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https://www.readbyqxmd.com/read/28338786/recombination-mediated-host-adaptation-by-avian-staphylococcus-aureus
#1
Susan Murray, Ben Pascoe, Guillaume Méric, Leonardos Mageiros, Koji Yahara, Matthew D Hitchings, Yasmin Friedmann, Thomas S Wilkinson, Fraser J Gormley, Dietrich Mack, James E Bray, Sarah Lamble, Rory Bowden, Keith A Jolley, Martin C J Maiden, Sarah Wendlandt, Stefan Schwarz, Jukka Corander, J Ross Fitzgerald, Samuel K Sheppard
Staphylococcus aureus are globally disseminated among farmed chickens causing skeletal muscle infections, dermatitis and septicaemia. The emergence of poultry-associated lineages has involved zoonotic transmission from humans to chickens but questions remain about the specific adaptations that promote proliferation of chicken pathogens. We characterised genetic variation in a population of genome-sequenced S. aureus isolates of poultry and human origin. Genealogical analysis identified a dominant poultry-associated sequence cluster within the CC5 clonal complex...
February 28, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28334237/dna-compass-a-secure-client-side-site-for-navigating-personal-genetic-information
#2
Charles Curnin, Assaf Gordon, Yaniv Erlich
Motivation: Millions of individuals have access to raw genomic data using direct-to-consumer companies. The advent of large-scale sequencing projects, such as the Precision Medicine Initiative, will further increase the number of individuals with access to their own genomic information. However, querying genomic data requires a computer terminal and computational skill to analyze the data - an impediment for the general public. Results: DNA Compass is a website designed to empower the public by enabling simple navigation of personal genomic data...
March 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28325067/deep-genealogical-analysis-of-a-large-cohort-of-participants-in-the-cartagene-project-quebec-canada
#3
Marc Tremblay, Gabrielle Rouleau
BACKGROUND: Genealogical analysis helps to better understand the genetic structure of populations. The population of Quebec (Canada) often serves as a model for this type of analysis, having one of the world's most complete genealogical databases. AIM: The main objective of this study was to reconstruct, analyse and compare the ascending genealogies of participants to CARTaGENE, a project that aims at building a database on various aspects of public health. SUBJECTS AND METHODS: In total, 5110 genealogies from four Quebec regions were reconstructed...
March 21, 2017: Annals of Human Biology
https://www.readbyqxmd.com/read/28317545/phylogeny-and-pathogenicity-of-lasiodiplodia-species-associated-with-dieback-of-mango-in-peru
#4
Edgar Rodríguez-Gálvez, Pakita Guerrero, Carla Barradas, Pedro W Crous, Artur Alves
Mango, which is an important tropical fruit crop in the region of Piura (Peru), is known to be prone to a range of diseases caused by Lasiodiplodia spp. The aim of this study was to evaluate the incidence and prevalence of mango dieback in the region of Piura, and to identify the species of Lasiodiplodia associated with the disease and evaluate their pathogenicity towards mango. Mango dieback was present in all orchards surveyed but incidence varied with location. Identification of fungal isolates was based on morphological and cultural characteristics as well as sequence data of the rDNA internal transcribed spacer region (ITS) and translation elongation factor 1-alpha gene (tef1-α)...
April 2017: Fungal Biology
https://www.readbyqxmd.com/read/28317541/mating-type-genes-in-the-genus-neofusicoccum-mating-strategies-and-usefulness-in-species-delimitation
#5
Anabela Lopes, Alan J L Phillips, Artur Alves
The genus Neofusicoccum includes species with wide geographical and plant host distribution, some of them of economic importance. The genus currently comprises 27 species that are difficult to identify based on morphological features alone. Thus, species differentiation is based on phylogenetic species recognition using multigene genealogies. In this study, we characterised the mating type genes of Neofusicoccum species. Specific primers were designed to amplify and sequence MAT genes in several species and a PCR-based mating type diagnostic assay was developed...
April 2017: Fungal Biology
https://www.readbyqxmd.com/read/28285392/a-consensus-method-for-ancestral-recombination-graphs
#6
Mary K Kuhner, Jon Yamato
We propose a consensus method for ancestral recombination graphs (ARGs) that generates a single ARG representing commonalities among a cloud of ARGs defined for the same genomic region and set of taxa. Our method, which we call "threshold consensus," treats a genomic location as a potential recombination breakpoint only if the number of ARGs in the cloud possessing a breakpoint at that location exceeds a chosen threshold. The estimate is further refined by ignoring recombinations that do not change the local tree topologies, as well as collapsing breakpoint locations separated only by invariant sites...
March 11, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28285141/mitigating-the-consequences-of-a-health-condition-the-role-of-intra-and-interhousehold-assistance
#7
Michael Dalton, Daniel LaFave
The behavior of noncoresident family members motivates much of the literature on consumption smoothing, risk-sharing, and informal networks, yet little is known empirically on the topic due to a lack of data simultaneously observing multiple households in an extended family. This study utilizes genealogically linked longitudinal data to examine how extended family networks insure against financial risks from severely limiting health conditions. We find that nonhealth consumption of unmarried households declines in response to worsening health, whereas married households smooth expenditures in a way that is consistent with full insurance...
