Quasispecies Theory for Evolution of Modularity

Biological systems are modular, and this modularity evolves over time and in different environments. A number of observations have been made of increased modularity in biological systems under increased environmental pressure. We here develop a quasispecies theory for the dynamics of modularity in populations of these systems. We show how the steady-state fitness in a randomly changing environment can be computed. We derive a fluctuation dissipation relation for the rate of change of modularity and use it to derive a relationship between rate of environmental changes and rate of growth of modularity. We also find a principle of least action for the evolved modularity at steady state. Finally, we compare our predictions to simulations of protein evolution and find them to be consistent.Comment: 21 pages, 4 figures; presentation reordered; to appear in Phys. Rev.

Quantitative surface normal measurement by a wavefront camera

A compact wavefront camera that allows users to quantitatively measure the intensity and wavefront at a remote object plane is reported. The camera is built from a chip-scale wavefront sensor that we previously developed. By measuring the wavefront of the image and calibrating the wavefront relationship between the image and object planes, the wavefront at the object plane can be computed and the surface normal of the object can be derived. We built a prototype camera and calibrated the wavefront relationship. In a proof-of-concept experiment, a set of concave mirrors with different focal lengths (50–200 mm), were imaged. The results agree well with their expected values. To demonstrate the application of the camera, we applied this method to measure the deformation of a microfluidic channel under pressure

Two Adjacent Phenylalanines In the NMDA Receptor GluN2A Subunit M3 Domain Interactively Regulate Alcohol Sensitivity and Ion Channel Gating

The N-methyl-d-aspartate (NMDA) receptor is a key target of ethanol action in the central nervous system. Alcohol inhibition of NMDA receptor function involves small clusters of residues in the third and fourth membrane-associated (M) domains. Previous results from this laboratory have shown that two adjacent positions in the M3 domain, F636 and F637, can powerfully regulate alcohol sensitivity and ion channel gating. In this study, we report that these positions interact with one another in the regulation of both NMDA receptor gating and alcohol action. Using dual mutant cycle analysis, we detected interactions among various substitution mutants at these positions with respect to regulation of glutamate EC50, steady-state to peak current ratios (Iss:Ip), mean open time, and ethanol IC50. This interaction apparently involves a balancing of forces on the M3 helix, such that the disruption of function due to a substitution at one position can be reversed by a similar substitution at the other position. For example, tryptophan substitution at F636 or F637 increased or decreased channel mean open time, respectively, but tryptophan substitution at both positions did not alter open time. Interestingly, the effects of a number of mutations on receptor kinetics and ethanol sensitivity appeared to depend upon subtle structural differences, such as those between the isomeric amino acids leucine and isoleucine, as they could not be explained on the basis of sidechain molecular volume or hydrophilicity

A new adaptive backpropagation algorithm based on Lyapunov stability theory for neural networks

A new adaptive backpropagation (BP) algorithm based on Lyapunov stability theory for neural networks is developed in this paper. It is shown that the candidate of a Lyapunov function V(k) of the tracking error between the output of a neural network and the desired reference signal is chosen first, and the weights of the neural network are then updated, from the output layer to the input layer, in the sense that DeltaV(k)=V(k)-V(k-1)<0. The output tracking error can then asymptotically converge to zero according to Lyapunov stability theory. Unlike gradient-based BP training algorithms, the new Lyapunov adaptive BP algorithm in this paper is not used for searching the global minimum point along the cost-function surface in the weight space, but it is aimed at constructing an energy surface with a single global minimum point through the adaptive adjustment of the weights as the time goes to infinity. Although a neural network may have bounded input disturbances, the effects of the disturbances can be eliminated, and asymptotic error convergence can be obtained. The new Lyapunov adaptive BP algorithm is then applied to the design of an adaptive filter in the simulation example to show the fast error convergence and strong robustness with respect to large bounded input disturbance

A novel consolidation-based representative volume element for granular materials and its application for the characterization of the mechanical response of sand during impact loading

Open Access funded by European Structural Integrity Society Defense Threat Reduction Agency (DTRA), Grant No: HDTRA1-12-1-004

