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https://www.readbyqxmd.com/read/28087782/mutation-supply-and-relative-fitness-shape-the-genotypes-of-ciprofloxacin-resistant-escherichia-coli
#1
Douglas L Huseby, Franziska Pietsch, Gerrit Brandis, Linnéa Garoff, Angelica Tegehall, Diarmaid Hughes
Ciprofloxacin is an important antibacterial drug targeting Type II topoisomerases, highly active against Gram-negatives including Escherichia coli The evolution of resistance to ciprofloxacin in E. coli always requires multiple genetic changes, usually including mutations affecting two different drug target genes, gyrA and parC Resistant mutants selected in vitro or in vivo can have many different mutations in target genes and efflux regulator genes that contribute to resistance. Among resistant clinical isolates the genotype, gyrA S83L D87N, parC S80I is significantly overrepresented suggesting that it has a selective advantage...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087070/can-evolution-supply-what-ecology-demands
#2
REVIEW
Hanna Kokko, Anurag Chaturvedi, Daniel Croll, Martin C Fischer, Frédéric Guillaume, Sophie Karrenberg, Ben Kerr, Gregor Rolshausen, Jessica Stapley
A simplistic view of the adaptive process pictures a hillside along which a population can climb: when ecological 'demands' change, evolution 'supplies' the variation needed for the population to climb to a new peak. Evolutionary ecologists point out that this simplistic view can be incomplete because the fitness landscape changes dynamically as the population evolves. Geneticists meanwhile have identified complexities relating to the nature of genetic variation and its architecture, and the importance of epigenetic variation is under debate...
January 10, 2017: Trends in Ecology & Evolution
https://www.readbyqxmd.com/read/28076351/ultra-fine-scale-spatially-integrated-mapping-of-habitat-and-occupancy-using-structure-from-motion
#3
Philip McDowall, Heather J Lynch
Organisms respond to and often simultaneously modify their environment. While these interactions are apparent at the landscape extent, the driving mechanisms often occur at very fine spatial scales. Structure-from-Motion (SfM), a computer vision technique, allows the simultaneous mapping of organisms and fine scale habitat, and will greatly improve our understanding of habitat suitability, ecophysiology, and the bi-directional relationship between geomorphology and habitat use. SfM can be used to create high-resolution (centimeter-scale) three-dimensional (3D) habitat models at low cost...
2017: PloS One
https://www.readbyqxmd.com/read/28074648/mispacking-and-the-fitness-landscape-of-the-green-fluorescent-protein-chromophore-milieu
#4
Shounak Banerjee, Christian D Schenkelberg, Thomas B Jordan, Julia M Reimertz, Emily E Crone, Donna E Crone, Christopher Bystroff
The auto-catalytic maturation of the chromophore in green fluorescent protein (GFP) was thought to require the precise positioning of the side chains surrounding it in the core of the protein, many of which are strongly conserved among homologous fluorescent proteins. In this study, we screened for green fluorescence in an exhaustive set of point mutations of seven residues that make up the chromophore microenvironment, excluding R96 and E222 because mutations of these positions have been previously characterized...
January 11, 2017: Biochemistry
https://www.readbyqxmd.com/read/28073389/the-distribution-of-echinostome-parasites-in-ponds-and-implications-for-larval-anuran-survival
#5
John A Marino, Manja P Holland, Earl E Werner
Parasites can influence host population dynamics, community composition and evolution. Prediction of these effects, however, requires an understanding of the influence of ecological context on parasite distributions and the consequences of infection for host fitness. We address these issues with an amphibian - trematode (Digenea: Echinostomatidae) host-parasite system. We initially performed a field survey of trematode infection in first (snail) and second (larval green frog, Rana clamitans) intermediate hosts over 5 years across a landscape of 23 ponds in southeastern Michigan...
January 11, 2017: Parasitology
https://www.readbyqxmd.com/read/28058767/do-group-dynamics-affect-colour-morph-clines-during-a-range-shift
#6
Lesley T Lancaster, Rachael Y Dudaniec, Bengt Hansson, Erik I Svensson
Species exhibiting colour-polymorphism are thought to have an ecological advantage at the landscape scale, because spatial segregation of alternatively-adapted ecotypes into diverse habitats can increase the total species' niche breadth and thus confer greater geographic range size. However, morph frequencies are also influenced by intra-populational processes such as frequency- or density-dependent social interactions. To identify how social feedback may affect clinal variation in morph frequencies, we investigated reciprocal interactions between morph-specific thermal tolerance, local climatic conditions, and social environments, in the context of a colour-morph frequency cline associated with a recent range expansion in blue-tailed damselflies (Ischnura elegans) in Sweden...
January 6, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28054831/lessons-learned-from-an-unstable-genomic-landscape
#7
Charles L Limoli
PURPOSE: This brief historical perspective will highlight the many accomplishments of the late William "Bill" Morgan, and how his laboratory during the mid-1990s shaped the field of genomic instability. Bill focused on the processes responsible for radiation-induced genomic instability, and while ionizing radiation was known to induce this phenomenon, the precise causes were poorly understood. Here we revisit Bill's unique approach to these problems, as he advocated the use of novel mammalian cell lines to tease apart the mechanisms responsible for destabilizing an otherwise stable nuclear genome...
