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https://www.readbyqxmd.com/read/27911438/evolutionary-convergence-in-experimental-pseudomonas-populations
#1
Peter A Lind, Andrew D Farr, Paul B Rainey
Model microbial systems provide opportunity to understand the genetic bases of ecological traits, their evolution, regulation and fitness contributions. Experimental populations of Pseudomonas fluorescens rapidly diverge in spatially structured microcosms producing a range of surface-colonising forms. Despite divergent molecular routes, wrinkly spreader (WS) niche specialist types overproduce a cellulosic polymer allowing mat formation at the air-liquid interface and access to oxygen. Given the range of ways by which cells can form mats, such phenotypic parallelism is unexpected...
December 2, 2016: ISME Journal
https://www.readbyqxmd.com/read/27905871/phyinformr-phylogenetic-experimental-design-and-phylogenomic-data-exploration-in-r
#2
Alex Dornburg, J Nick Fisk, Jules Tamagnan, Jeffrey P Townsend
BACKGROUND: Analyses of phylogenetic informativeness represent an important step in screening potential or existing datasets for their proclivity toward convergent or parallel evolution of molecular sites. However, while new theory has been developed from which to predict the utility of sequence data, adoption of these advances have been stymied by a lack of software enabling application of advances in theory, especially for large next-generation sequence data sets. Moreover, there are no theoretical barriers to application of the phylogenetic informativeness or the calculation of quartet internode resolution probabilities in a Bayesian setting that more robustly accounts for uncertainty, yet there is no software with which a computationally intensive Bayesian approach to experimental design could be implemented...
December 1, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27903662/patient-engagement-and-self-management-in-pulmonary-arterial-hypertension
#3
REVIEW
Jytte Graarup, Pisana Ferrari, Luke S Howard
Improved care in pulmonary arterial hypertension has led to increased longevity for patients, with a paralleled evolution in the nature of their needs. There is more focus on the impact of the disease on their day-to-day activities and quality of life, and a holistic approach is coming to the front of pulmonary arterial hypertension management, which places the patient at the centre of their own healthcare. Patients are thus becoming more proactive, involved and engaged in their self-care, and this engagement is an important factor if patient outcomes are to improve...
December 2016: European Respiratory Review: An Official Journal of the European Respiratory Society
https://www.readbyqxmd.com/read/27903631/genomics-of-compensatory-adaptation-in-experimental-populations-of-aspergillus-nidulans
#4
Jeremy R Dettman, Nicolas Rodrigue, Sijmen E Schoustra, Rees Kassen
Knowledge of the number and nature of genetic changes responsible for adaptation is essential for understanding and predicting evolutionary trajectories. Here, we study the genomic basis of compensatory adaptation to the fitness cost of fungicide resistance in experimentally evolved strains of the filamentous fungus Aspergillus nidulans The original selection experiment tracked the fitness recovery of lines founded by an ancestral strain that was resistant to fludioxonil, but paid a fitness cost in the absence of the fungicide...
November 30, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27897145/quantum-statistics-and-squeezing-for-a-microwave-driven-interacting-magnon-system
#5
Zahra Haghshenasfard, Michael G Cottam
Theoretical studies are reported for the statistical properties of a microwave-driven interacting magnon system. Both the magnetic dipole-dipole and the exchange interactions are included and the theory is developed for the case of parallel pumping allowing for the inclusion of the nonlinear processes due to the four-magnon interactions. The method of second quantization is used to transform the total Hamiltonian from spin operators to boson creation and annihilation operators. By using the coherent magnon state representation we have studied the magnon occupation number and the statistical behavior of the system...
