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https://www.readbyqxmd.com/read/28783909/an-underappreciated-hotspot-of-antibiotic-resistance-the-groundwater-near-the-municipal-solid-waste-landfill
#1
Qing-Lin Chen, Hu Li, Xin-Yuan Zhou, Yi Zhao, Jian-Qiang Su, Xian Zhang, Fu-Yi Huang
Landfills are so far the most common practice for the disposals of municipal solid waste (MSW) worldwide. Since MSW landfill receives miscellaneous wastes, including unused/expired antibiotics and bioactive wastes, it gradually becomes a huge potential bioreactor for breeding antibiotic resistance. Antibiotic resistance genes (ARGs) in landfill can flow to the environment through leakage of landfill leachate and pose a risk to public health. Using high throughput quantitative Polymerase Chain Reaction (HT-qPCR), we investigated the prevalence, diversity of ARGs and its association with various mobile genetic elements (MGEs) in MSW landfill groundwater...
July 31, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28725045/genomic-epidemiology-of-global-klebsiella-pneumoniae-carbapenemase-kpc-producing-escherichia-coli
#2
N Stoesser, A E Sheppard, G Peirano, L W Anson, L Pankhurst, R Sebra, H T T Phan, A Kasarskis, A J Mathers, T E A Peto, P Bradford, M R Motyl, A S Walker, D W Crook, J D Pitout
The dissemination of carbapenem resistance in Escherichia coli has major implications for the management of common infections. bla KPC, encoding a transmissible carbapenemase (KPC), has historically largely been associated with Klebsiella pneumoniae, a predominant plasmid (pKpQIL), and a specific transposable element (Tn4401, ~10 kb). Here we characterize the genetic features of bla KPC emergence in global E. coli, 2008-2013, using both long- and short-read whole-genome sequencing. Amongst 43/45 successfully sequenced bla KPC-E...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28720323/rapid-divergence-of-histones-in-hydrozoa-cnidaria-and-evolution-of-a-novel-histone-involved-in-dna-damage-response-in-hydra
#3
Puli Chandramouli Reddy, Suyog Ubhe, Neha Sirwani, Rasika Lohokare, Sanjeev Galande
Histones are fundamental components of chromatin in all eukaryotes. Hydra, an emerging model system belonging to the basal metazoan phylum Cnidaria, provides an ideal platform to understand the evolution of core histone components at the base of eumetazoan phyla. Hydra exhibits peculiar properties such as tremendous regenerative capacity, lack of organismal senescence and rarity of malignancy. In light of the role of histone modifications and histone variants in these processes it is important to understand the nature of histones themselves and their variants in hydra...
June 15, 2017: Zoology: Analysis of Complex Systems, ZACS
https://www.readbyqxmd.com/read/28715769/high-throughput-profiling-and-analysis-of-antibiotic-resistance-genes-in-east-tiaoxi-river-china
#4
Ji Zheng, Ruixia Gao, Yuanyuan Wei, Tao Chen, Jiqing Fan, Zhenchao Zhou, Tiimub Benjamin Makimilua, Yanan Jiao, Hong Chen
The rapid human activities and urbanization exacerbate the human health risks induced by antibiotic resistance genes (ARGs). In this study, the profiling of ARGs was investigated using high-throughput qPCR from water samples of 13 catchment areas in East Tiaoxi River, China. High prevalence of ARGs indicated significant antibiotic resistance pollution in the research area (absolute abundance: 6.1 × 10(8)-2.1 × 10(10) copies/L; relative abundance: 0.033-0.158 copies/cell). Conventional water qualities (COD, TN, TP, NH3-N), bacterial communities and mobile gene elements (MGEs) were detected and analyzed as factors of ARGs shift...