January 5, 2017: International Journal of Radiation Biology
https://www.readbyqxmd.com/read/28049817/global-urban-signatures-of-phenotypic-change-in-animal-and-plant-populations
#8
Marina Alberti, Cristian Correa, John M Marzluff, Andrew P Hendry, Eric P Palkovacs, Kiyoko M Gotanda, Victoria M Hunt, Travis M Apgar, Yuyu Zhou
Humans challenge the phenotypic, genetic, and cultural makeup of species by affecting the fitness landscapes on which they evolve. Recent studies show that cities might play a major role in contemporary evolution by accelerating phenotypic changes in wildlife, including animals, plants, fungi, and other organisms. Many studies of ecoevolutionary change have focused on anthropogenic drivers, but none of these studies has specifically examined the role that urbanization plays in ecoevolution or explicitly examined its mechanisms...
January 3, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28045264/exploring-the-mutational-robustness-of-nucleic-acids-by-searching-genotype-neighborhoods-in-sequence-space
#9
Qingtong Zhou, Xianbao Sun, Xiaole Xia, Zhou Fan, Zhaofeng Luo, Suwen Zhao, Eugene Shakhnovich, Haojun Liang
To assess the mutational robustness of nucleic acids, many genome- and protein-level studies have been performed, where nucleic acids are treated as genetic information carriers and transferrers. However, the molecular mechanisms through which mutations alter the structural, dynamic, and functional properties of nucleic acids are poorly understood. Here we performed a SELEX in silico study to investigate the fitness distribution of the l-Arm-binding aptamer genotype neighborhoods. Two novel functional genotype neighborhoods were isolated and experimentally verified to have comparable fitness as the wild-type...
January 5, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28028132/novel-candidate-genes-underlying-extreme-trophic-specialization-in-caribbean-pupfishes
#10
Joseph A McGirr, Christopher H Martin
The genetic changes responsible for evolutionary transitions from generalist to specialist phenotypes are poorly understood. Here we examine the genetic basis of craniofacial traits enabling novel trophic specialization in a sympatric radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas. This recent radiation consists of a generalist species and two novel specialists: a small-jawed 'snail-eater' and a large-jawed 'scale-eater.' We genotyped 12 million SNPs by whole-genome resequencing of 37 individuals of all three species from nine populations and integrated genome-wide divergence scans with association mapping to identify divergent regions containing putatively causal SNPs affecting jaw size - the most rapidly diversifying trait in this radiation...
December 26, 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28007889/spiraling-complexity-a-test-of-the-snowball-effect-in-a-computational-model-of-rna-folding
#11
Ata Kalirad, Ricardo B R Azevedo
As of January 9, 2017, this article has been removed at the request of the authors. Their re-evaluation of some of the data resulted in a change that does not alter the central conclusions of the paper, but changes the presentation of the data in some of the figures. A corrected version will be made available. In the meantime, we ask readers to refrain from citing or sharing the incorrect version of the article published on December 22, 2016.
22, 2016: Genetics
https://www.readbyqxmd.com/read/28003445/distance-decay-effect-in-stone-tool-transport-by-wild-chimpanzees
#12
Lydia V Luncz, Tomos Proffitt, Lars Kulik, Michael Haslam, Roman M Wittig
Stone tool transport leaves long-lasting behavioural evidence in the landscape. However, it remains unknown how large-scale patterns of stone distribution emerge through undirected, short-term transport behaviours. One of the longest studied groups of stone-tool-using primates are the chimpanzees of the Taï National Park in Ivory Coast, West Africa. Using hammerstones left behind at chimpanzee Panda nut-cracking sites, we tested for a distance-decay effect, in which the weight of material decreases with increasing distance from raw material sources...
December 28, 2016: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/27984632/local-epiphyte-establishment-and-future-metapopulation-dynamics-in-landscapes-with-different-spatio-temporal-properties
#13
Rocío Belinchón, Phil J Harrison, Louise Mair, Gergely Várkonyi, Tord Snäll
Understanding the relative importance of different ecological processes on the metapopulation dynamics of species is the basis for accurately forecasting metapopulation size in fragmented landscapes. Successful local colonization depends on both species dispersal range and how local habitat conditions affect establishment success. Moreover, there is limited understanding of the effects of different spatio-temporal landscape properties on future metapopulation size. We test which factors drive the future metapopulation size of the epiphytic model lichen species Lobaria pulmonaria in a managed forest landscape...
December 16, 2016: Ecology
https://www.readbyqxmd.com/read/27974464/affinity-maturation-of-a-cyclic-peptide-handle-for-therapeutic-antibodies-using-deep-mutational-scanning
#14
Martijn van Rosmalen, Brian M G Janssen, Nathalie M Hendrikse, Ardjan J van der Linden, Pascal A Pieters, Dave Wanders, Tom F A de Greef, Maarten Merkx
Meditopes are cyclic peptides that bind in a specific pocket in the antigen-binding fragment (Fab) of a therapeutic antibody such as cetuximab. Provided their moderate affinity can be enhanced, meditope peptides could be used as a specific non-covalent and paratope-independent handles in targeted drug delivery, molecular imaging and therapeutic drug monitoring. Here we show that the affinity of a recently reported meditope for cetuximab can be substantially enhanced using a combination of yeast display and deep mutational scanning...
