Biology subjects

Oliveira, H.

Publications and source records attributed to Oliveira, H..

5 recordsLinked to original sources

bioRxiv2025

Prolonged cell encapsulation and rapid filamented light biofabrication of muscle constructs in microgravity

The prospects of fabricating human tissue grafts or models using cell-laden bioresins in space has garnered significant interest in recent years. While there has been tremendous progress in extrusion or light-based bioprinting in microgravity conditions, printing of aligned tissues, such as those featuring anisotropic organization of cells and extracellular matrices (e.g., muscle, tendon, cardiac, etc.), remains a challenge. Furthermore, current photoresin formulations do not allow long-term cell encapsulation and are difficult to perform in microgravity. In this study, we demonstrate a new gravity-independent filamented light (G-FLight) biofabrication system with in-built refrigeration and heating units, which can create viable muscle constructs within seconds. We developed new photoresin formulations based on gelatin methacrylate (GelMA) for encapsulation of primary cells (murine myoblasts) and storage in printing cuvettes for at least a week at 4{degrees}C or -80{degrees}C. The tissues printed in microgravity based on the new formulations exhibited higher cell viability, number of proliferating cells and after maturation higher numbers of myotubes and fusion index compared to control formulations (i.e., GelMA dissolved in phosphate buffered saline). The microgravity-printed tissues also featured similar myotube density and fusion index to those printed using the same resins on-ground. The G-Flight printing concept, together with the new resins enabling refrigeration or cryopreservation with encapsulated cells, offers a promising solution for biofabrication in space.

bioengineering↗

bioRxiv2023

PhageDPO: Phage Depolymerase Finder

Bacteriophages are the most predominant and genetically diverse biological entities on Earth. They are bacterial viruses which encode numerous proteins with potential antibacterial activity. However, most bacteriophage-encoded proteins have no assigned function, hindering the discovery of novel antibacterial agents. In particular, there has been a growing interest in exploring recombinant bacteriophage depolymerases from the fundamental standpoint, but mostly for biotechnological applications to control bacterial pathogens. Due to the lack of efficient identification tools, we developed PhageDPO, the first developed tool that predicts depolymerases in bacteriophage genomes using machine learning methods. Availability and implementationPhageDPO was integrated into a Galaxy framework available online at: bit.ly/phagedpo.

bioinformatics↗

bioRxiv2022

Studies on the interaction of three lytic bacteriophages with a wide collection of Escherichia coli strains implicated in swine enteric colibacillosis

AO_SCPLOWBSTRACTC_SCPLOWThe misuse of antibiotics in the swine industry and their on-going restriction requires alternatives to control enterotoxigenic and shiga toxin-producing Escherichia coli (ETEC and STEC, respectively). This study evaluates the potential of three coliphages, vB_EcoM_FJ1, vB_EcoM_FN and vB_EcoM_SP1 against 104 ETEC, STEC and ETEC/STEC strains isolated from pig colibacillosis in Portuguese (2018-2020) and Spanish farms (2006-2016), encompassing 71.2% mcr-positive strains (33.7% with mcr-1, 1.9% mcr-2, 35.6% mcr-4 and 2.9% mcr-5) and 18.3% positive strains for TEM (1%), SHV (6.7%), and CTX-M (11.5%) extended-spectrum beta-lactamase-encoding genes. In general, all bacteriophages presented a narrow lytic spectrum (up to 2.9%) against the 104 ETEC, STEC and ETEC/STEC. Bacteriophages shared >80% overall nucleotide identity with E. coli phage T4 (Tevenvirinae subfamily), but a particular look at the distal part of the long tail fiber (gp38) revealed no homology. All bacteriophages recognize lipopolysaccharides as receptors, and additionally, FN binds to an outer membrane protein A. Bacteriophage-insensitive mutants of vB_EcoM_FJ1 (90%) and vB_EcoM_FN (100%) were shown to be more susceptible to pig serum inactivation comparatively to the parental strain and furthermore, their adhesion capacity to porcine intestinal cells was diminished by, approximately, 90%. Contrariwise, vB_EcoM_SP1 insensitive variants did not display phenotypic differences comparing to the wild-type strain. This study demonstrates that besides being T4-like, these bacteriophages revealed a narrow lytic spectrum against diarrhoeagenic E. coli strains and that the acquisition of novel bacteriophage-encoded adhesins (gp38) seems to be determinant for such results.

