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Genetic diversity

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https://www.readbyqxmd.com/read/29245019/genetic-polymorphism-of-21-non-codis-str-loci-in-chengdu-han-population-and-its-interpopulation-analysis-between-25-populations-in-china
#1
Ye Li, Hepei Li, Guanglin He, Weibo Liang, Haibo Luo, Miao Liao, Ji Zhang, Jing Yan, Yingbi Li, Yiping Hou, Jin Wu
AGCU 21+1 STR kit contains 21 non-combined DNA index system (non-CODIS) short tandem repeats (STR) loci and a sex-determining locus amelogenin. In this study, we evaluated the genetic diversity and forensically relevant population statistics of 21 non-CODIS loci in 210 Chinese Han individuals from Chengdu city, Sichuan province, Southwest China. No significant deviations from Hardy-Weinberg equilibrium were observed within the 21 non-CODIS STR loci. The combined power of discrimination (CPD) and combined power of exclusion (CPE) were 0...
December 9, 2017: Legal Medicine
https://www.readbyqxmd.com/read/29245013/combination-cancer-therapy-can-confer-benefit-via-patient-to-patient-variability-without-drug-additivity-or-synergy
#2
Adam C Palmer, Peter K Sorger
Combination cancer therapies aim to improve the probability and magnitude of therapeutic responses and reduce the likelihood of acquired resistance in an individual patient. However, drugs are tested in clinical trials on genetically diverse patient populations. We show here that patient-to-patient variability and independent drug action are sufficient to explain the superiority of many FDA-approved drug combinations in the absence of drug synergy or additivity. This is also true for combinations tested in patient-derived tumor xenografts...
December 14, 2017: Cell
https://www.readbyqxmd.com/read/29244833/genomic-characterization-and-molecular-evolution-analysis-of-subtype-b-and-bf-recombinant-hiv-1-strains-among-argentinean-men-who-have-sex-with-men-reveal-a-complex-scenario
#3
Cintia G Cevallos, Leandro R Jones, Maria A Pando, Jean K Carr, Maria M Avila, Jorge Quarleri
Currently, data on HIV-1 circulating strains among men who have sex with men (MSM) in Argentina is scarce. In South America, the distribution and the prevalence of BF recombinants are dissimilar and exhibit an underappreciated heterogeneity of recombinant structures. Here, we studied for the first time the genetic diversity of HIV-1 BF recombinants and their evolution over time through in-depth phylogenetic analysis and multiple recombination detection methods involving 337 HIV-1 nucleotide sequences (25 near full-length (NFL) and 312 partial pol gene) obtained from Argentinean MSM...
2017: PloS One
https://www.readbyqxmd.com/read/29244562/learning-to-cooperate-the-evolution-of-social-rewards-in-repeated-interactions
#4
Slimane Dridi, Erol Akçay
Understanding the behavioral and psychological mechanisms underlying social behaviors is one of the major goals of social evolutionary theory. In particular, a persistent question about animal cooperation is to what extent it is supported by other-regarding preferences-the motivation to increase the welfare of others. In many situations, animals adjust their behaviors through learning by responding to the rewards they experience as a consequence of their actions. Therefore, we may ask whether learning in social situations can be driven by evolved other-regarding rewards...
January 2018: American Naturalist
https://www.readbyqxmd.com/read/29244558/loss-of-color-pigmentation-is-maintained-at-high-frequency-in-a-monkey-flower-population
#5
Alex D Twyford, Aaron M Caola, Pratibha Choudhary, Ramesh Raina, Jannice Friedman
Color polymorphisms have long been of evolutionary interest for their diverse roles, including mate choice, predator avoidance, and pollinator attraction. While color variation is often under strong selection, some taxa demonstrate unexpectedly high frequencies of presumed deleterious color forms. Here we show that a genetic variant underlying complete loss of anthocyanin pigmentation has risen to an unexpectedly high frequency of >0.2 in a natural population of the plant Mimulus guttatus. Decreased expression of MYB5 transcription factor is associated with unpigmented morphs...
