iBB

Acetic acid is a major inhibitor of yeast cell growth in industrial settings and a key determinant of host colonization by pathogenic yeasts. Despite the importance of the understanding of the mechanisms underlying yeast response and tolerance to acetic acid and the numerous studies dedicated to the topic, the role of ion fluxes and their regulation is understated in scientific literature but crucial for the effective yeast adaption and tolerance to acetic acid stress. A review paper, just published in FEMS Yeast Research, offers a comprehensive overview of the mechanisms governing ion homeostasis in the context of acetic acid toxicity, adaptation, and tolerance in Saccharomyces cerevisiae and non-Saccharomyces species of clinical and biotechnological relevance. This new publication has as first-author the PhD student Miguel Antunes of the PhD programme in Biotechnology and Biosciences of the Department of Bioengineering  of  Instituto Superior Técnico and the FCT-DP BIOTECnico - and as a corresponding author his thesis supervisor, Professor Isabel Sá-Correia.

Marine bacteria present enzymatic activities that result from extensive evolution necessary for cell survival under the harsh and continuously changing conditions found in the marine environment. Metagenomic techniques and cultivation of not-yet-cultured bacteria, combined with high-throughput screening techniques, have allowed the identification of new biocatalysts and the development of industrial processes. In a recently published paper, Carlos J.C. Rodrigues and Carla C.C.R. de Carvalho (iBB) review the latest studies related to growth of marine bacteria under laboratorial conditions, screening techniques, and bioprocess development.

It is usually accepted that only 0.1-1% of marine bacteria may be cultivated under laboratory conditions. This resulted mainly from the observation that only a small fraction of the total bacteria determined by microscopic counts could be enumerated by culture plate techniques, and has been a justification for the widely implementation of cultivation-independent molecular techniques. In a recent published paper, Carlos J.C. Rodrigues and Carla C.C.R. de Carvalho (BERG-iBB) promoted the growth of bacteria from a marine rock pond by culture dependent techniques and compared the results with culture independent methods. The highest efficiency of cultivation was 45% attained in marine agar. The study shows that it is possible to grow more than the traditionally considered 1% of bacteria from a seawater sample using standard agar plate techniques and laboratorial conditions, and to find bacteria not detected by molecular approaches.

We owe a great debt to yeasts for their contributions to humankind. In the Food Industry alone, yeasts play a central role in breadmaking, winemaking, brewing, and more. The fact that yeasts present such spectacular diversity constitutes an opportunity to use different, unused yeasts to obtain fermented goods with distinct properties and organoleptic profiles. In his interactive poster submission to the international conference World Microbe Forum, a joint initiative by the American Society for Microbiology (ASM) and Federation of European Microbiological Sciences (FEMS) taking place online from 20-24 June 2021, Nuno Bourbon-Melo talks about the role of non-conventional yeasts seldom used in brewing, specifically Hanseniaspora opuntiae and H. guilliermondii, to improve the aroma and flavour of beer. Learn more about it by clicking here. The work was performed at iBB – Institute for Bioengineering and Biosciences, Instituto Superior Técnico, ULisboa, and advised by Prof. Isabel Sá-Correia and Dr. Margarida Palma.

A team of researchers from iBB-BERG, including Carlos Rodrigues, Ricardo Pereira, Pedro Fernandes, Prof. Joaquim Sampaio Cabral and led by Carla de Carvalho, will contribute to the development of enzymes for a new generation of environmentally friendly consumer products in the EU project FuturEnzyme. The consortium of 16 leading academic and industrial partners, led by Dr. Manuel Ferrer from CSIC (Spain), will develop innovative solutions that will combine big biodata mining and bio-prospecting, disruptive machine learning and protein engineering, nano-biotechnology, fermentation and downstream-processing systems, and pre-industrial testing. Innovative solutions will be proposed to discover, design, optimize and formulate new enzymes to develop detergents, textiles and cosmetics that combine a high level of functionality with improved sustainability, thus responding to the demands from consumers and industries.

B. cenocepacia is a contact-dependent bacterium known for its capacity of causing respiratory infections. Among a panel of adhesins used by B. cenocepacia to contact with host cells, trimeric autotransporter adhesins (TAAs) are of particular interest. In a recent paper published in Cellular Microbiology, a BSRG-iBB team (Andreia Pimenta, Nuno Bernardes, Dalila Mil-Homens and Arsénio M Fialho) together with Michelle Kilcoyne and Lokesh Joshi from the National University of Ireland Galway, Galway, Ireland, were able to uncover the roles of the TAA BCAM2418, as an adhesin and the type of host glycans that serve as recognition targets. This work reveals the importance of BCAM2418 as a mediator of early host-bacteria crosstalk.

