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population genome

Didier Clenet, Tatiana Vinit, Damien Soulet, Claire Maillet, Françoise Guinet-Morlot, Aure Saulnier
Vaccine thermostability is key to successful global immunization programs as it may have a significant impact on the continuous cold-chain maintenance logistics, as well as affect vaccine potency. Modern biological and biophysical techniques were combined to in-depth characterize the thermostability of a formulated rabies virus (RABV) in terms of antigenic and genomic titer, virus particle count and aggregation state. Tunable resistive pulse sensing (TRPS) and nanoparticle tracking analysis (NTA) were used to count virus particles while simultaneously determining their size distribution...
August 14, 2018: European Journal of Pharmaceutics and Biopharmaceutics
Han-Yuan Zhang, Zi-Xia Zhao, Jian Xu, Peng Xu, Qing-Li Bai, Shi-Yong Yang, Li-Kun Jiang, Bao-Hua Chen
Various salmonid species are cultivated in cold water aquaculture. However, due to limited genomic data resources, specific high-throughput genotyping tools are not available to many of the salmonid species. In this study, a 57K single nucleotide polymorphism (SNP) array for rainbow trout (Oncorhynchus mykiss) was utilized to detect polymorphisms in seven salmonid species, including Hucho taimen, Oncorhynchus masou, Salvelinus fontinalis, Brachymystax lenok, Salvelinus leucomaenis, O. kisutch, and O. mykiss...
2018: PloS One
John Soghigian, Theodore G Andreadis, Goudarz Molaei
BACKGROUND: Eastern Equine Encephalitis (EEE) (Togaviridae, Alphavirus) is a highly pathogenic mosquito-borne arbovirus that circulates in an enzootic cycle involving Culiseta melanura mosquitoes and wild Passeriformes birds in freshwater swamp habitats. Recently, the northeastern United States has experienced an intensification of virus activity with increased human involvement and northward expansion into new regions. In addition to its principal role in enzootic transmission of EEE virus among avian hosts, recent studies on the blood-feeding behavior of Cs...
August 17, 2018: PLoS Neglected Tropical Diseases
Lina M Valencia, Amely Martins, Edgardo M Ortiz, Anthony Di Fiore
Until recently, most phylogenetic and population genetics studies of nonhuman primates have relied on mitochondrial DNA and/or a small number of nuclear DNA markers, which can limit our understanding of primate evolutionary and population history. Here, we describe a cost-effective reduced representation method (ddRAD-seq) for identifying and genotyping large numbers of SNP loci for taxa from across the New World monkeys, a diverse radiation of primates that shared a common ancestor ~20-26 mya. We also estimate, for the first time, the phylogenetic relationships among 15 of the 22 currently-recognized genera of New World monkeys using ddRAD-seq SNP data using both maximum likelihood and quartet-based coalescent methods...
2018: PloS One
Mengyan Zhang, Ruolei Xin, Hua Li, Lifang Dong, Wenhui Chang
Sexual contact is the main route of transmission of HIV-1 pandemic in China. New unique recombinant forms (URFs) were increasingly characterized in sexual populations in recent years. We reported two URFs identified from two male HIV-1 positive patients who were infected through sexual exposure in Shaanxi, China. Phylogenetic analyses and bootscan analyses revealed the near full-length genomes (NFLGs) of the two URFs were both having four recombinant breakpoints, with two CRF07_BC fragments inserted into CRF01_AE backbones...
August 17, 2018: AIDS Research and Human Retroviruses
Qiao Huang, Weidong Ou, Yi Feng, Fan Li, Kang Li, Jia Sun, Zhangwen Ge, Hui Xing, Hao Liang, Yiming Shao
This study reports a novel HIV-1 recombinant form of CRF01_AE/B that was isolated from a 22 year-old, male individual (HE150308) residing in Hebei province, China. The near full-length genome (NFLG) phylogenetic tree showed that the strain was clustered with CRF01_AE reference sequences and placed at the peripheral position within the branch of CRF01_AE strains. The bootscaning and similarity plot analysis revealed that the NFLG of this novel recombinant was composed of 8 interlaced segments, including four CRF01_AE and four subtype B segments separated by 7 breakpoints observed in the gag, pol as well as nef regions of HIV-1 genome...
August 17, 2018: AIDS Research and Human Retroviruses
Nilesh Nayee, Goutam Sahana, Swapnil Gajjar, Ananthasayanam Sudhakar, Kamlesh Trivedi, Mogens Sandø Lund, Bernt Guldbrandtsen
Bos indicus cattle breeds are genetically distinct from Bos taurus breeds. We examined the performance of three SNP arrays, the Illumina BovineHD BeadChip (777k; Illumina Inc.), the Illumina BovineSNP50 BeadChip (50k) and the GeneSeek 70k Indicus chip (75Ki; GeneSeek) in four B. indicus breeds (Gir, Kankrej, Sahiwal and Red Sindhi) and their B. taurus crosses, along with two B. taurus breeds, Holstein and Jersey. More SNPs on both Illumina SNP chips were monomorphic in B. indicus breeds (average 20.3%-29...
