Robust filtering for stochastic genetic regulatory networks with time-varying delay

This paper addresses the robust filtering problem for a class of linear genetic regulatory networks (GRNs) with stochastic disturbances, parameter uncertainties and time delays. The parameter uncertainties are assumed to reside in a polytopic region, the stochastic disturbance is state-dependent described by a scalar Brownian motion, and the time-varying delays enter into both the translation process and the feedback regulation process. We aim to estimate the true concentrations of mRNA and protein by designing a linear filter such that, for all admissible time delays, stochastic disturbances as well as polytopic uncertainties, the augmented state estimation dynamics is exponentially mean square stable with an expected decay rate. A delay-dependent linear matrix inequality (LMI) approach is first developed to derive sufficient conditions that guarantee the exponential stability of the augmented dynamics, and then the filter gains are parameterized in terms of the solution to a set of LMIs. Note that LMIs can be easily solved by using standard software packages. A simulation example is exploited in order to illustrate the effectiveness of the proposed design procedures.     

Photosynthetic electron transport and proton flux under moderate heat stress

Moderate heat stress has been reported to increase PSI cyclic electron flow (CEF). We subjected leaves of Arabidopsis (Arabidopsis thaliana) mutants disrupted in the regulation of one or the other pathway of CEF flow—crr2 (chlororespiratory reduction, deficient in regulation of chloroplast NAD(P)H dehydrogenase-dependent CEF) and pgr5 (proton gradient regulation, proposed to have reduced efficiency of antimycin-A-sensitive-CEF regulation) to moderate heat stress. Light-adapted leaves were switched from 23 to 40°C in 2 min. Gas exchange, chlorophyll fluorescence, the electrochromic shift (ECS), and P700 were measured. Photosynthesis of crr2 and pgr5 was more sensitive to heat and had less ability to recover than the genetic background gl. The proton conductance in light was increased by heat and it was twice as much in pgr5, which had much smaller light-induced proton motive force. We confirmed that P700 becomes more reduced at high temperature and show that, in contrast, the proportion of PSII open centers (with Q _A oxidized) increases. The two mutants had much slower P700⁺ reduction rate during and after heat than gl. The proportion of light absorbed by PSI versus PSII was increased in gl and crr2 during and after heat treatment, but not in pgr5. We propose that heat alters the redox balance away from PSII and toward PSI and that the regulation of CEF helps photosynthesis tolerate heat stress.     

Circular permutation of ligand‐binding module improves dynamic range of genetically encoded FRET‐based nanosensor

Quantitative measurement of small molecules with high spatiotemporal resolution provides a solid basis for correct understanding and accurate modeling of metabolic regulation. A promising approach toward this goal is the FLIP (fluorescent indicator protein) nanosensor based on bacterial periplasmic binding proteins (PBPs) and fluorescence resonance energy transfer (FRET) between the yellow and cyan variants of green fluorescent protein (GFP). Each FLIP has a PBP module that specifically binds its ligand to induce a conformation change, leading to a change in FRET between the two GFP variant modules attached to the N‐ and C‐termini of the PBP. The larger is the dynamic range the more reliable is the measurement. Thus, we attempted to expand the dynamic range of FLIP by introducing a circular permutation with a hinge loop deletion to the PBP module. All the six circularly permutated PBPs tested, including structurally distinct Type I and Type II PBPs, showed larger dynamic ranges than their respective native forms when used for FLIP. Notably, the circular permutation made three PBPs, which totally failed to show FRET change when used as their native forms, fully capable of functioning as a ligand binding module of FLIP. These FLIPs were successfully used for the determination of amino acid concentration in complex solutions as well as real‐time measurement of amino acid influx in living yeast cells. Thus, the circular permutation strategy would not only improve the performance of each nanosensor but also expand the repertoire of metabolites that can be measured by the FLIP nanosensor technology.     

