Yeast biotechnology. For thousands of years, yeasts have been used for the making of bread and the production of fermented alcoholic drinks, such as wine and beer. Saccharomyces cerevisiae (bakers' and brewers' yeast) is the yeast species... more
Yeast biotechnology. For thousands of years, yeasts have been used for the making of bread and the production of fermented alcoholic drinks, such as wine and beer. Saccharomyces cerevisiae (bakers' and brewers' yeast) is the yeast species that is surely the most exploited by man. Nowadays, Saccharomyces is a cornerstone of modern biotechnology and also a top choice organism for industrial production of fuels, chemicals, and pharmaceuticals. Today, more and more different yeast species are explored for industrial applications. This Special Issue " Yeast Biotechnology 2.0 " is a continuation of the first issue " Yeast Biotechnology " (https://www.mdpi.com/books/pdfview/book/324). Yeast synthetic biology and strain engineering. Recently, important progress has been made in unlocking the key elements in the biochemical pathways involved in the synthesis of aroma compounds, as well as in methods to engineer these pathways. Recent advances in bioengineering of yeasts—including S. cerevisiae—to produce aroma compounds and bioflavors are reviewed in Reference [1]. This review presents yeast as a significant producer of bioflavors in a fresh context and proposes new directions for combining engineering and biology principles to improve the yield of targeted aroma compounds. In a proof-of-concept study, Yarrowia lipolytica was used as a whole cell factory for the de novo production of long chain dicarboxylic acid (LCDA-16 an-18) using glycerol as the sole carbon source [2]. The results provide basis for developing Y. lipolytica as a safe biorefinery platform for sustainable production of high-value LCDCAs from non-oily feedstock. It was demonstrated that a mutant strain of Y. lipolytica can be used to produce citric acid from renewable carbon sources such as rapeseed oil, glycerol, and glycerol-containing waste of the biodiesel industry and glucose-containing aspen waste [3]. The cost-effective production of cellulosic ethanol requires robust microorganisms for rapid co-fermentation of glucose and xylose. Therefore, a recombinant diploid xylose-fermenting S. cerevisiae strain was developed by integrating Piromyces sp. E2 xylose isomerase (PirXylA) and Orpinomyces sp. ukk1 xylose (OrpXylA) in the genome in multiple copies [4]. The development of a counter-selection method for phenyl auxotrophy could be a useful tool in the repertoire of yeast genetics. A fluorinated precursor, i.e., 4-fluorophenylpyruvate (FPP), was found to be toxic to several strains from Saccharomyces and Candida genera [5]. The results show that FPP could effectively be used for counter-selection, but not for enhanced phenylethanol production. New developments in efficient biomolecule production. In recent years, interest in the industrial production of yeast β-glucan has increased since it is an immunostimulant molecule for human and animal health. The β-glucan yield was optimised during anaerobic fermentation by evaluating the effect of the carbon source (glucose) and NaCl osmotic stress [6]. A yeast isolate, selected for its lipolytic activity from a meat product, was characterized as Pichia anomala [7]. Submerged fermentation optimization resulted in a significantly increased production of an extracellular lipolytic enzyme.
