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https://www.readbyqxmd.com/read/28549074/cwdprnp-a-tool-for-cervid-prion-sequence-analysis-in-program-r
#1
William L Miller, W David Walter
Summary: Chronic wasting disease is a fatal neurological, disease caused by an infectious prion protein, which affects economically and ecologically important members of the family Cervidae. Single nucleotide polymorphisms within the prion protein gene have been linked to differential susceptibility to the disease in many species. Wildlife managers are seeking to determine the frequencies of disease-associated alleles and genotypes and delineate spatial genetic patterns. The CWDPRNP package, implemented in program R, provides a unified framework for analyzing prion protein gene variability and spatial structure...
May 26, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28548882/finding-conducting-and-nurturing-science-a-virologist-s-memoir
#2
Anna Marie Ann Skalka Skalka
My laboratory investigations have been driven by an abiding interest in understanding the consequences of genetic rearrangement in evolution and disease, and in using viruses to elucidate fundamental mechanisms in biology. Starting with bacteriophages and moving to the retroviruses, my use of the tools of genetics, molecular biology, biochemistry, and biophysics has spanned more than half a century-from the time when DNA structure was just discovered to the present day of big data and epigenetics. Both riding and contributing to the successive waves of technology, my laboratory has elucidated fundamental mechanisms in DNA replication, repair, and recombination...
May 26, 2017: Annual Review of Virology
https://www.readbyqxmd.com/read/28548871/genetic-diversity-and-population-structure-of-acrossocheilus-yunnanensis-teleostei-cyprinidae-inferred-from-four-mitochondrial-gene-sequences
#3
Lan-Ping Zheng, Jun-Xing Yang
In this paper, we examine the genetic diversity, population structure and demographic history of Acrossocheilus yunnanensis inferred from four mitochondrial gene sequences. Twenty-two haplotypes were identified for A. yunnanensis. The total haplotype and nucleotide diversities of A. yunnanensis are 0.9206 and 0.024654, respectively. The monophyly of the haplotypes is supported by all phylogenetic analyses. All the haplotypes can be divided into four major lineages. The results of AMOVA and SAMOVA suggest that the best grouping pattern is to divide four groups, and that most of the variation of genetic divergence is present among these groups...
May 26, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28548703/microsporidians-xenomas-of-anglerfish-from-ne-atlantic-waters
#4
M Llarena-Reino, E Abollo, S Pascual
The presence of emergent visible parasites at commercial valuable fish species is increasingly causing problems at fisheries and seafood industries. Microsporidians have been previously reported to appear forming apparent xenomas complexes in anglerfish species, but no effort has been carried out to simultaneously integrate epidemiological data, phenotypic, genotypic and fine structural characterizations in the same parasite sample. In this work, specimens of Lophius budegassa and Lophius piscatorius from NE Atlantic waters were sampled and examined to provide information about specific site of infection and demographic data of two groups of different sizes of xenomas present at both fish species...
May 26, 2017: Journal of Fish Diseases
https://www.readbyqxmd.com/read/28548104/genomic-analysis-of-oesophageal-squamous-cell-carcinoma-identifies-alcohol-drinking-related-mutation-signature-and-genomic-alterations
#5
Jiang Chang, Wenle Tan, Zhiqiang Ling, Ruibin Xi, Mingming Shao, Mengjie Chen, Yingying Luo, Yanjie Zhao, Yun Liu, Xiancong Huang, Yuchao Xia, Jinlin Hu, Joel S Parker, David Marron, Qionghua Cui, Linna Peng, Jiahui Chu, Hongmin Li, Zhongli Du, Yaling Han, Wen Tan, Zhihua Liu, Qimin Zhan, Yun Li, Weimin Mao, Chen Wu, Dongxin Lin
Approximately half of the world's 500,000 new oesophageal squamous-cell carcinoma (ESCC) cases each year occur in China. Here, we show whole-genome sequencing of DNA and RNA in 94 Chinese individuals with ESCC. We identify six mutational signatures (E1-E6), and Signature E4 is unique in ESCC linked to alcohol intake and genetic variants in alcohol-metabolizing enzymes. We discover significantly recurrent mutations in 20 protein-coding genes, 4 long non-coding RNAs and 10 untranslational regions. Functional analyses show six genes that have recurrent copy-number variants in three squamous-cell carcinomas (oesophageal, head and neck and lung) significantly promote cancer cell proliferation, migration and invasion...
