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https://www.readbyqxmd.com/read/28534829/variation-in-the-genetic-repertoire-of-viruses-infecting-micromonas-pusilla-reflects-horizontal-gene-transfer-and-links-to-their-environmental-distribution
#1
Jan F Finke, Danielle M Winget, Amy M Chan, Curtis A Suttle
Prasinophytes, a group of eukaryotic phytoplankton, has a global distribution and is infected by large double-stranded DNA viruses (prasinoviruses) in the family Phycodnaviridae. This study examines the genetic repertoire, phylogeny, and environmental distribution of phycodnaviruses infecting Micromonas pusilla, other prasinophytes and chlorophytes. Based on comparisons among the genomes of viruses infecting M. pusilla and other phycodnaviruses, as well as the genome from a host isolate of M. pusilla, viruses infecting M...
May 19, 2017: Viruses
https://www.readbyqxmd.com/read/28534238/a-fast-algorithm-for-bayesian-multi-locus-model-in-genome-wide-association-studies
#2
Weiwei Duan, Yang Zhao, Yongyue Wei, Sheng Yang, Jianling Bai, Sipeng Shen, Mulong Du, Lihong Huang, Zhibin Hu, Feng Chen
Genome-wide association studies (GWAS) have identified a large amount of single-nucleotide polymorphisms (SNPs) associated with complex traits. A recently developed linear mixed model for estimating heritability by simultaneously fitting all SNPs suggests that common variants can explain a substantial fraction of heritability, which hints at the low power of single variant analysis typically used in GWAS. Consequently, many multi-locus shrinkage models have been proposed under a Bayesian framework. However, most use Markov Chain Monte Carlo (MCMC) algorithm, which are time-consuming and challenging to apply to GWAS data...
May 22, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28533378/pyrite-sulfur-isotopes-reveal-glacial-interglacial-environmental-changes
#3
Virgil Pasquier, Pierre Sansjofre, Marina Rabineau, Sidonie Revillon, Jennifer Houghton, David A Fike
The sulfur biogeochemical cycle plays a key role in regulating Earth's surface redox through diverse abiotic and biological reactions that have distinctive stable isotopic fractionations. As such, variations in the sulfur isotopic composition (δ(34)S) of sedimentary sulfate and sulfide phases over Earth history can be used to infer substantive changes to the Earth's surface environment, including the rise of atmospheric oxygen. Such inferences assume that individual δ(34)S records reflect temporal changes in the global sulfur cycle; this assumption may be well grounded for sulfate-bearing minerals but is less well established for pyrite-based records...
May 22, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28531368/molecular-phylogeny-of-loliginidae-inferred-from-mitochondrial-dna-sequence-variation
#4
Lisen Kang, Shuyi Zhang, Changwen Wu, Xiaoxu Liu, Mei Ying Xu, Lihua Jiang
Loliginidae includes many economically important species in trophic systems worldwide. Here, we investigated genetic relationships and diversity in this family. Sequence comparisons and phylogenetic analyses revealed considerable variations between mitochondrial 16 S rRNA gene and cytochrome coxidase subunit I gene among nine Loliginid species. We identified three similar non-coding regions in eight Loliginid species, but not in Sepioteuthislessoniana. We detected a single extended termination-associated sequence and three conserved sequence blocks among these eight species...
May 20, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28530240/controlling-for-the-species-area-effect-supports-constrained-long-term-mesozoic-terrestrial-vertebrate-diversification
#5
Roger A Close, Roger B J Benson, Paul Upchurch, Richard J Butler
Variation in the geographic spread of fossil localities strongly biases inferences about the evolution of biodiversity, due to the ubiquitous scaling of species richness with area. This obscures answers to key questions, such as how tetrapods attained their tremendous extant diversity. Here, we address this problem by applying sampling standardization methods to spatial regions of equal size, within a global Mesozoic-early Palaeogene data set of non-flying terrestrial tetrapods. We recover no significant increase in species richness between the Late Triassic and the Cretaceous/Palaeogene (K/Pg) boundary, strongly supporting bounded diversification in Mesozoic tetrapods...