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The cytoskeleton is a highly dynamical protein network that plays a central role in numerous cellular physiological processes, and is traditionally divided into three components according to its chemical composition, i.e. actin, tubulin... more
The cytoskeleton is a highly dynamical protein network that plays a central role in numerous cellular physiological processes, and is traditionally divided into three components according to its chemical composition, i.e. actin, tubulin and intermediate filament cytoskeletons. Understanding the cytoskeleton dynamics is of prime importance to unveil mechanisms involved in cell adaptation to any stress type. Fluorescence imaging of cytoskeleton structures allows analyzing the impact of mechanical stimulation in the cytoskeleton, but it also imposes additional challenges in the image processing stage, such as the presence of imaging-related artifacts and heavy blurring introduced by (high-throughput) automated scans. However, although there exists a considerable number of image-based analytical tools to address the image processing and analysis, most of them are unfit to cope with the aforementioned challenges. Filamentous structures in images can be considered as a piecewise composition of quasi-straight segments (at least in some finer or coarser scale). Based on this observation, we propose a three-steps actin filaments extraction methodology: (i) first the input image is decomposed into a 'cartoon' part corresponding to the filament structures in the image, and a noise/texture part, (ii) on the 'cartoon' image, we apply a multi-scale line detector coupled with a (iii) quasi-straight filaments merging algorithm for fiber extraction. The proposed robust actin filaments image analysis framework allows extracting individual filaments in the presence of noise, artifacts and heavy blurring. Moreover , it provides numerous parameters such as filaments orientation, position and length, useful for further analysis. Cell image decomposition is relatively under-exploited in biological images processing, and our study shows the benefits it provides when addressing such tasks. Experimental validation was conducted using publicly available datasets, and in oste-oblasts grown in two different conditions: static (control) and fluid shear stress. The proposed methodology exhibited higher sensitivity values and similar accuracy compared to state-of-the-art methods.
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The first step in the infection of humans by microbial pathogens is their adherence to host tissue cells, which is frequently based on the binding of carbohydrate-binding proteins (lectin-like adhesins) to human cell receptors that expose... more
The first step in the infection of humans by microbial pathogens is their adherence to host tissue cells, which is frequently based on the binding of carbohydrate-binding proteins (lectin-like adhesins) to human cell receptors that expose gly-cans. In only a few cases have the human receptors of pathogenic adhesins been described. A novel strategy— based on the construction of a lectin-glycan interaction (LGI) network—to identify the potential human binding receptors for pathogenic adhesins with lectin activity was developed. The new approach is based on linking glycan array screening results of these ad-hesins to a human glycoprotein database via the construction of an LGI network. This strategy was used to detect human receptors for virulent Escherichia coli (FimH adhesin), and the fungal pathogens Candida albicans (Als1p and Als3p adhesins) and C. glabrata (Epa1, Epa6, and Epa7 adhesins), which cause candidiasis. This LGI network strategy allows the profiling of potential adhesin binding receptors in the host with prioritization, based on experimental binding data, of the most relevant interactions. New potential targets for the selected adhesins were predicted and experimentally confirmed. This methodology was also used to predict lectin interactions with envelope glycoproteins of human-pathogenic viruses. It was shown that this strategy was successful in revealing that the FimH adhesin has anti-HIV activity. IMPORTANCE Microbial pathogens may express a wide range of carbohydrate-specific adhesion proteins that mediate adherence to host tissues. Pathogen attachment to host cells is achieved through the binding of these lectin-like adhesins to glycans on human glycoproteins. In only a few cases have the human receptors of pathogenic adhesins been described. We developed a new strategy to predict these interacting receptors. Therefore, we developed a novel LGI network that would allow the mapping of potential adhesin binding receptors in the host with prioritization, based on the experimental binding data, of the most relevant interactions. New potential targets for the selected adhesins (bacterial uroepithelial FimH from E. coli and fungal Epa and Als adhesins from C. glabrata and C. albicans) were predicted and experimentally confirmed. This methodology was also used to predict lectin interactions with human-pathogenic viruses and to discover whether FimH adhesin has anti-HIV activity.
