Identification of potential drug targets in Salmonella Typhimurium using metabolic modelling and experimental validation

almonella enterica serovar Typhimurium is an established model organism for Gram-negative, intracellular pathogens. Owing to the rapid spread of resistance to antibiotics among this group of pathogens, new approaches to identify suitable target proteins are required. Based on the genome sequence of Salmonella Typhimurium and associated databases, a genome-scale metabolic model was constructed. Output was based on an experimental determination of the biomass of Salmonella when growing in glucose minimal medium. Linear programming was used to simulate variations in energy demand, while growing in glucose minimal medium. By grouping reactions with similar flux responses, a sub-network of 34 reactions responding to this variation was identified (the catabolic core). This network was used to identify sets of one and two reactions, that when removed from the genome-scale model interfered with energy and biomass generation. 11 such sets were found to be essential for the production of biomass precursors. Experimental investigation of 7 of these showed that knock-outs of the associated genes resulted in attenuated growth for 4 pairs of reactions, while 3 single reactions were shown to be essential for growth.

The N-terminal SH2 domain of Syk is required for (hem)ITAM, but not integrin, signaling in mouse platelets

We have used a novel knockin mouse to investigate the effect of disruption of phosphotyrosine binding of the N-terminal SH2 domain of Syk on platelet activation by GPVI, CLEC-2, and integrin αIIbβ3. The Syk(R41Afl/fl) mouse was crossed to a PF4-Cre(+) mouse to induce expression of the Syk mutant in the megakaryocyte/platelet lineage. Syk(R41Afl/fl;PF4-Cre) mice are born at approximately 50% of the expected frequency and have a similar phenotype to Syk(fl/fl;PF4-Cre) mice, including blood-lymphatic mixing and chyloascites. Anastomosis of the venous and lymphatic vasculatures can be seen in the mesenteric circulation accounting for rapid and continuous mixing of the 2 vasculatures. Platelet activation by CLEC-2 and GPVI is abolished in Syk(R41Afl/fl;PF4-Cre) platelets. Syk phosphorylation on Tyr519/20 is blocked in CLEC-2-stimulated platelets, suggesting a model in which binding of Syk via its N-terminal SH2 domain regulates autophosphorylation. In contrast, outside-in signaling by integrin αIIbβ3 is not altered, but it is inhibited in the presence of inhibitors of Src and Syk tyrosine kinases. These results demonstrate that αIIbβ3 regulates Syk through an ITAM-independent pathway in mice and provide novel insight into the course of events underlying Syk activation and hemITAM phosphorylation by CLEC-2.

Physical analyses of compost from composting plants in Brazil

Nowadays the composting process has shown itself to be an alternative in the treatment of municipal solid wastes by composting plants. However, although more than 50% of the waste generated by the Brazilian population is composed of matter susceptible to organic composting, this process is, still today, insufficiently developed in Brazil, due to low compost quality and lack of investments in the sector. The objective of this work was to use physical analyses to evaluate the quality of the compost produced at 14 operative composting plants in the Sao Paulo State in Brazil. For this purpose, size distribution and total inert content tests were done. The results were analyzed by grouping the plants according to their productive processes: plants with a rotating drum, plants with shredders or mills, and plants without treatment after the sorting conveyor belt. Compost quality was analyzed considering the limits imposed by the Brazilian Legislation and the European standards for inert contents. The size distribution tests showed the influence of the machinery after the sorting conveyer on the granule sizes as well as the inert content, which contributes to the presence of materials that reduce the quality of the final product. (C) 2007 Elsevier Ltd. All rights reserved.

POLYGLYCOLIC ACID TUBE ASSOCIATED WITH GM1 IN REGENERATION OF PERIPHERAL NERVES

Introduction: Nerve allografting is regarded as a treatment of choice in large neural tissue losses preventing repair by primary anastomosis. In these cases, a synthetic polyglycolic acid tube is an alternative for nerve grafting. On the other hand, several studies have emphasized the importance of neurotrophic factors on neural regeneration, including substances with potential to optimize neural regeneration, especially the GM1, an neurotrophic enhancer factor. Objective: to compare, in rats, the neural regeneration degree using histological analysis, regenerated myelinized axons count, and functional analysis with the use of neurotube and GM1. Methods: This assessment was performed by interposing allograft (group A), polyglycolic acid tube (group B) and polyglycolic acid tube associated to GM1 (group C) on 5-mm sciatic nerve defects. Results: Neuroma formation was found only on group A. Groups A and C showed similar histological patterns, except for the regenerated axons on group C, which were shown to be better organized and myelinized than in group A. Conclusion: on functional recovery, no statistically significant difference was found for the three groups, despite of qualitative and quantitative histological differences found.

