Design and engineering of photosynthetic light-harvesting and electron transfer using length, time, and energy scales

Decades of research on the physical processes and chemical reaction-pathways in photosynthetic enzymes have resulted in an extensive database of kinetic information. Recently, this database has been augmented by a variety of high and medium resolution crystal structures of key photosynthetic enzymes that now include the two photosystems (PSI and PSII) of oxygenic photosynthetic organisms. Here, we examine the currently available structural and functional information from an engineer's point of view with the long-term goal of reproducing the key features of natural photosystems in de novo designed and custom-built molecular solar energy conversion devices. We find that the basic physics of the transfer processes, namely, the time constraints imposed by the rates of incoming photon flux and the various decay processes allow for a large degree of tolerance in the engineering parameters. Moreover, we find that the requirements to guarantee energy and electron transfer rates that yield high efficiency in natural photosystems are largely met by control of distance between chromophores and redox cofactors. Thus, for projected de novo designed constructions, the control of spatial organization of cofactor molecules within a dense array is initially given priority. Nevertheless, constructions accommodating dense arrays of different cofactors, some well within 1 nm from each other, still presents a significant challenge for protein design.     

Design and engineering of photosynthetic light-harvesting and electron transfer using length, time, and energy scales

Decades of research on the physical processes and chemical reaction-pathways in photosynthetic enzymes have resulted in an extensive database of kinetic information. Recently, this database has been augmented by a variety of high and medium resolution crystal structures of key photosynthetic enzymes that now include the two photosystems (PSI and PSII) of oxygenic photosynthetic organisms. Here, we examine the currently available structural and functional information from an engineer's point of view with the long-term goal of reproducing the key features of natural photosystems in de novo designed and custom-built molecular solar energy conversion devices. We find that the basic physics of the transfer processes, namely, the time constraints imposed by the rates of incoming photon flux and the various decay processes allow for a large degree of tolerance in the engineering parameters. Moreover, we find that the requirements to guarantee energy and electron transfer rates that yield high efficiency in natural photosystems are largely met by control of distance between chromophores and redox cofactors. Thus, for projected de novo designed constructions, the control of spatial organization of cofactor molecules within a dense array is initially given priority. Nevertheless, constructions accommodating dense arrays of different cofactors, some well within 1 nm from each other, still presents a significant challenge for protein design.     

植被对不同时间尺度干旱事件的响应特征及成因分析

利用标准化降雨蒸散发指数(SPEI)与归一化植被指数(NDVI)系统研究了中国不同区域、不同土地利用类型的植被对不同时间尺度干旱事件的响应特征,并对成因做出探讨。研究表明:(1)全国大部分区域NDVI与SPEI呈显著正相关,表明中国大部分区域植被生物量变化受干旱时空特征的影响。而沿北纬30度附近的长江流域区域,尤其是长江流域东南部、珠江流域下游等降水相对丰沛区域;黑龙江东北部及长白山地区、四川西部等高寒区域,NDVI与SPEI表现出弱相关性,受干旱影响较小;(2)多年平均水平衡是影响植被对干旱响应的关键因素,土壤水分变化是植被活力与生物量变化的关键影响因子。多年平均日照时数较长的区域,植被变化受干旱影响较大。从对干旱影响敏感性程度来讲,越是水量丰沛的区域,植被受干旱的影响越小,其中,草地对干旱的影响最为敏感,其次为灌木与森林。     

HIV-1 dynamics at different time scales under antiretroviral therapy

We exploit a model that considers three compartments: blood plasma (BP), lymphoid tissue-interstitial spaces (LT-IS), and follicular dendritic cells (FDC), for the HIV-1 dynamics under the application of highly active antiretroviral therapy (HAART) which allowed us to unravel distinct viral dynamics occurring in short- (2 days), middle- (21 days), and long-term (183 days) time scales. The different time scales are determined by the viral clearance rate, the ratio of productively infected CD4⁺ T cells to chronically infected cells, and the dissociation rate of HIV-1 complexes from FDC. This generates a scenario in which, after an initial transient stage, the viral BP dynamics decouples and becomes governed by the lymphoid tissue (LT) dynamics; in a later stage, a new decoupling occurs in which the LT-IS dynamics is slaved to that of the FDC dynamics. We observed an initial increase in the viremia after HAART in a patient who did not receive protease inhibitors (PI). By means of the above-mentioned model we were able to highlight the relevant parameters which need to be estimated at three different time scales after HAART.     

