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Genetic diversity

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https://www.readbyqxmd.com/read/29040729/csra-maximizes-expression-of-the-acrab-multidrug-resistance-transporter
#1
Vito Ricci, Victoria Attah, Tim Overton, David C Grainger, Laura J V Piddock
Carbon Storage Regulator A (CsrA) is an RNA binding protein that acts as a global regulator of diverse genes. Using a combination of genetics and biochemistry we show that CsrA binds directly to the 5' end of the transcript encoding AcrAB. Deletion of csrA or mutagenesis of the CsrA binding sites reduced production of both AcrA and AcrB. Nucleotide substitutions at the 5' UTR of acrA mRNA that could potentially weaken the inhibitory RNA secondary structure, allow for more efficient translation of the AcrAB proteins...
October 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29040727/whole-genome-sequencing-of-african-dogs-provides-insights-into-adaptations-against-tropical-parasites
#2
Yan-Hu Liu, Lu Wang, Tao Xu, Xiaomin Guo, Yang Li, Ting-Ting Yin, He-Chuan Yang, Hu Yang, Adeniyi C Adeola, Oscar J Sanke, Newton O Otecko, Meng Wang, Yaping Ma, Olaogun S Charles, Mikkel-Holger S Sinding, Shyam Gopalakrishnan, José Alfredo Samaniego, Anders J Hansen, Carlos Fernandes, Philippe Gaubert, Jane Budd, Philip M Dawuda, Eli Knispel Rueness, Lubin Jiang, Weiwei Zhai, M T P Gilbert, Min-Sheng Peng, Xiaopeng Qi, Guo-Dong Wang, Ya-Ping Zhang
Natural selection in domestic dogs is of great interest in evolutionary biology since dogs have migrated to every inhabited continent of the world alongside humans, and adapted to diverse environments. Here, we explored their demographic history and genetic basis of adaptation to the tropical African environment using whole genome analyses of 19 African indigenous dogs from Nigeria. Demographic analysis suggests that the ancestors of these dogs migrated into Africa from Eurasia 14,000 years ago and underwent a severe founder effect before population expansion...
October 10, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29040658/fire-does-not-strongly-affect-genetic-diversity-or-structure-of-a-common-treefrog-in-the-endangered-florida-scrub
#3
J M Robertson, S W Fitzpatrick, B B Rothermel, L M Chan
Fire regimes influence natural populations of organisms in diverse ways, via direct effects on population dynamics as well as indirect effects on habitat and ecosystem processes. Although many amphibian species have evolved to persist in fire-dependent ecosystems, the effects of fire on the genetic diversity of amphibian populations remain relatively unexplored. We examined how different aspects of fire history relate to population genetic diversity and structure of an abundant anuran, Hyla femoralis, in a large, intact area of Florida scrub containing hundreds of seasonally inundated ponds...
October 11, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29040585/emergence-of-mcr-1-and-carbapenemase-genes-in-hospital-sewage-water-in-beijing-china
#4
Longyang Jin, Ruobing Wang, Xiaojuan Wang, Qi Wang, Yawei Zhang, Yuyao Yin, Hui Wang
Objectives: This study identified and characterized mcr-1-positive Enterobacteriaceae (MCRPE) and carbapenemase-producing Enterobacteriaceae (CPE) in hospital sewage water. Methods: Influent and effluent sewage samples were collected from five tertiary hospitals in Beijing in December 2016. Samples were screened for MCRPE and CPE using antibiotic selection media. Results were confirmed by PCR amplification of β-lactamase and colistin resistance (mcr-1 and mcr-2) genes and by sequencing...
October 10, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29040583/taste-receptor-polymorphisms-and-male-infertility
#5
M Gentiluomo, L Crifasi, A Luddi, D Locci, R Barale, P Piomboni, D Campa
STUDY QUESTION: Are polymorphisms of taste receptor genes associated with male infertility? SUMMARY ANSWER: This study has showed the associations between three single nucleotide polymorphisms (SNPs) in taste receptors genes (TASR) and male infertility. WHAT IS KNOWN ALREADY: Recent studies showed the expression of taste receptors in the testis and in spermatozoa, suggesting their possible role in infertility. The vast genetic variability in taste genes results in a large degree of diversity in various human phenotypes...