HiPP: A Novel Hierarchical Point Placement Strategy and its Application to the Exploration of Document Collections

Point placement strategies aim at mapping data points represented in higher dimensions to bi-dimensional spaces and are frequently used to visualize relationships amongst data instances. They have been valuable tools for analysis and exploration of data sets of various kinds. Many conventional techniques, however, do not behave well when the number of dimensions is high, such as in the case of documents collections. Later approaches handle that shortcoming, but may cause too much clutter to allow flexible exploration to take place. In this work we present a novel hierarchical point placement technique that is capable of dealing with these problems. While good grouping and separation of data with high similarity is maintained without increasing computation cost, its hierarchical structure lends itself both to exploration in various levels of detail and to handling data in subsets, improving analysis capability and also allowing manipulation of larger data sets.

Study of environmental burden of lead in children using teeth as bioindicator

The south region of Sao Paulo city hosts the Guarapiranga dam, responsible for water supply to 25% of the city population. Their surroundings have been subject to intense and irregular occupation by people from very low socioeconomics classes. Measurements undertaken on sediment and particulate materials in the dam revealed concentrations of lead. copper, zinc and cadmium above internationally accepted limits. Epidemiological and toxicological studies undertaken by the World Health Organization in individuals exhibiting lead concentrations in blood, near or below the maximum recommended (10 mu g dl(-1)), surprisingly revealed that toxic effects are more intense in individuals belonging to low socioeconomics classes. Motivated by these facts, we aimed at the investigation of chronic incorporation of lead. as well as the use of our BIOKINETICS code, which is based on an accepted ICRP biokinetics model for lead, in order to extrapolate the results from teeth to other organs. The focus of our data taking was children from poor families, living in a small, restrict and allegedly contaminated area in Sao Paulo city. Thus, a total of 74 human teeth were collected. The average concentration of lead in teeth of children 5 to 10 years old was determined by means of a high-resolution inductively coupled plasma mass spectrometer (ICP-MS). For standardization of the measurements, an animal bone certified material (H-Animal Bone), from the International Atomic Energy Agency, was analyzed. The amount of lead in children living in the surroundings of the dam, was approximately 40% higher than those from the control region, and the average lead concentration was equal to 1.3 mu g g(-1) approximately. Grouping the results in terms of gender, tooth type and condition, it was concluded that a carious molar of boys is a much more efficient contamination pathway for lead, resulting in concentrations 70% higher than in the control region. We also inferred the average concentrations of lead in other organs of these children, by making use of our BIOKINETIC code. (C) 2008 Elsevier Ltd. All rights reserved.

The Aedes aegypti larval transcriptome: a comparative perspective with emphasis on trypsins and the domain structure of peritrophins

The genome sequence of Aedes aegypti was recently reported. A significant amount of Expressed Sequence Tags (ESTs) were sequenced to aid in the gene prediction process. In the present work we describe an integrated analysis of the genomic and EST data, focusing on genes with preferential expression in larvae (LG), adults (AG) and in both stages (SG). A total of 913 genes (5.4% of the transcript complement) are LG, including ion transporters and cuticle proteins that are important for ion homeostasis and defense. From a starting set of 245 genes encoding the trypsin domain, we identified 66 putative LG, AG, and SG trypsins by manual curation. Phylogenetic analyses showed that AG trypsins are divergent from their larval counterparts (LG), grouping with blood-induced trypsins from Anopheles gambiae and Simulium vittatum. These results support the hypothesis that blood-feeding arose only once, in the ancestral Culicomorpha. Peritrophins are proteins that interlock chitin fibrils to form the peritrophic membrane (PM) that compartmentalizes the food in the midgut. These proteins are recognized by having chitin-binding domains with 6 conserved Cys and may also present mucin-like domains (regions expected to be highly O-glycosylated). PM may be formed by a ring of cells (type 2, seen in Ae. aegypti larvae and Drosophila melanogaster) or by most midgut cells (type 1, found in Ae. aegypti adult and Tribolium castaneum). LG and D. melanogaster peritrophins have more complex domain structures than AG and T. castaneum peritrophins. Furthermore, mucin-like domains of peritrophins from T. castaneum (feeding on rough food) are lengthier than those of adult Ae. aegypti (blood-feeding). This suggests, for the first time, that type 1 and type 2 PM may have variable molecular architectures determined by different peritrophins and/or ancillary proteins, which may be partly modulated by diet.

