Cryoelectron microscopy (cryo-EM) and nuclear magnetic resonance (NMR) spectroscopy are routinely used to determine structures of macromolecules with molecular weights over 65 and under 25 kDa, ...respectively. We combined these techniques to study a 30 kDa HIV-1 dimer initiation site RNA (DIS2; 47 nt/strand). A 9 Å cryo-EM map clearly shows major groove features of the double helix and a right-handed superhelical twist. Simulated cryo-EM maps generated from time-averaged molecular dynamics trajectories (10 ns) exhibited levels of detail similar to those in the experimental maps, suggesting internal structural flexibility limits the cryo-EM resolution. Simultaneous inclusion of the cryo-EM map and 2H-edited NMR-derived distance restraints during structure refinement generates a structure consistent with both datasets and supporting a flipped-out base within a conserved purine-rich bulge. Our findings demonstrate the power of combining global and local structural information from these techniques for structure determination of modest-sized RNAs.
Display omitted
•Subnanometer resolution cryo-EM structure of 30 kDa HIV-1 RNA dimerization signal•The major groove of the RNA duplex was unambiguously resolved in the cryo-EM map•Atomic model of HIV-1 RNA duplex was obtained by integrating NMR, cryo-EM, and MD•Superhelical twist and flipped-out base were observed in this structure
Zhang, Keane et al. present the structure of the 30 kDa HIV-1 RNA dimerization signal using a hybrid approach combining global structural information from cryo-EM at subnanometer resolution with atomic resolution local structural information from NMR. Using MD simulations they found that cryo-EM resolution may be limited by internal structural flexibility.
SPINDLY (SPY) in Arabidopsis thaliana is a novel nucleocytoplasmic protein O-fucosyltransferase (POFUT), which regulates diverse developmental processes. Sequence analysis indicates that SPY is ...distinct from ER-localized POFUTs and contains N-terminal tetratricopeptide repeats (TPRs) and a C-terminal catalytic domain resembling the O-linked-N-acetylglucosamine (GlcNAc) transferases (OGTs). However, the structural feature that determines the distinct enzymatic selectivity of SPY remains unknown. Here we report the cryo-electron microscopy (cryo-EM) structure of SPY and its complex with GDP-fucose, revealing distinct active-site features enabling GDP-fucose instead of UDP-GlcNAc binding. SPY forms an antiparallel dimer instead of the X-shaped dimer in human OGT, and its catalytic domain interconverts among multiple conformations. Analysis of mass spectrometry, co-IP, fucosylation activity, and cryo-EM data further demonstrates that the N-terminal disordered peptide in SPY contains trans auto-fucosylation sites and inhibits the POFUT activity, whereas TPRs 1-5 dynamically regulate SPY activity by interfering with protein substrate binding.
We have examined several approaches for estimating the surface concentration of particulate organic carbon, POC, from optical measurements of spectral remote-sensing reflectance, Rrs(λ), using field ...data collected in tropical and subtropical waters of the eastern South Pacific and eastern Atlantic Oceans. These approaches include a direct empirical relationship between POC and the blue-to-green band ratio of reflectance, Rrs(λB)/Rrs(555), and two-step algorithms that consist of relationships linking reflectance to an inherent optical property IOP (beam attenuation or backscattering coefficient) and POC to the IOP. We considered two-step empirical algorithms that exclusively include pairs of empirical relationships and two-step hybrid algorithms that consist of semianalytical models and empirical relationships. The surface POC in our data set ranges from about 10 mg m−3 within the South Pacific Subtropical Gyre to 270 mg m−3 in the Chilean upwelling area, and ancillary data suggest a considerable variation in the characteristics of particulate assemblages in the investigated waters. The POC algorithm based on the direct relationship between POC and Rrs(λB)/Rrs(555) promises reasonably good performance in the vast areas of the open ocean covering different provinces from hyperoligotrophic and oligotrophic waters within subtropical gyres to eutrophic coastal upwelling regimes characteristic of eastern ocean boundaries. The best error statistics were found for power function fits to the data of POC vs. Rrs(443)/Rrs(555) and POC vs. Rrs(490)/Rrs(555). For our data set that includes over 50 data pairs, these relationships are characterized by the mean normalized bias of about 2% and the normalized root mean square error of about 20%. We recommend that these algorithms be implemented for routine processing of ocean color satellite data to produce maps of surface POC with the status of an evaluation data product for continued work on algorithm development and refinements. The two-step algorithms also deserve further attention because they can utilize various models for estimating IOPs from reflectance, offer advantages for developing an understanding of bio-optical variability underlying the algorithms, and provide flexibility for regional or seasonal parameterizations of the algorithms.
