goel
Long non-coding RNAs (lncRNAs) have been implicated in human pathology, however, their role in colorectal carcinogenesis have not been fully elucidated. In the current study, whole-transcriptome analysis was performed in 3 pairs of colorectal cancer (CRC) and matched normal mucosa (NM) by RNA sequencing (RNA-seq). Followed by confirmation using the Cancer Genome Atlas (TCGA) dataset, we identified 27 up-regulated and 22 down-regulated lncRNAs in CRC. Up-regulation of four lncRNAs, hereby named colorectal cancer associated lncRNA (CRCAL)-1 [AC021218...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330334/detection-of-heterozygous-mutation-in-hook-microtubule-tethering-protein-1-in-three-patients-with-decapitated-and-decaudated-spermatozoa-syndrome
#8
Huixing Chen, Yong Zhu, Zijue Zhu, Erlei Zhi, Keming Lu, Xiaobo Wang, Feng Liu, Zheng Li, Weiliang Xia
BACKGROUND: The mechanism of intramanchette transport is crucial to the transformation of sperm tail and the nuclear condensation during spermiogenesis. Although few dysfunctional proteins could result in abnormal junction between the head and tail of spermatozoon, little is known about the genetic cues in this process. OBJECTIVE: Based on patients with severe decapitated and decaudated spermatozoa (DDS) syndrome, the study aimed to validate whether new mutation exists on their Hook microtubule-tethering protein 1 (HOOK1) genes and follow their results of assisted reproduction treatment (ART)...
January 12, 2018: Journal of Medical Genetics
https://www.readbyqxmd.com/read/29330186/effect-of-plasmid-design-and-type-of-integration-event-on-recombinant-protein-expression-in-pichia-pastoris
#9
Thomas Vogl, Leigh Gebbie, Robin W Palfreyman, Robert Speight
Pichia pastoris (syn. Komagataella phaffii) is one of the most common eukaryotic expression systems for heterologous protein production. Expression cassettes are typically integrated in the genome to obtain stable expression strains. In contrast to Saccharomyces cerevisiae, where short overhangs are sufficient to target highly specific integration, long overhangs are more efficient in P. pastoris and ectopic integration of foreign DNA can occur. Here, we aimed to elucidate the influence of ectopic integration by high throughput screening of >700 transformants and whole genome sequencing of 27 transformants...
January 12, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29329757/challenges-of-francisella-classification-exemplified-by-an-atypical-clinical-isolate
#10
L M Matz, K Y Kamdar, M E Holder, G A Metcalf, G M Weissenberger, Q Meng, V Vee, Y Han, D M Muzny, R A Gibbs, C L Johnson, P A Revell, J F Petrosino
The accumulation of sequenced Francisella strains has made it increasingly apparent that the 16S rRNA gene alone is not enough to stratify the Francisella genus into precise and clinically useful classifications. Continued whole-genome sequencing of isolates will provide a larger base of knowledge for targeted approaches with broad applicability. Additionally, examination of genomic information on a case-by-case basis will help resolve outstanding questions regarding strain stratification. We report the complete genome sequence of a clinical isolate, designated here as F...
December 6, 2017: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/29329601/nicotiana-glauca-whole-genome-investigation-for-ct-dna-study
#11
Galina Khafizova, Pavel Dobrynin, Dmitrii Polev, Tatiana Matveeva
OBJECTIVE: Nicotiana glauca (tree tobacco) is a naturally transgenic plant, containing sequences acquired from Agrobacterium rhizogenes by horizontal gene transfer. Besides, N. glauca contains a wide profile of alkaloids of medical interest. DATA DESCRIPTION: We report a high-depth sequencing and de novo assembly of N. glauca full genome and analysis of genome elements with bacterial origin. The draft genome assembly is 3.2 Gb, with N50 size of 31.1 kbp. Comparative analysis confirmed the presence of single, previously described gT insertion...
