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https://www.readbyqxmd.com/read/29330536/carbon-limitation-drives-gc-content-evolution-of-a-marine-bacterium-in-an-individual-based-genome-scale-model
#1
Ferdi L Hellweger, Yongjie Huang, Haiwei Luo
An important unanswered question in evolutionary genomics is the source of considerable variation of genomic base composition (GC content) even among organisms that share one habitat. Evolution toward GC-poor genomes has been considered a major adaptive pathway in the oligotrophic ocean, but GC-rich bacteria are also prevalent and highly successful in this environment. We quantify the contribution of multiple factors to the change of genomic GC content of Ruegeria pomeroyi DSS-3, a representative and GC-rich member in the globally abundant Roseobacter clade, using an agent-based model...
January 12, 2018: ISME Journal
https://www.readbyqxmd.com/read/29330348/weak-epistasis-may-drive-adaptation-in-recombining-bacteria
#2
Brian J Arnold, Michael U Gutmann, Yonatan H Grad, Samuel K Sheppard, Jukka Corander, Marc Lipsitch, William P Hanage
The impact of epistasis on the evolution of multilocus traits depends on recombination. While sexually-reproducing eukaryotes recombine so frequently that epistasis between polymorphisms is not considered to play a large role in short-term adaptation, many bacteria also recombine, some to the degree that their populations are described as 'panmictic' or 'freely recombining'. However, whether this recombination is sufficient to limit the ability of selection to act on epistatic contributions to fitness is unknown...
January 12, 2018: Genetics
https://www.readbyqxmd.com/read/29328713/egalitarianism-among-bubbles-in-porous-media-an-ostwald-ripening-derived-anticoarsening-phenomenon
#3
Ke Xu, Roger Bonnecaze, Matthew Balhoff
We show that smaller gas bubbles grow at the expense of larger bubbles and all bubbles approach the same surface curvature after long times in porous media. This anticoarsening effect is contrary to typical Ostwald ripening and leads to uniformly sized bubbles in a homogeneous medium. Evolution dynamics of bubble populations were measured, and mathematical models were developed that fit the experimental data well. Ostwald ripening is shown to be the driving mechanism in this anticoarsening phenomenon; however, the relationship between surface curvature and bubble size determined by the pore-throat geometric confinement reverses the ripening direction...
December 29, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/29327998/a-novel-scale-for-describing-visual-outcomes-in-patients-following-resection-of-lesions-affecting-the-optic-apparatus-the-unified-visual-function-scale
#4
Serge Makarenko, Vincent Ye, Peter A Gooderham, Ryojo Akagami
OBJECTIVE Historically, descriptions of visual acuity and visual field change following intracranial procedures have been very rudimentary. Clinicians and researchers have often used basic descriptions, such as "improved," "worsened," and "unchanged," to describe outcomes following resections of tumors affecting the optic apparatus. These descriptors are vague, difficult to quantify, and challenging to apply in a clinical perspective. Several groups have attempted to combine visual acuity and visual fields into a single assessment score, but these are not user-friendly...
January 12, 2018: Journal of Neurosurgery
https://www.readbyqxmd.com/read/29326272/antagonism-toward-the-intestinal-microbiota-and-its-effect-on-vibrio-cholerae-virulence
#5
Wenjing Zhao, Florence Caro, William Robins, John J Mekalanos
The bacterial type VI secretion system (T6SS) is a nanomachine that delivers toxic effector proteins into target cells, killing them. In mice, we found that the Vibrio cholerae T6SS attacks members of the host commensal microbiota in vivo, facilitating the pathogen's colonization of the gut. This microbial antagonistic interaction drives measurable changes in the pathogenicity of V. cholerae through enhanced intestinal colonization, expression of bacterial virulence genes, and activation of host innate immune genes...
