Solution Structures of the cis- and trans-Pro30 Isomers of a Novel 38-Residue Toxin from the Venom of Hadronyche Infensa sp. that Contains a Cystine-Knot Motif within Its Four Disulfide Bonds

The primary sequence and three-dimensional structure of a novel peptide toxin isolated from the Australian funnel-web spider Hadronyche infensa sp. is reported. ACTX-HI:OB4219 contains 38 amino acids, including eight-cysteine residues that form four disulfide bonds. The connectivities of these disulfide bonds were previously unknown but have been unambiguously determined in this study. Three of these disulfide bonds are arranged in an inhibitor cystine-knot (ICK) motif, which is observed in a range of other disulfide-rich peptide toxins. The motif incorporates an embedded ring in the structure formed by two of the disulfides and their connecting backbone segments penetrated by a third disulfide bond. Using NMR spectroscopy, we determined that despite the isolation of a single native homologous product by RP-HPLC, ACTX-HI:OB4219 possesses two equally populated conformers in solution. These two conformers were determined to arise from cis/trans isomerization of the bond preceding Pro30. Full assignment of the NMR spectra for both conformers allowed for the calculation of their structures, revealing, the presence of a triple-stranded antiparallel sheet consistent with the inhibitor cystine-knot (ICK) motif.

ClC-5 chloride channel and kidney stones : what is the link?

Nephrolithiasis is one of the most common diseases in the Western world. The disease manifests itself with intensive pain, sporadic infections, and, sometimes, renal failure. The symptoms are due to the appearance of urinary stones (calculi) which are formed mainly by calcium salts. These calcium salts precipitate in the renal papillae and/or within the collecting ducts. Inherited forms of nephrolithiasis related to chromosome X (X-linked hypercalciuric nephrolithiasis or XLN) have been recently described. Hypercalciuria, nephrocalcinosis, and male predominance are the major characteristics of these diseases. The gene responsible for the XLN forms of kidney stones was cloned and characterized as a chloride channel called ClC-5. The ClC-5 chloride channel belongs to a superfamily of voltage-gated chloride channels, whose physiological roles are not completely understood. The objective of the present review is to identify recent advances in the molecular pathology of nephrolithiasis, with emphasis on XLN. We also try to establish a link between a chloride channel like ClC-5, hypercalciuria, failure in urine acidification and protein endocytosis, which could explain the symptoms exhibited by XLN patients.

Electrochemical and analytical investigation of passive films formed on stainless steels in alkaline media

Passive films were grown in potentiodynamic mode, by cyclic voltammetry on AISI 316 and AISI 304 stainless steels. The composition of these films was investigated by X-ray photoelectron spectroscopy (XPS). The electrochemical behaviour and the chemical composition of the passive films formed by cyclic voltammetry were compared to those of films grown under natural conditions (by immersion at open circuit potential, OCP) in alkaline solutions simulating concrete. The study included the effect of pH of the electrolyte and the effect of the presence of chloride ions. The XPS results revealed important changes in the passive film composition, which becomes enriched in chromium and depleted in magnetite as the pH decreases. On the other hand, the presence of chlorides promotes a more oxidised passive layer. The XPS results also showed relevant differences on the composition of the oxide layers for the films formed under cyclic voltammetry and/or under OCP.

Electrochemical response of 70Co-30Ni highly branched 3D-dendritic structures for charge storage electrodes

A 70Co-30Ni dendritic alloy was produced on stainless steel by pulse electrodeposition in the cathodic domain, and oxidized by potential cycling. X-ray diffraction (XRD) identified the presence of two phases and scanning electron microscopy (SEM) evidenced an open 3D highly branched dendritic morphology. After potential cycling in 1 M KOH, SEM and X-ray photoelectron spectroscopy (XPS) revealed, respectively, the presence of thin nanoplates, composed of Co and Ni oxi-hydroxides and hydroxides over the original dendritic film. Cyclic voltammetry tests showd the presence of redox peaks assigned to the oxidation and reduction of Ni and Co centres in the surface film. Charge/discharge measurements revealed capacity values of 121 mAh g(1) at 1 mA cm(2). The capacity retention under 8000 cycles was above 70%, stating the good reversibility of these redox materials and its suitability to be used as charge storage electrodes. Electrochemical impedance spectroscopy (EIS) spectra, taken under different applied bias, showed that the capacitance increased when the electrode was fully oxidized and decreased when the electrode was reduced, reflecting different states-of-charge of the electrode. (C) 2015 Elsevier Ltd. All rights reserved.

