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Institute for Bioengineering and Biosciences
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Hfq: A Multifaceted RNA Chaperone Involved in Virulence

Hfq: A Multifaceted RNA Chaperone Involved in Virulence | iBB | Scoop.it

The Hfq protein has emerged in recent years as a master regulator of gene expression in bacteria, mainly due to its ability to mediate the interaction of small noncoding RNAs with their mRNA targets,
including those related to virulence in Gram-negative bacteria. In a paper recently published in Future Microbiology, researchers from iBB/BSRG reviewed current knowledge on the involvement of Hfq in the regulation of virulence traits related to secretion systems, alternative sigma factors, outer membrane proteins, polysaccharides and iron metabolism. Recent data from transcriptomics and proteomics studies performed for major pathogens were included. Current knowledge on how Hfq protein impacts pathogenicity of bacterial pathogensis also summarized and correlated. Click on title to learn more.


Photo details: Hfq protein with a bound sRNA., Bob Plaag, Public Domain, https://en.wikipedia.org/wiki/Hfq_protein

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New Mechanisms of Flucytosine Resistance in C . glabrata Unveiled by a Chemogenomics Analysis in S . cerevisiae

New Mechanisms of Flucytosine Resistance in  C .  glabrata  Unveiled by a Chemogenomics Analysis in  S .  cerevisiae | iBB | Scoop.it

5-Flucytosine is currently used as an antifungal drug in combination therapy, but fungal pathogens are rapidly able to develop resistance against this drug, compromising its therapeutic action. The understanding of the underlying resistance mechanisms is crucial to deal with this problem. In a recent paper published in PLoS ONe by BSRG-iBB researchers, the S. cerevisiae knockout collection was screened for increased resistance to flucytosine. Base on this chemogenomics analysis, further studies were conducted in the pathogenic yeast Candida glabrata, leading to the discovery of new mechanisms of 5-flucytosine resistance, including cell wall remodeling and decreased drug accumulation mediated by the action of the aquaglyceroporins CgFps1 and CgFps2.

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Miniaturized Aqueous Two Phase Extraction of Recombinant HIV-like Particles from Cell Supernatants

Miniaturized Aqueous Two Phase Extraction of Recombinant HIV-like Particles from Cell Supernatants | iBB | Scoop.it
Virus-like particles (VLPs) are promising candidates for a new generation of biopharmaceuticals. In a recent publication in the Journal Separation and Purification Technology, BERG researchers led by Raquel Aires-Barros and working in collaboration with INESC-MN and the company Icosagen (Estonia) describe a microfluidic system for the recovery of  HIV-like particles from cell supernatants by aqueous two phase extraction. The system features 100 width × 20 μm wide microchannels and continuous pumping of the two immiscible phases. The results obtained show that it is possible to carry out extraction under miniaturized conditions. This opens up the possibility for the set up of a highthroughput microfluidic platform for the screening of optimal extraction conditions for the recovery of biologicals. 
Click on title to learn more.
Photo details: SEM micrograph of HIV particles infecting a human H9 T cell. NIAID 2009, PD, Wikimedia commons.
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Minimum Information About a Biosynthetic Gene Cluster (MIBiG)

Minimum Information About a Biosynthetic Gene Cluster (MIBiG) | iBB | Scoop.it

A wide variety of enzymatic pathways producing specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is dispersed throughout the literature, making it difficult to exploit. To facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters, in a recent publication in Nature Chemical Biology, an international consortium of researchers, including Leonilde M. Moreira from BSRG-iBB, proposed the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard (http://mibig.secondarymetabolites.org/). MIBiG will empower next-generation research on the biosynthesis, chemistry and ecology of broad classes of societally relevant bioactive secondary metabolites, guided by robust experimental evidence and rich metadata components. Click on title to learn more.

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Catching Breath: Monitoring Air Pollution Exposure Using Exhaled Breath Condensate

Catching Breath: Monitoring Air Pollution Exposure Using Exhaled Breath Condensate | iBB | Scoop.it

In a recent publication in the International Journal of Environmental Health Research, Teresa Pinheiro from BSRG-iBB together with researchers from C2TN/IST and from Hospital de Santa Maria in Lisbon, examined the capability of exhaled breath condensate (EBC) to provide biomarkers of exposure for the human respiratory system. Entirely non-invasive, this new method is easy to perform allowing for sampling from children and adults alike. In the reported study, three groups of workers exposed to different levels of fumes and particulate matter containing lead and other metals in their work environment were repeatedly assessed through time while performing their working activities.