January 2018: American Naturalist
https://www.readbyqxmd.com/read/29244212/detection-of-enteric-and-non-enteric-adenoviruses-in-gastroenteritis-patients-bangladesh-2012-2015
#6
Mokibul Hassan Afrad, Tasnuva Avzun, Jahurul Haque, Warda Haque, Mohammad Enayet Hossain, Afm Rajibur Rahman, Shahnawaz Ahmed, Abu Syed Golam Faruque, Mohammed Ziaur Rahman, Mustafizur Rahman
BACKGROUND: Human adenoviruses (HAdVs) are common cause of nonbacterial acute gastroenteritis worldwide. Limited data exist on HAdVs molecular epidemiology associated with acute gastroenteritis in Bangladesh. OBJECTIVE: We describe the genetic diversity and epidemiology of HAdVs among hospitalized diarrhea patients, including HAdV genotypes, clinical symptoms and co-infecting enteric pathogens. STUDY DESIGN: Stool samples were collected from ongoing diarrhea surveillance during 2012-2015...
December 15, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/29244129/dolutegravir-reshapes-the-genetic-diversity-of-hiv-1-reservoirs
#7
Pierre Gantner, Guinevere Q Lee, David Rey, Thibault Mesplede, Marialuisa Partisani, Christine Cheneau, Geneviève Beck-Wirth, Jean-Pierre Faller, Mahsa Mohseni-Zadeh, Martin Martinot, Mark A Wainberg, Samira Fafi-Kremer
Objectives: Better understanding of the dynamics of HIV reservoirs under ART is a critical step to achieve a functional HIV cure. Our objective was to assess the genetic diversity of archived HIV-1 DNA over 48 weeks in blood cells of individuals starting treatment with a dolutegravir-based regimen. Methods: Eighty blood samples were prospectively and longitudinally collected from 20 individuals (NCT02557997) including: acutely (n = 5) and chronically (n = 5) infected treatment-naive individuals, as well as treatment-experienced individuals who switched to a dolutegravir-based regimen and were either virologically suppressed (n = 5) or had experienced treatment failure (n = 5)...
December 13, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29244017/implications-of-segment-mismatch-for-influenza-a-virus-evolution
#8
Maria C White, Anice C Lowen
Influenza A virus (IAV) is an RNA virus with a segmented genome. These viral properties allow for the rapid evolution of IAV under selective pressure, due to mutation occurring from error-prone replication and the exchange of gene segments within a co-infected cell, termed reassortment. Both mutation and reassortment give rise to genetic diversity, but constraints shape their impact on viral evolution: just as most mutations are deleterious, most reassortment events result in genetic incompatibilities. The phenomenon of segment mismatch encompasses both RNA- and protein-based incompatibilities between co-infecting viruses and results in the production of progeny viruses with fitness defects...
December 15, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/29244005/ghost-global-hepatitis-outbreak-and-surveillance-technology
#9
Atkinson G Longmire, Seth Sims, Inna Rytsareva, David S Campo, Pavel Skums, Zoya Dimitrova, Sumathi Ramachandran, Magdalena Medrzycki, Hong Thai, Lilia Ganova-Raeva, Yulin Lin, Lili T Punkova, Amanda Sue, Massimo Mirabito, Silver Wang, Robin Tracy, Victor Bolet, Thom Sukalac, Chris Lynberg, Yury Khudyakov
BACKGROUND: Hepatitis C is a major public health problem in the United States and worldwide. Outbreaks of hepatitis C virus (HCV) infections associated with unsafe injection practices, drug diversion, and other exposures to blood are difficult to detect and investigate. Effective HCV outbreak investigation requires comprehensive surveillance and robust case investigation. We previously developed and validated a methodology for the rapid and cost-effective identification of HCV transmission clusters...
December 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29243868/genetic-diversity-of-small-populations-not-always-doom-and-gloom
#10
Dylan J Fraser
Is a key theory of evolutionary and conservation biology-that loss of genetic diversity can be predicted from population size-on shaky ground? In the face of increasing human-induced species depletion and habitat fragmentation, this question and the study of genetic diversity in small populations are paramount to understanding the limits of species' responses to environmental change and to providing remedies to endangered species conservation. Few empirical studies have investigated to what degree some small populations might be buffered against losses of genetic diversity...
