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https://www.readbyqxmd.com/read/28927096/laptm4b-2-allele-is-associated-with-the-development-of-papillary-thyroid-carcinoma-in-chinese-women
#1
Yue Meng, Rouli Zhou, Jianjun Xu, Qingyun Zhang
Lysosome-associated protein transmembrane 4-β (LAPTM4B) contains a polymorphic region that contributes to the increased risk of numerous types of tumor. However, no study has yet demonstrated an association between the expression of the LAPTM4B gene and tumor differentiation, and the reason that LAPTM4B polymorphisms affect the susceptibility of individuals to cancer remains to be elucidated. The present study assessed the possible association between LAPTM4B polymorphism and the risk of papillary thyroid carcinoma (PTC), and attempted to identify the underlying mechanism for variation in patient susceptibility with respect to transcription regulation in the polymorphism region...
September 2017: Oncology Letters
https://www.readbyqxmd.com/read/28927049/a-prognostic-model-for-lung-adenocarcinoma-patient-survival-with-a-focus-on-four-mirnas
#2
Xianqiu Li, Zhaoling An, Peihui Li, Haihua Liu
There is currently no effective biomarker for determining the survival of patients with lung adenocarcinoma. The purpose of the present study was to construct a prognostic survival model using microRNA (miRNA) expression data from patients with lung adenocarcinoma. miRNA data were obtained from The Cancer Genome Atlas, and patients with lung adenocarcinoma were divided into either the training or validation set based on the random allocation principle. The prognostic model focusing on miRNA was constructed, and patients were divided into high-risk or low-risk groups as per the scores, to assess their survival time...
September 2017: Oncology Letters
https://www.readbyqxmd.com/read/28926993/satellite-dna-an-evolving-topic
#3
REVIEW
Manuel A Garrido-Ramos
Satellite DNA represents one of the most fascinating parts of the repetitive fraction of the eukaryotic genome. Since the discovery of highly repetitive tandem DNA in the 1960s, a lot of literature has extensively covered various topics related to the structure, organization, function, and evolution of such sequences. Today, with the advent of genomic tools, the study of satellite DNA has regained a great interest. Thus, Next-Generation Sequencing (NGS), together with high-throughput in silico analysis of the information contained in NGS reads, has revolutionized the analysis of the repetitive fraction of the eukaryotic genomes...
September 18, 2017: Genes
https://www.readbyqxmd.com/read/28926847/probing-the-stochastic-property-of-endoreduplication-in-cell-size-determination-of-arabidopsis-thaliana-leaf-epidermal-tissue
#4
Kensuke Kawade, Hirokazu Tsukaya
Cell size distribution is highly reproducible, whereas the size of individual cells often varies greatly within a tissue. This is obvious in a population of Arabidopsis thaliana leaf epidermal cells, which ranged from 1,000 to 10,000 μm2 in size. Endoreduplication is a specialized cell cycle in which nuclear genome size (ploidy) is doubled in the absence of cell division. Although epidermal cells require endoreduplication to enhance cellular expansion, the issue of whether this mechanism is sufficient for explaining cell size distribution remains unclear due to a lack of quantitative understanding linking the occurrence of endoreduplication with cell size diversity...
2017: PloS One
https://www.readbyqxmd.com/read/28926843/the-genetic-basis-of-delayed-puberty
#5
S R Howard, Leo Dunkel
<br>The genetic control of puberty remains an important but mostly unanswered question. Late pubertal timing affects over 2% of adolescents and is associated with adverse health outcomes including short stature, reduced bone mineral density and compromised psychosocial health. Self-limited delayed puberty (DP) is a highly heritable trait, which often segregates in an autosomal dominant pattern; however, its neuroendocrine pathophysiology and genetic regulation remain unclear. Some insights into the genetic mutations that lead to familial DP have come from sequencing genes known to cause GnRH deficiency, most recently via next generation sequencing, and others from large-scale genome wide association studies in the general population...