Large-area homogeneous periodic surface structures generated on the surface sputtered boron carbide thin films by femtosecond laser processing

Amorphous and crystalline sputtered boron carbide thin films have a very high hardness even surpassing that of bulk crystalline boron carbide (≈41 GPa). However, magnetron sputtered B-C films have high friction coefficients (C.o.F) which limit their industrial application. Nanopatterning of materials surfaces has been proposed as a solution to decrease the C.o.F. The contact area of the nanopatterned surfaces is decreased due to the nanometre size of the asperities which results in a significant reduction of adhesion and friction. In the present work, the surface of amorphous and polycrystalline B-C thin films deposited by magnetron sputtering was nanopatterned using infrared femtosecond laser radiation. Successive parallel laser tracks 10 μm apart were overlapped in order to obtain a processed area of about 3 mm2. Sinusoidal-like undulations with the same spatial period as the laser tracks were formed on the surface of the amorphous boron carbide films after laser processing. The undulations amplitude increases with increasing laser fluence. The formation of undulations with a 10 μm period was also observed on the surface of the crystalline boron carbide film processed with a pulse energy of 72 μJ. The amplitude of the undulations is about 10 times higher than in the amorphous films processed at the same pulse energy due to the higher roughness of the films and consequent increase in laser radiation absorption. LIPSS formation on the surface of the films was achieved for the three B-C films under study. However, LIPSS are formed under different circumstances. Processing of the amorphous films at low fluence (72 μJ) results in LIPSS formation only on localized spots on the film surface. LIPSS formation was also observed on the top of the undulations formed after laser processing with 78 μJ of the amorphous film deposited at 800 °C. Finally, large-area homogeneous LIPSS coverage of the boron carbide crystalline films surface was achieved within a large range of laser fluences although holes are also formed at higher laser fluences.

Simulation of the velocity field in compound channel flow using different closure models

1st European IAHR Congress,6-4 May, Edinburg, Scotland

Projeto de torres metálicas de suporte de cabos de energia elétrica - Aplicação da parte 3-1 Eurocódigo 3

Mestrado em Engenharia Civil – Ramo Estruturas

Tectónica da cadeia da Arrábida

Geociências, Museu Nac. Hist. Nat. Univ. Lisboa, nº 2, 35-84

Robustness of corroded reinforced concrete structures. A structural performance approach

