TMFoldRec: a statistical potential-based transmembrane protein fold recognition tool.

BACKGROUND: Transmembrane proteins (TMPs) are the key components of signal transduction, cell-cell adhesion and energy and material transport into and out from the cells. For the deep understanding of these processes, structure determination of transmembrane proteins is indispensable. However, due to technical difficulties, only a few transmembrane protein structures have been determined experimentally. Large-scale genomic sequencing provides increasing amounts of sequence information on the proteins and whole proteomes of living organisms resulting in the challenge of bioinformatics; how the structural information should be gained from a sequence. RESULTS: Here, we present a novel method, TMFoldRec, for fold prediction of membrane segments in transmembrane proteins. TMFoldRec based on statistical potentials was tested on a benchmark set containing 124 TMP chains from the PDBTM database. Using a 10-fold jackknife method, the native folds were correctly identified in 77 % of the cases. This accuracy overcomes the state-of-the-art methods. In addition, a key feature of TMFoldRec algorithm is the ability to estimate the reliability of the prediction and to decide with an accuracy of 70 %, whether the obtained, lowest energy structure is the native one. CONCLUSION: These results imply that the membrane embedded parts of TMPs dictate the TM structures rather than the soluble parts. Moreover, predictions with reliability scores make in this way our algorithm applicable for proteome-wide analyses. AVAILABILITY: The program is available upon request for academic use

Krill Excretion Boosts Microbial Activity in the Southern Ocean

Antarctic krill are known to release large amounts of inorganic and organic nutrients to the water column. Here we test the role of krill excretion of dissolved products in stimulating heterotrophic bacteria on the basis of three experiments where ammonium and organic excretory products released by krill were added to bacterial assemblages, free of grazers. Our results demonstrate that the addition of krill excretion products (but not of ammonium alone), at levels expected in krill swarms, greatly stimulates bacteria resulting in an order-of-magnitude increase in growth and production. Furthermore, they suggest that bacterial growth rate in the Southern Ocean is suppressed well below their potential by resource limitation. Enhanced bacterial activity in the presence of krill, which are major sources of DOC in the Southern Ocean, would further increase recycling processes associated with krill activity, resulting in highly efficient krill-bacterial recycling that should be conducive to stimulating periods of high primary productivity in the Southern Ocean.This research is a contribution to projects ICEPOS (REN2002-04165-CO3-O2) and ATOS (POL2006-00550/CTM), funded by the Spanish Ministry of Science and Innovation

The importance of Antarctic krill in biogeochemical cycles

Antarctic krill (Euphausia superba) are swarming, oceanic crustaceans, up to two inches long, and best known as prey for whales and penguins – but they have another important role. With their large size, high biomass and daily vertical migrations they transport and transform essential nutrients, stimulate primary productivity and influence the carbon sink. Antarctic krill are also fished by the Southern Ocean’s largest fishery. Yet how krill fishing impacts nutrient fertilisation and the carbon sink in the Southern Ocean is poorly understood. Our synthesis shows fishery management should consider the influential biogeochemical role of both adult and larval Antarctic krill

Both loved and feared: third party punishers are viewed as formidable and likeable, but these reputational benefits may only be open to dominant individuals

Journal ArticleResearch Support, Non-U.S. Gov'tCopyright: © 2014 Gordon et al.The datasets associated with this article are available in ORE at http://hdl.handle.net/10871/15639Third party punishment can be evolutionarily stable if there is heterogeneity in the cost of punishment or if punishers receive a reputational benefit from their actions. A dominant position might allow some individuals to punish at a lower cost than others and by doing so access these reputational benefits. Three vignette-based studies measured participants' judgements of a third party punisher in comparison to those exhibiting other aggressive/dominant behaviours (Study 1), when there was variation in the success of punishment (Study 2), and variation in the status of the punisher and the type of punishment used (Study 3). Third party punishers were judged to be more likeable than (but equally dominant as) those who engaged in other types of dominant behaviour (Study 1), were judged to be equally likeable and dominant whether their intervention succeeded or failed (Study 2), and participants believed that only a dominant punisher could intervene successfully (regardless of whether punishment was violent or non-violent) and that subordinate punishers would face a higher risk of retaliation (Study 3). The results suggest that dominance can dramatically reduce the cost of punishment, and that while individuals can gain a great deal of reputational benefit from engaging in third party punishment, these benefits are only open to dominant individuals. Taking the status of punishers into account may therefore help explain the evolution of third party punishment.School of Psychology, University of Exete

