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Institute for Bioengineering and Biosciences
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Synthesis of Fluorescent Water-Soluble Block Co-polymers

Synthesis of Fluorescent Water-Soluble Block Co-polymers | iBB | Scoop.it

The ability of block co-polymers to self-assemble and form micelles in solution can potentially be explored to deliver poorly soluble chemotherapeutic agents. Researchers from BSIRG-iBB led by Vasco Bonifácio, working in collaboration with colleagues from Universidade Nova, have synthesized new block copolymers of oligo-2-oxazoline and linear oligo(ethylenimine) that are water-soluble and show an intrinsic blue fluorescence. The synthesis uses a green protocol and allows a precise control of the oligo(ethylenimine) backbone. The work was published in Advanced Materials Letters.

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Molecular and Physiological Basis of Yeast Tolerance to Adverse Lignocellulose-Based Process Conditions

Molecular and Physiological Basis of Yeast Tolerance to Adverse Lignocellulose-Based Process Conditions | iBB | Scoop.it

Lignocellulose-based biorefineries are an alternative to current petroleum-based refineries. However, the biomass pretreatment to break the recalcitrant lignocellulosic biomass structure results in the release of weak acids, furans, and phenolic compounds, which can be severely affect the performance of the common bioethanol producing yeast Saccharomyces cerevisiae. Moreover, pentose sugar utilization and the high temperatures required for an efficient simultaneous saccharification and fermentation step, are additional challenges. Therefore, a better understanding of the yeast response and adaptation towards the presence of the referred multiple stresses is of crucial importance to design strategies to improve yeast robustness and bioconversion capacity from lignocellulosic biomass. A recent review published in Applied Microbiology and Biotechnology describes the main inhibitors derived from different biomass pretreatments and the molecular and physiological mechanisms underlying yeast response to the above referred challenges. Successful cases of tolerance improvement are also highlighted. Decoding the overall yeast response mechanisms will pave the way for the integrated development of sustainable yeast cell-based biorefineries. This review paper was co-authored at iBB-BSRG by Prof Isabel Sá-Correia, in collaboration with the group of Prof Lucília Domingues at CEB, Universidade do Minho.

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Small Noncoding Regulatory RNAs from Pseudomonas aeruginosa and Burkholderia cepacia Complex

Small Noncoding Regulatory RNAs from Pseudomonas aeruginosa and Burkholderia cepacia Complex | iBB | Scoop.it

Cystic fibrosis (CF) is the most life-limiting autosomal recessive disorder in Caucasians, with chronic bacterial airway infections representing the major cause of early decease. Pseudomonas aeruginosa and bacteria from the Burkholderia cepacia complex (Bcc) are the leading pathogens of CF patients’ airways. A wide array of virulence factors is responsible for infections caused by these bacteria, which have tightly regulated responses to the host environment. Small noncoding RNAs (sRNAs) are major regulatory molecules in these bacteria. Several approaches have been developed to study P. aeruginosa sRNAs, many of which are involved in the virulence. On the other hand, the knowledge on Bcc sRNAs remains far behind. In a review published on International Journal of Molecular Sciences, Tiago Pita, Joana Feliciano and Jorge H. Leitão from BSRG-iBB updated the knowledge on characterized sRNAs involved in P. aeruginosa virulence, compiled data so far achieved on sRNAs from the Bcc and discuss their possible roles on bacteria virulence.

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Following the Evolution Towards Fluconazole Resistance in C. glabrata

Following the Evolution Towards Fluconazole Resistance in C. glabrata | iBB | Scoop.it

The effectiveness of Candida glabrata as an emerging human pathogen relies on its ability to acquire azole drug resistance. In a paper just published in Antimicrobial Agents and Chemotherapy, the first time-course evaluation of the global gene expression changes that lead a drug susceptible C. glabrata clinical isolate to step-wise acquisition of resistance to azole drugs was conducted. This work, which results from the collaboration of six different teams under the coordination of Miguel C Teixeira from BSRG-iBB, highlights the multifactorial nature of azole resistance acquisition, including the Epa3 adhesin as a new player, while providing fascinating clues on the underlying evolutionary path. This knowledge is of crucial importance to design more effective antifungal therapy.