Structure and Infrastructure Engineering, 1-17

The role of ribonuclease R in bacterial adaptation to cold shock

RESUMO:Os microrganismos reagem à súbita descida de temperatura através de uma resposta adaptativa específica que assegura a sua sobrevivência em condições desfavoráveis. Esta adaptação inclui alterações na composição da membrana, na maquinaria de tradução e transcrição. A resposta ao choque térmico pelo frio induz uma repressão da transcrição. No entanto, a descida de temperatura induz a produção de um grupo de proteínas específicas que ajudam a ajustar/re-ajustar o metabolismo celular às novas condições ambientais. Em E. coli o processo de adaptação demora apenas quatro horas, no qual um grupo de proteínas específicas são induzidas. Depois desde período recomeça lentamente a produção de proteínas.A ribonuclease R, uma das proteínas induzidas durante o choque térmico pelo frio, é uma das principais ribonucleases em E. coli envolvidas na degradação do RNA. É uma exoribonuclease que degrada RNA de cadeia dupla, possui funções importantes na maturação e “turnover” do RNA, libertação de ribossomas e controlo de qualidade de proteínas e RNAs. O nível celular desta enzima aumenta até dez vezes após exposição ao frio e estabiliza em células na fase estacionária. A capacidade de degradar RNA de dupla cadeia é importante a baixas temperaturas quando as estruturas de RNA estão mais estáveis. No entanto, este mecanismo é desconhecido. Embora a resposta específica ao “cold shock” tenha sido descoberta há mais de duas décadas e o número de proteínas envolvidas sugerirem que esta adaptação é rápida e simples, continuamos longe de compreender este processo. No nosso trabalho pretendemos descobrir proteínas que interactuem com a RNase R em condições ambientais diferentes através do método “TAP-tag” e espectrometria de massa. A informação obtida pode ser utilizada para deduzir algumas das novas funções da RNase R durante a adaptação bacteriana ao frio e durante a fase estacionária. Mais importante ainda, RNase R poderá ser recrutada para um complexo de proteínas de elevado peso molecular durante o “cold-shock”.------------ABSTRACT:Microorganisms react to the rapid temperature downshift with a specific adaptative response that ensures their survival in unfavorable conditions. Adaptation includes changes in membrane composition, in translation and transcription machinery. Cold shock response leads to overall repression of translation. However, temperature downshift induces production of a set of specific proteins that help to tune cell metabolism and readjust it to the new environmental conditions. For Escherichia coli the adaptation process takes only about four hours with a relatively small set of specifically induced proteins involved. After this time, protein production resumes, although at a slower rate. One of the cold inducible proteins is RNase R, one of the main E. coli ribonucleases involved in RNA degradation. RNase R is an exoribonuclease that digest double stranded RNA, serves important functions in RNA maturation and turnover, release of stalled ribosomes by trans-translation, and RNA and protein quality control. The level of this enzyme increases about ten-fold after cold induction, and it is also stabilised in cells growing in stationary phase. The RNase R ability to digest structured RNA is important at low temperatures where RNA structures are stabilized but the exact role of this mechanism remains unclear. Although specific bacterial cold shock response was discovered over two decades ago and the number of proteins involved suggests that this adaptation is fast and simple, we are still far from understanding this process. In our work we aimed to discover the proteins interacting with RNase R in different environmental conditions using TAP tag method and mass spectrometry analysis. The information obtained can be used to deduce some of the new functions of RNase R during adaptation of bacteria to cold and in stationary growth phase. Most importantly RNase R can be recruited into a high molecular mass complex of protein in cold shock.

Protein glycosylation of exosomes from ovarian carcinoma cells: structures and biological roles

Dissertation presented to obtain the Ph.D. degree in Biology

Assessing initial embodied energy in building structures using LCA methodology

The considerable amount of energy consumed on Earth is a major cause for not achieving sustainable development. Buildings are responsible for the highest worldwide energy consumption, nearly 40%. Strong efforts have been made in what concerns the reduction of buildings operational energy (heating, hot water, ventilation, electricity), since operational energy is so far the highest energy component in a building life cycle. However, as operational energy is being reduced the embodied energy increases. One of the building elements responsible for higher embodied energy consumption is the building structural system. Therefore, the present work is going to study part of embodied energy (initial embodied energy) in building structures using a life cycle assessment methodology, in order to contribute for a greater understanding of embodied energy in buildings structural systems. Initial embodied energy is estimated for a building structure by varying the span and the structural material type. The results are analysed and compared for different stages, and some conclusions are drawn. At the end of this work it was possible to conclude that the building span does not have considerable influence in embodied energy consumption of building structures. However, the structural material type has influence in the overall energetic performance. In fact, with this research it was possible that building structure that requires more initial embodied energy is the steel structure; then the glued laminated timber structure; and finally the concrete structure.

Acellular Gellan-gum based bilayered structures for the regeneration of osteochondral defects: a preclinical study