A quantum chemical study on a set of non-imidazole H(3) antihistamine molecules

Molecular orbital calculations were carried out on a set of 28 non-imidazole H(3) antihistamine compounds using the Hartree-Fock method in order to investigate the possible relationships between electronic structural properties and binding affinity for H3 receptors (pK(i)). It was observed that the frontier effective-for-reaction molecular orbital (FERMO) energies were better correlated with pK(i) values than highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy values. Exploratory data analysis through hierarchical cluster (HCA) and principal component analysis (PCA) showed a separation of the compounds in two sets, one grouping the molecules with high pK(i) values, the other gathering low pK(i) value compounds. This separation was obtained with the use of the following descriptors: FERMO energies (epsilon(FERMO)), charges derived from the electrostatic potential on the nitrogen atom (N(1)), electronic density indexes for FERMO on the N(1) atom (Sigma((FERMO))c(i)(2)). and electrophilicity (omega`). These electronic descriptors were used to construct a quantitative structure-activity relationship (QSAR) model through the partial least-squares (PLS) method with three principal components. This model generated Q(2) = 0.88 and R(2) = 0.927 values obtained from a training set and external validation of 23 and 5 molecules, respectively. After the analysis of the PLS regression equation and the values for the selected electronic descriptors, it is suggested that high values of FERMO energies and of Sigma((FERMO))c(i)(2), together with low values of electrophilicity and pronounced negative charges on N(1) appear as desirable properties for the conception of new molecules which might have high binding affinity. 2010 Elsevier Inc. All rights reserved.

Electrical Evaluation of a Low Concentrating PVT Collector Based on Performance Ratio

Photovoltaic Thermal/Hybrid collectors are an emerging technology that combines PV and solar thermal collectors by producing heat and electricity simultaneously. In this paper, the electrical performance evaluation of a low concentrating PVT collector was done through two testing parts: power comparison and performance ratio testing. For the performance ratio testing, it is required to identify and measure the factors affecting the performance ratio on a low concentrating PVT collector. Factors such as PV cell configuration, collector acceptance angle, flow rate, tracking the sun, temperature dependence and diffuse to irradiance ratio. Solarus low concentrating PVT collector V12 was tested at Dalarna University in Sweden using the electrical equipment at the solar laboratory. The PV testing has showed differences between the two receivers. Back2 was producing 1.8 energy output more than Back1 throughout the day. Front1 and Front2 were almost the same output performance. Performance tests showed that the cell configuration for Receiver2 with cells grouping (6- 32-32-6) has proved to have a better performance ratio when to it comes to minimizing the shading effect leading to more output power throughout the day because of lowering the mismatch losses. Different factors were measured and presented in this thesis in chapter 5. With the current design, it has been obtained a peak power at STC of 107W per receiver. The solar cells have an electrical efficiency of approximately 19% while the maximum measured electrical efficiency for the collector was approximately 18 % per active cell area, in addition to a temperature coefficient of -0.53%/ ˚C. Finally a recommendation was done to help Solarus AB to know how much the electrical performance is affected during variable ambient condition and be able to use the results for analyzing and introducing new modification if needed.

Hushållsavfall i Borlänge kommun : analyser av material en och flerfamiljshus

In Borlänge, source separation has been the basis for management of household waste for over five years. This report reviews today?s system and gives a model for further follow-up through waste grouping. In the basic system waste is separated into three fractions: biodegradable, waste to energy and waste to landfill. All waste is packed in plastic bags, put in separate containers for each fraction, and collected from the property. Separate analyses were made of waste from single family houses and apartment buildings. The amount of waste per household and week, number of non-sorted bags, purity, recovery rate and density of each fraction was calculated. The amount of packaging collected together with the household waste is given. Material collected under the Swedish law of Producers? Responsibility is not covered in this report.