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The Various Roles of Fatty Acids

The Various Roles of Fatty Acids | iBB | Scoop.it

Lipids comprise a large group of chemically heterogeneous compounds that, in general, have in their structure fatty acids (FA). In a review paper published this week in the Special Issue of Molecules edited by both authors and entitled “The Multiple Roles of Fatty Acids”, Dr. Carla CCR de Carvalho (BERG-iBB) and Dr. Maria José Caramujo (CE3C, FCUL) discuss the various roles of FA in prokaryotes and eukaryotes and highlight the application of FA analysis to elucidate ecological mechanisms. The authors briefly describe FA synthesis; analyse the role of FA as modulators of cell membrane properties and FA ability to store and supply energy to cells; and inspect the role of polyunsaturated FA (PUFA) and the suitability of using FA as biomarkers of organisms.

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Rapid Formation of Mineralized Bone Tissue Based on Stem Cell-mediated Osteogenesis

Rapid Formation of Mineralized Bone Tissue Based on Stem Cell-mediated Osteogenesis | iBB | Scoop.it

Bone regeneration, following fracture, relies on autologous and allogenic bone grafts. However, majority of fracture population consists of older individuals with poor quality bone associated with loss and/or modification of matrix proteins critical for bone formation and mineralization. Allografts sufer from same limitations and carry the risk of delayed healing, infection, immune rejection and eventual fracture. Researchers from SCERG-iBB, working in collaboration with colleagues from the Rensselaer Polytechnic Institute in the US, have applied a synergistic biomimetic strategy to develop matrices that rapidly form bone tissue. Collagen matrices, enhanced with osteocalcin and/or osteopontin, increased the rate and quantity of synthesized bone matrix by increasing mesenchymal stem/stromal (MSC) cell proliferation, accelerating osteogenic diferentiation and enhancing angiogenesis The work was published in Scientific Reports.

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The OmpR Regulator of Burkholderia multivorans Controls Properties Associated with Persistence in the Cystic Fibrosis Lung

The OmpR Regulator of Burkholderia multivorans Controls Properties Associated with Persistence in the Cystic Fibrosis Lung | iBB | Scoop.it

Within the cystic fibrosis (CF) lung, bacteria experience high-osmolarity conditions due to an ion unbalance resulting from defects in CF transmembrane conductance regulator (CFTR) protein activity in epithelial cells. Understanding how bacterial CF pathogens thrive in this environment might help the development of new therapeutic interventions to prevent chronic respiratory infections. In a recent publication in Journal of Bacteriology, researchers from BSRG-iBB led by Leonilde M. Moreira, in collaboration with Dr. Vaughn Cooper from University of Pittsburgh, USA, and Dr. Jörg Becker from Instituto Gulbenkian de Ciência, provide evidence that mutations in OmpR experience positive selection during the adaptation of Burkholderia to chronic infections of the CF airway, and these selective forces can be recapitulated in the laboratory. Characterization of OmpR shows that it is a major regulator of many traits related to cell envelope composition and central metabolism, in which loss-of-function mutants enable greater tolerance and growth under stress conditions but are costly for fitness under other conditions.

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Antimicrobial Properties of Camphor-Derived Silver Complexes

Antimicrobial Properties of Camphor-Derived Silver Complexes | iBB | Scoop.it

The emergence of bacterial resistance to available antimicrobials has prompted the search for novel antibacterial compounds to overcome this public health problem. Metal-based complexes have been much less explored than organic compounds as antimicrobials, leading to investigations of the antimicrobial properties of selected complexes in which silver may occupy the frontline due to its use as medicine since ancient times. Like silver, camphor has also long been used for medicinal purposes. However, in both cases, limited information exists concerning the mechanisms of their antimicrobial action. In a recent collaborative work by the research group headed by Jorge H. Leitão from BSRG/iBB and M. Fernanda Carvalho from CQE, the present knowledge of the antimicrobial properties of camphor-derived silver complexes is reviewed, focusing on recent research on the synthesis and antimicrobial properties of complexes based on silver and camphor imines. Selected examples of the structure and antimicrobial activity relationships of ligands studied so far are presented, showing the potential of silver camphorimine complexes as novel antimicrobials. The review was published in the journal Antibiotics.