EBC proved to be useful for occupational exposure assessment. In addition EBC may help estimating intake by inhalation and predicting temporal limits of exposure. Click on tilte to learn more.

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A SWOT Analysis of Aqueous Two-Phase Separation

A SWOT Analysis of Aqueous Two-Phase Separation | iBB | Scoop.it

For half a century aqueous two-phase systems (ATPSs) have been applied for the extraction and purification of biomolecules. In spite of their simplicity, selectivity, and relatively low cost they have not been significantly employed for industrial scale bioprocessing. Recently their ability to be readily scaled and interface easily in single-use, flexible biomanufacturing has led to industrial re-evaluation of ATPSs. Researchers of the Bioseparation Engineering Laboratory at BERG-iBB together with Dr. James V. Alstine, a former principal scientist at GE Healthcare recently published a review in the Biotechnology Journal providing a new perspective over aqueous two-phase separations focusing on the strengths, weaknesses, opportunities and threats to this separation technique with an industrial perspective.

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Production of Platelets and Their Progenitors From Umbilical Cord Blood

Production of  Platelets and Their Progenitors From Umbilical Cord Blood | iBB | Scoop.it

Platelet transfusion can be a life-saving procedure in different medical settings, but shelf-life of this plod product is only 5 days. The efficient ex vivobiomanufacturing of platelets would make it possible toovercome the shortages of donated platelets. The optimized protocol described by BERG researchers in a recent paper published in the journal Cythotherapy allows the efficient production of platelets and their progenitors from blood stem/progenitor cells by mimicking the bone marrow niche through a co-culture system with human mesenchymal stromal cells (MSC), in combination with different biological factors to prompt differentiation toward functional platelets. Click on title to learn more.


Photo details: SEM image from blood shwoing small disc-shaped platelets among other red and white blood cells. Bruce Wetzel, NCI, 1982, public domain. 

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Burkholderia Contaminans at a Cystic Fibrosis Center

Burkholderia Contaminans at a Cystic Fibrosis Center | iBB | Scoop.it

The taxonomy of Burkholderia cepacia complex (Bcc) has recently evolved significantly. The novel species B. contaminans and B. lata were proposed for a divergent group of bacteria formerly classified as B.cepacia recA K. In a recent publication in the Journal of Medical Microbiology, Carla Coutinho and Isabel Sá-Correia from BSRG-iBB, together with researchers from Hospital de Santa Maria (HSM) in Lisbon, have re-examined the taxonomic position, at the species level, of several isolates previously classified as B. cepacia recA K from a Bcc collection and also extended the identification to other isolates retrieved from CF patients under surveillance at the major Portuguese CF Center at HSM. During 15 years of epidemiological surveillance of respiratory infections involving Bcc in this Portuguese CF Center, B. contaminans was found to be involved in chronic and transient infections or to have been eradicated. The clinical outcome of the infected patients under study provided new information on the clinical impact of the rarely found B. contaminans species in CF respiratory infections. Click on tile to learn more.

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Neural Commitment of Human Pluripotent Stem Cells Under Defined Conditions Recapitulates Neural Development and Generates Patient-specific Neural Cells

Neural Commitment of Human Pluripotent Stem Cells Under Defined Conditions Recapitulates Neural Development and Generates Patient-specific Neural Cells | iBB | Scoop.it

In a recent publication in Biotechnology Journal researchers from the Stem Cell Bioengineering and Regenerative Medicine Laboratory (SCBL) at BERG-iBB describe a novel methodology capable of providing patient-specific neural cells under defined conditions using vitronectin and dual SMAD inhibition. The authors show how pluripotent stem cells can be used to generate patient-specific neural cells that could be used to gain a better understanding of disease mechanisms. This ability to recapitulate the development of the human nervous system in vitro could provide important insights on the mechanisms involved in the maturation of specific neural cell types, making this approach transversal to other related areas in neurodevelopmental research.

