iBB

The ability of block co-polymers to self-assemble and form micelles in solution can potentially be explored to deliver poorly soluble chemotherapeutic agents. Researchers from BSIRG-iBB led by Vasco Bonifácio, working in collaboration with colleagues from Universidade Nova, have synthesized new block copolymers of oligo-2-oxazoline and linear oligo(ethylenimine) that are water-soluble and show an intrinsic blue fluorescence. The synthesis uses a green protocol and allows a precise control of the oligo(ethylenimine) backbone. The work was published in Advanced Materials Letters.

Cystic fibrosis (CF) is the most life-limiting autosomal recessive disorder in Caucasians, with chronic bacterial airway infections representing the major cause of early decease. Pseudomonas aeruginosa and bacteria from the Burkholderia cepacia complex (Bcc) are the leading pathogens of CF patients’ airways. A wide array of virulence factors is responsible for infections caused by these bacteria, which have tightly regulated responses to the host environment. Small noncoding RNAs (sRNAs) are major regulatory molecules in these bacteria. Several approaches have been developed to study P. aeruginosa sRNAs, many of which are involved in the virulence. On the other hand, the knowledge on Bcc sRNAs remains far behind. In a review published on International Journal of Molecular Sciences, Tiago Pita, Joana Feliciano and Jorge H. Leitão from BSRG-iBB updated the knowledge on characterized sRNAs involved in P. aeruginosa virulence, compiled data so far achieved on sRNAs from the Bcc and discuss their possible roles on bacteria virulence.

Several membrane transporters from the ATP-binding cassette (ABC) superfamily present in yeast genomes are implicated in multidrug/multixenobiotic resistance (MDR/MXR). This is the case of Pdr18, that confers tolerance to ethanol and acetic acid and several other toxicants in yeast and has a biological role attributed in ergosterol transport at the plasma membrane. A recently iBB-BSRG paper published in Frontiers in Genetics, Evolutionary and Genomic Microbiology section, reconstructs the evolutionary history of the encoding gene PDR18 and the paralogue gene SNQ2. This publication results from the PhD thesis in Biotechnology and Biosciences of Cláudia P. Godinho advised by Prof. Isabel Sá-Correia with collaboration of Paulo J. Dias and Elise Ponçot. By combining phylogenetic gene neighborhood analysis for 117 yeast genomes belonging to 29 species across the Saccharomycetaceae family, the gene duplication event was traced to the last common ancestor of the Saccharomyces genus yeasts. The fact that Snq2 and Pdr18 confer resistance to different sets of chemical compounds with little overlapping is consistent with the subfunctionalization and neofunctionalization of these gene copies. Remarkably, PDR18 is only found in Saccharomyces genus genomes. 

The non-conventional food spoiling yeast species Zygosaccharomyces bailii is remarkably tolerant to acetic acid, a highly important microbial inhibitory compound in Food Industry and Biotechnology. The study recently published in Scientific Reports, coordinated by Isabel Sá-Correia and Margarida Palma and first authored by the BIOTECnico PhD student Miguel Antunes, investigates the genomic transcription changes occurring during the early response of Z. bailii to acetic acid or copper stresses and uncovers the regulatory network activated under the bifunctional transcriptional factor ZbHaa1 control. This study provides valuable insights regarding Z. bailii adaptation mechanisms to acetic acid or copper stresses, ZbHaa1-dependent regulatory network, and the evolution of transcription factors and regulatory networks in pre- whole genome duplication (WGD) and post-WGD yeast species.

Peripheral artery disease (PAD) is a debilitating condition characterized by the blockage of arteries, which leads to limb amputation in more severe cases. Researchers from SCERG- and BERG-iBB propose the use of human bone marrow (BM) MSC transiently transfected with minicircles encoding for VEGF as an ex vivo gene therapy strategy to enhance angiogenesis in PAD patients. The data shows that VEGF overexpression improved the angiogenic potential of MSC in vitro, as confirmed by endothelial cell tube formation and cell migration assays.These results suggest that minicircle-mediated VEGF gene delivery, combined with the unique properties of human MSC, could represent a promising ex vivo gene therapy approach to improve angiogenesis in the context of PAD. The work was published in Human Gene Therapy.

Innovation in construction materials (CM) implies changing their composition by incorporating raw materials (RM), usually non-traditional ones (e.g., processed or recycled RM), to confer particular characteristics. However, potential environmental risks associated with changing the conventional composition of CM are not completely known and need to be evaluated. Researchers from iBB-BSRG and CERIS - Civil Engineering Research and Innovation for Sustainability, at IST, proposed and applied a methodology for the assessment of the potential ecotoxicity associated with RM and cement-based CM considering a conservative scenario representative of the end of the materials life cycle. The work was published in the journal Materials.

