Finite element modelling of FRP-to-concrete bond behaviour using the concrete damage plasticity theory combined with a plastic degradation model

The technique of externally bonding fibre reinforced polymer (FRP) composites has been becoming popular worldwide for retrofitting existing reinforced concrete (RC) structures. A major failure mode in such strengthened structures is the debonding of FRP from the concrete substrate. The bond behaviour between FRP and concrete thus plays a crucial role in these structures. The FRP-to-concrete bond behaviour has been extensively investigated experimentally, commonly using the pull-off test of FRP-to-concrete bonded joint. Comparatively, much less research has been concerned with the numerical simulation of this bond behaviour, chiefly due to difficulties in accurately modelling the complex behaviour of concrete. This paper proposes a robust finite element (FE) model for simulating the bond behaviour in the entire loading process in the pull-off test. A concrete damage plasticity model based on the plastic degradation theory is proposed to overcome the weakness of the elastic degradation theory which has been commonly adopted in previous studies. The model produces results in very close agreement with test data. © Tsinghua University Press, Beijing and Springer-Verlag Berlin Heidelberg 2011.

Dengue Virus Inhibition of Autophagic Flux and Dependency of Viral Replication on Proteasomal Degradation of the Autophagy Receptor p62

Autophagic flux involves formation of autophagosomes and their degradation by lysosomes. Autophagy can either promote or restrict viral replication. In the case of Dengue virus (DENV) several studies report that autophagy supports the viral replication cycle, and describe an increase of autophagic vesicles (AVs) following infection. However, it is unknown how autophagic flux is altered to result in increased AVs. To address this question, and gain insight into the role of autophagy during DENV infection, we established an unbiased, image-based flow cytometry approach to quantify autophagic flux under normal growth conditions and in response to activation by nutrient deprivation or the mTOR inhibitor Torin1. We found that DENV induced an initial activation of autophagic flux, followed by inhibition of general and specific autophagy. Early after infection, basal and activated autophagic flux was enhanced. However, during established replication, basal and Torin1-activated autophagic flux was blocked, while autophagic flux activated by nutrient deprivation was reduced, indicating a block to AV formation and reduced AV degradation capacity. During late infection AV levels increased as a result of inefficient fusion of autophagosomes with lysosomes. Additionally, endo-lysosomal trafficking was suppressed, while lysosomal activities were increased. We further determined that DENV infection progressively reduced levels of the autophagy receptor SQSTM1/p62 via proteasomal degradation. Importantly, stable over-expression of p62 significantly suppressed DENV replication suggesting a novel role for p62 as viral restriction factor. Overall our findings indicate that in the course of DENV infection, autophagy shifts from a supporting to an anti-viral role, which is countered by DENV.

IMPORTANCE: Autophagic flux is a dynamic process starting with the formation of autophagosomes and ending with their degradation after fusion with lysosomes. Autophagy impacts the replication cycle of many viruses. However, thus far the dynamics of autophagy in case of Dengue virus (DENV) infections has not been systematically quantified. Therefore, we employed high-content, imaging-based flow cytometry to quantify autophagic flux and endo-lysosomal trafficking in response to DENV infection. We report that DENV induced an initial activation of autophagic flux, followed by inhibition of general and specific autophagy. Further, lysosomal activity was increased, but endo-lysosomal trafficking was suppressed confirming the block of autophagic flux. Importantly, we provide evidence that p62, an autophagy receptor, restrict DENV replication and was specifically depleted in DENV-infected cells via increased proteasomal degradation. These results suggest that during DENV infection autophagy shifts from a pro- to an antiviral cellular process, which is counteracted by the virus.

