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Benzyl Alcohol Production in Stirred and Packed Bed Reactors

Benzyl Alcohol Production in Stirred and Packed Bed Reactors | iBB | Scoop.it

The ocean is an excellent source for new biocatalysts due to the tremendous genetic diversity of marine microorganisms, and it may contribute to the development of sustainable industrial processes. In a recent paper published in Microorganisms, Carlos J.C. Rodrigues and Carla C.C.R. de Carvalho (iBB-BERG) used a marine bacterium for the conversion of benzaldehyde to benzyl alcohol, which is an important chemical employed as a precursor for producing esters for cosmetics and other industries. A stirred reactor, using a fed-batch approach, enabled a 1.5-fold increase in benzyl alcohol productivity when compared with batch mode. However, product accumulation in the reactor hindered the conversion. The use of a continuous flow reactor packed with immobilized cells enabled a 9.5-fold increase in productivity when compared with the fed-batch stirred reactor system.

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Characterization of a New Blastobotrys navarrensis Strain

Characterization of a New Blastobotrys navarrensis Strain | iBB | Scoop.it

A BSRG-iBB research paper just published in International Journal of Systematic and Evolutionary Microbiology reports the isolation, identification, and morphological and phylogenetic characterization of Blastobotrys navarrensis IST 508. The isolation of this yeast strain from a soil sample collected underneath an olive tree in Ferreira do Alentejo was essential to propose the taxonomic separation of B. navarrensis, so far represented by the single strain CBS 139.77, from Blastobotrys proliferans, which until this study was considered a synonym species. Molecular and phylogenetic data was used to propose B. navarrensis as an independent species and not a later synonym of B. proliferans. An emended description of B. navarrensis was also proposed. This research paper has as first- and corresponding- author Dr. Margarida Palma, who coordinated the investigation with contributions by Professor Isabel Sá-Correia. The article is also co-authored by former Master students Érica Vieira and Margarida Pataco, both from MSc in Biotechnology, IST.

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Modeling the Full Metabolism of the Human Pathogen Candida parapsilosis

Modeling the Full Metabolism of the Human Pathogen Candida parapsilosis | iBB | Scoop.it

Understanding the behavior of human pathogens is both a challenge and a need, if we are to address infectious diseases with the best possible tools. Genome-scale metabolic models are a way to meet this task, which was just used for the second most prevalent Candida species in Europe, Candida parapsilosis. The construction and validation of a global stoichiometric model describing the whole metabolic network in this human pathogen, as well as its exploitation in drug target discovery, stemming from a collaboration between researchers from BSRG/iBB (Miguel Cacho Teixeira), ITQB-NOVA (Isabel Rocha) and CEB-UMinho (Óscar Dias), was just published in Genes.

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Detection of mcr-1 gene in Vibrio Species Isolated From Clams

Detection of mcr-1 gene in Vibrio Species Isolated From Clams | iBB | Scoop.it

Pathogenic Vibrio species are responsible for human and animal illness and one of the main causes of human infection is related to the ingestion of undercooked seafood. Due to their filter-feeding habit, marine invertebrates, such as clams, are known to be a natural reservoir of specific microbial communities. In a recently published study carried out by researchers of ESTM, Polytechnic of Leiria, and Carla C.C.R. de Carvalho (BERG-iBB), the profile of antimicrobial resistance and the presence of virulence genes in the bacterial isolates from clams were evaluated. The presence of the mobilisable colistin resistance gene mcr-1 in three Vibrio spp. isolates highlights a potential threat to public health.

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Insights into Nanomedicine for Head and Neck Cancer Diagnosis and Treatment

Insights into Nanomedicine for Head and Neck Cancer Diagnosis and Treatment | iBB | Scoop.it

Head and neck cancers rank sixth among the most common cancers today, and the survival rate has remained virtually unchanged over the past 25 years, due to late diagnosis and ineffective treatments. These cancers affect areas of the body that are fundamental for the five senses. Therefore, it is necessary to treat them effectively and non-invasively as early as possible, to not compromise vital functions, which is not always possible with conventional treatments (chemotherapy or radiotherapy). Nanomedicine involves using nanocarriers to deliver drugs to sites of action and reducing the necessary doses and possible side effects. In a paper published in Materials, Pedro Fonte and co-workers from BERG-iBB performed an overview of the applications of nanocarrier systems to the diagnosis and treatment of head and neck cancer. Herein, several types of delivery strategies, radiation enhancement, inside-out hyperthermia, and theragnostic approaches were addressed.