microbiology↗

bioRxiv2019

Identifying relationships between imaging phenotypes and lung cancer-related mutation status: EGFR and KRAS

EGFR and KRAS are the most frequently mutated genes in lung cancer, being active research topics in targeted therapy. Biopsy is the traditional method to genetically characterise a tumour. However, it is a risky procedure, painful for the patient, and, occasionally, the tumour might be inaccessible. This work aims to study and debate the nature of the relationships between imaging phenotypes and lung cancer-related mutation status. Until now, the literature has failed to point to new research directions, mainly consisting of results-oriented works in a field where there is still not enough available data to train clinically viable models. We intend to open a discussion about critical points and to present new possibilities for future radiogenomics studies. We conducted high-dimensional data visualisation and developed classifiers, which allowed us to analyse the results for EGFR and KRAS biological markers according to different combinations of input features. We show that EGFR mutation status might be correlated to CT scans imaging phenotypes, however, the same does not seem to hold true for KRAS mutation status. Also, the experiments suggest that the best way to approach this problem is by combining nodule-related features with features from other lung structures.

bioengineering↗

bioRxiv2018

Antimicrobial activity of Mycobacteriophage D29 Lysin B during Mycobacterium ulcerans infection

Buruli Ulcer (BU) is a cutaneous disease caused by Mycobacterium ulcerans. The pathogenesis of this disease is closely related to the secretion of the toxin mycolactone that induces extensive destruction of the skin and soft tissues. Although the World Health Organization recommends a combination of rifampicin and streptomycin for the treatment of BU, clinical management of advanced stages often requires extensive surgical resection of the infected tissue. Therefore, it is important to develop alternative strategies for the treatment of BU.\n\nEndolysins (lysins) are phage encoded enzymes that degrade peptidoglycan of bacterial cell walls. Over the past years, lysins have been emerging as alternative antimicrobial agents against Gram-positive bacteria. Amongst Gram-positive bacteria, mycobacteria have an unusual outer membrane that is covalently attached to the mycolylarabinogalactan-peptidoglycan complex. To overcome this additional barrier to phage-mediated lysis, some mycobacteriophages encode a lipolytic enzyme, Lysin B (Lys B).\n\nIn this study, we demonstrated for the first time that recombinant Lys B displays lytic activity against M. ulcerans isolates. Moreover, using a mouse model of M. ulcerans footpad infection, we show that subcutaneous treatment with Lys B leads to a reduction in bacterial burdens, associated with IFN-{gamma} and TNF production in the draining lymph node. These findings highlight the potential use of lysins as a novel therapeutic approach against this neglected tropical disease.\n\nAUTHOR SUMMARYBuruli Ulcer (BU) is a necrotizing skin disease caused by Mycobacterium ulcerans. Standard treatment for BU lesions consists of a combination of rifampicin and streptomycin for 8 weeks. However, clinical management of advanced stages of the disease often requires extensive surgical resection of the infected tissue. Therefore, it is important to develop alternative strategies for the treatment of BU. In that sense, we tested the efficacy of Lysin B (Lys B), a phage encoded lipolytic enzyme that degrades the mycolylarabinogalactan-peptidoglycan complex present in the mycobacterial cell wall. In this study, we show that Lys B not only displays lytic activity against M. ulcerans isolates in vitro, but also leads to a reduction in bacterial burdens in M. ulcerans-infected mouse footpads. These findings highlight the potential use of lysins as a novel therapeutic approach against this neglected tropical disease.

microbiology↗