Synthesis, characterization, electrochemical behavior and in vitro protein tyrosine kinase inhibitory activity of the cymene-halogenobenzohydroxamato [Ru(eta(6)-cymene)(bha)Cl] complexes

The ruthenium(II)-cymene complexes [Ru(eta(6)-cymene)(bha)Cl] with substituted halogenobenzohydroxamato (bha) ligands (substituents = 4-F, 4-Cl, 4-Br, 2,4-F-2, 3,4-F-2, 2,5-F-2, 2,6-F-2) have been synthesized and characterized by elemental analysis, IR, H-1 NMR, C-13 NMR, cyclic voltammetry and controlled-potential electrolysis, and density functional theory (DFT) studies. The compositions of their frontier molecular orbitals (MOs) were established by DFT calculations, and the oxidation and reduction potentials are shown to follow the orders of the estimated vertical ionization potential and electron affinity, respectively. The electrochemical E-L Lever parameter is estimated for the first time for the various bha ligands, which can thus be ordered according to their electron-donor character. All complexes exhibit very strong protein tyrosine kinase (PTK) inhibitory activity, even much higher than that of genistein, the clinically used PTK inhibitory drug. The complex containing the 2,4-difluorobenzohydroxamato ligand is the most active one, and the dependences of the PTK activity of the complexes and of their redox potentials on the ring substituents are discussed. (C) 2012 Elsevier B.V. All rights reserved.

Open-source software in operations research in engineering teaching

ENEGI 2013: Atas do 2º Encontro Nacional de Engenharia e Gestão Industrial, Universidade de Aveiro, 17 e 18 de maio de 2013, Aveiro, Portugal.

Lipid content and fatty acid profile of Senegalese sole (Solea senegalensis Kaup, 1858) juveniles as affected by feed containing different amounts of plant protein sources

A growth trial with Senegalese Sole (Solea senegalensis Kaup, 1858) juveniles fed with diets containing increasing replacement levels of fishmeal by mixtures of plant protein sources was conducted over 12 weeks. Total fat contents of muscle, liver, viscera, skin, fins and head tissues were determined, as well as fatty acid profiles of muscle and liver (GC-FID analysis). Liver was the preferential local for fat deposition (5.5–10.8% of fat) followed by fins (3.4–6.7% fat). Increasing levels of plant protein in the diets seems to be related to increased levels of total lipids in the liver. Sole muscle is lean (2.4–4.0% fat), with total lipids being similar among treatments. Liver fatty acid profile varied significantly among treatments. Plant protein diets induced increased levels of C16:1 and C18:2 n -6 and a decrease in ARA and EPA levels. Muscle fatty acid profile also evidenced increasing levels of C18:2 n 6, while ARA and DHA remained similar among treatments. Substitution of fishmeal by plant protein is hence possible without major differences on the lipid content and fatty acid profile of the main edible portion of the fish – the muscle.

Translation termination and protein folding pathway genes are not correlated in gastric cancer

Background: The eukaryotic release factor 3 (eRF3) has been shown to affect both tubulin and actin cytoskeleton, suggesting a role in cytoskeleton assembly, mitotic spindle formation and chromosome segregation. Also, direct interactions between eRF3 and subunits of the cytosolic chaperonin CCT have been described. Moreover, both eRF3a and CCT subunits have been described to be up-regulated in cancer tissues. Our aim was to evaluate the hypothesis that eRF3 expression levels are correlated with the expression of genes encoding proteins involved in the tubulin folding pathways. Methods: Relative expression levels of eRF1, eRF3a/GSPT1, PFDN4, CCT2, CCT4, and TBCA genes in tumour samples relative to their adjacent normal tissues were investigated using real time-polymerase chain reaction in 20 gastric cancer patients. Results: The expression levels of eRF3a/GSPT1 were not correlated with the expression levels of the other genes studied. However, significant correlations were detected between the other genes, both within intestinal and diffuse type tumours. Conclusions: eRF3a/GSPT1 expression at the mRNA level is independent from both cell translation rates and from the expression of the genes involved in tubulin-folding pathways. The differences in the patterns of expression of the genes studied support the hypothesis of genetically independent pathways in the origin of intestinal and diffuse type gastric tumours.

