Proteasome activity profiling: a simple,robust and versatile method revealing subunit‐selective inhibitors and cytoplasmic,defense‐induced proteasome activities

The proteasome plays essential roles in nearly all biological processes in plant defense and development, yet simple methods for displaying proteasome activities in extracts and living tissues are not available to plant science. Here, we introduce an easy and robust method to simultaneously display the activities of all three catalytic proteasome subunits in plant extracts or living plant tissues. The method is based on a membrane‐permeable, small‐molecule fluorescent probe that irreversibly reacts with the catalytic site of the proteasome catalytic subunits in an activity‐dependent manner. Activities can be quantified from fluorescent protein gels and used to study proteasome activities in vitro and in vivo. We demonstrate that proteasome catalytic subunits can be selectively inhibited by aldehyde‐based inhibitors, including the notorious caspase‐3 inhibitor DEVD. Furthermore, we show that the proteasome activity, but not its abundance, is significantly increased in Arabidopsis upon treatment with benzothiadiazole (BTH). This upregulation of proteasome activity depends on NPR1, and occurs mostly in the cytoplasm. The simplicity, robustness and versatility of this method will make this method widely applicable in plant science.     

Interim analysis incorporating short‐ and long‐term binary endpoints

Designs incorporating more than one endpoint have become popular in drug development. One of such designs allows for incorporation of short‐term information in an interim analysis if the long‐term primary endpoint has not been yet observed for some of the patients. At first we consider a two‐stage design with binary endpoints allowing for futility stopping only based on conditional power under both fixed and observed effects. Design characteristics of three estimators: using primary long‐term endpoint only, short‐term endpoint only, and combining data from both are compared. For each approach, equivalent cut‐off point values for fixed and observed effect conditional power calculations can be derived resulting in the same overall power. While in trials stopping for futility the type I error rate cannot get inflated (it usually decreases), there is loss of power. In this study, we consider different scenarios, including different thresholds for conditional power, different amount of information available at the interim, different correlations and probabilities of success. We further extend the methods to adaptive designs with unblinded sample size reassessments based on conditional power with inverse normal method as the combination function. Two different futility stopping rules are considered: one based on the conditional power, and one from P‐values based on Z‐statistics of the estimators. Average sample size, probability to stop for futility and overall power of the trial are compared and the influence of the choice of weights is investigated.     

Roles of Soil Organic Matter and Humic Substance Structure in Cu and Pb Adsorption in Histosols

ABSTRACT

Histosols have a high organic matter content and therefore a high variability of structures and chemical functional groups with adsorptive capacity. This study aimed to select the most appropriate models to describe the sorption phenomena of Cu and Pb in Histosols, identify the types of bonds between these metals and soil samples, and assess the influence of soil attributes and soil humic substance structures on these bonds. The Freundlich and Langmuir models were selected based on the values of the corrected Akaike information criterion and variation of Akaike information criterion as the best models for describing Cu and Pb sorption in Histosols. The values of the adsorption coefficients provided by the models indicated that Pb has higher affinity with the studied soil relative to Cu. However, Cu adsorption to soil occurs specifically and Pb is adsorbed nonspecifically. In general, the contents of N and fulvic acids were the factors that most influenced Pb sorption. Pb has a higher association with more aliphatic fulvic character structures, while Cu has a higher association with soil humic character structures. Therefore, compared to Cu, Pb in the studied Histosol has greater bioavailability potential and, consequently, greater risks of contamination and entering the food chain.     

Analysis of binding properties and specificity through identification of the interface forming residues (IFR) for serine proteases <Emphasis Type="Italic">in silico</Emphasis> docked to different inhibitors

Background  

Enzymes belonging to the same super family of proteins in general operate on variety of substrates and are inhibited by wide selection of inhibitors. In this work our main objective was to expand the scope of studies that consider only the catalytic and binding pocket amino acids while analyzing enzyme specificity and instead, include a wider category which we have named the Interface Forming Residues (IFR). We were motivated to identify those amino acids with decreased accessibility to solvent after docking of different types of inhibitors to sub classes of serine proteases and then create a table (matrix) of all amino acid positions at the interface as well as their respective occupancies. Our goal is to establish a platform for analysis of the relationship between IFR characteristics and binding properties/specificity for bi-molecular complexes.     

Drosophila Nimrod proteins bind bacteria

Engulfment of foreign particles by phagocytes is initiated by the engagement of phagocytic receptors. We have previously reported that NimC1 is involved in the phagocytosis of bacteria in Drosophila melanogaster. We have identified a family of genes, the Nimrod gene superfamily, encoding characteristic NIM domain containing structural homologues of NimC1. In this work we studied the bacterium-binding properties of the Nimrod proteins by using a novel immunofluorescencebased flow cytometric assay. This method proved to be highly reproducible and suitable for investigations of the bacteriumbinding capacities of putative phagocytosis receptors. We found that NimC1, NimA, NimB1 and NimB2 bind bacteria significantly but differently. In this respect they are similar to other NIM domain containing receptors Eater and Draper.