The goal of the Arabian Sea section of the TARA oceans expedition was to study large particulate matter (LPM > 100 μm) distributions and possible impact of associated midwater biological processes on ...vertical carbon export through the oxygen minimum zone (OMZ) of this region. We propose that observed spatial patterns in LPM distribution resulted from the timing and location of surface phytoplankton bloom, lateral transport, microbial processes in the core of the OMZ, and enhanced biological processes mediated by bacteria and zooplankton at the lower oxycline. Indeed, satellite-derived net primary production maps showed that the northern stations of the transect were under the influence of a previous major bloom event while the most southern stations were in a more oligotrophic situation. Lagrangian simulations of particle transport showed that deep particles of the northern stations could originate from the surface bloom while the southern stations could be considered as driven by 1-D vertical processes. In the first 200 m of the OMZ core, minima in nitrate concentrations and the intermediate nepheloid layer (INL) coincided with high concentrations of 100 μm < LPM < 200 μm. These particles could correspond to colonies of bacteria or detritus produced by anaerobic microbial activity. However, the calculated carbon flux through this layer was not affected. Vertical profiles of carbon flux indicate low flux attenuation in the OMZ, with a Martin model b exponent value of 0.22. At three stations, the lower oxycline was associated to a deep nepheloid layer, an increase of calculated carbon flux and an increase in mesozooplankton abundance. Enhanced bacterial activity and zooplankton feeding in the deep OMZ is proposed as a mechanism for the observed deep particle aggregation. Estimated lower flux attenuation in the upper OMZ and re-aggregation at the lower oxycline suggest that OMZ may be regions of enhanced carbon flux to the deep sea relative to non OMZ regions.
The objectives of the BIOSOPE (BIogeochemistry and Optics SOuth Pacific Experiment) project was to study, during the austral summer, the biological, biogeochemical and bio-optical properties of ...different trophic regimes in the South East Pacific: the eutrophic zone associated with the upwelling regime off the Chilean coast, the mesotrophic area associated with the plume of the Marquises Islands in the HNLC (High Nutrient Low Chlorophyll) waters of this subequatorial area, and the extremely oligotrophic area associated with the central part of the South Pacific Gyre (SPG). At the end of 2004, a 55-day international cruise with 32 scientists on board took place between Tahiti and Chile, crossing the SPG along a North-West South-East transect. This paper describes in detail the objectives of the BIOSOPE project, the implementation plan of the cruise, the main hydrological entities encountered along the ~8000 km South East Pacific transect, and ends with a general overview of the 32 other papers published in this special issue.
Avoiding biases in binned fits Gligorov, V.V.; Hageboeck, S.; Nanut, T. ...
Journal of instrumentation,
08/2021, Letnik:
16, Številka:
8
Journal Article
Recenzirano
Odprti dostop
Abstract
Binned maximum likelihood fits are an attractive option when analysing large datasets, but require care when computing likelihoods of continuous PDFs in bins.
For many years the widely used ...statistical modelling package evaluated probabilities at the bin centre, leading to significant biases for strongly curved probability density functions.
We demonstrate the biases with real-world examples, and introduce a PDF class to that removes these biases.
The physics and computation performance of this new class are discussed.