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Comparative Transcriptomic Analysis of Pesticide Action in Saccharomyces cerevisiae

Comparative Transcriptomic Analysis of Pesticide Action in Saccharomyces cerevisiae | iBB | Scoop.it

Accidental spills or careless storage and disposal of pesticides may lead to environmental contamination posing possible risks for non-target microbes and higher eukaryotes in ecosystems. In a recent publication in the journal Ecotoxicology, iBB-BSRG researchers led by Cristina A. Viegas, in collaboration with Jörg D. Becker from IGC, reported a comparative transcriptomic analysis of the responses to sub-lethal levels of six environmentally relevant pesticides in the Saccharomyces cerevisiae model species. A number of predictions of biological pathways and mechanisms emerged from this study in yeast, which are relevant to better understand the potential mode of action and adverse side-effects of these pesticides in biological systems.

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Azurin Perturbs Lipid Rafts’ Organization and Enhances Sensitivity to Anti-cancer Drugs

Azurin Perturbs Lipid Rafts’ Organization and Enhances Sensitivity to Anti-cancer Drugs | iBB | Scoop.it

A new determinant of the interaction of the bacterial anti-cancer protein azurin with the lipid rafts present in the membrane of cancer cells has been uncovered by a team led by Arsénio Fialho from BSRG-iBB, in collaboration with Sandra Pinto and Fábio Fernandes from CQFM-IN and iBB. The lipid rafts in these cells contribute to increase membrane order, rigidity and resistance to anti-cancer drugs. As a consequence of the interaction with lipid rafts, we demonstrate that treating cells with azurin increases membrane fluidity, and ultimately benefits the action of other drugs, probably by facilitating its entry in cancer cells. The work was recently published in the journal Cell Cycle.

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Expansion of Human Induced Pluripotent Stem Cells in Vertical-Wheel Bioreactors

Expansion of Human Induced Pluripotent Stem Cells in Vertical-Wheel Bioreactors | iBB | Scoop.it

The successful use of Human induced Pluripotent Stem Cells (hiPSC) for disease modelling, drug discovery and, ultimately, for regenerative therapies depends on the development of robust bioprocesses capable of generating large numbers of hiPSC and derivatives. SCERG-iBB researchers developed a bioprocess for the scalable generation of hiPSC in a microcarrier-based system using, for the first time, single-use Vertical-Wheel bioreactors. hiPSC culture was performed in working volumes up to 300 mL, maintaining the pluripotency and genomic integrity of the cells, providing an important tool for the successful manufacturing of hiPSC-based products.  The work was published in the Journal of Chemical Technology and Biotechnology.

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Re-engineering E. coli for Interferon Production

Re-engineering E. coli for Interferon Production | iBB | Scoop.it

The bacterial genome can be modified to favour the synthesis of recombinant protein. Such productivity gains can contribute to lower costs and increase the affordabiliy of protein pharmaceuticals. BERG-iBB researchers and colleagues from the Institute of Technology Guwahati (India) have shown that deletion of the pgi (phosphoglucose isomerase) gene in Escherichia coli favours the production of the pharmaceutically important protein interferon gamma (IFN-gamma). Specific IFN-gamma yields were 3.0-fold higher in mutant compared to native strain. Furthermore, a metabolic model analysis showed that pgi deletion raises flux efficiency towards IFN-gamma synthesis. The work was published in Enzyme Microbial Technology.

 

Photo details: 3D model of pgi by Emw, own work, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=8814547

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Microalgae for Wastewater Treatment

Microalgae for Wastewater Treatment | iBB | Scoop.it

Microalgae are an attractive, low cost and sustainable option for the treatment of wastewaters (WW). A collaborative study by portuguese (iBB, LNEG) and brazilian researchers shows that poultry, swine, cattle, brewery, dairy and urban WW can be treated with the microalgae Scenedesmus obliquus. Removal efficiency ranges were 95–100% for N, 63–99% for P and 48–70% for COD. Higher biohydrogen production yields were obtained using poultry and swine WW. The study, co-authored by Helena Pinheiro from BERG-iBB, was published in Environmental Research.

