Imaging cellular signalling: many `moving tales' in MAP kinase odyssey

Cellular signalling events are at the core of every adaptive response. Signalling events link environmental changes to physiological responses, consequently allowing cellular and organismal sustenance and survival. Classical approaches to study cellular signalling have relied on a variety of cell disruptive techniques which yield limited kinetic information, while the underlying events are much more complex. In this article, we discuss how modern live cell imaging microscopy has found increasing utilization in revealing spatio temporal dynamics of various signalling pathways. Utilizing the well studied mitogen-activated protein kinase (MAPK) signalling cascade as a template, the design, construction and utilization of `mobile' (translocation proficient) biosensors, suitable for studying MAPK signalling in living cells are described in detail. Experimental setup and results obtained from these biosensors, based on different proteins involved in the MAPK signalling cascade, have been described along with the setup of a microscope optimal for live cell imaging applications. Utilizing the ability to activate or deactivate signalling pathways using defined activators and specific pharmacological inhibitors, we also show how these sensors can yield unique spatial and temporal kinetic information of signalling in living cells.

Imaging cellular signalling: many `moving tales' in MAP kinase odyssey

Cellular signalling events are at the core of every adaptive response. Signalling events link environmental changes to physiological responses, consequently allowing cellular and organismal sustenance and survival. Classical approaches to study cellular signalling have relied on a variety of cell disruptive techniques which yield limited kinetic information, while the underlying events are much more complex. In this article, we discuss how modern live cell imaging microscopy has found increasing utilization in revealing spatio temporal dynamics of various signalling pathways. Utilizing the well studied mitogen-activated protein kinase (MAPK) signalling cascade as a template, the design, construction and utilization of `mobile' (translocation proficient) biosensors, suitable for studying MAPK signalling in living cells are described in detail. Experimental setup and results obtained from these biosensors, based on different proteins involved in the MAPK signalling cascade, have been described along with the setup of a microscope optimal for live cell imaging applications. Utilizing the ability to activate or deactivate signalling pathways using defined activators and specific pharmacological inhibitors, we also show how these sensors can yield unique spatial and temporal kinetic information of signalling in living cells.

Bacterial growth rate and host factors as determinants of intracellular bacterial distributions in systemic Salmonella enterica infections.

Bacteria of the species Salmonella enterica cause a range of life-threatening diseases in humans and animals worldwide. The within-host quantitative, spatial, and temporal dynamics of S. enterica interactions are key to understanding how immunity acts on these infections and how bacteria evade immune surveillance. In this study, we test hypotheses generated from mathematical models of in vivo dynamics of Salmonella infections with experimental observation of bacteria at the single-cell level in infected mouse organs to improve our understanding of the dynamic interactions between host and bacterial mechanisms that determine net growth rates of S. enterica within the host. We show that both bacterial and host factors determine the numerical distributions of bacteria within host cells and thus the level of dispersiveness of the infection.

Spread of Salmonella enterica in the body during systemic infection: unravelling host and pathogen determinants.

Salmonella enterica causes a range of life-threatening diseases in humans and animals worldwide. Current treatments for S. enterica infections are not sufficiently effective, and there is a need to develop new vaccines and therapeutics. An understanding of how S. enterica spreads in tissues has very important implications for targeting bacteria with vaccine-induced immune responses and antimicrobial drugs. Development of new control strategies would benefit from a more sophisticated evaluation of bacterial location, spatiotemporal patterns of spread and distribution in the tissues, and sites of microbial persistence. We review here recent studies of S. enterica serovar Typhimurium (S. Typhimurium) infections in mice, an established model of systemic typhoid fever in humans, which suggest that continuous bacterial spread to new infection foci and host phagocytes is an essential trait in the virulence of S. enterica during systemic infections. We further highlight how infections within host tissues are truly heterogeneous processes despite the fact that they are caused by the expansion of a genetically homogeneous microbial population. We conclude by discussing how understanding the within-host quantitative, spatial and temporal dynamics of S. enterica infections might aid the development of novel targeted preventative measures and drug regimens.

Estudo do efeito das cargas de nutrientes no reservatório APM-Manso: uma abordagem através da modelagem numérica tridimensional.

