Structural elucidation of polymethoxyflavones from shift reagent proton NMR measurements

The quantitative shift reagent behavior of polymethoxylated flavones in the presence of Pr(fod)₃ shows that for structural elucidation of these molecules the degree of substitution in the neighborhood of the carbonyl group can be determined from the number of signals that are strongly shifted and broadened. The induced shifts of the remaining signals are of complementary help and even the resonances of individual methoxyl groups can be ascribed.     

Factors initiating algal life-form shift from sediment to water

In enclosure and whole-lake experiments, I tested whether life-form shift (recruitment) is a passive process induced by turbulence, a seasonal phenomenon, or a behavior that can be induced by alterations in environmental variables. The number of algal cells recruited from the sediment varied considerably during the experimental period. The most important migrating genera in this study were: Cryptomonas, Dinobryon, Gonyostomum, Gymnodinium, Peridinium, and Synura. An obvious conclusion is that it is not the same factor in each case that causes life-form shift, but that different triggering factors operate in different algal species. Turbulence and temperature were similar in all treatments and therefore did not cause the considerable fluctuations and trends in algal recruitment in the enclosures. This suggests that life0form shift is not a passive process driven by wind and temperature-induced currents. In the enclosure experiment, alterations in the light régime explained a major part (up to 53%) of the variation in recruitment for most genera. For Gymnodinium this was corroborated in the whole-lake experiment, where the depth of the euphotic zone explained 41% of the variation in recruitment. For Cryptomonas, however, 64% of the variation in recruitment was explained by the depth of the oxycline, whereas 52% of the variation in recruitment of Synura were explained by the depths of the euphotic zone and the oxyline. Peridinium pusillum and P. wisconsinense showed low recruitment at high zooplankton abundance and high recruitment at low zoo-plankton abundance in the lake experiment, as well as in the enclosure experiment. Thus, the hypothesis that the presence of grazers can induce shifts in behaviour of some algal groups cannot be rejected.     

The role of competitive learning in the generation of DG fields from EC inputs

We follow up on a suggestion by Rolls and co-workers, that the effects of competitive learning should be assessed on the shape and number of spatial fields that dentate gyrus (DG) granule cells may form when receiving input from medial entorhinal cortex (mEC) grid units. We consider a simple non-dynamical model where DG units are described by a threshold-linear transfer function, and receive feedforward inputs from 1,000 mEC model grid units of various spacing, orientation and spatial phase. Feedforward weights are updated according to a Hebbian rule as the virtual rodent follows a long simulated trajectory through a single environment. Dentate activity is constrained to be very sparse. We find that indeed competitive Hebbian learning tends to result in a few active DG units with a single place field each, rounded in shape and made larger by iterative weight changes. These effects are more pronounced when produced with thousands of DG units and inputs per DG unit, which the realistic system has available, than with fewer units and inputs, in which case several DG units persists with multiple fields. The emergence of single-field units with learning is in contrast, however, to recent data indicating that most active DG units do have multiple fields. We show how multiple irregularly arranged fields can be produced by the addition of non-space selective lateral entorhinal cortex (lEC) units, which are modelled as simply providing an additional effective input specific to each DG unit. The mean number of such multiple DG fields is enhanced, in particular, when lEC and mEC inputs have overall similar variance across DG units. Finally, we show that in a restricted environment the mean size of the fields is unaltered, while their mean number is scaled down with the area of the environment.

Extraction of bovine serum albumin with reverse micelles from glucosylammonium and lactosylammonium surfactants

Reverse micelle extraction is still in the stage of laboratory. Major limitation associated with use of synthetic surfactants in reverse micelle extraction process is the unfolding or denaturation of proteins. Sugar surfactants are thought non-toxic and environmentally benign, and can exhibit interesting interfacial properties, but the application of sugar-based surfactants in protein extraction is still limited. In the present study, we extracted bovine serum albumin (BSA) by using reverse micelles from glucosylammonium (GA) and lactosylammonium (LA) surfactants (with dicarboxylate as counter ion). It was found that under optimum condition, (1) the maximum forward extraction efficiency was ca. 86% with GA, while only around 50% with LA, and (2) almost all BSA solubilized in reverse micelles prepared from GA could be recovered into aqueous phase, while the recovery of BSA from the reverse micelles of LA was lower. In addition, the optimum extraction parameters were closely related to surfactant structure. Therefore, the electrostatic interaction, H-bonding and sugar head size should be important for BSA transfer.     

