1,422 research outputs found
Target search on a dynamic DNA molecule
We study a protein-DNA target search model with explicit DNA dynamics
applicable to in vitro experiments. We show that the DNA dynamics plays a
crucial role for the effectiveness of protein "jumps" between sites distant
along the DNA contour but close in 3D space. A strongly binding protein that
searches by 1D sliding and jumping alone, explores the search space less
redundantly when the DNA dynamics is fast on the timescale of protein jumps
than in the opposite "frozen DNA" limit. We characterize the crossover between
these limits using simulations and scaling theory. We also rationalize the slow
exploration in the frozen limit as a subtle interplay between long jumps and
long trapping times of the protein in "islands" within random DNA
configurations in solution.Comment: manuscript and supplementary material combined into a single documen
Reduced tillage, but not organic matter input, increased nematode diversity and food web stability in European longâterm field experiments
Soil nematode communities and food web indices can inform about the complexity, nutrient flows and decomposition pathways of soil food webs, reflecting soil quality. Relative abundance of nematode feeding and lifeâhistory groups are used for calculating food web indices, i.e., maturity index (MI), enrichment index (EI), structure index (SI) and channel index (CI). Molecular methods to study nematode communities potentially offer advantages compared to traditional methods in terms of resolution, throughput, cost and time. In spite of such advantages, molecular data have not often been adopted so far to assess the effects of soil management on nematode communities and to calculate these food web indices. Here, we used highâthroughput amplicon sequencing to investigate the effects of tillage (conventional vs. reduced) and organic matter addition (low vs. high) on nematode communities and food web indices in 10 European longâterm field experiments and we assessed the relationship between nematode communities and soil parameters. We found that nematode communities were more strongly affected by tillage than by organic matter addition. Compared to conventional tillage, reduced tillage increased nematode diversity (23% higher Shannon diversity index), nematode community stability (12% higher MI), structure (24% higher SI), and the fungal decomposition channel (59% higher CI), and also the number of herbivorous nematodes (70% higher). Total and labile organic carbon, available K and microbial parameters explained nematode community structure. Our findings show that nematode communities are sensitive indicators of soil quality and that molecular profiling of nematode communities has the potential to reveal the effects of soil management on soil quality
Poisson transition rates from time-domain measurements with finite bandwidth
In time-domain measurements of a Poisson two-level system, the observed
transition rates are always smaller than those of the actual system, a general
consequence of finite measurement bandwidth in an experiment. This
underestimation of the rates is significant even when the measurement and
detection apparatus is ten times faster than the process under study. We derive
here a quantitative form for this correction using a straightforward
state-transition model that includes the detection apparatus, and provide a
method for determining a system's actual transition rates from
bandwidth-limited measurements. We support our results with computer
simulations and experimental data from time-domain measurements of
quasiparticle tunneling in a single-Cooper-pair transistor.Comment: 4 pages, 5 figure
On the action potential as a propagating density pulse and the role of anesthetics
The Hodgkin-Huxley model of nerve pulse propagation relies on ion currents
through specific resistors called ion channels. We discuss a number of
classical thermodynamic findings on nerves that are not contained in this
classical theory. Particularly striking is the finding of reversible heat
changes, thickness and phase changes of the membrane during the action
potential. Data on various nerves rather suggest that a reversible density
pulse accompanies the action potential of nerves. Here, we attempted to explain
these phenomena by propagating solitons that depend on the presence of
cooperative phase transitions in the nerve membrane. These transitions are,
however, strongly influenced by the presence of anesthetics. Therefore, the
thermodynamic theory of nerve pulses suggests a explanation for the famous
Meyer-Overton rule that states that the critical anesthetic dose is linearly
related to the solubility of the drug in the membranes.Comment: 13 pages, 8 figure
Adaptive evolution of molecular phenotypes
Molecular phenotypes link genomic information with organismic functions,
fitness, and evolution. Quantitative traits are complex phenotypes that depend
on multiple genomic loci. In this paper, we study the adaptive evolution of a
quantitative trait under time-dependent selection, which arises from
environmental changes or through fitness interactions with other co-evolving
phenotypes. We analyze a model of trait evolution under mutations and genetic
drift in a single-peak fitness seascape. The fitness peak performs a
constrained random walk in the trait amplitude, which determines the
time-dependent trait optimum in a given population. We derive analytical
expressions for the distribution of the time-dependent trait divergence between
populations and of the trait diversity within populations. Based on this
solution, we develop a method to infer adaptive evolution of quantitative
traits. Specifically, we show that the ratio of the average trait divergence
and the diversity is a universal function of evolutionary time, which predicts
the stabilizing strength and the driving rate of the fitness seascape. From an
information-theoretic point of view, this function measures the
macro-evolutionary entropy in a population ensemble, which determines the
predictability of the evolutionary process. Our solution also quantifies two
key characteristics of adapting populations: the cumulative fitness flux, which
measures the total amount of adaptation, and the adaptive load, which is the
fitness cost due to a population's lag behind the fitness peak.Comment: Figures are not optimally displayed in Firefo
Molecular mechanisms of inflammation and tissue injury after major trauma-is complement the "bad guy"?