Os gestores de recursos hídricos estão encarregados da gestão de longo prazo, a regulação e a proteção dos recursos hídricos. No entanto, reconhece-se que a estes gestores devem levar em conta a multiplicidade de usos dos recursos hídricos que são apresentadas pelas partes interessadas, tais como agricultores, fornecedores de água e grupos de ambientalistas. Dada a complexidade do sistema hidrológico, o desenvolvimento e a utilização de modelos matemáticos são muitas das vezes necessários. Neste contexto a modelagem ambiental é frequentemente realizada para avaliar os impactos da degradação do ecossistema devido à ação humana. Essa aplicação orientada a investigações proporciona um importante meio pelo qual os cientistas podem interagir e influenciar nas políticas a nível local, regional, nacional e internacional. No Mato Grosso, durante a implantação da hidroelétrica de Aproveitamento Múltiplo de Manso foram adotadas medidas de mitigação dos impactos socioeconômicos causados. Essas medidas geram uma tendência de aumento populacional associado a uma mudança das características sócio-econômicas, para toda a região do entorno do Reservatório, o que agrava o problema de poluição por nutrientes e denota que existe uma necessidade proeminente de estudos do impacto que estas cargas causariam no ecossistema do reservatório. Utilizando o modelo hidrodinâmico e termodinâmico tridimensional ELCOM, associado ao modelo biogeoquímico Caedym, este trabalho tem a finalidade de criar uma modelagem representativa das cargas dos principais nutrientes causadores da eutrofização cultural, sendo eles: a amônia (NH4), o nitrato (NO3) e o Ortofosfato (PO4), com a finalidade de estudar os efeitos das dinâmicas espaciais e temporais destas cargas no estado trófico deste reservatório no em torno dos pontos de lançamento de esgoto e na sua totalidade.