May 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/28529731/a-bayesian-supervised-dual-dimensionality-reduction-model-for-simultaneous-decoding-of-lfp-and-spike-train-signals
#6
Andrew Holbrook, Alexander Vandenberg-Rodes, Norbert Fortin, Babak Shahbaba
Neuroscientists are increasingly collecting multimodal data during experiments and observational studies. Different data modalities-such as EEG, fMRI, LFP, and spike trains-offer different views of the complex systems contributing to neural phenomena. Here, we focus on joint modeling of LFP and spike train data, and present a novel Bayesian method for neural decoding to infer behavioral and experimental conditions. This model performs supervised dual-dimensionality reduction: it learns low-dimensional representations of two different sources of information that not only explain variation in the input data itself, but also predict extra-neuronal outcomes...
2017: Stat: the ISI's Journal for Rapid Dissemination of Statistics Research
https://www.readbyqxmd.com/read/28529729/characterization-of-the-novel-in1059-harbouring-vim-gene-cassette
#7
Dongguo Wang, Jinhong Yang, Meiyu Fang, Wei He, Ying Zhang, Caixia Liu, Dongsheng Zhou
BACKGROUND: VIM-type enzyme encodes the most widely acquired metallo-β-lactamases in Gram- negative bacteria. To obtain current epidemiological data for integrons from enterobacteriae in hospital, the study characterizes the genetic structure in In1059 by comparison with In846 integrons harbouring VIM gene and other class 1 integrons including In37, In62, In843 and In1021 with the aim of identifying the putative mechanisms involved integron mobilization and infer evolution of relevant integrons...
2017: Antimicrobial Resistance and Infection Control
https://www.readbyqxmd.com/read/28528256/evaluation-of-artificial-time-series-microarray-data-for-dynamic-gene-regulatory-network-inference
#8
P Xenitidis, I Seimenis, S Kakolyris, A Adamopoulos
High-throughput technology like microarrays is widely used in the inference of gene regulatory networks (GRNs). We focused on time series data since we are interested in the dynamics of GRNs and the identification of dynamic networks. We evaluated the amount of information that exists in artificial time series microarray data and the ability of an inference process to produce accurate models based on them. We used dynamic artificial gene regulatory networks in order to create artificial microarray data. Key features that characterize microarray data such as the time separation of directly triggered genes, the percentage of directly triggered genes and the triggering function type were altered in order to reveal the limits that are imposed by the nature of microarray data on the inference process...
May 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28522998/genetic-polymorphism-in-wine-yeasts-mechanisms-and-methods-for-its-detection
#9
REVIEW
José M Guillamón, Eladio Barrio
The processes of yeast selection for using as wine fermentation starters have revealed a great phenotypic diversity both at interspecific and intraspecific level, which is explained by a corresponding genetic variation among different yeast isolates. Thus, the mechanisms involved in promoting these genetic changes are the main engine generating yeast biodiversity. Currently, an important task to understand biodiversity, population structure and evolutionary history of wine yeasts is the study of the molecular mechanisms involved in yeast adaptation to wine fermentation, and on remodeling the genomic features of wine yeast, unconsciously selected since the advent of winemaking...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28522444/harmonization-of-serum-thyroid-stimulating-hormone-measurements-paves-the-way-for-the-adoption-of-a-more-uniform-reference-interval
#10
Linda M Thienpont, Katleen Van Uytfanghe, Linde A C De Grande, Dries Reynders, Barnali Das, James D Faix, Finlay MacKenzie, Brigitte Decallonne, Akira Hishinuma, Bruno Lapauw, Paul Taelman, Paul Van Crombrugge, Annick Van den Bruel, Brigitte Velkeniers, Paul Williams
BACKGROUND: The IFCC Committee for Standardization of Thyroid Function Tests developed a global harmonization approach for thyroid-stimulating hormone measurements. It is based on a multiassay method comparison study with clinical serum samples and target setting with a robust factor analysis method. Here we describe the Phase IV method comparison and reference interval (RI) studies conducted with the objective to recalibrate the participating assays and demonstrate the proof-of-concept...
