An open and parallel multiresolution framework using block-based adaptive grids

A numerical approach for solving evolutionary partial differential equations in two and three space dimensions on block-based adaptive grids is presented. The numerical discretization is based on high-order, central finite-differences and explicit time integration. Grid refinement and coarsening are triggered by multiresolution analysis, i.e. thresholding of wavelet coefficients, which allow controlling the precision of the adaptive approximation of the solution with respect to uniform grid computations. The implementation of the scheme is fully parallel using MPI with a hybrid data structure. Load balancing relies on space filling curves techniques. Validation tests for 2D advection equations allow to assess the precision and performance of the developed code. Computations of the compressible Navier-Stokes equations for a temporally developing 2D mixing layer illustrate the properties of the code for nonlinear multi-scale problems. The code is open source

Bacterial cellulose : production and applications

Bacterial cellulose (BC), excreted by Gluconacetobacter xylinus, is a unique nanofibrilar biopolymer with a wide range of applications in human and veterinary medicine, odonthology, pharmaceutical industry, biotechnological, food and paper industry. The major research activities of our research group include the following headlines: - Surface-modification of BC matrices and BC whiskers for the design of novel functional BC nanocomposite systems. This domain includes the surface-activation of BC with CBMs (Carbohydrate Binding Modules) conjugated with bioactive peptides for biomedical applications.[1] CEB-UM has already shown that the adsorption of CBM-RGD (the minimal essential cell adhesion recognition motifs) onto BC improves its ability to adsorb fibroblasts.[2] Also, research on the use of BC tubes as new guides for neuronal growth (CAPES, 3989/05-4) and, for the first time, on assessing the in vivo cytotoxicity of BC nanofibers (SFRH/BD/18418/2004), is on course. - Design of novel BC structures with tailored microporosity, for biomedical applications (SFRH/BD/48759/2008). - Engineering of electro-conductive and electro-active BC scaffolds with potential applications in neuronal growth. The embedded polymeric directionally of the BC nanofibers is expected to exhibit shear piezoelectricity which, coupled with a high in situ moldability, thrusts a promising future for novel BC-based materials such as lightweight, biodegradable electro-actives, biosensors and flexible electric displays, with a tailored oriented stiffness and strength. - Exploring the large-scale fermentation of BC. A novel bioreactor, based on a surfaceculture method was designed. A simple and low-cost piece of equipment is capable of direct nebulization of a high volume of dispersed and microparticulated subtrate over the growing bacteria. The developed system may reveal to be an interesting economic solution for the large-scale production of BC

Development of a strategy to functionalize a dextrin-based hydrogel for animal cell cultures using a starch-binding module fused to RGD sequence

Several approaches can be used to functionalize biomaterials, such as hydrogels, for biomedical applications. One of the molecules often used to improve cells adhesion is the peptide Arg-Gly-Asp (RGD). The RGD sequence, present in several proteins from the extra-cellular matrix (ECM), is a ligand for integrin-mediated cell adhesion; this sequence was recognized as a major functional group responsible for cellular adhesion. In this work a bi-functional recombinant protein, containing a starch binding module (SBM) and RGD sequence was used to functionalize a dextrin-based hydrogel. The SBM, which belongs to an α-amylase from Bacillus sp. TS-23, has starch (and dextrin, depolymerized starch) affinity, acting as a binding molecule to adsorb the RGD sequence to the hydrogel surface. Results The recombinant proteins SBM and RGD-SBM were cloned, expressed, purified and tested in in vitro assays. The evaluation of cell attachment, spreading and proliferation on the dextrin-based hydrogel surface activated with recombinant proteins were performed using mouse embryo fibroblasts 3T3. A polystyrene cell culture plate was used as control. The results showed that the RGD-SBM recombinant protein improved, by more than 30%, the adhesion of fibroblasts to dextrin-based hydrogel. In fact, cell spreading on the hydrogel surface was observed only in the presence of the RGD-SBM. Conclusion The fusion protein RGD-SBM provides an efficient way to functionalize the dextrin-based hydrogel. Many proteins in nature that hold a RGD sequence are not cell adhesive, probably due to the conformation/accessibility of the peptide. We therefore emphasise the successful expression of a bi-functional protein with potential for different applications.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES, Brazil)Fundação para a Ciência e a Tecnologia (FCT

