LC-MS for protein characterization: current capabilities and future trends

With advances in ionization methods and instrumentation, liquid chromatography (LC)/mass spectrometry (MS) has become a powerful technology for protein characterization. This review article will describe the general approaches on LC-MS analysis in protein characterization, including bottom-up and top-down strategies. Discussions will be given on characterization of recombinant proteins, and post-translational and protein modifications such as disulfide bonds, glycosylation and phosphorylation using LC-MS. New research directions in this area will also be presented to illustrate future prospects of LC-MS in protein characterization, including application to proteomics.     

Feature-based attention: it is all bottom-up priming

Feature-based attention (FBA) enhances the representation of image characteristics throughout the visual field, a mechanism that is particularly useful when searching for a specific stimulus feature. Even though most theories of visual search implicitly or explicitly assume that FBA is under top-down control, we argue that the role of top-down processing in FBA may be limited. Our review of the literature indicates that all behavioural and neuro-imaging studies investigating FBA suffer from the shortcoming that they cannot rule out an effect of priming. The mere attending to a feature enhances the mandatory processing of that feature across the visual field, an effect that is likely to occur in an automatic, bottom-up way. Studies that have investigated the feasibility of FBA by means of cueing paradigms suggest that the role of top-down processing in FBA is limited (e.g. prepare for red). Instead, the actual processing of the stimulus is needed to cause the mandatory tuning of responses throughout the visual field. We conclude that it is likely that all FBA effects reported previously are the result of bottom-up priming.     

Towards understanding of the cortical network underlying associative memory

Declarative knowledge and experiences are represented in the association cortex and are recalled by reactivation of the neural representation. Electrophysiological experiments have revealed that associations between semantically linked visual objects are formed in neural representations in the temporal and limbic cortices. Memory traces are created by the reorganization of neural circuits. These regions are reactivated during retrieval and contribute to the contents of a memory. Two different types of retrieval signals are suggested as follows: automatic and active. One flows backward from the medial temporal lobe during the automatic retrieval process, whereas the other is conveyed as a top-down signal from the prefrontal cortex to the temporal cortex during the active retrieval process. By sending the top-down signal, the prefrontal cortex manipulates and organizes to-be-remembered information, devises strategies for retrieval and monitors the outcome. To further understand the neural mechanism of memory, the following two complementary views are needed: how the multiple cortical areas in the brain-wide network interact to orchestrate cognitive functions and how the properties of single neurons and their synaptic connections with neighbouring neurons combine to form local circuits and to exhibit the function of each cortical area. We will discuss some new methodological innovations that tackle these challenges.     

Shorebirds, snails, and the amphipod (Corophium volutator) in the upper Bay of Fundy: top–down vs. bottom–up factors, and the influence of compensatory interactions on mudflat ecology

During their annual mid- to late-summer southward migration, Semipalmated Sandpipers (Calidris pusilla) feed intensively on the amphipod Corophium volutator on intertidal mudflats in the Bay of Fundy. Corophium, in turn, feed on diatoms and bacteria. Using a series of bird exclosures and fertilizer addition, we examined top–down and bottom–up effects, and investigated the presence of a trophic cascade in the mudflat community during the period when birds are abundant. Although both top–down and bottom–up forces were present in this system, neither transmitted beyond a single trophic link. Predation by shorebirds, which may be less size-selective than previously thought, reduced Corophium abundance in control plots by approximately 80% relative to exclosures, but most other species were unaffected. Shorebird predation did not result in an increase in diatom abundance, as predicted under the trophic cascade hypothesis. Fertilizer increased diatom abundance, but had no effect on Corophium abundance or bird predation, and little effect on other mudflat invertebrates. The only indirect effect observed was on mud snails (Ilyanassa obsoleta), which, by rapidly responding to changes in diatom abundance, compensated for both bird exclusion and fertilizer addition, and prevented the trophic cascade. This population response by snails, possibly stemming from competition with Corophium, probably contributed to the stability of the community. Our results provide an example of short-term compensation in a simple intertidal community, and highlight the importance of considering direct and indirect effects in community ecological studies. We conclude that while compensatory interactions that block trophic cascades may be more common in more complex ecosystems, they are not restricted to them.     

Top-down control of natural phyto- and bacterioplankton prey communities by Daphnia magna and by the natural zooplankton community of the hypertrophic Lake Blankaart

Biomanipulation, through the reduction of fish abundance resulting in an increase of large filter feeders and a stronger top-down control on algae, is commonly used as a lake restoration tool in eutrophic lakes. However, cyanobacteria, often found in eutrophic ponds, can influence the grazing capacity of filter feeding zooplankton. We performed grazing experiments in hypertrophic Lake Blankaart during two consecutive summers (1998, with and 1999, without cyanobacteria) to elucidate the influence of cyanobacteria on the grazing pressure of zooplankton communities. We compared the grazing pressure of the natural macrozooplankton community (mainly small to medium-sized cladocerans and copepods) with that of large Daphnia magna on the natural bacterioplankton and phytoplankton prey communities. Our results showed that in the absence of cyanobacteria, Daphnia magna grazing pressure on bacteria was higher compared to the grazing pressure of the natural zooplankton community. However, Daphnia grazing rates on phytoplankton were not significantly different compared to the grazing rates of the natural zooplankton community. When cyanobacteria were abundant, grazing pressure of Daphnia magnaseemed to be inhibited, and the grazing pressure on bacteria and phytoplankton was similar to that of the natural macrozooplankton community. Our results suggest that biomanipulation may not always result in a more effective top-down control of the algal biomass.     