July 14, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28710822/prevalence-and-significance-of-hmga2-expression-in-esophageal-adenocarcinoma
#5
Jeffrey K Mito, Agoston T Agoston, Paola Dal Cin, Amitabh Srivastava
AIMS: Esophageal adenocarcinoma (EAC) tumorigenesis has been primarily linked to loss-of-function mutations in tumor suppressor genes. Knowledge of specific oncogenes that drive tumor progression, and their relationship to outcomes, is limited. High Mobility Group AT-Hook 2 (HMGA2) has been reported to be amplified in a subset of EACs, but the clinicopathologic and prognostic implications of HMGA2 expression in EAC is unknown. METHODS AND RESULTS: We performed HMGA2 immunohistochemistry and fluorescence in-situ hybridization (FISH) in EAC to determine its clinicopathologic and prognostic significance...
July 15, 2017: Histopathology
https://www.readbyqxmd.com/read/28704934/functioning-of-fluorescent-proteins-in-aggregates-in-anthozoa-species-and-in-recombinant-artificial-models
#6
Natalia V Povarova, Natalia D Petri, Anna E Blokhina, Alexey M Bogdanov, Nadya G Gurskaya, Konstantin A Lukyanov
Despite great advances in practical applications of fluorescent proteins (FPs), their natural function is poorly understood. FPs display complex spatio-temporal expression patterns in living Anthozoa coral polyps. Here we applied confocal microscopy, specifically, the fluorescence recovery after photobleaching (FRAP) technique to analyze intracellular localization and mobility of endogenous FPs in live tissues. We observed three distinct types of protein distributions in living tissues. One type of distribution, characteristic for Anemonia, Discosoma and Zoanthus, is free, highly mobile cytoplasmic localization...
July 12, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28701230/plasmid-composition-in-aeromonas-salmonicida-subsp-salmonicida-01-b526-unravels-unsuspected-type-three-secretion-system-loss-patterns
#7
Katherine H Tanaka, Antony T Vincent, Jean-Guillaume Emond-Rheault, Marcin Adamczuk, Michel Frenette, Steve J Charette
BACKGROUND: Aeromonas salmonicida subsp. salmonicida is a ubiquitous psychrophilic waterborne bacterium and a fish pathogen. The numerous mobile elements, especially insertion sequences (IS), in its genome promote rearrangements that impact its phenotype. One of the main virulence factors of this bacterium, its type three secretion system (TTSS), is affected by these rearrangements. In Aeromonas salmonicida subsp. salmonicida most of the TTSS genes are encoded in a single locus on a large plasmid called pAsa5, and may be lost when the bacterium is cultivated at a higher temperature (25 °C), producing non-virulent mutants...
July 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28700423/sox2-gene-amplification-and-overexpression-is-linked-to-hpv-positive-vulvar-carcinomas
#8
André Gut, Holger Moch, Matthias Choschzick
SOX2 (SRY-related HMG-box 2) belongs to the SOX gene family of high-mobility transcription factors indispensably involved in gene regulation in pluripotent stem cells and neural differentiation. SOX2 copy number increases have been frequently reported in various types of squamous cell cancer. To better understand the effect of SOX2 aberrations on vulvar cancer phenotype and patient prognosis, we analyzed SOX2 copy number changes using fluorescence in situ hybridization and SOX2 expression by immunohistochemistry in 55 squamous cell carcinomas of the vulva...
July 11, 2017: International Journal of Gynecological Pathology
https://www.readbyqxmd.com/read/28687080/inhibition-of-rna-polymerase-ii-allows-controlled-mobilisation-of-retrotransposons-for-plant-breeding
#9
Michael Thieme, Sophie Lanciano, Sandrine Balzergue, Nicolas Daccord, Marie Mirouze, Etienne Bucher
BACKGROUND: Retrotransposons play a central role in plant evolution and could be a powerful endogenous source of genetic and epigenetic variability for crop breeding. To ensure genome integrity several silencing mechanisms have evolved to repress retrotransposon mobility. Even though retrotransposons fully depend on transcriptional activity of the host RNA polymerase II (Pol II) for their mobility, it was so far unclear whether Pol II is directly involved in repressing their activity...
