Small proteins in bacteria – Big challenges in prediction and identification

Proteins with up to 100 amino acids have been largely overlooked due to the challenges associated with predicting and identifying them using traditional methods. Recent advances in bioinformatics and machine learning, DNA sequencing, RNA and Ribo-seq technologies, and mass spectrometry (MS) have greatly facilitated the detection and characterisation of these elusive proteins in recent years. This has revealed their crucial role in various cellular processes including regulation, signalling and transport, as toxins and as folding helpers for protein complexes. Consequently, the systematic identification and characterisation of these proteins in bacteria have emerged as a prominent field of interest within the microbial research community. This review provides an overview of different strategies for predicting and identifying these proteins on a large scale, leveraging the power of these advanced technologies. Furthermore, the review offers insights into the future developments that may be expected in this field.     

Predicting human visuomotor behaviour in a driving task

The sequential deployment of gaze to regions of interest is an integral part of human visual function. Owing to its central importance, decades of research have focused on predicting gaze locations, but there has been relatively little formal attempt to predict the temporal aspects of gaze deployment in natural multi-tasking situations. We approach this problem by decomposing complex visual behaviour into individual task modules that require independent sources of visual information for control, in order to model human gaze deployment on different task-relevant objects. We introduce a softmax barrier model for gaze selection that uses two key elements: a priority parameter that represents task importance per module, and noise estimates that allow modules to represent uncertainty about the state of task-relevant visual information. Comparisons with human gaze data gathered in a virtual driving environment show that the model closely approximates human performance.     

Hydrogen-Deuterium Exchange Coupled to Top- and Middle-Down Mass Spectrometry Reveals Histone Tail Dynamics before and after Nucleosome Assembly

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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.     

Constraints on food chain length arising from regional metacommunity dynamics

Classical ecological theory has proposed several determinants of food chain length, but the role of metacommunity dynamics has not yet been fully considered. By modelling patchy predator-prey metacommunities with extinction-colonization dynamics, we identify two distinct constraints on food chain length. First, finite colonization rates limit predator occupancy to a subset of prey-occupied sites. Second, intrinsic extinction rates accumulate along trophic chains. We show how both processes concur to decrease maximal and average food chain length in metacommunities. This decrease is mitigated if predators track their prey during colonization (habitat selection) and can be reinforced by top-down control of prey vital rates (especially extinction). Moreover, top-down control of colonization and habitat selection can interact to produce a counterintuitive positive relationship between perturbation rate and food chain length. Our results show how novel limits to food chain length emerge in spatially structured communities. We discuss the connections between these constraints and the ones commonly discussed, and suggest ways to test for metacommunity effects in food webs.     

Time tells: long-term patterns in the population dynamics of the yew gall midge, Taxomyia taxi (Cecidomyiidae), over 35 years

Abstract. 1. Three populations of the yew gall midge, Taxomyia taxi, and its two chalcid parasitoids, Mesopolobus diffinis and Torymus nigritarsus, from Kingley Vale, West Sussex, U.K., were monitored each year between 1966 and 2002. Taxomyia taxi's life cycles are either hemivoltine or univoltine and the parasitoids' are univoltine (T. nigritarsus) or multivoltine (M. diffinis). 2. Growth of the host trees, yew Taxus baccata, each year between 1950 and 1997 was assessed by width of annual rings in cores taken in 1998. Temperature and rainfall data were provided by the weather station in Southampton, representative of the climate of central southern England. 3. Time‐series analyses were conducted to explore the effects of climate, tree growth, and parasitoids on each T. taxi population and on the three populations combined. Four time‐delayed models were developed: for hemivoltine and univoltine T. taxi and for each of the parasitoids. 4. Hemivoltine T. taxi populations showed troughs in density in the periods 1972–1975 and 1991–1992, which were more pronounced in even than odd years; these were closely tracked by M. diffinis and followed, after a delay, by T. nigritarsus. Time‐series models showed that, for T. taxi, its current density depended on the density of its hemivoltine parents moderated by the negative effects of T. nigritarsus on these parents. In reciprocal fashion, T. nigritarsus density was influenced by that of its hemivoltine host as well as by its own previous density. Host and parasitoid appear to participate in a coupled interaction that regulates the populations of both via delayed density dependence, resulting in cycles of at least 14 years. Mesopolobus diffinis had no effect on the dynamics of hemivoltine T. taxi, most of which escaped its parasitism. Although univoltine T. taxi can give rise to hemivoltine offspring, there was no evidence that they affected hemivoltine dynamics. 5. The density of univoltine T. taxi was usually much lower than hemivoltine density and varied irregularly over time. It was not attacked by T. nigritarsus but parasitism by M. diffinis was always high. Despite this, its density depended only on the density of its parents, especially the hemivoltine parents. Parasitism had no effect on the dynamics of univoltine T. taxi. Conversely, M. diffinis density depended solely on the densities of both univoltine and hemivoltine hosts. 6. Tree growth appeared to have little effect on the dynamics of the host or parasitoids and there was no evidence that gall density had any effect on growth of the tree. The primary effect of climate appeared to be in maintaining the cyclic nature of the T. taxi–T. nigritarsus interaction. If stochastic weather variables are removed from the models, the oscillations are of equivalent periodicity but dampen to equilibrium.     

Bottom-up regulation of a pelagic community through spatial aggregations

The importance of spatial pattern in ecosystems has long been recognized. However, incorporating patchiness into our understanding of forces regulating ecosystems has proved challenging. We used a combination of continuously sampling moored sensors, complemented by shipboard sampling, to measure the temporal variation, abundance and vertical distribution of four trophic levels in Hawaii's near shore pelagic ecosystem. Using an analysis approach from trophic dynamics, we found that the frequency and intensity of spatial aggregations-rather than total biomass-in each step of a food chain involving phytoplankton, copepods, mesopelagic micronekton and spinner dolphins (Stenella longirostris) were the most significant predictors of variation in adjacent trophic levels. Patches of organisms had impacts disproportionate to the biomass of organisms within them. Our results are in accordance with resource limitation-mediated by patch dynamics-regulating structure at each trophic step in this ecosystem, as well as the foraging behaviour of the top predator. Because of their high degree of heterogeneity, ecosystem-level effects of patchiness such as this may be common in many pelagic marine systems.     

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.