RNA-binding proteins (RBPs) are important regulators of cellular functions, playing critical roles on the survival of bacteria and in the case of pathogens, on their interaction with the host. RBPs are involved in transcriptional, post-transcriptional, and translational processes. However, except for model organisms like Escherichia coli, there is little information about the identification or characterization of RBPs in other bacteria, namely in members of the Burkholderia cepacia complex (Bcc). Bcc is a group of bacterial species associated with a poor clinical prognosis in cystic fibrosis patients. These species have some of the largest bacterial genomes, and except for the presence of two-distinct Hfq-like proteins, their RBP repertoire has not been analyzed so far. Using in silico approaches, we identified 186 conventional putative RBPs in Burkholderia cenocepacia J2315, an epidemic and multidrug resistant pathogen of cystic fibrosis patients. In a work recently published in the journal GENES, Joana Feliciano, António Seixas, Tiago Pita and Jorge H. Leitão described the comparative genomics and phylogenetic analysis of RBPs present in multiple copies and predicted to play a role in transcription, protein synthesis, and RNA decay in Bcc bacteria. The analysis suggest the existence, in B. cenocepacia and in other Bcc bacteria, of some extra and unexplored functions for the mentioned RBPs, as well as of alternative mechanisms involved in RNA regulation and metabolism in these bacteria.

The conjugation of dye-labelled DNA oligonucleotides with gold nanorods has been widely explored for the development of multifunctional fluorescent nanoprobes. In a recent publication in Nanoscale, BERG-iBB researchers in collaboration with colleagues from Centro de Química Estrutural and Centro de Ciências do Mar show that the functionalization route is crucial to achieve enhanced emission in dye nano-assemblies based on gold nanorods. By using a tip-selective approach for thiol attachment of dye molecules onto gold nanorods, it was possible to effectively increase the emission by more than 10-fold relatively to that of free dye. The results could improve significantly the performance of dye nano-assemblies for imaging or sensing applications.The work is part of the PhD thesis of David Botequim, which is supervised by Pedro Paulo (CQE) and Miguel Prazeres (BERG-iBB).

FCT will be accepting PhD applications for fellowships from the 2nd march until the 31st March 2020. Click here to learn more.

Evguenia Bekman and Tiago Fernandes from SCERG-iBB together with Simão Teixeira da Rocha from IMM-FMUL have been awarded by the Amélia de Mello Foundation (FAM) with the Pedro Maria José de Mello Costa Duarte Scholarship to carry out the project “Exploring new therapeutic strategies for Angelman syndrome: A disease modeling approach based on 3D cerebellar organoids derived from patient iPSCs”. The Angelman Syndrome is a genetic-neurological disease discovered in the 60s of the last century by the English pediatrician Harry Angelman, which is estimated to affect 1 in every 15,000 live births and which is characterized by developmental delay, difficulty in speech, sleep disorders, convulsions, disconnected movements and a frequent smile.

Intrinsically disordered proteins/regions (IDPs/IDRs) are widespread in the human proteome and play critical roles in distinct biological processes and dysfunction. Contrary to the classical “structure–function” paradigm, IDPs lack stable secondary/tertiary structures under physiological conditions, and instead adopt a dynamic ensemble of multiple conformations. Moreover, several neurodegenerative disorders are associated with the pathological self-assembly of neuronal IDPs, including tau (Alzheimer’s disease), α-synuclein (Parkinson’s disease), and huntingtin exon 1 (Huntington’s disease). Therefore, there is an emerging medical interest in understanding their physical and structural features. However, their characterization is inherently challenging by traditional ensemble and time-averaging methodologies. A recent review co-authored by Ana Melo from BSIRG-iBB, and published in Frontiers in Molecular Neurosciences the advantages of employing cutting-edge single-molecule fluorescence techniques are discussed to characterize the conformational ensemble of neurodegeneration-promoting IDPs under normal and disease conditions to obtain insights into their gain- or loss-of-function.

In a paper recently published in the journal Antibiotics, a series of cyclam- and cyclen-derived salts were designed and studied as antibacterials by the research groups headed by JH Leitão (BSRG) and AM Martins and LG Alves (CQE). The compounds were designed specifically to gain insights into their structure and antibacterial activity towards Staphylococcus aureus and Escherichia coli, used respectively, as Gram-positive and Gram-negative model organisms. The newly synthesized compounds are monosubstituted and trans-disubstituted tetraazamacrocycles that display benzyl, methylbenzyl, trifluoromethylbenzyl, or trifluoroethylbenzyl substituents appended on the nitrogen atoms of the macrocyclic ring. The results obtained show that the chemical nature, polarity, and substitution patterns of the benzyl groups, as well as the number of pendant arms, are critical parameters for the antibacterial activity of the cyclam-based salts. The paper was published as part of the journal Special Issue New Insights into Antibacterial Compounds: From Synthesis and Discovery to Molecular Mechanisms of Action, guest-edited by Jorge H. Leitão.

Ricardo Ribeiro, IST PhD student in Biotechnology and Biosciences
from the FCT doctoral programme in Applied and Environmental
Microbiology (DP_AEM), at iBB-BSRG, presented his work during the symposium on “Molecular Microbiology and Microbial Physiology” of the Congress of Microbiology and Biotechnology 2019 (Microbiotec’19) which was held between the 5th and 7th of December 2019 in Coimbra, Portugal. The presentation was entitled “Yeast response and tolerance to acetic acid: focus on the cell envelope” This work was carried out under supervision of Prof. Dr. Isabel Sá- Correia (iBB-BSRG) and the collaboration of Dr. Mário Rodrigues’s team (BioISI), for the atomic force microscopy characterization of cell wall properties.

