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Marine Bioprospecting, Biocatalysis and Process Development

Marine Bioprospecting, Biocatalysis and Process Development | iBB | Scoop.it

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-2BRG) review the latest studies related to growth of marine bacteria under laboratorial conditions, screening techniques, and bioprocess development.

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Overcoming the “unculturable” dogma

Overcoming the “unculturable” dogma | iBB | Scoop.it

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.

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Check paper at:

https://www.frontiersin.org/articles/10.3389/fbioe.2022.964589/full

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Magnetic Particles for the Purification of DNA Scaffolds for Biomanufacturing DNA-Origami Nanostructures

Magnetic Particles for the Purification of DNA Scaffolds for Biomanufacturing DNA-Origami Nanostructures | iBB | Scoop.it

Asymmetric PCR (aPCR) is often used to generate single-stranded DNA (ssDNA) scaffolds, which can then be assembled into nanoobjects by the DNA-origami technique. The scaffolds are usually purified by agarose gel extraction, a laborious, time consuming, limited, and non-scalable technique that presents low recovery yields, delivers low-quality products. To overcome such pitfalls, Ana Silva-Santos, Rui Silva, Sara Rosa and Miguel Prazeres from BERG-iBB, in collaboration with Pedro Paulo from CQE developed a simple, fast, and potentially scalable affinity-based method comprising magnetic particles. Specifically, scaffolds were synthesized by aPCR and purifed using magnetic particles functionalized with a 20 nt oligonucleotide complementary to the 3′ end of the target. The purified scaffolds were used to assemble 31 and 63 bp edge length tetrahedra with short oligonucleotides and thermal annealing, demonstrating the potential of affinity-based magnetic beads in the production of DNA-origami nanostructures. The work was published in ACS Applied Nanomaterials.

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Nuno Melo Participates in World Microbe Forum

Nuno Melo Participates in World Microbe Forum | iBB | Scoop.it

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.

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Participation in the EU Project FuturEnzyme

Participation in the EU Project FuturEnzyme | iBB | Scoop.it

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.

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BERG Research Presented at SBCN 2021

BERG Research Presented at SBCN 2021 | iBB | Scoop.it

The 15th international symposium on Biochromatography and Nanoseparations, which is taking place from 17-20th May in virtual mode, aims to highlight the recent progress on the purification and characterization of biomolecules from lab to industrial scale. BERG-IBB researchers will be presenting their work with oral (Ana Azevedo, Ana Rita Santos, Amin Javidanbardan and Malik Wahab) and poster (Jorge João) communications.

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Cláudia Alves to Defend PhD Thesis in Biotechnology and Biosciences

Cláudia Alves to Defend PhD Thesis in Biotechnology and Biosciences | iBB | Scoop.it

Cláudia Patrícia Almeida Alves will be defending her PhD thesis in Biotechnology and Biosciences at Instituto Superior Técnico, Friday the 14th of May 2021, at 14:00 am (https://videoconf-colibri.zoom.us/j/82471896554). During the last years, and under the supervision of Gabriel Monteiro and Miguel Prazeres from iBB, Cláudia engineered Escherichia coli strains for the production of minicircle vectors by resolvase-catalyzed in vivo recombination. The title of her thesis is “Escherichia coli Genome Engineering For Improved Minicircle Production". Yo can check more about Cláudia's work here.

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Burkholderia cenocepacia BCAM2418-induced Antibody Inhibits Bacterial Adhesion

Burkholderia cenocepacia BCAM2418-induced Antibody Inhibits Bacterial Adhesion | iBB | Scoop.it

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.

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Burkholderia cenocepacia Transcriptome During the Early Contacts with Giant Plasma Membrane Vesicles

Burkholderia cenocepacia Transcriptome During the Early Contacts with Giant Plasma Membrane Vesicles | iBB | Scoop.it

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.

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BIOTECnico PhD Alumni Seminar: Pedro Pais

BIOTECnico PhD Alumni Seminar: Pedro Pais | iBB | Scoop.it

Pedro Pais will be giving a talk entitled "Unveiling the complex regulatory network governing antifungal drug resistance in Candida glabrata: from new regulators to new effectors", Tuesday the 16th february at 16:00 h via zoom. Pedro obtained his PhD in Biotechnology and Biosciences in 2019 and is currently an Assistant Researcher at iBB.