An ecological framework linking scales across space and time based on self-thinning

Scaling up from measurements made at small spatial and short temporal scales is a central challenge in the ecological and related sciences, where predictions at larger scales and over long time periods are required. It involves two quite distinct aspects: a formulation of a theoretical framework for calculating space-time averages, and an acquisition of data to support that framework. In this paper, we address the theoretical part of the question, and although our primary motivation was an understanding of carbon accounting our formulation is more general. To that end, we adopt a dynamical systems approach, and incorporate a new dynamical formulation of self-thinning. We show how to calculate rates of change for total (and average) plant dry mass, volume, and carbon, in terms of the properties of the individual plants. The results emphasize how local scale statistics (such as, variation in the size of individuals) lead to nonlinear variation at larger scales. Further, we describe how regular and stochastic disturbance can be readily incorporated into this framework. It is shown that stochastic disturbance at patch-scales, results in (to first approximation) regular disturbance at ecosystem scales, and hence can be formulated as such. We conclude that a dynamical formulation of self-thinning can be used as a generic framework for scaling ecological processes in space and time.     

A dual layer hair array of the brown lacewing: repelling water at different length scales

Additional weight due to contamination (water and/or contaminating particles) can potentially have a detrimental effect on the flight capabilities of large winged insects such as butterflies and dragonflies. Insects where the wing surface area-body mass ratio is very high will be even more susceptible to these effects. Water droplets tend to move spontaneously off the wing surface of these insects. In the case of the brown lacewing, the drops effectively encounter a dual bed of hair springs with a topographical structure which aids in the hairs resisting penetration into water bodies. In this article, we demonstrate experimentally how this protective defense system employed by the brown lacewing (Micromus tasmaniae) aids in resisting contamination from water and how the micro- and nanostructures found on these hairs are responsible for quickly shedding water from the wing which demonstrates an active liquid-repelling surface.     

Imaging mass spectrometry at cellular length scales

Imaging mass spectrometry (IMS) allows the direct investigation of both the identity and the spatial distribution of the molecular content directly in tissue sections, single cells and many other biological surfaces. In this protocol, we present the steps required to retrieve the molecular information from tissue sections using matrix-enhanced (ME) and metal-assisted (MetA) secondary ion mass spectrometry (SIMS) as well as matrix-assisted laser desorption/ionization (MALDI) IMS. These techniques require specific sample preparation steps directed at optimal signal intensity with minimal redistribution or modification of the sample analytes. After careful sample preparation, different IMS methods offer a unique discovery tool in, for example, the investigation of (i) drug transport and uptake, (ii) biological processing steps and (iii) biomarker distributions. To extract the relevant information from the huge datasets produced by IMS, new bioinformatics approaches have been developed. The duration of the protocol is highly dependent on sample size and technique used, but on average takes approximately 5 h.     

Biofilm development in a membrane-aerated biofilm reactor: effect of flow velocity on performance

The effect of liquid flow velocity on biofilm development in a membrane-aerated biofilm reactor was investigated both by mathematical modeling and by experiment, using Vibrio natriegens as a test organism and acetate as carbon substrate. It was shown that velocity influenced mass transfer in the diffusion boundary layer, the biomass detachment rate from the biofilm, and the maximum biofilm thickness attained. Values of the overall mass transfer coefficient of a tracer through the diffusion boundary layer, the biofilm, and the membrane were shown to be identical during different experiments at the maximum biofilm thickness. Comparison of the results with published values of this parameter in membrane attached biofilms showed a similar trend. Therefore, it was postulated that this result might indicate the mechanism that determines the maximum biofilm thickness in membrane attached biofilms. In a series of experiments, where conditions were set so that the active layer of the membrane attached biofilm was located close to the membrane biofilm interface, it was shown that the most critical effect on process performance was the effect of velocity on biofilm structure. Biofilm thickness and effective diffusivity influenced reaction and diffusion in a complex manner such that the yield of biomass on acetate was highly variable. Consideration of endogenous respiration in the mathematical model was validated by direct experimental measurements of yield coefficients. Good agreement between experimental measurements of acetate and oxygen uptake rates and their prediction by the mathematical model was achieved.     

