Development of advanced cell/tissue culture systems, based on enhanced polymeric scaffolds and sophisticated bioreactors, for tissue engineering applications

Programa Doutoral em Engenharia Biomédica

High-level of viral genomic diversity in cervical cancers: a Brazilian study on human papillomavirus type 16

Invasive cervical cancer (ICC) is the third most frequent cancer among women worldwide and is associated with persistent infection by carcinogenic human papillomaviruses (HPVs). The combination of large populations of viral progeny and decades of sustained infection may allow for the generation of intra-patient diversity, in spite of the assumedly low mutation rates of PVs. While the natural history of chronic HPVs infections has been comprehensively described, within-host viral diversity remains largely unexplored. In this study we have applied next generation sequencing to the analysis of intra-host genetic diversity in ten ICC and one condyloma cases associated to single HPV16 infection. We retrieved from all cases near full-length genomic sequences. All samples analyzed contained polymorphic sites, ranging from 3 to 125 polymorphic positions per genome, and the median probability of a viral genome picked at random to be identical to the consensus sequence in the lesion was only 40%. We have also identified two independent putative duplication events in two samples, spanning the L2 and the L1 gene, respectively. Finally, we have identified with good support a chimera of human and viral DNA. We propose that viral diversity generated during HPVs chronic infection may be fueled by innate and adaptive immune pressures. Further research will be needed to understand the dynamics of viral DNA variability, differentially in benign and malignant lesions, as well as in tissues with differential intensity of immune surveillance. Finally, the impact of intralesion viral diversity on the long-term oncogenic potential may deserve closer attention.

Automatic distinction of Fernando Pessoas’ heteronyms

Text Mining has opened a vast array of possibilities concerning automatic information retrieval from large amounts of text documents. A variety of themes and types of documents can be easily analyzed. More complex features such as those used in Forensic Linguistics can gather deeper understanding from the documents, making possible performing di cult tasks such as author identi cation. In this work we explore the capabilities of simpler Text Mining approaches to author identification of unstructured documents, in particular the ability to distinguish poetic works from two of Fernando Pessoas' heteronyms: Alvaro de Campos and Ricardo Reis. Several processing options were tested and accuracies of 97% were reached, which encourage further developments.

Parameter identification of the fermentative production of fructo-oligosaccharides by Aureobasidium pullulans

In this study, a mathematical model for the production of Fructo-oligosaccharides (FOS) by Aureobasidium pullulans is developed. This model contains a relatively large set of unknown parameters, and the identification problem is analyzed using simulation data, as well as experimental data. Batch experiments were not sufficiently informative to uniquely estimate all the unknown parameters, thus, additional experiments have to be achieved in fed-batch mode to supplement the missing information. © 2015 IEEE.

Development of an intelligent earthwork optimization system

Tese de Doutoramento em Engenharia Civil.

Inactivation of PNKP by mutant ATXN3 triggers apoptosis by activating the DNA damage-response pathway in SCA3.

Spinocerebellar ataxia type 3 (SCA3), also known as Machado-Joseph disease (MJD), is an untreatable autosomal dominant neurodegenerative disease, and the most common such inherited ataxia worldwide. The mutation in SCA3 is the expansion of a polymorphic CAG tri-nucleotide repeat sequence in the C-terminal coding region of the ATXN3 gene at chromosomal locus 14q32.1. The mutant ATXN3 protein encoding expanded glutamine (polyQ) sequences interacts with multiple proteins in vivo, and is deposited as aggregates in the SCA3 brain. A large body of literature suggests that the loss of function of the native ATNX3-interacting proteins that are deposited in the polyQ aggregates contributes to cellular toxicity, systemic neurodegeneration and the pathogenic mechanism in SCA3. Nonetheless, a significant understanding of the disease etiology of SCA3, the molecular mechanism by which the polyQ expansions in the mutant ATXN3 induce neurodegeneration in SCA3 has remained elusive. In the present study, we show that the essential DNA strand break repair enzyme PNKP (polynucleotide kinase 3'-phosphatase) interacts with, and is inactivated by, the mutant ATXN3, resulting in inefficient DNA repair, persistent accumulation of DNA damage/strand breaks, and subsequent chronic activation of the DNA damage-response ataxia telangiectasia-mutated (ATM) signaling pathway in SCA3. We report that persistent accumulation of DNA damage/strand breaks and chronic activation of the serine/threonine kinase ATM and the downstream p53 and protein kinase C-d pro-apoptotic pathways trigger neuronal dysfunction and eventually neuronal death in SCA3. Either PNKP overexpression or pharmacological inhibition of ATM dramatically blocked mutant ATXN3-mediated cell death. Discovery of the mechanism by which mutant ATXN3 induces DNA damage and amplifies the pro-death signaling pathways provides a molecular basis for neurodegeneration due to PNKP inactivation in SCA3, and for the first time offers a possible approach to treatment.