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Genome Sequence and Analysis of the Flavinogenic Yeast Candida membranifaciens

Genome Sequence and Analysis of the Flavinogenic Yeast Candida membranifaciens | iBB | Scoop.it

A BSRG-iBB research paper just published in Journal of Fungi (special issue “New Trends in Yeast Genomics”) reports the isolation of Candida membranifaciens strains from soil, their physiological characterization and comparison regarding the production of riboflavin (vitamin B2). The first annotated genome sequence of C. membranifaciens IST 626 is provided, as well as the comparative genomic analysis with other relevant yeast species. This research work is first-authored by Dr. Margarida Palma, who coordinated the investigation with Professor Isabel Sá-Correia. The work has contributions from Master students Mariana Pereira and Érica Vieira and researchers from Joint Genome Institute, Berkeley, USA.

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The Effect of Recombinant Protein Production in Lactococcus lactis Transcriptome and Proteome

The Effect of Recombinant Protein Production in Lactococcus lactis Transcriptome and Proteome | iBB | Scoop.it

Lactococcus lactis is a food-grade, and generally recognized as safe, bacterium, which making it ideal for producing plasmid DNA (pDNA) or recombinant proteins for industrial or pharmaceutical applications. A paper published in Microorganisms by Sofia Duarte and Gabriel Monteiro from BERG-iBB reviews the major findings from L. lactis transcriptome and proteome studies, with an overexpression of native or recombinant proteins. These studies provide important insights on how to engineer the plasmid vectors and/or the strains in order to achieve high pDNA or recombinant proteins yields, with high quality standards. 

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Microchromatography Integrated with Impedance Sensor for Bioprocess Optimization

Microchromatography Integrated with Impedance Sensor for Bioprocess Optimization | iBB | Scoop.it

The development of new scale-down models for accelerated and cost-effective biopharmaceutical process development has been receiving considerable attention in the last decade. Microfluidic systems have emerged as a particularly attractive candidate by offering miniaturization, parallelization, and allowing continuous and precise pumping and online monitoring possible. In a collaborative work, published in Journal of Chromatography A, BERG-iBB researchers Ana Azevedo and Amin Javidanbardan, together with INESC-MN researchers João Pedro Conde and Virginia Chu, propose a simple and cost-effective method for developing microfluidic chromatographic systems with integrated sensors. Fabrication and integration of microsensors, in this case, an impedance sensor, in each microcolumn provided the possibility of parallelizing experiments with separate online monitoring. The work was performed under the Marie Skłodowska-Curie grant agreement No. 812909 CODOBIO, within the Marie Skłodowska-Curie European Training Networks framework.

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Integral Analysis of Liquid-Hot-Water Pretreatment of Wheat Straw

Integral Analysis of Liquid-Hot-Water Pretreatment of Wheat Straw | iBB | Scoop.it

Developing viable biorefineries is urgent to support the transition to a sustainable society. Lignocellulosic biomass is a crucial renewable feedstock, but usually a combination of pretreatments is necessary to extract both sugars and lignin. In a recent paper published in the journal Sustainability, the M.Sc. student Manuel Dias and Carla C.C.R. de Carvalho (BERG-iBB) collaborated with researchers from Technische Universität Wien (Vienna, Austria) under supervision of Prof Anton Friedl, to study liquid-hot-water (LHW) as pretreatment for hemicellulose hydrolysis. Assessment of different LHW conditions allowed the determination of those leading to high sugar concentration and low concentration of degradation products. The lignin remaining in the solid phase could be extracted and hydrolysed. By including the analysis of lignin hydrolysis into the standard sugar and degradation products in LHW, it was possible to make an integrated decision to valorize the different lignocellulosic components of wheat straw.

