Bacterial Killing Via A Type Iv Secretion System.

Type IV secretion systems (T4SSs) are multiprotein complexes that transport effector proteins and protein-DNA complexes through bacterial membranes to the extracellular milieu or directly into the cytoplasm of other cells. Many bacteria of the family Xanthomonadaceae, which occupy diverse environmental niches, carry a T4SS with unknown function but with several characteristics that distinguishes it from other T4SSs. Here we show that the Xanthomonas citri T4SS provides these cells the capacity to kill other Gram-negative bacterial species in a contact-dependent manner. The secretion of one type IV bacterial effector protein is shown to require a conserved C-terminal domain and its bacteriolytic activity is neutralized by a cognate immunity protein whose 3D structure is similar to peptidoglycan hydrolase inhibitors. This is the first demonstration of the involvement of a T4SS in bacterial killing and points to this special class of T4SS as a mediator of both antagonistic and cooperative interbacterial interactions.

A Component of the Xanthomonadaceae Type IV Secretion System Combines a VirB7 Motif with a N0 Domain Found in Outer Membrane Transport Proteins

Type IV secretion systems (T4SS) are used by Gram-negative bacteria to translocate protein and DNA substrates across the cell envelope and into target cells. Translocation across the outer membrane is achieved via a ringed tetradecameric outer membrane complex made up of a small VirB7 lipoprotein (normally 30 to 45 residues in the mature form) and the C-terminal domains of the VirB9 and VirB10 subunits. Several species from the genera of Xanthomonas phytopathogens possess an uncharacterized type IV secretion system with some distinguishing features, one of which is an unusually large VirB7 subunit (118 residues in the mature form). Here, we report the NMR and 1.0 angstrom X-ray structures of the VirB7 subunit from Xanthomonas citri subsp. citri (VirB7(XAC2622)) and its interaction with VirB9. NMR solution studies show that residues 27-41 of the disordered flexible N-terminal region of VirB7(XAC2622) interact specifically with the VirB9 C-terminal domain, resulting in a significant reduction in the conformational freedom of both regions. VirB7(XAC2622) has a unique C-terminal domain whose topology is strikingly similar to that of N0 domains found in proteins from different systems involved in transport across the bacterial outer membrane. We show that VirB7(XAC2622) oligomerizes through interactions involving conserved residues in the N0 domain and residues 42-49 within the flexible N-terminal region and that these homotropic interactions can persist in the presence of heterotropic interactions with VirB9. Finally, we propose that VirB(7XAC2622) oligomerization is compatible with the core complex structure in a manner such that the N0 domains form an extra layer on the perimeter of the tetradecameric ring.

Structure-Function Analysis of the HrpB2-HrcU Interaction in the Xanthomonas citri Type III Secretion System

Bacterial type III secretion systems deliver protein virulence factors to host cells. Here we characterize the interaction between HrpB2, a small protein secreted by the Xanthomonas citri subsp. citri type III secretion system, and the cytosolic domain of the inner membrane protein HrcU, a paralog of the flagellar protein FlhB. We show that a recombinant fragment corresponding to the C-terminal cytosolic domain of HrcU produced in E. coli suffers cleavage within a conserved Asn264-Pro265-Thr266-His267 (NPTH) sequence. A recombinant HrcU cytosolic domain with N264A, P265A, T266A mutations at the cleavage site (HrcU(AAAH)) was not cleaved and interacted with HrpB2. Furthermore, a polypeptide corresponding to the sequence following the NPTH cleavage site also interacted with HrpB2 indicating that the site for interaction is located after the NPTH site. Non-polar deletion mutants of the hrcU and hrpB2 genes resulted in a total loss of pathogenicity in susceptible citrus plants and disease symptoms could be recovered by expression of HrpB2 and HrcU from extrachromossomal plasmids. Complementation of the Delta hrcU mutant with HrcU(AAAH) produced canker lesions similar to those observed when complemented with wild-type HrcU. HrpB2 secretion however, was significantly reduced in the Delta hrcU mutant complemented with HrcU(AAAH), suggesting that an intact and cleavable NPTH site in HrcU is necessary for total functionally of T3SS in X. citri subsp. citri. Complementation of the Delta hrpB2 X. citri subsp. citri strain with a series of hrpB2 gene mutants revealed that the highly conserved HrpB2 C-terminus is essential for T3SS-dependent development of citrus canker symptoms in planta.