 

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Perturbing the Dynamics and Organization of Cell Membrane Components: A New Paradigm for Cancer-Targeted Therapies

Perturbing the Dynamics and Organization of Cell Membrane Components: A New Paradigm for Cancer-Targeted Therapies | iBB | Scoop.it

https://www.scoop.it/t/ibb/?&tag=Ars%C3%A9nio+FialhoUnlike the current paradigm of “one drug one target”, nowadays multiple-target approaches taking place at the cancer cell membrane are gaining much more relevance. The rational is based on the use of a new class of molecules that can exert significant changes in the dynamics and organization of cell membranes thereby affecting growth factor signaling, invasiveness and drug resistance. In a review published in a Special Issue “Receptor-Targeted Cancer Therapy” of the International Journal of Molecular Sciences, BSRG-iBB team members Nuno Bernardes and Arsenio M Fialho present and discuss novel approaches for cancer therapy, including the anticancer bacterial protein azurin.

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Bioactive Secondary Metabolites from Octocoral-Associated Microbes—New Chances for Blue Growth

Bioactive Secondary Metabolites from Octocoral-Associated Microbes—New Chances for Blue Growth | iBB | Scoop.it

Octocorals (Cnidaria, Anthozoa Octocorallia) are magnificent repositories of natural products with fascinating and unusual chemical structures and bioactivities of interest to medicine and biotechnology. Microorganisms associated with octocorals possess a widespread yet uncharted capacity to synthetize a broad range of these natural products. In this review article published in Marine Drugs, Inês Raimundo, Sandra Silva, Rodrigo Costa and Tina Keller-Costa from BSRG-iBB uncover a wide diversity of bioactive natural products, particularly alkaloids, cyclopeptides, terpenoids and polyketides, reported to date for octocoral-derived microbes, with remarkable antibacterial, antifungal, antiviral, antifouling and anticancer activities. Beyond providing an overview of these bioactive compounds, the authors reveal hundreds of putative secondary metabolite biosynthetic gene clusters across 15 genomes of bacteria isolated from octocorals in Portugal, highlighting their potential as sources of novel metabolites suitable for bioprospection studies. They finish by discussing how to harness this biotechnological potential using multidisciplinary laboratory experimentation. This review provides the scientific community with an integrated view of the current status of secondary metabolite biosynthesis by octocoral-associated microbes and the methodological challenges that are to be met in order to achieve a sustainable response to the urgent industrial demand for novel drugs and enzyme varieties from the blue economy sector.

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Expansion and Harvesting Of Human Induced Pluripotent Stem Cells on Dissolvable Microcarriers

Expansion and Harvesting Of Human Induced Pluripotent Stem Cells on Dissolvable Microcarriers | iBB | Scoop.it

Development of efficient bioprocesses for human induced pluripotent stem cells (hiPSC) is critical for their medical and biotechnological applications. Scalable expansion of hiPSC is often performed using polystyrene microcarriers, which have to be removed using a time-consuming separation step. At the Stem Cell Engineering Research Group, novel xeno-free dissolvable microcarriers were applied for the first time for the integrated expansion and harvesting of hiPSC. After expansion, microcarriers were dissolved inside the bioreactor, allowing the recovery of more than 90% of the cells, which represents a significantly higher cell yield when compared with microcarrier filtration (45%). These results represent a major improvement for the downstream processing of hiPSC. Find more on the paper on Biotechnology Journal.