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Exploring the Biological Function of Efflux Pumps for the Development of Superior Industrial Yeasts

Exploring the Biological Function of Efflux Pumps for the Development of Superior Industrial Yeasts | iBB | Scoop.it

The economic competitiveness of yeast-mediated bioprocesses in Chemical Biotechnology requires high tolerance of industrial strains to the multiple stresses that occur. Among the mechanisms used by yeast to overcome those deleterious effects is the activity of plasma membrane transporters involved in multidrug/multixenobiotic resistance (MDR/MXR). A new review article on these still poorly characterized transporters belonging to the MFS and the ABC Superfamily in yeasts of biotechnological relevance has just been published. The reported role of specific transporters in increasing the secretion of metabolites and other added-value bioproducts is also highlighted. The review article is co-authored by the BSRG-iBB researchers Isabel Sá-Correia and Cláudia P. Godinho and was published in the journal Current Opinion in Biotechnology (special Issue: Chemical Biotechnology 2022).

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Implementation of Synthetic Pathways towards Microbe-Based Production of Non-Natural Carboxylic Acids

Implementation of Synthetic Pathways towards Microbe-Based Production of Non-Natural Carboxylic Acids | iBB | Scoop.it

Carboxylic acids (CAs) are considered key players in the implementation of more sustainable industrial processes due to their potential to replace a set of oil-derived commodity chemicals and there is growing interest in producing them through microbial processes. While many CAs are intermediates of microbial central carbon metabolism, and therefore envisaging their production in a host of choice is relatively straightforward; for other CAs this approach is difficult. This could be because they do not occur naturally (as is the case for levulinic acid) or because the described production pathway cannot be easily ported (as it is the case for adipic, muconic or glucaric acids). In a review published in Journal of Fungi, Nuno Mira’s team (iBB) reviewed the synthetic biology approaches that have been made towards enabling the production of non-natural CAs in microbes, with a large emphasis on metabolic retrobiosynthesis methodologies. Additionally, the authors also reviewed the pathway prospecting studies towards microbial levulinic, poly-lactic and methacrylic acid production, as two case-studies where there is a need to bridge the gap between natural CAs and their non-natural industrial derivatives.

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Acyl-chain Saturation Regulates the Order of Phosphatidylinositol 4,5-bisphosphate Nanodomains

Acyl-chain Saturation Regulates the Order of Phosphatidylinositol 4,5-bisphosphate Nanodomains | iBB | Scoop.it

PI(4,5)P2 is a phospholipid found mostly in the plasma membrane of eukaryotic cells, where it plays a crucial role in processes like vesicle trafficking, cytoskeletal regulation, ion channel function, viral assembly and budding. While most phospholipids show considerable acyl-chain diversity, PI(4,5)P2 lipids are exceptionally enriched in specific acyl-chains, the most frequent composition in mammalian cells being 1-stearoyl-2-arachidonyl (18:0 20:4). The biological functions that call for this specific enrichment are still not fully clear. In a recent paper published in Communications Chemistry, a BSIRG-iBB team led by Fábio Fernandes together with the teams of Dr. Nuno Santos (IMM) and Dr. Manuel Melo (ITQB) identified a previously unreported increase in membrane order upon calcium-dependent PI(4,5)P2 clustering. Remarkably, the interaction of saturated PI(4,5)P2 with calcium culminated in the formation of gel nanodomains for fully saturated PI(4,5)P2, and the formation of these gel domains was abrogated in the presence of 18:0 20:4 polyunsaturated PI(4,5)P2. These results support a role of (18:0 20:4)PI(4,5)P2 in inhibiting the formation of highly ordered PI(4,5)P2 nanodomains in the plasma membrane.