Expert system for the assessment of power transformer insulation condition based on type-2 fuzzy logic systems

An efficient expert system for the power transformer condition assessment is presented in this paper. Through the application of Duval`s triangle and the method of the gas ratios a first assessment of the transformer condition is obtained in the form of a dissolved gas analysis (DGA) diagnosis according IEC 60599. As a second step, a knowledge mining procedure is performed, by conducting surveys whose results are fed into a first Type-2 Fuzzy Logic System (T2-FLS), in order to initially evaluate the condition of the equipment taking only the results of dissolved gas analysis into account. The output of this first T2-FLS is used as the input of a second T2-FLS, which additionally weighs up the condition of the paper-oil system. The output of this last T2-FLS is given in terms of words easily understandable by the maintenance personnel. The proposed assessing methodology has been validated for several cases of transformers in service. (C) 2010 Elsevier Ltd. All rights reserved.

Continuous extraction of alpha-toxin from a fermented broth of Clostridium perfringens Type A in perforated rotating disc contactor using aqueous two-phase PEG-phosphate system

A 2(3-1) factorial experimental design was used to evaluate the performance of a perforated rotating disc contactor to extract alpha-toxin from the fermented broth of Clostridium perfringens Type A by aqueous two-phase system of polyethylene glycol-phosphate salts. The influence of three independent variables, specifically the dispersed phase flowrate, the continuous phase flowrate and the disc rotational speed, was investigated on the hold up, the mass transfer coefficient, the separation efficiency and the purification factor, taken as the response variables. The optimum dispersed phase flowrate was 3.0 mL/min for all these responses. Besides, maximum values of hold up (0.80), separation efficiency (0. 10) and purification factor (2.4) were obtained at this flowrate using the lowest disc rotational speed (35 rpm), while the optimum mass transfer coefficient (0. 165 h(-1)) was achieved at the highest agitation level (140 rpm). The results of this study demonstrated that the dispersed phase flowrate strongly influenced the performance of PRDC, in that both the mass transfer coefficient and hold up increased with this parameter. (c) 2007 Elsevier B. V. All rights reserved.

Differences in the post-translational modifications of human papillomavirus type 6b major capsid protein expressed from a baculovirus system compared with a vaccinia virus system

Virus-like particles (VLPs) are being currently investigated in vaccines against viral infections in humans. There are different recombinant-protein-expression systems available for obtaining the necessary VLP preparation for vaccination. However, the differences in post-translational modifications of the recombinant proteins obtained and their differences in efficacy in eliciting an anti-viral response in vaccines are not well established. In this study we have compared the posttranslational modifications of human papillomavirus type-6b major capsid protein L1 (HPV 6bL1) expressed using recombinant baculovirus (rBV) in Sf9 (Spodoptera frugiperda) insect cells, with the protein expressed using recombinant vaccinia virus (rVV) in CV-1 kidney epithelial cells, Two-dimensional gel electrophoresis of biosynthetically labelled rBV-expressed HPV 6bL1 showed several post-translationally modified variants of the protein, whereas rVV-expressed HPV 6bL1 showed only a few variants. Phosphorylations were detected at threonine and serine residues for the L1 expressed from rBV compared with phosphorylation at serine residues only for the L1 expressed from rVV. HPV 6bL1 expressed using rBV incorporated [H-3]mannose and [H-3]galactose, whereas HPV 6bL1 expressed using rVV incorporated only [H-3]galactose. We conclude that post-translational modification of recombinant HPV 6bL1 can differ according to the system used for its expression. Since recombinant L1 protein is a potential human-vaccine candidate, the implication of the observed differences in post-translational modifications on immunogenicity of L1 VLPs warrants investigation.

Assessment of guanylin peptides system in type 2 diabetes

Os doentes com diabetes mellitus tipo 2 apresentam predisposição para a retenção de sódio e são frequentemente hipertensos. No entanto, os mecanismos implicados na dificuldade do rim diabético em mobilizar o sódio são, ainda, pouco compreendidos. Os peptídeos da família das guanilinas estão envolvidos na regulação do transporte de electrólitos e água nos epitélios intestinal e renal, através da activação do receptor guanilato ciclase-C (GC-C) e subsequente libertação intracelular de GMPc. O objectivo do presente estudo foi a avaliação da actividade do sistema dos peptídeos das guanilinas (SPG) e do seu papel na regulação do balanço de sódio num modelo animal de diabetes tipo 2. Ratinhos machos C57BL/6 foram submetidos a uma dieta com alto teor de gordura e rica em hidratos de carbono simples (ratinhos diabéticos) ou a uma dieta normal (ratinhos controlo). A expressão renal e intestinal da guanilina (GN), uroguanilina (UGN) e do receptor GC-C assim como os níveis de GMPc na urina e plasma foram avaliados nos ratinhos controlo e diabéticos, durante a ingestão de dietas normo (NS) e hiper-salina (HS). Nos ratinhos diabéticos, durante a dieta NS verificou-se um aumento significativo da pressão arterial que foi acompanhado de redução da expressão do ARNm da GN, UGN e do GC-C no intestino e de aumento da expressão de ARNm da UGN no rim. A dieta HS induziu um aumento da expressão do ARNm da UGN no jejuno dos ratinhos controlo mas não nos diabéticos. Os ratinhos diabéticos apresentaram níveis urinários de GMPc inferiores aos controlos, em condições de dieta NS. Em conclusão, os nossos resultados sugerem que na diabetes tipo 2 ocorre uma redução da actividade intestinal do SPG que é acompanhada por um aumento compensatório da actividade renal do SPG. A diminuição da actividade do SPG intestinal na diabetes tipo 2 deve-se não só a uma redução da expressão dos peptídeos GN e UGN, mas também a uma redução da expressão do seu receptor, GC-C. Estes resultados sugerem que o SPG pode contribuir para a sensibilidade ao sódio na diabetes.

