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https://www.readbyqxmd.com/read/28749613/linked-selection-demography-and-the-evolution-of-correlated-genomic-landscapes-in-birds-and-beyond
#1
Reto Burri
Selection has a deep impact on the distribution of genetic diversity and population differentiation along the genome (the genomic landscapes of diversity and differentiation), reducing diversity and elevating differentiation not only at the sites it targets, but also at linked neutral sites. Fuelled by the high-throughput sequencing revolution, these genomic footprints of selection have been extensively exploited over the past decade with the aim to identify genomic regions involved in adaptation and speciation...
August 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28749478/molecular-autopsy-in-maternal-fetal-medicine
#2
Hanan E Shamseldin, Wesam Kurdi, Fatima Almusafri, Maha Alnemer, Alya Alkaff, Zeneb Babay, Amal Alhashem, Maha Tulbah, Nada Alsahan, Rubina Khan, Bahauddin Sallout, Elham Al Mardawi, Mohamed Zain Seidahmed, Niema Meriki, Yasser Alsaber, Alya Qari, Ola Khalifa, Wafaa Eyaid, Zuhair Rahbeeni, Ahmed Kurdi, Mais Hashem, Tarfa Alshidi, Eman Al-Obeid, Firdous Abdulwahab, Niema Ibrahim, Nour Ewida, Karen El-Akouri, Mariam Al Mulla, Tawfeg Ben-Omran, Matthias Pergande, Sebahattin Cirak, Saeed Al Tala, Ranad Shaheen, Eissa Faqeih, Fowzan S Alkuraya
PurposeThe application of genomic sequencing to investigate unexplained death during early human development, a form of lethality likely enriched for severe Mendelian disorders, has been limited.MethodsIn this study, we employed exome sequencing as a molecular autopsy tool in a cohort of 44 families with at least one death or lethal fetal malformation at any stage of in utero development. Where no DNA was available from the fetus, we performed molecular autopsy by proxy, i.e., through parental testing.ResultsPathogenic or likely pathogenic variants were identified in 22 families (50%), and variants of unknown significance were identified in further 15 families (34%)...
July 27, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28749451/characterization-of-two-historic-smallpox-specimens-from-a-czech-museum
#3
Petr Pajer, Jiri Dresler, Hana Kabíckova, Libor Písa, Pavel Aganov, Karel Fucik, Daniel Elleder, Tomas Hron, Vitezslav Kuzelka, Petr Velemínsky, Jana Klimentova, Alena Fucikova, Jaroslav Pejchal, Rita Hrabakova, Vladimir Benes, Tobias Rausch, Pavel Dundr, Alexander Pilin, Radomir Cabala, Martin Hubalek, Jan Stríbrny, Markus H Antwerpen, Hermann Meyer
Although smallpox has been known for centuries, the oldest available variola virus strains were isolated in the early 1940s. At that time, large regions of the world were already smallpox-free. Therefore, genetic information of these strains can represent only the very last fraction of a long evolutionary process. Based on the genomes of 48 strains, two clades are differentiated: Clade 1 includes variants of variola major, and clade 2 includes West African and variola minor (Alastrim) strains. Recently, the genome of an almost 400-year-old Lithuanian mummy was determined, which fell basal to all currently sequenced strains of variola virus on phylogenetic trees...
July 27, 2017: Viruses
https://www.readbyqxmd.com/read/28749355/hardware-accelerator-for-the-multifractal-analysis-of-dna-sequences
#4
Jorge E Duarte-Sanchez, Jaime Velasco-Medina, Pedro A Moreno
The multifractal analysis has allowed to quantify the genetic variability and non-linear stability along the human genome sequence. It has some implications in explaining several genetic diseases given by some chromosome abnormalities, among other genetic particularities. The multifractal analysis of a genome is carried out by dividing the complete DNA sequence in smaller fragments and calculating the generalized dimension spectrum of each fragment using the chaos game representation and the box-counting method...
July 24, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28749283/seroprevalence-and-molecular-characterization-of-ferlavirus-in-captive-vipers-of-costa-rica
#5
Cristina Solis, Randall Arguedas, Mario Baldi, Martha Piche, Carlos Jimenez
Ferlaviruses (FV, previously referred to as ophidian paramyxoviruses, OPMV), are enveloped viruses with a negative-strand RNA genome, affecting snakes in captivity worldwide. Infection is characterized by respiratory and nervous clinical signs and carries high mortality rates, but no specific treatment or vaccine is currently available. Costa Rica has 16 species of vipers, found in captivity in collections essential for antivenom production, reintroduction, and public education. FV circulation in these populations was previously unknown, and the risk of introducing the viruses into naïve collections or free-ranging populations exists if the virus's presence is confirmed...
