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Genetic diversity

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https://www.readbyqxmd.com/read/29452359/convergent-amino-acid-signatures-in-polyphyletic-campylobacter-jejuni-sub-populations-suggest-human-niche-tropism
#1
Guillaume Méric, Alan McNally, Alberto Pessia, Evangelos Mourkas, Ben Pascoe, Leonardos Mageiros, Minna Vehkala, Jukka Corander, Samuel K Sheppard
Human infection with the gastrointestinal pathogen C. jejuni is dependent upon the opportunity for zoonotic transmission and the ability of strains to colonize the human host. Certain lineages of this diverse organism are more common in human infection but the factors underlying this overrepresentation are not fully understood. We analysed 601 isolate genomes from agricultural animals and human clinical cases, including isolates from the multi-host (ecological generalist) ST-21 and ST-45 clonal complexes (CCs)...
February 14, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29452350/extra-virgin-olive-oil-contains-a-metabolo-epigenetic-inhibitor-of-cancer-stem-cells
#2
Bruna Corominas-Faja, Elisabet Cuyàs, Jesús Lozano-Sánchez, Sílvia Cufí, Sara Verdura, Salvador Fernández-Arroyo, Isabel Borrás-Linares, Begoña Martin-Castillo, Ángel G Martin, Ruth Lupu, Alfons Nonell-Canals, Melchor Sanchez-Martinez, Vicente Micol, Jorge Joven, Antonio Segura-Carretero, Javier A Menendez
Targeting tumor-initiating, drug-resistant populations of cancer stem cells (CSC) with phytochemicals is a novel paradigm for cancer prevention and treatment. We herein employed a phenotypic drug discovery approach coupled to mechanism-of-action profiling and target deconvolution to identify phenolic components of extra virgin olive oil (EVOO) capable of suppressing the functional traits of CSC in breast cancer (BC). In vitro screening revealed that the secoiridoid decarboxymethyl oleuropein aglycone (DOA) could selectively target sub-populations of epithelial-like, aldehyde dehydrogenase (ALDH)-positive and mesenchymal-like, CD44+CD24-/low CSC...
February 14, 2018: Carcinogenesis
https://www.readbyqxmd.com/read/29452311/phylogenetic-relationships-and-cryptic-species-diversity-in-the-brazilian-egg-brooding-tree-frog-genus-fritziana-mello-leit%C3%A3-o-1937-anura-hemiphractidae
#3
Marina Walker, Mariana L Lyra, Célio F B Haddad
The genus Fritziana (Anura: Hemiphractidae) comprises six described species (F. goeldii, F. ohausi, F. fissilis, F. ulei, F. tonimi, and F. izecksohni) that are endemic to the Brazilian Atlantic Forest. Although the genus has been the subject of studies dealing with its taxonomy, phylogeny, and systematics, there is considerable evidence for cryptic diversity hidden among the species. The present study aims to understand the genetic diversity and phylogenetic relationships among the species of Fritziana, as well as the relationships among populations within species...
February 13, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29452293/genetic-diversity-and-functional-analysis-of-oipa-gene-in-association-with-other-virulence-factors-among-helicobacter-pylori-isolates-from-iranian-patients-with-different-gastric-diseases
#4
Nastaran Farzi, Abbas Yadegar, Hamid Asadzadeh Aghdaei, Yoshio Yamaoka, Mohammad Reza Zali
Helicobacter pylori (H. pylori) is one of the most genetically diverse bacterial pathogens that persistently colonizes the human gastric epithelium. This remarkable genomic plasticity may act as a driving force for successful adaptation and persistence of the bacteria in the harsh gastric environment. Outer inflammatory protein A (OipA) encoded by oipA gene (HP0638/hopH) is a member of the outer membrane proteins (OMPs) of H. pylori involved in induction of IL-8 secretion and is associated with development of peptic ulcer and gastric cancer...
February 13, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29451715/transitions-in-sex-determination-and-sex-chromosomes-across-vertebrate-species
#5
Matthew W Pennell, Judith E Mank, Catherine L Peichel
Despite the prevalence of sexual reproduction across eukaryotes, there is a remarkable diversity of sex determination mechanisms. The underlying causes of this diversity remain unclear, and it is unknown if there are convergent trends in the directionality of turnover in sex determination mechanisms. We used the recently assembled Tree of Sex database to assess patterns in the evolution of sex determination systems in the remarkably diverse vertebrate clades of teleost fish, squamate reptiles, and amphibians...