Design of a balanced scorecard-type management system for a back-office department in a bank

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Finance from the NOVA – School of Business and Economics

Verificación de Sistemas Basada en Teoría de Tipos. System verification in type theory

Este proyecto se enmarca en la utlización de métodos formales (más precisamente, en la utilización de teoría de tipos) para garantizar la ausencia de errores en programas. Por un lado se plantea el diseño de nuevos algoritmos de chequeo de tipos. Para ello, se proponen nuevos algoritmos basados en la idea de normalización por evaluación que sean extensibles a otros sistemas de tipos. En el futuro próximo extenderemos resultados que hemos conseguido recientemente [16,17] para obtener: una simplificación de los trabajos realizados para sistemas sin regla eta (acá se estudiarán dos sistemas: a la Martin Löf y a la PTS), la formulación de estos chequeadores para sistemas con variables, generalizar la noción de categoría con familia utilizada para dar semántica a teoría de tipos, obtener una formulación categórica de la noción de normalización por evaluación y finalmente, aplicar estos algoritmos a sistemas con reescrituras. Para los primeros resultados esperados mencionados, nos proponemos como método adaptar las pruebas de [16,17] a los nuevos sistemas. La importancia radica en que permitirán tornar más automatizables (y por ello, más fácilmente utilizables) los asistentes de demostración basados en teoría de tipos. Por otro lado, se utilizará la teoría de tipos para certificar compiladores, intentando llevar adelante la propuesta nunca explorada de [22] de utilizar un enfoque abstracto basado en categorías funtoriales. El método consistirá en certificar el lenguaje "Peal" [29] y luego agregar sucesivamente funcionalidad hasta obtener Forsythe [23]. En este período esperamos poder agregar varias extensiones. La importancia de este proyecto radica en que sólo un compilador certificado garantiza que un programa fuente correcto se compile a un programa objeto correcto. Es por ello, crucial para todo proceso de verificación que se base en verificar código fuente. Finalmente, se abordará la formalización de sistemas con session types. Los mismos han demostrado tener fallas en sus formulaciones [30], por lo que parece conveniente su formalización. Durante la marcha de este proyecto, esperamos tener alguna formalización que dé lugar a un algoritmo de chequeo de tipos y a demostrar las propiedades usuales de los sistemas. La contribución es arrojar un poco de luz sobre estas formulaciones cuyos errores revelan que el tema no ha adquirido aún suficiente madurez o comprensión por parte de la comunidad. This project is about using type theory to garantee program correctness. It follows three different directions: 1) Finding new type-checking algorithms based on normalization by evaluation. First, we would show that recent results like [16,17] extend to other type systems like: Martin-Löf´s type theory without eta rule, PTSs, type systems with variables (in addition to systems in [16,17] which are a la de Bruijn), systems with rewrite rules. This will be done by adjusting the proofs in [16,17] so that they apply to such systems as well. We will also try to obtain a more general definition of categories with families and normalization by evaluation, formulated in categorical terms. We expect this may turn proof-assistants more automatic and useful. 2) Exploring the proposal in [22] to compiler construction for Algol-like languages using functorial categories. According to [22] such approach is suitable for verifying compiler correctness, claim which was never explored. First, the language Peal [29] will be certified in type theory and we will gradually add funtionality to it until a correct compiler for the language Forsythe [23] is obtained. 3) Formilizing systems for session types. Several proposals have shown to be faulty [30]. This means that a formalization of it may contribute to the general understanding of session types.

The identity type weak factorisation system

We show that the classifying category C(T)of a dependent type theory T with axioms for identity types admits a nontrivial weak factorisation system. After characterising this weak factorisation system explicitly, we relate it to the homotopy theory of groupoids.

Early expression of the type III secretion system of Parachlamydia acanthamoebae during a replicative cycle within its natural host cell Acanthamoeba castellanii.

