Browsing by Subject "220 Industrial biotechnology"

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  • Barmaki, Samineh; Jokinen, Ville; Obermaier, Daniela; Blokhina, Daria; Korhonen, Matti; Ras, Robin H. A.; Vuola, Jyrki; Franssila, Sami; Kankuri, Esko (2018)
    Physiological oxygen levels within the tissue microenvironment are usually lower than 14%, in stem cell niches these levels can be as low as 0-1%. In cell cultures, such low oxygen levels are usually mimicked by altering the global culture environment either by O-2 removal (vacuum or oxygen absorption) or by N-2 supplementation for O-2 replacement. To generate a targeted cellular hypoxic microenvironment under ambient atmospheric conditions, we characterised the ability of the dissolved oxygen-depleting sodium sulfite to generate an in-liquid oxygen sink. We utilised a microfluidic design to place the cultured cells in the vertical oxygen gradient and to physically separate the cells from the liquid. We demonstrate generation of a chemical in-liquid oxygen sink that modifies the surrounding O-2 concentrations. O-2 level control in the sink-generated hypoxia gradient is achievable by varying the thickness of the polydimethylsiloxane membrane. We show that intracellular hypoxia and hypoxia response element-dependent signalling is instigated in cells exposed to the microfluidic in-liquid O-2 sink-generated hypoxia gradient. Moreover, we show that microfluidic flow controls site-specific microenvironmental kinetics of the chemical O-2 sink reaction, which enables generation of intermittent hypoxia/re-oxygenation cycles. The microfluidic O-2 sink chip targets hypoxia to the cell culture microenvironment exposed to the microfluidic channel architecture solely by depleting O-2 while other sites in the same culture well remain unaffected. Thus, responses of both hypoxic and bystander cells can be characterised. Moreover, control of microfluidic flow enables generation of intermittent hypoxia or hypoxia/re-oxygenation cycles. (C) 2018 Published by Elsevier Ltd on behalf of Acta Materialia Inc.
  • Sodupe-Ortega, Enrique; Sanz-Garcia, Andres; Pernia-Espinoza, Alpha; Escobedo-Lucea, Carmen (2018)
    Most of the studies in three-dimensional (3D) bioprinting have been traditionally based on printing a single bioink. Addressing the complexity of organ and tissue engineering, however, will require combining multiple building and sacrificial biomaterials and several cells types in a single biofabrication session. This is a significant challenge, and, to tackle that, we must focus on the complex relationships between the printing parameters and the print resolution. In this paper, we study the influence of the main parameters driven multi-material 3D bioprinting and we present a method to calibrate these systems and control the print resolution accurately. Firstly, poloxamer hydrogels were extruded using a desktop 3D printer modified to incorporate four microextrusion-based bioprinting (MEBB) printheads. The printed hydrogels provided us the particular range of printing parameters (mainly printing pressure, deposition speed, and nozzle z-offset) to assure the correct calibration of the multi-material 3D bioprinter. Using the printheads, we demonstrated the excellent performance of the calibrated system extruding different fluorescent bioinks. Representative multi-material structures were printed in both poloxamer and cell-laden gelatin-alginate bioinks in a single session corroborating the capabilities of our system and the calibration method. Cell viability was not significantly affected by any of the changes proposed. We conclude that our proposal has enormous potential to help with advancing in the creation of complex 3D constructs and vascular networks for tissue engineering.
  • Helfenstein, Andreas; Tammela, Päivi (2017)
    Motivation: Ethnopharmacology, or the scientific validation of traditional medicine, is a respected starting point in drug discovery. Home remedies and traditional use of plants are still widespread, also in Western societies. Instead of perusing ancient pharmacopeias, we developed MedCrawler, which we used to analyze blog posts for mentions of home remedies and their applications. This method is free and accessible from the office computer. Results: We developed MedCrawler, a data mining tool for analyzing user-generated blog posts aiming to find modern 'traditional' medicine or home remedies. It searches user-generated blog posts and analyzes them for correlations between medically relevant terms. We also present examples and show that this method is capable of delivering both scientifically validated uses as well as not so well documented applications, which might serve as a starting point for follow-up research.
  • Perri, Giuseppe; Rizzello, Carlo Giuseppe; Ampollini, Marco; Celano, Giuseppe; Coda, Rossana; Gobbetti, Marco; De Angelis, Maria; Calasso, Maria (2021)
    A comprehensive study into the potential of bioprocessing techniques (sprouting and sourdough fermentation) for improving the technological and nutritional properties of wheat breads produced using barley and lentil grains was undertaken. Dextran biosynthesis in situ during fermentation of native or sprouted barley flour (B or SB) alone or by mixing SB flour with native or sprouted lentil flour (SB-L or SB-SL) by Weissella paramesenteroides SLA5, Weissella confusa SLA4, Leuconostoc pseudomesenteroides DSM 20193 or Weissella confusa DSM 20194 was assessed. The acidification and the viscosity increase during 24 h of fermentation with and without 16% sucrose (on flour weight), to promote the dextran synthesis, were followed. After the selection of the fermentation parameters, the bioprocessing was carried out by using Leuconostoc pseudomesenteroides DSM 20193 (the best LAB dextran producer, up to 2.7% of flour weight) and a mixture of SB-SL (30:70% w/w) grains, enabling also the decrease in the raffinose family oligosaccharides. Then, the SB-SL sourdoughs containing dextran or control were mixed with the wheat flour (30% of the final dough) and leavened with baker’s yeast before baking. The use of dextran-containing sourdough allowed the production of bread with structural improvements, compared to the control sourdough bread. Compared to a baker’s yeast bread, it also markedly reduced the predicted glycemic index, increased the soluble (1.26% of dry matter) and total fibers (3.76% of dry matter) content, giving peculiar and appreciable sensory attributes.
