In Silico Analysis of the Molecular-Level Impact of SMPD1 Variants on Niemann-Pick Disease Severity

Sphingomyelin phosphodiesterase (SMPD1) is a key enzyme in the sphingolipid metabolism. Genetic SMPD1 variants have been related to the Niemann-Pick lysosomal storage disorder, which has different degrees of phenotypic severity ranging from severe symptomatology involving the central nervous system (type A) to milder ones (type B). They have also been linked to neurodegenerative disorders such as Parkinson and Alzheimer. In this paper, we leveraged structural, evolutionary and stability information on SMPD1 to predict and analyze the impact of variants at the molecular level. We developed the SMPD1-ZooM algorithm, which is able to predict with good accuracy whether variants cause Niemann-Pick disease and its phenotypic severity; the predictor is freely available for download. We performed a large-scale analysis of all possible SMPD1 variants, which led us to identify protein regions that are either robust or fragile with respect to amino acid variations, and show the importance of aromatic-involving interactions in SMPD1 function and stability. Our study also revealed a good correlation between SMPD1-ZooM scores and in vitro loss of SMPD1 activity. The understanding of the molecular effects of SMPD1 variants is of crucial importance to improve genetic screening of SMPD1-related disorders and to develop personalized treatments that restore SMPD1 functionality.     

The use of epilithic Antarctic lichens (Usnea aurantiacoatra and U. antartica) to determine deposition patterns of heavy metals in the Shetland Islands, Antarctica

Trace-metal contents were recorded for the epilithic antarctic lichens Usnea aurantiacoatra and U. antartica, sampled close to the Argentine scientific station 'Jubany' on '25 de Mayo' (King George) Island, in the Southern Shetland Archipelago (Antarctica). The corresponding heavy-metal levels have been measured through atomic absorption spectrophotometry, following internationally accepted analytical methods. The results obtained support the hypothesis that an atmospheric circulation of trace metals exists on the assessed area, and the activities developed at the different scientific stations located on this island would be a potential source of heavy metals to the evaluated environment. The geographical distribution of trace metals atmospherically transported in the area close to 'Jubany Station' was studied through the corresponding metal contents of the assessed lichens. Finally, the suitability of both analyzed lichen species, Usnea aurantiacoatra and U. antartica, as biological indicators for quantitative monitoring of airborne metals for this antarctic environment was recognized.     

Proinflammatory Interleukin-33 Induces Dichotomic Effects on Cell Proliferation in Normal Gastric Epithelium and Gastric Cancer

Interleukin (IL)-33 is a member of the interleukin (IL)-1 family of cytokines linked to the development of inflammatory conditions and cancer in the gastrointestinal tract. This study is designed to investigate whether IL-33 has a direct effect on human gastric epithelial cells (GES-1), the human gastric adenocarcinoma cell line (AGS), and the gastric carcinoma cell line (NCI-N87) by assessing its role in the regulation of cell proliferation, migration, cell cycle, and apoptosis. Cell cycle regulation was also determined in ex vivo gastric cancer samples obtained during endoscopy and surgical procedures. Cell lines and tissue samples underwent stimulation with rhIL-33. Proliferation was assessed by XTT and CFSE assays, migration by wound healing assay, and apoptosis by caspase 3/7 activity assay and annexin V assay. Cell cycle was analyzed by means of propidium iodine assay, and gene expression regulation was assessed by RT-PCR profiling. We found that IL-33 has an antiproliferative and proapoptotic effect on cancer cell lines, and it can stimulate proliferation and reduce apoptosis in normal epithelial cell lines. These effects were also confirmed by the analysis of cell cycle gene expression, which showed a reduced expression of pro-proliferative genes in cancer cells, particularly in genes involved in G0/G1 and G2/M checkpoints. These results were confirmed by gene expression analysis on bioptic and surgical specimens. The aforementioned results indicate that IL-33 may be involved in cell proliferation in an environment- and cell-type-dependent manner.     