February 20, 2017: Journal of Health Economics
https://www.readbyqxmd.com/read/28267748/inferring-fitness-landscapes-and-selection-on-phenotypic-states-from-single-cell-genealogical-data
#8
Takashi Nozoe, Edo Kussell, Yuichi Wakamoto
Recent advances in single-cell time-lapse microscopy have revealed non-genetic heterogeneity and temporal fluctuations of cellular phenotypes. While different phenotypic traits such as abundance of growth-related proteins in single cells may have differential effects on the reproductive success of cells, rigorous experimental quantification of this process has remained elusive due to the complexity of single cell physiology within the context of a proliferating population. We introduce and apply a practical empirical method to quantify the fitness landscapes of arbitrary phenotypic traits, using genealogical data in the form of population lineage trees which can include phenotypic data of various kinds...
March 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28253846/digging-up-the-roots-of-an-insular-hotspot-of-genetic-diversity-decoupled-mito-nuclear-histories-in-the-evolution-of-the-corsican-sardinian-endemic-lizard-podarcis-tiliguerta
#9
Daniele Salvi, Catarina Pinho, D James Harris
BACKGROUND: Mediterranean islands host a disproportionately high level of biodiversity and endemisms. Growing phylogeographic evidence on island endemics has unveiled unexpectedly complex patterns of intra-island diversification, which originated at diverse spatial and temporal scales. We investigated multilocus genetic variation of the Corsican-Sardinian endemic lizard Podarcis tiliguerta with the aim of shedding more light on the evolutionary processes underlying the origin of Mediterranean island biodiversity...
March 2, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28251872/phylogeography-of-human-y-chromosome-haplogroup-q3-l275-from-an-academic-citizen-science-collaboration
#10
Oleg Balanovsky, Vladimir Gurianov, Valery Zaporozhchenko, Olga Balaganskaya, Vadim Urasin, Maxat Zhabagin, Viola Grugni, Rebekah Canada, Nadia Al-Zahery, Alessandro Raveane, Shao-Qing Wen, Shi Yan, Xianpin Wang, Pierre Zalloua, Abdullah Marafi, Sergey Koshel, Ornella Semino, Chris Tyler-Smith, Elena Balanovska
BACKGROUND: The Y-chromosome haplogroup Q has three major branches: Q1, Q2, and Q3. Q1 is found in both Asia and the Americas where it accounts for about 90% of indigenous Native American Y-chromosomes; Q2 is found in North and Central Asia; but little is known about the third branch, Q3, also named Q1b-L275. Here, we combined the efforts of population geneticists and genetic genealogists to use the potential of full Y-chromosome sequencing for reconstructing haplogroup Q3 phylogeography and suggest possible linkages to events in population history...
February 7, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28241078/genetic-evidence-from-mitochondrial-dna-corroborates-the-origin-of-tibetan-chickens
#11
Long Zhang, Pu Zhang, Qingqing Li, Uma Gaur, Yiping Liu, Qing Zhu, Xiaoling Zhao, Yan Wang, Huadong Yin, Yaodong Hu, Aiping Liu, Diyan Li
Chicken is the most common poultry species and is important to human societies. Tibetan chicken (Gallus gallus domesticus) is a breed endemic to China that is distributed mainly on the Qinghai-Tibet Plateau. However, its origin has not been well characterized. In the present study, we sequenced partial mitochondrial DNA (mtDNA) control region of 239 and 283 samples from Tibetan and Sichuan indigenous chickens, respectively. Incorporating 1091 published sequences, we constructed the matrilineal genealogy of Tibetan chickens to further document their domestication history...
2017: PloS One
https://www.readbyqxmd.com/read/28237797/identification-of-nascent-memory-cd8-t-cells-and-modeling-of-their-ontogeny
#12
Fabien Crauste, Julien Mafille, Lilia Boucinha, Sophia Djebali, Olivier Gandrillon, Jacqueline Marvel, Christophe Arpin
Primary immune responses generate short-term effectors and long-term protective memory cells. The delineation of the genealogy linking naive, effector, and memory cells has been complicated by the lack of phenotypes discriminating effector from memory differentiation stages. Using transcriptomics and phenotypic analyses, we identify Bcl2 and Mki67 as a marker combination that enables the tracking of nascent memory cells within the effector phase. We then use a formal approach based on mathematical models describing the dynamics of population size evolution to test potential progeny links and demonstrate that most cells follow a linear naive→early effector→late effector→memory pathway...
March 22, 2017: Cell Systems
https://www.readbyqxmd.com/read/28228572/opposed-to-the-being-of-henrietta-bioslavery-pop-culture-and-the-third-life-of-hela-cells
#13
Marlon Rachquel Moore
Operating at the intersection of thanatopolitics and African-American cultural studies, this essay argues that the commercial sale of HeLa-themed art and other bioproducts perpetuates the bioslavery of HeLa cells, a circumstance created by legal and medical discourses tracing back to US racial slavery. Racial slavery normalised economic, social and legal inequities that the nation continues to struggle with and, the article posits, laid foundation for the dynamics that currently exist between Henrietta Lacks' genealogical family, the HeLa cell line, and the medical-pharmaceutical establishment...
