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https://www.readbyqxmd.com/read/28324890/regulation-of-itga3-by-the-dual-stranded-microrna-199-family-as-a-potential-prognostic-marker-in-bladder-cancer
#1
Takashi Sakaguchi, Hirofumi Yoshino, Masaya Yonemori, Kazutaka Miyamoto, Satoshi Sugita, Ryosuke Matsushita, Toshihiko Itesako, Shuichi Tatarano, Masayuki Nakagawa, Hideki Enokida
BACKGROUND: Based on the microRNA (miRNA) signature of bladder cancer (BC) by deep sequencing, we recently found that several double-stranded mature miRNAs derived from the same pre-miRNAs were sufficiently expressed and acted as tumour suppressors by regulating common target genes in BC. Our deep-sequencing signature of BC showed that all miR-199 family members (miR-199a-3p/-5p and miR-199b-3p/-5p) were also downregulated. We hypothesised that these miRNAs may function as tumour suppressors by regulating common target genes...
March 21, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28324612/quantitative-image-analysis-of-single-molecule-mrna-dynamics-in-living-cells
#2
José Rino, Ana C de Jesus, Maria Carmo-Fonseca
Single mRNA molecules can be imaged in living cells by a method that consists in genetically inserting binding sites for a bacteriophage protein in the gene of interest. The resulting reporter transgene is then integrated in the genome of cells that express the phage protein fused to a fluorescent tag. Upon transcription, binding of the fluorescent protein to its target sequence makes the RNA visible. With this approach it is possible to track, in real time, the life cycle of a precursor mRNA at the site of transcription in the nucleus and transport of mature mRNA to the cytoplasm...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28324502/telomeres-and-nextgen-co-fish-directional-genomic-hybridization-telo-dgh%C3%A2
#3
Miles J McKenna, Erin Robinson, Edwin H Goodwin, Michael N Cornforth, Susan M Bailey
The cytogenomics-based methodology of Directional Genomic Hybridization (dGH™) emerged from the concept of strand-specific hybridization, first made possible by Chromosome Orientation FISH (CO-FISH), the utility of which was demonstrated in a variety of early applications, often involving telomeres. Similar to standard whole chromosome painting (FISH), dGH™ is capable of identifying inter-chromosomal rearrangements (translocations between chromosomes), but its distinctive strength stems from its ability to detect intra-chromosomal rearrangements (inversions within chromosomes), and to do so at higher resolution than previously possible...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28324217/rare-slc1a1-variants-in-hot-water-epilepsy
#4
Kalpita Rashimi Karan, P Satishchandra, Sanjib Sinha, Anuranjan Anand
Hot water epilepsy is sensory epilepsy, wherein seizures are triggered by an unusual stimulus: contact with hot water. Although genetic factors contribute to the etiology of hot water epilepsy, molecular underpinnings of the disorder remain largely unknown. We aimed to identify the molecular genetic basis of the disorder by studying families with two or more of their members affected with hot water epilepsy. Using a combination of genome-wide linkage mapping and whole exome sequencing, a missense variant was identified in SLC1A1 in a three-generation family...
March 21, 2017: Human Genetics
https://www.readbyqxmd.com/read/28324178/complete-genome-sequence-analysis-of-a-novel-staphylococcus-phage-stap1-and-proposal-of-a-new-species-in-the-genus-silviavirus
#5
Amal Senevirathne, Kuntal Ghosh, Eunjung Roh, Kwang-Pyo Kim
Bacteriophage StAP1 was isolated from a soil sample infecting Staphylococcus aureus and S. xylosus. Its genome was found to be 135,502 base pairs (bp) long with 30.00 mol% G+C content and 192 open reading frames. While no tRNA encoding genes were identified, 7 mobile elements were found to interrupt five StAP1 open reading frames. Comparative genomic and proteomic analysis consistently supports the establishment of a new species in the genus Silviavirus.
March 21, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28324026/gonadotropin-inhibitory-hormone-gnih-the-piscine-ortholog-of-lpxrfa-participates-in-17%C3%AE-estradiol-feedback-in-female-goldfish-reproduction
#6
Xin Qi, Wenyi Zhou, Qingqing Wang, Liang Guo, Danqi Lu, Haoran Lin
Gonadotropin-inhibitory hormone (GnIH) plays a critical role in regulating GnRH, GtH and steroidogenesis in teleosts. In the present study, we sought to determine whether E2 (17β-estradiol) acts directly on GnIH neurons to regulate reproduction in goldfish, a seasonal breeder, and we investigated the role of estrogen receptors in mediating this process. We found that GnIH neurons co-express three types of ERs. Ovariectomy and letrozole implantation into female goldfish at the vitellogenic stage elicited a significant decrease in the expression of GnIH mRNA, and E2 supplementation abolished this effect...