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Quantitative FRET Microscopy Reveals a Crucial Role of Cytoskeleton in Promoting PI(4,5)P2 Confinement

Quantitative FRET Microscopy Reveals a Crucial Role of Cytoskeleton in Promoting PI(4,5)P2 Confinement | iBB | Scoop.it

Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) is crucial to many cellular processes in eukaryotes, including membrane trafficking, signal transduction, ion channel function  and cytoskeleton dynamics. This function multiplicity is partially achieved through a dynamic spatiotemporal organization of PI(4,5)P2 within the membrane. In a recent paper published in IJMS, an IBB team (Maria J. Sarmento, Luís Borges-Araújo, Sandra N.Pinto, Nuno Bernardes, Joana Ricardo, Ana Coutinho, Manuel Prieto and Fábio Fernandes) was able to quantify PI(4,5)P2 confinement in living cells making use of FRET imaging measurements. PI(4,5)P2 was found to be significantly compartmentalized at the plasma membrane of HeLa cells. These PI(4,5)P2 enriched domains were shown to not depend on cholesterol content, ruling out an association with lipid rafts. On the other hand, upon inhibition of actin polymerization, compartmentalization of PI(4,5)P2 was almost entirely eliminated, confirming that the cytoskeleton network is the critical component responsible for the formation of nanoscale PI(4,5)P2 domains.

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Greener Strategy for Lupanine Purification from Lupin Bean Wastewaters Using a Molecularly Imprinted Polymer

Greener Strategy for Lupanine Purification from Lupin Bean Wastewaters Using a Molecularly Imprinted Polymer | iBB | Scoop.it

Lupanine is used as a building block in the synthesis of sparteine, a chiral selector in drug synthesis. This alkaloid is found in wastewaters derived from the debittering process that makes lupin beans edible. In a recently published work, carried out by researchers of the Faculty of Sciences and Faculty of Pharmacy from the University of Lisbon, and Teresa Esteves, Frederico Ferreira, Flávio Ferreira and Ana Mota from BERG-iBB, a computational chemistry approach was taken to design molecularly imprinted polymers (MIPs) selecting itaconic acid, a biobased building block, as a functional monomer that can provide higher affinities for lupanine. In this work, lupanine was concentrated from lupin bean wastewater by nanofiltration, extracted with ethyl acetate, and purified using the synthesized MIP, which was able to selectively recognize lupanine and improve its purity to 88%, with 82% recovery of the alkaloid, showing the potential application of this strategy to render the industrial process more sustainable.

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Additive Manufactured PCL-Graphene Scaffolds for Tissue Engineering

Additive Manufactured PCL-Graphene Scaffolds for Tissue Engineering | iBB | Scoop.it

Understanding the mechano–biological coupling mechanisms of biomaterials for tissue engineering is of major importance to assure proper scaffold performance in situ. Therefore, it is of paramount importance to establish correlations between biomaterials, their processing conditions, and their mechanical behaviour, as well as their biological performance. In a collaborative work between CDRSP-Politécnico de Leiria and SCERG-iBB  (João C. Silva and Frederico Ferreira), it was possible to infer a correlation between the addition of different concentrations of graphene nanoparticles (GPN) in three-dimensional poly(ε-caprolactone) (PCL)-based scaffolds, their extrusion-based processing parameters, and the lamellar crystal orientation observed in the different scaffolds through small-angle X-ray scattering experiments. Moreover, in vitro cell culture studies performed at SCERG-iBB demonstrated the suitability and potential of these novel 3D PCL/GPN scaffolds for tissue engineering applications. The results of this study were just published in Polymers.

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Cellulose-based LFA for Detection of Cystatin C

Cellulose-based LFA for Detection of Cystatin C | iBB | Scoop.it

The relevance and impact of Lateral Flow Assays (LFA) as point-of-care devices has been amply demonstrated with the current SARS-CoV-2 pandemic. However, and despite their usefulness, drawbacks like low sensitivity, low specificity, and lack of quantitation are often associated with LFAs. In a paper published in Scientific Reports, Miguel Prazeres from BERG-IST and colleagues from the Indian Institute of Technology (Madras) propose a new LFA architecture that combines nitrocellulose strips with layered cellulose, ZZ-CBM3 fusions and fluorescently labeled Fab fragments. The system was successfully applied to the the quantitative, fluorescence-based detection of the kidney biomarker cystatin C. The work was funded by project CBM-X.