Recording and Using Provenance in a Protein Compressibility Experiment

Very large scale computations are now becoming routinely used as a methodology to undertake scientific research. In this context, `provenance systems' are regarded as the equivalent of the scientist's logbook for in silico experimentation: provenance captures the documentation of the process that led to some result. Using a protein compressibility analysis application, we derive a set of generic use cases for a provenance system. In order to support these, we address the following fundamental questions: what is provenance? how to record it? what is the performance impact for grid execution? what is the performance of reasoning? In doing so, we define a technologyindependent notion of provenance that captures interactions between components, internal component information and grouping of interactions, so as to allow us to analyse and reason about the execution of scientific processes. In order to support persistent provenance in heterogeneous applications, we introduce a separate provenance store, in which provenance documentation can be stored, archived and queried independently of the technology used to run the application. Through a series of practical tests, we evaluate the performance impact of such a provenance system. In summary, we demonstrate that provenance recording overhead of our prototype system remains under 10% of execution time, and we show that the recorded information successfully supports our use cases in a performant manner.

Reasoning about Requirements Evolution Using Clustered Belief Revision

During the development of system requirements, software system specifications are often inconsistent. Inconsistencies may arise for different reasons, for example, when multiple conflicting viewpoints are embodied in the specification, or when the specification itself is at a transient stage of evolution. These inconsistencies cannot always be resolved immediately. As a result, we argue that a formal framework for the analysis of evolving specifications should be able to tolerate inconsistency by allowing reasoning in the presence of inconsistency without trivialisation, and circumvent inconsistency by enabling impact analyses of potential changes to be carried out. This paper shows how clustered belief revision can help in this process. Clustered belief revision allows for the grouping of requirements with similar functionality into clusters and the assignment of priorities between them. By analysing the result of a cluster, an engineer can either choose to rectify problems in the specification or to postpone the changes until more information becomes available.

Estudo da incidência de complicações da anastomose brônquica em pacientes submetidos à transplante de pulmão em um período de 10 anos

Uma das complicações cirúrgicas que mais afeta o resultado do transplante pulmonar é a complicação da anastomose brônquica. Esta pode apresentar-se com um espectro que vai desde a isquemia transitória da anastomose sem outras alterações até a deiscência total com mediastinite e sépsis. Embora a sua ocorrência tenha diminuído nos últimos anos, continua sendo uma das complicações mais frequentes no pós-operatório. Em nosso trabalho, foi analisada a ocorrência de complicações de anastomose brônquica que necessitaram algum tipo de intervenção cirúrgica na população de pacientes transplantados de pulmão durante um período de dez anos (1989-1999). Este grupo representa a quase totalidade dos transplantes pulmonares realizados no Brasil neste período. Pacientes e Métodos: Foram avaliados todos os transplantes de pulmão realizados em um período de 10 anos (1989-1999) no Pavilhão Pereira Filho, Santa Casa de Misericórdia, Porto Alegre, RS, Brasil, para a ocorrência de complicação da anastomose brônquica e possíveis fatores de risco. Resultados: Em um total de 76 pacientes e 81 anastomoses com o risco de complicação, ocorreram 12 complicações (15,79%). Entre os fatores analisados para risco possivelmente associado à complicação, não houve diferença estatisticamente significativa para o tempo de isquemia superior ou inferior a quatro horas (Teste de Fischer com p=1,00), entre um ou mais de um episódio de rejeição (Teste de Fischer com p=0,756), um ou mais de um pulsos de metilprednisolona (p=0,58), a ocorrência de infecção por citomegalovírus ou não ( teste de Fischer com p=0,169), e nem houve maior número de complicações brônquicas nos pacientes que tiveram maior número de episódios de infecção. Houve diferença estatisticamente entre a técnica de anastomose brônquica término-terminal e a telescopagem brônquica, sendo a ocorrência de complicações bem menor no segundo grupo (teste de Fischer com p=0,005), e também ocorreu diferença estatisticamente significativa entre dois períodos de transplante, de 1989 a 1993 e de 1994 a 1999, sendo a ocorrência menor no segundo grupo (teste exato de Fischer com p=0,037). Conclusões: A técnica de telescopagem brônquica apresentou menor número de complicações da anastomose brônquica, e a maior experiência da equipe de transplantes também contribuiu para a redução das complicações da anastomose.