January 4, 2017: Endocrinology
https://www.readbyqxmd.com/read/28324015/paternally-inherited-dlk1-deletion-associated-with-familial-central-precocious-puberty
#7
Andrew Dauber, Marina Cunha-Silva, Delanie B Macedo, Vinicius N Brito, Ana Paula Abreu, Stephanie A Roberts, Luciana R Montenegro, Melissa Andrew, Andrew Kirby, Matthew T Weirauch, Guillaume Labilloy, Danielle S Bessa, Rona S Carroll, Dakota C Jacobs, Patrick E Chappell, Berenice B Mendonca, David Haig, Ursula B Kaiser, Ana Claudia Latronico
Context: Central precocious puberty (CPP) results from premature activation of the hypothalamic-pituitary-gonadal axis. Few genetic causes of CPP have been identified with the most common being mutations in the paternally expressed imprinted gene MKRN3. Objective: To identify the genetic etiology of CPP in a large multigenerational family. Design: Linkage analysis followed by whole genome sequencing was performed in a family with 5 female members with nonsyndromic CPP...
January 27, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28324014/variation-in-the-insulin-like-growth-factor-1-gene-in-primates
#8
Peter Rotwein
Insulin-like growth factor 1 (IGF1) is a multifunctional peptide that is involved in a wide range of physiological and patho-physiological processes in many animal species, ranging from somatic growth in children to metabolism, and tissue regeneration and repair in adults. The IGF1 gene is under multifactorial regulation in the few species in which it has been studied, with major control being exerted by growth hormone (GH) through a gene expression pathway involving inducible binding of the STAT5b transcription factor to dispersed enhancer elements...
January 18, 2017: Endocrinology
https://www.readbyqxmd.com/read/28324009/whole-exome-sequencing-for-diagnosis-of-turner-syndrome-towards-next-generation-sequencing-and-newborn-screening
#9
David R Murdock, Frank X Donovan, Settara C Chandrasekharappa, Nicole Banks, Carolyn Bondy, Maximilian Muenke, Paul Kruszka
Context, Objectives: Turner syndrome (TS) is due to a complete or partial loss of an X chromosome in females and is not currently part of newborn screening. Diagnosis is often delayed resulting in missed crucial diagnostic and therapeutic opportunities. This study sought to determine if whole-exome sequencing (WES) as part of a potential newborn screening program could be used to diagnose TS. Design, Setting, Patients: Karyotype, chromosomal microarray, and WES were performed on women with TS (n=27) enrolled in the Personalized Genomic Research study at the National Institutes of Health...
January 24, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28323875/the-clinical-features-outcomes-and-genetic-characteristics-of-hypertrophic-cardiomyopathy-patients-with-severe-right-ventricular-hypertrophy
#10
Xiying Guo, Chaomei Fan, Lei Tian, Yanling Liu, Hongyue Wang, Shihua Zhao, Fujian Duan, Xiuling Zhang, Xing Zhao, Fengqi Wang, Hongguang Zhu, Aiqing Lin, Xia Wu, Yishi Li
INTRODUCTION: Severe right ventricular hypertrophy (SRVH) is a rare phenotype in hypertrophic cardiomyopathy (HCM) for which limited information is available. This study was undertaken to investigate the clinical, prognostic and genetic characteristics of HCM patients with SRVH. METHODS: HCM with SRVH was defined as HCM with a maximum right ventricular wall thickness ≥10 mm. Whole-genome sequencing (WGS) was performed in HCM patients with SRVH. Multivariate Cox proportional hazards regression models were used to identify risk factors for cardiac death and events in HCM with SRVH...