Burkholderia cenocepacia is a human contact-dependent pathogenic bacterium known for its capacity of causing severe opportunistic respiratory infections. B. cenocepacia uses a complex machinery for primary adherence with host cells. In a recent paper published in Scientific Reports, a BSRG-iBB team (Andreia Pimenta, Nuno Bernardes, Dalila Mil-Homens and Arsénio M Fialho) together with Marta M Alves from CQE, IST, have developed a RNASeq-based approach that led to identify adhesion candidate genes that were not previously reported in the context of a B. cenocepacia infection. This study presents a innovative technique in which their use Giant Plasma Membrane Vesicles (GPMVs) from a bronchial epithelial cell line as a cell-like alternative to investigate the steps involved in the adhesion process of B. cenocepacia.

Diana Marques, a PhD candidate at the Institute for Bioengineering and Biosciences (iBB), was challenged by Fernando Gaspar to answer this question.

In an interview for the podcast "Consórcio do Bem-Estar," Diana discussed the Algae2Fish project's goals with Fernando Gaspar, José Alberto Maia Pereira, and Alvaro Cidrais. Diana is developing research on unique techniques for generating 3D bioprinted fish fillets.

The Algae2Fish project is currently ongoing at iBB and aims to produce seabass fish fillets using 3D bioprinting. These scaffolds will support fish cell growth, provide adequate mechanical and structural properties, and contribute to the final tissue nutritional and organoleptic features.

Organized at Instituto Superior Técnico by Isabel Sá-Correia and Jorge Leitão, a joint workshop of two FCT-funded doctoral programs in which  DBE and iBB participate or direct, AEM-Applied and Environmental Microbiology and BIOTECnico- Biotechnology and Biosciences, took place at the Zoom platform on February 15 (dedicated to AEM) and 16 (dedicated to BIOTECnico). The external supervisory committee (ESC) of the two programs were present and participated very actively. They are highly renowned academics in the areas of the PhD programs: Tom Coyne from Gent University, William de Vos from Wageningen University, Jack Pronk from Delft University, Prof Steve Oliver, University of  Cambridge, Michael Hoare, University College London. 

PhD students and alumni of both programs were present and program that we set up via Zoom allowed us to demonstrate the work carried out in terms of advanced training in the framework of BIOTECnico and AEM programs. The ESCs were very impressed about the way how “the two fabulous programs were designed and managed and built a culture that encourages PhD candidates to take initiative, grow and prosper.” Congratulations to the directive boards of both programs, the students, the alumni, and their supervisors and collaborators.

Protein kinases are essential as signal transductors for a proper cellular response to extracellular stimuli. A BSRG-iBB review paper, just published in Computational and Structural Biotechnology Journal gathers the available information regarding the NPR/Hal5 family of kinases in Saccharomyces cerevisiae and non-Saccharomyces species of clinical and biotechnological relevance. These kinases - for which information is scarce and scattered across scientific literature - are essential modulators of yeast nutrient availability responses and ion homeostasis. This publication has as first-author the PhD student Miguel Antunes of the IST PhD programme in Biotechnology and Biosciences and the FCT-DP BIOTECnico - and as a corresponding author his thesis supervisor, Professor Isabel Sá-Correia.

The role of the cell wall in yeast response and tolerance to stress is frequently neglected. A BSRG-iBB research paper just published in Scientific Reports, provides, for the first time, a comprehensive view of the alterations occurring at the cell wall in a yeast population adapting to sub-lethal stress induced by acetic acid. The results reveal changes to the cell wall polysaccharide composition and nanomechanical properties, as well as alterations in the transcript levels of key cell wall biosynthetic genes. This paper reinforces the notion that the adaptive yeast response to acetic acid involves coordinated alterations of the cell wall at the biophysical and molecular levels. The gathered knowledge is important for the design of superior industrial strains and for the efficient control of the deleterious activity of spoilage yeasts, particularly in the Food Industry. This research work is first-authored by the PhD student of the PhD programme in Biotechnology and Biosciences Ricardo Ribeiro (FCT_DP AEM fellowship), performed under the supervision of Isabel Sá-Correia. This collaborative study with Fábio Fernandes (BSIRG-iBB) and Mário S. Rodrigues and his team (BioISI, Faculty of Sciences, ULisboa), is also coauthored by Cláudia Godinho (posdoc researcher) and the PhD student Nuno Bourbon-Melo (FCT_DP BIOTECnico) from the BSRG-iBB team.

The determination of the recombination efficiency and the monitoring of parental plasmids (PP), minicircles (MC) and miniplasmid (MP) species during processing and in the final product are critical aspects of minicircle manufacturing. A paper published in Analytical Biochemistry by BERG-iBB researchers Cláudia Alves, Miguel Prazeres and Gabriel Monteiro describes a real-time PCR method for the specific identification of PP, MP or MC that uses sets of primers specific for each species. The results presented indicate that the method can be applied for the determination of recombination efficiency in pure DNA samples.

Carlos JC Rodrigues and Carla CCR de Carvalho (iBB-BERG) presented their work in EFB2021, the major scientific conference organised by the European Federation of Biotechnology. The two studies presented focused on the marine environment as a source of biocatalysts for suitable bioprocesses, and on using microbial heterogeneity to improve bioprocesses. The virtual conference took place during May 10th-14th.