Anoxia-induced dopamine release from rat striatal slices: involvement of reverse transport mechanism

Incubation of rat striatal slices in the absence of oxygen (anoxia), glucose (aglycemia), or oxygen plus glucose (ischemia) caused significant increases in dopamine (DA) release. Whereas anoxia decreased extracellular 3,4-dihydroxyphenylacetic acid levels by 50%, aglycemia doubled it, and ischemia returned this aglycemia-induced enhancement to its control level. Although nomifensine, a DA uptake blocker, completely protected the slices against anoxia-induced DA depletion, aglycemia- and ischemia-induced increases were not altered. Moreover, hypothermia differentially affected DA release stimulated by anoxia, aglycemia, and ischemia. Involvement of glutamate in DA release induced by each experimental condition was tested by using MK-801 and also by comparing the glutamate-induced DA release with that during anoxia, aglycemia, or ischemia. MK-801 decreased the anoxia-induced DA depletion in a dose-dependent manner. This treatment, however, showed a partial protection in aglycemic conditions but failed to improve ischemia-induced DA depletion. Like anoxia, DA release induced by exogenous glutamate was also sensitive to nomifensine and hypothermia. These results indicate that anoxia enhances DA release by a mechanism involving both the reversed DA transporter and endogenous glutamate. Partial or complete lack of effect of nomifensine, hypothermia, or MK-801 in the absence of glucose or oxygen plus glucose also suggests that experimental conditions, such as the degree of anoxia/ischemia, may alter the mechanism(s) involved in DA depletion.     

De novo protein structure generation from incomplete chemical shift assignments

NMR chemical shifts provide important local structural information for proteins. Consistent structure generation from NMR chemical shift data has recently become feasible for proteins with sizes of up to 130 residues, and such structures are of a quality comparable to those obtained with the standard NMR protocol. This study investigates the influence of the completeness of chemical shift assignments on structures generated from chemical shifts. The Chemical-Shift-Rosetta (CS-Rosetta) protocol was used for de novo protein structure generation with various degrees of completeness of the chemical shift assignment, simulated by omission of entries in the experimental chemical shift data previously used for the initial demonstration of the CS-Rosetta approach. In addition, a new CS-Rosetta protocol is described that improves robustness of the method for proteins with missing or erroneous NMR chemical shift input data. This strategy, which uses traditional Rosetta for pre-filtering of the fragment selection process, is demonstrated for two paramagnetic proteins and also for two proteins with solid-state NMR chemical shift assignments. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Bacteriorhodopsin (BR570) bathochromic band shift in an external electric field

In dry films of bacteriorhodopsin-containing purple membranes from Halobacterium halobium the external electric field (10⁴–10⁵ V · cm^?1) induces the appearance of a product spectrally close to the initial intermediate of bacteriorhodopsin (BR) photochromic cycle (batho form, K). This result and also preliminary data of the electret-thermal analysis of the preparations suggest that the dielectric polarization in chromophore-protein-lipid complexes might be an essential step of the primary stabilization of light energy in photo-bioenergetic processes.     

Stability and Enzymatic Studies of Glucose Dehydrogenase from the Archaeon Haloferax mediterranei in reverse micelles

Reverse micelles were used as a cytoplasmic model to study the kinetics of an extreme halophilic enzyme such as the recombinant glucose dehydrogenase from the Archaeon Haloferax mediterranei. This enzyme was solubilized in reverse micelles of hexadecyltrimethylammoniumbromide in cyclohexane, with 1-butanol as co-surfactant. Glucose dehydrogenase retained its catalytic properties in this organic medium, showing good stability at low water content, even at low salt concentration (125 mM NaCl). The dependence of the enzymatic activity on the molar water surfactant ratio (w₀=[H₂O]/[surfactant]) increased with rising water content. Surprisingly, the activity of this extreme halophilic enzyme did not depend on the salt concentration in reverse micelles. The kinetic of the enzymatic oxidation of β-D-glucose to D-glucono-1,5-lactone using NADP⁺ as coenzyme for the glucose dehydrogenase from Haloferax mediterranei was also studied in the reverse micellar system.     

SimShiftDB; local conformational restraints derived from chemical shift similarity searches on a large synthetic database

We present SimShiftDB, a new program to extract conformational data from protein chemical shifts using structural alignments. The alignments are obtained in searches of a large database containing 13,000 structures and corresponding back-calculated chemical shifts. SimShiftDB makes use of chemical shift data to provide accurate results even in the case of low sequence similarity, and with even coverage of the conformational search space. We compare SimShiftDB to HHSearch, a state-of-the-art sequence-based search tool, and to TALOS, the current standard tool for the task. We show that for a significant fraction of the predicted similarities, SimShiftDB outperforms the other two methods. Particularly, the high coverage afforded by the larger database often allows predictions to be made for residues not involved in canonical secondary structure, where TALOS predictions are both less frequent and more error prone. Thus SimShiftDB can be seen as a complement to currently available methods.     

Purification of nattokinase by reverse micelles extraction from fermentation broth: effect of temperature and phase volume ratio

Nattokinase is a novel fibrinolytic enzyme that is considered to be a promising agent for thrombosis therapy. In this study, reverse micelles extraction was applied to purify and concentrate nattokinase from fermentation broth. The effects of temperature and phase volume ratio used for the forward and backward extraction on the extraction process were examined. The optimal temperature for forward and backward extraction were 25°C and 35°C respectively. Nattokinase became more thermosensitive during reverse micelles extraction. And it could be enriched in the stripping phase eight times during backward extraction. It was found that nattokinase could be purified by AOT reverse micelles with up to 80% activity recovery and with a purification factor of 3.9.     

