Publications

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Conference Paper
Moreira, IP, Sato L, Alves C, Palma S, Roque AC.  2021.  Fish gelatin-based films for gas sensing. BIODEVICES 2021 - 14th International Conference on Biomedical Electronics and Devices; Part of the 14th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2021. :32–39.: SciTePress Abstract102062.pdf

Electronic noses (e-noses) mimic the complex biological olfactory system, usually including an array of gas sensors to act as the olfactory receptors and a trained computer with signal-processing and pattern recognition tools as the brain. In this work, a new stimuli-responsive material is shown, consisting of self-assembled droplets of liquid crystal and ionic liquid stabilised within a fish gelatin matrix. These materials change their opto/electrical properties upon contact with volatile organic compounds (VOCs). By using an in-house developed e-nose, these new gas-sensing films yield characteristic optical signals for VOCs from different chemical classes. A support vector machine classifier was implemented based on 12 features of the signals. The results show that the films are excellent identifying hydrocarbon VOCs (toluene, heptane and hexane) (95% accuracy) but lower performance was found to other VOCs, resulting in an overall 60.4% accuracy. Even though they are not reusable, these sustainable gas-sensing films are stable throughout time and reproducible, opening several opportunities for future optoelectronic devices and artificial olfaction systems.

Roque, ACA, Fred A, Gamboa H.  2019.  Foreword, January 2019. BIODEVICES 2019 - 12th International Conference on Biomedical Electronics and Devices, Proceedings; Part of 12th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2019. , Prague: SciTePress
Padua, A, Gruber J, Gamboa H, Roque ACA.  2019.  Impact of Sensing Film’s Production Method on Classification Accuracy by Electronic Nose. Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 1: BIODEVICES. , Prague, Czech Republic AbstractPDF

The development of gas sensing materials is relevant in the field of non-invasive biodevices. In this work, we used an electronic nose (E-nose) developed by our research group, which possess versatile and unique sensing materials. These are gels that can be spread over the substrate by Film Coating or Spin Coating. This study aims to evaluate the influence of the sensing film spreading method selected on the classification capabilities of the E-nose. The methodology followed consisted of performing an experiment where the E-nose was exposed to 13 different pure volatile organic compounds. The sensor array had two sensing films produced by Film Coating, and other two produced by Spin Coating. After data collection, a set of features was extracted from the original signal curves, and the best were selected by Recursive Feature Elimination. Then, the classification performance of Multinomial Logistic regression, Decision Tree, and Naíve Bayes was evaluated. The results showed that both s preading methods for sensing film’s production are adequate since the estimated error of classification was inferior to 4 % for all the classification tools applied.

Book Chapter
Roque, ACA, Lowe CR.  2007.  Affinity chromatography: History, Perspectives, Limitations and Prospects. Affinity Chromatography: Methods and Protocols. (M. Zachariou, Ed.).:1-23., U.S.A.: Humana Press Inc. Abstract

Biomolecule separation and purification has until very recently steadfastly remained one of the more empirical aspects of modern biotechnology. Affinity chromatography, one of several types of adsorption chromatography, is particularly suited for the efficient isolation of biomolecules. This technique relies on the adsorbent bed material that has biological affinity for the substance to be isolated. This review is intended to place affinity chromatography in historical perspective and describe the current status, limitations and future prospects for the technique in modern biotechnology.

Pina, AS, Batalha IL, Roque ACA.  2014.  Affinity Tags in Protein Purification and Peptide Enrichment: An Overview. Protein Downstream Processing: Design, Development and Application of High and Low-Resolution Methods. (Labrou, Nikolaos, Ed.).:147-168.: Springer Abstract

The reversible interaction between an affinity ligand and a complementary receptor has been widely explored in purification systems for several biomolecules. The development of tailored affinity ligands highly specific towards particular target biomolecules is one of the options in affinity purification systems. However, both genetic and chemical modifications on proteins and peptides widen the application of affinity ligand-tag receptor pairs towards universal capture and purification strategies. In particular, this chapter will focus on two case studies highly relevant for biotechnology and biomedical areas, namely, the affinity tags and receptors employed on the production of recombinant fusion proteins and the chemical modification of phosphate groups on proteins and peptides and the subsequent specific capture and enrichment, a mandatory step before further proteomic analysis.

Pina, AS, Batalha IL, Dias AMGC, Roque ACA.  2021.  Affinity tags in protein purification and peptide enrichment: An overview, in Protein Downstream Processing: Design, Development, and Application of High and Low-Resolution Methods. Methods in Molecular Biology. :107-132.: Springer-Humana Press
Fernandes, CSM, Teixeira GDG, Iranzo O, Roque ACA.  2018.  Engineered protein variants for bioconjugation. Biomedical Applications of Functionalized Nanomaterials - Concepts, Development and Clinical Translation. (Sarmento, Bruno, Jose Das Neves, Eds.).: Elsevier
Pina, AS, Hussain A, Roque ACA.  2009.  An historical overview of drug discovery. Ligand-Macromolecule Interactions in Drug Discovery. (Roque, A. C. A., Ed.).:3-12., USA: Humana Press Inc. Abstract

Drug Discovery in modern times straddles three main periods. The first notable period can be traced to the nineteenth century where the basis of drug discovery relied on the serendipity of the medicinal chemists. The second period commenced around the early twentieth century when new drug structures were found, which contributed for a new era of antibiotics discovery. Based on these known structures, and with the development of powerful new techniques such as molecular modelling, combinatorial chemistry, and automated high-throughput screening, rapid advances occurred in drug discovery towards the end of the century. The period also was revolutionized by the emergence of recombinant DNA technology, where it became possible to develop potential drugs target candidates. With all the expansion of new technologies and the onset of the "Omics" revolution in the twenty-first century, the third period has kick-started with an increase in biopharmaceutical drugs approved by FDA/EMEA for therapeutic use.

Carvalho, HF, Barbosa A, Roque ACA, Iranzo O, Branco RJF.  2017.  Integration of Molecular Dynamics Based Predictions into the Optimization of de novo Protein Designs: Limitations and Benefits. Computation Protein Design. :181-201.
Roque, ACA, Lowe CR.  2007.  Rationally designed ligands for use in Affinity Chromatography: An artificial Protein L. Affinity Chromatography: Methods and Protocols. (M. Zachariou, Ed.).:93-110., U.S.A.: Humana Press Inc. Abstract

Synthetic affinity ligands can circumvent the drawbacks of natural immunoglobulin (Ig)-binding proteins by imparting resistance to chemical and biochemical degradation and to in situ sterilization, as well as ease and low cost of production. Protein L (PpL), isolated from Peptostreptococcus magnus strains, interacts with the Fab (antigen-binding fragment) portion of Igs, specifically with kappa light chains, and represents an almost universal ligand for the purification of antibodies. The concepts of rational design and solid-phase combinatorial chemistry were used for the discovery of a synthetic PpL mimic affinity ligand. The procedure presented in this chapter represents a general approach with the potential to be applied to different systems and target proteins.

Book
Roque, ACA.  2009.  Ligand-Macromolecule Interactions in Drug Discovery. , U.S.A.: Methods in Molecular Biology, Humana Press Inc.Website