May 18, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28515871/wolf-in-sheep-s-clothing-model-misspecification-undermines-tests-of-the-neutral-theory-for-life-histories
#11
Matthieu Authier, Lise M Aubry, Emmanuelle Cam
Understanding the processes behind change in reproductive state along life-history trajectories is a salient research program in evolutionary ecology. Two processes, state dependence and heterogeneity, can drive the dynamics of change among states. Both processes can operate simultaneously, begging the difficult question of how to tease them apart in practice. The Neutral Theory for Life Histories (NTLH) holds that the bulk of variations in life-history trajectories is due to state dependence and is hence neutral: Once previous (breeding) state is taken into account, variations are mostly random...
May 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28510204/microarray-meta-analysis-to-explore-abiotic-stress-specific-gene-expression-patterns-in-arabidopsis
#12
Po-Chih Shen, Ai-Ling Hour, Li-Yu Daisy Liu
BACKGROUND: Abiotic stresses are the major limiting factors that affect plant growth, development, yield and final quality. Deciphering the underlying mechanisms of plants' adaptations to stresses using few datasets might overlook the different aspects of stress tolerance in plants, which might be simultaneously and consequently operated in the system. Fortunately, the accumulated microarray expression data offer an opportunity to infer abiotic stress-specific gene expression patterns through meta-analysis...
December 2017: Botanical Studies (Taipei, Taiwan)
https://www.readbyqxmd.com/read/28509342/morphological-and-molecular-characterization-of-bysmatrum-subsalsum-dinophyceae-from-the-western-mediterranean-sea-reveals-the-existence-of-cryptic-species
#13
Sílvia Anglès, Albert Reñé, Esther Garcés, Antonella Lugliè, Nicola Sechi, Jordi Camp, Cecilia Teodora Satta
Bysmatrum subsalsum is a cosmopolitan dinoflagellate species that inhabits marine and transitional habitats. Despite its wide distribution, information on the morphological variability, phylogeny and ecology of B. subsalsum is scarce. In this study, we provide morphological and molecular data on B. subsalsum strains and wild cells from different locations in the Mediterranean Basin. The dynamics of cell abundances and the associated environmental conditions during a field bloom are also described. Genetic sequences of B...
May 16, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28505156/an-independent-component-analysis-confounding-factor-correction-framework-for-identifying-broad-impact-expression-quantitative-trait-loci
#14
Jin Hyun Ju, Sushila A Shenoy, Ronald G Crystal, Jason G Mezey
Genome-wide expression Quantitative Trait Loci (eQTL) studies in humans have provided numerous insights into the genetics of both gene expression and complex diseases. While the majority of eQTL identified in genome-wide analyses impact a single gene, eQTL that impact many genes are particularly valuable for network modeling and disease analysis. To enable the identification of such broad impact eQTL, we introduce CONFETI: Confounding Factor Estimation Through Independent component analysis. CONFETI is designed to address two conflicting issues when searching for broad impact eQTL: the need to account for non-genetic confounding factors that can lower the power of the analysis or produce broad impact eQTL false positives, and the tendency of methods that account for confounding factors to model broad impact eQTL as non-genetic variation...
May 15, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28502018/evolutionary-processes-in-populations-of-cryptosporidium-inferred-from-gp60-sequence-data
#15
Juan C Garcia-R, David T S Hayman
Cryptosporidiosis is one of the most common human infectious diseases globally. The gp60 gene has been adopted as a key marker for molecular epidemiological investigations into this protozoan disease because of the capability to characterize genotypes and detect variants within Cryptosporidium species infecting humans. However, we know relatively little about the potential spatial and temporal variation in population demography that can be inferred from this gene beyond that it is recognized to be under selective pressure...