The feasibility of applying Flow Microcalorimetry to evaluate the complex phenomena involved in the adsorption of monoclonal antibodies to phenylboronate ligands has been demonstrated by BERG-iBB researchers led by Ana Azevedo, in collaboration with Ana Cristina Dias-Cabral from CICS-UBI. The thermodynamic studies evidence the role of affinity and non-specific effects that contribute to the complex, phenylboronate-mediated multimodal adsorption process. This deeper understanding, combined with the economic advantages associated with the employment of the PBA ligand, may lead industry to adopt such a chromatographic process as a reliable alternative to protein A-based capture steps in the current downstream processing of mAbs. The work is part of Sara Rosa’s PhD thesis in Biotechnology and Biosciences. The paper was published on J. Chromatography A.

 Bacteria of the Burkholderia cepacia complex (Bcc) remain an important cause of morbidity and mortality among patients suffering from cystic fibrosis. Eradication of these pathogens by antimicrobial therapy often fails, highlighting the need to develop novel strategies to eradicate infections. Vaccines are attractive since they can confer protection to particularly vulnerable patients, as is the case of cystic fibrosis patients. Several studies have identified specific virulence factors and proteins as potential subunit vaccine candidates. So far, no vaccine is available to protect from Bcc infections. In a recent publication in the journal Vaccines, iBB-BSRG researchers Sílvia Sousa, António M. Seixas and Jorge H. Leitão review the most promising postgenomic approaches and selected web tools available to speed up the identification of immunogenic proteins with the potential of conferring protection against Bcc infections.

Most microorganisms cannot be cultivated in the laboratory, what hinders our understanding of their physiology, evolution and functional roles. In collaboration with GEOMAR, University of Kiel, iBB researchers used modern nucleotide composition binning methodologies to assemble the genome of an “unculturable” bacterial symbiont from microbial metagenomes. The research led to the identification of a novel alphaproteobacterial lineage found to be intimately associated with marine sponges, termed "SERC" (sponge-enriched Rhodospirillales clade), characterized by the lack of chemotaxis and motility traits and enrichment of genes required for the utilization of organic sulfur, biosynthesis of natural products, and cell detoxification processes. The work was published in FEMS Microbiology Ecology.

Microfluidic devices with integrated photodetectors can address the need for compact and portable biosensing platforms for medical, veterinary, environmental and food safety applications. However, depending on the application, performance requirements like the minimum detectable limits, the target sensitivity, and the detection time can vary dramatically. To improve the engineering of fit-for-purpose bead-based microfluidic biosensors, researchers at BERG-iBB and INESC-MN developed a simple quantitative methodology to determine (1) equilibrium constants, (2) binding kinetics, (3) rate at which photons are generated/absorbed per captured molecule, and (4) molecular capture efficiencies. These parameters provide an effective trade-off between required sensitivity, cost effectiveness and assay complexity. This work was published in the IOP Journal of Micromechanics and Microengineering.

The ability to differentiate neural progenitors (NP) from human induced pluripotent stem cells (hiPSCs) provides an opportunity to develop new applications for cellular therapy, disease modelling and drug screening. SCERG-iBB researchers developed a platform that can be applied towards the study of the effect of neurotoxic molecules that impair normal embryonic development, such as the antiepileptic drug valproic acid (VPA). It was verified that exposure to VPA led to a prevalence of NP structures over neuronal differentiation, confirmed by analysis of the expression of neural cell adhesion molecule, and neural rosette number and morphology. This methodology can potentially complement current toxicity tests for the detection of teratogenic compounds that can interfere with normal embryonic development. The work was published in Toxicology Letters.

https://www.scoop.it/t/ibb/?&tag=Ars%C3%A9nio+FialhoUnlike the current paradigm of “one drug one target”, nowadays multiple-target approaches taking place at the cancer cell membrane are gaining much more relevance. The rational is based on the use of a new class of molecules that can exert significant changes in the dynamics and organization of cell membranes thereby affecting growth factor signaling, invasiveness and drug resistance. In a review published in a Special Issue “Receptor-Targeted Cancer Therapy” of the International Journal of Molecular Sciences, BSRG-iBB team members Nuno Bernardes and Arsenio M Fialho present and discuss novel approaches for cancer therapy, including the anticancer bacterial protein azurin.