根茎克隆植物羊草分株种群对去叶干扰的生长对策

克隆植物具有多种不同于非克隆植物的生长和繁殖策略。本研究首先综述了这些生长与繁殖策略之中，与我们的实验研究相关的尤其是对于去叶干扰适应策略的四个方面，包括克隆整合、克隆分株大小与密度之权衡( tradeoff)过程、碳水化合物贮备与利用、营养繁殖和芽种群(bud population)调节等。预测克隆植物选择什么样的对策以及某种对策发生作用的条件及程度如何，对克隆植物生态学研究者来说，将是富有挑战意味的课题。 羊草(Leymus chinensis (Trin,) Tzvel.)是禾本科的一种多年生根茎型克隆植物，常常处于由放牧或刈割造成的去叶干扰( defoliation)的胁迫下。在我们的第一个实验（2002年）中，考察了去叶干扰和根茎切割( rhizome severing)是否影响根茎本身和分株地上部分的生长、以及营养繁殖芽的数量特征。同时我们检验如下的假设：直接受到去叶干扰的分株除了会受益于可能的补偿作用之外，还会受益于克隆整合作用，即与之保持根茎联系的未受去叶处理的分株将转移碳水化合物或养分给受去叶干扰的分株，使之得以尽快恢复光合组织。实验结果显示：单次去叶干扰影响根茎生长和芽的产生，而对地上部分的生长影响甚微。只有重度去叶干扰才显著影响营养繁殖芽的产生，而轻度去叶干扰作用不明显。所以，当去叶强度不大时，补偿作用机制将弥补植物由于去叶干扰而受到的损失。我们的实验并未检测到克隆整合的发生，可能的原因是本实验持续的时间不足够长或者是由于根茎中的碳水化合物贮备在去叶干扰发生后发挥了作用，缓解了去叶干扰对羊草分株生长及芽生产的所造成的冲击。 在第二个实验（200 3年）中，为了考查相继数次的去叶干扰是否能够启动羊草分株间的克隆整合，以及启动克隆整合所需达到的去叶干扰的频次，我们将实验样方设计为两部分：核心区( Core section)和外围区(Periphery section)。不同频次的去叶处理（0去叶，作为对照; 1次去叶;3次去叶;5次去叶）仅施加于实验样方的核心区。结果表明，经历3次和5次去叶处理的样方外围区的生物量及水溶性碳水化合物( wsc)含量均明显少于经历1次去叶处理及0去叶处理的样方外围区，这意味着克隆整合在3次去叶和5次去叶两种处理中发生了，而在其它两种处理中没有发生。此外，分株的大小一数目之权衡可能在基株(genet)水平上发生，因此，一个克隆植物基株，当部分分株受到去叶干扰后，将增加其分株数目，但优先增加未受到去叶干扰部分的分株数目。我们将羊草的这种行为视为克隆基株试图逃避干扰的“逃逸行为”( escaping behavior)。 同时在实验中，我们监测了实验样方核心区分株的wsc浓度，目的是查明羊草枝条与根茎中wsc浓度随时间的变化格局及其对去叶干扰的响应，意在发现羊草枝条地上、地下部分和根茎中wsc浓度的时间变化之间的联系。在生长旺季，对照处理（即O去叶处理）的wsc浓度显著降低，这是由于植物在此时期的高生长速率和高呼吸速率所致;相比之下，其它经历去叶干扰的三个处理中羊草wsc浓度降低不如对照处理那么明显和迅速，甚至在高频次去叶处理中还有所上升，其原因大概是由于去叶而使叶面积减小，引起枝条的总呼吸下降所致。羊草枝条中最终的wsc浓度没有受到单次去叶处理的显著影响，却很可观地受到相继数次去叶干扰（3次和5次去叶处理）的影响。去叶干扰可能加速了碳水化合物在气温降低时自地上向地下的转移。枝条的地下部分wsc浓度比地上部分更稳定。在地上部分受到去叶干扰后，根茎中的wsc必然向上输出到地上枝条，而强烈的生长会消耗wsc，但可能的克隆整合（通常在相对频繁的去叶干扰条件下发生）将在一定程度上缓解这种wsc消耗。 在此实验中，我们还监测了羊草平均每分株所拥有的芽的数目，包括每分株分蘖节芽（tiller bud）数目和根茎芽(thizomatous bud)数目。从平均每分株芽数目的时间动态来看，各种去叶处理之间的差异程度不大，这主要是羊草在受到去叶干扰后补偿作用的贡献。与对照处理相比，受不同频次去叶干扰的三个处理的根茎芽具有相对于分蘖节的更强的增长优势。去叶干扰对根茎芽生长的促进作用大于对分蘖节芽的促进作用。我们认为这种反应是羊草克隆基株的一种逃避干扰的适应性努力，可视为一种“逃逸行为”，也可看作克隆植物觅养行为(foraging behavior)的一种特殊形式。芽的增长在中等频度的去叶干扰条件下最强，似乎同样符合中度干扰理论。有趣的是，特定频度的去叶干扰可能会造成芽种群中两大类型芽之间比例（根茎芽／分蘖节芽）的振荡现象（Oscillation）。 最后展望了对于羊草今后应继续开展的工作主要集中在两大方面：一是有性繁殖与无性繁殖之间在不同生境或不同干扰条件下的权衡关系;二是处于不同斑块对比度( patch contrast)的生境中的羊草克隆分株之问的生理整合，及其强度与斑块对比度的定量关系。