Besnoitia besnoiti protein disulfide isomerase (BbPDI): molecular characterization, expression and in silico modelling

Besnoitia besnoiti is an apicomplexan parasite responsible for bovine besnoitiosis, a disease with a high prevalence in tropical and subtropical regions and re-emerging in Europe. Despite the great economical losses associated with besnoitiosis, this disease has been underestimated and poorly studied, and neither an effective therapy nor an efficacious vaccine is available. Protein disulfide isomerase (PDI) is an essential enzyme for the acquisition of the correct three-dimensional structure of proteins. Current evidence suggests that in Neosporacaninum and Toxoplasmagondii, which are closely related to B. besnoiti, PDI play an important role in host cell invasion, is a relevant target for the host immune response, and represents a promising drug target and/or vaccine candidate. In this work, we present the nucleotide sequence of the B. besnoiti PDI gene. BbPDI belongs to the thioredoxin-like superfamily (cluster 00388) and is included in the PDI_a family (cluster defined cd02961) and the PDI_a_PDI_a'_c subfamily (cd02995). A 3D theoretical model was built by comparative homology using Swiss-Model server, using as a template the crystallographic deduced model of Tapasin-ERp57 (PDB code 3F8U chain C). Analysis of the phylogenetic tree for PDI within the phylum apicomplexa reinforces the close relationship among B. besnoiti, N. caninum and T. gondii. When subjected to a PDI-assay based on the polymerisation of reduced insulin, recombinant BbPDI expressed in E. coli exhibited enzymatic activity, which was inhibited by bacitracin. Antiserum directed against recombinant BbPDI reacted with PDI in Western blots and by immunofluorescence with B. besnoiti tachyzoites and bradyzoites.

Effect of a sardine supplement on C-reactive protein in patients receiving hemodialysis

Objective - The study evaluated the effect of a canned sardine supplement in C-reactive protein (CRP) in patients on hemodialysis (HD) and the compliance and adherence to this supplement. Design - This was a quasi-experimental study: Participants with a serum CRP of 5 mg/dL or less volunteered to consume a sardine supplement or were maintained on the usual cheese/ham sandwich supplement. Setting - The study took place in two outpatient dialysis units in Lisbon, Portugal. Patients - The study comprised 63 patients receiving maintenance HD three times per week for at least 6 months and an initial CRP concentration of 5 mg/dL or less. Exclusion criteria included the presence of graft vascular access or history of cancer. Intervention - After a 4-week washout period, the nutritional intervention included a canned sardine sandwich for the case group (n = 31) and a cheese or ham sandwich for the control group (n = 32), to be ingested during each routine HD session, 3 times per week, for 8 weeks. Main outcome measure - Serum levels of high-sensitivity CRP were the outcome measure. Results - Only 65 patients from the invited 186 patients met the inclusion criteria and agreed to eat the sardine sandwich supplement three times per week and were involved in the study. A significant proportion of 48% (n = 31, case group) consumed the sardine sandwich supplement three times per week for 8 weeks, fulfilling the requirements and completing the study. The present investigation showed that a sardine sandwich supplement had no effect on CRP levels among patients on HD. However, when participants were stratified according to tertiles of CRP distribution values at baseline, a reduction in CRP levels was found for those in the higher tertile, being higher for the case group (P = .047). Although diabetic patients were excluded from the analysis (eight in the sardine supplementation group and seven in the control group) a significant CRP reduction was found (P = .034). Conclusion - Although a supplement of low-dose n-3 long-chain polyunsaturated fatty acids had no effect on the plasma high-sensitivity CRP of the supplemented group, a reduction in CRP levels was found when patients were stratified for tertiles of CRP (for the upper tertile) and diabetic status (for nondiabetic patients). These findings need to be further confirmed. This canned sardine supplement was accepted by an important proportion of patients, enhancing diet variety and contributing for a greater n-3 long-chain polyunsaturated fatty acids eicosapentaenoic acid and docosahexaenoic acid intake.