The type three secretion system (T3SS) operons of Chlamydiales bacteria are distributed in different clusters along their chromosomes and are conserved at both the level of sequence and genetic organization. A complete characterization of the temporal expression of multiple T3SS components at the transcriptional and protein levels has been performed in Parachlamydia acanthamoebae, replicating in its natural host cell Acanthamoeba castellanii. The T3SS components were classified in four different temporal clusters depending on their pattern of expression during the early, mid- and late phases of the infectious cycle. The putative T3SS transcription units predicted in Parachlamydia are similar to those described in Chlamydia trachomatis, suggesting that T3SS units of transcriptional expression are highly conserved among Chlamydiales bacteria. The maximal expression and activation of the T3SS of Parachlamydia occurred during the early to mid-phase of the infectious cycle corresponding to a critical phase during which the intracellular bacterium has (1) to evade and/or block the lytic pathway of the amoeba, (2) to differentiate from elementary bodies (EBs) to reticulate bodies (RBs), and (3) to modulate the maturation of its vacuole to create a replicative niche able to sustain efficient bacterial growth.

Construction and characterisation of a complete reverse genetics system of dengue virus type 3

Dengue virulence and fitness are important factors that determine disease outcome. However, dengue virus (DENV) molecular biology and pathogenesis are not completely elucidated. New insights on those mechanisms have been facilitated by the development of reverse genetic systems in the past decades. Unfortunately, instability of flavivirus genomes cloned in Escherichia coli has been a major problem in these systems. Here, we describe the development of a complete reverse genetics system, based on the construction of an infectious clone and replicon for a low passage DENV-3 genotype III of a clinical isolate. Both constructs were assembled into a newly designed yeast- E. coli shuttle vector by homologous recombination technique and propagated in yeast to prevent any possible genome instability in E. coli . RNA transcripts derived from the infectious clone are infectious upon transfection into BHK-21 cells even after repeated passages of the plasmid in yeast. Transcript-derived DENV-3 exhibited growth kinetics, focus formation size comparable to original DENV-3 in mosquito C6/36 cell culture. In vitro characterisation of DENV-3 replicon confirmed its identity and ability to replicate transiently in BHK-21 cells. The reverse genetics system reported here is a valuable tool that will facilitate further molecular studies in DENV replication, virus attenuation and pathogenesis.

An Automatic Approach for Learning and Tuning Gaussian Interval Type-2 Fuzzy Membership Functions Applied to Lung CAD Classification System

The potential of type-2 fuzzy sets for managing high levels of uncertainty in the subjective knowledge of experts or of numerical information has focused on control and pattern classification systems in recent years. One of the main challenges in designing a type-2 fuzzy logic system is how to estimate the parameters of type-2 fuzzy membership function (T2MF) and the Footprint of Uncertainty (FOU) from imperfect and noisy datasets. This paper presents an automatic approach for learning and tuning Gaussian interval type-2 membership functions (IT2MFs) with application to multi-dimensional pattern classification problems. T2MFs and their FOUs are tuned according to the uncertainties in the training dataset by a combination of genetic algorithm (GA) and crossvalidation techniques. In our GA-based approach, the structure of the chromosome has fewer genes than other GA methods and chromosome initialization is more precise. The proposed approach addresses the application of the interval type-2 fuzzy logic system (IT2FLS) for the problem of nodule classification in a lung Computer Aided Detection (CAD) system. The designed IT2FLS is compared with its type-1 fuzzy logic system (T1FLS) counterpart. The results demonstrate that the IT2FLS outperforms the T1FLS by more than 30% in terms of classification accuracy.

The TetR-type MfsR protein of the integrative and conjugative element (ICE) ICEclc controls both a putative efflux system and initiation of ICE transfer.

Integrative and conjugating elements (ICE) are self-transferable DNAs widely present in bacterial genomes, which often carry a variety of auxiliary genes of potential adaptive benefit. One of the model ICE is ICEclc, an element originally found in Pseudomonas knackmussii B13 and known for its propensity to provide its host with the capacity to metabolize chlorocatechols and 2-aminophenol. In this work, we studied the mechanism and target of regulation of MfsR, a TetR-type repressor previously found to exert global control on ICEclc horizontal transfer. By using a combination of ICEclc mutant and transcriptome analysis, gene reporter fusions, and DNA binding assays, we found that MfsR is a repressor of both its own expression and that of a gene cluster putatively coding for a major facilitator superfamily efflux system on ICEclc (named mfsABC). Phylogenetic analysis suggests that mfsR was originally located immediately adjacent to the efflux pump genes but became displaced from its original cis target DNA by a gene insertion. This resulted in divergence of the original bidirectional promoters into two separated individual regulatory units. Deletion of mfsABC did not result in a strong phenotype, and despite screening a large number of compounds and conditions, we were unable to define the precise current function or target of the putative efflux pump. Our data reconstruct how the separation of an ancestor mfsR-mfsABC system led to global control of ICEclc transfer by MfsR.