Fate of organo-mineral particles in streams: Microbial degradation by streamwater & biofilm assemblages

Inland waters are of global biogeochemical importance. They receive carbon inputs of ~ 4.8 Pg C/ y of which, 12 % is buried, 18 % transported to the oceans, and 70 % supports aquatic secondary production. However, the mechanisms that determine the fate of organic matter (OM) in these systems are poorly defined. One aspect of this is the formation of organo-mineral complexes in aquatic systems and their potential as a route for OM transport and burial vs. their use as carbon (C) and nitrogen (N) sources within aquatic systems. Organo-mineral particles form by sorption of dissolved OM to freshly eroded mineral surfaces and may contribute to ecosystem-scale particulate OM fluxes. We experimentally tested the availability of mineral-sorbed OM as a C & N source for streamwater microbial assemblages and streambed biofilms. Organo-mineral particles were constructed in vitro by sorption of ¹³C:¹⁵N-labelled amino acids to hydrated kaolin particles, and microbial degradation of these particles compared with equivalent doses of ¹³C:¹⁵N-labelled free amino acids. Experiments were conducted in 120 ml mesocosms over 7 days using biofilms and water sampled from the Oberer Seebach stream (Austria). Each incubation experienced a 16:8 light:dark regime, with metabolism monitored via changes in oxygen concentrations between photoperiods. The relative fate of the organo-mineral particles was quantified by tracing the mineralization of the ¹³C and ¹⁵N labels and their incorporation into microbial biomass. Here we present the initial results of ¹³C-label mineralization, incorporation and retention within dissolved organic carbon pool. The results indicate that 514 (± 219) μmol/ mmol of the ¹³:¹⁵N labeled free amino acids were mineralized over the 7-day incubations. By contrast, 186 (± 97) μmol/ mmol of the mineral-sorbed amino acids were mineralized over a similar period. Thus, organo-mineral complexation reduced amino acid mineralization by ~ 60 %, with no differences observed between the streamwater and biofilm assemblages. Throughout the incubations, biofilms were observed to leach dissolved organic carbon (DOC). However, within the streamwater assemblage the presence of both organo-mineral particles and kaolin particles was associated with significant DOC removal (-1.7 % and -7.5 % respectively). Consequently, the study demonstrates that mineral and organo-mineral particles can limit the availability of DOC in aquatic systems, providing nucleation sites for flocculation and fresh mineral surfaces, which facilitate OM-sorption. The formation of these organo-mineral particles subsequently restricts microbial OM degradation, potentially altering the transport and facilitating the burial of OM within streams.

Comparison of granulometric methods and sampling strategies used in marine habitat classification and Ecological Status assessment

Sediment particle size analysis (PSA) is routinely used to support benthic macrofaunal community distribution data in habitat mapping and Ecological Status (ES) assessment. No optimal PSA Method to explain variability in multivariate macrofaunal distribution has been identified nor have the effects of changing sampling strategy been examined. Here, we use benthic macrofaunal and PSA grabs from two embayments in the south of Ireland. Four frequently used PSA Methods and two common sampling strategies are applied. A combination of laser particle sizing and wet/dry sieving without peroxide pre-treatment to remove organics was identified as the optimal Method for explaining macrofaunal distributions. ES classifications and EUNIS sediment classification were robust to changes in PSA Method. Fauna and PSA samples returned from the same grab sample significantly decreased macrofaunal variance explained by PSA and caused ES to be classified as lower. Employing the optimal PSA Method and sampling strategy will improve benthic monitoring. © 2012 Elsevier Ltd.

Behaviour-time budget and functional habitat use of a free-ranging European badger (Meles meles)

Background: The European badger (Melesmeles) is involved in the maintenance of bovine tuberculosis infection and onward spread to cattle. However, little is known about how transmission occurs. One possible route could be through direct contact between infected badgers and cattle. It is also possible that indirect contact between cattle and infected badger excretory products such as faeces or urine may occur either on pasture or within and around farm buildings. A better understanding of behaviour patterns in wild badgers may help to develop biosecurity measures to minimise direct and indirect contact between badgers and cattle. However, monitoring the behaviour of free-ranging badgers can be logistically challenging and labour intensive due to their nocturnal and semi-fossorial nature.We trialled a GPS and tri-axial accelerometer-equipped collar on a free-ranging badger to assess its potential value to elucidate behaviour-time budgets and functional habitat use. Results: During the recording period between 16:00 and 08:00 on a single night, resting was the most commonly identified behaviour (67.4%) followed by walking (20.9%), snuffling (9.5%) and trotting (2.3%).When examining accelerometer data associated with each GPS fix and habitat type (occurring 2 min 30 s before and after), walking was themost common behaviour in woodland (40.3%) and arable habitats (53.8%), while snuffling was themost common behaviour in pasture (61.9%). Several nocturnal resting periods were also observed. The total distance travelled was 2.28 km. Conclusions: In the present report, we demonstrate proof of principle in the application of a combined GPS and accelerometer device to collect detailed quantitative data on wild badger behaviour. Behaviour-time budgets allow us to investigate how badgers allocate energy to different activities and how thismight change with disease status. Such information could be useful in the development of measures to reduce opportunities for onward transmission of bovine tuberculosis from badgers to cattle.