A remote virtual experiment in mechanical engineering

Conferência: 2nd Experiment at International Conference (Exp at)- Univ Coimbra, Coimbra, Portugal - Sep 18-20, 2013

Endothelialization of chitosan porous conduits via immobilization of a recombinant fibronectin fragment (rhFNIII7–10)

The present study aimed to develop a pre-endothelialized chitosan (CH) porous hollowed scaffold for application in spinal cord regenerative therapies. CH conduits with different degrees of acetylation (DA; 4% and 15%) were prepared, characterized (microstructure, porosity and water uptake) and functionalized with a recombinant fragment of human fibronectin (rhFNIII7–10). Immobilized rhFNIII7–10 was characterized in terms of amount (125I-radiolabelling), exposure of cell-binding domains (immunofluorescence) and ability to mediate endothelial cell (EC) adhesion and cytoskeletal rearrangement. Functionalized conduits revealed a linear increase in immobilized rhFNIII7–10 with rhFNIII7–10 concentration, and, for the same concentration, higher amounts of rhFNIII7–10 on DA 4% compared with DA 15%. Moreover, rhFNIII7–10 concentrations as low as 5 and 20 lgml 1 in the coupling reaction were shown to provide DA 4% and 15% scaffolds, respectively, with levels of exposed cell-binding domains exceeding those observed on the control (DA 4% scaffolds incubated in a 20 lgml 1 human fibronectin solution). These grafting conditions proved to be effective in mediating EC adhesion/cytoskeletal organization on CH with DA 4% and 15%, without affecting the endothelial angiogenic potential. rhFNIII7–10 grafting to CH could be a strategy of particular interest in tissue engineering applications requiring the use of endothelialized porous matrices with tunable degradation rates.

Adding value [valorization] to tannery fleshings: part II – effect of protein hydrolysates on leather dyeing

The tanning industry generates a high quantity of solid wastes. Therefore, there is a need to create valorization [added value] options for these wastes. The main objective of the present work was to study the effect of protein hydrolysates (HP) prepared from fleshings on leather dyeing. During previous studies it was found that the application of HP products, obtained from fleshings, in leather retannage intensified the colour of crust leather. In this work the CIELAB colour system was used to evaluate the effect of HP on retannage processes. The main conclusions of this study were: (i) HP can be used instead of a dicyanodiamide resin (Fortan DC) if the colour parameters of the standard procedure are to be maintained, and (ii) the replacement of an acrylic resin (Fortan A40) by glutaraldehyde-modified HP (GHP) results in a darker skin, and can therefore be interesting for the reduction of the quantity of dye used.

Engineering hybrid wired/wireless fieldbus networks - a case study

Advances in networking and information technologies are transforming factory-floor communication systems into a mainstream activity within industrial automation. It is now recognized that future industrial computer systems will be intimately tied to real-time computing and to communication technologies. For this vision to succeed, complex heterogeneous factory-floor communication networks (including mobile/wireless components) need to function in a predictable, flawless, efficient and interoperable way. In this paper we re-visit the issue of supporting real-time communications in hybrid wired/wireless fieldbus-based networks, bringing into it some experimental results obtained in the framework of the RFieldbus ISEP pilot.

Engineering real-time applications with WorldFIP: tools and analysis

WorldFIP is standardised as European Norm EN 50170 - General Purpose Field Communication System. Field communication systems (fieldbuses) started to be widely used as the communication support for distributed computer-controlled systems (DCCS), and are being used in all sorts of process control and manufacturing applications within different types of industries. There are several advantages in using fieldbuses as a replacement of for the traditional point-to-point links between sensors/actuators and computer-based control systems. Indeed they concern economical ones (cable savings) but, importantly, fieldbuses allow an increased decentralisation and distribution of the processing power over the field. Typically DCCS have real-time requirements that must be fulfilled. By this, we mean that process data must be transferred between network computing nodes within a maximum admissible time span. WorldFIP has very interesting mechanisms to schedule data transfers. It explicit distinguishes to types of traffic: periodic and aperiodic. In this paper we describe how WorldFIP handles these two types of traffic, and more importantly, we provide a comprehensive analysis for guaranteeing the real-time requirements of both types of traffic. A major contribution is made in the analysis of worst-case response time of aperiodic transfer requests.

