Involvement of sulfoquinovosyl diacylglycerol in the structural integrity and heat-tolerance of photosystem II

To examine the role of sulfoquinovosyl diacylglycerol (SQDG) in thylakoid membranes, we compared the structural and functional properties of photosystem II (PSII) between a mutant of Chlamydomonas reinhardtii defective in SQDG ( hf-2) and the wild type. The PSII core complex of hf-2, as compared with that of the wild type, showed structural fragility when solubilized with a detergent, dodecyl beta- d-maltoside, suggesting that the physical properties of the PSII complex were altered by the loss of SQDG. On the other hand, exposure of the cells to 41 degrees C for 120 min in the dark decreased the PSII activity to 70% and 50% of the initial levels in the wild type and hf-2, respectively, which implies that the PSII activity, in the absence of SQDG, becomes less stable under heat-stress conditions. PSII inactivated to 60% of the initial level by dark incubation at 41 degrees C was reactivated by following illumination even at 41 degrees C to more than 90% in the wild type, but only to 70% in hf-2. These results suggest that PSII inactivated by heat recovers through some mechanism dependent on light, and that SQDG participates in functioning of the mechanism. The conformational disorder of PSII caused by the defect in SQDG might be correlated with the increased susceptibility of its activity to heat-stress.     

Characterization of α-nitromethyl ketone as a new zinc-binding group based on structural analysis of its complex with carboxypeptidase A

Zinc-binding groups (ZBGs) are exhaustively applied in the development of the new inhibitors against a wide variety of physiologically and pathologically important zinc proteases. Here the α-nitro ketone was presented as a new ZBG, which is a transition-state analog featured by the unique bifurcated hydrogen bonds at the active site of carboxypeptidase A based on the structural analysis. Introduction of a nitro group at the α-position of the ketone could provide more non-covalent interactions without loss of the abilities to form a tetrahedral transition-state analog.     

Thermodynamic and structural analysis of homodimeric proteins: model of β-lactoglobulin

The energetics of protein homo-oligomerization was analyzed in detail with the application of a general thermodynamic model. We have studied the thermodynamic aspects of protein-protein interaction employing β-lactoglobulin A from bovine milk at pH=6.7 where the protein is mainly in its dimeric form. We performed differential calorimetric scans at different total protein concentration and the resulting thermograms were analyzed with the thermodynamic model for oligomeric proteins previously developed. The thermodynamic model employed, allowed the prediction of the sign of the enthalpy of dimerization, the analysis of complex calorimetric profiles without transitions baselines subtraction and the obtainment of the thermodynamic parameters from the unfolding and the association processes and the compared with association parameters obtained with Isothermal Titration Calorimetry performed at different temperatures. The dissociation and unfolding reactions were also monitored by Fourier-transform infrared spectroscopy and the results indicated that the dimer of β-lactoglobulin (N(2)) reversibly dissociates into monomeric units (N) which are structurally distinguishable by changes in their infrared absorbance spectra upon heating. Hence, it is proposed that β-lactoglobulin follows the conformational path induced by temperature:N(2)?2N?2D. The general model was validated with these results indicating that it can be employed in the study of the thermodynamics of other homo-oligomeric protein systems.     

The structural integrity of TDP-43?N-terminus is required for efficient aggregate entrapment and consequent loss of protein function

ABSTRACT. Nuclear factor TDP-43 has been shown to play a key role in Amyotrophic Lateral Sclerosis and Frontotemporal Dementia, where TDP-43 aggregates accumulate in patient''s affected neurons and this event can cause neuronal dysfunction. A major focus of today''s research is to discover the critical factors that lead to TDP-43 aggregation and the consequences for neuronal metabolism. From a structural point of view, several lines of evidence point toward TDP-43 C-terminus as a key domain able to mediate this process. Regarding this region, we have recently described a novel cellular TDP-43 aggregation model based on 12 tandem repetitions of its 339-366 Q/N rich prion-like domain. In addition, we have shown and confirmed that a minimal TDP-43 construct constituted by the N and C-terminal regions, but lacking both RRM domains, induce aggregation of endogenous TDP-43 and leads to its total loss of function as seen by changes in the alternative splicing of endogenous genes. In this work, we further characterize this model and show the importance of the N-terminus structure in the loss of function process. In addition, from a biochemical point of view we report that, as shown in a previous version of this model (GFP 12×Q/N), the endogenous TDP-43 trapped in the aggregates undergoes the 2 most important post-translational modifications seen in pathological TDP-43 inclusions: ubiquitination and hyperphosphorylation.     