Coccolithophores, a key phytoplankton group, are one of the most studied organisms regarding their physiological response to ocean acidification/carbonation. The biogenic production of calcareous ...coccoliths has made coccolithophores a promising group for paleoceanographic research aiming to reconstruct past environmental conditions. Recently, geochemical and morphological analyses of fossil coccoliths have gained increased interest in regard to changes in seawater carbonate chemistry. The cosmopolitan coccolithophore Emiliania huxleyi (Lohm.) Hay and Mohler was cultured over a range of pCO2 levels in controlled laboratory experiments under nutrient replete and nitrogen limited conditions. Measurements of photosynthesis and calcification revealed, as previously published, an increase in particulate organic carbon production and a moderate decrease in calcification from ambient to elevated pCO2 . The enhancement in particulate organic carbon production was accompanied by an increase in cell diameter. Changes in coccolith volume were best correlated with the coccosphere/cell diameter and no significant correlation was found between the coccolith volume and the particulate inorganic carbon production. The conducted experiments revealed that the coccolith volume of E. huxleyi is variable with aquatic CO2 concentration but its sensitivity is rather small in comparison with its sensitivity to nitrogen limitation. Comparing coccolith morphological and geometrical parameters like volume, mass and size to physiological parameters under controlled laboratory conditions is an important step to understand variations in fossil coccolith geometry.
The microalgae Dunaliella salina has the capacity to grow in salterns at high salinity. In this particular shallow environment, D. salina is exposed to strong light and temperature variations and has ...developed various strategies such as cell cycle adaptation and storage of dedicated metabolites. The effects of light/dark cycles have already been studied, but few works focused on the concomitant effects of light and temperature variations characterizing salterns and outdoor conditions. In this study, growth, carbon and nitrogen storage, pigments and lipid production of D. Salina were measured in laboratory conditions mimicking the outdoor light and temperature conditions. A control experiment with constant temperature was carried out with light variations only. During the night, cell respiration was correlated with temperature, following an Arrhenius law. Many differences with the control at constant temperature confirmed that temperature variations are a crucial parameter in outdoor conditions and should be taken into account to predict growth. Triglyceride and pigment production was tightly linked to the light dark cycle.
The aim of this study is to evaluate the consequences of accounting for variable Chl:C (chlorophyll:carbon) and C:N (carbon:nitrogen) ratios in the formulation of phytoplankton growth in ...biogeochemical models. We compare the qualitative behavior of a suite of phytoplankton growth formulations with increasing complexity: 1) a Redfield formulation (constant C:N ratio) without photo-acclimation (constant Chl:C ratio), 2) a Redfield formulation with diagnostic chlorophyll (variable and empirical Chl:C ratio), 3) a quota formulation (variable C:N ratio) with diagnostic chlorophyll, and 4) a quota formulation with prognostic chlorophyll (dynamic variable). These phytoplankton growth formulations are embedded in a simple marine ecosystem model in a 1D framework at the Bermuda Atlantic Time-series (BATS) station. The model parameters are tuned using a stochastic assimilation method (micro-genetic algorithm) and skill assessment techniques are used to compare results. The lowest misfits with observations are obtained when photo-acclimation is taken into account (variable Chl:C ratio) and with non-Redfield stoichiometry (variable C:N ratio), both under spring and summer conditions. This indicates that the most flexible models (i.e., with variable ratios) are necessary to reproduce observations. As seen previously, photo-acclimation is essential in reproducing the observed deep chlorophyll maximum and subsurface production present during summer. Although Redfield and quota formulations of C:N ratios can equally reproduce chlorophyll data the higher primary production that arises from the quota model is in better agreement with observations. Under the oligotrophic conditions that typify the BATS site no clear difference was detected between quota formulations with diagnostic or prognostic chlorophyll.
► We compare phytoplankton growth formulations with increasing complexity, after tuning through microgenetic algorithm. ► The most flexible models, i.e., with variable ratios, are necessary to reproduce observations under oligotrophic regimes. ► Photo-acclimation (variable Chl:C) is needed to reproduce the subsurface chlorophyll maximum in summer. ► Non-Redfield stoichiometry (variable C:N) is needed to simulate more realistic primary production estimates. ► No clear difference is detected between quota (non-Redfield) formulations with diagnostic or prognostic chlorophyll.
PDF