Nuno Bourbon, PhD student from the BIOTECnico doctoral programme at iBB-BSRG, presented his work during the symposium on “Industrial and Food Microbiology” of the Congress of Microbiology and Biotechnology 2019 (Microbiotec’19), which was held between the 5th and 7th of December 2019 in Coimbra, Portugal. The presentation, entitled “Use of Hanseniaspora guilliermondii and Hanseniaspora opuntiae in co-fermentation with Saccharomyces cerevisiae to enhance the aromatic profile of craft beer”, focused on the potential of using two distinct Hanseniaspora yeast species to improve the organoleptic properties of beer. This work was carried out under the supervision of Prof. Isabel Sá-Correia (iBB-BSRG) and Dr. Margarida Palma (iBB-BSRG), in collaboration with Prof. Maria Rosário Bronze’s team (IBET and Faculty of Pharmacy, ULisboa, for the analysis of volatile compounds).

Ana Azevedo from BERG-iBB was invited to deliver a presention on continuous purification of antibodies at the European Summit of Industrial Biotecnology, in a special session dedicated to the Continuous Downstream Processing of the Biomolecules of the future. The section included also presentations from Novartis, Merck and Sanofi. The summit was held on the 18th – 20th November 2019, in Graz, Austria.

Due to the exceptional measures decreed by the Government in the context of the Covid-19 pandemic, the Directive Council of the portuguese Foundation for Science and Technology (FCT) took the decision to automatically extend for one month the duration of all scholarship contracts. The measure is valid for all contracts funded by FCT that were in force on on the March 13, 2020. Click here to learn more.

Illustration by David S. Goodsell, RCSB Protein Data Bank; doi: 10.2210/rcsb_pdb/goodsell-gallery-019

The buccal route has been used as alternative for delivery of drugs that undergo first-pass metabolism or are susceptible to pH and enzymatic degradation. However, the drug concentration absorbed in the buccal mucosa is often low. The encapsulation of drugs into nanoparticles is an important strategy to improve their buccal delivery. In a recently published review paper in Journal of Controlled Release, Ana Macedo, Pedro Fonte (BERG-iBB) and colleagues overview the nanotechnological approaches developed so far to improve the buccal delivery of drugs. Several types of delivery strategies are addressed and a special focus is placed on pipeline products.

A biological process for the production of xylonic acid (XA) from xylose or from xylose-rich lignocellulosic hydrolysates has been patented by BERG-iBB researchers Teresa Cesário, Manuela Fonseca and Maryna Bondar (PT 115970). The ability of the wild strain Paraburkholderia sacchari (previously classified as Burkholderia sacchari) DSM 17165 to produce xylonic acid from renewable and sustainable feedstocks is claimed. XA is a potential substitute for gluconic acid (GA), namely in the pharma industry, as a chelating agent, as a precursor of 1,2,4-butanetriol, polyamides and polyesters, as well as in the production of solvents, paints, adhesives and dyes. Moreover, XA, like GA, can be used as a retardant of the setting time of cement paste. XA productivities in the range 4.8 g/(L.h) to 7.1 g/(L.h) and yields between 89% e 100% were achieved, with XA titres of 360 to 390 g/L, using one single, non-pressurised stirred tank reactor operating in the fed-batch mode under dissolved oxygen concentrations higher than 10%  saturation.

Ana Margarida Rosa will be defending her PhD thesis in Biotechnology and Biosciences on Wednesday the 29th january 2020 (10:30 H, amphitheater PA-3, Mathematics Building). During the last years, and under the supervision of Miguel Prazeres from BERG-iBB and Pedro Paulo from CQE-IST, Ana developed a cellulose-based system for the colorimetric detection of nucleic acids by exploring the recognition of biotin-labeled DNA hybrids by anti-biotin antibodies immobilized through ZZ-CBM chimeric proteins. These fusions combine carbohydrate-binding modules (CBM) with affinity to cellulose and double Z domains (ZZ) that bind to IgG antibodies. The title of the thesis is “DNA recognition system on bioactive paper using fusions of carbohydrate-binding modules and IgG-binding Z domains”.

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Nuno Bourbon, PhD student from the BIOTECnico doctoral programme at iBB-BSRG, was awarded 1st place in the “GENERAL” category of the competition “Science Communication in Microbiology”, promoted by the Portuguese Society of Microbiology (SPM) to commemorate the International Microorganism Day 2019. The competition seeks to encourage and facilitate the communication of relevant microbiology topics to the general public in a concise and attractive fashion by asking contestants to summarise the topic in an image which, if selected, is to be published in an eBook accompanied by a short explanatory description. His entry, entitled “Microbiology of beer”, provides an overview of the main yeast and bacterium species used in brewing and how different volatile compounds arising from their metabolism can impact the flavour and aroma of this alcoholic beverage.

Luís Miguel Martins, PhD student from the AEM doctoral programme in Applied and Environmental Microbiology, at iBB-BSRG, presented his work during the symposium on “Bioeconomy and Sustainable Development“   of the Congress of Microbiology and Biotechnology 2019 (Microbiotec’19), which was held between the 5th and 7th of December 2019 in Coimbra, Portugal. The presentation was entitled “Isolation and potential of non-conventional yeasts for the production of added-value compounds from pectin-rich residues, in particular sugar beet pulp”. This work was carried out under the supervision of Prof. Isabel Sá-Correia (iBB-BSRG) in the framework of ERANET-Industrial Biotechnology project ERA-IB-2/0003/2015 “Engineering of the yeast Saccharomyces cerevisiae for bioconversion of pectin-containing agro-industrial side-streams”.