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https://www.readbyqxmd.com/read/28528574/esc-track-a-computer-workflow-for-4-d-segmentation-tracking-lineage-tracing-and-dynamic-context-analysis-of-escs
#1
Laura Fernández-de-Manúel, Covadonga Díaz-Díaz, Daniel Jiménez-Carretero, Miguel Torres, María C Montoya
Embryonic stem cells (ESCs) can be established as permanent cell lines, and their potential to differentiate into adult tissues has led to widespread use for studying the mechanisms and dynamics of stem cell differentiation and exploring strategies for tissue repair. Imaging live ESCs during development is now feasible due to advances in optical imaging and engineering of genetically encoded fluorescent reporters; however, a major limitation is the low spatio-temporal resolution of long-term 3-D imaging required for generational and neighboring reconstructions...
May 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/28512346/cryptic-diversity-in-the-japanese-mantis-shrimp-oratosquilla-oratoria-crustacea-squillidae-allopatric-diversification-secondary-contact-and-hybridization
#2
Jiao Cheng, Zhong-Li Sha
Mounting evidence of cryptic species in the marine realm emphasizes the necessity to thoroughly revise our current perceptions of marine biodiversity and species distributions. Here, we used mitochondrial cytochrome oxidase subunit I (mtDNA COI) and nuclear ribosomal internal transcribed spacer (nrDNA ITS) to investigate cryptic diversity and potential hybridization in the Japanese mantis shrimp Oratosquilla oratoria in the Northwestern (NW) Pacific. Both mitochondrial and nuclear gene genealogies revealed two cryptic species in this morphotaxon, which was further confirmed by extensive population-level analyses...
May 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28508479/prediction-of-complex-traits-conciliating-genetics-and-statistics
#3
E Manfredi, L Tusell, Z G Vitezica
This review focuses on methods used to predict complex traits. Main characteristics of prediction approaches are given: the deterministic or stochastic nature of prediction, the objects of prediction, the sources of information and the main statistical methods. Sources of information discussed are the traditional genealogies and phenotypes, nucleotide sequences, expression data and epigenetics marks. Statistical methods are presented as successive degrees of generalization from the definition of the conditional expectation as the prediction rule, to best linear unbiased prediction, then Bayesian and, recently, machine learning methods, including meta-methods...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28503367/etiology-of-triarchic-psychopathy-dimensions-in-chimpanzees-pan-troglodytes
#4
Robert D Latzman, Christopher J Patrick, Hani J Freeman, Steven J Schapiro, William D Hopkins
The current study undertook analyses of genealogical data from a sample of 178 socially-housed chimpanzees (Pan troglodytes) with well-documented pedigrees, to clarify the etiologic bases of triarchic psychopathy dimensions and the influence of early social rearing experiences. Whereas biometric analyses for the full sample indicated significant heritability for the boldness dimension of psychopathy only, heritability estimates varied by early rearing, with all three triarchic dimensions showing significant heritabilities among mother-reared but not nursery-reared apes...
March 2017: Clinical Psychological Science
https://www.readbyqxmd.com/read/28476403/the-genealogical-decomposition-of-a-matrix-population-model-with-applications-to-the-aggregation-of-stages
#5
François Bienvenu, Erol Akçay, Stéphane Legendre, David M McCandlish
Matrix projection models are a central tool in many areas of population biology. In most applications, one starts from the projection matrix to quantify the asymptotic growth rate of the population (the dominant eigenvalue), the stable stage distribution, and the reproductive values (the dominant right and left eigenvectors, respectively). Any primitive projection matrix also has an associated ergodic Markov chain that contains information about the genealogy of the population. In this paper, we show that these facts can be used to specify any matrix population model as a triple consisting of the ergodic Markov matrix, the dominant eigenvalue and one of the corresponding eigenvectors...