January 12, 2018: BMC Research Notes
https://www.readbyqxmd.com/read/29329552/correction-to-linkage-whole-genome-sequence-and-biological-data-implicate-variants-in-rab10-in-alzheimer-s-disease-resilience
#12
Perry G Ridge, Celeste M Karch, Simon Hsu, Ivan Arano, Craig C Teerlink, Mark T W Ebbert, Josue D Gonzalez Murcia, James M Farnham, Anna R Damato, Mariet Allen, Xue Wang, Oscar Harari, Victoria M Fernandez, Rita Guerreiro, Jose Bras, John Hardy, Ronald Munger, Maria Norton, Celeste Sassi, Andrew Singleton, Steven G Younkin, Dennis W Dickson, Todd E Golde, Nathan D Price, Nilüfer Ertekin-Taner, Carlos Cruchaga, Alison M Goate, Christopher Corcoran, JoAnn Tschanz, Lisa A Cannon-Albright, John S K Kauwe
The original version of this article [1] unfortunately contained a typographical error. The 'Alzheimer's Disease Neuroimaging Initiative' was erroneously included as 'Alzheimer's Disease Neuroimaging Initative' in the author list of the article.
January 12, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29329546/whole-genome-sequencing-of-genotype-vi-newcastle-disease-viruses-from-formalin-fixed-paraffin-embedded-tissues-from-wild-pigeons-reveals-continuous-evolution-and-previously-unrecognized-genetic-diversity-in-the-u-s
#13
Ying He, Tonya L Taylor, Kiril M Dimitrov, Salman L Butt, James B Stanton, Iryna V Goraichuk, Heather Fenton, Rebecca Poulson, Jian Zhang, Corrie C Brown, Hon S Ip, Marcos Isidoro-Ayza, Claudio L Afonso
BACKGROUND: Newcastle disease viruses (NDV) are highly contagious and cause disease in both wild birds and poultry. A pigeon-adapted variant of genotype VI NDV, often termed pigeon paramyxovirus 1, is commonly isolated from columbids in the United States and worldwide. Complete genomic characterization of these genotype VI viruses circulating in wild columbids in the United States is limited, and due to the genetic variability of the virus, failure of rapid diagnostic detection has been reported...
January 12, 2018: Virology Journal
https://www.readbyqxmd.com/read/29328655/identification-of-novel-coumestan-derivatives-as-polyketide-synthase-13-inhibitors-against-mycobacterium-tuberculosis
#14
Wei Zhang, Shichun Lun, Shu-Huan Wang, Xingwu Jiang, Fan Yang, Jie Tang, Abigail L Manson, Ashlee M Earl, Hendra Gunosewoyo, William R Bishai, Li-Fang Yu
Inhibition of the mycolic acid pathway has proven a viable strategy in antitubercular drug discovery. The AccA3/AccD4/FadD32/Pks13 complex of Mycobacterium tuberculosis constitutes an essential biosynthetic mechanism for mycolic acids. Small molecules targeting the thioesterase domain of Pks13 have been reported, including a benzofuran-based compound, whose X-ray co-crystal structure has been very recently solved. Its initial inactivity in a serum inhibition titration (SIT) assay led us to further probe other structurally-related benzofurans with the aim to improve their potency and bioavailability...
January 12, 2018: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29328368/identification-of-significant-biomarkers-and-pathways-associated-with-gastric-carcinogenesis-by-whole-genome-wide-expression-profiling-analysis
#15
Hong-Jun Fei, Song-Chang Chen, Jun-Yu Zhang, Shu-Yuan Li, Lan-Lan Zhang, Yi-Yao Chen, Chun-Xin Chang, Chen-Ming Xu
The incidence of gastric cancer (GC) is extremely high in East Asia. GC is also one of the most common and lethal forms of cancer from a global perspective. However, to date, we have not been able to determine one or several genes as biomarkers in the diagnosis of GC and have also been unable to identify the genes which are important in the therapy of GC. In this study, we analyzed all genome-wide expression profiling arrays uploaded onto the Gene Expression Omnibus (GEO) database to filtrate the differentially expressed genes (DEGs) between normal stomach tissues and GC tissues...
January 11, 2018: International Journal of Oncology
https://www.readbyqxmd.com/read/29327728/diverse-modes-of-clonal-evolution-in-hbv-related-hepatocellular-carcinoma-revealed-by-single-cell-genome-sequencing
#16
Meng Duan, Junfeng Hao, Sijia Cui, Daniel L Worthley, Shu Zhang, Zhichao Wang, Jieyi Shi, Longzi Liu, Xiaoying Wang, Aiwu Ke, Ya Cao, Ruibin Xi, Xiaoming Zhang, Jian Zhou, Jia Fan, Chong Li, Qiang Gao
Hepatocellular carcinoma (HCC) is a cancer of substantial morphologic, genetic and phenotypic diversity. Yet we do not understand the relationship between intratumor heterogeneity and the associated morphologic/histological characteristics of the tumor. Using single-cell whole-genome sequencing to profile 96 tumor cells (30-36 each) and 15 normal liver cells (5 each), collected from three male patients with HBV-associated HCC, we confirmed that copy number variations occur early in hepatocarcinogenesis but thereafter remain relatively stable throughout tumor progression...