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Bacterial Lipids for Biodiesel Blends

Bacterial Lipids for Biodiesel Blends | iBB | Scoop.it

The quest for renewable fuels from sustainable and ecologically friendly processes has identified biodiesel as a promising candidate. Carla de Carvalho and Maria  Cortes of BERG-iBB recently showed that bacterial cells of Rhodococcus erythropolis DCL14 and R. opacus PWD4 can accumulate triacylglycerols, the most relevant lipids for biodiesel production, and other lipids which contain fatty acids that may be esterified. Appropriate growth conditions, such as N and P limitation, increased lipid accumulation in the cells. The cetane numbers of the fatty acid blends produced, which measure the quality of diesel fuels and biodiesel, are in accordance to biodiesel standards.

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Control of Aggregation Directs Human Pluripotent Stem Cells Towards Neural Commitment

Control of Aggregation Directs Human Pluripotent Stem Cells Towards Neural Commitment | iBB | Scoop.it

3D suspension culture is generally considered a promising method to achieve efficient expansion and controlled differentiation of human pluripotent stem cells (hPSCs). In a recent publication in Biotechnology Journal,  researchers from the Stem Cell Bioengineering and Regenerative Medicine Laboratory (SCBL) at BERG-iBB led by Margarida Diogo describe the development of an integrated culture platform for expansion and neural commitment of hPSCs into neural precursors using 3D suspension conditions and chemically-defined culture media. The results obtained in the study constitute an important contribution to the definition of a robust method for production of hPSC-derived neural precursors that minimizes processing steps and has high potential for scale-up.

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New Review on Yeast Toxicogenomics

New Review on Yeast Toxicogenomics | iBB | Scoop.it

The 2015 edition of the special issue Environmental Biotechnology published by Current Opinion in Biotechnology features a review on the field of yeast toxicogenomics, focusing on the role of this organism both as a cell model and as a cell factory. Toxicogenomics has emerged in the past decade as a transdisciplinary area that merges genome-wide methodologies with traditional toxicology studies to provide an integrated assessment of the cellular response to different toxicants at multiple levels. The invitation to write this review was made on the basis of the longstanding contribution of the Biological Sciences Research Group-iBB and its PI Isabel Sá-Correia to this field.
The still highly relevant role of yeast as a model organism is highlighted in this review, supported by the pioneering exploitation of multiple Omics approaches (genomics, proteomics, metabolomics, transcriptomics, lipidomics...) and synthetic biology, in fields ranging from the pharmaceutical industry to food preservation processes and identification of toxicological outcomes of exposure to environmental toxicants and agrochemicals. The review also describes the most recent advances in the production of next-generation biofuels based on renewable feedstocks such as lignocellulosic hydrolysates. Yeast is a cell factory of choice in biorefineries, where genomic and metabolic engineering are greatly contributing to develop more cost-efficient bioprocess conditions and more robust engineered strains. Click on the title to learn more.

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Membrane Proteome-wide Response to the Antifungal Drug Clotrimazole in Candida glabrata

Membrane Proteome-wide Response to the Antifungal Drug Clotrimazole in Candida glabrata | iBB | Scoop.it

Candida glabrata is the second most common cause of candidemia worldwide and presents high levels of intrinsic azole resistance, thus being an interesting subject for the study of azole resistance mechanisms in fungal pathogens. In a recent paper, published by BSRG-iBB researchers in the Molecular and Cellular Proteomics journal, an iTRAQ-based membrane proteomics analysis was performed to identify all the membrane-associated proteins whose abundance changes in C. glabrata cells exposed to the azole drug clotrimazole. Based on this analysis, two new multidrug transporters, CgTpo1_1 and CgTpo1_2, were characterized as azole drug resistance determinants. Additionally, this study highlighted the existence of unforeseen targets of the transcription factor CgPdr1, recognized as a major regulator of azole drug resistance in clinical isolates. Click on title to learn more.


Image details: Ball-and-stick model of the clotrimazole molecule. PD, Wikimedia commons.

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Intracoronary Delivery of Human Mesenchymal/Stromal Stem Cells

Intracoronary Delivery of Human Mesenchymal/Stromal Stem Cells | iBB | Scoop.it

Mesenchymal stem/stromal cells have unique properties favorable to their use in clinical practice and have been studied for cardiac repair. However, these cells are larger than coronary microvessels and there is controversy about the risk of embolization and microinfarctions, which could jeopardize the safety and efficacy of intracoronary route for their delivery. The index of microcirculatory resistance (IMR) is an invasive method for quantitatively assessing the coronary microcirculation status. In a recent publication in PlosOne, BERG-iBB researchers in collaboration with colleagues from the Department of Cardiology at Hospital de Santa Marta and from the Faculty of Veterinary Medicine at University of Lisbon have examined heart microcirculation in a swine model after intracoronary injection of mesenchymal stem/stromal cells with the index of microcirculatory resistance. Overall, the study provides definitive evidence of microcirculatory disruption upon intracoronary administration of mesenchymal stem/stromal cells, in a large animal model closely resembling human cardiac physiology, function and anatomy.