Design, synthesis and validation of an inhibitor of CGRP degradation

Introduction: In addition to their afferent role in detection and signalling noxious stimuli, neuropeptide-containing sensory nerves may initiate and maintain chronic inflammation in diseases such as periodontitis by an efferent process known as neurogenic inflammation. Neuropeptides are susceptible to cleavage by peptidases, and therefore, the exact location and level of expression of peptidases are major determinants of neuropeptide action. Previous studies in our laboratory showed that enzyme components of gingival crevicular fluid (GCF) from periodontitis sites selectively inactivated the neuropeptide calcitonin gene-related peptide (CGRP), known to have a role in inhibiting osteoclastic bone resorption. Objectives: The aim of this study was to design and synthesise a specific inhibitor to prevent the degradation of CGRP by components of GCF. Methods: A hydroxamate-based inhibitor with a biotinylated tag was designed to ensure selectivity for CGRP and ease of use for future purification strategies. The biotinylated peptide hydroxamate contained the P1-P4 amino acid sequence of the potential CGRP cleavage site and was synthesised by solid-phase methods using standard Fmoc chemistry. Inhibition of CGRP metabolism by GCF was determined by MALDI-mass spectrometry (MALDI-MS) using pooled GCF samples from periodontitis patients as a crude source of the CGRP-degrading enzyme. Results: MALDI-MS analysis of CGRP degradation showed almost complete inhibition in the presence of the biotinylated inhibitor. Our results showed that the rate-limiting step in the cleavage of CGRP is endopeptidase cleavage, followed by carboxypeptidase attack. Conclusion: This study demonstrates that the enzyme component of GCF responsible for the degradation of CGRP can be inhibited by a biotinylated hydroxamate modelled on a potential endopeptidase cleavage site. The biotin tag on the inhibitor will facilitate our future purification of the CGRP-cleavage enzyme using a streptavidin-agarose column.

LL-37 Degradation by GCF: A Role for Porphyromonas gingivalis Proteinases?

Background: LL-37, composed of 37 amino acid residues, is an innate host defence peptide of the cathelicidin family. It is expressed by neutrophils, monocytes and epithelial cells and exhibits both anti-bacterial and immunomodulatory properties. LL-37 is however prone to proteolytic degradation by proteinases, thus potentially limiting its inherent host defence properties in the inflammatory milieu. Objectives: The present study was designed to determine whether LL-37 was degraded by components of gingival crevicular fluid (GCF) from healthy subjects or those with periodontitis. In addition, we aimed to deduce whether degradation of the peptide was accelerated in GCF samples which were determined to be positive for the periodontopathic bacterium Porphyromonas gingivalis. Methods: GCF and bacterial plaque samples, pre- and post non-surgical periodontal treatment, were collected from 4 individual sites in patients presenting with advanced periodontitis. In healthy subjects, GCF samples only were collected. Plaque samples were analysed by QPCR for the presence or absence of P. gingivalis. Pooled GCF samples from healthy sites; periodontitis sites which were P. gingivalis negative (Pg-); or periodontitis sites which were P. gingivalis positive (Pg+), were incubated with synthetic LL-37 for 0 – 180 min. The degradation products were then analysed by matrix-assisted laser desorption/ionisation time of flight mass spectrometry (MALDI-TOF MS). Results: LL-37 was not degraded when incubated with GCF from healthy subjects. In contrast, LL-37 was degraded after 30 min when incubated with Pg- GCF. However degradation of LL-37 was apparent after only 2 min incubation with Pg+ GCF and the parent molecule was almost completely degraded after 30 min. Conclusions: The rapid degradation of LL-37, particularly in Pg+ sites, highlights the limited role which this host defence peptide may play in the presence of biologically active proteinases. It also underscores a potent virulence mechanism of P. gingivalis used to circumvent innate host responses.