Living cell microarrays have been combined with microfluidic bioreactors, which provide multiple advantages for multiplex dynamic analyses and high-throughput screening. In the last decade, many developments in this new field have been... more
Living cell microarrays have been combined with microfluidic bioreactors, which provide multiple advantages for multiplex dynamic analyses and high-throughput screening. In the last decade, many developments in this new field have been introduced. The technology has evolved from fixed cell analysis towards living single-cell dynamic systems' biology and high content analyses. The aim of this review is to provide an updated overview of the developments of living cellular microarrays in microfluidic bioreactors. Cell arrays in microfluidic bioreactors constructed with adherent mammalian cells are compared to non-adherent cells (mainly microbial cells). An overview is given on the design and construction of these microfluidic devices with a particular focus on cell patterning techniques. Cell patterning on adhesive micropatterns using techniques such as microcontact printing, microfluidic patterning, dip-pen nanolithography and polymer pen lithography as well as photo-patterning and laser-patterning strategies are discussed. Additionally, developments in mechanical cell patterning methods and robotic cell printing are reviewed. Two-dimensional (2D) as well as recently developed 3D cell arraying are discussed. Finally, cell array microfluidic setups and operation for single-cell types versus cell population variants are illustrated and compared on the basis of some illustrative examples in the field of drug screening, cytotoxicity evaluation, and basic cellular and microbiology research.
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RH Wijffels, RM Buitelaar, C. Bucke and J. Tramper (Eds) Immobilized Cells: Basics and Applications 1996 Elsevier Science BV All rights reserved. Modellin g th e immobilisation of cells in a packe d be d of porous carriers Ronnie... more
RH Wijffels, RM Buitelaar, C. Bucke and J. Tramper (Eds) Immobilized Cells: Basics and Applications 1996 Elsevier Science BV All rights reserved. Modellin g th e immobilisation of cells in a packe d be d of porous carriers Ronnie Willaert, Luc De Backer and Gino V. ...
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ABSTRACT Progress in pharmaceutical and biotechnological research relies on the availability of a variety of analytical measurement tools. In this paper we discuss the progress on our research in the field of a novel real-time label-free,... more
ABSTRACT Progress in pharmaceutical and biotechnological research relies on the availability of a variety of analytical measurement tools. In this paper we discuss the progress on our research in the field of a novel real-time label-free, and immobilization-free integrated sensor in silicon for monitoring biological substances in nano-liter liquids flowing through a capillary tube. The performance of various sensor generations is benchmarked with water-alcohol mixtures: we demonstrate an dynamic range increase from 15 to 60 dB. A selection of measurements on biological species dissolved in liquids is presented.
Immobilized yeast cells are being used in various bio-industries but also could be beneficially implemented in industries based on ethanol fermentation. For reasons including faster fermentation rates in comparison to traditional... more
Immobilized yeast cells are being used in various bio-industries but also could be beneficially implemented in industries based on ethanol fermentation. For reasons including faster fermentation rates in comparison to traditional processes, increased volumetric ...
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... Chapter 11 Bioprocess Intensification of Beer Fermentation Using Immobilised Cells Pieter J. Verbelen, Viktor A. Nedović, Verica Manojlović, Freddy R. Delvaux, Ida Laskošek-Čukalović, Branko Bugarski, and Ronnie Willaert ...
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Natural flavours and fragrances play nowadays an important role in the quality of food and beverages. Due to food-processing operations such as premature harvesting, extended storage and physical treatment, aromas may be lost and the... more
Natural flavours and fragrances play nowadays an important role in the quality of food and beverages. Due to food-processing operations such as premature harvesting, extended storage and physical treatment, aromas may be lost and the addition of flavour supplements to ...
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Gel immobilised living cell systems represent a special form of heterogeneous catalysis. Due to mass transfer limitations on substrate delivery and product removal, time-dependent spatial variations in growth rate and biomass densities... more
Gel immobilised living cell systems represent a special form of heterogeneous catalysis. Due to mass transfer limitations on substrate delivery and product removal, time-dependent spatial variations in growth rate and biomass densities are created. A dynamic ...