November 29, 2016: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/27892802/longitudinal-changes-and-correlations-of-bio-impedance-and-anthropometric-measurements-in-pregnancy-simple-possible-bed-side-tools-to-assess-pregnancy-evolution
#6
Gabriele Piuri, Enrico Ferrazzi, Camilla Bulfoni, Luciana Mastricci, Daniela Di Martino, Attilio Francesco Speciani
PURPOSE: the aim of this study was to assess longitudinal changes of bio-impedance analysis compared with anthropometric measurements in low risk pregnant woman recruited in the first trimester, and to observe possible differences in these indices in women who developed high risk pregnancies. MATERIAL AND METHODS: bio-impedance indices, for the three trimesters of pregnancies were calculated separately for uneventful pregnancies delivered of newborns > the 10(th) centile...
November 28, 2016: Journal of Maternal-fetal & Neonatal Medicine
https://www.readbyqxmd.com/read/27886568/deep-sequencing-methods-for-protein-engineering-and-design
#7
REVIEW
Emily E Wrenbeck, Matthew S Faber, Timothy A Whitehead
The advent of next-generation sequencing (NGS) has revolutionized protein science, and the development of complementary methods enabling NGS-driven protein engineering have followed. In general, these experiments address the functional consequences of thousands of protein variants in a massively parallel manner using genotype-phenotype linked high-throughput functional screens followed by DNA counting via deep sequencing. We highlight the use of information rich datasets to engineer protein molecular recognition...
November 22, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27885777/variable-time-normalization-analysis-general-graphical-elucidation-of-reaction-orders-from-concentration-profiles
#8
Jordi Burés
The recent technological evolution of reaction monitoring techniques has not been paralleled by the development of modern kinetic analyses. The analyses currently used disregard part of the data acquired, thus requiring an increased number of experiments to obtain sufficient kinetic information for a given chemical reaction. Herein, we present a simple graphical analysis method that takes advantage of the data-rich results provided by modern reaction monitoring tools. This analysis uses a variable normalization of the time scale to enable the visual comparison of entire concentration reaction profiles...
November 25, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27880966/age-dependency-of-location-of-epileptic-foci-in-continuous-spike-and-waves-during-sleep-a-parallel-to-the-posterior-anterior-trajectory-of-slow-wave-activity
#9
Bigna Katrin Bölsterli Heinzle, Thomas Bast, Hanne Critelli, Reto Huber, Bernhard Schmitt
Background Epileptic encephalopathy with continuous spike-and-waves during sleep (CSWS) occurs during childhood and is characterized by an activation of spike wave complexes during slow wave sleep. The location of epileptic foci is variable, as is etiology. A relationship between the epileptic focus and age has been shown in various focal epilepsies following a posterior-anterior trajectory, and a link to brain maturation has been proposed.We hypothesize that in CSWS, maximal spike wave activity, corresponding to the epileptic focus, is related to age and shows a posterior-anterior evolution...
November 23, 2016: Neuropediatrics
https://www.readbyqxmd.com/read/27879948/efficacy-and-local-tolerability-of-different-spray-products-in-the-treatment-of-mild-to-moderate-acne-of-the-back-and-chest-a-controlled-3-arm-assessor-blinded-prospective-trial
#10
Ada Lo Schiavo, Rosa V Puca, Francesca Romano, Massimo Milani
BACKGROUND: A spray formulation containing 2 vitamin-A derivatives (hydroxypinacolone retinoate and retinol) carried in glycospheres (RetinSphere®) combined with an antimicrobial peptide (BIOPEP-15), salicylic acid and vitamin E (BR) has been recently developed for the treatment of truncal acne. We evaluated clinical efficacy of BR in comparison with two commonly used sprays, containing triethylcitrate and ethylinoleate (AK) and containing betaine, glycine and salicylic acid 2% (SP)...
November 23, 2016: Giornale Italiano di Dermatologia e Venereologia: Organo Ufficiale, Società Italiana di Dermatologia e Sifilografia
https://www.readbyqxmd.com/read/27870264/a-hot-topic-the-genetics-of-adaptation-to-geothermal-vents-in-mimulus-guttatus
#11
Kathleen G Ferris
Identifying the individual loci and mutations that underlie adaptation to extreme environments has long been a goal of evolutionary biology. However, finding the genes that underlie adaptive traits is difficult for several reasons. First, because many traits and genes evolve simultaneously as populations diverge, it is difficult to disentangle adaptation from neutral demographic processes. Second, finding the individual loci involved in any trait is challenging given the respective limitations of quantitative and population genetic methods...