中部天山林线动态对气候变化的响应研究

中部天山高山林线构成一个对气候变化及其变化程度的理想而敏感的代表性指标，低温、干旱和水分胁迫等都可能限制森林的分布和影响林线的形成。本文通过沿海拔梯度定位调查高山林线样地天山云杉种群的更新情况，利用树木年轮气候学和生态学方法，研究了林线天山云杉种群的时间动态和空间动态及其与气候变化的关系，并取得了一些初步结果。 利用不同年龄的树木年轮序列建立了三个不同年龄的树木年轮宽度年表，幼龄(<100年)，中龄(100-200年)和老龄(>200年) 树木都与当年生长季前期1-3月份的温度显著正相关，和当年1月份和7月份的降水显著正相关。但不同年龄的天山云杉对气候变化的响应结果不同，幼龄(<100年)天山云杉对气候变化的响应程度随年龄的增加而增加，但变化趋势不明显；中龄树木(100-200年)对气候变化的响应随年龄的增加而降低；老龄(>200年)天山云杉受年龄的影响不大。 有关古气候变化的相关研究中，都是尽可能采取年代长的树木年轮样本建立年代较长的年表，并利用最近几十年的气候资料与最近几十年的树木生长的相关关系来重建古气候变化情况。本文的研究结果表明，将不同年龄天山云杉的树木年轮宽度序列放在一起所建成的多年龄复合年表包含有更多的气候信息，显示出当地天山云杉种群对气候变化反应的共性。研究结果表明在建树木年轮的宽度年表时，选用一定数量的不同年龄的树木年轮宽度序列可增强年表对气候变化的响应关系。 利用不同年龄的天山云杉样本建成的复合年龄的树木年轮宽度年表对冬季的最低温度的响应关系，重建了中部天山高山林线地区过去300年来的冬季最低温度。重建的冬季最低温度的有几个明显的暖期和冷期，20世纪50年代以来冬季低温则表现出显著增高的变化趋势。 中部天山高山林线天山云杉种群的胸径和年龄结构以都呈倒-J型分布，说明天山云杉种群更新良好，处于稳定发展时期。随着全球变暖和温度的升高，20世纪以来中部天山高山林线天山云杉的种群更新数量较多，天山云杉的密度有所增加，但林线位置并没有显著的上升，不同年代内更新的树木所到达的海拔高度也不一样。中部天山高山林线天山云杉种群发生的时间动态主要和冬季最低温度正相关，而不同时间内更新的天山云杉种群空间动态形成原因比较复杂，主要和冬季低温负相关。

Dicke superradiance in GaN quantum wells

We numerically modeled the spatio-temporal dynamics of Dicke superradiance in GaN/InGaN heterostructure quantum wells in a ridge waveguide cavity. Model predictions envisage ultrashort pulses of intensities superior to what can be obtained in mode-locked lasers. ©2010 IEEE.

Spatial analysis for spring bloom and nutrient limitation in Xiangxi bay of three Gorges Reservoir

The spatial and temporal dynamics of physical variables, inorganic nutrients and phytoplankton chlorophyll a were investigated in Xiangxi Bay from 23 Feb. to 28 Apr. every six days, including one daily sampling site and one bidaily sampling site. The concentrations of nutrient variables showed ranges of 0.02-3.20 mg/L for dissolved silicate (Si); 0.06-2.40 mg/L for DIN (NH4N + NO2N + NO3N); 0.03-0.56 mg/L for PO4P and 0.22-193.37 mu g/L for chlorophyll a, respectively. The concentration of chlorophyll a and inorganic nutrients were interpolated using GIS techniques. The results indicated that the spring bloom was occurred twice in space during the whole monitoring period (The first one: 26 Feb.-23 Mar.; the second one: 23 Mar.-28 Apr.). The concentration of DIN was always high in the mouth of Xiangxi Bay, and PO4P was high in the upstream of Xiangxi Bay during the whole bloom period. Si seems no obvious difference in space in the beginning of the spring bloom, but showed high heterogeneity in space and time with the development of spring bloom. By comparing the interpolated maps of chlorophyll a and inorganic variables, obvious consumptions of Si and DIN were found when the bloom status was serious. However, no obvious depletion of PO4P was found. Spatial regression analysis could explained most variation of Chl-a except at the begin of the first and second bloom. The result indicated that Si was the factor limiting Chl-a in space before achieved the max area of hypertrophic in the first and second bloom period. When Si was obviously exhausted, DIN became the factor limiting the Chl-a in space. Daily and bidaily monitoring of Site A and B, representing for high DIN: PO4P ratio and low DIN:PO4P ratio, indicated that the concentration of Si was decreased with times at both site A and B, and the dramatically drop of DIN was found in the end monitoring at site B. Multiple stepwise regression analysis indicated that Si was the most important factor affect the development of spring bloom both at site A and B in time series.