June 2017: Journal of Zoo and Wildlife Medicine: Official Publication of the American Association of Zoo Veterinarians
https://www.readbyqxmd.com/read/28749196/double-stranded-telomeric-dna-binding-proteins-diversity-matters
#6
Filip Červenák, Katarína Juríková, Regina Sepšiová, Martina Neboháčová, Jozef Nosek, Ľubomír Tomáška
Telomeric sequences constitute only a small fraction of the whole genome yet they are crucial for ensuring genomic stability. This function is in large part mediated by protein complexes recruited to telomeric sequences by specific telomere-binding proteins (TBPs). Although the principal tasks of nuclear telomeres are the same in all eukaryotes, TBPs in various taxa exhibit a surprising diversity indicating their distinct evolutionary origin. This diversity is especially pronounced in ascomycetous yeasts where they must have co-evolved with rapidly diversifying sequences of telomeric repeats...
July 27, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28748849/a-novel-missense-mutation-in-peripheral-myelin-protein-22-causes-charcot-marie-tooth-disease
#7
Li-Xi Li, Hai-Lin Dong, Bao-Guo Xiao, Zhi-Ying Wu
BACKGROUND: Charcot-Marie-Tooth disease (CMT) is the most common inherited peripheral neuropathy. A great number of causative genes have been described in CMT, and among them, the heterozygous duplication of peripheral myelin protein-22 (PMP22) is the major cause. Although the missense mutation in PMP22 is rarely reported, it has been demonstrated to be associated with CMT. This study described a novel missense mutation of PMP22 in a Chinese family with CMT phenotype. METHODS: Targeted next-generation sequencing (NGS) was used to screen the causative genes in a family featured with an autosomal dominant demyelinating form of CMT...
August 5, 2017: Chinese Medical Journal
https://www.readbyqxmd.com/read/28748640/expression-of-nad-p-h-quinone-dehydrogenase-1-nqo1-is-increased-in-the-endometrium-of-women-with-endometrial-cancer-and-women-with-polycystic-ovary-syndrome
#8
William Atiomo, Mohamad Nasir Shafiee, Caroline Chapman, Veronika M Metzler, Jad Abouzeid, Ayşe Latif, Amy Chadwick, Sarah Kitson, Vanitha N Sivalingam, Ian J Stratford, Catrin S Rutland, Jenny L Persson, Niels Ødum, Pablo Fuentes-Utrillia, Jennie N Jeyapalan, David M Heery, Emma J Crosbie, Nigel P Mongan
OBJECTIVE: Women with a prior history of polycystic ovary syndrome (PCOS) have an increased risk of endometrial cancer (EC). AIM: To investigate whether the endometrium of women with PCOS possess gene expression changes similar to those found in EC. DESIGN AND METHODS: Patients with EC, PCOS and control women unaffected by either PCOS or EC were recruited into a cross-sectional study at the Nottingham University Hospital, UK. For RNA sequencing, representative individual endometrial biopsies were obtained from women with EC, PCOS and a woman unaffected by PCOS or EC...
July 27, 2017: Clinical Endocrinology
https://www.readbyqxmd.com/read/28748527/the-prevalence-of-dicer1-pathogenic-variation-in-population-databases
#9
Jung Kim, Amanda Field, Kris Ann P Schultz, D Ashley Hill, Douglas R Stewart
The DICER1 syndrome is associated with a variety of rare benign and malignant tumors, including pleuropulmonary blastoma (PPB), cystic nephroma (CN) and Sertoli-Leydig cell tumor (SLCT). The prevalence and penetrance of pathogenic DICER1 variation in the general population is unknown. We examined three publicly-available germline whole exome sequence datasets: Exome Aggregation Consortium (ExAC), 1000 Genomes (1000G), and the Exome Sequencing Project (ESP). To avoid over-estimation of pathogenic DICER1 variation from cancer-associated exomes, we excluded The Cancer Genome Atlas (TCGA) variants from ExAC...