Magnitude differences in bioactive compounds, chemical functional groups, fatty acid profiles, nutrient degradation and digestion, molecular structure and metabolic characteristics of protein in newly developed yellow-seeded and black-seeded canola lines.

Recently, new lines of yellow-seeded (CS-Y) and black-seeded canola (CS-B) have been developed with chemical and structural alteration through modern breeding technology. However, no systematic study was found on the bioactive compounds, chemical functional groups, fatty acid profiles, inherent structure, nutrient degradation and absorption, or metabolic characteristics between the newly developed yellow- and black-seeded canola lines. This study aimed to systematically characterize chemical, structural, and nutritional features in these canola lines. The parameters accessed include bioactive compounds and antinutrition factors, chemical functional groups, detailed chemical and nutrient profiles, energy value, nutrient fractions, protein structure, degradation kinetics, intestinal digestion, true intestinal protein supply, and feed milk value. The results showed that the CS-Y line was lower (P ≤ 0.05) in neutral detergent fiber (122 vs 154 g/kg DM), acid detergent fiber (61 vs 99 g/kg DM), lignin (58 vs 77 g/kg DM), nonprotein nitrogen (56 vs 68 g/kg DM), and acid detergent insoluble protein (11 vs 35 g/kg DM) than the CS-B line. There was no difference in fatty acid profiles except C20:1 eicosenoic acid content (omega-9) which was in lower in the CS-Y line (P < 0.05) compared to the CS-B line. The glucosinolate compounds differed (P < 0.05) in terms of 4-pentenyl, phenylethyl, 3-CH3-indolyl, and 3-butenyl glucosinolates (2.9 vs 1.0 μmol/g) between the CS-Y and CS-B lines. For bioactive compounds, total polyphenols tended to be different (6.3 vs 7.2 g/kg DM), but there were no differences in erucic acid and condensed tannins with averages of 0.3 and 3.1 g/kg DM, respectively. When protein was portioned into five subfractions, significant differences were found in PA, PB1 (65 vs 79 g/kg CP), PB2, and PC fractions (10 vs 33 g/kg CP), indicating protein degradation and supply to small intestine differed between two new lines. In terms of protein structure spectral profile, there were no significant differences in functional groups of amides I and II, α helix, and β-sheet structure as well as their ratio between the two new lines, indicating no difference in protein structure makeup and conformation between the two lines. In terms of energy values, there were significant differences in total digestible nutrient (TDN; 149 vs 133 g/kg DM), metabolizable energy (ME; 58 vs 52 MJ/kg DM), and net energy for lactation (NEL; 42 vs 37 MJ/kg DM) between CS-Y and CS-B lines. For in situ rumen degradation kinetics, the two lines differed in soluble fraction (S; 284 vs 341 g/kg CP), potential degradation fraction (D; 672 vs 590 g/kg CP), and effective degraded organic matter (EDOM; 710 vs 684 g/kg OM), but no difference in degradation rate. CS-Y had higher digestibility of rumen bypass protein in the intestine than CS-B (566 vs 446 g/kg of RUP, P < 0.05). Modeling nutrient supply results showed that microbial protein synthesis (MCP; 148 vs 171 g/kg DM) and rumen protein degraded balance (DPB; 108 vs 127 g/kg DM) were lower in the CS-Y line, but there were no differences in total truly digested protein in small intestine (DVE) and feed milk value (FMV) between the two lines. In conclusion, the new yellow line had different nutritional, chemical, and structural features compared to the black line. CS-Y provided better nutrient utilization and availability.