May 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28547520/small-scale-intraspecific-patterns-of-adaptive-immunogenetic-polymorphisms-and-neutral-variation-in-lake-superior-lake-trout
#6
Shauna M Baillie, Riley R Hemstock, Andrew M Muir, Charles C Krueger, Paul Bentzen
Many fishes express high levels of intraspecific variability, often linked to resource partitioning. Several studies show that a species' evolutionary trajectory of adaptive divergence can undergo reversals caused by changes in its environment. Such a reversal in neutral genetic and morphological variation among lake trout Salvelinus namaycush ecomorphs appears to be underway in Lake Superior. However, a water depth gradient in neutral genetic divergence was found to be associated with intraspecific diversity in the lake...
May 25, 2017: Immunogenetics
https://www.readbyqxmd.com/read/28547213/evolutionary-dynamics-in-the-two-locus-two-allele-model-with-weak-selection
#7
Martin Pontz, Josef Hofbauer, Reinhard Bürger
Two-locus two-allele models are among the most studied models in population genetics. The reason is that they are the simplest models to explore the role of epistasis for a variety of important evolutionary problems, including the maintenance of polymorphism and the evolution of genetic incompatibilities. Many specific types of models have been explored. However, due to the mathematical complexity arising from the fact that epistasis generates linkage disequilibrium, few general insights have emerged. Here, we study a simpler problem by assuming that linkage disequilibrium can be ignored...
May 25, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28546999/a-birth-of-bipartite-exon-by-intragenic-deletion
#8
Kandai Nozu, Kazumoto Iijima, Toru Igarashi, Shiro Yamada, Jana Kralovicova, Yoshimi Nozu, Tomohiko Yamamura, Shogo Minamikawa, Ichiro Morioka, Takeshi Ninchoji, Hiroshi Kaito, Koichi Nakanishi, Igor Vorechovsky
BACKGROUND: Disease-causing mutations that activate transposon-derived exons without creating a new splice-site consensus have been reported rarely, but they provided unique insights into our understanding of structural motifs required for inclusion of intronic sequences in mature transcripts. METHODS: We employ a combination of experimental and computational techniques to characterize the first de novo bipartite exon activation in genetic disease. RESULTS: The exon originated from two separate introns as a result of an in-frame COL4A5 deletion associated with a typical Alport syndrome...
May 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28546994/sdha-related-tumorigenesis-a-new-case-series-and-literature-review-for-variant-interpretation-and-pathogenicity
#9
Ruth T Casey, David B Ascher, Eleanor Rattenberry, Louise Izatt, Katrina A Andrews, Helen L Simpson, Benjamen Challis, Soo-Mi Park, Venkata R Bulusu, Fiona Lalloo, Douglas E V Pires, Hannah West, Graeme R Clark, Philip S Smith, James Whitworth, Thomas G Papathomas, Phillipe Taniere, Rosina Savisaar, Laurence D Hurst, Emma R Woodward, Eamonn R Maher
PURPOSE: To evaluate the role of germline SDHA mutation analysis by (1) comprehensive literature review, (2) description of novel germline SDHA mutations and (3) in silico structural prediction analysis of missense substitutions in SDHA. PATIENTS AND METHODS: A systematic literature review and a retrospective review of the molecular and clinical features of patients identified with putative germline variants in UK molecular genetic laboratories was performed. To evaluate the molecular consequences of SDHA missense variants, a novel model of the SDHA/B/C/D complex was generated and the structural effects of missense substitutions identified in the literature, our UK novel cohort and a further 32 "control missense variants" were predicted by the mCSM computational platform...
May 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28546921/a-novel-frameshift-mutation-in-cx46-associated-with-hereditary-dominant-cataracts-in-a-chinese-family
#10
Xiu-Kun Cui, Ke-Ke Zhu, Zheng Zhou, Si-Min Wan, Yi Dong, Xuan-Ce Wang, Jing Li, Jing Zhang, Hong-Mei Mu, Lei Qin, Yan-Zhong Hu
AIM: To investigate the genetic mutations that are associated the hereditary autosomal dominant cataract in a Chinese family. METHODS: A Chinese family consisting of 20 cataract patients (including 9 male and 11 female) and 2 unaffected individuals from 5 generations were diagnosed to be a typical autosomal dominant cataract pedigree. Genomic DNA samples were extracted from the peripheral blood cells of the participants in this pedigree. Exon sequence was used for genetic mutation screening...