Can self-report instruments of shoulder function capture functional differences in older adults with and without a rotator cuff tear?

Rotator cuff tears (RCT) are prevalent in older individuals and may compound age-associated functional declines. Our purpose was to determine whether self-report measures of perceived functional ability are valid for older patients with RCT. Twenty five subjects participated (12M/13F; age = 63.9 ± 3.0 years); 13 with RCT and 12 controls (CON). Participants completed self-report measures of shoulder function (SST, ASES, WORC) and health-related quality of life (SF-36). Isometric joint moment and range of motion (ROM) were measured at the shoulder. Relationships among functional self-reports, and between these measures and joint moment and ROM were assessed; group differences for total and subcategory scores were evaluated. There were significant correlations among self-reports (r_s = 0.62–0.71, p ⩽ 0.02). For RCT subjects, ASES was associated with all joint moments except adduction (p ⩽ 0.02); SST, ASES, and WORC were associated with abduction and external rotation ROM (p ⩽ 0.04). For RCT subjects, SST and WORC were associated with SF-36 physical function subcategory scores (p ⩽ 0.05). The RCT group scored worse than CON on all functional self-reports (p < 0.01) and WORC and ASES subcategories (p < 0.01). In conclusion, SST, ASES, and WORC demonstrate utility and discriminant validity for older individuals by distinguishing those with RCT, but this work suggests prioritizing ASES given its stronger association with functional group strength.     

Can the presence of structural phosphorus help to discriminate between abiogenic and biogenic magnetites?

The influence of phosphate on the competitive formation of magnetite and lepidocrocite and the properties of magnetite prepared from mixtures of Fe(II) and Fe(III) salts were studied. Products were prepared at 90 °C and pH 12.5 (series 1), 50 °C and pH 7 (series 2) and 20 °C and pH 8 (series 3). The P/Fe atomic ratio in the initial solution ranged from 0 to 3% and the pH was kept at the desired value with NaOH or KOH. Air was used as oxidant in series 2 and 3. All products, which were characterized by X-ray diffraction, transmission electron microscopy, chemical analysis and IR spectroscopy, contained a phase intermediate between magnetite and maghemite (referred to as magnetite in this paper). The products of series 1 consisted only of magnetite at all P/Fe ratios, whereas both magnetite and lepidocrocite formed in series 2 and 3 above a certain P/Fe ratio. On increasing the P/Fe ratio in the initial solution, the magnetite crystals became smaller and more oxidized (i.e. closer to maghemite) and the lepidocrocite/magnetite ratio increased. The P associated with magnetite was partly in the form of occluded P, i.e. non-surface-adsorbed phosphate. IR spectra suggested this P to be structural and occurring as low-symmetry PO₄ units. Because abiogenic magnetites produced in various environments incorporate structural P but some well-characterized biogenic magnetites seem to contain no P or be formed in P-poor environments, we hypothesize that natural magnetites containing occluded P are unlikely to be biogenic. However, more studies are needed to discard the presence of P in biogenic magnetites.     