October 12, 2017: Human Reproduction
https://www.readbyqxmd.com/read/29040419/high-rates-of-human-fecal-carriage-of-mcr-1-positive-multi-drug-resistant-enterobacteriaceae-isolates-emerge-in-china-in-association-with-successful-plasmid-families
#6
Lan-Lan Zhong, Hang T T Phan, Cong Shen, Karina Doris-Vihta, Anna E Sheppard, Xi Huang, Kun-Jiao Zeng, Hong-Yu Li, Xue-Fei Zhang, Sandip Patil, Derrick W Crook, A Sarah Walker, Yong Xing, Jia-Lin Lin, Lian-Qiang Feng, Yohei Doi, Yong Xia, Nicole Stoesser, Guo-Bao Tian
Objectives: mcr-1-mediated colistin resistance in Enterobacteriaceae is concerning, as colistin is used in treating multidrug-resistant Enterobacteriaceae infections. Rates of human mcr-1 gastrointestinal carriage have historically been low. We identified trends in human fecal mcr-1-positivity rates and colonization with mcr-1-positive+third-generation cephalosporin-resistant (3GC-R) Enterobacteriaceae in Guangzhou, China, and investigated the genetic contexts of mcr-1 in a subset of mcr-1-positive+3GC-R strains...
October 10, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/29040265/analysis-of-peripheral-b-cells-and-autoantibodies-against-the-anti-nicotinic-acetylcholine-receptor-derived-from-patients-with-myasthenia-gravis-using-single-cell-manipulation-tools
#7
Tomohiro Makino, Ryuichi Nakamura, Maki Terakawa, Satoshi Muneoka, Kazuhiro Nagahira, Yuriko Nagane, Jyoji Yamate, Masakatsu Motomura, Kimiaki Utsugisawa
The majority of patients with myasthenia gravis (MG), an organ-specific autoimmune disease, harbor autoantibodies that attack the nicotinic acetylcholine receptor (nAChR-Abs) at the neuromuscular junction of skeletal muscles, resulting in muscle weakness. Single cell manipulation technologies coupled with genetic engineering are very powerful tools to examine T cell and B cell repertoires and the dynamics of adaptive immunity. These tools have been utilized to develop mAbs in parallel with hybridomas, phage display technologies and B-cell immortalization...
2017: PloS One
https://www.readbyqxmd.com/read/29040078/genetic-diversity-of-escherichia-coli-isolates-from-surface-water-and-groundwater-in-a-rural-environment
#8
Maria Laura Gambero, Monica Blarasin, Susana Bettera, Jesica Giuliano Albo
The genetic characteristics among Escherichia coli strains can be grouped by origin of isolation. Then, it is possible to use the genotypes as a tool to determine the source of water contamination. The aim of this study was to define water aptitude for human consumption in a rural basin and to assess the diversity of E. coli water populations. Thus, it was possible to identify the main sources of fecal contamination and to explore linkages with the hydrogeological environment and land uses. The bacteriological analysis showed that more than 50% of samples were unfit for human consumption...
October 2017: Journal of Water and Health
https://www.readbyqxmd.com/read/29036709/deep-learning-of-the-splicing-epi-genetic-code-reveals-a-novel-candidate-mechanism-linking-histone-modifications-to-esc-fate-decision
#9
Yungang Xu, Yongcui Wang, Jiesi Luo, Weiling Zhao, Xiaobo Zhou
Alternative splicing (AS) is a genetically and epigenetically regulated pre-mRNA processing to increase transcriptome and proteome diversity. Comprehensively decoding these regulatory mechanisms holds promise in getting deeper insights into a variety of biological contexts involving in AS, such as development and diseases. We assembled splicing (epi)genetic code, DeepCode, for human embryonic stem cell (hESC) differentiation by integrating heterogeneous features of genomic sequences, 16 histone modifications with a multi-label deep neural network...
September 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036574/differential-expression-of-hypertensive-phenotypes-in-bxd-mouse-strains-in-response-to-angiotensin-ii
#10
Wenyuan Zhao, Tieqiang Zhao, Yuanjian Chen, Syamal K Bhattacharya, Lu Lu, Yao Sun
BACKGROUND: Besides environmental risk factors, genetic factors play a crucial role in the pathogenesis of primary hypertension. The current study is to unravel whether hypertensive phenotypes vary in mice with different genetic background. METHODS: Hypertension was induced in C57BL/6J (B6), DBA/2J (D2), and 25 BXD strains by administrating angiotensin (Ang)II (2.5 mg/kg/day infused by osmotic minipump) for 4 weeks. Systolic blood pressure was monitored before (baseline) and after 4 weeks of AngII treatment by tail cuff...