The interaction of season length and development time alters size at maturity

An end-of-season penalty, with late-maturing individuals being smaller than early-maturing individuals, has been observed in a variety of univoltine terrestrial arthropods. The current study extends these observations, utilizing multiple populations of a single sexually dimorphic species to examine the ecological correlates and fitness consequences of late maturation at a small size. The orb-weaving spider, Nephila clavipes, inhabits a broad range of habitats that vary from mild to strong seasonality. Because males mature several instars earlier than females, they can reach maturity much earlier in the growing season. Within a cohort, I found that female size at maturity was negatively correlated with timing of maturation in strongly seasonal sites. At a less seasonal site, there was no correlation between female size and timing of maturation within a cohort. In most populations studied, male size was not correlated with the timing of maturation within a cohort. Within populations in strongly seasonal sites, late-maturing females had reduced fecundity. The probability of copulation, survivorship from maturity to first clutch, clutch size relative to female size, and the number of possible clutches were all reduced with delayed maturation. The probability of pre-reproductive death for late-maturing females was strongly affected by stochasticity in the timing of the end of the growing season. Received: 30 December 1998 / Accepted: 1 September 1999     

Linear discrete models with different time scales

Aggregation of variables allows to approximate a large scale dynamical system (the micro-system) involving many variables into a reduced system (the macro-system) described by a few number of global variables. Approximate aggregation can be performed when different time scales are involved in the dynamics of the micro-system. Perturbation methods enable to approximate the large micro-system by a macro-system going on at a slow time scale. Aggregation has been performed for systems of ordinary differential equations in which time is a continuous variable. In this contribution, we extend aggregation methods to time-discrete models of population dynamics. Time discrete micro-models with two time scales are presented. We use perturbation methods to obtain a slow macro-model. The asymptotic behaviours of the micro and macro-systems are characterized by the main eigenvalues and the associated eigenvectors. We compare the asymptotic behaviours of both systems which are shown to be similar to a certain order.     

不同时间尺度下华北落叶松人工林冠层蒸腾与环境因子的关系

在半干旱区连续2年监测华北落叶松(Larix principis-rupprechtii)的树干液流、气象因子和土壤体积含水量,分析不同时间尺度下人工林冠层蒸腾与环境因子的关系。结果表明：不同时间尺度下,华北落叶松人工林冠层蒸腾的季节变化均呈单峰曲线,即先增大后减小的趋势;2016年、2017年日蒸腾量分别为1.58 mm/d和1.71 mm/d,生长季蒸腾总量分别为241.30 mm和260.97 mm。在日尺度下,气温、太阳辐射强度和饱和水汽压差是影响华北落叶松人工林冠层蒸腾主要环境因子;月尺度下,气温、风速、降水和土壤水分是冠层蒸腾的主要影响因子;冠层蒸腾与降水、大气相对湿度的相关关系由日尺度下的负相关到月尺度的正相关,相关性增强。总体来看,随时间尺度由小到大,气温、风速、大气相对湿度、降水、土壤水分对冠层蒸腾的影响作用增大,而太阳辐射强度、饱和水汽压差的作用减弱;在未来增温增雨趋势下,研究区生长季将延长,华北落叶松人工林冠层蒸腾量可能会加大。     

Biofilm development and enhanced stress resistance of a model,mixed-species community biofilm

Most studies of biofilm biology have taken a reductionist approach, where single-species biofilms have been extensively investigated. However, biofilms in nature mostly comprise multiple species, where interspecies interactions can shape the development, structure and function of these communities differently from biofilm populations. Hence, a reproducible mixed-species biofilm comprising Pseudomonas aeruginosa, Pseudomonas protegens and Klebsiella pneumoniae was adapted to study how interspecies interactions affect biofilm development, structure and stress responses. Each species was fluorescently tagged to determine its abundance and spatial localization within the biofilm. The mixed-species biofilm exhibited distinct structures that were not observed in comparable single-species biofilms. In addition, development of the mixed-species biofilm was delayed 1–2 days compared with the single-species biofilms. Composition and spatial organization of the mixed-species biofilm also changed along the flow cell channel, where nutrient conditions and growth rate of each species could have a part in community assembly. Intriguingly, the mixed-species biofilm was more resistant to the antimicrobials sodium dodecyl sulfate and tobramycin than the single-species biofilms. Crucially, such community level resilience was found to be a protection offered by the resistant species to the whole community rather than selection for the resistant species. In contrast, community-level resilience was not observed for mixed-species planktonic cultures. These findings suggest that community-level interactions, such as sharing of public goods, are unique to the structured biofilm community, where the members are closely associated with each other.     