In vivo studies on toxin accumulation in liver and ultrastructural changes of hepatocytes of the phytoplanktivorous bighead carp i.p.-injected with extracted microcystins

Phytoplanktivorous bighead carp were injected i.p. with extracted microcystins (mainly MC-RR and -LR) at two doses, 200 and 500 MC-LReq. mu g kg(-1) bw, and the changes in extractable MCs in liver and in the ultrastructure of hepatocytes were studied at 1, 3, 12, 24 and 48 h after injection. Quantitative and qualitative determinations of MCs in the liver were conducted by HPLC and LC-MS, respectively. MC concentration in the liver reached the maxima at 12 It (2.89 mu g MCs g(-1) dry weight at the lower dose) or at 3 h (5.43 mu g MCs g(-1) dry weight at the higher dose) post-injection, followed by sharp declines afterwards, whereas the ultrastructural changes of hepatocytes in both dose groups suggest progressive increases in severity toward the directions of apoptosis and necrosis from I to 24 h, respectively. There were two new findings in fish: widening of intercellular spaces was among the early ultrastructural changes induced by MCs and ultrastructural recovery of hepatocytes was evident at 48 h post-injection in both dose groups. Both the present and previous studies suggest that with in vivo or in vitro exposure to microcystins, hepatocyte damage in fish tends to proceed toward the direction of apoptosis at lower MC concentrations but toward the direction of necrosis at high MC concentrations. The temporal dynamics of MCs in the liver suggest that bighead carp may have a mechanism to degrade or bind MC-LR actively after it enters the blood system. (c) 2005 Elsevier Ltd. All rights reserved.

The environment effect on fish assemblage structure in waters adjacent to the Changjiang (Yangtze) River estuary (1998-2001)

We collected fish abundance data in the Changjiang (Yangtze River) estuary and adjacent waters in November 1998, May 1999, November 2000, and May 2001. Using the data, we evaluated the characteristics of the fish assemblages at each site and investigated the effect of several environmental factors. We used a multivariate analysis, including community ordination methods such as detrended correspondence analysis (DCA) and canonical correspondence analysis (CCA), and two-way indicator species analysis (TWINSPAN). We analyzed the biological community structure and environmental factors to determine their spatial distributions, temporal dynamics, and seasonal variations. Among the fish species, five exceeded 5% of the total abundance: Harpodon nehereus (42.82%), Benthosema pterotum (13.85%), Setipinna taty (11.64%), Thryssa kammalensis (9.17%) and Apogonichthys lineatus (6.49%). These were separated into four ecological assemblages: hypsithermal-saline, hypsithermal-brackish, hypothermal-brackish, and hypothermal-saline. We evaluated the degree of influence of environmental factors on the fish community. Our analyses suggested that environmental factors including water depth, salinity, turbidity, transparency, nutrient, and suspended matter formed a synthetic spatial gradient between the coastal and pelagic areas. Ecological and environmental factors changed temporally from 1998 to 2001, and drove the fish community succession. The environmental factors driving the fish community structure included bottom temperature, water depth, bottom and surface pH, surface total phosphorous, and bottom dissolved oxygen. This investigation was completed before completion of the Three Gorges Dam; therefore the results of this study provide an important foundation for evaluating the influence of the human activities.

The broad-scale distribution and abundance of Scyphomedusae in Irish waters

Scyphomedusae are receiving increasing recognition as key components of marine ecosystems. However, information on their distribution and abundance beyond coastal waters is generally lacking. Organising access to such data is critical to effectively transpose findings from laboratory, mesocosm and small scale studies to the scale of ecological processes. These data are also required to identify the risks of detrimental impacts of jellyfish blooms on human activities. In Ireland, such risks raise concerns among the public, but foremost amongst the professionals of the aquaculture and fishing sectors. The present work looked at the opportunity to get access to new information on the distribution of jellyfish around Ireland mostly by using existing infrastructures and programmes. The analysis of bycatch data collected during the Irish groundfish surveys provided new insights into the distribution of Pelagia noctiluca over an area >160 000 km2, a scale never reached before in a region of the Northeast Atlantic (140 sampling stations). Similarly, 4 years of data collected during the Irish Sea juvenile gadoid fish survey provided the first spatially, explicit, information on the abundance of Aurelia aurita and Cyanea spp. (Cyanea capillata and Cyanea lamarckii) throughout the Irish Sea (> 200 sampling events). In addition, the use of ships of opportunity allowed repeated samplings (N = 37) of an >100 km long transect between Dublin (Ireland) and Holyhead (Wales, UK), therefore providing two years of seasonal monitoring of the occurrence of scyphomedusae in that region. Finally, in order to inform the movements of C. capillata in an area where many negative interactions with bathers occur, the horizontal and vertical movements of 5 individual C. capillata were investigated through acoustic tracking.