September 18, 2017: Neuroendocrinology
https://www.readbyqxmd.com/read/28926565/a-snp-panel-and-online-tool-for-checking-genotype-concordance-through-comparing-qr-codes
#6
Yonghong Du, Joshua S Martin, John McGee, Yuchen Yang, Eric Yi Liu, Yingrui Sun, Matthias Geihs, Xuejun Kong, Eric Lingfeng Zhou, Yun Li, Jie Huang
In the current precision medicine era, more and more samples get genotyped and sequenced. Both researchers and commercial companies expend significant time and resources to reduce the error rate. However, it has been reported that there is a sample mix-up rate of between 0.1% and 1%, not to mention the possibly higher mix-up rate during the down-stream genetic reporting processes. Even on the low end of this estimate, this translates to a significant number of mislabeled samples, especially over the projected one billion people that will be sequenced within the next decade...
2017: PloS One
https://www.readbyqxmd.com/read/28926213/whole-genome-amplification-and-sequencing-of-a-daphnia-resting-egg
#7
Justin B Lack, Lawrence J Weider, Punidan D Jeyasingh
Resting eggs banks are unique windows that allow us to directly observe shifts in population genetics, and phenotypes over time as natural populations evolve. Although a variety of planktonic organisms also produce resting stages, the keystone freshwater consumer, Daphnia, is a well-known model for paleogenetics and resurrection ecology. Nevertheless, paleogenomic investigations are limited largely because resting eggs do not contain enough DNA for genomic sequencing. In fact, genomic studies even on extant populations include a laborious preparatory phase of batch culturing dozens of individuals to generate sufficient genomic DNA...
September 19, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28926156/the-roles-of-plasticity-and-evolutionary-change-in-shaping-gene-expression-variation-in-natural-populations-of-extremophile-fish
#8
Courtney N Passow, Chathurika Henpita, Jennifer H Shaw, Corey R Quackenbush, Wesley C Warren, Manfred Schartl, Lenin Arias-Rodriguez, Joanna L Kelley, Michael Tobler
The notorious plasticity of gene expression responses and the complexity of environmental gradients complicate the identification of adaptive differences in gene regulation among populations. We combined transcriptome analyses in nature with common garden and exposure experiments to establish cause and effect relationships between the presence of a physiochemical stressor and expression differences, as well as to test how evolutionary change and plasticity interact to shape gene expression variation in natural systems...
September 19, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28926153/comparative-and-population-genomics-landscape-of-phellinus-noxius-a-hypervariable-fungus-causing-root-rot-in-trees
#9
Chia-Lin Chung, Tracy J Lee, Mitsuteru Akiba, Hsin-Han Lee, Tzu-Hao Kuo, Dang Liu, Huei-Mien Ke, Toshiro Yokoi, Marylette B Roa, Meiyeh J Lu, Ya-Yun Chang, Pao-Jen Ann, Jyh-Nong Tsai, Chien-Yu Chen, Shean-Shong Tzean, Yuko Ota, Tsutomu Hattori, Norio Sahashi, Ruey-Fen Liou, Taisei Kikuchi, Isheng J Tsai
The order Hymenochaetales of white rot fungi contain some of the most aggressive wood decayers causing tree deaths around the world. Despite their ecological importance and the impact of diseases they cause, little is known about the evolution and transmission patterns of these pathogens. Here, we sequenced and undertook comparative genomics analyses of Hymenochaetales genomes using brown root rot fungus Phellinus noxius, wood-decomposing fungus Phellinus lamaensis, laminated root rot fungus Phellinus sulphurascens, and trunk pathogen Porodaedalea pini...
September 19, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28925547/biogeographic-conservation-of-the-cytosine-epigenome-in-the-globally-important-marine-nitrogen-fixing-cyanobacterium-trichodesmium
#10
Nathan G Walworth, David A Hutchins, Egor Dolzhenko, Michael D Lee, Feixue Fu, Andrew D Smith, Eric A Webb
Cytosine methylation has been shown to regulate essential cellular processes and impact biological adaptation. Despite its evolutionary importance, only a handful of bacterial, genome-wide cytosine studies have been conducted, with none for marine bacteria. Here, we examine the genome-wide, C(5) -Methyl-cytosine (m5C) methylome and its correlation to global transcription in the marine nitrogen-fixing cyanobacterium Trichodesmium. We characterize genome-wide methylation and highlight conserved motifs across 3 Trichodesmium isolates and 2 Trichodesmium metagenomes, thereby identifying highly conserved, novel genomic signatures of potential gene regulation in Trichodesmium...