Integrated diversity analysis of the microbial community in a reverse osmosis system from a Brazilian oil refinery

Oil refineries are known for the large volume of water used in their processes, as well as the amount of wastewater generated at the end of the production chain. Due to strict environmental regulations, the recycling of water has now become a viable alternative for refineries. Among the many methods available to treat wastewater for reuse, the use of membranes in reverse osmosis systems stands out due to several economic and environmental benefits. However, these systems are vulnerable to contamination and deposition of microorganisms, mainly because of the feedwater quality. In this study, the microbial diversity of feedwater and reverse osmosis membranes was investigated using a combination of culture-dependent and culture-independent methods in order to characterize the microorganisms colonizing and deteriorating the membranes. In total, 37 bacterial isolates, 17 filamentous fungi and approximately 400 clones were obtained and analyzed. Among the bacterial genera identified, the most represented were Sphingobium, Acidovorax, Microbacterium, Rhizobium and Shinella. The results revealed genera that acted as candidate key players in initial biofilm formation in membrane systems, and provided important information concerning the microbial ecology of oligotrophic aquatic systems.     

Over-shading is critical for inducing a regime shift from heathland to grassland under nitrogen enrichment

The mass conversion of heathland to grassland in north-western Europe the past decades is a typical example of how tipping points threaten the biodiversity and ecosystem services delivered by biota. Different explanations have been provided for this conversion, with nitrogen enrichment resulting from anthropogenic activities being a commonly supported hypothesis. Here we present a mathematical model to investigate the conditions under which the conversion of heathland to grassland can occur. The model describes indirect competition for light and nitrogen between heather dwarf shrub (Calluna vulgaris) and wavy hair-grass (Deschampsia flexuosa), while both species also over-shade each other. Nutrient co-limitation in the model is described using the Synthesizing Unit concept. Over-shading is found to play a pivotal role in the existence of alternative stable states in the model. Under constant light availability a combination of over-shading and enrichment with ammonia leads to a regime shift from heathland to grassland, while under enrichment with ammonia alone there is coexistence between the two species. These results are supported by experimental findings in the literature.     

Estimation of protein secondary structure content directly from NMR spectra using an improved empirical correlation with averaged chemical shift

We have recently shown that the averaged chemical shift (ACS) of a nucleus in the protein backbone correlates well empirically to its secondary structure content (SSC). This allows the estimation of SSC directly from the NMR spectrum without the time intensive process of chemical shift assignment. Here, we present an empirical correlation that accounts both for contributions to the relevant protein and chemical shift databases made subsequent to the original analysis, and for missing or inconsistently referenced resonances. Our results affirm that this method provides a significant tool for initial structural prediction from NMR data prior to complete chemical shift assignment.     

沉积物记录揭示的深圳湾红树林生态系统稳态转变

稳态转换作为滨海生态系统的一种灾变现象,其过程伴随着生态系统质量下降和功能退化。深圳湾位于粤港澳大湾区的核心区域,深入理解其生态系统演化过程是进行适应性管理的重要前提。2014年于深圳湾福田红树林湿地获得4根岩芯沉积柱,通过分析沉积和生物地球化学指标（包括金属元素、营养盐、粒度和有机质指标）,重建半个世纪以来深圳湾环境的历史变迁,揭示其生态系统发生的稳态转变过程。结果表明：稳态转换发生前（1954-1980）,福田红树林沉积物中重金属、无机营养和有机物含量稳定增加,但处于较低水平;稳态转换发生后（1990-2014）,深圳湾中污染输入增加,沉积物中重金属和营养盐含量发生明显变化,深圳湾生态系统质量持续下降。通过揭示深圳湾生态系统演变过程及其稳态转变的发生规律,为粤港澳大湾区生态系统修复和管理提供重要的理论依据和参考。     

Three-dimensional electron microscopy of the reverse gyrase from Sulfolobus tokodaii

Reverse gyrase is a type IA topoisomerase, found in various hyperthermophiles and promotes ATP-dependent positive supercoiling of DNA. Electron microscopy combined with single particle analyses revealed the three-dimensional structure of the DNA-free Sulfolobus tokodaii reverse gyrase and two-dimensional average images of both the protein alone and that complexed with double-stranded DNA. The 23A resolution map exhibited a parallelogrammatic morphology of 110 x 87 x 43A, which is in good agreement with the crystal structure of the Archaeoglobus fulgidus reverse gyrase. The average image of the complex revealed that the monomeric enzyme binds DNA duplex. Together with this average image of the complex, the three-dimensional map implies that, at the beginning of the supercoiling reaction, DNA is bound within a 10-20A wide cleft in the helicase-like domain. We also speculate that DNA may pass through a 20A wide hole at the end of the cleft.