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https://www.readbyqxmd.com/read/29346534/microbial-community-structure-of-sea-spray-aerosols-at-three-california-beaches
#1
Katherine Graham, Linsey C Marr, Lauren M Sassoubre, Alexandria B Boehm
We characterized the microbial communities in SSA, water, and sand of three beaches in central California (Cowell Beach, Baker Beach, and Lovers Point) by sequencing the V4 region of the 16S rRNA gene. Average concentrations of 16S rRNA genes in SSA ranged from 2.4 × 104 to 1.4 × 105 gene copies per m3 of air. A total of 9,781 distinct OTUs were identified in SSA and of these, 1,042 OTUs were found in SSA of all beaches. SSA microbial communities included marine taxa, as well as some associated with the terrestrial environment...
January 15, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29343833/dopamine-d3-receptor-antagonist-reveals-a-cryptic-pocket-in-aminergic-gpcrs
#2
Noelia Ferruz, Stefan Doerr, Michelle A Vanase-Frawley, Yaozhong Zou, Xiaomin Chen, Eric S Marr, Robin T Nelson, Bethany L Kormos, Travis T Wager, Xinjun Hou, Anabella Villalobos, Simone Sciabola, Gianni De Fabritiis
The recent increase in the number of X-ray crystal structures of G-protein coupled receptors (GPCRs) has been enabling for structure-based drug design (SBDD) efforts. These structures have revealed that GPCRs are highly dynamic macromolecules whose function is dependent on their intrinsic flexibility. Unfortunately, the use of static structures to understand ligand binding can potentially be misleading, especially in systems with an inherently high degree of conformational flexibility. Here, we show that docking a set of dopamine D3 receptor compounds into the existing eticlopride-bound dopamine D3 receptor (D3R) X-ray crystal structure resulted in poses that were not consistent with results obtained from site-directed mutagenesis experiments...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29343817/associations-between-body-mass-index-and-the-risk-of-renal-events-in-patients-with-type-2-diabetes
#3
Kamel Mohammedi, John Chalmers, William Herrington, Qiang Li, Giuseppe Mancia, Michel Marre, Neil Poulter, Anthony Rodgers, Bryan Williams, Vlado Perkovic, Josef Coresh, Mark Woodward
BACKGROUND/OBJECTIVES: We aimed to evaluate the relationship between BMI and the risk of renal disease in patients with type 2 diabetes in the Action in Diabetes and Vascular Disease: PreterAx and DiamicroN Modified-Release Controlled Evaluation (ADVANCE) study. SUBJECTS/METHODS: Participants were divided into six baseline BMI categories: <18.5 (underweight, n = 58); ≥18.5 to <25 (normal, n = 2894); ≥25 to <30 (overweight, n = 4340); ≥30 to <35 (obesity grade 1, n = 2265); ≥35 to <40 (obesity grade 2, n = 744); and ≥40 kg/m2 (obesity grade 3, n = 294); those underweight were excluded...
January 17, 2018: Nutrition & Diabetes
https://www.readbyqxmd.com/read/29332123/braf-nras-and-gnaq-mutations-in-conjunctival-melanocytic-nevi
#4
Jasmine H Francis, Hans E Grossniklaus, Larissa A Habib, Brian Marr, David H Abramson, Klaus J Busam
Purpose: To evaluate BRAF, NRAS, and GNAQ mutations in surgical specimens of common and blue conjunctival melanocytic nevi. Methods: Surgical specimens from 25 conjunctival melanocytic nevi (23 common and 2 blue) of 25 patients were evaluated. All common nevi were analyzed immunohistochemically for the expression of BRAF V600E or NRAS Q61R. One lesion with negative immunoreactivity and for all blue nevi, a hybridization capture-based next-generation sequencing method was employed for mutation analysis...
January 1, 2018: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29325551/relationship-between-cardiac-microvascular-dysfunction-measured-with-82rubidium-pet-and-albuminuria-in-patients-with-diabetes-mellitus
#5
Louis Potier, Renata Chequer, Ronan Roussel, Kamel Mohammedi, Souad Sismail, Agnès Hartemann, Chloé Amouyal, Michel Marre, Dominique Le Guludec, Fabien Hyafil
BACKGROUND: Albuminuria is of one the strongest predictors of cardiovascular disease (CVD) in diabetes. Diabetes is associated with cardiac microvascular dysfunction (CMD), a powerful, independent prognostic factor for cardiac mortality. The aim of this study was to evaluate the relationship between CMD and microvascular complications in patients without known CVD. METHODS: In this monocentric study, myocardial flow reserve (MFR) was measured with cardiac 82Rubidium positron emission tomography (Rb-PET) in 311 patients referred to nuclear medicine department of Bichat University Hospital for screening of coronary artery disease from 2012 to 2014...