May 13, 2017: Parasitology Research
https://www.readbyqxmd.com/read/28498987/genetic-structure-and-phylogeography-of-the-leopard-cat-prionailurus-bengalensis-inferred-from-mitochondrial-genomes
#16
Riddhi P Patel, Saskia Wutke, Dorina Lenz, Shomita Mukherjee, Uma Ramakrishnan, Géraldine Veron, Jörns Fickel, Andreas Wilting, Daniel W Förster
The Leopard cat Prionailurus bengalensis is a habitat generalist that is widely distributed across Southeast Asia. Based on morphological traits, this species has been subdivided into 12 subspecies. Thus far, there have been few molecular studies investigating intraspecific variation, and those had been limited in geographic scope. For this reason, we aimed to study the genetic structure and evolutionary history of this species across its very large distribution range in Asia. We employed both PCR-based (short mtDNA fragments, 94 samples) and high throughput sequencing based methods (whole mitochondrial genomes, 52 samples) on archival, noninvasively collected and fresh samples to investigate the distribution of intraspecific genetic variation...
June 1, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28498950/igess-a-statistical-approach-to-integrating-individual-level-genotype-data-and-summary-statistics-in-genome-wide-association-studies
#17
Mingwei Dai, Jingsi Ming, Mingxuan Cai, Jin Liu, Can Yang, Xiang Wan, Zongben Xu
Motivation: Results from genome-wide association studies (GWAS) suggest that a complex phenotype is often affected by many variants with small effects, known as "polygenicity". Tens of thousands of samples are often required to ensure statistical power of identifying these variants with small effects. However, it is often the case that a research group can only get approval for the access to individual-level genotype data with a limited sample size (e.g., a few hundreds or thousands)...
May 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28496285/partial-identification-in-the-statistical-matching-problem
#18
Daniel Ahfock, Saumyadipta Pyne, Sharon X Lee, Geoffrey J McLachlan
The statistical matching problem involves the integration of multiple datasets where some variables are not observed jointly. This missing data pattern leaves most statistical models unidentifiable. Statistical inference is still possible when operating under the framework of partially identified models, where the goal is to bound the parameters rather than to estimate them precisely. In many matching problems, developing feasible bounds on the parameters is equivalent to finding the set of positive-definite completions of a partially specified covariance matrix...
December 2016: Computational Statistics & Data Analysis
https://www.readbyqxmd.com/read/28495960/inferring-the-joint-demographic-history-of-multiple-populations-beyond-the-diffusion-approximation
#19
Julien Jouganous, Will Long, Aaron P Ragsdale, Simon Gravel
Understanding variation in allele frequencies across populations is a central goal of population genetics. Classical models for the distribution of allele frequencies, using forward simulation, coalescent theory, or the diffusion approximation, have been applied extensively for demographic inference, medical study design, and evolutionary studies. Here we propose a tractable model of ordinary differential equations for the evolution of allele frequencies that is closely related to the diffusion approximation but avoids many of its limitations and approximations...
May 11, 2017: Genetics
https://www.readbyqxmd.com/read/28495267/the-evolutionary-interplay-between-adaptation-and-self-fertilization
#20
REVIEW
Matthew Hartfield, Thomas Bataillon, Sylvain Glémin
Genome-wide surveys of nucleotide polymorphisms, obtained from next-generation sequencing, have uncovered numerous examples of adaptation in self-fertilizing organisms, especially regarding changes to climate, geography, and reproductive systems. Yet existing models for inferring attributes of adaptive mutations often assume idealized outcrossing populations, which risks mischaracterizing properties of these variants. Recent theoretical work is emphasizing how various aspects of self-fertilization affects adaptation, yet empirical data on these properties are lacking...
May 8, 2017: Trends in Genetics: TIG
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