Rapid Invasion of Spartina alterniflora in the Coastal Zone of Mainland China: New Observations from Landsat OLI Images

Plant invasion imposes significant threats to biodiversity and ecosystem function. Thus, monitoring the spatial pattern of invasive plants is vital for effective ecosystem management. Spartina alterniflora (S. alterniflora) has been one of the most prevalent invasive plants along the China coast, and its spread has had severe ecological consequences. Here, we provide new observation from Landsat operational land imager (OLI) images. Specifically, 43 Landsat-8 OLI images from 2014 to 2016, a combination of object-based image analysis (OBIA) and support vector machine (SVM) methods, and field surveys covering the whole coast were used to construct an up-to-date dataset for 2015 and investigate the spatial variability of S. alterniflora in the coastal zone of mainland China. The classification results achieved good estimation, with a kappa coefficient of 0.86 and 96% overall accuracy. Our results revealed that there was approximately 545.80 km2 of S. alterniflora distributed in the coastal zone of mainland China in 2015, from Hebei to Guangxi provinces. Nearly 92% of the total area of S. alterniflora was distributed within four provinces: Jiangsu, Shanghai, Zhejiang, and Fujian. Seven national nature reserves invaded by S. alterniflora encompassed approximately one-third (174.35 km2) of the total area of S. alterniflora over mainland China. The Yancheng National Nature Reserve exhibited the largest area of S. alterniflora (115.62 km2) among the reserves. Given the rapid and extensive expansion of S. alterniflora in the 40 years since its introduction and its various ecological effects, geospatially varied responding decisions are needed to promote sustainable coastal ecosystems

Dynamics of photosynthesis in Eichhornia crassipes Solms of Jiangsu of China and their influencing factors

With LI-6400 portable photosynthesis system, the photosynthetic characteristics of artificially cultured Eichhornia crassipes in Jiangsu, China, were monitored from June 1 to November 14, 2009. Both the net photosynthetic rate (Pn) in different positions and light and temperature-response curves of the top fourth leaf were measured in an open-circuit gas channel system in June, July, and August, respectively. The top third to sixth leaves matured with a high Pn in August, 2009. The values of the maximum net photosynthesis (Pmax), light component point (LCP) and apparent quantum efficiency (AQE) of the top fourth leaf of E. crassipes were 34.5±0.72 and 20.25±3.6 μmol m-2s-1 as well as 0.0532±0.0014, respectively, significantly higher than those in rice and maize. The light-saturation point (LSP) of leaves of E. crassipes was 2358±69 μmol m-2s-1, significantly higher than that in rice and much close to that in maize. The natural light intensity and temperatures in Jiangsu are suitable for E. crassipes to rapidly grow but not good enough for it to show the maximum internal photosynthetic capacity from the perspective of photosynthetic physiology, thus resulting in its low biomass in this region.Key words: Eichhornia crassipes, photosynthetic characteristics, environmental influencing factors

Autophagy regulation in heme-induced neutrophil activation is associated with microRNA expression on transfusion-related acute lung injury

AbstractTransfusion-related acute lung injury (TRALI) is the leading cause of death after transfusion therapy. The pathogenesis of TRALI is associated with neutrophil activation in the lungs, causing endothelial damage and capillary leakage, and thus neutrophil extravasation. Heme-related molecules derived from the hemolysis of red blood cell components have been recognized as a stimulator, inducing neutrophil activation at TRALI. To investigate post-transcriptional changes of the neutrophil at TRALI, we performed heme-related molecules induced reactive oxygen species production in the neutrophil as a model. Neutrophils were isolated from heparinized peripheral blood and stimulated with heme-related molecules. After stimulation, reactive oxygen species production, degranulation, phagocytosis activity, and miRNA expression profile of neutrophil were analyzed by luminol assay, flow cytometry, and real-time polymerase chain reaction. The expression of miRNA targeting NADPH oxidase and autophagy in the neutrophil activation of TRALI was explored. The expression profile of miRNAs will be a useful predictor of disease severity and for the grading of patients for transfusion