iBB

Microbial life present in the marine environment has to be able to adapt to rapidly changing and often extreme conditions. In a recently published paper, Ricardo F.S. Pereira and Carla C.C.R. de Carvalho form iBB and colleagues from CQE and ISEL, used genomic, lipidomic and biochemical approaches to characterise a Serratia rubidaea, isolated from a sample taken at a shallow water hydrothermal vent, and its red product. Several state-of-the-art techniques, such as DSC, FTIR, NMR, and Ultra-High Resolution Qq-Time-of-Flight mass spectrometry, were used to characterize the structure of the red pigment which was found to be prodigiosin.

Carla CCR de Carvalho and the Ph.D. student Ricardo FS Pereira presented their work during the FEMS2023 congress in Hamburg, Germany. The congress organized by Federation of European Microbiological Societies is the largest event in the field of microbiology in Europe. Carla de Carvalho presented the talk entitled “Development of efficient bioprocesses using isolated marine bacteria” in the Industrial Microbiology and Bioeconomy session. Ricardo Pereira did a flash presentation entitled “Marine bioprocess development: targeting the production of prodigiosin” during the Biotechnology & Synthetic Microbiology session.

The production of recombinant proteins is gaining increasing importance as several applications request high quality proteins. However, several process parameters affect both the growth of cells and product yields. In a paper recently published in the journal Molecules, Ricardo FS Pereira and Carla CCR de Carvalho (iBB-BERG) used high throughput systems and statistical methods to assess the influence of fermentation conditions in lab-scale bioreactors. Using partial least squares, it was found that the height-to-diameter ratio of the bioreactor, aeration rate, and PID controller parameters contributed significantly to the final biomass and cytochrome concentrations. This information was used to fine-tune the process parameters, which increased cytochrome production and yield several-fold.

Carla C. C. R. de Carvalho and Ricardo Pereira (2BRG-iBB) participated in the annual meeting of the EU funded project FuturEnzyme (https://www.futurenzyme.eu). The 16 partners that integrate the project met during July 6 and 7, in the house of UHAM members, the Institute of Plant Science and Microbiology (IPM, Hamburg, Germany), next to the Botanical Garden. The work carried out during the first 24M of the project was presented and discussed between partners and in the presence of members of the Advisory Board.

In the past 22nd and 23rd of May, PhD students from the Biotechnology and Biosciences doctoral program, Luís Sousa and Ricardo Pereira, attended the First Workshop on Computational Enzyme Bioprospecting and Engineering at the Barcelona Supercomputing Center (BSC). As a part of a joint program between two European projects, Oxipro (DOI 10.3030/101000607) and FuturEnzyme (DOI 10.3030/101000327), the last where IST-ID is a working partner headed by  Carla C. C. R. de Carvalho (iBB), the attendees were able to use the leading softwares for computational protein engineering. With Galaxy, attendees were able to create and develop their own workflows for Computational Bioprospecting, HMM routines, and basic sequence similarity analysis. For Protein Engineering, the Schrodinger Suite and the AsiteDesign Galaxy were made available to perform analysis and visualization of enzyme structures, perform tasks such as system preparation, visualization, sitemap calculations, ligand docking and enzyme redesign. The workshop promoted interdisciplinary thinking and collaboration between different fields, highlighted the real-world applications of computational protein engineering, and its importance in advancing our understanding of biological systems and developing new solutions for global challenges.