Production of recombinant carbohydrate-binding modules fused to RGD : functional studies using bacterial cellulose

The attachment of cells to biomedical materials can be improved by using adhesion molecules, present in the extracellular matrix substances, such as fibronectin, vitronectin, or laminin. In many cases, Arg-Gly-Asp (RGD) was found to be the major functional amino acid sequence responsible for cellular adhesion. In the present study, a method for producing chimerics proteins, RGDCBM, with functions similar to fibronectin, which contains a cellulose-binding module (CBM), was developed. The CBM used was from the cellulosoma of the bacteria Clostridium thermocellum. The genes encoding these CBM-containing chimeric proteins were cloned, and the protein expressed and purified. Bacterial cellulose (BC) secreted by Gluconacetobacter xylinus was produced. Polystyrene surfaces and bacterial cellulose sheets where ‘‘coated’’ with these RGD-containing proteins, and then used in adhesion/biocompatibility tests, using a mouse embryo fibroblasts culture. The results showed that the proteins containing the RGD or GRGDY sequence were able to improve the adhesion of the fibroblast on the polystyrene plate, furthermore proteins containing the RGD sequence were more effective than the proteins containing the GRGDY sequence. Preliminary adhesion studies of fibroblast cultures on cellulose sheets, functionalized with the recombinant proteins, showed positive effects on the adhesion and proliferation of the cells. The results demonstrated that the proteins containing the RGD sequence were able to increase significantly the adhesion of fibroblast to BC surfaces when compared with the controls (cellulose treated with the CBM or buffer). The results also demonstrated that the protein containing one RGD sequence have a stronger effect than the protein containing two RGDs

Improving bacterial cellulose for blood vessel replacement: functionalization with a chimeric protein containing a cellulose-binding module and an adhesion peptide

Chimeric proteins containing a cellulose-binding module (CBM) and an adhesion peptide (RGD or GRGDY) were produced and used to improve the adhesion of human microvascular endothelial cells (HMEC) to bacterial cellulose (BC). The effect of these proteins on the HMEC–BC interaction was studied. The results obtained demonstrated that recombinant proteins containing adhesion sequences were able to significantly increase the attachment of HMEC to BC surfaces, especially the RGD sequence. The images obtained by scanning electron microscopy showed that the cells on the RGD-treated BC present a more elongated morphology 48 h after cell seeding. The results also showed that RGD decreased the in-growth of HMEC cells through the BC and stimulated the early formation of cord-like structures by these endothelial cells. Thus, the use of recombinant proteins containing a CBM domain, with high affinity and specificity for cellulose surfaces allows control of the interaction of this material with cells. CBM may be combined with virtually any biologically active protein for the modification of cellulose-based materials, for in vitro or in vivo applications.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES, Brazil)Fundação para a Ciência e a Tecnologia (FCT

Combining Animal Welfare With Experimental Rigor to Improve Reproducibility in Behavioral Neuroscience

Grants of Alexander von Humboldt Foundation (Germany) to CLi. CML was recipient of Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) research fellowship through the Instituto Nacional de Ciência e Tecnologia Translacional em Medicina (INCT-TM), Brazil. FM was supported by Post-doctoral fellowship grant #2018/25857-5, São Paulo Research Foundation (FAPESP), Brazil. KD was supported by Fellow BIPD/FCT Proj2020/i3S/26040705/2021, Fundação para a Ciência e Tecnologia, Portugal. This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brasil (CAPES) – Finance Code 001