September 23, 2017: American Journal of Hypertension
https://www.readbyqxmd.com/read/29036456/role-of-free-dna-ends-and-protospacer-adjacent-motifs-for-crispr-dna-uptake-in-pyrococcus-furiosus
#11
Masami Shiimori, Sandra C Garrett, Dwain P Chambers, Claiborne V C Glover, Brenton R Graveley, Michael P Terns
To acquire CRISPR-Cas immunity against invasive mobile genetic elements, prokaryotes must first integrate fragments of foreign DNA into their genomic CRISPR arrays for use in future invader silencing. Here, we found that the hyperthermophilic archaeaon, Pyrococcus furiosus, actively incorporates DNA fragments (spacers) from both plasmid (foreign) and host genome (self) sequences into its seven CRISPR loci. The majority of new spacers were derived from DNA immediately downstream from a 5'-CCN-3' protospacer adjacent motif (PAM) that is critical for invader targeting...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036451/genetic-mapping-and-phylogenetic-analysis-reveal-intraspecific-variation-in-sex-chromosomes-of-the-virginian-strawberry
#12
Na Wei, Rajanikanth Govindarajulu, Jacob A Tennessen, Aaron Liston, Tia-Lynn Ashman
With their extraordinary diversity in sexual systems, flowering plants offer unparalleled opportunities to understand sex determination and to reveal generalities in the evolution of sex chromosomes. Comparative genetic mapping of related taxa with good phylogenetic resolution can delineate the extent of sex chromosome diversity within plant groups, and lead the way to understanding the evolutionary drivers of such diversity. The North American octoploid wild strawberries provide such an opportunity. We performed linkage mapping using targeted sequence capture for the subdioecious western Fragaria virginiana ssp...
September 27, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29036328/phylogeography-and-population-genetic-analyses-in-the-iberian-toothcarp-aphanius-iberus-valenciennes-1846-at-different-time-scales
#13
Elena G Gonzalez, Carina Cunha, Hamid R Ghanavi, Francisco J Oliva-Paterna, Mar Torralva, Ignacio Doadrio
Secondary freshwater fish species inhabiting fluctuating and extreme environments are susceptible to changes in dispersion, effective population size, and genetic structure. The Iberian toothcarp Aphanius iberus is an endemic cyprinodontid of the Iberian Peninsula restricted to brackish water of salt marshes and coastal lagoons on the eastern Spanish Mediterranean coast. In this study we analysed mitochondrial cytochrome b DNA and microsatellite variation to evaluate ways in which the processes of extinction, dispersal, and colonization of A...
September 22, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29036305/breeding-for-cuticle-associated-traits-in-crop-species-traits-targets-and-strategies
#14
Johann Petit, Cécile Bres, Jean-Philippe Mauxion, Bénédicte Bakan, Christophe Rothan
Improving crop productivity and quality while promoting sustainable agriculture have become major goals in plant breeding. The cuticle is a natural film covering the aerial organs of plants and consists of lipid polyesters covered and embedded with wax. The cuticle protects plants against water loss and pathogens and affects traits with strong impacts on crop quality such as, for horticultural crops, fruit brightness, cracking, russeting, netting, and shelf life. Here we provide an overview of the most important cuticle-associated traits that can be targeted for crop improvement...
September 27, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29036297/genetic-evidence-for-sexuality-in-cochliopodium-amoebozoa
#15
Fiona C Wood, Alireza Heidari, Yonas I Tekle
Microbial eukaryotes, including amoeboids, display diverse and complex life cycles that may or may not involve sexual reproduction. A recent comprehensive gene inventory study concluded that the Amoebozoa are ancestrally sexual. However, the detection of sex genes in some lineages known for their potentially sexual life cycle was very low. Particularly, the genus Cochliopodium, known to undergo a process of cell fusion, karyogamy, and subsequent fission previously described as parasexual, had no meiosis genes detected...
