Simultaneous Quantification of Protein Expression and Modifications by Top-down Targeted Proteomics: A Case of the Sarcomeric Subproteome

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Highlights

• •A new strategy for simultaneous quantification of protein expression and modification.
• •This top-down LC/MS-based method shows high reproducibility and high throughput.
• •Quantification at the intact protein level with results comparable to Western blot.
• •This top-down proteomics method is applicable to different species and tissues.

     

From population ecology to metabolism: growth of Trypanosoma evansi,and implications of glucose depletion,in a live host

Little attention has been paid to the potential top-down effects of population ecology on metabolism. Because it is capable of a fast growth that dramatically modifies its blood environment, the parasitic protozoan, Trypanosoma evansi, is a promising model for the study of density-dependent metabolic processes. We assess the in vivo growth rate, doubling time, biomass yield, glycolytic flux, and enzyme expression of T. evansi. Then, we explore the metabolic changes likely occurring during its growth. At low T. evansi densities, most host glucose is used to produce energy, which results in the release of pyruvate. Part of glucose is used for NADPH production through the pentose phosphate pathway. At high T. evansi densities, fructose, mannose, and glycerol become additional energy sources. Part of host glucose is used for biosynthesis and for NADPH production through alternative metabolic pathways, which results in the release of succinate, alanine, and acetate. The ability of organisms to adjust to resource changes is crucial to their survival. Irrespective if the triggering mechanism is direct (nutrient limitation) or indirect (a pheromone-like factor), nutrient availability is necessarily the main evolutionary factor responsible for the density-dependent metabolic properties of trypanosome populations.     

Effects of consumers and enrichment on abundance and diversity of benthic algae in a rocky intertidal community

Human alteration of nutrient cycling and the densities of important consumers have intensified the importance of understanding how nutrients and consumers influence the structure of ecological systems. We examined the effects of both grazing and nutrient enrichment on algal abundance and diversity in a high-intertidal limpet-macroalgal community on the South Island of New Zealand, a relatively nutrient-poor environment. We used a fully factorial design with three levels each of grazing (manipulations of limpet and snail densities) and nutrients (nutrient-diffusers attached to the rock). Top-down control by grazers appears to be the driving organizing mechanism for algal communities in this system, with strong negative effects of grazing on algal diversity and abundance across all levels of nutrient enrichment. However, in contrast to the conclusions drawn from the analysis of the whole algal community, there was an interactive effect of grazing and enrichment on foliose algae, an important component of the algal system. When herbivory was reduced to very low levels, enrichment generated increases in the abundance and biomass of foliose algae. As expected, top-down control was the primary determinant of algal community structure in this system, controlling abundance and diversity of macrophytes on the upper shore. Contrary to expectations, however, increased nutrients had no community-wide effects, although foliose algal abundance increases were greatest with high nutrients and reduced grazing. It seems likely that most of the corticated algal species have limited capacity to respond to nutrient pulses in this nutrient-poor environment.     

Combined effects of nutrients and grazers on bacterioplankton and phytoplankton abundance in an Antarctic lake with even food-chain links

The goal of this study was to address the top-down and bottom-up controls on different microbial web components (bacterioplankton, picophytoplankton, and >3 μm phytoplankton) in an Antarctic lake. Two experiments using a size fractionation approach and nutrient addition were conducted at microcosm scale (2.5 l). The variation in net growth rates (k′) of bacterioplankton and phytoplankton size fractions was analyzed after 5 days. The results determined significant differences; whereas bacterioplankton and large phytoplankton showed an increase in their k′ when their predators were removed, the picophytoplankton showed a decrease. All the studied plankton components presented the highest k′ when nutrients were added. It is suggested that, in this lake, both the top-down and bottom-up regulations account for the regulation of bacterioplankton and large phytoplankton. As for picophytoplankton, the bottom-up control was evident and grazing did not pose a negative impact and rather, had a positive effect probably due to liberation of nutrients.     