February 16, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29451433/populations-of-phytophthora-rubi-show-little-differentiation-and-high-rates-of-migration-among-states-in-the-western-united-states
#6
Javier F Tabima, Michael D Coffey, Inga Zasada, Niklaus J Grünwald
Population genetics is a powerful tool to understand patterns and evolutionary processes that are involved in plant pathogen emergence and adaptation to agricultural ecosystems. We are interested in studying the population dynamics of Phytophthora rubi, the causal agent of Phytophthora root rot in raspberry. P. rubi is found in the western U.S., where the majority of the fresh and processed raspberries are produced. We used genotyping-by-sequencing to characterize genetic diversity in populations of P. rubi sampled in the U...
February 16, 2018: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29450668/genetic-variation-and-selection-of-mhc-class-i-loci-differ-in-two-congeneric-frogs
#7
Karen M Kiemnec-Tyburczy, Karen E Tracy, Karen R Lips, Kelly R Zamudio
Major histocompatibility complex (MHC) genes encode proteins in the acquired immune response pathway that often show distinctive selection-driven patterns in wild vertebrate populations. We examined genetic variation and signatures of selection in the MHC class I alpha 1 (A1)- and alpha 2 (A2)-domain encoding exons of two frog congeners [Agalychnis callidryas (n = 20) and A. lemur (n = 20)] from a single locality in Panama. We also investigated how historical demographic processes may have impacted MHC genetic diversity by analyzing a neutral mitochondrial marker...
February 15, 2018: Genetica
https://www.readbyqxmd.com/read/29450233/pharmacogenomics-guided-policy-in-opioid-use-disorder-oud-management-an-ethnically-diverse-case-based-approach
#8
Earl B Ettienne, Edwin Chapman, Mary Maneno, Adaku Ofoegbu, Bradford Wilson, Beverlyn Settles-Reaves, Melissa Clarke, Georgia Dunston, Kevin Rosenblatt
Introduction: Opioid use disorder (OUD) is characterized by a problematic pattern of opioid use leading to clinically-significant impairment or distress. Opioid agonist treatment is an integral component of OUD management, and buprenorphine is often utilized in OUD management due to strong clinical evidence for efficacy. However, interindividual genetic differences in buprenorphine metabolism may result in variable treatment response, leaving some patients undertreated and at increased risk for relapse...
December 2017: Addictive Behaviors Reports
https://www.readbyqxmd.com/read/29449965/genetic-diversity-and-cross-species-transmission-of-kobuviruses-in-vietnam
#9
Lu Lu, Nguyen Van Dung, Alasdair Ivens, Carlijn Bogaardt, Aine O'Toole, Juliet E Bryant, Juan Carrique-Mas, Nguyen Van Cuong, Pham Hong Anh, Maia A Rabaa, Ngo Tri Tue, Guy E Thwaites, Stephen Baker, Peter Simmonds, Mark Ej Woolhouse
Cross-species transmission of viruses poses a sustained threat to public health. Due to increased contact between humans and other animal species the possibility exists for cross-species transmissions and ensuing disease outbreaks. By using conventional PCR amplification and next generation sequencing, we obtained 130 partial or full genome kobuvirus sequences from humans in a sentinel cohort in Vietnam and various mammalian hosts including bats, rodents, pigs, cats, and civets. The evolution of kobuviruses in different hosts was analysed using Bayesian phylogenetic methods...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29449860/adaptive-genetic-divergence-despite-significant-isolation-by-distance-in-populations-of-taiwan-cow-tail-fir-keteleeria-davidiana-var-formosana
#10
Kai-Ming Shih, Chung-Te Chang, Jeng-Der Chung, Yu-Chung Chiang, Shih-Ying Hwang
Double digest restriction site-associated DNA sequencing (ddRADseq) is a tool for delivering genome-wide single nucleotide polymorphism (SNP) markers for non-model organisms useful in resolving fine-scale population structure and detecting signatures of selection. This study performs population genetic analysis, based on ddRADseq data, of a coniferous species, Keteleeria davidiana var. formosana , disjunctly distributed in northern and southern Taiwan, for investigation of population adaptive divergence in response to environmental heterogeneity...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29449618/codon-based-co-occurrence-network-motifs-in-human-mitochondria
#11
Pramod Shinde, Camellia Sarkar, Sarika Jalan
The nucleotide polymorphism in the human mitochondrial genome (mtDNA) tolled by codon position bias plays an indispensable role in human population dispersion and expansion. Herein, genome-wide nucleotide co-occurrence networks were constructed using data comprised of five different geographical regions and around 3000 samples for each region. We developed a powerful network model to describe complex mitochondrial evolutionary patterns among codon and non-codon positions. We found evidence that the evolution of human mitochondria DNA is dominated by adaptive forces, particularly mutation and selection, which was supported by many previous studies...