August 16, 2018: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
Yangfan Wang, Guidong Sun, Qifan Zeng, Zhihui Chen, Xiaoli Hu, Hengde Li, Shi Wang, Zhenmin Bao
Selective breeding is a common and effective approach for genetic improvement of aquaculture stocks with parental selection as the key factor. Genomic selection (GS) has been proposed as a promising tool to facilitate selective breeding. Here, we evaluated the predictability of four GS methods in Zhikong scallop (Chlamys farreri) through real dataset analyses of four economical traits (e.g., shell length, shell height, shell width, and whole weight). Our analysis revealed that different GS models exhibited variable performance in prediction accuracy depending on genetic and statistical factors, but non-parametric method, including reproducing kernel Hilbert spaces regression (RKHS) and sparse neural networks (SNN), generally outperformed parametric linear method, such as genomic best linear unbiased prediction (GBLUP) and BayesB...
August 16, 2018: Marine Biotechnology
Ahmed El-Sharkawy, Lobna Al Zaidan, Ahmed Malki
The Epstein-Barr virus (EBV) is the first herpesvirus identified to be associated with human cancers known to infect the majority of the world population. EBV-associated malignancies are associated with a latent form of infection, and several of the EBV-encoded latent proteins are known to mediate cellular transformation. These include six nuclear antigens and three latent membrane proteins (LMPs). In lymphoid and epithelial tumors, viral latent gene expressions have distinct pattern. In both primary and metastatic tumors, the constant expression of latent membrane protein 2A (LMP2A) at the RNA level suggests that this protein is the key player in the EBV-associated tumorigenesis...
2018: Frontiers in Oncology
Sayed M Hosseini-Vardanjani, Mohammad M Shariati, Hossein Moradi Shahrebabak, Mojtaba Tahmoorespur
Genomic prediction using a large number of markers is challenging, due to the curse of dimensionality as well as multicollinearity arising from linkage disequilibrium between markers. Several methods have been proposed to solve these problems such as Principal Component Analysis (PCA) that is commonly used to reduce the dimension of predictor variables by generating orthogonal variables. Usually, the knowledge from PCA is incorporated in genomic prediction, assuming equal variance for the PCs or a variance proportional to the eigenvalues, both treat variances as fixed...
2018: Frontiers in Genetics
Qiang Li, Juan Guo, Kaixiang Chao, Jinye Yang, Weiyun Yue, Dongfang Ma, Baotong Wang
Stripe rust, caused by the biotrophic fungus Puccinia striiformis f. sp. tritici ( Pst ), is one of the most widespread and destructive wheat diseases worldwide. Growing resistant cultivars is an effective approach for controlling this disease. However, because host resistance genes were easily overcome by new virulent Pst races, there is a continuous demand for identifying new effective wheat stripe rust resistance genes and develop closely linked markers for marker-assisted selection (MAS). Baidatou, an old Chinese wheat landrace, has been grown for several decades in Longnan region, Gansu Province, where stripe rust epidemics are frequent and severe...
2018: Frontiers in Plant Science
Stephanie L Servetas, Ryan S Doster, Aeryun Kim, Ian H Windham, Jeong-Heon Cha, Jennifer A Gaddy, D Scott Merrell
One elusive area in the Helicobacter pylori field is an understanding of why some infections result in gastric cancer, yet others persist asymptomatically for the life-span of the individual. Even before the genomic era, the high level of intraspecies diversity of H. pylori was well recognized and became an intriguing area of investigation with respect to disease progression. Of interest in this regard is the unique repertoire of over 60 outer membrane proteins (OMPs), several of which have been associated with disease outcome...
2018: Frontiers in Microbiology
Stephen P Robertson, Jennie Harre Hindmarsh, Sarah Berry, Vicky A Cameron, Murray P Cox, Ofa Dewes, Robert N Doughty, George Gray, Jessie C Jacobsen, Albert Laurence, Elizabeth Matisoo-Smith, Susan Morton, Andrew N Shelling, Dianne Sika-Paotonu, Anna Rolleston, Jonathan R Skinner, Russell G Snell, Andrew Sporle, Cristin Print, Tony R Merriman, Maui Hudson, Philip Wilcox
Precision medicine seeks to draw on data from both individuals and populations across disparate domains to influence and support diagnosis, management and prevention in healthcare at the level of the individual patient and their family/whānau. Central to this initiative is incorporating the effects of the inherent variation that lies within genomes and can influence health outcomes. Identifying and interpreting such variation requires an accurate, valid and representative dataset to firstly define what variants are present and then assess the potential relevance for the health of a person, their family/whānau and the wider community to which they belong...