July 7, 2017: Genome Biology
https://www.readbyqxmd.com/read/28684862/direct-and-convenient-measurement-of-plasmid-stability-in-lab-and-clinical-isolates-of-e-coli
#10
Siyi Chen, Mårten Larsson, Robert C Robinson, Swaine L Chen
Plasmids are important mobile elements in bacteria, contributing to evolution, virulence, and antibiotic resistance. Natural plasmids are generally large and maintained at low copy number and thus prone to be lost. Therefore, dedicated plasmid maintenance systems have evolved, leading to plasmid loss rates as low as 1 per 10(7) divisions. These low rates complicate studies of plasmid loss, as traditional techniques for measuring plasmid loss are laborious and not quantitative. To overcome these limitations, we leveraged a stringent negative selection system to develop a method for performing direct, quantitative measurements of plasmid loss in E...
July 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28676355/nanos-driven-expression-of-piggybac-transposase-induces-mobilization-of-a-synthetic-autonomous-transposon-in-the-malaria-vector-mosquito-anopheles-stephensi
#11
Vanessa M Macias, Alyssa J Jimenez, Bianca Burini-Kojin, David Pledger, Nijole Jasinskiene, Celine Hien Phong, Karen Chu, Aniko Fazekas, Kelcie Martin, Osvaldo Marinotti, Anthony A James
Transposons are a class of selfish DNA elements that can mobilize within a genome. If mobilization is accompanied by an increase in copy number (replicative transposition), the transposon may sweep through a population until it is fixed in all of its interbreeding members. This introgression has been proposed as the basis for drive systems to move genes with desirable phenotypes into target species. One such application would be to use them to move a gene conferring resistance to malaria parasites throughout a population of vector mosquitos...
August 2017: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28667117/reduced-mutation-rate-and-increased-transformability-of-transposon-free-acinetobacter-baylyi-adp1-isx
#12
Gabriel A Suárez, Brian A Renda, Aurko Dasgupta, Jeffrey E Barrick
The genomes of most bacteria contain mobile DNA elements that can contribute to undesirable genetic instability in engineered cells. In particular, transposable insertion sequence (IS) elements can rapidly inactivate genes that are important for a designed function. We deleted all six copies of IS1236 from the genome of the naturally transformable bacterium Acinetobacter baylyi ADP1. The natural competence of ADP1 made it possible to rapidly repair deleterious point mutations that arose during strain construction...
June 30, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28652353/disentangling-the-effects-of-selection-and-loss-bias-on-gene-dynamics
#13
Jaime Iranzo, José A Cuesta, Susanna Manrubia, Mikhail I Katsnelson, Eugene V Koonin
We combine mathematical modeling of genome evolution with comparative analysis of prokaryotic genomes to estimate the relative contributions of selection and intrinsic loss bias to the evolution of different functional classes of genes and mobile genetic elements (MGE). An exact solution for the dynamics of gene family size was obtained under a linear duplication-transfer-loss model with selection. With the exception of genes involved in information processing, particularly translation, which are maintained by strong selection, the average selection coefficient for most nonparasitic genes is low albeit positive, compatible with observed positive correlation between genome size and effective population size...
July 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28642606/transposable-elements-in-cancer
#14
REVIEW
Kathleen H Burns
Transposable elements give rise to interspersed repeats, sequences that comprise most of our genomes. These mobile DNAs have been historically underappreciated - both because they have been presumed to be unimportant, and because their high copy number and variability pose unique technical challenges. Neither impediment now seems steadfast. Interest in the human mobilome has never been greater, and methods enabling its study are maturing at a fast pace. This Review describes the activity of transposable elements in human cancers, particularly long interspersed element-1 (LINE-1)...
July 2017: Nature Reviews. Cancer
https://www.readbyqxmd.com/read/28630288/intact-pirna-pathway-prevents-l1-mobilization-in-male-meiosis
#15
Simon J Newkirk, Suman Lee, Fiorella C Grandi, Valeriya Gaysinskaya, James M Rosser, Nicole Vanden Berg, Cathryn A Hogarth, Maria C N Marchetto, Alysson R Muotri, Michael D Griswold, Ping Ye, Alex Bortvin, Fred H Gage, Jef D Boeke, Wenfeng An
The PIWI-interacting RNA (piRNA) pathway is essential for retrotransposon silencing. In piRNA-deficient mice, L1-overexpressing male germ cells exhibit excessive DNA damage and meiotic defects. It remains unknown whether L1 expression simply highlights piRNA deficiency or actually drives the germ-cell demise. Specifically, the sheer abundance of genomic L1 copies prevents reliable quantification of new insertions. Here, we developed a codon-optimized L1 transgene that is controlled by an endogenous mouse L1 promoter...