Ativação linfocitária durante a cirurgia de revascularização miocárdica : papel da circulação extracorpórea

Introdução: Sabe-se que a cirurgia de revascularização miocárdica está associada com alteração dos mediadores inflamatórios e da função imunitária, com ativação precoce dos linfócitos que poderia ser responsável pela linfopenia e diminuição da atividade dos linfócitos no pós-operatório. A elevação enzimática está diminuída na cirurgia sem circulação extracorpórea mas este achado não está associado a melhor evolução clínica. Nesta tese, testamos a hipótese de que a cirurgia de revascularização miocárdica realizada sem circulação extracorpórea pode levar a uma ativação linfocitária de menor intensidade do que a cirurgia com circulação extracorpórea. Métodos: A resposta da ativação linfocitária foi estudada durante o período trans e pósoperatório em 28 pacientes randomizados para cirurgia de coronária sem circulação extracorpórea (n=13) ou cirurgia convencional com circulação extracorpórea (n=15), utilizando citometria de fluxo para determinar a expressão de CD25, CD26, CD69 e DR em linfócitos T (CD3+) e B (CD19+), em sangue periférico. No mesmo período foram realizadas dosagens de troponina I por quimioluminescência e realizado ecocardiograma uni-bidimensional antes e após a cirurgia. Resultados: Não houve diferença estatisticamente significativa para nenhum dos marcadores de ativação linfocitária quando comparados os grupos operados sem ou com circulação extracorpórea (ANOVA bicaudal para medidas repetidas, p>0,05). Considerando todos os pacientes estudados, houve uma elevação da expressão proporcional de CD25 e CD69 em linfócitos T (CD3+) e B (CD19+). Nos linfócitos T, o valor proporcional médio mais elevado (+ EP) de CD69 foi observado 6 horas após terem sido completadas as anastomoses (+75 + 476%) e CD25 teve uma elevação mais gradual, com o pico de seu valor médio (+48 + 24 %) ocorrendo 24 horas após a revascularização. Em linfócitos B, o pico do valor médio de CD69 (+104 + 269 %) ocorreu também após o fim das anastomoses. CD25 teve seu pico de valor médio (+150 + 773 %) 112 horas após a revascularização e seu último valor medido ainda estava elevado. A expressão de CD26 em linfócitos T teve um aparente declínio nos seus valores proporcionais médios (-42 + 32 %) 12 horas após o fim das anastomoses. Não houve diferença significativa na elevação enzimática entre os dois grupos (teste estatístico >0,05). No ecocardiograma, o grupo operado sem circulação extracorpórea apresentou diminuição do volume diastólico (p=0,001) de da fração de ejeção (P=0,012), enquanto no grupo com circulação extracorpórea, diminuíram os volumes diastólico (p=0,006) e sistólico (p=0,01). Conclusões: 1) Comparando a cirurgia de revascularização miocárdica com circulação extracorpórea, a cirurgia sem circulação extracorpórea não reduz a ativação dos linfócitos. 2) A cirurgia de revascularização miocárdica produz uma ativação precoce dos linfócitos, com aumento da expressão de CD69 e CD25 em linfócitos T (CD3+) e B (CD19+), em sangue periférico. A elevação precoce de CD69, e elevação mais tardia de CD25, pode indicar duas partes de uma seqüência de ativação linfocitária. 3) O comportamento das enzimas cardíacas e dos achados ecocardiográficos não sugere benefício da cirurgia sem circulação extracorpórea sobre o dano miocárdio.

Perfil da indústria de alimentos no Brasil: 1990-1995

A pesquisa sobre o perfil da indústria de alimentos no período de 1990-95 observou uma superior participação do grupo de produtos de maior valor agregado, com destaque para os laticínios, assim como um aumento do consumo de alimentos em geral propiciado pelo aumento da renda real dos trabalhadores após o Plano Real. Constataram-se, também, ajustes aos novos padrões de competitividade devido à abertura de mercado, com conseqüências na diminuição das margens líquidas e do número de emprego.