 In orthopaedics, the management and treatment of osteochondral (OC) defects remains an ongoing clinical challenge. Autologous osteochondral mosaicplasty has been used as a valid option for OC treatments although donor site morbidity remains a source of concern [1]. Engineering a whole structure capable of mimicking different tissues (cartilage and subchondral bone) in an integrated manner could be a possible approach to regenerate OC defects. In our group we have been proposing the use of bilayered structures to regenerate osteochondral defects [2,3]. The present study aims to investigate the pre-clinical performance of bilayered hydrogels and spongy-like hydrogels in in vivo  models (mice and rabbit, respectively), in both subcutaneous and orthotopic models. The bilayered structures were produced from Low Acyl Gellan Gum (LAGG) from Sigma-Aldrich, USA. Cartilage-like layers were obtained from a 2wt% LAGG solution. The bone-like layers were made of 2wt% LAGG with incorporation of hydroxyapatite at 20% and 30% (w/v). Hydrogels and spongy-like were subcutaneouly implanted in mice to evaluate the inflammatory response. Then, OC defects were induced in rabbit knee to create a critical size defect (4 mm diameter and 5 mm depth), and then hydrogels and sponges implanted. Both structures followed different processing methods. The hydrogels were injected allowing in situ  crosslinking. Unlike, the spongy-like were pre-formed by freeze-drying. The studies concerning subcutaneous implantation and critical size OC defect were performed for 2 and 4 weeks time, respectively. Cellular behavior and inflammatory responses were assessed by means of histology staining and biochemical function and matrix deposition by immunohistochemistry. Additionally, both OC structures stability and new cartilage and bone formation were evaluated by using vivo- computed tomography (Scanco 80). The results showed no acute inflammatory response for both approaches. New tissue formation and integration in the adjacent tissues were also observed, which present different characteristic behaviors when comparing hydrogels and sponges response. As future insights, a novel strategy for regeneration of OC defects can be designed encompassing both, hydrogels and spongy-like structures and cellular approaches. References: 1. Espregueira-Mendes J. et al. Osteochondral transplantation using autografts from the upper tibio-fibular joint for the treatment of knee cartilage lesions. Knee Surgery, Sports Traumatology, Arthroscopy 20,1136, 2012. 2. Oliveira JM. et al, Novel hydroxyapatite/chitosan bilayered scaffold for osteochondral tissue-engineering applications: Scaffold design and its performance when seeded with goat bone marrow stromal cells. Biomaterials 27, 6123, 2006. 3. Pereira D R. et al. Gellan Gum-Based Hydrogel Bilayered Scaffolds for Osteochondral Tissue Engineering. Key Engineering Materials 587, 255, 2013.

Self-monitoring of freeze–thaw damage using triphasic electric conductive concrete

The effect of freeze–thaw cycles on concrete is of great importance for durability evaluation of concrete structures in cold regions. In this paper, damage accumulation was studied by following the fractional change of impedance (FCI) with number of freeze–thaw cycles (N). The nano-carbon black (NCB), carbon fiber (CF) and steel fiber (SF) were added to plain concrete to produce the triphasic electrical conductive (TEC) and ductile concrete. The effects of NCB, CF and SF on the compressive strength, flexural properties, electrical impedance were investigated. The concrete beams with different dosages of conductive materials were studied for FCI, N and mass loss (ML), the relationship between FCI and N of conductive concrete can be well defined by a first order exponential decay curve. It is noted that this nondestructive and sensitive real-time testing method is meaningful for evaluating of freeze–thaw damage in concrete.

A FEM-based model to study the behaviour of corroded RC beams shear repaired by NSM CFRP rods technique

This paper presents the main features of finite element FE numerical model developed using the computer code FEMIX to predict the near-surface mounted NSM carbon-fiber-reinforced polymer CFRP rods shear repair contribution to corroded reinforced concrete RC beams. In the RC beams shear repaired with NSM technique, the Carbon Fibre Reinforced Polymer (CFRP) rods are placed inside pre-cut grooves onto the concrete cover of the RC beam’s lateral faces and are bonded to the concrete with high epoxy adhesive. Experimental and 3D numerical modelling results are presented in this paper in terms of load-deflection curves, and failure modes for 4 short corroded beams: two corroded beams (A1CL3-B and A1CL3-SB) and two control beams (A1T-B and A1T-SB), the beams noted with B were let repaired in bending only with NSM CFRP rods while the ones noted with SB were repaired in both bending and shear with NSM technique. The corrosion of the tensile steel bars and its effect on the shear capacity of the RC beams was discussed. Results showed that the FE model was able to capture the main aspects of the experimental load-deflection curves of the RC beams, moreover it has presented the experimental failure modes and FE numerical modelling crack patterns and both gave similar results for non-shear repaired beams which failed in diagonal tension mode of failure and for shear-repaired beams which failed due to large flexural crack at the middle of the beams along with the concrete crushing, three dimensional crack patterns were produced for shear-repaired beams in order to investigate the splitting cracks occurred at the middle of the beams and near the support.