January 12, 2018: Cell Research
https://www.readbyqxmd.com/read/29327725/whole-genome-sequencing-reveals-principles-of-brain-retrotransposition-in-neurodevelopmental-disorders
#17
Jasmine Jacob-Hirsch, Eran Eyal, Binyamin A Knisbacher, Jonathan Roth, Karen Cesarkas, Chen Dor, Sarit Farage-Barhom, Vered Kunik, Amos J Simon, Moran Gal, Michal Yalon, Sharon Moshitch-Moshkovitz, Rick Tearle, Shlomi Constantini, Erez Y Levanon, Ninette Amariglio, Gideon Rechavi
Neural progenitor cells undergo somatic retrotransposition events, mainly involving L1 elements, which can be potentially deleterious. Here, we analyze the whole genomes of 20 brain samples and 80 non-brain samples, and characterized the retrotransposition landscape of patients affected by a variety of neurodevelopmental disorders including Rett syndrome, tuberous sclerosis, ataxia-telangiectasia and autism. We report that the number of retrotranspositions in brain tissues is higher than that observed in non-brain samples and even higher in pathologic vs normal brains...
January 12, 2018: Cell Research
https://www.readbyqxmd.com/read/29327208/analysis-of-dna-modifications-in-aging-research
#18
REVIEW
Dustin R Masser, Niran Hadad, Hunter Porter, Michael B Stout, Archana Unnikrishnan, David R Stanford, Willard M Freeman
As geroscience research extends into the role of epigenetics in aging and age-related disease, researchers are being confronted with unfamiliar molecular techniques and data analysis methods that can be difficult to integrate into their work. In this review, we focus on the analysis of DNA modifications, namely cytosine methylation and hydroxymethylation, through next-generation sequencing methods. While older techniques for modification analysis performed relative quantitation across regions of the genome or examined average genome levels, these analyses lack the desired specificity, rigor, and genomic coverage to firmly establish the nature of genomic methylation patterns and their response to aging...
January 11, 2018: GeroScience
https://www.readbyqxmd.com/read/29326230/base-resolution-analysis-of-dna-methylation-patterns-downstream-of-dnmt3a-in-mouse-na%C3%A3-ve-b-cells
#19
Christopher G Duncan, Hrisavgi D Kondilis-Mangum, Sara A Grimm, Pierre R Bushel, Kaliopi Chrysovergis, John D Roberts, Frederick L Tyson, B Alex Merrick, Paul A Wade
The DNA methyltransferase, Dnmt3a, is dynamically regulated throughout mammalian B cell development and upon activation by antigenic stimulation. Dnmt3a inactivation in hematopoietic stem cells has been shown to drive B cell-related malignancies, including chronic lymphocytic leukemia (CLL), and associates with specific DNA methylation patterns in transformed cells. However, while it is clear that inactivation of Dnmt3a in hematopoietic stem cells has profound functional impacts, the consequences of Dnmt3a inactivation in cells of the B lineage are unclear...
January 11, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29326229/genomic-understanding-of-an-infectious-brain-disease-from-the-desert
#20
Leandro F Moreno, Abdalla A O Ahmed, Balázs Brankovics, Christina A Cuomo, Steph B J Menken, Saad J Taj-Aldeen, Hani Faidah, J Benjamin Stielow, Marcus de M Teixeira, Francesc X Prenafeta-Boldú, Vania A Vicente, Sybren de Hoog
Rhinocladiella mackenziei accounts for the majority of fungal brain infections in the Middle East and is restricted to the arid climate zone between Saudi Arabia and Pakistan. Neurotropic dissemination caused by this fungus has been reported in immunocompromised, but also immunocompetent individuals. If untreated, the infection is fatal. Outside of humans, the environmental niche of R. mackenziei is unknown, and the fungus has been only cultured from brain biopsies. In this paper we describe the whole genome re-sequencing of two Rhinocladiella mackenziei strains from patients in Saudi Arabia and Qatar...
January 11, 2018: G3: Genes—Genomes—Genetics
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