July 27, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28748462/in-vivo-rat-t-lymphocyte-pig-a-assay-detection-and-expansion-of-cells-deficient-in-the-gpi-anchored-cd48-surface-marker-for-analysis-of-mutation-in-the-endogenous-pig-a-gene
#10
Vasily N Dobrovolsky, Javier Revollo, Dayton M Petibone, Robert H Heflich
The Pig-a assay is being developed as an in vivo gene mutation assay for regulatory safety assessments. The assay is based on detecting mutation in the endogenous Pig-a gene of treated rats by using flow cytometry to measure changes in cell surface markers of peripheral blood cells. Here we present a methodology for demonstrating that phenotypically mutant rat T-cells identified by flow cytometry contain mutations in the Pig-a gene, an important step for validating the assay. In our approach, the mutant phenotype T-cells are sorted into individual wells of 96-well plates and expanded into clones...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28748394/association-mapping-analysis-of-fiber-yield-and-quality-traits-in-upland-cotton-gossypium-hirsutum-l
#11
Mulugeta Seyoum Ademe, Shoupu He, Zhaoe Pan, Junling Sun, Qinglian Wang, Hongde Qin, Jinhai Liu, Hui Liu, Jun Yang, Dongyong Xu, Jinlong Yang, Zhiying Ma, Jinbiao Zhang, Zhikun Li, Zhongmin Cai, Xuelin Zhang, Xin Zhang, Aifen Huang, Xianda Yi, Guanyin Zhou, Lin Li, Haiyong Zhu, Baoyin Pang, Liru Wang, Yinhua Jia, Xiongming Du
Fiber yield and quality are the most important traits for Upland cotton (Gossypium hirsutum L.). Identifying high yield and good fiber quality genes are the prime concern of researchers in cotton breeding. Association mapping offers an alternative and powerful method for detecting those complex agronomic traits. In this study, 198 simple sequence repeats (SSRs) were used to screen markers associated with fiber yield and quality traits with 302 elite Upland cotton accessions that were evaluated in 12 locations representing the Yellow River and Yangtze River cotton growing regions of China...
July 26, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28748222/an-improved-plasmodium-cynomolgi-genome-assembly-reveals-an-unexpected-methyltransferase-gene-expansion
#12
Erica M Pasini, Ulrike Böhme, Gavin G Rutledge, Annemarie Voorberg-Van der Wel, Mandy Sanders, Matt Berriman, Clemens Hm Kocken, Thomas Dan Otto
BACKGROUND: Plasmodium cynomolgi, a non-human primate malaria parasite species, has been an important model parasite since its discovery in 1907. Similarities in the biology of P. cynomolgi to the closely related, but less tractable, human malaria parasite P. vivax make it the model parasite of choice for liver biology and vaccine studies pertinent to P. vivax malaria. Molecular and genome-scale studies of P. cynomolgi have relied on the current reference genome sequence, which remains highly fragmented with 1,649 unassigned scaffolds and little representation of the subtelomeres...
2017: Wellcome Open Research
https://www.readbyqxmd.com/read/28748134/genomic-characterization-reconfirms-the-taxonomic-status-of-lactobacillus-parakefiri
#13
Yasuhiro Tanizawa, Hisami Kobayashi, Eli Kaminuma, Mitsuo Sakamoto, Moriya Ohkuma, Yasukazu Nakamura, Masanori Arita, Masanori Tohno
Whole-genome sequencing was performed for Lactobacillus parakefiri JCM 8573(T) to confirm its hitherto controversial taxonomic position. Here, we report its first reliable reference genome. Genome-wide metrics, such as average nucleotide identity and digital DNA-DNA hybridization, and phylogenomic analysis based on multiple genes supported its taxonomic status as a distinct species in the genus Lactobacillus. The availability of a reliable genome sequence will aid future investigations on the industrial applications of L...
2017: Bioscience of Microbiota, Food and Health
https://www.readbyqxmd.com/read/28748024/insights-into-cedecea-neteri-strain-m006-through-complete-genome-sequence-a-rare-bacterium-from-aquatic-environment
#14
Kok-Gan Chan, Wen-Si Tan
Cedecea neteri M006 is a rare bacterium typically found as an environmental isolate from the tropical rainforest Sungai Tua waterfall (Gombak, Selangor, Malaysia). It is a Gram-reaction-negative, facultative anaerobic, bacillus. Here, we explore the features of Cedecea neteri M006, together with its genome sequence and annotation. The genome comprised 4,965,436 bp with 4447 protein-coding genes and 103 RNA genes.