May 2, 2017: Theoretical Population Biology
https://www.readbyqxmd.com/read/28460352/characterization-of-nist-human-mitochondrial-dna-srm-2392-and-srm-2392-i-standard-reference-materials-by-next-generation-sequencing
#6
Sarah Riman, Kevin M Kiesler, Lisa A Borsuk, Peter M Vallone
Standard Reference Materials SRM 2392 and 2392-I are intended to provide quality control when amplifying and sequencing human mitochondrial genome sequences. The National Institute of Standards and Technology (NIST) offers these SRMs to laboratories performing DNA-based forensic human identification, molecular diagnosis of mitochondrial diseases, mutation detection, evolutionary anthropology, and genetic genealogy. The entire mtGenome (∼16569bp) of SRM 2392 and 2392-I have previously been characterized at NIST by Sanger sequencing...
April 15, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28455625/toward-a-consensus-on-snp-and-str-mutation-rates-on-the-human-y-chromosome
#7
REVIEW
O Balanovsky
The mutation rate on the Y-chromosome matters for estimating the time-to-the-most-recent-common-ancestor (TMRCA, i.e. haplogroup age) in population genetics, as well as for forensic, medical, and genealogical studies. Large-scale sequencing efforts have produced several independent estimates of Y-SNP mutation rates. Genealogical, or pedigree, rates tend to be slightly faster than evolutionary rates obtained from ancient DNA or calibrations using dated (pre)historical events. It is, therefore, suggested to report TMRCAs using an envelope defined by the average aDNA-based rate and the average pedigree-based rate...
May 2017: Human Genetics
https://www.readbyqxmd.com/read/28454930/integrative-inference-of-population-history-in-the-ibero-maghrebian-endemic-pleurodeles-waltl-salamandridae
#8
Jorge Gutiérrez-Rodríguez, A Márcia Barbosa, Íñigo Martínez-Solano
Inference of population histories from the molecular signatures of past demographic processes is challenging, but recent methodological advances in species distribution models and their integration in time-calibrated phylogeographic studies allow detailed reconstruction of complex biogeographic scenarios. We apply an integrative approach to infer the evolutionary history of the Iberian ribbed newt (Pleurodeles waltl), an Ibero-Maghrebian endemic with populations north and south of the Strait of Gibraltar. We analyzed an extensive multilocus dataset (mitochondrial and nuclear DNA sequences and ten polymorphic microsatellite loci) and found a deep east-west phylogeographic break in Iberian populations dating back to the Plio-Pleistocene...
April 25, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28437587/relationship-type-affects-the-reliability-of-dispersal-distance-estimated-using-pedigree-inferences-in-partially-sampled-populations-a-case-study-involving-invasive-american-mink-in-scotland
#9
Y Melero, M K Oliver, X Lambin
Estimating dispersal-a key parameter for population ecology and management-is notoriously difficult. The use of pedigree assignments, aided by likelihood-based software, has become popular to estimate dispersal rate and distance. However, the partial sampling of populations may produce false assignments. Further, it is unknown how the accuracy of assignment is affected by the genealogical relationships of individuals and is reflected by software-derived assignment probabilities. Inspired by a project managing invasive American mink (Neovison vison), we estimated individual dispersal distances using inferred pairwise relationships of culled individuals...
April 24, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28433481/genetics-of-common-complex-diseases-a-view-from-iceland
#10
REVIEW
David O Arnar, Runolfur Palsson
In the past decade, large scale genotyping has led to discoveries of numerous sequence variants that confer increased risk of many common complex diseases. Interestingly, a substantial proportion of pioneering genetic work has originated from the small nation of Iceland and has been facilitated by an extensive genealogy database. We provide examples of relevant observations made so far in several major disease categories central to internal medicine practice. Some of these findings offer new mechanistic clues into the pathophysiology of common disorders and may suggest novel approaches in diagnosis and drug therapy...