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Probiotics in Fish Aquaculture

Probiotics in Fish Aquaculture | iBB | Scoop.it

Aquaculture is the fastest-growing sector in food production worldwide. BSRG-iBB researchers Nuno Borges, Tina Keller-Costa, PhD candidate Gracinda Sanches-Fernandes and Prof. Rodrigo Costa, together with colleagues from the University of Aveiro, have recently published a review in Annual Review of Animal Biosciences examining molecular studies of bacterial diversity, function, and host immunity modulation at early stages of fish development, where microbial infections cause important economic losses. The authors uncover host colonization and virulence factors from a synthetic assemblage of fish pathogens using comparative genomics and address the use of probiotics and paraprobiotics as disease-prevention strategies in fish larval and juvenile rearing. They also propose guidelines for future microbiome research of presumed relevance to fish larviculture.

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BIOTECnico PhD Alumni Seminar: Amir Hassan

BIOTECnico PhD Alumni Seminar: Amir Hassan | iBB | Scoop.it

Amir Hassan will be giving a talk entitled "Adaptation of Burkholderia cepacia complex bacteria to the cystic fibrosis lung: focus on lipopolysaccharide O-antigen and cell wall physical properties", Tuesday the 19th january at 16:00 h via zoom. Amir obtained his PhD in Biotechnology and Biosciences in 2020 and is currently at the Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium.

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Andreia Pimenta to Defend PhD Thesis in Biotechnology and Biosciences

Andreia Pimenta to Defend PhD Thesis in Biotechnology and Biosciences | iBB | Scoop.it

Andreia Isabel de Melo Pimenta will be defending her PhD thesis in Biotechnology and Biosciences at Instituto Superior Técnico, Tuesday the 22nd of December 2020, at 10:00 am (https://videoconf-colibri.zoom.us/j/87589426644). During the last years, and under the supervision of Arsénio Fialho from BSRG-iBB, Andreia studied the role of Trimeric autotransporter adhesins in the pathogenesis of Burkholderia cenocepacia. The title of her thesis is “New insights into the interaction of Burkholderia cenocepacia with host cells: Trimeric autotransporter adhesins as pathogenicity factors”.

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The NPR/Hal family of kinases in S. cerevisiae and other yeasts

The NPR/Hal family of kinases in S. cerevisiae and other yeasts | iBB | Scoop.it

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.

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Check full paper at: https://doi.org/10.1016/j.csbj.2022.10.006

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Carlos Rodrigues to Defend PhD Thesis in Biotechnology and Biosciences

Carlos Rodrigues to Defend PhD Thesis in Biotechnology and Biosciences | iBB | Scoop.it

Carlos Júnio Caridade Rodrigues will be defending his PhD thesis in Biotechnology and Biosciences at Instituto Superior Técnico, Friday the 26th of July 2022, at 10:00 am (Amphitheater PA-3, floor -1, Mathematics building, Alameda campus). During the last years, and under the supervision of Carla Carvalho from iBB, Carlos focused on the development of novel integrative bioprocesses by accessing the enzymatic machinery of marine bacteria and improving cultivation techniques of ‘unculturable’ bacteria. The title of his thesis is “Developing bioprocesses with marine bacteria for sustainable industrial applications". Check some of Carlo´s PhD outputs here.

Ana Azevedo's comment, July 22, 2022 3:15 AM
Best of luck Carlos!
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Controlling Biofilm Establishment Since the First Touch

Controlling Biofilm Establishment Since the First Touch | iBB | Scoop.it

Candida glabrata’s ability to cause human infections is tightly linked to its impressive ability to form persistent biofilms. The molecular control of this process is far from being clarified, as it lacks many of the typical features displayed by other Candida species. In this study, a combination of genetic screening, RNA-seq based transcriptomics, and Single-Cell Force Spectroscopy (SCFS), enabled the observation that the transcription factor CgEfg1, but not CgTec1, is necessary for the initial interaction of C. glabrata cells with both abiotic surfaces used in medical devices and epithelial cells, while both transcription factors orchestrate biofilm maturation. The knowledge gathered through this study by former PhD student Mafalda Cavalheiro, and an international team led by Miguel Cacho Teixeira, BSRG-iBB, including Etienne Dague, LAAS-CNRS, Geraldine Butler, University College Dublin, and Arsénio Fialho, BSRG-iBB, and just published in Communications Biology, is expected to contribute to guide the design of more successful therapeutic approaches.

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Adaptation to Acetic Acid Stress Involves Structural Alterations and Increased Stiffness of the Yeast Cell Wall

Adaptation to Acetic Acid Stress Involves Structural Alterations and Increased Stiffness of the Yeast Cell Wall | iBB | Scoop.it

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.

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Determination of Recombination Efficiency in Minicircle Production by Real-time PCR

Determination of Recombination Efficiency in Minicircle Production by Real-time PCR | iBB | Scoop.it

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.

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Participation in the EFB2021

Participation in the EFB2021 | iBB | Scoop.it

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.