September 27, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29036178/substantial-population-structure-of-plasmodium-vivax-in-thailand-facilitates-identification-of-the-sources-of-residual-transmission
#16
Veerayuth Kittichai, Cristian Koepfli, Wang Nguitragool, Jetsumon Sattabongkot, Liwang Cui
BACKGROUND: Plasmodium vivax transmission in Thailand has been substantially reduced over the past 10 years, yet it remains highly endemic along international borders. Understanding the genetic relationship of residual parasite populations can help track the origins of the parasites that are reintroduced into malaria-free regions within the country. METHODOLOGY/RESULTS: A total of 127 P. vivax isolates were genotyped from two western provinces (Tak and Kanchanaburi) and one eastern province (Ubon Ratchathani) of Thailand using 10 microsatellite markers...
October 16, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29035322/analysis-of-genetic-diversity-and-structure-pattern-of-indigofera-pseudotinctoria-in-karst-habitats-of-the-wushan-mountains-using-aflp-markers
#17
Yan Fan, Chenglin Zhang, Wendan Wu, Wei He, Li Zhang, Xiao Ma
Indigofera pseudotinctoria Mats is an agronomically and economically important perennial legume shrub with a high forage yield, protein content and strong adaptability, which is subject to natural habitat fragmentation and serious human disturbance. Until now, our knowledge of the genetic relationships and intraspecific genetic diversity for its wild collections is still poor, especially at small spatial scales. Here amplified fragment length polymorphism (AFLP) technology was employed for analysis of genetic diversity, differentiation, and structure of 364 genotypes of I...
October 16, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29035133/genetic-polymorphism-and-bottleneck-analysis-of-balkhi-hashtnagri-and-michni-sheep-populations-using-microsatellite-markers
#18
Muhammad Ibrahim, Sohail Ahmad, Irfan Safdar Durrani, Aqib Iqbal, Iqbal Munir, Zahoor Ahmad Swati
Pakistan is rich in sheep genetic resources. Balkhi, Hashtnagri, and Michni are neighboring sheep populations found in Khyber Pakhtunkhwa province of Pakistan. In this study, we analyzed the genetic structures and bottleneck incidents within these sheep populations using 31 microsatellite DNA markers. Total numbers of 116, 100, and 95 alleles, with average numbers of 3.20, 3.26, and 3.74 alleles per locus were observed, respectively, in Balkhi, Hashtnagri, and Michni population. Mean observed heterozygosity was 0...
October 16, 2017: Animal Biotechnology
https://www.readbyqxmd.com/read/29034956/homoeologous-exchanges-cause-extensive-dosage-dependent-gene-expression-changes-in-an-allopolyploid-crop
#19
Andrew Lloyd, Aurélien Blary, Delphine Charif, Catherine Charpentier, Joseph Tran, Sandrine Balzergue, Etienne Delannoy, Guillem Rigaill, Eric Jenczewski
Structural variation is a major source of genetic diversity and an important substrate for selection. In allopolyploids, homoeologous exchanges (i.e. between the constituent subgenomes) are a very frequent type of structural variant. However, their direct impact on gene content and gene expression had not been determined. Here, we used a tissue-specific mRNA-Seq dataset to measure the consequences of homoeologous exchanges (HE) on gene expression in Brassica napus, a representative allotetraploid crop. We demonstrate that expression changes are proportional to the change in gene copy number triggered by the HEs...
October 16, 2017: New Phytologist
https://www.readbyqxmd.com/read/29034850/pseudomonas-aeruginosa-variants-obtained-from-veterinary-clinical-samples-reveal-a-role-for-cyclic-di-gmp-in-biofilm-formation-and-colony-morphology
#20
Maria T Brock, Galya C Fedderly, Grace I Borlee, Michael M Russell, Liliana K Filipowska, Doreene R Hyatt, Ryan A Ferris, Bradley R Borlee
Overuse of antibiotics is contributing to an emerging antimicrobial resistance crisis. To better understand how bacteria adapt tolerance and resist antibiotic treatment, Pseudomonas aeruginosa isolates obtained from infection sites sampled from companion animals were collected and evaluated for phenotypic differences. Selected pairs of clonal isolates were obtained from individual infection samples and were assessed for antibiotic susceptibility, cyclic di-GMP levels, biofilm production, motility and genetic-relatedness...
October 16, 2017: Microbiology
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