146 research outputs found

    Simulation, Experiment, and Evolution: Understanding Nucleation in Protein S6 Folding

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    In this study, we explore nucleation and the transition state ensemble of the ribosomal protein S6 using a Monte Carlo Go model in conjunction with restraints from experiment. The results are analyzed in the context of extensive experimental and evolutionary data. The roles of individual residues in the folding nucleus are identified and the order of events in the S6 folding mechanism is explored in detail. Interpretation of our results agrees with, and extends the utility of, experiments that shift f-values by modulating denaturant concentration and presents strong evidence for the realism of the mechanistic details in our Monte Carlo Go model and the structural interpretation of experimental f-values. We also observe plasticity in the contacts of the hydrophobic core that support the specific nucleus. For S6, which binds to RNA and protein after folding, this plasticity may result from the conformational flexibility required to achieve biological function. These results present a theoretical and conceptual picture that is relevant in understanding the mechanism of nucleation in protein folding.Comment: PNAS in pres

    Spatial differences in dissolved silicon utilisation in Lake Baikal, Siberia: examining the impact of high diatom biomass events and eutrophication

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    Recent research has highlighted how Lake Baikal, Siberia, has responded to the direct and indirect effects of climate change (e.g., ice-cover duration), nutrient loading, and pollution, manifesting as changes in phytoplankton/zooplankton populations, community structure, and seasonal succession. Here, we combine and compare= analyses of chlorophyll a (an estimate of total algal biomass), carotenoid pigments (biomarkers of algal groups), and lake water silicon isotope geochemistry (d30SiDSi) to differentiate spatial patterns in dissolved silicon (DSi) uptake at Lake Baikal. A total of 15 sites across the three basins (south, central, and north) of Lake Baikal were sampled in August 2013 along a depth gradient of 0–180 m. Strong, significant correlations were found between vertical profiles of photic zone DSi concentrations and d30SiDSi compositions (r 5 20.81, p < 0.001), although these are strongest in the central basin aphotic zone (r 5 20.98, p < 0.001). Data refute the hypothesis of DSi uptake by picocyanobacteria. Algal biomass profiles and high surface d30SiDSi compositions suggest greater productivity in the south basin and more oligotrophic conditions in the north basin. d30SiDSi signatures are highest at depth (20 m) in central basin sites, indicating greater (10–40%) DSi utilization at deep chlorophyll maxima. DSi limitation occurs in the pelagic central basin, probably reflecting a high diatom biomass bloom event (Aulacoseira baicalensis). Meanwhile in the more hydrologically restricted, shallow Maloe More region (central basin), both high d30SiDSi compositions and picocyanobacteria (zeaxanthin) concentrations, respectively point to the legacy of an “Aulacoseira bloom year” and continuous nutrient supply in summer months (e.g., localized eutrophication)

    Locomotor activity of the Holarctic molluscs Radix auricularia (from Lake Baikal) in various light pollution conditions

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    Light pollution is a modern environmental problem. The scale of light pollution is increasing yearly and is negatively affecting the functioning of terrestrial and aquatic ecosystems. Of the aquatic ecosystems, marine ecosystems are the most studied, while there is very little information on the effect of artificial lighting on freshwater ecosystems. Among freshwater aquatic organisms, there are relatively little data on the effect of artificial light on crustaceans and fish, while we could find no meaningful data on the effect of artificial light on molluscs are practically absent. Here we test whether different types of artificial lighting, differing in their spectra, affect the activity of the Holarctic mollusc Radix auricularia. For this, we used two light sources (with warm and cold light) and a 1-m long aquarium. We found that both light sources affect individuals of this species, but the effects of this exposure are different. Artificial lighting (depending on the spectral characteristics) can increase the activity of molluscs of this species or reduce it. In the long term, the impact on the ecosystem will depend on the type of water body where light pollution is present, where individuals of this species live, and the type of light sources

    Rapid and highly variable warming of lake surface waters around the globe

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    In this first worldwide synthesis of in situ and satellite-derived lake data, we find that lake summer surface water temperatures rose rapidly (global mean = 0.34°C decade−1) between 1985 and 2009. Our analyses show that surface water warming rates are dependent on combinations of climate and local characteristics, rather than just lake location, leading to the counterintuitive result that regional consistency in lake warming is the exception, rather than the rule. The most rapidly warming lakes are widely geographically distributed, and their warming is associated with interactions among different climatic factors—from seasonally ice-covered lakes in areas where temperature and solar radiation are increasing while cloud cover is diminishing (0.72°C decade−1) to ice-free lakes experiencing increases in air temperature and solar radiation (0.53°C decade−1). The pervasive and rapid warming observed here signals the urgent need to incorporate climate impacts into vulnerability assessments and adaptation efforts for lakes.Peer reviewe

    Lake surface water temperature [in “State of the Climate in 2019”]

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    Regional Climates is one chapter from the State of the Climate in 2019 annual report. Compiled by NOAA’s National Centers for Environmental Information, State of the Climate in 2019 is based on contributions from scientists from around the world. It provides a detailed update on global climate indicators, notable weather events, and other data collected by environmental monitoring stations and instruments located on land, water, ice, and in space.Universidad de Costa Rica/[805-B9-454]/UCR/Costa RicaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigaciones Geofísicas (CIGEFI
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