Can patterns of spatial autocorrelation reveal population processes? An analysis with the fire salamander

Spatial autocorrelation (SAC) is often observed in species distribution data, and can be caused by exogenous, autocorrelated factors determining species distribution, or by endogenous population processes determining clustering such as dispersal. However, it remains debated whether SAC patterns can actually reveal endogenous processes. We reviewed studies measuring dispersal of the salamander Salamandra salamandra, to formulate a priori hypotheses on the scale at which dispersal is expected to determine population distribution. We then tested the hypotheses by analysing SAC in distribution data, and evaluating whether controlling for the effect of environmental variables can reveal endogenous processes. We surveyed 565 streams to obtain species distribution data; we also recorded landscape and microhabitat features known to affect the species. We used multiple approaches to tease apart endogenous and exogenous SAC: the analysis of residuals of logistic regression models considering different environmental variables; the analysis of eigenvectors extracted by several implementations of spatial eigenvector mapping. In capture–mark–recapture studies, 98% of individuals moved 500 m or less. Both species distribution and environmental features were strongly autocorrelated. The residuals of logistic regression relating species to environmental variables were autocorrelated at distances up to 500 m; analyses considering different sets of environmental variables, or assuming non‐linear species habitat relationships, yielded identical results. The results of spatial eigenvector mapping strongly depended on the matrix of distances used. Nevertheless, the eigenvectors of models with best fit were autocorrelated at distances up to 200–500 m. The concordance between multiple approaches suggests that 500 m is the scale at which dispersal connects breeding localities, increasing probability of occurrence. If exogenous variables are correctly identified, the analysis of SAC can provide important insights on endogenous population processes, such as the flow of individuals. SAC analysis can also provide important information for conservation, as the existence of metapopulations or population networks is essential for long term persistence of amphibians.     

Can learning style predict student satisfaction with different instruction methods and academic achievement in medical education?

The curriculum of our medical school has a hybrid structure including both traditional training (lectures) and problem-based learning (PBL) applications. The purpose of this study was to determine the learning styles of our medical students and investigate the relation of learning styles with each of satisfaction with different instruction methods and academic achievement in them. This study was carried out with the participation of 170 first-year medical students (the participation rate was 91.4%). The researchers prepared sociodemographic and satisfaction questionnaires to determine the characteristics of the participants and their satisfaction levels with traditional training and PBL. The Kolb learning styles inventory was used to explore the learning styles of the study group. The participants completed all forms at the end of the first year of medical education. Indicators of academic achievement were scores of five theoretical block exams and five PBL exams performed throughout the academic year of 2008-2009. The majority of the participants took part in the "diverging" (n = 84, 47.7%) and "assimilating" (n = 73, 41.5%) groups. Numbers of students in the "converging" and "accommodating" groups were 11 (6.3%) and 8 (4.5%), respectively. In all learning style groups, PBL satisfaction scores were significantly higher than those of traditional training. Exam scores for "PBL and traditional training" did not differ among the four learning styles. In logistic regression analysis, learning style (assimilating) predicted student satisfaction with traditional training and success in theoretical block exams. Nothing predicted PBL satisfaction and success. This is the first study conducted among medical students evaluating the relation of learning style with student satisfaction and academic achievement. More research with larger groups is needed to generalize our results. Some learning styles may relate to satisfaction with and achievement in some instruction methods.     

Conjugation of α-amylase with dextran for enhanced stability: Process details, kinetics and structural analysis

The influence of enzyme polysaccharide interaction on enzyme stability and activity was elucidated by covalently binding dextran to a model enzyme, α-amylase. The conjugation process was optimized with respect to concentration of oxidizing agent, pH of enzyme solution, ratio of dextran to enzyme concentration, temperature and time of conjugate formation, and was found to affect the stability of α-amylase. α-Amylase conjugated under optimized conditions showed 5% loss of activity but with enhanced thermal and pH stability. Lower inactivation rate constant of conjugated α-amylase within the temperature range of 60-80°C implied its better stability. Activation energy for denaturation of α-amylase increased by 8.81kJ/mol on conjugation with dextran. Analysis of secondary structure of α-amylase after covalent binding with dextran showed helix to turn conversion without loss of functional properties of α-amylase. Covalent bonding was found to be mandatory for the formation of conjugate.     

Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?