August 17, 2018: New Zealand Medical Journal
Annette Erlangsen, Vivek Appadurai, Yunpeng Wang, Gustavo Turecki, Ole Mors, Thomas Werge, Preben B Mortensen, Anna Starnawska, Anders D Børglum, Andrew Schork, Ron Nudel, Marie Bækvad-Hansen, Jonas Bybjerg-Grauholm, David M Hougaard, Wesley K Thompson, Merete Nordentoft, Esben Agerbo
Family studies have shown an aggregation of suicidal behavior in families. Yet, molecular studies are needed to identify loci accounting for genetic heritability. We conducted a genome-wide association study and estimated single nucleotide polymorphisms (SNP) heritability for a suicide attempt. In a case-cohort study, national data on all individuals born in Denmark after 1981 and diagnosed with severe mental disorders prior to 2013 (n = 57,377) and individuals from the general population (n = 30,000) were obtained...
August 16, 2018: Molecular Psychiatry
Patrick Vudriko, Rika Umemiya-Shirafuji, James Okwee-Acai, Dickson Stuart Tayebwa, Joseph Byaruhanga, John Son Bbira, Kozo Fujisaki, Xuenan Xuan, Hiroshi Suzuki
This study investigated the target site mutations in the partial sequence of voltage-sensitive sodium channel (VSSC) domain II of synthetic pyrethroid (SP)-resistant Rhipicephalus appendiculatus. Genomic DNA was extracted from seven tick populations (two susceptible and five resistant) collected from central, eastern and southwestern Uganda. The PCR amplicons of the VSSC domain II were cloned and sequenced to determine novel single nucleotide polymorphisms (SNP). A non-synonymous mutation C78 A corresponding to C190 A was found in all the five SP-resistant ticks...
August 8, 2018: Ticks and Tick-borne Diseases
Mohit Yadav, Jitendra Singh Rathore
Here we report the first essentially complete TAome analysis for type II toxin-antitoxin (TA) system, a major class of TA modules found in bacterial system, from entomopathogenic bacterium Xenorhabdus nematophila ATCC 19061 (NCBI RefSeq NC_014228). We summarize this analysis in terms of TA locus, accession identifier, hits in conserved domain database, toxin superfamily, antitoxin superfamily and chromosomal/mobile genome/plasmid occurrences. Moreover, for TA context analyses we use six different specifications namely virulence factors, mobile genetic elements (MGE), antibiotic resistance genes, secretion systems, prophage and a classification of mobile genetic elements (ACLAME); among these hits are found for only MGE, ACLAME and prophage...
July 11, 2018: Computational Biology and Chemistry
Jiao Gong, Tingcai Cheng, Yuqian Wu, Xi Yang, Qili Feng, Kazuei Mita
Spodoptera litura is a polyphagous pest and can feed on >100 species of plants, causing great damage to agricultural production. The SNP results showed that there were gene exchanges between different regions. To explore the variations of larger segments in S. litura genome, we used genome resequencing samples from 14 regions of China, India, and Japan to study the copy number variations (CNVs). We identified 3976 CNV events and 1581 unique copy number variation regions (CNVRs) occupying the 108.5 Mb genome of S...
August 13, 2018: Genomics
Dana Šafářová, Karolína Vavroušková, Thierry Candresse, Milan Navrátil
A novel virus infecting elderberry was identified by high-throughput Illumina sequencing of double strand RNAs isolated form elderberry leaves. The complete genome sequence obtained (4512 nucleotides in length) shows an organization typical for aureusviruses, with five open reading frames (ORFs) and the typical ORF1-RT expression by the readthrough of an amber stop codon. The analysis of the RNA-dependent RNA polymerase (RdRp) and coat protein (CP) sequences showed the highest identity (respectively 75.7% and 55%) with the corresponding amino acid sequences of Pothos latent virus...
2018: PloS One
Hussain Bahbahani, Arwa Afana, David Wragg
Although classified as an African taurine breed, the genomes of Sheko cattle are an admixture of Asian zebu and African taurine ancestries. They populate the humid Bench Maji zone in Sheko and Bench districts in the south-western part of Ethiopia and are considered as a trypanotolerant breed with high potential for dairy production. Here, we investigate the genome of Sheko cattle for candidate signatures of adaptive introgression and positive selection using medium density genome-wide SNP data. Following locus-ancestry deviation analysis, 15 and 72 genome regions show substantial excess and deficiency in Asian zebu ancestry, respectively...
2018: PloS One
Eda Altan, Kristen Aiemjoy, Tung G Phan, Xutao Deng, Solomon Aragie, Zerihun Tadesse, Kelly E Callahan, Jeremy Keenan, Eric Delwart
BACKGROUND: The enteric viruses shed by different populations can be influenced by multiple factors including access to clean drinking water. We describe here the eukaryotic viral genomes in the feces of Ethiopian children participating in a clean water intervention trial. METHODOLOGY/PRINCIPAL FINDINGS: Fecal samples from 269 children with a mean age of 2.7 years were collected from 14 villages in the Amhara region of Ethiopia, half of which received a new hand-dug water well...
2018: PloS One
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