December 14, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27973606/evolution-at-sutures-and-centers-recombination-can-aid-adaptation-of-spatially-structured-populations-on-rugged-fitness-landscapes
#15
Jacob D Cooper, Benjamin Kerr
Epistatic interactions among genes can give rise to rugged fitness landscapes, in which multiple "peaks" of high-fitness allele combinations are separated by "valleys" of low-fitness genotypes. How populations traverse rugged fitness landscapes is a long-standing question in evolutionary biology. Sexual reproduction may affect how a population moves within a rugged fitness landscape. Sex may generate new high-fitness genotypes by recombination, but it may also destroy high-fitness genotypes by shuffling the genes of a fit parent with a genetically distinct mate, creating low-fitness offspring...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27941984/tropical-forest-fragmentation-limits-movements-but-not-occurrence-of-a-generalist-pollinator-species
#16
Noelia L Volpe, W Douglas Robinson, Sarah J K Frey, Adam S Hadley, Matthew G Betts
Habitat loss and fragmentation influence species distributions and therefore ecological processes that depend upon them. Pollination may be particularly susceptible to fragmentation, as it depends on frequent pollinator movement. Unfortunately, most pollinators are too small to track efficiently which has precluded testing the hypothesis that habitat fragmentation reduces or eliminates pollen flow by disrupting pollinator movement. We used radio-telemetry to examine space use of the green hermit hummingbird (Phaethornis guy), an important 'hub' pollinator of understory flowering plants across substantial portions of the neotropics and the primary pollinator of a keystone plant which shows reduced pollination success in fragmented landscapes...
2016: PloS One
https://www.readbyqxmd.com/read/27936909/variation-in-the-use-of-open-pyeloplasty-minimally-invasive-pyeloplasty-and-endopyelotomy-for-the-treatment-of-ureteropelvic-junction-obstruction-in-adults
#17
Bruce L Jacobs, Julie C Lai, Rachana Seelam, Janet M Hanley, J Stuart Wolf, Brent K Hollenbeck, John M Hollingsworth, Andrew W Dick, Claude M Setodji, Christopher S Saigal
BACKGROUND AND PURPOSE: Ureteropelvic junction obstruction is a common condition that can be treated with open pyeloplasty, minimally invasive pyeloplasty, and endopyelotomy. While all these treatments are effective, the extent to which they are used is unclear. We sought to examine the dissemination of these treatments. PATIENTS AND METHODS: Using the MarketScan(®) database, we identified adults 18 to 64 years old who underwent treatment for ureteropelvic junction obstruction between 2002 and 2010...
January 5, 2017: Journal of Endourology
https://www.readbyqxmd.com/read/27935934/beyond-the-hypercube-evolutionary-accessibility-of-fitness-landscapes-with-realistic-mutational-networks
#18
Marcin Zagorski, Zdzislaw Burda, Bartlomiej Waclaw
Evolutionary pathways describe trajectories of biological evolution in the space of different variants of organisms (genotypes). The probability of existence and the number of evolutionary pathways that lead from a given genotype to a better-adapted genotype are important measures of accessibility of local fitness optima and the reproducibility of evolution. Both quantities have been studied in simple mathematical models where genotypes are represented as binary sequences of two types of basic units, and the network of permitted mutations between the genotypes is a hypercube graph...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27933091/spatially-heterogeneous-environmental-selection-strengthens-evolution-of-reproductively-isolated-populations-in-a-dobzhansky-muller-system-of-hybrid-incompatibility
#19
Samuel A Cushman, Erin L Landguth
Within-species hybrid incompatibility can arise when combinations of alleles at more than one locus have low fitness but where possession of one of those alleles has little or no fitness consequence for the carriers. Limited dispersal with small numbers of mate potentials alone can lead to the evolution of clusters of reproductively isolated genotypes despite the absence of any geographical barriers or heterogeneous selection. In this paper, we explore how adding heterogeneous natural selection on the genotypes (e...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27932215/the-land-use-legacy-effect-towards-a-mechanistic-understanding-of-time-lagged-water-quality-responses-to-land-use-cover
#20
Sherry L Martin, Daniel B Hayes, Anthony D Kendall, David W Hyndman
Numerous studies have linked land use/land cover (LULC) to aquatic ecosystem responses, however only a few have included the dynamics of changing LULC in their analysis. In this study, we explicitly recognize changing LULC by linking mechanistic groundwater flow and travel time models to a historical time series of LULC, creating a land-use legacy map. We then illustrate the utility of legacy maps to explore relationships between dynamic LULC and lake water chemistry. We tested two main concepts about mechanisms linking LULC and lake water chemistry: groundwater pathways are an important mechanism driving legacy effects; and, LULC over multiple spatial scales is more closely related to lake chemistry than LULC over a single spatial scale...
February 1, 2017: Science of the Total Environment
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