Rúben Fernandes

1. Cell physiology

We use several technologies for understanding cell viability, metabolic activity, cell proliferation, cell invasion and migration, cell death, apoptosis, senescence, among others;

2. Cell biochemistry

We study central metabolic pathways and cell signaling cascades, and organelle dynamics, using both gene expression, western-blotting, and cytochemistry stainings.

3. Computational metabolic analysis

By mens of computer tools such as COPASI, BRENDA, REACTOME, KEGG and others, we modulate metabolic pathways for drug predictive mathematic modultation.

4. Mitochondria and oxidative stress

Oxidative stress results on the imbalance of redox biochemistry. We analise glutathione reduced (GSH) and oxidized forms (GSSG), as well as the antioxidant enzymes that use them as co-factors such as glutathione peroxidase, glutathione reductase, was well as catalase, SOD, and lipid peroxidation by  thiobarbituric acid (TBA) test and its product malondialdehyde (MDA). Also by means of flow cytometry reative oxigen species are measured using fluorescent dyes DCFDA / H2DCFDA.

5. Genotoxicity and Molecular cytogenetics

By means of fluorescence in situ hybridization (FISH) we may analyze aneuploidies and microdelections. FISH is also used micronuclei genotoxicity induced by radiation. Our panel of genotoxicity assays include Ames Test in engineered E.coli, evaluation, endocrine dysruptor analysis in engineered yeasts, and also nuclei dysruption by means of single cell gel electroforesis (SCGE) or comet assay.

6. Engineered cell sensors

Our research team is developing real-time biosensors for glucose and lactate using Förster resonant energy transfer (FRET) protein interations.

7. Analytic cytometry

We use flow cytometry for determining DNA content, cell viability, mitocondrial membrane potential, mutliparametric analysis using specific antibodies, cell death and organelle dynamics.

1. Viral infection and Cancer

Viruses are associated with a great number of cancer cases. The human papillomaviruses (HPVs), cause cervical cancer and several other epithelial malignancies, and the hepatitis viruses HBV and HCV, which are responsible for the majority of hepatocellular cancer. Nevertheless, some viruses have receptor for some types of cancer, thus being considered as oncolytic virus. One recent example of oncolytic virus is SARS-CoV-2 which as been associated to remission of NK lymphomas. The ongoing research is exploring oncolytic effects of SARS-CoV-2.

2. Parasite infections and Cancer

Schistosoma haematobium, a parasitic flatworm that infects more than 100 million people, mostly in the developing world, is the causative agent of urogenital schistosomiasis, and is associated with a high incidence of squamous cell carcinoma (SCC) of the bladder. During infection, eggs are deposited in the bladder causing an intense inflammatory reaction. Thus, identifying biomarkers of this process plays an important role in the study of cancer.

3. Biofilm formation and stress response

Bacterial biofilms do serious harm to the diabetic foot ulcer because they play a crucial role in infection invasion and spread. Staphylococcus aureus and Pseudomonas aeruginosa the predominant Gram-positive and Gram-negative bacteria in diabetic foot infection and are often associated with colonization and biofilm formation. Biofilm formation also prevents the access of the antibiotics to microbial agents that are causing infection.  Thus biofilm formation are bacteria defense mechanisms against antibiotics. Antibiotics trigger a genomic mechanism in bacteria that activate SOS response. Cell signaling in bacteria mediated by recA cascade activates several mechanism such as quorum sensing and biofilm formation.

4. Phage biotechnology

Bacteriophages or simply phages are bacteria infecting viruses. In terms of pharmaceutical classification in EU and United States, phages are considered as anti-infectious medicinal products and biological products, given the intended use and their live nature. Phages are envisioned for a variety of uses including (1) the biocontrol of pathogenic bacteria in agriculture and food industries, (2) the modulation of dysbiotic flora, (3) the eradication of pathogenic bacteria infecting humans or animals. The research group is devoted to the bioprospecting of new phages intending to contribute to the control and phage therapy of drug resistant Gram-negative pathogens such as Pseudomonas spp. and Klebsiella spp., Salmonella enterica, Escherichia coli, and Gram-positive Staphylococci and Streptococci.

5. Microbiome and dysbiosis

Normal Gut microbiota is an important mediator several physiological processes (eubiosis). Conversely alteration in number and diversity of certain taxa (dysbiosis) has emerged as implicated in the development and the outcomes of certain diseases.  Still far from being completely understood and analyzed is the complexity of this ecosystem. Certain medicines, such as antibiotics, alterations to lifestyle, stress are among the diversity of causes that disturbes microbiota. The research team is focusing in describing microbial biomarkers in dysbiosis of several conditions such as gut-metabolic axis, gut-brain axis, and gut-lung axis: metabolic syndrome, obesity, cardiovascular disease, pneumonia, mood and, neurogenerative diseases.

6. Diabetic foot infections

The diabetic foot is one of the major complications of this disease, with an estimated 10% to 25% of diabetic patients developing a diabetic foot ulcer (DFU) in their lifetimes causing a considerable burden in health care and patient well-being. Foot infections are common in patients with diabetes and are associated with high morbidity and risk of lower extremity amputation. Diabetic foot infections (DFIs) are classified as mild, moderate, or severe. DFIs aggravate with antibiotic resistance and with increased virulence of bacterial flora in the infected ulcer in particular due to biofilm formation. Staphylococcus aureus but gram-negative such as P. aeruginosa bacteria are most commonly pathogens causing biofilms. The research group is particular interested in new therapeutic approaches such as hyperbaric oxygen therapy, phage therapy and photodynamic therapy.

7. Antimicrobial Resistance

The burden of antibiotics in the environment and in medical prescription is still a major matter of concern. Our group is focusing in drug resistance genes in the taxon of γ-proteobacteria in particular Enterobacteriaceae, Pseudomonacea and Vibrionaceae. This group is interested in the enzymes conferring resistance to broad spectrum cephalosporins such as ESBL or AmpC and in permeation mechanisms such as mutation in porins or drug efflux pumps.