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The surface of a biomaterial interacts with the body fluid upon implantation in the human body. The biocompatibility of a material is strongly influenced by the adsorption of proteins onto the surface. Titanium is frequently used as a... more
The surface of a biomaterial interacts with the body fluid upon implantation in the human body. The biocompatibility of a material is strongly influenced by the adsorption of proteins onto the surface. Titanium is frequently used as a biomaterial for implants in orthopedics and cardiovascular devices. Understanding the biocompatibility is very important to improve implants. The surface chemistry of an implant material and its influence on the interaction with body fluid is crucial in that perspective. The main goal of this study was to investigate the conformation of human plasma fibrinogen (HPF) adsorbed on commercially pure titanium (CP Ti) on a molecular level by means of ex situ atomic force microscopy (AFM). With X-ray photoelectron spectroscopy combined with argon ion beam depth profiling, it was shown that the oxide layer present at the surface was mainly composed of TiO2, with a small percentage of Ti2O3. Ex situ AFM imaging showed the conformation of HPF on CP Ti. Single molecules and aggregates of fibrinogen were observed. The trinodular structure of single HPF molecules (two spherical D domains at the distal ends of the extended molecule and the central spherical E domain) adsorbed onto CP Ti was visualized. Aggregate formation through the connection of the D domains of the HPF molecules was observed on CP Ti. The alphaC domains of HPF were not visible on CP Ti. The ex situ AFM images indicated conformational changes of HPF upon adsorption onto CP Ti. The conformation of the adsorbed HPF molecules was different on mica and titanium. The difference in wettability between both substrates caused a larger spread of the protein on the CP Ti surface and thus resulted in a larger perturbation to the native structure of HPF as compared to mica.
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Research Interests: Engineering, Physics, Chemistry, Biology, Medicine, and 23 moreGene expression, Multidisciplinary, Antibiotic Resistance, Quorum Sensing, Genome Analysis, Quinolones, Phenotype, PLoS one, Pseudomonas aeruginosa, Anti-Bacterial Agents, Reproducibility of Results, Microbial Sensitivity Tests, Genetic variation, Proteome analysis, Efflux Pumps, Pseudomonas Aeruginosa, Proteome, Expression analysis, Environmental, Nucleotides, Gene expression profiling, Down-Regulation, and Gentamicins
Abstract The crystallisation by counterdiffusion is a very efficient technique for obtaining high-quality protein crystals. A prerequisite for the use of counterdiffusion techniques is that mass transport must be controlled by diffusion... more
Abstract The crystallisation by counterdiffusion is a very efficient technique for obtaining high-quality protein crystals. A prerequisite for the use of counterdiffusion techniques is that mass transport must be controlled by diffusion alone. Sedimentation and convection can be ...
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Flo1p and Lg-Flo1p are two cell-wall adhesins belonging to the Flo (flocculation) protein family from the yeasts Saccharomyces cerevisiae and S. pastorianus. The main function of these modular proteins endowed with calcium-dependent... more
Flo1p and Lg-Flo1p are two cell-wall adhesins belonging to the Flo (flocculation) protein family from the yeasts Saccharomyces cerevisiae and S. pastorianus. The main function of these modular proteins endowed with calcium-dependent lectin activity is to mediate cell-cell adhesion events during yeast flocculation, a process which is well known at the cellular level but still not fully characterized from a molecular perspective. Recently, structural features of the N-terminal Flo lectin domains, including the N-terminal domain of Lg-Flo1p (N-Lg-Flo1p), and their interactions with carbohydrate molecules have been investigated. However, structural data concerning the N-terminal domain of Flo1p (N-Flo1p), which is the most specific among the Flo proteins, are missing and information about the N-Lg-Flo1p-carbohydrate interaction still lacks detailed structural insight. Here, the crystallization and preliminary X-ray characterization of the apo form and the mannose complex of N-Flo1p and X-ray analysis of N-Lg-Flo1p crystals soaked in α-1,2-mannobiose are reported. The N-Flo1p crystals diffracted to a resolution of 1.43 Å in the case of the apo form and to 2.12 Å resolution for the mannose complex. Both crystals were orthorhombic and belonged to space group P212121, with one molecule in the asymmetric unit. The N-Lg-Flo1p-α-1,2-mannobiose complex crystal diffracted to 1.73 Å resolution and belonged to the monoclinic space group P1211 with two molecules in the asymmetric unit.