Mining protein structure data

The principal topic of this work is the application of data mining techniques, in particular of machine learning, to the discovery of knowledge in a protein database. In the first chapter a general background is presented. Namely, in section 1.1 we overview the methodology of a Data Mining project and its main algorithms. In section 1.2 an introduction to the proteins and its supporting file formats is outlined. This chapter is concluded with section 1.3 which defines that main problem we pretend to address with this work: determine if an amino acid is exposed or buried in a protein, in a discrete way (i.e.: not continuous), for five exposition levels: 2%, 10%, 20%, 25% and 30%. In the second chapter, following closely the CRISP-DM methodology, whole the process of construction the database that supported this work is presented. Namely, it is described the process of loading data from the Protein Data Bank, DSSP and SCOP. Then an initial data exploration is performed and a simple prediction model (baseline) of the relative solvent accessibility of an amino acid is introduced. It is also introduced the Data Mining Table Creator, a program developed to produce the data mining tables required for this problem. In the third chapter the results obtained are analyzed with statistical significance tests. Initially the several used classifiers (Neural Networks, C5.0, CART and Chaid) are compared and it is concluded that C5.0 is the most suitable for the problem at stake. It is also compared the influence of parameters like the amino acid information level, the amino acid window size and the SCOP class type in the accuracy of the predictive models. The fourth chapter starts with a brief revision of the literature about amino acid relative solvent accessibility. Then, we overview the main results achieved and finally discuss about possible future work. The fifth and last chapter consists of appendices. Appendix A has the schema of the database that supported this thesis. Appendix B has a set of tables with additional information. Appendix C describes the software provided in the DVD accompanying this thesis that allows the reconstruction of the present work.

The dark side of DEMMON: what is behind the scene in engineering large-scale wireless sensor networks

Most research work on WSNs has focused on protocols or on specific applications. There is a clear lack of easy/ready-to-use WSN technologies and tools for planning, implementing, testing and commissioning WSN systems in an integrated fashion. While there exists a plethora of papers about network planning and deployment methodologies, to the best of our knowledge none of them helps the designer to match coverage requirements with network performance evaluation. In this paper we aim at filling this gap by presenting an unified toolset, i.e., a framework able to provide a global picture of the system, from the network deployment planning to system test and validation. This toolset has been designed to back up the EMMON WSN system architecture for large-scale, dense, real-time embedded monitoring. It includes network deployment planning, worst-case analysis and dimensioning, protocol simulation and automatic remote programming and hardware testing tools. This toolset has been paramount to validate the system architecture through DEMMON1, the first EMMON demonstrator, i.e., a 300+ node test-bed, which is, to the best of our knowledge, the largest single-site WSN test-bed in Europe to date.

Bilirubin directly disrupts membrane lipid polarity and fluidity, protein order, and redox status in rat mitochondria

Background/Aims: Unconjugated bilirubin (UCB) impairs crucial aspects of cell function and induces apoptosis in primary cultured neurones. While mechanisms of cytotoxicity begin to unfold, mitochondria appear as potential primary targets. Methods: We used electron paramagnetic resonance spectroscopy analysis of isolated rat mitochondria to test the hypothesis that UCB physically interacts with mitochondria to induce structural membrane perturbation, leading to increased permeability, and subsequent release of apoptotic factors. Results: Our data demonstrate profound changes on mitochondrial membrane properties during incubation with UCB, including modified membrane lipid polarity and fluidity (P , 0:01), as well as disrupted protein mobility(P , 0:001). Consistent with increased permeability, cytochrome c was released from the intermembrane space(P , 0:01), perhaps uncoupling the respiratory chain and further increasing oxidative stress (P , 0:01). Both ursodeoxycholate, a mitochondrial-membrane stabilising agent, and cyclosporine A, an inhibitor of the permeability transition, almost completely abrogated UCB-induced perturbation. Conclusions: UCB directly interacts with mitochondria influencing membrane lipid and protein properties, redox status, and cytochrome c content. Thus, apoptosis induced by UCB may be mediated, at least in part, by physical perturbation of the mitochondrial membrane. These novel findings should ultimately prove useful to our evolving understanding of UCB cytotoxicity.

Engineering a search and rescue application with a wireless sensor network - based localization mechanism

The advent of Wireless Sensor Network (WSN) technologies is paving the way for a panoply of new ubiquitous computing applications, some of them with critical requirements. In the ART-WiSe framework, we are designing a two-tiered communication architecture for supporting real-time and reliable communications in WSNs. Within this context, we have been developing a test-bed application, for testing, validating and demonstrating our theoretical findings - a search&rescue/pursuit-evasion application. Basically, a WSN deployment is used to detect, localize and track a target robot and a station controls a rescuer/pursuer robot until it gets close enough to the target robot. This paper describes how this application was engineered, particularly focusing on the implementation of the localization mechanism.