January 12, 2018: Science
https://www.readbyqxmd.com/read/29322557/veni-vidi-vici-the-success-of-wtf-meiotic-drivers-in-fission-yeast
#6
José Fabricio López Hernández, Sarah E Zanders
Meiotic drivers are selfish DNA loci that can bias their own transmission into gametes. Due to their transmission advantages, meiotic drivers can spread in populations even if the drivers or linked variants decrease organismal fitness. Meiotic drive was first formally described in the 1950s and is thought to be a powerful force shaping eukaryotic genomes. Classic genetic analyses have detected the action of meiotic drivers in plants, filamentous fungi, insects, and vertebrates. Several of these drive systems have limited experimental tractability and relatively little is known about the molecular mechanisms of meiotic drive...
January 11, 2018: Yeast
https://www.readbyqxmd.com/read/29321898/sap-flow-characteristics-and-responses-to-summer-rainfall-for-pinus-tabulaeformis-and-hippophae-rhamnoides-in-the-loess-hilly-region-of-china
#7
Xu Wu, Yakun Tang, Yunming Chen, Jie Wen, Yuli Xie, Senbao Lu
As a major driving element of the structure and function of arid and semiarid ecosystems, rainfall is the essential factor limiting plant biological processes. To clarify the characteristics of transpiration and responses to summer rainfall, sap flow density (Fd) of Pinus tabulaeformis and Hippophae rhamnoides was monitored using thermal dissipation probes. In addition, midday leaf water potential (ψm) and leaf stomatal conductance (Gs) were also analyzed to determine water use strategies. The results indicated that the diurnal variation in the normalized Fd values exhibited a single-peak curve for P...
January 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29307030/the-neurobiology-of-climate-change
#8
Sean O'Donnell
Directional climate change (global warming) is causing rapid alterations in animals' environments. Because the nervous system is at the forefront of animals' interactions with the environment, the neurobiological implications of climate change are central to understanding how individuals, and ultimately populations, will respond to global warming. Evidence is accumulating for individual level, mechanistic effects of climate change on nervous system development and performance. Climate change can also alter sensory stimuli, changing the effectiveness of sensory and cognitive systems for achieving biological fitness...
January 6, 2018: Die Naturwissenschaften
https://www.readbyqxmd.com/read/29304821/impact-of-the-hiv-1-genetic-background-and-hiv-1-population-size-on-the-evolution-of-raltegravir-resistance
#9
Axel Fun, Thomas Leitner, Linos Vandekerckhove, Martin Däumer, Alexander Thielen, Bernd Buchholz, Andy I M Hoepelman, Elizabeth H Gisolf, Pauline J Schipper, Annemarie M J Wensing, Monique Nijhuis
BACKGROUND: Emergence of resistance against integrase inhibitor raltegravir in human immunodeficiency virus type 1 (HIV-1) patients is generally associated with selection of one of three signature mutations: Y143C/R, Q148K/H/R or N155H, representing three distinct resistance pathways. The mechanisms that drive selection of a specific pathway are still poorly understood. We investigated the impact of the HIV-1 genetic background and population dynamics on the emergence of raltegravir resistance...
January 5, 2018: Retrovirology
https://www.readbyqxmd.com/read/29303475/the-active-conceptual-framework-as-a-structural-equation-model
#10
Alden L Gross, Brennan R Payne, Ramon Casanova, Pega Davoudzadeh, Joseph M Dzierzewski, Sarah Farias, Tania Giovannetti, Edward H Ip, Michael Marsiske, George W Rebok, K Warner Schaie, Kelsey Thomas, Sherry Willis, Richard N Jones
Background/Study Context: Conceptual frameworks are analytic models at a high level of abstraction. Their operationalization can inform randomized trial design and sample size considerations. METHODS: The Advanced Cognitive Training for Independent and Vital Elderly (ACTIVE) conceptual framework was empirically tested using structural equation modeling (N=2,802). ACTIVE was guided by a conceptual framework for cognitive training in which proximal cognitive abilities (memory, inductive reasoning, speed of processing) mediate treatment-related improvement in primary outcomes (everyday problem-solving, difficulty with activities of daily living, everyday speed, driving difficulty), which in turn lead to improved secondary outcomes (health-related quality of life, health service utilization, mobility)...