April 19, 2017: European Journal of Internal Medicine
https://www.readbyqxmd.com/read/28415890/correction-to-deep-genealogical-analysis-of-a-large-cohort-of-participants-in-the-cartagene-project-quebec-canada
#11
(no author information available yet)
No abstract text is available yet for this article.
April 18, 2017: Annals of Human Biology
https://www.readbyqxmd.com/read/28410396/evolution-of-the-neuraminidase-gene-of-seasonal-influenza-a-and-b-viruses-in-thailand-between-2010-and-2015
#12
Nipaporn Tewawong, Preeyaporn Vichiwattana, Sumeth Korkong, Sirapa Klinfueng, Nungruthai Suntronwong, Thanunrat Thongmee, Apiradee Theamboonlers, Sompong Vongpunsawad, Yong Poovorawan
The neuraminidase inhibitors (NAIs) oseltamivir and zanamivir are commonly used for the treatment and control of influenza A and B virus infection. However, the emergence of new influenza virus strains with reduced susceptibility to NAIs may appear with the use of these antivirals or even naturally. We therefore screened the neuraminidase (NA) sequences of seasonal influenza virus A(H1N1), A(H1N1)pdm09, A(H3N2), and influenza B virus strains identified in Thailand for the presence of substitutions previously reported to reduce susceptibility to NAIs...
2017: PloS One
https://www.readbyqxmd.com/read/28397796/geographic-barriers-and-pleistocene-climate-change-shaped-patterns-of-genetic-variation-in-the-eastern-afromontane-biodiversity-hotspot
#13
Mario Mairal, Isabel Sanmartín, Alberto Herrero, Lisa Pokorny, Pablo Vargas, Juan J Aldasoro, Marisa Alarcón
The Eastern African Afromontane forest is getting increased attention in conservation studies because of its high endemicity levels and shrinking geographic distribution. Phylogeographic studies have found evidence of high levels of genetic variation structured across the Great Rift System. Here, we use the epiphytic plant species Canarina eminii to explore causal explanations for this pattern. Phylogeographic analyses were undertaken using plastid regions and AFLP fragments. Population genetic analyses, Statistical Parsimony, and Bayesian methods were used to infer genetic diversity, genealogical relationships, structure, gene flow barriers, and the spatiotemporal evolution of populations...
April 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28393289/practically-delineating-bacterial-species-with-genealogical-concordance
#14
Stephanus N Venter, Marike Palmer, Chrizelle W Beukes, Wai-Yin Chan, Giyoon Shin, Elritha van Zyl, Tarren Seale, Teresa A Coutinho, Emma T Steenkamp
Bacterial species are commonly defined by applying a set of predetermined criteria, including DNA-DNA hybridization values, 16S rRNA gene sequence similarity, phenotypic data as well as genome-based criteria such as average nucleotide identity or digital DNA-DNA hybridization. These criteria mostly allow for the delimitation of taxa that resemble typical bacterial species. Their application is often complicated when the objective is to delineate new species that are characterized by significant population-level diversity or recent speciation...
April 9, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28390909/deep-reticulation-and-incomplete-lineage-sorting-obscure-the-diploid-phylogeny-of-rain-lilies-and-allies-amaryllidaceae-tribe-hippeastreae
#15
Nicolás García, Ryan A Folk, Alan W Meerow, Srikar Chamala, Matthew A Gitzendanner, Renata Souza de Oliveira, Douglas E Soltis, Pamela S Soltis
Hybridization is a frequent and important force in plant evolution. Next-generation sequencing (NGS) methods offer new possibilities for clade resolution and ambitious sampling of gene genealogies, yet difficulty remains in detecting deep reticulation events using currently available methods. We reconstructed the phylogeny of diploid representatives of Amaryllidaceae tribe Hippeastreae to test the hypothesis of ancient hybridizations preceding the radiation of its major subclade, Hippeastrinae. Through hybrid enrichment of DNA libraries and NGS, we obtained data for 18 nuclear loci through a curated assembly approach and nearly complete plastid genomes for 35 ingroup taxa plus 5 outgroups...
