Localization studies of the FemXAB protein family in Staphylococcus aureus

Dissertação apresentada para a obtenção do Grau de Mestre em Genética Molecular e Biomedicina, pela Universidade Nova de Lisboa, Faculdade de Ciências e TecnologiaThe public health burden of methicillin-resistant Staphylococcus aureus (MRSA) strains and the emergence of vancomycin resistance in S. aureus call for alternative strategies in chemotherapy. The FemXAB family of proteins is responsible for the assembly of the characteristic pentaglycine cross-bridge in the peptidoglycan of S. aureus, which is essential both for cell viability and for the expression of high level methicillin resistance. Fem proteins are, therefore, good candidate targets for the development of pathogen specific antimicrobial compounds, acting alone or synergistically with -lactams. In this work, we characterized the localization of the FemX, FemA and FemB proteins (which add the 1st; 2nd and 3rd; 4th and 5th glycines of the crossbridge, respectively) during the bacterial cell cycle, using fluorescence microscopy. These proteins localized preferably at the membrane, including the septum, and de-localized in the absence of the peptidoglycan precursor. FemA and FemB proteins colocalized in all cells observed during the different stages of the cell cycle, whilst FemX and FemA proteins co-localized in 64% of the cells. To determine if the FemB protein was dependent on FemA for proper localization, different approaches were used to attempt inactivation of the femA gene, but all were unsuccessful, suggesting that femA may be a lethaltarget

C++ é inadequado para ensinar OO

Num curso superior de Informática não deve haver preocupação em ensinar a última novidade tecnológica, mas antes os fundamentos que permitam aos diplomados uma capacidade para aprender continuamente. No ensino da programação orientada ao objecto (POO) é importante utilizar-se uma linguagem com suporte coerente dos conceitos fundamentais do paradigma, sem características que entrem em contradição com o modelo central, sob pena da linguagem se tornar um obstáculo à aprendizagem. Neste artigo argumenta-se precisamente que C++ é um obstáculo à aprendizagem da POO. Muitos alunos acreditam que aprender C++ lhes dará todas as competências na área da programação de que necessitarão no futuro. Esta visão errada tem como consequência que poderão ficar pior preparados para se adaptarem às mudanças a que a informática está sujeita. C++ foi criado tendo em vista a compatibilidade com o C, pelo que todas as decisões de concepção do C++ estiveram dependentes das características, boas ou más, da linguagem anterior. Só este facto já permite questionar se tudo o que o C++ oferece será coerente, sobretudo se se considerar que o próprio C, por vezes classificado de “linguagem assembly estruturada”, dá suporte a vários paradigmas da programação. Na verdade C++ não é uma linguagem orientada ao objecto (LOO), mas uma linguagem multiparadigma, dotada dum suporte imperfeito dos conceitos da OO, misturados com conceitos oriundos de modelos de programação mais antigos. A seguir alude-se a alguns dos principais aspectos técnicos em que C++ apresenta imperfeições no suporte à POO. São feitas comparações com algumas das LOOs mais importantes, sobretudo Eiffel e Java

An illustrative example of refactoring object-oriented source code with aspect-oriented mechanisms

This paper describes a refactoring process that transforms a Java source code base into a functionally equivalent AspectJ source code base. The process illustrates the use of a collection of refactorings for aspect-oriented source code, covering the extraction of scattered implementation elements to aspects, the internal reorganization of the extracted aspects and the extraction of commonalities to super-aspects.Fundação para a Ciência e a Tecnologia (FCT)Fundo Europeu de Desenvolvimento Regional (FEDER) - POSC/EIA/60189/200

Some thoughts on refactoring objects to aspects

The prospect of aspect-orientation receiving widespread acceptance and adoption in the near future begs the question of how to deal with a large base of object-oriented legacy code. We propose to investigate refactoring techniques for restructuring object-oriented source code so that it can leverage the mechanisms of aspect-orientation in order to become easier to adapt, extend and evolve. Our approach is to adopt an object-oriented framework in the area of workflow as a non-trivial case study. We plan to analyse its source code, develop an aspect-oriented version through the progressive use of manual refactorings, and build a catalogue of refactoring operations based on the experience gained through the process

Pitfalls of aspectJ implementations of some of the gang-of-four design patterns

For the previous edition of this workshop [8], the authors wrote a paper presenting the aims of the first author’s Ph.D. project [13], which includes the development of a catalogue of refactorings [3] for the AspectJ programming language [1]. Case studies are be used for refactoring experiments, to gain the necessary insights. In this paper, we present several considerations on some code examples in AspectJ [10] from our second case study. They look like a critique, which may lead readers to assume we have a low opinion of them. That is not the case: we largely consider them a success, and proved to be a rich source of insights. Our intent is to simply point out some problems in using the code examples, thus contributing to their analysis. This is done in section 2. We take the opportunity provided by this paper to present, in section 3, an update on a style rule proposed in the previous paper [13]. In section 4 we conclude the paper.PRODEP III - Medida 5 - Acção 5.3 - Eixo 3 - Formação Avançada de Docentes do Ensino Superior; PPC-VM - POSI/CHS/47158/2002

Mechanisms coordinating peptidoglycan synthesis with the cell cycle in Staphylococcus aureus

"The emergence and spread of antibiotic resistance in bacteria constitutes one of the major challenges to global public health and is predicted to further escalate during the 21st century. One of the most frequent multi-drug resistant pathogens is methicillin-resistant Staphylococcus aureus (MRSA), a gram-positive coccoid bacterium that causes difficult to treat infections with severe morbidity and mortality rates. Many of the commonly used antibiotics target steps in the biosynthesis of peptidoglycan (PG), a robust but flexible meshlike macromolecule that withstands the intense internal turgor in the cell, among other functions. The integrity of the PG layer is of the utmost importance to bacteria, which must ensure that incorporation of new PG strands and remodelling of the existing ones is timely coordinated with the progression of the cell cycle. Despite its clinical relevance, many fundamental biological processes in S. aureus remain to be elucidated.(...)"

Refactoring a java code base to aspectJ: an illustrative example

This paper describes a refactoring process transforming a Java code base into an AspectJ equivalent. The process illustrates 17 aspect-oriented refactorings covering extraction of implementation elements to aspects, internal reorganization of extracted aspects, and extraction of commonalities to superaspects.(undefined

Coding mode decision algorithm for binary descriptor coding

In visual sensor networks, local feature descriptors can be computed at the sensing nodes, which work collaboratively on the data obtained to make an efficient visual analysis. In fact, with a minimal amount of computational effort, the detection and extraction of local features, such as binary descriptors, can provide a reliable and compact image representation. In this paper, it is proposed to extract and code binary descriptors to meet the energy and bandwidth constraints at each sensing node. The major contribution is a binary descriptor coding technique that exploits the correlation using two different coding modes: Intra, which exploits the correlation between the elements that compose a descriptor; and Inter, which exploits the correlation between descriptors of the same image. The experimental results show bitrate savings up to 35% without any impact in the performance efficiency of the image retrieval task. © 2014 EURASIP