Top-down control in a patchy environment: revisiting the stabilizing role of food-dependent predator dispersal

In this paper, we revisit the stabilizing role that predator dispersal and aggregation have in the top-down regulation of predator-prey systems in a heterogeneous environment. We consider an environment consisting of sites interconnected by dispersal, and propose a novel mechanism of stabilization for the case with a non-sigmoid functional response of predators. We assume that the carrying capacity of the prey is infinitely large in each site, and show that successful top-down regulation of this otherwise globally unstable system is made possible through an interplay between the unevenness of prey fitness across the sites and the rapid food-dependent migration of predators. We argue that this mechanism of stabilization is different from those previously reported in the literature: in particular, it requires a high degree of synchronicity in local oscillations of species densities across the sites. Prey outbreaks take place synchronously, but the unevenness of prey growth rates across the sites results in a pronounced difference in the species densities, and so the predator quickly disperses to the sites with the highest prey abundances. For this reason, the consumption of prey mostly takes place in the sites with high densities of prey, which assures an efficient suppression of outbreaks. Furthermore, when the total size of prey population is low, the distribution of both species among the sites becomes more even, and this prevents overconsumption of the prey by the predator. Finally, we put forward the hypothesis that this mechanism, when considered in a tri-trophic plankton community in the water column, can explain the stability of the nutrient-rich low-chlorophyll open ocean regions.     

Invasive litter, not an invasive insectivore, determines invertebrate communities in Hawaiian forests

In Hawaii, invasive plants have the ability to alter litter-based food chains because they often have litter traits that differ from native species. Additionally, abundant invasive predators, especially those representing new trophic levels, can reduce prey. The relative importance of these two processes on the litter invertebrate community in Hawaii is important, because they could affect the large number of endemic and endangered invertebrates. We determined the relative importance of litter resources, represented by leaf litter of two trees, an invasive nitrogen-fixer, Falcataria moluccana, and a native tree, Metrosideros polymorpha, and predation of an invasive terrestrial frog, Eleutherodactylus coqui, on leaf litter invertebrate abundance and composition. Principle component analysis revealed that F. moluccana litter creates an invertebrate community that greatly differs from that found in M. polymorpha litter. We found that F. moluccana increased the abundance of non-native fragmenters (Amphipoda and Isopoda) by 400% and non-native predaceous ants (Hymenoptera: Formicidae) by 200%. E. coqui had less effect on the litter invertebrate community; it reduced microbivores by 40% in F. moluccana and non-native ants by 30% across litter types. E. coqui stomach contents were similar in abundance and composition in both litter treatments, despite dramatic differences in the invertebrate community. Additionally, our results suggest that invertebrate community differences between litter types did not cascade to influence E. coqui growth or survivorship. In conclusion, it appears that an invasive nitrogen-fixing tree species has a greater influence on litter invertebrate community abundance and composition than the invasive predator, E. coqui.     

The relative importance of herbivory and carnivory on the distribution of energy in a stochastic tri-trophic food web

A three-state, discrete-time Markov chain is used to model the dynamics of energy flow in a tri-trophic food web. The distribution of energy in the three trophic levels is related to the rates of flow between the trophic levels and calculated for the entire range of possible flow values. These distributions are then analysed for stability and used to test the idea that plants are resource-limited and herbivores are predation-limited. Low rates of death and decomposition, when coupled with low rates of herbivory and carnivory, tend to destabilize this food web. Food webs with higher rates of death and decomposition are relatively more stable regardless of rates of herbivory and carnivory. Plants are more prone to resource-limitation and herbivores are, in general, limited by their predators, which supports Hairston et al. (Am. Nat. 94 (1960) 421). The rate of decomposition often mediates the roles of top-down and bottom-up control of energy flow in the food web.     