2017: International Journal of Ophthalmology
https://www.readbyqxmd.com/read/28546913/genetic-assembly-of-double-layered-fluorescent-protein-nanoparticles-for-cancer-targeting-and-imaging
#11
Seong-Eun Kim, Sung Duk Jo, Koo Chul Kwon, You-Yeon Won, Jeewon Lee
Hepatitis B virus capsid (HBVC), a self-assembled protein nanoparticle comprised of 180 or 240 subunit proteins, is used as a cage for genetic encapsulation of fluorescent proteins (FPs). The self-quenching of FPs is controlled by varying the spacing between FPs within the capsid structure. Double-layered FP nanoparticle possessing cancer cell-targeting capabilities is also produced by additionally attaching FPs and cancer cell receptor-binding peptides (affibodies) to the outer surface of the capsid. The generically modified HBVC with double layers of mCardinal FPs and affibodies (mC-DL-HBVC) exhibit a high fluorescence intensity and a strong photostability, and is efficiently internalized by cancer cells and significantly stable against intracellular degradation...
May 2017: Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
https://www.readbyqxmd.com/read/28546842/opportunities-and-challenges-for-the-sustainable-production-of-structurally-complex-diterpenoids-in-recombinant-microbial-systems
#12
REVIEW
Katarina Kemper, Max Hirte, Markus Reinbold, Monika Fuchs, Thomas Brück
With over 50.000 identified compounds terpenes are the largest and most structurally diverse group of natural products. They are ubiquitous in bacteria, plants, animals and fungi, conducting several biological functions such as cell wall components or defense mechanisms. Industrial applications entail among others pharmaceuticals, food additives, vitamins, fragrances, fuels and fuel additives. Central building blocks of all terpenes are the isoprenoid compounds isopentenyl diphosphate and dimethylallyl diphosphate...
2017: Beilstein Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28546787/pepsinogen-c-expression-regulation-and-its-relationship-with-cancer
#13
REVIEW
Shixuan Shen, Jingyi Jiang, Yuan Yuan
Pepsinogen C (PGC) belongs to the aspartic protease family and is secreted by gastric chief cells. PGC could be activated to pepsin C and digests polypeptides and amino acids, but as a zymogen PGC's functions is unclear. In normal physiological conditions, PGC is initially detected in the late embryonic stage and is mainly expressed in gastric mucosa. The in situ expression of PGC in gastric mucosa is decreased considerably in the process of superficial gastritis → atrophic gastritis → gastric cancer (GC), proving that PGC is a comparatively ideal negative marker of GC...
2017: Cancer Cell International
https://www.readbyqxmd.com/read/28546232/genetic-defects-in-pediatric-onset-adrenal-insufficiency-in-japan
#14
Naoko Amano, Satoshi Narumi, Mie Hayashi, Masaki Takagi, Kazuhide Imai, Toshirou Nakamura, Rumi Hachiya, Goro Sasaki, Keiko Homma, Tomohiro Ishii, Tomonobu Hasegawa
CONTEXT: Most patients with pediatric-onset primary adrenal insufficiency (PAI), such as 21-hydroxylase deficiency, can be diagnosed by measuring the urine or serum levels of steroid metabolites. However, the etiology is often difficult to determine in a subset of patients lacking characteristic biochemical findings. OBJECTIVE: To assess the frequency of genetic defects in Japanese children with biochemically uncharacterized PAI, and characterize the phenotypes of mutation-carrying patients...
May 25, 2017: European Journal of Endocrinology
https://www.readbyqxmd.com/read/28546079/pioneer-study-of-population-genetics-of-rhodnius-ecuadoriensis-hemiptera-reduviidae-from-the-central-coast-and-southern-andean-regions-of-ecuador
#15
Anita G Villacís, Paula L Marcet, César A Yumiseva, Ellen M Dotson, Michel Tibayrenc, Simone Frédérique Brenière, Mario J Grijalva
Effective control of Chagas disease vector populations requires a good understanding of the epidemiological components, including a reliable analysis of the genetic structure of vector populations. Rhodnius ecuadoriensis is the most widespread vector of Chagas disease in Ecuador, occupying domestic, peridomestic and sylvatic habitats. It is widely distributed in the central coast and southern highlands regions of Ecuador, two very different regions in terms of bio-geographical characteristics. To evaluate the genetic relationship among R...