2017: PloS One
https://www.readbyqxmd.com/read/28323863/discovery-of-genome-widesnps-by-rad-seqand-the-genetic-diversity-of-captive-hog-deer-axis-porcinus
#11
Wei Wang, Huijuan Yan, Jianqiu Yu, Jun Yi, Yu Qu, Maozhong Fu, Ang Chen, Hui Tang, Lili Niu
The hog deer (Axis porcinus) is a small deer whose natural habitat is the wet or moist tall grasslands in South and Southeast Asia. Wild populations have dramatically decreased in recent decades. While wild hog deer were recently acknowledged to be extinct in China, a few captive populations have been maintained. In the present study, we successfully employed the restriction-site-associated DNA sequencing (RAD-seq) technique to generate a genome-wide profile of single-nucleotide polymorphisms (SNPs) in the captive population of hog deer from Chengdu Zoo, China (N = 11)...
2017: PloS One
https://www.readbyqxmd.com/read/28323839/on-dna-numerical-representations-for-genomic-similarity-computation
#12
Gerardo Mendizabal-Ruiz, Israel Román-Godínez, Sulema Torres-Ramos, Ricardo A Salido-Ruiz, J Alejandro Morales
Genomic signal processing (GSP) refers to the use of signal processing for the analysis of genomic data. GSP methods require the transformation or mapping of the genomic data to a numeric representation. To date, several DNA numeric representations (DNR) have been proposed; however, it is not clear what the properties of each DNR are and how the selection of one will affect the results when using a signal processing technique to analyze them. In this paper, we present an experimental study of the characteristics of nine of the most frequently-used DNR...
2017: PloS One
https://www.readbyqxmd.com/read/28323836/single-nucleotide-variants-and-indels-identified-from-whole-genome-re-sequencing-of-guzerat-gyr-girolando-and-holstein-cattle-breeds
#13
Nedenia Bonvino Stafuzza, Adhemar Zerlotini, Francisco Pereira Lobo, Michel Eduardo Beleza Yamagishi, Tatiane Cristina Seleguim Chud, Alexandre Rodrigues Caetano, Danísio Prado Munari, Dorian J Garrick, Marco Antonio Machado, Marta Fonseca Martins, Maria Raquel Carvalho, John Bruce Cole, Marcos Vinicius Gualberto Barbosa da Silva
Whole-genome re-sequencing, alignment and annotation analyses were undertaken for 12 sires representing four important cattle breeds in Brazil: Guzerat (multi-purpose), Gyr, Girolando and Holstein (dairy production). A total of approximately 4.3 billion reads from an Illumina HiSeq 2000 sequencer generated for each animal 10.7 to 16.4-fold genome coverage. A total of 27,441,279 single nucleotide variations (SNVs) and 3,828,041 insertions/deletions (InDels) were detected in the samples, of which 2,557,670 SNVs and 883,219 InDels were novel...
2017: PloS One
https://www.readbyqxmd.com/read/28323658/changing-face-of-metastatic-prostate-cancer-the-law-of-diminishing-returns-holds-true
#14
Ulka N Vaishampayan
PURPOSE OF REVIEW: Prostate cancer presents with a multitude of faces. It ranges from localized cancers staying quiescent for many years during active surveillance to the raging diffuse liver metastases causing terminal disease. The incidence of metastatic disease is increasing. This review will highlight some of the recent developments as well as ongoing challenges of managing advanced prostate cancer. RECENT FINDINGS: Significant strides are being made in managing metastatic prostate cancer...
March 18, 2017: Current Opinion in Oncology
https://www.readbyqxmd.com/read/28323563/isolation-of-an-h5n8-highly-pathogenic-avian-influenza-virus-strain-from-wild-birds-in-seoul-a-highly-urbanized-area-in-south-korea
#15
Jung-Hoon Kwon, Dong-Hun Lee, Jei-Hyun Jeong, Seong-Su Yuk, Tseren-Ochir Erdene-Ochir, Jin-Yong Noh, Woo-Tack Hong, Sol Jeong, Gyeong-Bin Gwon, Sang-Won Lee, In-Soo Choi, Chang-Seon Song
Asian-lineage H5 highly pathogenic avian influenza viruses (HPAIV) have caused recurrent outbreaks in poultry and wild birds. In January 2014, H5N8 HPAIV caused outbreaks in South Korea and subsequently spread to East Asia, Europe, and North America. We report the isolation of an H5N8 HPAIV strain from wild birds in Seoul, the most-developed city in South Korea. We analyzed the complete genome sequence of this isolate and estimated its origin using a phylogenetic analysis. The Seoul H5N8 isolate clustered phylogenetically with strains isolated from migratory wild birds but was distinct from Korean poultry isolates...