Preference-performance linkage in a herbivorous lady beetle: consequences of variability of natural enemies

We investigated the relationship between oviposition preference and offspring performance in a herbivorous lady beetle Epilachna pustulosa on two co-occurring plant species, thistle Cirsium kamtschaticum and blue cohosh Caulophyllum robustum, in 1994 and 1995. The relative importance of bottom-up effects by host plants and top-down effects by natural enemies on offspring performance were determined using field and laboratory experiments. In both years, egg density on blue cohosh was significantly higher than on thistle. A laboratory experiment demonstrated that larval survival from hatching to adult emergence was significantly higher, and developmental period shorter when larvae were reared on blue cohosh compared to thistle. The positive preference-performance linkage varied between years in the field. Top-down effects had a different impact on larval survival on the two host plant species. Arthropod predators, a lady beetle Harmonia axyridis and an earwig Forficula mikado, considerably depressed immature survival on thistle, while they were negligible on blue cohosh. Although the lack of effective predation increased larval survival on blue cohosh, it led to defoliation due to increased larval feeding late in the season. Because of severe intraspecific competition, old larvae had significantly lower survival on blue cohosh than on thistle. In 1994, as larval survival decreased due to defoliation on blue cohosh, the overall survival rate was significantly higher on thistle than on blue cohosh. This survival pattern was opposite to that found in the laboratory experiment. In contrast, in 1995, the increase in predatory lady beetles on thistle caused greater larval mortality. Thus, the overall survival was significantly lower on thistle than on blue cohosh, although severe intraspecific competition occurred on blue cohosh as it had in 1994. Consequently, the offspring performance on the two host plants is largely determined by the relative importance of arthropod predation determining larval survival on thistle and host plant defoliation reducing late larval survival on blue cohosh. These results indicate the important role of spatial and temporal variability of natural enemies on the preference-performance linkage of herbivorous insects. Received: 19 August 1998 / Accepted: 11 January 1999     

Evolution mediates the effects of apex predation on aquatic food webs

Ecological and evolutionary mechanisms are increasingly thought to shape local community dynamics. Here, I evaluate if the local adaptation of a meso-predator to an apex predator alters local food webs. The marbled salamander (Ambystoma opacum) is an apex predator that consumes both the spotted salamander (Ambystoma maculatum) and shared zooplankton prey. Common garden experiments reveal that spotted salamander populations which co-occur with marbled salamanders forage more intensely than those that face other predator species. These foraging differences, in turn, alter the diversity, abundance and composition of zooplankton communities in common garden experiments and natural ponds. Locally adapted spotted salamanders exacerbate prey biomass declines associated with apex predation, but dampen the top-down effects of apex predation on prey diversity. Countergradient selection on foraging explains why locally adapted spotted salamanders exacerbate prey biomass declines. The two salamander species prefer different prey species, which explains why adapted spotted salamanders buffer changes in prey composition owing to apex predation. Results suggest that local adaptation can strongly mediate effects from apex predation on local food webs. Community ecologists might often need to consider the evolutionary history of populations to understand local diversity patterns, food web dynamics, resource gradients and their responses to disturbance.     

Influence of drought on interactions between Rhopalosiphum padi and ground dwelling predators – A mesocosm study

Climate change will lead to extreme droughts, but it is difficult to predict how this will affect crop pests. In particular, it is unclear how interactions between natural enemies and pests will be influenced. In the field, bird cherry-oat aphids (Rhopalosiphum padi (L.)) have been observed to reside close to, or below the ground surface during dry conditions. We hypothesized that this will increase the niche overlap between R. padi and ground-dwelling predators such as carabid beetles and wolf spiders and that aphid numbers will therefore decline during dry conditions. A fully factorial mesocosm experiment was conducted testing the combined effects of drought and predator presence on aphid position and abundance on barley (Hordeum vulgare) plants. In support of our hypothesis, we found that (a) aphids moved below ground during dry conditions, (b) predators reduced aphid numbers, but only during dry conditions, and (c) predators reduced the proportion of aphids below ground in dry conditions. This increased predation effect during dry conditions was, however, compensated for by a corresponding increase in aphid performance on the plants and so the net effect of drought on aphid numbers ended up being neutral. Thus, pests can be affected by drought in complex ways via a combination top-down and bottom-up mechanisms. Predicting how pest populations will be affected by droughts in the future is thus a formidable research challenge.