Quality-of-life indicators at different scales: Theoretical background

The article is presenting the general analysis of the systems approach and model approaches for the development of QoL indicators and indices. In our study we propose the method of response function as a method of the construction of purposeful, credible integrated models from data and prior knowledge or information. The method of response function implies credible models in the sense that they are identifiable, and, hopefully, explains system output behaviour satisfactorily.Using response function method for the development of QoL models, we are able to obtain QoL indices as the direct output of the models.     

Shewanella biofilm development and engineering for environmental and bioenergy applications

The genus Shewanella comprises about 70 species of Gram-negative, facultative anaerobic bacteria inhabiting various environments, which have shown great potential in various biotechnological applications ranging from environmental bioremediation, metal(loid) recovery and material synthesis to bioenergy generation. Most environmental and energy applications of Shewanella involve the biofilm mode of growth on surfaces of solid minerals or electrodes. In this article, we first provide an overview of Shewanella biofilm biology with the focus on biofilm dynamics, biofilm matrix, and key signalling systems involved in Shewanella biofilm development. Then we review strategies recently exploited to engineer Shewanella biofilms to improve biofilm-mediated bioprocesses.     

物种灭绝对不同时间尺度人类活动的响应机制研究

通过修改Tilman的多物种共存的经典模式中栖息地毁坏率（D）,使D随时间的推移呈线性增长情况下,本文模拟了百万年、万年和百年尺度人类活动对栖息地的破坏下,物种灭绝对栖息地毁坏的响应特征。结果表明,大时间尺度人类活动对栖息地毁坏导致物种的强弱关系发生变化,并且强物种先灭绝,而小时间尺度人类活动对栖息地破坏是弱物种先灭绝;在百万年和万年尺度上,物种对栖息地毁坏的响应是减幅振荡衰退直至灭绝,并且最强物种对栖息地的占有率（q）越大,振幅越大,而在百年尺度上,物种的演化几乎是直线衰退;在大时间尺度的栖息地毁坏情况下,q越大,则物种灭绝起始时间和所有物种灭绝的时间越长;而在较小的时间尺度的栖息地毁坏情况下,q越大,灭绝起始时间和所有物种最终灭绝的时间则越短。     

Biofilm development in a membrane-aerated biofilm reactor: effect of intra-membrane oxygen pressure on performance

The effect on intra-membrane oxygen pressure at a constant carbon substrate loading rate on the development of biofilms of Vibrio natrigens in a membrane aerated biofilm reactor (MABR) was investigated experimentally and by mathematical modelling. A recently reported technique (Zhang et al., 1998. Biotechnol. Bioeng. 59: 80-89) for the in situ measurement of the substrate diffusion coefficients in a growing biofilm and the mass transfer coefficients in the boundary layer at the biofilm liquid interface was used. This aided the study of the effect of the heterogeneous biofilm structure and also improved the reliability of the model predictions. The different intra-membrane oxygen pressures used, 12.5, 25 and 50 kPa, with acetate as the carbon substrate, showed a marked effect on the initial biofilm growth rate, on acetate removal rate, particularly in thick biofilms and on biofilm structure. The model predicted the substrate limitation regimes, the location of the active biomass layer within the biofilms and the trends in oxygen uptake rate through the membrane into the biofilms. During the development of the biofilms, the biofilm thickness and the intra-membrane oxygen pressure were found to be the most important parameters influencing the MABR performance while the effect of biofilm structure was less marked.     

Epigenetic responses to heat stress at different time scales and the involvement of small RNAs

The hypothesis that plants can benefit from a memory of past stress exposure has recently attracted a lot of attention. Here, we discuss two different examples of heat stress memory to elucidate the potential benefits that epigenetic responses may provide at both the level of acclimation of the individual plant and adaptation at a species-wide level. Specifically, we discuss how microRNAs regulate the heat stress memory and thereby increase survival upon a recurring heat stress. Secondly, we review how a prolonged heat stress in a small interfering RNA-deficient background induces retrotransposition that is transmitted to the next generation, thus creating genetic variation for natural selection to act on. Collectively, these studies reveal a crucial role of short RNAs in heat stress memory across different time scales.