Observing change in pelagic animals as sampling methods shift: the case of Antarctic krill

Understanding and managing the response of marine ecosystems to human pressures including climate change requires reliable large-scale and multi�decadal information on the state of key populations. These populations include the pelagic animals that support ecosystem services including carbon export and fisheries. The use of research vessels to collect information using scientific nets and acoustics is being replaced with technologies such as autonomous moorings, gliders, and meta-genetics. Paradoxically, these newer methods sample pelagic populations at ever-smaller spatial scales, and ecological change might go undetected in the time needed to build up large-scale, long time series. These global-scale issues are epitomised by Antarctic krill (Euphausia superba), which is concentrated in rapidly warming areas, exports substantial quantities of carbon and supports an expanding fishery, but opinion is divided on how resilient their stocks are to climatic change. Based on a workshop of 137 krill experts we identify the challenges of observing climate change impacts with shifting sampling methods and suggest three tractable solutions. These are to: improve overlap and calibration of new with traditional methods; improve communication to harmonise, link and scale up the capacity of new but localised sampling programs; and expand opportunities from other research platforms and data sources, including the fishing industry. Contrasting evidence for both change and stability in krill stocks illustrates how the risks of false negative and false positive diagnoses of change are related to the temporal and spatial scale of sampling. Given the uncertainty about how krill are responding to rapid warming we recommend a shift towards a fishery management approach that prioritises monitoring of stock status and can adapt to variability and change

Plankton and nekton community structure in the vicinity of the South Sandwich Islands (Southern Ocean) and the influence of environmental factors

The South Sandwich Islands (SSI) are a biologically productive archipelago situated in the eastern Scotia Sea to the south of the eastward flowing Antarctic Circumpolar Current (ACC). The islands support important populations of higher predators, including several penguin species, seals and humpback whales. Despite this, the plankton ecology of the region has been little studied and information on mesoscale structure and environmental forcing of plankton ecology is particularly limited. We conducted a comprehensive oceanographic and net sampling campaign during the CCAMLR Area 48 Survey (January and February 2019), incorporating phytoplankton, mesozooplankton and macrozooplankton/nekton. Satellite chlorophyll-a (chl-a) data showed the development of a large bloom that was initiated two months prior to our study period at the south-eastern edge of the archipelago and propagated northwards along the eastern side, limited to the east by mesoscale features associated with the southern boundary of the ACC (SB). Multivariate cluster analysis revealed distinct mesoscale structure within the plankton community, with four spatially defined groups of phytoplankton and macrozooplankton/nekton, and three cluster groups of mesozooplankton. North of the SB, we found some spatial congruence between the three plankton assemblages, with a distinct, spatially coherent, cluster in each, corresponding to a warmer water community. Here, biomass was dominated by mesozooplankton, particularly calanoid copepods Rhincalanus gigas, Calanus propinquus, C. simillimus and Euchaetidae. The corresponding phytoplankton community was dominated by small diatoms, particularly Thalassionema spp., Pseudo-nitzschia spp., Fragilariopsis spp. and Chaetoceros spp., whilst Themisto gaudichaudii, Euphausia triacantha and myctophids were the major contributors to the macrozooplankton/nekton community. South of the SB, there was some spatial congruence between phytoplankton and macrozooplankton/nekton community structure on the western side of the archipelago, as well as on the eastern side that corresponded to the location of the bloom, but less association with mesozooplankton structure. Macrozooplankton/nekton structure was strongly driven by environmental conditions 1–2 months prior to the survey, including sea-ice distribution, surface phytoplankton concentration and productivity, whilst mesozooplankton was more tightly coupled to in-situ prevailing conditions such as surface temperature and integrated chl-a. Top-down pressure between trophic levels may have also had an influence on spatial patterns although direct evidence is lacking. Antarctic krill (Euphausia superba) was found with relatively low biomass at our net sampling sites (median biomass of 0.04 mg m−3 or <0.01 g m−2) while myctophids and the euphausiid Thysanoessa spp. predominated. We suggest that the highly productive and species rich pelagic community of the SSI supports multiple trophic pathways, and that off-shelf these may operate independently of Antarctic krill