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Advanced Qualification of Pharmaceutical Excipient Suppliers

Advanced Qualification of Pharmaceutical Excipient Suppliers | iBB | Scoop.it

Pharmaceutical excipients have different functions within a drug formulation and can influence the manufacturability and/or performance of medicinal products.  Sometimes it may be necessary to qualify a second supplier, but its product will not be completely equal to the first supplier product. In a recent study co-authored by José Cardoso Menezes from BERG-iBB, Multivariate Analysis is used to extract relevant information  from Raman spectroscopy, laser diffraction and Xray powder diffraction analysis of calcium hydrogen phosphate from two suppliers. The two lots of CaHPO4 could be discriminated by their supplier and the  gained knowledge made it possible to specify an enhanced strategy for second supplier qualification. Click on title to learn more. 

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Phenotypic Characterisation of An International Pseudomonas aeruginosa Reference Panel

Phenotypic Characterisation of An International Pseudomonas aeruginosa Reference Panel | iBB | Scoop.it

Pseudomonas aeruginosa causes chronic lung infections in people with cystic fibrosis (CF) and acute opportunistic infections in people without CF. In a recently published article, an international consortium of researchers, members of the EU COST Action BM1003: Microbial cell surface determinants of virulence as targets for new therapeutics in cystic fibrosis, including Isabel Sá-Correia from BSRG-iBB and the students of the IST PhD programme in Biotechnology and Biosciences, Rita F. Maldonado, Ana S. Moreira, collated forty two P. aeruginosa strains from a range of clinical and environmental sources into a single reference strain panel to harmonise research on this diverse opportunistic pathogen .The panel strains were characterized for growth rates, motility, virulence in the Galleria mellonella infection model, pyocyanin and alginate production, mucoid phenotype, lipopolysaccharide (LPS) pattern, biofilm formation, urease activity, antimicrobial and phage susceptibilities. Overall, the full phenotypic characterization of the defined panel of P. aeruginosa strains increased the current  understanding of the virulence and pathogenesis of P. aeruginosa and may provide a valuable resource for the testing of novel therapies against this problematic pathogen. Click on title to learn more.


Photo details: SEM of Pseudomonas aeruginosa. CDC/ Janice Haney Carr, Public domain. 

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Biomarkers of Metal Pollution Vulnerability

Biomarkers of Metal Pollution Vulnerability | iBB | Scoop.it

The metal imbalance in fish caused by water pollution is thought to play a critical role in neurodegeneration and neuronal dysfunctions. In a recent publication in Metallomics, Teresa Pinheiro from BSRG-iBB, together with researchers from IPMA, CESAM and CIMAR have examined the elemental distributions in brains of wild Liza aurata a teleost fish captured in polluted and reference coastal systems in the vicinity of Lisbon. This study evaluates major and trace elemental contents, essential and toxic, and their compartmentalization in optic lobe structures providing insights into species physiological requirements and vulnerability to metal toxicity. This is the first multi-elemental mapping of neuronal tissue of teleost fish.

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Environmental Tenacity of Mycobacteria

Environmental Tenacity of Mycobacteria | iBB | Scoop.it

Mycobacteria are associated to several diseases, including tuberculosis, but little is known about their behavior in natural ecosystems. In an international study involving Ricardo Santos from Laboratório de Análises, Carla C.C.R. de Carvalho from iBB-BERG and researchers from the Queen’s University Belfast, it was showed that mycobacteria have solute tolerances close to those of eukaryotes. The Mycobacterium strains isolated from Yellowstone and Glacier National Parks (USA), grew at a temperature range of >60ºC, in super-saturated concentrations of hydrophobic stressors and under osmotic stress and chaotropic activity. The study demonstrates that certain mycobacteria strains are as resilient to key solute induced stresses as some of the most stress-tolerant microbes known to science. Click on title to learn more. 