EarpieceHub's comment, June 7, 2021 8:11 AM
nicew
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Minicircle‐based Expression of VEGF in Mesenchymal Stromal Cells from Human Tissues

Minicircle‐based Expression of VEGF in Mesenchymal Stromal Cells from Human Tissues | iBB | Scoop.it

Mesenchymal stromal cells (MSC) have been exploited for the treatment of ischemic diseases given their angiogenic potential. A recent study published in the Journal of Gene Medicine by BERG and SCERG researchers compares the angiogenic potential of MSC obtained from bone marrow (BM), adipose tissue (AT) and umbilical cord matrix (UCM) that were genetically modified with VEGF‐encoding minicircle vectors. Transfected cells displayed higher in vitro angiogenic potential than non‐transfected controls, as demonstrated by functional in vitro assays, but no significant differences were observed among cells from different sources.

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BIOTECnico PhD Alumni Seminar: Mafalda Cavalheiro

BIOTECnico PhD Alumni Seminar: Mafalda Cavalheiro | iBB | Scoop.it

Mafalda Cavalheiro will be giving a talk entitled "Deciphering Mechanisms of Pathogenesis in Candida glabrata: in the Crossroad Between Drug Resistance and Virulence ", Tuesday the 16th of March at 16:00 h via zoom. Mafalda obtained her PhD in Biotechnology and Biosciences in 2020 and is currently working at A4F – Algae for Future, as a Junior R&D Project Manager.

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Asymmetric Synthesis with a Marine Transaminase

Asymmetric Synthesis with a Marine Transaminase | iBB | Scoop.it

w-Transaminases (w-TA) have a pivotal role in the synthesis of chiral amines used as building blocks for drugs and pharmaceuticals. In a recently published paper, Carlos JC Rodrigues (iBB-BERG), Manuel Ferrer (CSIC, Spain) and Carla CCR de Carvalho (iBB-BERG) used a w-TA from a marine bacterium to synthesize the fluorine chiral amine (S)-1-(4-trifluoromethylphenyl)ethylamine from a bulky ketone. An in situ product removal (ISPR) approach using an aqueous organic two-phase system was used to mitigate product inhibition, and engineering tools were used to increase substrate mass transfer without affecting the ability of the organic phase to prevent inhibition of the enzyme activity. The insights gained during process development may be valuable for future process applications of TA reactions.

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Development of Anti-Fouling Materials that Reduce Microbial Pathogen Adhesion

Development of Anti-Fouling Materials that Reduce Microbial Pathogen Adhesion | iBB | Scoop.it

The attachment of bacteria and other microbes to natural and artificial surfaces leads to the development of biofilms, which can further cause nosocomial infections. Thus, an important field of research is the development of new materials capable of preventing the initial adhesion of pathogenic microorganisms. In this work, novel polymer/particle composite materials were developed and characterized with respect to their mechanical, chemical and surface properties. Both S. aureus and C. glabrata exhibit a reduced capacity to adhere to the newly developed nanomaterials used in this study, thus showing their potential for bio-medical applications. This study, led by researchers from LAAS-CNRS, Toulouse, and co-authored by Mafalda Cavalheiro and Miguel Cacho Teixeira from BSRG-iBB, was just published in Nanomaterials.

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Minicircle Biopharmaceuticals: An Overview of Purification Strategies

Minicircle Biopharmaceuticals: An Overview of Purification Strategies | iBB | Scoop.it

Minicircles are non-viral delivery vectors with promising features for biopharmaceutical applications. These vectors are obtained in vivo in Escherichia coli by the intramolecular recombination of a parental plasmid, which generates the minicircle of interest and an unwanted miniplasmid. Several strategies have been proposed over the years to meet the challenge of purifying and obtaining high quality minicircles. The characteristics of the strain and parental plasmid used have a high impact and strongly affect the purification strategy that can be applied. In a review published in Frontiers in Chemical Engineering, Cláudia Alves, Miguel Prazeres and Gabriel Monteiro from BERG-IST summarize the different methods developed so far, focusing not only on the purification method itself but also on its dependence on the upstream production strategy used.

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BIOTECnico PhD Program Seminar Cycle 2021

BIOTECnico PhD Program Seminar Cycle 2021 | iBB | Scoop.it

The BIOTECnico PhD program will initiate a cycle of alumni seminars on the 19th of January 2021. Until the 30th of March, every 2 weeks, on Tuesdays at 4 pm, BIOTECnico alumni will deliver a 20 min presentation describing the main achievements of the PhD projects they developed at iBB, as well as their current professional activities and institution. The seminars will be delivered via zoom and the full list can be found here.

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