January 5, 2018: Experimental Aging Research
https://www.readbyqxmd.com/read/29302610/what-theory-for-whom-and-in-which-context-reflections-on-the-application-of-theory-in-the-development-and-evaluation-of-complex-population-health-interventions
#11
Graham F Moore, Rhiannon E Evans
Recent years have seen a growing emphasis on the value of building and testing middle range theory throughout the development and evaluation of complex population health interventions. We agree that a coherent theoretical basis for intervention development, and use of evaluation to test key causal assumptions and build theory, are crucial. However, in this editorial, we argue that such recommendations have often been operationalised in somewhat simplistic terms with potentially perverse consequences, and that an uncritical assumption that an intervention explicitly based on theory is inherently superior carries significant risks...
December 2017: SSM—Population Health
https://www.readbyqxmd.com/read/29302276/haemoglobin-mediated-response-to-hyper-thermal-stress-in-the-keystone-species-daphnia-magna
#12
Maria Cuenca Cambronero, Bettina Zeis, Luisa Orsini
Anthropogenic global warming has become a major geological and environmental force driving drastic changes in natural ecosystems. Due to the high thermal conductivity of water and the effects of temperature on metabolic processes, freshwater ecosystems are among the most impacted by these changes. The ability to tolerate changes in temperature may determine species long-term survival and fitness. Therefore, it is critical to identify coping mechanisms to thermal and hyper-thermal stress in aquatic organisms...
January 2018: Evolutionary Applications
https://www.readbyqxmd.com/read/29299289/high-level-of-sperm-competition-may-increase-transfer-of-accessory-gland-products-carried-by-the-love-dart-of-land-snails
#13
Monica Lodi, Alexandra Staikou, Ruben Janssen, Joris M Koene
Postcopulatory adaptations that increase reproductive success compared to rivals, like the transfer of accessory gland products that promote paternity, are common when sperm competition occurs among males. In land snails, the dart shooting behavior and its adaptive significance, in promoting individual fitness through enhanced paternity of the successful dart shooter, have been considered such an adaptation. The fitness result gained is mediated by the transfer of mucus components on the love dart capable of altering the physiology of the receiver's reproductive tract...
December 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/29298052/new-insights-to-compare-and-choose-tktd-models-for-survival-based-on-an-inter-laboratory-study-for-lymnaea-stagnalis-exposed-to-cd
#14
Virgile Baudrot, Sara Preux, Virginie Ducrot, Alain Pavé, Sandrine Charles
Toxicokinetic-toxicodynamic (TKTD) models, as the General Unified Threshold model of Survival (GUTS), provide a consistent process-based framework compared to classical dose-response models to analyze both time and concentration-dependent data sets. However, the extent to which GUTS models (Stochastic Death (SD) and Individual Tolerance (IT)) lead to a better fitting than classical dose-response model at a given target time (TT) has poorly been investigated. Our paper highlights that GUTS estimates are generally more conservative and have a reduced uncertainty through smaller credible intervals for the studied data sets than classical TT approaches...
January 3, 2018: Environmental Science & Technology
https://www.readbyqxmd.com/read/29297505/determinants-and-clinical-implications-of-chromosomal-instability-in-cancer
#15
REVIEW
Laurent Sansregret, Bart Vanhaesebroeck, Charles Swanton
Aberrant chromosomal architecture, ranging from small insertions or deletions to large chromosomal alterations, is one of the most common characteristics of cancer genomes. Chromosomal instability (CIN) underpins much of the intratumoural heterogeneity observed in cancers and drives phenotypic adaptation during tumour evolution. Thus, an urgent need exists to increase our efforts to target CIN as if it were a molecular entity. Indeed, CIN accelerates the development of anticancer drug resistance, often leading to treatment failure and disease recurrence, which limit the effectiveness of most current therapies...