Habitat-species interactions in a carnivore community

Na maioria das area protegidas nacionais existe uma considerável falta de informação científica relativa aos mamíferos carnívoros. A Reserva Natural da Serra da Malcata, localizada no centro-este de Portugal, tem vindo a desenvolver, desde os últimos 20 anos, estudos de ecologia e esta tese pretende dar seguimento a esse esforço de monitorização, através do desenvolvimento de métodos simples e eficientes, de monitorização de carnívoros, que possam servir como percursores de trabalhos a longo-prazo em áreas relevantes para a conservação. Através do uso de armadilhagem fotográfica, foram estudadas relações espécies-habitats para 5 espécies: gato-bravo (Felis silvestris), fuinha (Martes foina), raposa (Vulpes vulpes), gineta (Genetta genetta), e sacarrabos (Herpestes ichneumon). Foram desenvolvidos métodos para se determinar a densidade absoluta de raposa e gineta e a população de gato-bravo foi estudada em detalhe. As principais conclusões do estudo foram: 1) a ocupação de raposas é uniforme e parece ser independente de variáveis ambientais; 2) a ocupação de fuinha encontra-se relacionada com variáveis de habitat, estrutura paisagística e presas; 3) a ocupação de gineta está relacionada com a cobertura de folhosas e distribuição de presas; 4) para o sacarrabos verificase que a ocupação é influenciada pelas extensões de habitat arbustivos, 5) a população de gato-bravo sofreu um forte declínio durante o trabalho e requer urgentes medidas de conservação. Metodologicamente foi demonstrada a importância da modelação das probabilidades de detecção para espécies para as quais este parâmetros apresenta valores baixos ou é muito variável. Esta tese também demonstrou a grande importância da Serra da Malcata para a conservação de carnívoros e a necessidade do desenvolvimento de técnicas de monitorização padronizadas para uma correcta gestão adaptativa das áreas protegidas.

Biodiversity and conservation of the middle-Araguaia herpetofauna

A conservação da biodiversidade nunca foi uma assunto tão popular como nas últimas décadas, mas esta popularidade crescente é devida à pior das razões: o passo acelerado da extinção de espécies e habitats. Os ecossistemas tropicais são, ao mesmo tempo, os mais diversos e os mais ameaçados, em parte porque muitos países destas regiões emergem ainda de situações de instabilidade social, económica e política. O Brasil é o maior país Neotropical, onde se encontram alguns dos biomas com maior diversidade e mais ameaçados do planeta. Actualmente, é também um país líder ao nível da planificação e implementação de medidas de conservação da biodiversidade. Vários dos biomas tropicais mais diversos e ameaçados encontram-se em território brasileiro. Dois destes biomas, a Amazónia e o Cerrado, convergem numa região ecotonal sujeita a uma elevada pressão humana, conhecida como o arco do desmatamento. O Araguaia, um dos maiores rios do Brasil, corre ao longo desta paisagem e os efeitos do desmatamento são já evidentes em toda a sua bacia. Por causa do acelerado ritmo de degradação deste ecossistema, torna-se urgente obter uma imagem clara da biodiversidade regional e compreender como e se a estratégia de conservação para esta região é capaz de lidar com as correntes ameaças e alcançar o seu objectivo a longo prazo: conservar a biota regional. Tendo a herpetofauna como grupo-alvo, os nossos objectivos principais foram: aumentar o conhecimento das comunidades de anfíbios e répteis squamata da região do curso médio do Rio Araguaia; compreender a importância deste rio nos padrões intraespecíficos de estrutura e diversidade genética para diferentes espécies com diferentes características ecológicas; avaliar o potencial de diferentes metodologias para o estudo e monitorização da herpetofauna regional. Os nossos resultados revelam que a amostragem continuada e o uso de diferentes técnicas são essenciais para a obtenção de uma imagem precisa da diversidade da herpetofauna local. As comunidades locais de anfíbios e lagartos apresentaram maior riqueza específica na Área de Protecção Ambiental Bananal/Cantão (APABC), uma área tampão, do no Parque Estadual do Cantão (PEC), uma área de conservação estrita. A APABC é caracterizada por uma maior heterogeneidade de habitats e os nosso resultados corroboram a teoria da heterogeneidade espacial e resultados recentes que revelam uma maior diversidade de lagartos nas zonas interfluviais do Cerrado, do que nas matas de galeria. Os resultados aqui apresentados não corroboram a hipótese de que os ecótonos apresentam maior diversidade do que os biomas em redor. Os nossos resultados revelaram ainda que o Rio Araguaia afecta de forma diferente a estrutura genética de várias espécies de anfíbios e lagartos. Estas diferenças poderão estar relacionadas com a ecologia das espécies, nomeadamente com o uso de diferentes habitats, a vagilidade, ou a estratégia alimentar. Sugerimos que a gestão integração de diferentes unidades de conservação, com diferentes estatutos, podem ajudar a preservar melhor a biota regional.