September 19, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28925404/ing5-activity-in-self-renewal-of-glioblastoma-stem-cells-via-calcium-and-follicle-stimulating-hormone-pathways
#11
F Wang, A Y Wang, C Chesnelong, Y Yang, A Nabbi, S Thalappilly, V Alekseev, K Riabowol
Stem cell-like brain tumor initiating cells (BTICs) cause recurrence of glioblastomas, with BTIC 'stemness' affected by epigenetic mechanisms. The ING family of epigenetic regulators (ING1-5) function by targeting histone acetyltransferase (HAT) or histone deacetylase complexes to the H3K4me3 mark to alter histone acetylation and subsequently, gene expression. Here we find that ectopic expression of ING5, the targeting subunit of HBO1, MOZ and MORF HAT complexes increases expression of the Oct4, Olig2 and Nestin stem cell markers, promotes self-renewal, prevents lineage differentiation and increases stem cell pools in BTIC populations...
September 18, 2017: Oncogene
https://www.readbyqxmd.com/read/28924516/characterization-and-transferability-of-microsatellites-for-the-kangaroo-paw-anigozanthos-manglesii-haemodoraceae
#12
Bronwyn M Ayre, Janet M Anthony, David G Roberts, Richard J N Allcock, Siegfried L Krauss
PREMISE OF THE STUDY: Microsatellites were developed for the future assessment of population genetic structure, mating system, and dispersal of the perennial kangaroo paw, Anigozanthos manglesii (Haemodoraceae), and related species. METHODS AND RESULTS: Using a Personal Genome Machine (PGM) semiconductor sequencer, ca. 4.03 million sequence reads were generated. QDD pipeline software was used to identify 190,000 microsatellite-containing regions and priming sites...
August 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28924514/isolation-and-characterization-of-microsatellite-loci-from-arthropodium-cirratum-asparagaceae
#13
Mariana Bulgarella, Patrick J Biggs, Peter J de Lange, Lara D Shepherd
PREMISE OF THE STUDY: Microsatellite markers were developed for Arthropodium cirratum (Asparagaceae) to study population genetic structure and translocation of this species. These markers were tested for cross-amplification in two other Arthropodium species. METHODS AND RESULTS: Sixteen microsatellite markers were developed from a genomic library and tested in three populations of A. cirratum. The loci exhibited one to five alleles per locus, with private alleles present in each of the populations...
August 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28924513/identification-and-characterization-of-microsatellite-loci-in-the-tuliptree-liriodendron-tulipifera-magnoliaceae
#14
Ricardo Gutiérrez-Ozuna, Matthew B Hamilton
PREMISE OF THE STUDY: Twenty-three polymorphic microsatellite loci (simple sequence repeats) were identified and characterized for Liriodendron tulipifera (Magnoliaceae), a species native to eastern North America, to investigate its genetic diversity, population structure, and mating system. METHODS AND RESULTS: Using Illumina HiSeq paired-end reads from genomic DNA, searches for repeat motifs identified approximately 280,000 potentially amplifiable loci. Of 77 loci tested, 51 amplified consistently...
August 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28924231/population-genomics-of-virulence-genes-of-plasmodium-falciparum-in-clinical-isolates-from-uganda
#15
Shazia Ruybal-Pesántez, Kathryn E Tiedje, Gerry Tonkin-Hill, Thomas S Rask, Moses R Kamya, Bryan Greenhouse, Grant Dorsey, Michael F Duffy, Karen P Day
Plasmodium falciparum causes a spectrum of malarial disease from asymptomatic to uncomplicated through to severe. Investigations of parasite virulence have associated the expression of distinct variants of the major surface antigen of the blood stages known as Pf EMP1 encoded by up to 60 var genes per genome. Looking at the population genomics of var genes in cases of uncomplicated malaria, we set out to determine if there was any evidence of a selective sweep of specific var genes or clonal epidemic structure related to the incidence of uncomplicated disease in children...