May 22, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28545973/evolutionary-and-ecological-forces-influencing-population-diversification-in-bornean-montane-passerines
#16
Vivien L Chua, Brian Tilston Smith, Ryan C Burner, Mustafa Abdul Rahman, Maklarin Lakim, Dewi M Prawiradilaga, Robert G Moyle, Frederick H Sheldon
The mountains of Borneo are well known for their high endemicity and historical role in preserving Southeast Asian rainforest biodiversity, but the diversification of populations inhabiting these mountains is poorly studied. Here we examine the genetic structure of 12 Bornean montane passerines by comparing complete mtDNA ND2 gene sequences of populations spanning the island. Maximum likelihood and Bayesian phylogenetic trees and haplotype networks are examined for common patterns that might signal important historical events or boundaries to dispersal...
May 22, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28545862/a-novel-pathogenic-variant-in-the-fzd6-gene-causes-recessive-nail-dysplasia-in-a-large-iranian-kindred
#17
Javad Mohammadi-Asl, Mohammad Reza Pourreza, Aliasgar Mohammadi, Ameneh Eskandari, Sima Mozafar-Jalali, Mohammad Amin Tabatabaiefar
BACKGROUND: Nail disorder nonsyndromic congenital (NDNC) is a very rare clinically and genetically heterogeneous disease inherited both in recessive or dominant modes. FZD6 is a component of Wnt-FZD signaling pathway in which recessive loss-of-function variants in the corresponding genes could lead to nail anomalies. OBJECTIVE: A large multiplex family with NDNC was referred for genetic counselling. Thorough genetic evaluation was performed. METHODS: PCR-Sanger sequencing was carried out for the coding exons and exon-intron boundaries of the FZD6 gene...
May 13, 2017: Journal of Dermatological Science
https://www.readbyqxmd.com/read/28545623/genetic-determinants-of-hereditary-bradyarrhythmias-a-contemporary-review-of-a-diverse-group-of-disorders
#18
REVIEW
Saman Rezazadeh, Henry J Duff
Bradyarrhythmia is a common clinical presentation. Although the majority of cases are acquired, genetic screening of families with bradyarrhythmia has led to the discovery of a growing number of causative hereditary mutations. These mutations can interfere with any of the steps required for the occurrence of each cardiac cycle, including generation of an action potential in the sinoatrial node, successful exit of the action potential from the node, propagation of the action potential throughout the atria until the depolarization waves reach the atrioventricular node, and finally transmission of the action potential to the ventricles through the His-Purkinje system...
June 2017: Canadian Journal of Cardiology
https://www.readbyqxmd.com/read/28545432/the-impact-of-migratory-flyways-on-the-spread-of-avian-influenza-virus-in-north-america
#19
Mathieu Fourment, Aaron E Darling, Edward C Holmes
BACKGROUND: Wild birds are the major reservoir hosts for influenza A viruses (AIVs) and have been implicated in the emergence of pandemic events in livestock and human populations. Understanding how AIVs spread within and across continents is therefore critical to the development of successful strategies to manage and reduce the impact of influenza outbreaks. In North America many bird species undergo seasonal migratory movements along a North-South axis, thereby providing opportunities for viruses to spread over long distances...
May 25, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28545396/transcriptomic-resources-for-the-medicinal-legume-mucuna-pruriens-de-novo-transcriptome-assembly-annotation-identification-and-validation-of-est-ssr-markers
#20
N Sathyanarayana, Ranjith Kumar Pittala, Pankaj Kumar Tripathi, Ratan Chopra, Heikham Russiachand Singh, Vikas Belamkar, Pardeep Kumar Bhardwaj, Jeff J Doyle, Ashley N Egan
BACKGROUND: The medicinal legume Mucuna pruriens (L.) DC. has attracted attention worldwide as a source of the anti-Parkinson's drug L-Dopa. It is also a popular green manure cover crop that offers many agronomic benefits including high protein content, nitrogen fixation and soil nutrients. The plant currently lacks genomic resources and there is limited knowledge on gene expression, metabolic pathways, and genetics of secondary metabolite production. Here, we present transcriptomic resources for M...
May 25, 2017: BMC Genomics
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