Incorporation of antimicrobial peptides on functionalized cotton gauzes for medical applications

A large group of low molecular weight natural compounds that exhibit antimicrobial activity has been isolated from animals and plants during the past two decades. Among them, peptides are the most widespread resulting in a new generation of antimicrobial agents with higher specific activity. In the present study we have developed a new strategy to obtain antimicrobial wound-dressings based on the incorporation of antimicrobial peptides into polyelectrolyte multilayer films built by the alternate deposition of polycation (chitosan) and polyanion (alginic acid sodium salt) over cotton gauzes. Energy dispersive X ray microanalysis technique was used to determine if antimicrobial peptides penetrated within the films. FTIR analysis was performed to assess the chemical linkages, and antimicrobial assays were performed with two strains: Staphylococcus aureus (Gram-positive bacterium) and Klebsiella pneumonia (Gram-negative bacterium). Results showed that all antimicrobial peptides used in this work have provided a higher antimicrobial effect (in the range of 4 log–6 log reduction) for both microorganisms, in comparison with the controls, and are non-cytotoxic to normal human dermal fibroblasts at the concentrations tested.

Real-time monitoring of progression towards renal failure in primary care patients

First published online: December 16, 2014.

Current situation on the occurrence of mycotoxins and toxigenic fungi in Portugal

Mycotoxins are secondary metabolites produced by filamentous fungi that are toxic for humans and animals in small amounts and that are found worldwide in a large number of agricultural commodities. They are usually ingested involuntarily, when contaminated plant products are consumed, and represent a great risk for public health. Therefore, governments throughout the world have imposed strict legal limits for their levels in food and feed products in order to reduce potential health risks for consumers. Despite of its ubiquity, the mycotoxin problem is mainly dependent on regional factors, such as the mycotoxigenic characteristics of the local mycoflora, the local climate conditions, and the local agricultural practices. For this reason, a constant vigilance from local governmental food safety agencies and from the local researcher community is needed. This communication will review the current situation on the occurrence of mycotoxigenic fungi in some Portuguese cultures, such as wine grapes, corn and dried fruits. Particular attention will be given to the incidence of mycotoxigenic Aspergillus strains in those cultures and to the levels of ochratoxin A, aflatoxins, cyclopiazonic acid and fumonisin B2 produced. Data will be discussed taking into account the geographical origin of the isolates and the particular climate conditions of each sampling region. An updated review on the levels of the main mycotoxins found in local products and in imported commodities will also be presented.

A review of sustainable approaches in transport infrastructure geotechnics

Transportation geotechnics associated with constructing and maintaining properly functioning transportation infrastructure is a very resource intensive activity. Large amounts of materials and natural resources are required, consuming proportionately large amounts of energy and fuel. Thus, the implementation of the principles of sustainability is important to reduce energy consumption, carbon footprint, greenhouse gas emissions, and to increase material reuse/recycling, for example. This paper focusses on some issues and activities relevant to sustainable earthwork construction aimed at minimising the use of energy and the production of CO2 while improving the in-situ ground to enable its use as a foundation without the consumption of large amounts of primary aggregate as additional foundation layers. The use of recycled materials is discussed, including steel slag and tyre bales, alongside a conceptual framework for evaluating the utility of applications for recycled materials in transportation infrastructure.

An R package for the integrated analysis of metabolomics and spectral data

Recently, there has been a growing interest in the field of metabolomics, materialized by a remarkable growth in experimental techniques, available data and related biological applications. Indeed, techniques as Nuclear Magnetic Resonance, Gas or Liquid Chromatography, Mass Spectrometry, Infrared and UV-visible spectroscopies have provided extensive datasets that can help in tasks as biological and biomedical discovery, biotechnology and drug development. However, as it happens with other omics data, the analysis of metabolomics datasets provides multiple challenges, both in terms of methodologies and in the development of appropriate computational tools. Indeed, from the available software tools, none addresses the multiplicity of existing techniques and data analysis tasks. In this work, we make available a novel R package, named specmine, which provides a set of methods for metabolomics data analysis, including data loading in different formats, pre-processing, metabolite identification, univariate and multivariate data analysis, machine learning, and feature selection. Importantly, the implemented methods provide adequate support for the analysis of data from diverse experimental techniques, integrating a large set of functions from several R packages in a powerful, yet simple to use environment. The package, already available in CRAN, is accompanied by a web site where users can deposit datasets, scripts and analysis reports to be shared with the community, promoting the efficient sharing of metabolomics data analysis pipelines.

The role of macroH2A1 in prostate carcinogenesis

Dissertação de mestrado em Genética Molecular

Advances in preservation of fruits and vegetables with bioactive coatings

Bioactive compounds are a large group of compounds (antimicrobials, antioxidants, nutrients, etc.), but its use in edible fi lms and coatings for application on fruits and vegetables has been very important because nowadays the consumers demand fruits and vegetables that are fresh, healthy, high quality and easy to prepare. A number of investigations have shown that the use of additives in edible fi lms and coatings improve its functionability and provide compounds for human health. However, it is necessary to continue research that can generate specifi c or tailor-made edible fi lms and coatings for each product with the best characteristics for preservation. In this review we present and analyze the concepts, progress and perspectives in the design and application of edible fi lms and coatings for fruits and vegetables in order to defi ne the challenges and opportunities that this topic of study in the fi eld of science, technology and food engineering.

Development of nanohydrogels as a vehicle for the release of bioactive compounds in food matrices

PhD in Chemical and Biological Engineering

From perfect strangers to research partners: a study of relationships, resource sharing and perceived benefits within R&D cooperation networks

Doctoral thesis in Marketing and Strategy.