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The ABC Transporters Pdr18 and Snq2 Derive from a Recent Gene Duplication Event

The ABC Transporters Pdr18 and Snq2 Derive from a Recent Gene Duplication Event | iBB | Scoop.it

Several membrane transporters from the ATP-binding cassette (ABC) superfamily present in yeast genomes are implicated in multidrug/multixenobiotic resistance (MDR/MXR). This is the case of Pdr18, that confers tolerance to ethanol and acetic acid and several other toxicants in yeast and has a biological role attributed in ergosterol transport at the plasma membrane. A recently iBB-BSRG paper published in Frontiers in Genetics, Evolutionary and Genomic Microbiology section, reconstructs the evolutionary history of the encoding gene PDR18 and the paralogue gene SNQ2. This publication results from the PhD thesis in Biotechnology and Biosciences of Cláudia P. Godinho advised by Prof. Isabel Sá-Correia with collaboration of Paulo J. Dias and Elise Ponçot. By combining phylogenetic gene neighborhood analysis for 117 yeast genomes belonging to 29 species across the Saccharomycetaceae family, the gene duplication event was traced to the last common ancestor of the Saccharomyces genus yeasts. The fact that Snq2 and Pdr18 confer resistance to different sets of chemical compounds with little overlapping is consistent with the subfunctionalization and neofunctionalization of these gene copies. Remarkably, PDR18 is only found in Saccharomyces genus genomes. 

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Regulation of Zygosaccharomyces bailii Early Response to Acetic Acid and Copper Stress

Regulation of Zygosaccharomyces bailii Early Response to Acetic Acid and Copper Stress | iBB | Scoop.it

The non-conventional food spoiling yeast species Zygosaccharomyces bailii is remarkably tolerant to acetic acid, a highly important microbial inhibitory compound in Food Industry and Biotechnology. The study recently published in Scientific Reports, coordinated by Isabel Sá-Correia and Margarida Palma and first authored by the BIOTECnico PhD student Miguel Antunes, investigates the genomic transcription changes occurring during the early response of Z. bailii to acetic acid or copper stresses and uncovers the regulatory network activated under the bifunctional transcriptional factor ZbHaa1 control. This study provides valuable insights regarding Z. bailii adaptation mechanisms to acetic acid or copper stresses, ZbHaa1-dependent regulatory network, and the evolution of transcription factors and regulatory networks in pre- whole genome duplication (WGD) and post-WGD yeast species.

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Engineering Human MSC with VEGF-encoding Minicircles for Angiogenic Gene Therapy

Engineering Human MSC with VEGF-encoding Minicircles for Angiogenic Gene Therapy | iBB | Scoop.it

Peripheral artery disease (PAD) is a debilitating condition characterized by the blockage of arteries, which leads to limb amputation in more severe cases. Researchers from SCERG- and BERG-iBB propose the use of human bone marrow (BM) MSC transiently transfected with minicircles encoding for VEGF as an ex vivo gene therapy strategy to enhance angiogenesis in PAD patients. The data shows that VEGF overexpression improved the angiogenic potential of MSC in vitro, as confirmed by endothelial cell tube formation and cell migration assays.These results suggest that minicircle-mediated VEGF gene delivery, combined with the unique properties of human MSC, could represent a promising ex vivo gene therapy approach to improve angiogenesis in the context of PAD. The work was published in Human Gene Therapy.

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Production and Purification of Supercoiled Minicircles

Production and Purification of Supercoiled Minicircles | iBB | Scoop.it

A wider application of minicircle (MC) vectors in gene therapy research depends critically on the ability to purify supercoiled MC from related miniplasmid (MP) and parental plasmid (PP) impurities. BERG-iBB researchers published a protocol that describes a purification strategy that combines the in vitro enzymatic relaxation of supercoiled MP and PP impurities by a nicking endonuclease, and topoisomer separation and RNA clearance by hydrophobic interaction chromatography. The time required to follow the full protocol, from production to isolation of sc MC is, approximately, 50 hr. The process delivers supercoiled MCs that are virtually free from MP, PP, RNA and protein impurities. The work was published in Human Gene Therapy Methods.

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Assessment of Ecotoxicological Potential of Cement-based Construction Materials

Assessment of Ecotoxicological  Potential of Cement-based Construction Materials | iBB | Scoop.it

Innovation in construction materials (CM) implies changing their composition by incorporating raw materials (RM), usually non-traditional ones (e.g., processed or recycled RM), to confer particular characteristics. However, potential environmental risks associated with changing the conventional composition of CM are not completely known and need to be evaluated. Researchers from iBB-BSRG and CERIS - Civil Engineering Research and Innovation for Sustainability, at IST, proposed and applied a methodology for the assessment of the potential ecotoxicity associated with RM and cement-based CM considering a conservative scenario representative of the end of the materials life cycle. The work was published in the journal Materials.