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Piezoelectric Nanofibers for Osteochondral Tissue Engineering

Piezoelectric Nanofibers for Osteochondral Tissue Engineering | iBB | Scoop.it

Osteochondral (OC) tissue disorders, particularly osteoarthritis, number among the most prevalent and debilitating diseases in the adult population worldwide. However, despite the recent achievements in the field, no satisfactory clinical treatments have been developed to date to resolve this unmet medical issue. Notably, while the piezoelectric nature of the OC tissue has been extensively reported in different studies, this feature keep being neglected in the design of novel biomaterial scaffolds for OC regeneration. Thus, piezoelectric electrospun scaffolds capable of both recapitulating the piezoelectric nature of the tissue’s fibrous extracellular matrix and of providing a platform for electrical and mechanical stimulation of cells/tissues are promising platforms to promote OC regeneration. In a recent publication in the International Journal of Molecular Sciences, SCERG-iBB researchers MSc Frederico Barbosa, Prof. Frederico Ferreira and Dr. João Silva review and discuss the current state of the art of such piezoelectric biomimetic scaffolds for OC tissue engineering strategies.

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A CBM-Hexapeptide Fusion Confers Antimicrobial Properties to Cellulose

A CBM-Hexapeptide Fusion Confers Antimicrobial Properties to Cellulose | iBB | Scoop.it

A new strategy to modify cellulose with the short antimicrobial hexapeptide MP196 (RWRWRW-NH2) is proposed by BERG and BSIRG researchers that uses fusions of Cys-terminated derivatives of MP196 and a carbohydrate binding module (CBM). CBM3-MP196-modified cellulose hydrogels displayed antibacterial activity that was significantly higher when compared with controls. This versatile concept offers a toolbox for the functionalization of different cellulose materials with a broad choice in peptides. the paper was published in Acta Biomaterialia. The work was funded by project CBM-X.

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Optimization of the Brewing Parameters on Coffee Extraction Using a Central Composite Rotatable Design

Optimization of the Brewing Parameters on Coffee Extraction Using a Central Composite Rotatable Design | iBB | Scoop.it

When an idea in a coffee break in an international meeting turns into a paper, Pedro Fonte from BERG-iBB in collaboration with researchers from UFVJM, Brazil just published a work in JSFA Reports performing an optimization of the brewing parameters on coffee extraction using a central composite rotatable design. The effects of extraction time, particle size of ground coffee, extraction temperature, coffee-to-water ratio, stirring on caffeine yield, and soluble solids on caffeine concentrations were studied. Optimized parameters showed 45 min sufficed to perform a cold extraction at 4°C and 24°C. The parameters selected for validation were 24°C, 30% coffee-to-water ratio, a stirring of 400 rpm resulting in 3.98 mg/ml of extracted caffeine, 11.20 °Brix, and 93.9% of caffeine yield. The smaller particle size (595 μm) displayed the higher caffeine extraction of about 4 mg/ml. This study reveals the high efficiency of cold brew extraction and its potential at the industrial scale, decreasing costs with energy and extraction time, and producing a coffee rich in caffeine and soluble solids.

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Development of 3D High-Quality PDMS Microfluidic Chips Based on Micromilling Technology

Development of 3D High-Quality PDMS Microfluidic Chips Based on Micromilling Technology | iBB | Scoop.it

In recent years, there has been an increased interest in exploring the potential of micro-and mesoscale milling technologies for developing cost-effective microfluidic systems with high design flexibility and a rapid microfabrication process that does not require a cleanroom. Nevertheless, the number of current studies aiming to fully understand and establish the benefits of this technique in developing high-quality microsystems with simple integrability is still limited. In a recent paper published in Micromachines, BERG-iBB researches, Ana Azevedo and Amin Javidanbardan, in collaboration, with João Pedro Conde and Virginia Chu from INESC-MN, describe a systematic methodology for developing 3D high-quality thermoplastic-based molds for microfluidic structures based on micromilling technology. The work was performed under the Marie Skłodowska-Curie grant agreement No. 812909 CODOBIO, within the Marie Skłodowska-Curie European Training Networks framework.