March 21, 2017: Journal of Wildlife Diseases
https://www.readbyqxmd.com/read/28323522/detection-of-cytosine-and-cpg-density-in-proto-oncogenes-and-tumor-suppressor-genes-in-promoter-sequences-of-acute-myeloid-leukemia
#16
Senol Dogan, Anis Cilic, Damir Marjanovic, Amina Kurtovic-Kozaric
Aberrant methylation is one of the driving forces of cancer genome development. Although the rate of methylation appears massively variable across the genome, it is mainly observed in histone modification, chromatin organization, DNA accessibility, or promoter sequence. Methylation of promoter sequence occurs mostly to cytosine nucleotides, which can affect transcription factors' binding affinities. In this study, we demonstrated that cytosine repeats (C types density), consisting of CC, CCC, CCCC, CCCCC, CCCCCC, CCCCCCC motifs and CpG islands density in 25 proto-oncogenes, tumor suppressor genes and control genes may play a role in the pathogenesis of acute myeloid leukemia...
March 21, 2017: Nucleosides, Nucleotides & Nucleic Acids
https://www.readbyqxmd.com/read/28323406/affinity-selection-mass-spectrometry-identifies-a-novel-antibacterial-rna-polymerase-inhibitor
#17
Scott S Walker, David Degen, Elliott Nickbarg, Donna Carr, Aileen Soriano, Mihir Baran Mandal, Ronald E Painter, Payal R Sheth, Li Xiao, Xinwei Sher, Nicholas Murgolo, Jing Su, David B Olsen, Richard H Ebright, Katherine Young
The growing prevalence of drug-resistant Gram-negative bacteria is a significant global threat to human health. Rifampicin, an RNA polymerase-targeting agent, is an important part of the antibacterial armamentarium; however the emergence of resistance requires that it be used against only certain infections and usually in combination with another antibiotic. While rifampicin has significant clinical limitations, it does show that bacterial RNA polymerase can be an effective target for antibacterial intervention...
March 21, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28320202/identification-and-expression-of-equine-mer-derived-mirnas
#18
Jeong-An Gim, Heui-Soo Kim
MicroRNAs (miRNAs) are single-stranded, small RNAs (21-23 nucleotides) that function in gene silencing and translational inhibition via the RNA interference mechanism. Most miRNAs originate from host genomic regions, such as intergenic regions, introns, exons, and transposable elements (TEs). Here, we focused on the palindromic structure of medium reiteration frequencies (MERs), which are similar to precursor miRNAs. Five MER consensus sequences (MER5A1, MER53, MER81, MER91C, and MER117) were matched with paralogous transcripts predicted to be precursor miRNAs in the horse genome (equCab2) and located in either intergenic regions or introns...
March 21, 2017: Molecules and Cells
https://www.readbyqxmd.com/read/28319736/structural-variants-in-snca-gene-and-the-implication-to-synucleinopathies
#19
REVIEW
Ornit Chiba-Falek
Synucleinopathies are a group of neurodegenerative diseases that share a common pathological lesion of intracellular protein inclusions largely composed of aggregates of alpha-synuclein protein. Accumulating evidence, including genome-wide association studies, has implicated the alpha-synuclein (SNCA) gene in the etiology of synucleinopathies and it has been suggested that SNCA expression levels are critical for the development of these diseases. This review focuses on genetic variants from the class of structural variants (SVs), including multiplication of large genomic segments and short (<50bp) genomic variants such as simple sequence repeats (SSRs), within the SNCA locus...
March 2, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28319670/identification-of-candidate-genes-for-the-seed-coat-colour-change-in-a-brachypodium-distachyon-mutant-induced-by-gamma-radiation-using-whole-genome-re-sequencing
#20
Man Bo Lee, Dae Yeon Kim, Yong Weon Seo
Brachypodium distachyon has been proposed as a model plant for agriculturally important cereal crops such as wheat and barley. Seed coat colour change from brown-red to yellow was observed in a mutant line (142-3) of B. distachyon, which was induced by chronic gamma radiation. In addition, dwarf phenotypes were observed in each of the lines 142-3, 421-2, and 1376-1. In order to identify causal mutations for the seed coat colour change, the three mutant lines and the wild type were subjected to whole-genome re-sequencing...
March 20, 2017: Genome Génome / Conseil National de Recherches Canada
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