Ecology and conservation of felids in the Brazilian pantanal

Habitat conversion and environmental degradation have reached alarming levels in the Pantanal, endangering all its biodiversity. This scenario is complicated by the fact that the biome relies on only a few protected areas, which combined do not exceed 10% of the territory. Felids, as predators, play a vital role in the maintenance of this ecosystem, but require large areas, have low population densities and, typically, are very sensitive to environmental disturbances. Amolar Mountain Ridge is considered an area of extreme importance and high priority for conservation within the biome. There are four species of felids in this region: the jaguar (Panthera onca), the puma (Puma concolor), the ocelot (Leopardus pardalis), and jaguarundi (Puma yagouaroundi). However, little is known about the ecology of these species in this region or the magnitude of interaction between the communities living around the protected areas and the animals. The goal of this study was to increase our knowledge about these felids and understand how people interact with them in order to contribute to their conservation in the network of parks within Amolar. Camera trapping surveys were carried out in two areas of the network, covering approximately 83,000 hectares, in order to identify the species of mammals occurring in the region, those that may be potential prey for the felids, and to obtain basic ecological data about both felids and prey. In addition, we conducted surveys in three riverside schools in order to assess the knowledge, perceptions and attitudes of schoolchildren regarding the four focal felids, and surveys among the adult population to assess their perceptions and attitudes towards the jaguar. We recorded a total of 33 species of mammals from both study areas. The large cats were cathemeral, reflecting the temporal activity of larger prey, whereas the ocelot was nocturnal, mirroring the activity of smaller prey. Jaguar occupancy was influenced by prey abundance, while puma occupancy was influenced by patch density in drier dense forest. Jaguars and pumas may be competitors over temporal and spatial scales, while no resource overlap was found for ocelots. Overall, both adults and children tended to have negative perceptions about the cats, which were related to the fear of being attacked. To increase awareness about the species and to maximize the effectiveness of protective measures in the network of reserves, it is recommended to develop and implement an Environmental Educational Program in the medium- to long-term in order to minimize the fear of these felids and to counsel locals on the role of felids in the maintenance of the Pantanal’s biodiversity.

Pathways of oxidative degradation of wine

The production of color/flavor compounds in wine is the result of different interrelated mechanism reactions. Among these, the oxidation phenomenon and the Maillard reaction stands out with particular relevance due to their large impact on the sensory quality of wines and consequently on the product shelflife. The aim of this thesis is to achieve a global vision of wine degradation mechanisms. The identification of mediators’ reactions involved in oxidative browning and aromatic degradation will be attempted based on different detectors. Two approaches are implemented in this work: a “non-target” approach by which relevant analytical tools will be used to merge the information of cyclic voltammetry and Diode-Array (DAD) detectors, allowing a broader overview of the system and the note of interesting compounds, and a “target” approach by which the identification and quantification of the different compounds related to the wine degradation process will be performed using different detectors (HPLC-UV/Vis, LC-MS, GC-MS, and FID). Two different patterns of degradation will be used in this study: wines generated by O2 and temperature perturbations, and synthetic solutions with relevant wine constituents for mechanisms validation. Results clearly demonstrate a “convolution” of chemical mechanisms. The presence of oxygen combined with temperature had a synergistic effect on the formation of several key odorant compounds.The results of this work could be translated to the wine-making and wine-storage environment from the modelling of the analysed compounds.