January 3, 2018: Nature Reviews. Clinical Oncology
https://www.readbyqxmd.com/read/29296711/klf1-directly-activates-expression-of-the-novel-fetal-globin-repressor-zbtb7a-lrf-in-erythroid-cells
#16
Laura J Norton, Alister P W Funnell, Jon Burdach, Beeke Wienert, Ryo Kurita, Yukio Nakamura, Sjaak Philipsen, Richard C M Pearson, Kate G R Quinlan, Merlin Crossley
Genes encoding the human β-like hemoglobin proteins undergo a developmental switch from fetal γ-globin to adult β-globin expression around the time of birth. β-hemoglobinopathies, such as sickle-cell disease and β-thalassemia, result from mutations affecting the adult β-globin gene. The only treatment options currently available carry significant adverse effects. Analyses of heritable variations in fetal hemoglobin (HbF) levels have provided evidence that reactivation of the silenced fetal γ-globin genes in adult erythroid cells is a promising therapy...
April 25, 2017: Blood Advances
https://www.readbyqxmd.com/read/29295937/hamilton-s-inclusive-fitness-maintains-heritable-altruism-polymorphism-through-rb-c
#17
Changcao Wang, Xin Lu
How can altruism evolve or be maintained in a selfish world? Hamilton's rule shows that the former process will occur when rb > c-the benefits to the recipients of an altruistic act b, weighted by the relatedness between the social partners r, exceed the costs to the altruists c-drives altruistic genotypes spreading against nonaltruistic ones. From this rule, we infer that altruistic genotypes will persist in a population by forming a stable heritable polymorphism with nonaltruistic genotypes if rb = c makes inclusive fitness of the two morphs equal...
January 2, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29291074/frequency-patterns-of-semantic-change-corpus-based-evidence-of-a-near-critical-dynamics-in-language-change
#18
Q Feltgen, B Fagard, J-P Nadal
It is generally believed that when a linguistic item acquires a new meaning, its overall frequency of use rises with time with an S-shaped growth curve. Yet, this claim has only been supported by a limited number of case studies. In this paper, we provide the first corpus-based large-scale confirmation of the S-curve in language change. Moreover, we uncover another generic pattern, a latency phase preceding the S-growth, during which the frequency remains close to constant. We propose a usage-based model which predicts both phases, the latency and the S-growth...
November 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/29290103/mechanisms-of-thermal-adaptation-and-evolutionary-potential-of-conspecific-populations-to-changing-environments
#19
Zhongqi Chen, Anthony P Farrell, Amanda Matala, Shawn R Narum
Heterogeneous and ever-changing thermal environments drive the evolution of populations and species, especially when extreme conditions increase selection pressure for traits influencing fitness. However, projections of biological diversity under scenarios of climate change rarely consider evolutionary adaptive potential of natural species. In this study, we tested for mechanistic evidence of evolutionary thermal adaptation among ecologically divergent redband trout populations (Oncorhynchus mykiss gairdneri) in cardiorespiratory function, cellular response and genomic variation...
December 31, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29273640/using-cellular-fitness-to-map-the-structure-and-function-of-a-major-facilitator-superfamily-effluxer
#20
Anisha M Perez, Marcella M Gomez, Prashant Kalvapalle, Erin O'Brien-Gilbert, Matthew R Bennett, Yousif Shamoo
The major facilitator superfamily (MFS) effluxers are prominent mediators of antimicrobial resistance. The biochemical characterization of MFS proteins is hindered by their complex membrane environment that makes in vitro biochemical analysis challenging. Since the physicochemical properties of proteins drive the fitness of an organism, we posed the question of whether we could reverse that relationship and derive meaningful biochemical parameters for a single protein simply from fitness changes it confers under varying strengths of selection...
December 22, 2017: Molecular Systems Biology
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