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Purification Technologies for Monoclonal Antibodies

Purification Technologies for Monoclonal Antibodies | iBB | Scoop.it

The commercial potential of monoclonal antibodies (mAbs) has been continuously increasing during the last years alongside with the number of approved mAb-based drugs and clinical trials. Despite their effectiveness and safety, the general access to this class of biopharmaceuticals is barred by high selling prices. Downstream processing is now considered the bottleneck in the manufacturing of mAbs. Therefore, the design of novel and economic operations and their implementation in the current technology platforms constitutes a pressing need. A recent review published by researchers from the Bioseparation Engineering Laboratory at BERG-iBB, provides an insight into the current state-of-the-art in mAbs purification, focusing on multimodal chromatography as one of the viable options to upgrade the established purification train. Multimodal chromatography has been receiving considerable attention over the last years, with about 152 publications published in ISI-index journals in the last decade (2004-2013). The number of publications per year has been steadily increasing, with a paper-boom starting in 2008.

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A Microcarrier-based Stirred Culture System for the Scalable expansion of Human Mesenchymal Stem/Stromal Cells

A Microcarrier-based Stirred Culture System for the Scalable expansion of Human Mesenchymal Stem/Stromal Cells | iBB | Scoop.it

The therapeutic use of human mesenchymal stem/stromal cells (MSC) for a wide range of diseases is at the front line of stem cell-based cellular therapies. Through a bioprocess engineering approach, researchers at BERG-iBB led by Cláudia Lobato Silva and Joaquim Cabral, were able to maximize the production of MSC from different human sources – bone marrow and adipose tissue - in a microcarrier-based stirred culture system. The advances, reported in a recent paper on Biotechnology Journal, clearly improve the scalability and cost-effectiveness of MSC manufacturing, while facilitating the translation to a Good Manufacturing Practices (GMP)-compliant bioprocess.


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Assessing the Potential of Aerobic Granular Sludge for Industrial Wastewater Treatment

Assessing the Potential of Aerobic Granular Sludge for Industrial Wastewater Treatment | iBB | Scoop.it

Aerobic granular sludge (AGS) is a compact and energy-saving biotechnology pointed as the next generation of wastewater treatment. In a recent publication, BERG-iBB and BSRG-iBB researchers led by Nídia Lourenço compare the performance of AGS with conventional activated sludge in the treatment of textile industry wastewater. High efficiencies were attained in both systems, with AGS providing higher yields and excellent biomass settling properties. Yeast-based toxicity assays also highlighted the better wastewater detoxification performance of AGS, supporting its potential application for industrial wastewater treatment as an effective alternative to the conventional technology based on floc-forming bacteria.

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Bioprocess Intensification Through Enzymatic Microreactors

Bioprocess Intensification Through Enzymatic Microreactors | iBB | Scoop.it

Microreactors have been gaining increased relevance as preferred process intensification tools. Microreactors present several advantages over conventional batch reactors, namely mass and heat transfer, high surface to volume ratios, minute consumption of chemicals, ease of automation and better process control. Within the scope of this exciting area of research, Pedro Fernandes and Filipe Carvalho from BERG-iBB recently designed, assembled and run a low-cost continuous flow enzyme microreactor, allowing for detailed characterization of biocatalytic systems with immobilized enzymes in particulate form. Moreover, the microreactor enabled continuous enzymatic sucrose hydrolysis for 1 month, with sustained substrate conversion of roughly 100%.

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Heparin as a Capture Step in the Purification of Monoclonal Antibodies

Heparin as a Capture Step in the Purification of Monoclonal Antibodies | iBB | Scoop.it

Heparin is a naturally occurring sulfonated glycosaminoglycan, characterized by a high density and distribution of negative charges that is widely used as an injectable anticoagulant. In a recent pubication, BERG-iBB researchers led by Ana Azevedo explore the strong cation exchanger potential of an heparin resin, namely its  ability to capture a basic mAb from CHO cell culture supernatants. The performance of the proposed capture step was estimated in terms of yield, protein purity and purification factor, and compared to the traditional protein A affinity chromatography.

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Krishan Maggon 's curator insight, May 30, 2015 9:38 AM
Biochemical Engineering Journal

Available online 14 May 2015

In Press, Corrected Proof — Note to users

 Exploring the use of heparin as a first capture step in the purification of monoclonal antibodies from cell culture supernatantsInês F. Pinto, Sara A.S.L. Rosa, M. Raquel Aires-Barros, Ana M. Azevedo,  doi:10.1016/j.bej.2015.05.011