December 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29243083/enhancing-the-copper-sensing-capability-of-escherichia-coli-based-whole-cell-bioreporters-by-genetic-engineering
#11
Yerin Kang, Woonwoo Lee, Sunghoon Kim, Geupil Jang, Bong-Gyu Kim, Youngdae Yoon
Metals are essential to all organisms; accordingly, cells employ numerous genes to maintain metal homeostasis as high levels can be toxic. In the present study, the gene operons responsive to metal(loid)s were employed to generate bacterial cell-based biosensors to detect target metal(loid)s. The cluster of genes related to copper transport known as the cop-operon is regulated by the interaction between the copA promoter region (copAp) and CueR, turning on and off gene expression upon copper ion binding. Therefore, the detection of copper ions could be achieved by inserting a plasmid harboring the fusion of copAp and reporter genes, such as enzymes and fluorescent genes...
December 15, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29242837/the-human-gut-microbial-metabolome-modulates-fungal-growth-via-the-tor-signaling-pathway
#12
Carlos García, Faiza Tebbji, Michelle Daigneault, Ning-Ning Liu, Julia R Köhler, Emma Allen-Vercoe, Adnane Sellam
Candida albicans is well known as a major human fungal pathogen, but it is also a permanent resident of healthy gastrointestinal tracts. Recent studies have shown that the human gut microbial metabolome represents an interesting source of bioactive molecules with a significant degree of chemical diversity. Some of these bioactive molecules may have useful antivirulence activities. For instance, intestinal bacterial species belonging to the Lachnospiraceae family were found to secrete molecules that attenuate Salmonella pathogenicity and repress the expression of virulence genes...
November 2017: MSphere
https://www.readbyqxmd.com/read/29242678/keap1-and-done-targeting-the-nrf2-pathway-with-sulforaphane
#13
Albena T Dinkova-Kostova, Jed W Fahey, Rumen V Kostov, Thomas W Kensler
Background: Since the re-discovery of sulforaphane in 1992 and the recognition of the bioactivity of this phytochemical, many studies have examined its mode of action in cells, animals and humans. Broccoli, especially as young sprouts, is a rich source of sulforaphane and broccoli-based preparations are now used in clinical studies probing efficacy in health preservation and disease mitigation. Many putative cellular targets are affected by sulforaphane although only one, KEAP1-NRF2 signaling, can be considered a validated target at this time...
November 2017: Trends in Food Science & Technology
https://www.readbyqxmd.com/read/29242387/inbred-or-outbred-genetic-diversity-in-laboratory-rodent-colonies
#14
Thomas D Brekke, Katherine A Steele, John F Mulley
Non-model rodents are widely used as subjects for both basic and applied biological research, but the genetic diversity of the study individuals is rarely quantified. University-housed colonies tend to be small and subject to founder effects and genetic drift and so may be highly inbred or show substantial genetic divergence from other colonies, even those derived from the same source. Disregard for the levels of genetic diversity in an animal colony may result in a failure to replicate results if a different colony is used to repeat an experiment, as different colonies may have fixed alternative variants...
December 13, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29242287/the-local-co-existence-pattern-of-selfing-genotypes-in-caenorhabditis-elegans-natural-metapopulations
#15
Aurélien Richaud, Gaotian Zhang, Daehan Lee, Junho Lee, Marie-Anne Félix
To study the interplay of rare outcrossing and metapopulation structure, we focus on the nematode Caenorhabditis elegans Its remarkably low outcrossing rate is at the extreme end of the spectrum for facultative selfing organisms. At the demographic level, C. elegans natural populations undergo boom and bust dynamics on ephemeral resources, the dauer diapause larva acting as the dispersal form. Here we investigate the small-scale genetic structure of C. elegans populations in two localities over several years, using 2b-RAD (Restriction-Associated DNA) sequencing of nearly a thousand individuals...