April 6, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28385666/optimal-point-process-filtering-and-estimation-of-the-coalescent-process
#16
Kris V Parag, Oliver G Pybus
The coalescent process is a widely used approach for inferring the demographic history of a population, from samples of its genetic diversity. Several parametric and non-parametric coalescent inference methods, involving Markov chain Monte Carlo, Gaussian processes, and other algorithms, already exist. However, these techniques are not always easy to adapt and apply, thus creating a need for alternative methodologies. We introduce the Bayesian Snyder filter as an easily implementable and flexible minimum mean square error estimator for parametric demographic functions on fixed genealogies...
April 3, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28379570/gene-tree-discordance-does-not-explain-away-the-temporal-decline-of-convergence-in-mammalian-protein-sequence-evolution
#17
Zhengting Zou, Jianzhi Zhang
Several authors reported lower frequencies of protein sequence convergence between more distantly related evolutionary lineages and attributed this trend to epistasis, which renders the acceptable amino acids at a site more different and convergence less likely in more divergent lineages. A recent primate study, however, suggested that this trend is at least partially and potentially entirely an artifact of gene tree discordance (GTD). Here we demonstrate in a genome-wide dataset from 17 mammals that the temporal trend remains (1) upon the control of the GTD level, (2) in genes whose genealogies are concordant with the species tree, and (3) for convergent changes, which are extremely unlikely to be caused by GTD...
April 3, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28371627/the-problem-of-choice-from-the-voluntary-way-to-affordable-care-act-health-insurance-exchanges
#18
Jessica Mulligan
This article takes a genealogical and ethnographic approach to the problem of choice, arguing that what choice means has been reworked several times since health insurance first figured prominently in national debates about health reform. Whereas voluntary choice of doctor and hospital used to be framed as an American right, contemporary choice rhetoric includes consumer choice of insurance plan. Understanding who has deployed choice rhetoric and to what ends helps explain how offering choices has become the common sense justification for defending and preserving the exclusionary health care system in the United States...
May 2017: Social Science & Medicine
https://www.readbyqxmd.com/read/28355314/ideology-science-and-people-in-am%C3%A3-lcar-cabral
#19
José Neves
The present article contributes to the debate on how historians and social scientists perceive and understand relations between ideology and science, which are often seen as realms belonging to rival kingdoms. Following an analysis and critical positioning vis-à-vis Cabralian studies, the text examines how scholars of Cabral have portrayed his agronomic activities. It then undertakes a genealogical analysis of the Cabralian concept of people and suggests that the emergence of this concept in Cabral's discourse derives from the intersection of the development of anti-colonial nationalist thought in the former Portuguese Empire and the development of agrarian studies in metropolitan Portugal...
March 23, 2017: História, Ciências, Saúde—Manguinhos
https://www.readbyqxmd.com/read/28351409/identification-of-a-novel-merozoite-surface-antigen-of-plasmodium-vivax-pvmsa180
#20
Fauzi Muh, Jin-Hee Han, Myat Htut Nyunt, Seong-Kyun Lee, Hye-Yoon Jeon, Kwon-Soo Ha, Won Sun Park, Seok-Ho Hong, Md Atique Ahmed, Sunghun Na, Eizo Takashima, Takafumi Tsuboi, Eun-Taek Han
BACKGROUND: Although a number of Plasmodium vivax proteins have been identified, few have been investigated as potential vaccine candidates. This study characterized the Plasmodium vivax merozoite surface antigen 180 (PvMSA180, PVX_094920), a novel P. vivax antigenic protein. METHODS: The target gene was amplified as four overlapping domains (D1, D2, D3 and D4) to enable expression of the recombinant protein using cell-free and bacterial expression systems. The recombinant PvMSA180 proteins were used in protein microarrays to evaluate the humoral immune response of 72 vivax-infected patients and 24 vivax-naïve individuals...
March 28, 2017: Malaria Journal
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