The effectiveness of Candida glabrata as an emerging human pathogen relies on its ability to acquire azole drug resistance. In a paper just published in Antimicrobial Agents and Chemotherapy, the first time-course evaluation of the global gene expression changes that lead a drug susceptible C. glabrata clinical isolate to step-wise acquisition of resistance to azole drugs was conducted. This work, which results from the collaboration of six different teams under the coordination of Miguel C Teixeira from BSRG-iBB, highlights the multifactorial nature of azole resistance acquisition, including the Epa3 adhesin as a new player, while providing fascinating clues on the underlying evolutionary path. This knowledge is of crucial importance to design more effective antifungal therapy.

Within the cystic fibrosis (CF) lung, bacteria experience high-osmolarity conditions due to an ion unbalance resulting from defects in CF transmembrane conductance regulator (CFTR) protein activity in epithelial cells. Understanding how bacterial CF pathogens thrive in this environment might help the development of new therapeutic interventions to prevent chronic respiratory infections. In a recent publication in Journal of Bacteriology, researchers from BSRG-iBB led by Leonilde M. Moreira, in collaboration with Dr. Vaughn Cooper from University of Pittsburgh, USA, and Dr. Jörg Becker from Instituto Gulbenkian de Ciência, provide evidence that mutations in OmpR experience positive selection during the adaptation of Burkholderia to chronic infections of the CF airway, and these selective forces can be recapitulated in the laboratory. Characterization of OmpR shows that it is a major regulator of many traits related to cell envelope composition and central metabolism, in which loss-of-function mutants enable greater tolerance and growth under stress conditions but are costly for fitness under other conditions.

The emergence of bacterial resistance to available antimicrobials has prompted the search for novel antibacterial compounds to overcome this public health problem. Metal-based complexes have been much less explored than organic compounds as antimicrobials, leading to investigations of the antimicrobial properties of selected complexes in which silver may occupy the frontline due to its use as medicine since ancient times. Like silver, camphor has also long been used for medicinal purposes. However, in both cases, limited information exists concerning the mechanisms of their antimicrobial action. In a recent collaborative work by the research group headed by Jorge H. Leitão from BSRG/iBB and M. Fernanda Carvalho from CQE, the present knowledge of the antimicrobial properties of camphor-derived silver complexes is reviewed, focusing on recent research on the synthesis and antimicrobial properties of complexes based on silver and camphor imines. Selected examples of the structure and antimicrobial activity relationships of ligands studied so far are presented, showing the potential of silver camphorimine complexes as novel antimicrobials. The review was published in the journal Antibiotics.

Accidental spills or careless storage and disposal of pesticides may lead to environmental contamination posing possible risks for non-target microbes and higher eukaryotes in ecosystems. In a recent publication in the journal Ecotoxicology, iBB-BSRG researchers led by Cristina A. Viegas, in collaboration with Jörg D. Becker from IGC, reported a comparative transcriptomic analysis of the responses to sub-lethal levels of six environmentally relevant pesticides in the Saccharomyces cerevisiae model species. A number of predictions of biological pathways and mechanisms emerged from this study in yeast, which are relevant to better understand the potential mode of action and adverse side-effects of these pesticides in biological systems.

The bacterial genome can be modified to favour the synthesis of recombinant protein. Such productivity gains can contribute to lower costs and increase the affordabiliy of protein pharmaceuticals. BERG-iBB researchers and colleagues from the Institute of Technology Guwahati (India) have shown that deletion of the pgi (phosphoglucose isomerase) gene in Escherichia coli favours the production of the pharmaceutically important protein interferon gamma (IFN-gamma). Specific IFN-gamma yields were 3.0-fold higher in mutant compared to native strain. Furthermore, a metabolic model analysis showed that pgi deletion raises flux efficiency towards IFN-gamma synthesis. The work was published in Enzyme Microbial Technology.

Photo details: 3D model of pgi by Emw, own work, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=8814547

The ability of Saccharomyces cerevisiae to overcome the stress induced by cytotoxic compounds depends on the activity of plasma membrane transporters of the ABC superfamily, presumably through the questionable unspecific efflux of multiple drugs and xenobiotic compounds. A recent paper by iBB researchers provides new insights into the biological role of the ABC transporter of the pleiotropic drug resistance family of putative drug efflux pumps Pdr18, proposed to mediate ergosterol incorporation in plasma membrane. Pdr18 expression was found to help cells to counteract acetic acid-induced decrease of plasma membrane lipid order, increase the non-specific membrane permeability and decrease the transmembrane electrochemical potential. Results support the notion that Pdr18-mediated multistress resistance is linked to the status of plasma membrane lipid environment related with ergosterol content and the associated plasma membrane properties. The paper, published in Scientific Reports, results from the PhD project of Cláudia Godinho, advised by Prof. Isabel Sá-Correia from BSRG-iBB in collaboration with Fábio Fernandes and Sandra Pinto from BSIRG-iBB).