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Flow Microcalorimetry Analysis of the Adsorption of mAbs in Phenylboronate Chromatography

Flow Microcalorimetry Analysis of the Adsorption of mAbs in Phenylboronate Chromatography | iBB | Scoop.it

The feasibility of applying Flow Microcalorimetry to evaluate the complex phenomena involved in the adsorption of monoclonal antibodies to phenylboronate ligands has been demonstrated by BERG-iBB researchers led by Ana Azevedo, in collaboration with Ana Cristina Dias-Cabral from CICS-UBI. The thermodynamic studies evidence the role of affinity and non-specific effects that contribute to the complex, phenylboronate-mediated multimodal adsorption process. This deeper understanding, combined with the economic advantages associated with the employment of the PBA ligand, may lead industry to adopt such a chromatographic process as a reliable alternative to protein A-based capture steps in the current downstream processing of mAbs. The work is part of Sara Rosa’s PhD thesis in Biotechnology and Biosciences. The paper was published on J. Chromatography A.

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Advancing the Development of Vaccines Against Bacteria of the Burkholderia cepacia complex

Advancing the Development of Vaccines Against Bacteria of the Burkholderia cepacia complex | iBB | Scoop.it

 Bacteria of the Burkholderia cepacia complex (Bcc) remain an important cause of morbidity and mortality among patients suffering from cystic fibrosis. Eradication of these pathogens by antimicrobial therapy often fails, highlighting the need to develop novel strategies to eradicate infections. Vaccines are attractive since they can confer protection to particularly vulnerable patients, as is the case of cystic fibrosis patients. Several studies have identified specific virulence factors and proteins as potential subunit vaccine candidates. So far, no vaccine is available to protect from Bcc infections. In a recent publication in the journal Vaccines, iBB-BSRG researchers Sílvia Sousa, António M. Seixas and Jorge H. Leitão review the most promising postgenomic approaches and selected web tools available to speed up the identification of immunogenic proteins with the potential of conferring protection against Bcc infections.

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Metagenomic Binning Illuminates the Evolution of Unculturable, Symbiotic Bacteria

Metagenomic Binning Illuminates the Evolution of Unculturable, Symbiotic Bacteria | iBB | Scoop.it

Most microorganisms cannot be cultivated in the laboratory, what hinders our understanding of their physiology, evolution and functional roles. In collaboration with GEOMAR, University of Kiel, iBB researchers used modern nucleotide composition binning methodologies to assemble the genome of an “unculturable” bacterial symbiont from microbial metagenomes. The research led to the identification of a novel alphaproteobacterial lineage found to be intimately associated with marine sponges, termed "SERC" (sponge-enriched Rhodospirillales clade), characterized by the lack of chemotaxis and motility traits and enrichment of genes required for the utilization of organic sulfur, biosynthesis of natural products, and cell detoxification processes. The work was published in FEMS Microbiology Ecology.

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Quantitative Analysis of Bead-Based Microfluidic Optical Biosensors

Quantitative Analysis of Bead-Based Microfluidic Optical Biosensors | iBB | Scoop.it

Microfluidic devices with integrated photodetectors can address the need for compact and portable biosensing platforms for medical, veterinary, environmental and food safety applications. However, depending on the application, performance requirements like the minimum detectable limits, the target sensitivity, and the detection time can vary dramatically. To improve the engineering of fit-for-purpose bead-based microfluidic biosensors, researchers at BERG-iBB and INESC-MN developed a simple quantitative methodology to determine (1) equilibrium constants, (2) binding kinetics, (3) rate at which photons are generated/absorbed per captured molecule, and (4) molecular capture efficiencies. These parameters provide an effective trade-off between required sensitivity, cost effectiveness and assay complexity. This work was published in the IOP Journal of Micromechanics and Microengineering.

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