January 11, 2018: Cardiovascular Diabetology
https://www.readbyqxmd.com/read/29324326/studying-the-recognition-mechanism-of-tcar-and-ssdna-using-molecular-dynamic-simulations
#6
Jing-Rong Fan, Hong-Xing Zhang, Yu-Guang Mu, Qing-Chuan Zheng
The transcription regulator teicoplanin-associate locus regulator (TcaR) plays a vital role in interfering with ssDNA replication and resisting ssDNA phage invasion. Although recent studies demonstrated that TcaR had strong interaction with ssDNA, the dynamics and interaction mechanism of dimeric TcaR bound to ssDNA have not been rationalized at the atomic level. In our study, MD simulations combined with MM-GB/SA calculations were employed to study recognition mechanism between TcaR and ssDNA. The results illuminate that electrostatic interaction is the main driving force for the binding process...
December 5, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29316570/the-randomized-shortened-dental-arch-study-tooth-loss-over-10-years
#7
Michael H Walter, Jens Dreyhaupt, Wolfgang Hannak, Stefan Wolfart, Ralph G Luthardt, Helmut Stark, Peter Pospiech, Torsten Mundt, Matthias Kern, Klaus Walter Böning, Bernd Wöstmann, Herbert Scheller, Florentine Jahn, Wilfried Reinhardt, Joerg Strub, Birgit Marré, Guido Heydecke
PURPOSE: This study aimed to compare the long-term outcomes of two different nonimplant treatments in the bilateral shortened dental arch (SDA). MATERIALS AND METHODS: In a multicenter randomized controlled clinical trial, patients with complete molar loss in one arch were assigned to one of two different nonimplant treatments. In the partial removable dental prosthesis (PRDP) group, patients were provided with a distal-extension prosthesis retained with precision attachments...
January 2018: International Journal of Prosthodontics
https://www.readbyqxmd.com/read/29308539/haemoglobin-glycation-index-and-risk-for-diabetes-related-complications-in-the-action-in-diabetes-and-vascular-disease-preterax-and-diamicron-modified-release-controlled-evaluation-advance-trial
#8
Sigrid C van Steen, Mark Woodward, John Chalmers, Qiang Li, Michel Marre, Mark E Cooper, Pavel Hamet, Giuseppe Mancia, Stephen Colagiuri, Bryan Williams, Diederick E Grobbee, J Hans DeVries
AIMS/HYPOTHESIS: Previous studies have suggested that the haemoglobin glycation index (HGI) can be used as a predictor of diabetes-related complications in individuals with type 1 and type 2 diabetes. We investigated whether HGI was a predictor of adverse outcomes of intensive glucose lowering and of diabetes-related complications in general, using data from the Action in Diabetes and Vascular Disease: Preterax and Diamicron Modified Release Controlled Evaluation (ADVANCE) trial. METHODS: We studied participants in the ADVANCE trial with data available for baseline HbA1c and fasting plasma glucose (FPG) (n = 11,083)...
January 8, 2018: Diabetologia
https://www.readbyqxmd.com/read/29297851/ram-locus-is-a-key-regulator-to-trigger-multidrug-resistance-in-enterobacter-aerogenes
#9
Alexander Molitor, Chloë E James, Séamus Fanning, Jean-Marie Pagès, Anne Davin-Regli
PURPOSE: Several genetic regulators belonging to AraC family are involved in the emergence of MDR isolates of E. aerogenes due to alterations in membrane permeability. Compared with the genetic regulator Mar, RamA may be more relevant towards the emergence of antibiotic resistance. METHODOLOGY: Focusing on the global regulators, Mar and Ram, we compared the amino acid sequences of the Ram repressor in 59 clinical isolates and laboratory strains of E. aerogenes. Sequence types were associated with their corresponding multi-drug resistance phenotypes and membrane protein expression profiles using MIC and immunoblot assays...