February 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29449565/amphibian-chytridiomycosis-outbreak-dynamics-are-linked-with-host-skin-bacterial-community-structure
#12
Kieran A Bates, Frances C Clare, Simon O'Hanlon, Jaime Bosch, Lola Brookes, Kevin Hopkins, Emilia J McLaughlin, Olivia Daniel, Trenton W J Garner, Matthew C Fisher, Xavier A Harrison
Host-associated microbes are vital for combatting infections and maintaining health. In amphibians, certain skin-associated bacteria inhibit the fungal pathogen Batrachochytrium dendrobatidis (Bd), yet our understanding of host microbial ecology and its role in disease outbreaks is limited. We sampled skin-associated bacteria and Bd from Pyrenean midwife toad populations exhibiting enzootic or epizootic disease dynamics. We demonstrate that bacterial communities differ between life stages with few shared taxa, indicative of restructuring at metamorphosis...
February 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29449488/natural-noncanonical-protein-splicing-yields-products-with-diverse-%C3%AE-amino-acid-residues
#13
Brandon I Morinaka, Edgars Lakis, Marjan Verest, Maximilian J Helf, Thibault Scalvenzi, Anna L Vagstad, James Sims, Shinichi Sunagawa, Muriel Gugger, Jörn Piel
Current textbook knowledge holds that the structural scope of ribosomal biosynthesis is based exclusively on α-amino acid backbone topology. Here we report the genome-guided discovery of bacterial pathways that posttranslationally create β-amino acid-containing products. The transformation is widespread in bacteria and is catalyzed by an enzyme belonging to a previously uncharacterized radical S -adenosylmethionine family. We show that the β-amino acids result from an unusual protein splicing process involving backbone carbon-carbon bond cleavage and net excision of tyramine...
February 16, 2018: Science
https://www.readbyqxmd.com/read/29449437/dynamic-clonal-progression-in-xenografts-of-acute-lymphoblastic-leukemia-with-intrachromosomal-amplification-of-chromosome-21
#14
Paul B Sinclair, Helen H Blair, Sarra L Ryan, Lars Buechler, Joanna Cheng, Jake Clayton, Rebecca Hanna, Shaun Hollern, Zoe Hawking, Matthew Bashton, Claire J Schwab, Lisa Jones, Lisa J Russell, Helen Marr, Peter Carey, Christina Halsey, Olaf Heidenreich, Anthony V Moorman, Christine J Harrison
Intrachromosomal amplification of chromosome 21 is a heterogeneous chromosomal rearrangement occurring in 2% of childhood precursor B-cell acute lymphoblastic leukemia. There are no cell lines with iAMP21 and these abnormalities are too complex to faithfully engineer in animal models. As a resource for future functional and pre-clinical studies, we have created xenografts from intrachromosomal amplification of chromosome 21 leukemia patient blasts and characterised them by in-vivo and ex-vivo luminescent imaging, FLOW immunophenotyping, and histological and ultrastructural analysis of bone marrow and the central nervous system...
February 15, 2018: Haematologica
https://www.readbyqxmd.com/read/29449045/how-to-measure-glucocorticoid-receptor-s-sensitivity-in-patients-with-stress-related-psychiatric-disorders
#15
REVIEW
Carolin Leistner, Andreas Menke
Stress is a state of derailed homeostasis and a main environmental risk factor for psychiatric diseases. Chronic or uncontrollable stress may lead to a dysregulation of the hypothalamic-pituitary-adrenal (HPA) axis, which is a common feature of stress-related psychiatric disorders. One of the key mechanisms underlying a disturbed HPA axis is an impaired function of the glucocorticoid receptor (GR) with an enhanced or reduced feedback sensitivity for glucocorticoids and subsequently altered concentrations of peripheral cortisol...