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A Neofunctionalized Transcription Factor Controls Azole Resistance in C. glabrata

A Neofunctionalized Transcription Factor Controls Azole Resistance in C. glabrata | iBB | Scoop.it

The prevalence of antifungal resistance in Candida glabrata, especially against azole drugs, results in difficult-to-treat and potentially life-threatening infections. In this study, the role of a newly described transcription factor, Mar1, in azole susceptibility was explored. Using RNA-sequencing, its role in the transcriptome-wide response to fluconazole is assessed, leading to the elucidation of its role in modulating azole susceptibility, dependent on membrane sphingolipid incorporation, membrane permeability, and intracellular drug accumulation. Altogether, a regulatory pathway modulating azole susceptibility in C. glabrata is proposed, resulting from what appears to be a neofunctionalization of a Hap1-like transcription factor. These results obtained by an international team led by Miguel Cacho Teixeira, BSRG-iBB, just published in Journal of Fungi, are expected to contribute to maintain the usability of this drug in antifungal therapy.

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Engineering Organoids for Modeling PKU

Engineering Organoids for Modeling PKU | iBB | Scoop.it

Phenylketonuria (PKU) is a recessive genetic disorder of amino-acid metabolism, where impaired phenylalanine hydroxylase function in the liver of patients leads to the accumulation of neurotoxic phenylalanine levels in the brain. Despite the current knowledge, the chronic effect of PKU in the brain is still poorly understood. In a recent publication in Frontiers in Molecular Neurosciences, DBE faculty and SCERG-iBB researcher Tiago Fernandes, discusses the need for better predictive models, able to recapitulate specific mechanisms of this disease. New exciting in vitro platforms to model specific PKU-derived neuronal impairment are presented in a attempt to understand the impact of phenylalanine in the brain of patients, and ultimately contribute to the understanding of this disease.

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Metabolic Engineering of Saccharomyces cerevisiae Towards the Valorization of Pectin-rich Residues

Metabolic Engineering of Saccharomyces cerevisiae Towards the Valorization of Pectin-rich Residues | iBB | Scoop.it

A recent article published in the journal Metabolic Engineering reports the metabolic engineering of the yeast Saccharomyces cerevisiae envisaging the fast and complete consumption of D-galacturonic acid (d-GalUA) in crude sugar beet pulp hydrolysate under aerobic conditions. To this end, the fungal d-GalUA pathway was inserted in an S cerevisiae strain equipped with an NAD-dependent glycerol catabolic pathway. The constructed strain was able to consume d-GalUA with the highest reported maximum specific rate in synthetic minimal medium when glycerol was added. This work is the result of joint research in the framework of project YEASTPEC (Engineering of the yeast Saccharomyces cerevisiae for bioconversion of pectin-containing agro-industrial side-streams), funded through the ERA-IB scheme. In Portugal, the project was led by Isabel Sá-Correia (BSRG/iBB), in Germany by Elke Nevoigt, Jacobs University (corresponding author) and Wolfgang Liebl, TUM, and at VTT, Finland, by Peter Richard. The BSRG/iBB PhD graduate in Biotechnology and Biosciences Luis Martins also co-authored this article.

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Special Issue "Bioprocess Engineering: Sustainable Manufacturing for a Green Society"

Special Issue "Bioprocess Engineering: Sustainable Manufacturing for a Green Society" | iBB | Scoop.it

The mild operational conditions typically required by biobased production processes, together with the selective nature of biocatalysts, microbial diversity and tunability, and the century-long record of fermentation, clearly place bioprocesses as the primary contenders, by far, in achieving the generalized implementation of efficient, green manufacturing strategies. Moreover, by overlapping with the biorefinery approach, the foundations needed for bioprocesses to embrace the circular economy concept are set. In this Special Issue on “Bioprocess Engineering: Sustainable Manufacturing for a Green Society", guest edited by Pedro Fernandes and Carla de Carvalho (iBB-BERG) in Processes, the papers will discuss new bioproducts and concomitant bioengineering approaches to achieve a sustainable and environmentally friendly economy.

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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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