Characterisation of mortar morphology in thin sections by digital image processing

A digital imaging approach was applied to investigate mortar morphology in thin sections; in particular, the binder/aggregate ratio and the grading curve of five mortar bars were attained by digital image processing (DIP), using the Image Pro Plus 4.1 software package. The imaging procedure employed image segmentation, to extract mortar aggregate, and image filtering, to fix grain boundaries. The results show that digital image processing may be considered as an alternative method to mechanical sieving for the characterisation of mortar morphology, as it appears to be quicker and more accurate than the traditional method. However, digital image processing exhibits limits, which are discussed in the text.     

Sketching human character animations by composing sequences from large motion database

Quick creation of 3D character animations is an important task in game design, simulations, forensic animation, education, training, and more. We present a framework for creating 3D animated characters using a simple sketching interface coupled with a large, unannotated motion database that is used to find the appropriate motion sequences corresponding to the input sketches. Contrary to the previous work that deals with static sketches, our input sketches can be enhanced by motion and rotation curves that improve matching in the context of the existing animation sequences. Our framework uses animated sequences as the basic building blocks of the final animated scenes, and allows for various operations with them such as trimming, resampling, or connecting by use of blending and interpolation. A database of significant and unique poses, together with a two-pass search running on the GPU, allows for interactive matching even for large amounts of poses in a template database. The system provides intuitive interfaces, an immediate feedback, and poses very small requirements on the user. A user study showed that the system can be used by novice users with no animation experience or artistic talent, as well as by users with an animation background. Both groups were able to create animated scenes consisting of complex and varied actions in less than 20 minutes.     

Alder ene functionalization of polyisobutene oligomer and styrene-butadiene-styrene triblock copolymer

The Alder ene functionalization reaction of double bonds containing macromolecules such as polyisobutene oligomer (PIB) and a styrene-butadiene-styrene triblock copolymer (SBS) samples with maleic anhydride (MAH) or diethyl maleate (DEM) as enophiles is described. The analysis of the products by means of different techniques assesses the addition of the polar molecules to the reactive vinylidene units of the polymer with functional degrees (FD) depending on the type of enophile and polymer reactivity. The role of the reaction conditions and the use as Lewis acids as catalysts are discussed in terms of their influence on the addition reaction extent and on the polymer molecular weight.     

Kinetic folding mechanism of PDZ2 from PTP-BL

PDZ domains represent a large family of protein-interaction modules associated with a variety of unrelated proteins with different functions. We report a complete characterization of the kinetic folding mechanism of a fluorescent variant of PDZ2 from PTP-BL, investigated under a variety of different experimental conditions. For this purpose, we engineered a fluorescent variant of this protein Y43W (called pseudo-wild-type, pWT43). The results suggest the presence of a high-energy intermediate in the folding of PDZ2, as revealed by a pronounced non-linear dependence of the unfolding rate constant on denaturant concentration. Such an intermediate may or may not be detectable depending on the experimental conditions, giving rise to apparent two-state folding under stabilizing conditions (e.g. in the presence of sodium sulfate). Interestingly, even under these conditions, three-state folding can be restored by selectively destabilizing the native-like rate-limiting barrier by one specific mutation (V44A). Finally, we show that data taken on pWT43 under different experimental conditions (e.g. different pH values from 2.1 to 8.0 or in the presence of a stabilizing salt) and also data on a site-directed conservative mutant can be rationalized in terms of a simple reaction scheme involving a single set of intermediates and transition states.     

Artificial institutions: a model of institutional reality for open multiagent systems

Software agents’ ability to interact within different open systems, designed by different groups, presupposes an agreement on an unambiguous definition of a set of concepts, used to describe the context of the interaction and the communication language the agents can use. Agents’ interactions ought to allow for reliable expectations on the possible evolution of the system; however, in open systems interacting agents may not conform to predefined specifications. A possible solution is to define interaction environments including a normative component, with suitable rules to regulate the behaviour of agents. To tackle this problem we propose an application-independent metamodel of artificial institutions that can be used to define open multiagent systems. In our view an artificial institution is made up by an ontology that models the social context of the interaction, a set of authorizations to act on the institutional context, a set of linguistic conventions for the performance of institutional actions and a system of norms that are necessary to constrain the agents’ actions.