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28747923/mapping-qtl-for-seed-germinability-under-low-temperature-using-a-new-high-density-genetic-map-of-rice
#15
Ningfei Jiang, Shilai Shi, Huan Shi, Hira Khanzada, Ghulam M Wassan, Changlan Zhu, Xiaosong Peng, Qiuying Yu, Xiaorong Chen, Xiaopeng He, Junru Fu, Lifang Hu, Jie Xu, Linjuan Ouyang, Xiaotang Sun, Dahu Zhou, Haohua He, Jianmin Bian
Mapping major quantitative trait loci (QTL) responsible for rice seed germinability under low temperature (GULT) can provide valuable genetic source for improving cold tolerance in rice breeding. In this study, 124 rice backcross recombinant inbred lines (BRILs) derived from a cross indica cv. Changhui 891 and japonica cv. 02428 were genotyped through re-sequencing technology. A bin map was generated which includes 3057 bins covering distance of 1266.5 cM with an average of 0.41 cM between markers. On the basis of newly constructed high-density genetic map, six QTL were detected ranging from 40 to 140 kb on Nipponbare genome...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28747921/unreduced-megagametophyte-production-in-lemon-occurs-via-three-meiotic-mechanisms-predominantly-second-division-restitution
#16
Houssem Rouiss, José Cuenca, Luis Navarro, Patrick Ollitrault, Pablo Aleza
Unreduced (2n) gametes have played a pivotal role in polyploid plant evolution and are useful for sexual polyploid breeding in various species, particularly for developing new seedless citrus varieties. The underlying mechanisms of 2n gamete formation were recently revealed for Citrus reticulata but remain poorly understood for other citrus species, including lemon (C. limon [L.] Burm. f.). Here, we investigated the frequency and causal meiotic mechanisms of 2n megagametophyte production in lemon. We genotyped 48progeny plants of two lemon genotypes, "Eureka Frost" and "Fino", using 16 Simple Sequence Repeat (SSR) and 18 Single Nucleotide Polymorphism (SNP) markers to determine the genetic origin of the progenies and the underlying mechanisms for 2n gamete formation...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28747909/the-physiological-functions-and-structural-determinants-of-catalytic-bias-in-the-fefe-hydrogenases-cpi-and-cpii-of-clostridium-pasteurianum-strain-w5
#17
Jesse B Therien, Jacob H Artz, Saroj Poudel, Trinity L Hamilton, Zhenfeng Liu, Seth M Noone, Michael W W Adams, Paul W King, Donald A Bryant, Eric S Boyd, John W Peters
The first generation of biochemical studies of complex, iron-sulfur-cluster-containing [FeFe]-hydrogenases and Mo-nitrogenase were carried out on enzymes purified from Clostridium pasteurianum (strain W5). Previous studies suggested that two distinct [FeFe]-hydrogenases are expressed differentially under nitrogen-fixing and non-nitrogen-fixing conditions. As a result, the first characterized [FeFe]-hydrogenase (CpI) is presumed to have a primary role in central metabolism, recycling reduced electron carriers that accumulate during fermentation via proton reduction...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28747902/in-silico-taxonomic-classification-of-373-genomes-reveals-species-misidentification-and-new-genospecies-within-the-genus-pseudomonas
#18
Phuong N Tran, Michael A Savka, Han Ming Gan
The genus Pseudomonas has one of the largest diversity of species within the Bacteria kingdom. To date, its taxonomy is still being revised and updated. Due to the non-standardized procedure and ambiguous thresholds at species level, largely based on 16S rRNA gene or conventional biochemical assay, species identification of publicly available Pseudomonas genomes remains questionable. In this study, we performed a large-scale analysis of all Pseudomonas genomes with species designation (excluding the well-defined P...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28747754/corrigendum-whole-genome-sequencing-identifies-rare-genotypes-in-comp-and-chadl-associated-with-high-risk-of-hip-osteoarthritis
#19
Unnur Styrkarsdottir, Hannes Helgason, Asgeir Sigurdsson, Gudmundur L Norddahl, Arna B Agustsdottir, Louise N Reynard, Amanda Villalvilla, Gisli H Halldorsson, Aslaug Jonasdottir, Audur Magnusdottir, Asmundur Oddson, Gerald Sulem, Florian Zink, Gardar Sveinbjornsson, Agnar Helgason, Hrefna S Johannsdottir, Anna Helgadottir, Hreinn Stefansson, Solveig Gretarsdottir, Thorunn Rafnar, Ina S Almdahl, Anne Brækhus, Tormod Fladby, Geir Selbæk, Farhad Hosseinpanah, Fereidoun Azizi, Jung Min Koh, Nelson L S Tang, Maryams Danesphour, Jose I Mayordomo, Corrine Welt, Peter S Braund, Nilesh J Samani, Lambertus A Kiemeney, L Stefan Lohmander, Claus Christiansen, Ole A Andreassen, arcOGEN Consortium, Olafur Magnusson, Gisli Masson, Augustine Kong, Ingileif Jonsdottir, Daniel Gudbjartsson, Patrick Sulem, Helgi Jonsson, John Loughlin, Thorvaldur Ingvarsson, Unnur Thorsteinsdottir, Kari Stefansson
No abstract text is available yet for this article.
July 27, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28747720/mitochondrial-genomes-of-two-bombycoidea-insects-and-implications-for-their-phylogeny
#20
Zhao-Zhe Xin, Yu Liu, Xiao-Yu Zhu, Ying Wang, Hua-Bin Zhang, Dai-Zhen Zhang, Chun-Lin Zhou, Bo-Ping Tang, Qiu-Ning Liu
The mitochondrial genome (mt genome) provides important information for understanding molecular evolution and phylogenetics. As such, the two complete mt genomes of Ampelophaga rubiginosa and Rondotia menciana were sequenced and annotated. The two circular genomes of A. rubiginosa and R. menciana are 15,282 and 15,636 bp long, respectively, including 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and an A + T-rich region. The nucleotide composition of the A. rubiginosa mt genome is A + T rich (81...
July 26, 2017: Scientific Reports
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