September 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28924186/interactome-analysis-reveals-znf804a-a-schizophrenia-risk-gene-as-a-novel-component-of-protein-translational-machinery-critical-for-embryonic-neurodevelopment
#16
Y Zhou, F Dong, T A Lanz, V Reinhart, M Li, L Liu, J Zou, H S Xi, Y Mao
Recent genome-wide association studies identified over 100 genetic loci that significantly associate with schizophrenia (SZ). A top candidate gene, ZNF804A, was robustly replicated in different populations. However, its neural functions are largely unknown. Here we show in mouse that ZFP804A, the homolog of ZNF804A, is required for normal progenitor proliferation and neuronal migration. Using a yeast two-hybrid genome-wide screen, we identified novel interacting proteins of ZNF804A. Rather than transcriptional factors, genes involved in mRNA translation are highly represented in our interactome result...
September 19, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28924158/genome-wide-association-analysis-of-powdery-mildew-resistance-in-u-s-winter-wheat
#17
Na Liu, Guihua Bai, Meng Lin, Xiangyang Xu, Wenming Zheng
Wheat powdery mildew (PM), caused by Blumeria graminis f. sp. tritici, is a major fungal disease of wheat worldwide. It can cause considerable yield losses when epidemics occur. Use of genetic resistance is the most effective approach to control the disease. To determine the genomic regions responsible for PM resistance in a set of U.S. winter wheat and identify DNA markers in these regions, we conducted a genome-wide association study on a set of 185 U.S. winter wheat accessions using single nucleotide polymorphism (SNP) markers from 90 K wheat SNP arrays...
September 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28923882/mutational-profiling-of-acute-myeloid-leukemia-with-normal-cytogenetics-in-brazilian-patients-the-value-of-next-generation-sequencing-for-genomic-classification
#18
Thiago Rodrigo de Noronha, Miguel Mitne-Neto, Maria de Lourdes Chauffaille
Karyotype (KT) aberrations are important prognostic factors for acute myeloid leukemia (AML); however, around 50% of cases present normal results. Single nucleotide polymorphism array can detect chromosomal gains, losses or uniparental disomy that are invisible to KT, thus improving patients' risk assessment. However, when both tests are normal, important driver mutations can be detected by the use of next-generation sequencing (NGS). Fourteen adult patients with AML with normal cytogenetics were investigated by NGS for 19 AML-related genes...
September 18, 2017: Journal of Investigative Medicine: the Official Publication of the American Federation for Clinical Research
https://www.readbyqxmd.com/read/28923540/the-contribution-of-admixture-to-primate-evolution
#19
REVIEW
Jenny Tung, Luis B Barreiro
Genome-wide data on genetic variation are now available for multiple primate species and populations, facilitating analyses of evolutionary history within and across taxa. One emerging theme from these studies involves the central role of admixture. Genomic data sets indicate that both ancient gene flow following initial taxonomic divergence and ongoing gene flow at current species boundaries are common. These findings are of particular interest given evidence for a complex history of admixture in our own lineage, including examples of ecologically driven adaptive introgression...
September 15, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28923510/first-characterization-of-a-middle-east-gi-23-lineage-var2-like-of-infectious-bronchitis-virus-in-europe
#20
Anna Lisowska, Joanna Sajewicz-Krukowska, Alice Fusaro, Anna Pikula, Katarzyna Domanska-Blicharz
Variants assigned to GI-23 lineage of infectious bronchitis virus (IBV), formerly called Var2, have circulated for nearly 20 years only in countries of the Middle East. Strains of this lineage were first identified in Israel in 1998. More severe form of the virus appeared in 2006, when the second wave of Var2 epidemic has spread over the Middle East region. The present study describes the detection and detailed genetic characterization of the GI-23 viruses in Poland. The full-length genome of gammaCoV/Ck/Poland/G052/2016 strain consists of 27596 nucleotides and has typical organization for IBV (UTR5'-POl-S-3a-3b-E-M-5a-5b-N-UTR3')...
September 15, 2017: Virus Research
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