Formalizing Darwinism and inclusive fitness theory

Inclusive fitness maximization is a basic building block for biological contributions to any theory of the evolution of society. There is a view in mathematical population genetics that nothing is caused to be maximized in the process of natural selection, but this is explained as arising from a misunderstanding about the meaning of fitness maximization. Current theoretical work on inclusive fitness is discussed, with emphasis on the author''s ‘formal Darwinism project’. Generally, favourable conclusions are drawn about the validity of assuming fitness maximization, but the need for continuing work is emphasized, along with the possibility that substantive exceptions may be uncovered. The formal Darwinism project aims more ambitiously to represent in a formal mathematical framework the central point of Darwin''s Origin of Species, that the mechanical processes of inheritance and reproduction can give rise to the appearance of design, and it is a fitting ambition in Darwin''s bicentenary year to capture his most profound discovery in the lingua franca of science.     

基于最大熵原理的浙江毛竹胸径分布及测量不确定度评定

应用最大熵原理构造了测树因子概率分布的统一模型,这样构造的模型具有明确的解析表达式,并能克服常用方法无法解释测树因子服从某种概率分布的真正原因,从而为测树因子统计分布建模提供了一种有效方法.使用1-3阶样本矩、1-4阶样本矩与1-5阶样本矩,用所构建的概率分布统一模型分别对浙江省域毛竹胸径分布分别作了仿真试验,结果表明当采用1-4阶样本矩时,仿真效果最好,而且比通过假设检验的Weibull分布仿真结果理想:(1)图形非常相似,对实测数据都能很好的模拟;(2)最大熵法的离差平方和为0.00018,Weibull分布的为0.00045[1].由于各种系统与非系统的原因,都会影响测量结果的准确性,对所构建的模型作了不确定度评定,表明结果具有很大的可靠性,测量结果的估计:7.85100,测量结果的标准不确定度:1.82710,置信概率:0.96020.     

The development and in vitro characterisation of an intracellular nanosensor responsive to reactive oxygen species

Advances in sensor technologies have enhanced our understanding of the roles played by reactive oxygen species (ROS) in a number of physiological and pathological processes. However, high inter-reactivity and short life spans has made real-time monitoring of ROS in cellular systems challenging. Fluorescent dyes capable of intracellular ROS measurements have been reported. However, these dyes are known to be intrinsically cytotoxic and thus can potentially significantly alter cellular metabolism and adversely influence in vitro data. Reported here is the development and in vitro application of a novel ROS responsive nanosensor, based on PEBBLE (Probes Encapsulated By Biologically Localised Embedding) technology. The ROS sensitive fluorescent probe dihydrorhodamine 123 (DHR 123) was employed as the sensing element of the PEBBLE through entrapment within a porous, bio-inert polyacrylamide nanostructure enabling passive monitoring of free radical flux within the intracellular environment. Successful delivery of the nanosensors into NR8383 rat alveolar macrophage cells via phagocytosis was achieved. Stimulation of PEBBLE loaded NR8383 cells with phorbol-12-myristate-13-acetate (PMA) enabled real time monitoring of ROS generation within the cell without affecting cellular viability. These data suggest that PEBBLE nanosensors could offer significant advantages over existing technologies used in monitoring the intracellular environment.     

Potential errors in the quantitative evaluation of biogas production in anaerobic digestion processes

Errors that are commonly made in the quantification of biogas from anaerobic digestion experiments were investigated.For liquid displacement gasometers where a barrier solution separates the biogas and the atmosphere, inaccuracy due to gas diffusion was examined experimentally. Acidified saturated saline solution was the most suitable barrier solution, as biogas characteristics changed least with time. Using acidified or tap water caused considerable biogas losses and should therefore be avoided where biogas is stored before measurement.Errors associated with volume calculation from three common liquid displacement gasometer types were investigated theoretically. Corrections that must be made to obtain gas volumes at standard temperature and pressure when using this equipment are discussed. Regarding experimental errors, gasometer designs where displaced liquid is weighed to determine the volume are the most versatile since errors depend mainly upon balance sensitivity. Using liquid heights to calculate volume requires appropriate sizing of the gasometer relative to the volume of gas measured.The calibration of a low flow gas meter was investigated and an approximately linear variation with flow rate was found; hence in situ calibration is advised for this type of instrument. Correction for atmospheric conditions should be performed in real time to reduce errors.     