November 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27861590/phylosymbiosis-relationships-and-functional-effects-of-microbial-communities-across-host-evolutionary-history
#12
Andrew W Brooks, Kevin D Kohl, Robert M Brucker, Edward J van Opstal, Seth R Bordenstein
Phylosymbiosis was recently proposed to describe the eco-evolutionary pattern, whereby the ecological relatedness of host-associated microbial communities parallels the phylogeny of related host species. Here, we test the prevalence of phylosymbiosis and its functional significance under highly controlled conditions by characterizing the microbiota of 24 animal species from four different groups (Peromyscus deer mice, Drosophila flies, mosquitoes, and Nasonia wasps), and we reevaluate the phylosymbiotic relationships of seven species of wild hominids...
November 2016: PLoS Biology
https://www.readbyqxmd.com/read/27859467/what-drives-parallel-evolution-how-population-size-and-mutational-variation-contribute-to-repeated-evolution
#13
Susan F Bailey, François Blanquart, Thomas Bataillon, Rees Kassen
Parallel evolution is the repeated evolution of the same phenotype or genotype in evolutionarily independent populations. Here, we use evolve-and-resequence experiments with bacteria and yeast to dissect the drivers of parallel evolution at the gene level. A meta-analysis shows that parallel evolution is often rare, but there is a positive relationship between population size and the probability of parallelism. We present a modeling approach to estimate the contributions of mutational and selective heterogeneity across a genome to parallel evolution...
November 15, 2016: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/27859247/repeated-intra-specific-divergence-in-lifespan-and-ageing-of-african-annual-fishes-along-an-aridity-gradient
#14
Radim Blažek, Matej Polačik, Petr Kačer, Alessandro Cellerino, Radomil Řežucha, Caroline Methling, Oldřich Tomášek, Kamila Syslová, Eva Terzibasi Tozzini, Tomáš Albrecht, Milan Vrtílek, Martin Reichard
Lifespan and ageing are substantially modified by natural selection. Across species, higher extrinsic (environmentally-related) mortality (and hence shorter life expectancy) selects for the evolution of more rapid ageing. However, among populations within species, high extrinsic mortality can lead to extended lifespan and slower ageing as a consequence of condition-dependent survival. Using within-species contrasts of eight natural populations of Nothobranchius fishes in common garden experiments, we demonstrate that populations originating from dry regions (with short life expectancy) had shorter intrinsic lifespans and a greater increase in mortality with age, more pronounced cellular and physiological deterioration (oxidative damage, tumor load), and a faster decline in fertility than populations from wetter regions...
November 17, 2016: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/27845672/gpu-based-point-cloud-superpositioning-for-structural-comparisons-of-protein-binding-sites
#15
Matthias Leinweber, Thomas Fober, Bernd Freisleben
In this paper, we present a novel approach to solve the labeled point cloud superpositioning problem for performing structural comparisons of protein binding sites. The solution is based on a parallel evolution strategy that operates on large populations and runs on GPU hardware. The proposed evolution strategy reduces the likelihood of getting stuck in a local optimum of the multimodal real-valued optimization problem represented by labeled point cloud superpositioning. The performance of the GPU-based parallel evolution strategy is compared to a previously proposed CPU-based sequential approach for labeled point cloud superpositioning, indicating that the GPU-based parallel evolution strategy leads to qualitatively better results and significantly shorter runtimes, with speed improvements of up to a factor of 1,500 for large populations...