January 3, 2018: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/29277727/antimicrobial-resistance-in-urine-and-skin-isolates-in-timor-leste
#10
Ian Marr, Nevio Sarmento, Matt O'Brien, Karl Lee, Celia Gusmao, Gloria de Castro, Sonja Janson, Steven Y C Tong, Rob W Baird, Joshua R Francis
OBJECTIVES: High rates of antimicrobial resistance are seen throughout Southeast Asia. Limited antimicrobial resistance data exists for Timor-Leste, which is situated on the south-eastern portion of the Malay Archipelago. The purpose of this study was to identify antimicrobial resistance in bacteria isolated from urine and skin swabs from patients in Dili, Timor-Leste. METHODS: Urine and skin swabs were collected from symptomatic patients and processed for bacterial culture in Timor-Leste...
December 22, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/29259111/toward-a-unified-theory-of-efficient-predictive-and-sparse-coding
#11
Matthew Chalk, Olivier Marre, Gašper Tkačik
A central goal in theoretical neuroscience is to predict the response properties of sensory neurons from first principles. To this end, "efficient coding" posits that sensory neurons encode maximal information about their inputs given internal constraints. There exist, however, many variants of efficient coding (e.g., redundancy reduction, different formulations of predictive coding, robust coding, sparse coding, etc.), differing in their regimes of applicability, in the relevance of signals to be encoded, and in the choice of constraints...
December 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29258889/association-of-escherichia-coli-st131-lineage-with-risk-of-urinary-tract-infection-recurrence-among-young-women
#12
Miriam D Ismail, Ihsan Ali, Savannah Hatt, Elizabeth A Salzman, Anna W Cronenwett, Carl F Marrs, Alexander H Rickard, Betsy Foxman
OBJECTIVES: Test the hypothesis that urinary tract infections (UTI) caused by Escherichia coli of the ST131 lineage are more likely to recur than UTI cause by other E. coli lineages. METHODS: We used isolates from 221 young women with UTI caused by Escherichia coli participating in a randomized controlled trial. Participants were followed for 6 months or until recurrence. RESULTS: Sequence type was not associated with risk of recurrence. Isolates in the ST131 lineage were more resistant to quinolones (6% vs 1%) than other STs, but not trimethoprim sulfamethoxazole (15% vs 15%)...
December 16, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/29247320/time-dependent-propagators-for-stochastic-models-of-gene-expression-an-analytical-method
#13
Frits Veerman, Carsten Marr, Nikola Popović
The inherent stochasticity of gene expression in the context of regulatory networks profoundly influences the dynamics of the involved species. Mathematically speaking, the propagators which describe the evolution of such networks in time are typically defined as solutions of the corresponding chemical master equation (CME). However, it is not possible in general to obtain exact solutions to the CME in closed form, which is due largely to its high dimensionality. In the present article, we propose an analytical method for the efficient approximation of these propagators...
December 15, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/29240826/pamr-a-new-marr-like-regulator-affecting-prophages-and-metabolic-genes-expression-in-bacillus-subtilis
#14
Alba De San Eustaquio-Campillo, Charlène Cornilleau, Cyprien Guérin, Rut Carballido-López, Arnaud Chastanet
B. subtilis adapts to changing environments by reprogramming its genetic expression through a variety of transcriptional regulators from the global transition state regulators that allow a complete resetting of the cell genetic expression, to stress specific regulators controlling only a limited number of key genes required for optimal adaptation. Among them, MarR-type transcriptional regulators are known to respond to a variety of stresses including antibiotics or oxidative stress, and to control catabolic or virulence gene expression...
2017: PloS One
https://www.readbyqxmd.com/read/29229866/allosteric-histidine-switch-for-regulation-of-intracellular-zinc-ii-fluctuation
#15
Rongfeng Zhu, Yanqun Song, Haiping Liu, Yufei Yang, Shenlin Wang, Chengqi Yi, Peng R Chen
Metalloregulators allosterically control transcriptional activity through metal binding-induced reorganization of ligand residues and/or hydrogen bonding networks, while the coordination atoms on the same ligand residues remain seldom changed. Here we show that the MarR-type zinc transcriptional regulator ZitR switches one of its histidine nitrogen atoms for zinc coordination during the allosteric control of DNA binding. The Zn(II)-coordination nitrogen on histidine 42 within ZitR's high-affinity zinc site (site 1) switches from Nε2 to Nδ1 upon Zn(II) binding to its low-affinity zinc site (site 2), which facilitates ZitR's conversion from the nonoptimal to the optimal DNA-binding conformation...