March 2017: Medical Humanities
https://www.readbyqxmd.com/read/28219291/the-genealogy-of-a-gene-patents-hiv-aids-and-race
#14
Matt James
No abstract text is available yet for this article.
July 2016: New Bioethics: a Multidisciplinary Journal of Biotechnology and the Body
https://www.readbyqxmd.com/read/28202101/berber-genealogy-and-the-politics-of-prehistoric-archaeology-and-craniology-in-french-algeria-1860s-1880s
#15
Bonnie Effros
Following the conquest of Algiers and its surrounding territory by the French army in 1830, officers noted an abundance of standing stones in this region of North Africa. Although they attracted considerably less attention among their cohort than more familiar Roman monuments such as triumphal arches and bridges, these prehistoric remains were similar to formations found in Brittany and other parts of France. The first effort to document these remains occurred in 1863, when Laurent-Charles Féraud, a French army interpreter, recorded thousands of dolmens and stone formations south-west of Constantine...
February 16, 2017: British Journal for the History of Science
https://www.readbyqxmd.com/read/28196347/disentangling-life-darwin-selectionism-and-the-postgenomic-return-of-the-environment
#16
Maurizio Meloni
In this paper, I analyze the disruptive impact of Darwinian selectionism for the century-long tradition in which the environment had a direct causative role in shaping an organism's traits. In the case of humans, the surrounding environment often determined not only the physical, but also the mental and moral features of individuals and whole populations. With its apparatus of indirect effects, random variations, and a much less harmonious view of nature and adaptation, Darwinian selectionism severed the deep imbrication of organism and milieu posited by these traditional environmentalist models...
February 11, 2017: Studies in History and Philosophy of Biological and Biomedical Sciences
https://www.readbyqxmd.com/read/28194930/representation-archaeology-and-genealogy-three-spatial-metaphors-for-inquiring-into-nursing-phenomena-with%C3%A2-foucauldian-discourse-analysis
#17
Michael E Clinton, Rusla Anne Springer
Foucault used the "Quadrilateral of Language" metaphor to describe how language functioned in what the French called the Classic Age, roughly 1650 to 1800, the period from Descartes to Kant. His purpose was to show how the functions of language changed radically with the arrival of the Modern Age (~1800). Foucault developed his archaeological methods to investigate the impact of this change, but later revised his methods to introduce genealogical strategies to conduct "histories of the present". Our purpose in this paper is to clarify Foucault's thinking about ruptures in the functions of language and to show their implications for analyzing nursing discourse...
February 14, 2017: Nursing Philosophy: An International Journal for Healthcare Professionals
https://www.readbyqxmd.com/read/28192145/population-based-familial-aggregation-of-eosinophilic-esophagitis-suggests-a-genetic-contribution
#18
Kristina Allen-Brady, Rafael Firszt, John C Fang, Jathine Wong, Ken R Smith, Kathryn A Peterson
BACKGROUND: Prior familial clustering studies have observed an increased risk of eosinophilic esophagitis (EoE) mostly among first-degree relatives, suggesting a genetic contribution to EoE, and twin studies have suggested a powerful contribution from environmental factors. OBJECTIVE: This study sought to clarify the contribution of genetic factors to EoE through estimation of familial aggregation and risk of EoE in extended relatives. METHODS: The Utah Population Database, a population-based genealogy resource linked to electronic medical records for health care systems across the state of Utah, was used to identify EoE cases and age, sex, and birthplace-matched controls at a 5:1 ratio...
February 10, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28188662/population-genetics-of-reef-coral-endosymbionts-symbiodinium-dinophyceae
#19
D J Thornhill, E J Howells, D C Wham, T D Steury, S R Santos
Symbiodinium is a diverse genus of unicellular dinoflagellate symbionts associating with various marine protists and invertebrates. Although the broad-scale diversity and phylogenetics of the Symbiodinium complex is well established, there have been surprisingly few data on fine-scale population structure and biogeography of these dinoflagellates. Yet population level processes contribute strongly to the biology of Symbiodinium, including how anthropogenic-driven global climate change impacts these symbionts and their host associations...
February 11, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28187711/poppante-population-and-pedigree-association-testing-for-quantitative-data
#20
Alessia Visconti, Mashael Al-Shafai, Wadha A Al Muftah, Shaza B Zaghlool, Massimo Mangino, Karsten Suhre, Mario Falchi
BACKGROUND: Family-based designs, from twin studies to isolated populations with their complex genealogical data, are a valuable resource for genetic studies of heritable molecular biomarkers. Existing software for family-based studies have mainly focused on facilitating association between response phenotypes and genetic markers, and no user-friendly tools are at present available to straightforwardly extend association studies in related samples to large datasets of generic quantitative data, as those generated by current -omics technologies...
February 10, 2017: BMC Genomics
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