December 13, 2017: Genetics
https://www.readbyqxmd.com/read/29241572/genome-wide-association-mapping-of-qtl-underlying-seed-oil-and-protein-contents-of-a-diverse-panel-of-soybean-accessions
#16
Ying-Hui Li, Jochen C Reif, Hui-Long Hong, Hui-Hui Li, Zhang-Xiong Liu, Yan-Song Ma, Jun Li, Yun Tian, Yan-Fei Li, Wen-Bin Li, Li-Juan Qiu
To investigate the genetic basis of variation in oil and protein contents in soybean seeds, a diverse collection of 421 mainly Chinese soybean cultivars was genotyped using 1536 SNPs, mostly from candidate genes related to acyl-lipid metabolism and from regions harboring known QTL. Six significant associations were identified for each of seed oil and protein contents which individually explained 2.7-5.9% of the phenotypic variance. Six associations occurred in or near known QTL and the remaining are putative novel QTL...
January 2018: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/29241456/designer-rhamnolipids-by-reduction-of-congener-diversity-production-and-characterization
#17
Till Tiso, Rabea Zauter, Hannah Tulke, Bernd Leuchtle, Wing-Jin Li, Beate Behrens, Andreas Wittgens, Frank Rosenau, Heiko Hayen, Lars Mathias Blank
BACKGROUND: Rhamnolipids are biosurfactants featuring surface-active properties that render them suitable for a broad range of industrial applications. These properties include their emulsification and foaming capacity, critical micelle concentration, and ability to lower surface tension. Further, aspects like biocompatibility and environmental friendliness are becoming increasingly important. Rhamnolipids are mainly produced by pathogenic bacteria like Pseudomonas aeruginosa. We previously designed and constructed a recombinant Pseudomonas putida KT2440, which synthesizes rhamnolipids by decoupling production from host-intrinsic regulations and cell growth...
December 14, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/29241118/plhint-a-knowledge-driven-computational-approach-based-on-the-intermolecular-h-bond-interactions-at-the-protein-ligand-interface-from-docking-solutions
#18
Sivakumar Prasanth Kumar
The tendency of docking scoring functions to generate crystal close conformations of ligands bound to protein structures face limitations in not reproducing the exact crystal intermolecular contacts in dock poses. Intermolecular H bond contacts enumerated at the protein-docked ligand interface can be used to train scoring models and improve virtual screening performance. There is a need to incorporate additional knowledge of protein-ligand H bond contacts in extension to crystal contacts from docking solutions within the reproducibility efficiency of the docking program...
December 6, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29241022/evolution-as-an-ecosystem-process-insights-from-genomics
#19
Blake Matthews, Rebecca J Best, Philine G D Feulner, Anita Narwani, Romana Limberger
Evolution is a fundamental ecosystem process. The study of genomic variation of organisms can not only improve our understanding of evolutionary processes, but also of contemporary and future ecosystem dynamics. We argue that integrative research between the fields of genomics and ecosystem ecology could generate new insights. Specifically, studies of biodiversity and ecosystem functioning, evolutionary rescue, and eco-evolutionary dynamics could all benefit from information about variation in genome structure and the genetic architecture of traits, whereas genomic studies could benefit from information about the ecological context of evolutionary dynamics...
December 14, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29240932/homogenization-of-populations-in-the-wildflower-texas-bluebonnet-lupinus-texensis
#20
Kathryn G Turner, Daisie I Huang, Quentin C B Cronk, Loren H Rieseberg
Wildflower seeds are routinely spread along highways and thoroughfares throughout North America as part of federal beautification policy, but the genetic effect of the introduction of these cultivated populations on wild populations of the same species is unknown. Interbreeding may occur between these seeded and wild populations, resulting in several possible outcomes. Here we sample 187 individuals in 12 matched pairs of neighboring wild and seeded populations of the Texas bluebonnet (Lupinus texensis), a species popular in commercially available wildflower seed mixes used by both the Texas Department of Transportation and the public...
December 12, 2017: Journal of Heredity
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