February 2, 2018: Psychoneuroendocrinology
https://www.readbyqxmd.com/read/29449029/development-of-alcohol-expectancies-and-early-alcohol-use-in-children-and-adolescents-a-systematic-review
#16
REVIEW
Koen Smit, Carmen Voogt, Marieke Hiemstra, Marloes Kleinjan, Roy Otten, Emmanuel Kuntsche
PURPOSE: Developmental changes in alcohol expectancies (AE) have been proposed to lead to alcohol use initiation and later alcohol use in adolescence. This systematic review aims to provide longitudinal evidence of the development of AE and the relation of AE to alcohol outcomes from childhood to late adolescence (4-18 years old). METHODS: A computer-assisted search of relevant articles identified 1602 studies, of which 43 studies (conducted between 1996 and 2016) were selected...
February 6, 2018: Clinical Psychology Review
https://www.readbyqxmd.com/read/29448955/analysis-of-the-genetic-diversity-and-mrna-expression-level-in-porcine-reproductive-and-respiratory-syndrome-virus-vaccinated-pigs-that-developed-short-or-long-viremias-after-challenge
#17
Martí Cortey, Gaston Arocena, Tahar Ait-Ali, Anna Vidal, Yanli Li, Gerard Martín-Valls, Alison D Wilson, Allan L Archibald, Enric Mateu, Laila Darwich
Porcine reproductive and respiratory syndrome virus (PRRSv) infection alters the host's cellular and humoral immune response. Immunity against PRRSv is multigenic and vary between individuals. The aim of the present study was to compare several genes that encode for molecules involved in the immune response between two groups of vaccinated pigs that experienced short or long viremic periods after PRRSv challenge. These analyses include the sequencing of four SLA Class I, two Class II allele groups, and CD163, plus the analysis by quantitative realtime qRT-PCR of the constitutive expression of TLR2, TLR3, TLR4, TLR7, TLR8 and TLR9 mRNA and other molecules in peripheral blood mononuclear cells...
February 15, 2018: Veterinary Research
https://www.readbyqxmd.com/read/29448954/new-therapeutic-strategies-to-treat-human-cancers-expressing-mutant-p53-proteins
#18
REVIEW
Giovanni Blandino, Silvia Di Agostino
The tumor suppressor p53 plays a critical role to preserve DNA fidelity from diverse insults through the regulation of cell-cycle checkpoints, DNA repair, senescence and apoptosis. The TP53 is the most frequently inactivated gene in human cancers. This leads to the production of mutant p53 proteins that loose wild-type p53 tumor suppression functions and concomitantly acquire new oncogenic properties among which deregulated cell proliferation, increased chemoresistance, disruption of tissue architecture, promotion of migration, invasion and metastasis and several other pro-oncogenic activities...
February 15, 2018: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/29448209/metagenomic-analysis-revealed-the-prevalence-of-antibiotic-resistance-genes-in-the-gut-and-living-environment-of-freshwater-shrimp
#19
Yanting Zhao, Xu-Xiang Zhang, Zhonghua Zhao, Cuilan Duan, Huangen Chen, Miaomiao Wang, Hongqiang Ren, Ying Yin, Lin Ye
Antibiotic resistance disseminating from animals and their environments is a public issue that poses significant threats to human health. In the present study, the diversity and abundance of antibiotic resistance genes (ARGs) in 15 samples from the guts and related aquaculture environments (water and sediment) of shrimp were investigated. In total, 60 ARGs, 102 ARGs and 67 ARGs primarily belonging to 13, 15 and 15 different types were detected in the shrimp gut, pond water and sediment samples, respectively...
February 6, 2018: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/29448052/kir-and-hla-ligands-demonstrate-genetic-inheritance-diversity-in-japanese-descendants-from-paran%C3%A3-brazil
#20
Josiane Bazzo de Alencar, Joana Maira Valentini Zacarias, Barbara Leticia da Silva Guedes de Moura, Marco Antônio Braga, Jeane Eliete Laguila Visentainer, Ana Maria Sell
In order to investigate killer immunoglobulin-like receptors (KIR) and their ligands, human leukocyte antigen (HLA), diversity in the Brazilian population influenced by migrations, unrelated Brazilian Japanese descendants were selected and genotyped for the KIR genes and HLA class I allele groups. Genetic heterogeneity in Brazil Paraná Japanese was observed for KIR genes, whose frequency distributions demonstrated similarity with mixed Brazilian populations and with the Japanese population, suggesting gene flow...
February 12, 2018: Human Immunology
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