November 7, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/27833851/overexpression-of-cop9-signalosome-subunits-csn7a-and-csn7b-exerts-different-effects-on-adipogenic-differentiation
#16
Xiaohua Huang, Jürgen Ordemann, Johann Pratschke, Wolfgang Dubiel
The COP9 signalosome (CSN) is an essential regulator of cullin-RING-ubiquitin (Ub) ligases (CRLs), which ubiquitinate important cellular regulators and target them for degradation by the Ub proteasome system (UPS). The CSN exhibits deneddylating activity localized on subunit CSN5, which removes the ubiquitin-like protein Nedd8 from the cullins of CRLs. CSN-mediated deneddylation is an important step in the process of CRL remodeling, in which new substrate recognition units are incorporated into Ub ligases to meet changed requirements for proteolysis in cells...
November 2016: FEBS Open Bio
https://www.readbyqxmd.com/read/27833102/parallel-evolution-of-passive-and-active-defence-in-land-snails
#17
Yuta Morii, Larisa Prozorova, Satoshi Chiba
Predator-prey interactions are major processes promoting phenotypic evolution. However, it remains unclear how predation causes morphological and behavioural diversity in prey species and how it might lead to speciation. Here, we show that substantial divergence in the phenotypic traits of prey species has occurred among closely related land snails as a result of adaptation to predator attacks. This caused the divergence of defensive strategies into two alternatives: passive defence and active defence. Phenotypic traits of the subarctic Karaftohelix land snail have undergone radiation in northeast Asia, and distinctive morphotypes generally coexist in the same regions...
November 11, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27832161/molecular-analysis-of-stromal-cells-induced-neural-differentiation-of-mouse-embryonic-stem-cells
#18
Ramila Joshi, James Carlton Buchanan, Sailaja Paruchuri, Nathan Morris, Hossein Tavana
Deriving specific neural cells from embryonic stem cells (ESCs) is a promising approach for cell replacement therapies of neurodegenerative diseases. When co-cultured with certain stromal cells, mouse ESCs (mESCs) differentiate efficiently to neural cells. In this study, a comprehensive gene and protein expression analysis of differentiating mESCs is performed over a two-week culture period to track temporal progression of cells from a pluripotent state to specific terminally-differentiated neural cells such as neurons, astrocytes, and oligodendrocytes...
2016: PloS One
https://www.readbyqxmd.com/read/27829356/alternative-evolution-of-a-spheroidal-colony-in-volvocine-algae-developmental-analysis-of-embryogenesis-in-astrephomene-volvocales-chlorophyta
#19
Shota Yamashita, Yoko Arakaki, Hiroko Kawai-Toyooka, Akira Noga, Masafumi Hirono, Hisayoshi Nozaki
BACKGROUND: Volvocine algae, which range from the unicellular Chlamydomonas to the multicellular Volvox with a germ-soma division of labor, are a model for the evolution of multicellularity. Within this group, the spheroidal colony might have evolved in two independent lineages: Volvocaceae and the goniacean Astrephomene. Astrephomene produces spheroidal colonies with posterior somatic cells. The feature that distinguishes Astrephomene from the volvocacean algae is lack of inversion during embryogenesis; the volvocacean embryo undergoes inversion after successive divisions to orient flagella toward the outside...
November 9, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27825516/adaptation-of-escherichia-coli-traversing-from-the-faecal-environment-to-the-urinary-tract
#20
Karen L Nielsen, Marc Stegger, Paul A Godfrey, Michael Feldgarden, Paal S Andersen, Niels Frimodt-Møller
The majority of extraintestinal pathogenic Escherichia coli (ExPEC) causing urinary tract infections (UTI) are found in the patient's own gut flora, but only limited knowledge is available on the potential adaptation that may occur in the bacteria in order to traverse the perineum and successfully infect the urinary tract. Here, matching pairs of faecal and UTI isolates from 42 patients were compared pairwise using in-depth whole-genome sequencing to investigate whether genetic changes were evident for successful colonization in these two different environments...
November 4, 2016: International Journal of Medical Microbiology: IJMM
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