Trauma represents the leading cause of death among young people in industrialized countries. Recent clinical and experimental studies have brought increasing evidence for activation of the innate immune system in contributing to the pathogenesis of trauma-induced sequelae and adverse outcome. As the "first line of defense", the complement system represents a potent effector arm of innate immunity, and has been implicated in mediating the early posttraumatic inflammatory response. Despite its generic beneficial functions, including pathogen elimination and immediate response to danger signals, complement activation may exert detrimental effects after trauma, in terms of mounting an "innocent bystander" attack on host tissue. Posttraumatic ischemia/reperfusion injuries represent the classic entity of complement-mediated tissue damage, adding to the "antigenic load" by exacerbation of local and systemic inflammation and release of toxic mediators. These pathophysiological sequelae have been shown to sustain the systemic inflammatory response syndrome after major trauma, and can ultimately contribute to remote organ injury and death. Numerous experimental models have been designed in recent years with the aim of mimicking the inflammatory reaction after trauma and to allow the testing of new pharmacological approaches, including the emergent concept of site-targeted complement inhibition. The present review provides an overview on the current understanding of the cellular and molecular mechanisms of complement activation after major trauma, with an emphasis of emerging therapeutic concepts which may provide the rationale for a "bench-to-bedside" approach in the design of future pharmacological strategies
Relationship between food waste, diet quality, and environmental sustainability
Improving diet quality while simultaneously reducing environmental impact is a critical focus globally. Metrics linking diet quality and sustainability have typically focused on a limited suite of indicators, and have not included food waste. To address this important research gap, we examine the relationship between food waste, diet quality, nutrient waste, and multiple measures of sustainability: use of cropland, irrigation water, pesticides, and fertilizers. Data on food intake, food waste, and application rates of agricultural amendments were collected from diverse US government sources. Diet quality was assessed using the Healthy Eating Index-2015. A biophysical simulation model was used to estimate the amount of cropland associated with wasted food. This analysis finds that US consumers wasted 422g of food per person daily, with 30 million acres of cropland used to produce this food every year. This accounts for 30% of daily calories available for consumption, one-quarter of daily food (by weight) available for consumption, and 7% of annual cropland acreage. Higher quality diets were associated with greater amounts of food waste and greater amounts of wasted irrigation water and pesticides, but less cropland waste. This is largely due to fruits and vegetables, which are health-promoting and require small amounts of cropland, but require substantial amounts of agricultural inputs. These results suggest that simultaneous efforts to improve diet quality and reduce food waste are necessary. Increasing consumersâ knowledge about how to prepare and store fruits and vegetables will be one of the practical solutions to reducing food waste
Impact of charge transport on current voltage characteristics and power conversion efficiency of organic solar cells
This work elucidates the impact of charge transport on the photovoltaic properties of organic solar cells. Here we show that the analysis of current-voltage curves of organic solar cells under illumination with the Shockley equation results in values for ideality factor, photo-current and parallel resistance, which lack physical meaning. Drift-diffusion simulations for a wide range of charge-carrier mobilities and illumination intensities reveal significant carrier accumulation caused by poor transport properties, which is not included in the Shockley equation. As a consequence, the separation of the quasi Fermi levels in the organic photoactive layer (internal voltage) differs substantially from the external voltage for almost all conditions. We present a new analytical model, which considers carrier transport explicitly. The model shows excellent agreement with full drift-diffusion simulations over a wide range of mobilities and illumination intensities, making it suitable for realistic efficiency predictions for organic solar cells
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