Stochastic E2F activation and reconciliation of phenomenological cell-cycle models.

The transition of the mammalian cell from quiescence to proliferation is a highly variable process. Over the last four decades, two lines of apparently contradictory, phenomenological models have been proposed to account for such temporal variability. These include various forms of the transition probability (TP) model and the growth control (GC) model, which lack mechanistic details. The GC model was further proposed as an alternative explanation for the concept of the restriction point, which we recently demonstrated as being controlled by a bistable Rb-E2F switch. Here, through a combination of modeling and experiments, we show that these different lines of models in essence reflect different aspects of stochastic dynamics in cell cycle entry. In particular, we show that the variable activation of E2F can be described by stochastic activation of the bistable Rb-E2F switch, which in turn may account for the temporal variability in cell cycle entry. Moreover, we show that temporal dynamics of E2F activation can be recast into the frameworks of both the TP model and the GC model via parameter mapping. This mapping suggests that the two lines of phenomenological models can be reconciled through the stochastic dynamics of the Rb-E2F switch. It also suggests a potential utility of the TP or GC models in defining concise, quantitative phenotypes of cell physiology. This may have implications in classifying cell types or states.

Scale-dependent foraging ecology of a marine top predator modelled using passive acoustic data

1.Understanding which environmental factors drive foraging preferences is critical for the development of effective management measures, but resource use patterns may emerge from processes that occur at different spatial and temporal scales. Direct observations of foraging are also especially challenging in marine predators, but passive acoustic techniques provide opportunities to study the behaviour of echolocating species over a range of scales. 2.We used an extensive passive acoustic data set to investigate the distribution and temporal dynamics of foraging in bottlenose dolphins using the Moray Firth (Scotland, UK). Echolocation buzzes were identified with a mixture model of detected echolocation inter-click intervals and used as a proxy of foraging activity. A robust modelling approach accounting for autocorrelation in the data was then used to evaluate which environmental factors were associated with the observed dynamics at two different spatial and temporal scales. 3.At a broad scale, foraging varied seasonally and was also affected by seabed slope and shelf-sea fronts. At a finer scale, we identified variation in seasonal use and local interactions with tidal processes. Foraging was best predicted at a daily scale, accounting for site specificity in the shape of the estimated relationships. 4.This study demonstrates how passive acoustic data can be used to understand foraging ecology in echolocating species and provides a robust analytical procedure for describing spatio-temporal patterns. Associations between foraging and environmental characteristics varied according to spatial and temporal scale, highlighting the need for a multi-scale approach. Our results indicate that dolphins respond to coarser scale temporal dynamics, but have a detailed understanding of finer-scale spatial distribution of resources.

Bridging the gap between energy and the environment

Meeting the world’s energy demand is a major challenge for society over the coming century. To identify the most sustainable energy pathways to meet this demand, analysis of energy systems on which policy is based must move beyond the current primary focus on carbon to include a broad range of ecosystem services on which human well-being depends. Incorporation of a broad set of ecosystem services into the design of energy policy will differentiates between energy technology options to identify policy options that reconcile national and international obligations to address climate change and the loss of biodiversity and ecosystem services. In this paper we consider our current understanding of the implications of energy systems for ecosystem services and identify key elements of an assessment. Analysis must consider the full life cycle of energy systems, the territorial and international footprint, use a consistent ecosystem service framework that incorporates the value of both market and non-market goods, and consider the spatial and temporal dynamics of both the energy and environmental system. While significant methodological challenges exist, the approach we detail can provide the holistic view of energy and ecosystem services interactions required to inform the future of global energy policy.