The determination of G protein-coupled receptor (GPCR) structures at atomic resolution has improved understanding of cellular signaling and will accelerate the development of new drug candidates. However, experimental structures still remain unavailable for a majority of the GPCR family. GPCR structures and their interactions with ligands can also be modelled computationally, but such predictions have limited accuracy. In this work, we explored if molecular dynamics (MD) simulations could be used to refine the accuracy of in silico models of receptor-ligand complexes that were submitted to a community-wide assessment of GPCR structure prediction (GPCR Dock). Two simulation protocols were used to refine 30 models of the D₃ dopamine receptor (D₃R) in complex with an antagonist. Close to 60 μs of simulation time was generated and the resulting MD refined models were compared to a D₃R crystal structure. In the MD simulations, the receptor models generally drifted further away from the crystal structure conformation. However, MD refinement was able to improve the accuracy of the ligand binding mode. The best refinement protocol improved agreement with the experimentally observed ligand binding mode for a majority of the models. Receptor structures with improved virtual screening performance, which was assessed by molecular docking of ligands and decoys, could also be identified among the MD refined models. Application of weak restraints to the transmembrane helixes in the MD simulations further improved predictions of the ligand binding mode and second extracellular loop. These results provide guidelines for application of MD refinement in prediction of GPCR-ligand complexes and directions for further method development.     

Hormones and root-shoot relationships in flooded plants — an analysis of methods and results

Two aspects of root to shoot communication in flooded plants are discussed (i) the formation of porous aerenchyma that enhances the passage of oxygen, and other gases, from shoots to roots and (ii) the movement of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) from roots to shoots in the transpiration stream, and the effect of this on ethylene production and epinastic curvature in the shoots. For aerenchyma studies a highly sensitive photoacoustic laser detector for ethylene was used to avoid interference associated with other methods of ethylene measurement that require tissue excision. ACC concentrations in xylem sap were measured by physico-chemical means to ensure correct identification and account for processing losses. Solute concentrations, e.g., abscisic acid (ABA), in xylem sap are shown to be distorted by temporary contamination caused by the method used to collect sap. Concentrations of solutes in xylem sap (e.g., ACC) are also altered by changes in sap flow brought about by conventional methods of sap collection or by experimental treatments such as flooding the soil. Ways of for overcoming these problems are described together with a summary of preliminary results.     

How to identify and quantify the members of the Bacillus genus?

Members of the Bacillus genus are widely distributed throughout natural environments and have been studied for decades among others for their physiology, genetics, ecological functions, and applications. However, despite its prevalence in nature, the characterization and classification of Bacillus remain challenging due to its complex and ever-evolving taxonomic framework. This review addresses the current state of the Bacillus taxonomic landscape and summarizes the critical points in the development of Bacillus phylogeny. With a clear view of Bacillus phylogeny as a foundation, we subsequently review the methodologies applied in identifying and quantifying Bacillus, while also discussing their respective advantages and disadvantages.     

Prognostic analysis of Behçet’s disease with aortic regurgitation or involvement

Background

Aortic regurgitation is the most common cardiovascular damage in Chinese patients with Behçet’s disease (BD) and is usually associated with aortic disease. These patients are easily misdiagnosed, and their prognosis is poor, even after surgical treatment. This study aimed to analyse potential factors that can improve the prognosis of BD patients with aortic regurgitation and/or aortic involvement.

Methods

Twenty-two patients with diagnosed or suspected BD as well as aortic regurgitation and/or aortic involvement in our hospital from 2012 through 2017 were collected in this study. Their clinical characteristics were listed, and the diagnosis of BD was evaluated by two different criteria sets. The influences of surgical treatment and immunosuppressive therapy (IST) on their prognosis were also explored.

Results

The diagnostic positive rate of the International Criteria for Behçet’s Disease was higher than that of the International Study Group criteria (kappa value 0.31, p?<?0.05), indicating that the diagnostic consistency between the criteria sets was poor. There was no significant difference in survival between patients who had undergone ≤?1 operation and those with ≥?2 operations. Aortic valve replacement alone or in combination with aortic root replacement had no significant effect on the incidence of reoperation or death, but IST did significantly reduce this incidence (p?<?0.05). However, there was no significant difference in the occurrence of reoperation or death between preoperative and postoperative IST versus postoperative IST only.

Conclusion

IST significantly improved the prognosis of BD patients with aortic regurgitation and/or aortic involvement.