Estimating ancestral distributions of lineages with uncertain sister groups： a statistical approach to Dispersal-Vicariance Analysis and a case using Aesculus L. （Sapindaceae） including fossils

We propose a simple statistical approach for using Dispersal-Vicariance Analysis （DIVA） software to infer biogeographic histories without fully bifurcating trees. In this approach, ancestral ranges are first optimized for a sample of Bayesian trees. The probability P of an ancestral range r at a node is then calculated as P（rY） = ∑t^n=1 F（rY）t Pt where Y is a node, and F（rY） is the frequency of range r among all the optimal solutions resulting from DIVA optimization at node Y, t is one of n topologies optimized, and Pt is the probability of topology t. Node Y is a hypothesized ancestor shared by a specific crown lineage and the sister of that lineage ＂x＂, where x may vary due to phylogenetic uncertainty （polytomies and nodes with posterior probability 〈 100%）. Using this method, the ancestral distribution at Y can be estimated to provide inference of the geographic origins of the specific crown group of interest. This approach takes into account phylogenetic uncertainty as well as uncertainty from DIVA optimization. It is an extension of the previously described method called Bayes-DIVA, which pairs Bayesian phylogenetic analysis with biogeographic analysis using DIVA. Further, we show that the probability P of an ancestral range at Y calculated using this method does not equate to pp＊F（rY） on the Bayesian consensus tree when both variables are 〈 100%, where pp is the posterior probability and F（rY） is the frequency of range r for the node containing the specific crown group. We tested our DIVA-Bayes approach using Aesculus L., which has major lineages unresolved as a polytomy. We inferred the most probable geographic origins of the five traditional sections of Aesculus and ofAesculus californica Nutt. and examined range subdivisions at parental nodes of these lineages. Additionally, we used the DIVA-Bayes data from Aesculus to quantify the effects on biogeographic inference of including two wildcard fossil taxa in phylogenetic analysis. Our analysis resolved the geographic     

Single-fluorophore monitoring of DNA hybridization for investigating the effect of secondary structure on the nucleation step

Nucleic acid hybridization is one of the essential biological processes involved in storage and transmission of genetic information. Here we quantitatively determined the effect of secondary structure on the hybridization activation energy using structurally defined oligonucleotides. It turned out that activation energy is linearly proportional to the length of a single-stranded region flanking a nucleation site, generating a 0.18 kcal/mol energy barrier per nucleotide. Based on this result, we propose that the presence of single-stranded segments available for non-productive base pairing with a nucleation counterpart extends the searching process for nucleation sites to find a perfect match. This result may provide insights into rational selection of a target mRNA site for siRNA and antisense gene silencing.     

Measuring tendon properties in mdx mice: Cell viability and viscoelastic characteristics

Muscular dystrophy is a genetic disorder of skeletal muscle characterized by progressive muscle weakness. Here we assessed whether muscle wasting affects cell viability and mechanical properties of extensor digitorum longus (EDL) and of tibialis anterior (TA) tendons from mdx dystrophic mice compared to wild type (WT) mice. mdx mice represent the classical animal model for human Duchenne muscular dystrophy, and show several signs of the pathology, including a decrease in specific force and an increase of fibrotic index. Cell viability of tendons was evaluated by histological analysis, and viscoelastic properties have been assessed by a rapid measurement protocol that allowed us to compute, at the same time, tissue complex compliance for all the frequencies of interest. Confocal microscopy and mechanical properties measurements revealed that mdx tendons, compared to WT ones, have an increase in the number of dead cells and a significant reduction in tissue elasticity for all the frequencies that were tested. These findings indicate a reduced quality of the tissue. Moreover, mdx tendons have an increase in the viscous response, indicating that during dynamic loading, they dissipate more energy compared to WT. Our results demonstrate that muscular dystrophy involves not only muscle wasting, but also alteration in the viscoelastic properties of tendons, suggesting a paracrine effect of altered skeletal muscle on tendinous tissue.