July 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28626737/high-level-bacterial-contamination-of-secondary-school-students-mobile-phones
#16
Siiri Kõljalg, Rando Mändar, Tiina Sõber, Tiiu Rööp, Reet Mändar
INTRODUCTION: While contamination of mobile phones in the hospital has been found to be common in several studies, little information about bacterial abundance on phones used in the community is available. Our aim was to quantitatively determine the bacterial contamination of secondary school students' mobile phones. METHODS: Altogether 27 mobile phones were studied. The contact plate method and microbial identification using MALDI-TOF mass spectrometer were used for culture studies...
June 2017: Germs
https://www.readbyqxmd.com/read/28599766/plastic-and-immobile-unequal-intergenerational-mobility-by-genetic-sensitivity-score-within-sibling-pairs
#17
Emily Rauscher
Contrary to traditional biological arguments, the differential susceptibility model suggests genotype may moderate rather than mediate parent-child economic similarity. Using family fixed effects models of Add Health sibling data, I investigate the relationship between an index of sensitive genotypes and intergenerational mobility. Full, same sex sibling comparisons hold constant parental characteristics and address the non-random distribution of genotype that reduces internal validity in nationally representative samples...
July 2017: Social Science Research
https://www.readbyqxmd.com/read/28593349/transcriptomic-analysis-of-the-swarm-motility-phenotype-of-salmonella-enterica-serovar-typhimurium-mutant-defective-in-periplasmic-glucan-synthesis
#18
Arvind A Bhagwat, Lynn Young, Allen D Smith, Medha Bhagwat
Movement of food-borne pathogens on moist surfaces enables them to migrate towards more favorable niches and facilitate their survival for extended periods of time. Salmonella enterica serovar Typhimurium mutants defective in Osmoregulated periplasmic glucans (OPG) synthesis are unable to exhibit motility on moist surfaces (swarming); however, their mobility in liquid (swim motility) remains unaffected. In order to understand the role of OPG in swarm motility, transcriptomic analysis was performed using cells growing on a moist agar surface...
September 2017: Current Microbiology
https://www.readbyqxmd.com/read/28577759/pip40a-a-type-1-incc-plasmid-from-1969-carries-the-integrative-element-gisul2-and-a-novel-class-ii-mercury-resistance-transposon
#19
Christopher J Harmer, Mohammad Hamidian, Ruth M Hall
The 167.5kb sequence of the conjugative IncC plasmid pIP40a, isolated from a Pseudomonas aeruginosa in 1969, was analysed. pIP40a confers resistance to kanamycin, neomycin, ampicillin, sulphonamides and mercuric ions, and several insertions in a type 1 IncC backbone were found, including copies of IS3, Tn1000 and a novel mercury resistance transposon, Tn6182. The antibiotic resistance genes were in two locations. Tn6023, containing the aphA1 kanamycin and neomycin resistance gene, is in a partial copy of Tn1/Tn2/Tn3 (blaTEM, ampicillin resistance) in the kfrA gene, and the sul2 sulphonamide resistance gene is in the integrative element GIsul2 in the position of ARI-B islands...
May 31, 2017: Plasmid
https://www.readbyqxmd.com/read/28573589/low-resolution-refinement-of-atomic-models-against-crystallographic-data
#20
Robert A Nicholls, Oleg Kovalevskiy, Garib N Murshudov
This review describes some of the problems encountered during low-resolution refinement and map calculation. Refinement is considered as an application of Bayes' theorem, allowing combination of information from various sources including crystallographic experimental data and prior chemical and structural knowledge. The sources of prior knowledge relevant to macromolecules include basic chemical information such as bonds and angles, structural information from reference models of known homologs, knowledge about secondary structures, hydrogen bonding patterns, and similarity of non-crystallographically related copies of a molecule...
2017: Methods in Molecular Biology
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