December 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29223475/insights-from-clinical-experience-in-treating-ivf-poor-responders
#16
REVIEW
Kelly J Gonda, Alice D Domar, Norbert Gleicher, Richard P Marrs
'Poor responders' is a term used to describe a subpopulation of IVF patients who do not respond well to ovarian stimulation with gonadotrophins. While there is no standard definition of a poor responder, these patients tend to be of advanced maternal age (≥40 years), have a history of poor ovarian response with conventional stimulation protocols, and/or have low ovarian reserve. Despite the heterogeneity of this patient group, there are characteristics and needs common to many poor responders that can be addressed through a holistic approach...
October 24, 2017: Reproductive Biomedicine Online
https://www.readbyqxmd.com/read/29222838/results-of-a-systematic-literature-review-of-treatment-modalities-for-jugulotympanic-paraganglioma-stratified-per-fisch-class
#17
Thijs T G Jansen, Henri J L M Timmers, Henri A M Marres, Johannes H A M Kaanders, Henricus P M Kunst
OBJECTIVE: Key for successful jugulotympanic paraganglioma management is a personalized approach aiming for the best practice for each individual patient. To this end, a systematic review is performed, evaluating the local control- and complication rates for the different treatment modalities stratified by the broadly accepted Fisch classification. DESIGN: A systematic literature review according to the PRISMA statement was performed. A detailed overview of individual treatment outcomes per Fisch class is provided...
December 8, 2017: Clinical Otolaryngology
https://www.readbyqxmd.com/read/29216271/genomic-and-phenotypic-characteristics-of-swedish-c-jejuni-water-isolates
#18
Anna Nilsson, Cecilia Johansson, Astrid Skarp, René Kaden, Lars Engstrand, Hilpi Rautelin
Campylobacter jejuni is the most common cause of bacterial gastroenteritis. Major reservoirs are warm-blooded animals, poultry in particular, but Campylobacter can also be transmitted via water. In this paper, we have taken a closer look at the biology and potential virulence of C. jejuni water isolates. Seven C. jejuni isolates from incoming surface water at water plants in Sweden were characterized with whole genome sequencing and phenotypical testing. Multi locus sequence typing analysis revealed that these isolates belonged to groups known to include both common (ST48CC) and uncommon (ST1275CC, ST683, ST793 and ST8853) human pathogens...
2017: PloS One
https://www.readbyqxmd.com/read/29214529/a-rapid-and-reagent-free-bioassay-for-the-detection-of-dioxin-like-compounds-and-other-aryl-hydrocarbon-receptor-ahr-agonists-using-autobioluminescent-yeast
#19
Tingting Xu, Anna Young, Enolia Marr, Gary Sayler, Steven Ripp, Dan Close
An autonomously bioluminescent Saccharomyces cerevisiae BLYAhS bioreporter was developed in this study for the simple and rapid detection of dioxin-like compounds (DLCs) and aryl hydrocarbon receptor (AhR) agonists. This recombinant yeast reporter was based on a synthetic bacterial luciferase reporter gene cassette (lux) that can produce the luciferase as well as the enzymes capable of self-synthesizing the requisite substrates for bioluminescent production from endogenous cellular metabolites. As a result, bioluminescent signal production is generated continuously and autonomously without cell lysis or exogenous reagent addition...
December 6, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/29213097/multiplexed-computations-in-retinal-ganglion-cells-of-a-single-type
#20
Stéphane Deny, Ulisse Ferrari, Emilie Macé, Pierre Yger, Romain Caplette, Serge Picaud, Gašper Tkačik, Olivier Marre
In the early visual system, cells of the same type perform the same computation in different places of the visual field. How these cells code together a complex visual scene is unclear. A common assumption is that cells of a single-type extract a single-stimulus feature to form a feature map, but this has rarely been observed directly. Using large-scale recordings in the rat retina, we show that a homogeneous population of fast OFF ganglion cells simultaneously encodes two radically different features of a visual scene...
December 6, 2017: Nature Communications
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