视觉图像辨认眼动中的Top－down信息处理

在视觉图像辨认过程中,眼球不是均匀地扫描全幅图像,而是通过一系列快速的眼球跳动来改变注视点位置,有选择地通过注视停顿来采集图象中的关键信息。通过实验对不同图像刺激时的眼动轨迹进行记录与分析,发现：（１）对于简单的几何图形,眼动注视停顿主要集中在图像中几何特征之处,亦即与周围不同的奇异点上;（２）对复杂图象刺激,眼动注视点位置决定于受试者的已有概念模型及其兴趣所在;（３）对中文单字进行辩认时,其眼动模式也是取决于受试者对该单字的知识（也即概念模型）。以上结果提示,视觉图象辨认主要是通过自上而下（ｔｏｐ－ｄｏｗｎ）的信息处理方式才完成．由中枢控制眼球运动,将注视点落到中枢决定的图形奇点上来,通过注视停顿对中枢认为的关键信息之处进行抽提,以实现辨认。这种处理方式不是只取决于输入的图像信息,也不必对目标图像的每个象素进行处理,而只需对图象中少量的关键信息部位进行重点的检测和处理,从而提高了图象信息处理的能力及效率。     

Bottom-up versus top-down effects on ciliate community composition in four eutrophic lakes (China)

Previous studies have shown that ciliate plankton is generally controlled by food resources (e.g., algae) and predators (e.g., metazooplankton). Among lakes with similar trophic levels but different distributions of phyto- and metazooplankton, the main forces acting on ciliate assemblages may be different. We investigated the relationship between ciliate communities and bottom-up versus top-down variables based on a survey of four subtropical eutrophic lakes (China). Two of the lakes (Chaohu, Taihu) are located on the Mid-lower Yangtze Plain near sea level, and the other two (Dianchi, Xingyunhu) on the Yunnan-Kweichow Plateau at 1700 m above sea level. Blooms of cyanobacteria developed during summer in Lakes Chaohu and Taihu and throughout the year in Lakes Dianchi and Xingyunhu. Ciliate functional feeding groups differed significantly between lakes. The results of canonical correspondence analysis (CCA) and variation partitioning showed that cyanobacteria significantly influence ciliate species, whereas ‘edible’ algae (cryptophytes, diatoms) and cladocerans were the important variables in explaining the ciliate community structure of Lakes Dianchi and Xingyunhu compared with Lakes Taihu and Chaohu. Our results highlight the importance of consistent cyanobacterial blooms in shaping the ciliate community in subtropical eutrophic shallow lakes by interacting with top-down and bottom-up factors.     

Regulation of boreal forest understory vegetation: the roles of resources and herbivores

To understand inter-trophic linkages between components of the boreal forest understory vegetation, three hypotheses were tested: survival, growth and abundance of grasses and legumes were controlled by (i) resource availability alone, (ii) by herbivores alone, and (iii) by both resource availability and herbivores. The hypotheses were tested using three experimental treatments – fertilization, herbivore exclusion, and fertilization plus herbivore exclusion – in three areas having different densities of resident herbivores, mostly snowshoe hares and ground squirrels. The highest density of snowshoe hares is comparable to natural levels during peaks in the snowshoe hare cycle. As the density of herbivores increased so too did the level of response by the measured variables – survival, growth of transplants and leaf area index of established vegetation. In general, fertilization resulted in a decrease in survival and growth of transplants, and fences increased survival and growth; both responses were more noticeable at higher herbivore densities. Fertilizer and herbivore exclosure fences had only negligible effects on established grass and legume abundance at all hare densities. We have shown that some hypotheses of vegetation regulation are over-simplified because different species groups (i.e., grasses and legumes) are regulated by different factors, at different life history stages, and sometimes these factors act in opposing directions. We argue that during the increase phase and peak of the snowshoe hare cycle (high herbivore density), growth and survival of establishing plants is regulated by herbivores. During the decline and low phases of the snowshoe hare cycle herbivores will have little impact on early life stages, whereas the established, mature, vegetation will be resource-regulated. Because of the variability in responses to the same manipulations we may begin to understand which plant life history stages are most vulnerable to consumer and resource regulation, the magnitudes of these sources of regulation at each of these stages, and how these vary among species groups and types of environments.