  • Kinaret, Pia Anneli Sofia; Scala, Giovanni; Federico, Antonio; Sund, Jukka; Greco, Dario (2020)
    Toxic effects of certain carbon nanomaterials (CNM) have been observed in several exposure scenarios both in vivo and in vitro. However, most of the data currently available has been generated in a high-dose/acute exposure setup, limiting the understanding of their immunomodulatory mechanisms. Here, macrophage-like THP-1 cells, exposed to ten different CNM for 48 h in low-cytotoxic concentration of 10 mu g mL(-1), are characterized by secretion of different cytokines and global transcriptional changes. Subsequently, the relationships between cytokine secretion and transcriptional patterns are modeled, highlighting specific pathways related to alternative macrophage activation. Finally, time- and dose-dependent activation of transcription and secretion of M1 marker genes IL-1 beta and tumor necrosis factor, and M2 marker genes IL-10 and CSF1 is confirmed among the three most responsive CNM, with concentrations of 5, 10, and 20 mu g mL(-1) at 24, 48, and 72 h of exposure. These results underline CNM effects on the formation of cell microenvironment and gene expression leading to specific patterns of macrophage polarization. Taken together, these findings imply that, instead of a high and toxic CNM dose, a sub-lethal dose in controlled exposure setup can be utilized to alter the cell microenvironment and program antigen presenting cells, with fascinating implications for novel therapeutic strategies.
  • Wang, Yaqin; Maina, Ndegwa Henry; Coda, Rossana; Katina, Kati (2021)
    Background: The use of grains as an alternative to wheat in breadmaking has rapidly grown in the last few years, driven by the Sustainable Development Goals toward improving food security and promoting sustainable agriculture. Flours from legumes, pseudo-cereals, minor cereals and milling by-products, such as bran, are of particular interest. The production of partially substituted or wheat-free bread is, however, a challenging task in terms of texture and flavour attributes. Scope and approach: The present review covers recent advances in the application of dextrans in improving dough rheology, baking performance and bread flavour characteristics. Emphasis has been given to in situ application of dextran via sourdough technology as a & lsquo;clean label & rsquo; alternative to commercial hydrocolloid additives. Key findings and conclusions: In-situ dextran production leads to bread with higher specific volume, softer crumbs and increased moisture content. Dextran also provides an anti-staling effect attributable to its ability to reduce water mobility and retard starch retrogradation. A structure & ndash;function relationship has suggested that dextran with high molecular weight and less branching is superior in enhancing bread quality. Furthermore, mild acidification favours the functionality of dextran in dough and bread systems, while intensive acidification results in adverse effects. Lactic acid bacterial strains belonging to the genus Weissella exhibiting mild acidification are therefore appreciated in regard to the utilisation of in-situ produced dextran. This review highlights the novel application of dextran as a flavour masking agent to minimise off-flavours (e.g. beany flavour, bitter taste, and aftertaste) originating from non-wheat grains, consequently improving the acceptability of the final products.
  • Lubbers, Ronnie J. M.; Dilokpimol, Adiphol; Navarro, Jorge; Peng, Mao; Wang, Mei; Lipzen, Anna; Ng, Vivian; Grigoriev, Igor V.; Visser, Jaap; Hildén, Kristiina S.; de Vries, Ronald P. (2019)
    Cinnamic acid is an aromatic compound commonly found in plants and functions as a central intermediate in lignin synthesis. Filamentous fungi are able to degrade cinnamic acid through multiple metabolic pathways. One of the best studied pathways is the non-oxidative decarboxylation of cinnamic acid to styrene. In Aspergillus niger, the enzymes cinnamic acid decarboxylase (CdcA, formally ferulic acid decarboxylase) and the flavin prenyltransferase (PadA) catalyze together the non-oxidative decarboxylation of cinnamic acid and sorbic acid. The corresponding genes, cdcA and padA, are clustered in the genome together with a putative transcription factor previously named sorbic acid decarboxylase regulator (SdrA). While SdrA was predicted to be involved in the regulation of the non-oxidative decarboxylation of cinnamic acid and sorbic acid, this was never functionally analyzed. In this study, A. niger deletion mutants of sdrA, cdcA, and padA were made to further investigate the role of SdrA in cinnamic acid metabolism. Phenotypic analysis revealed that cdcA, sdrA and padA are exclusively involved in the degradation of cinnamic acid and sorbic acid and not required for other related aromatic compounds. Whole genome transcriptome analysis of ΔsdrA grown on different cinnamic acid related compounds, revealed additional target genes, which were also clustered with cdcA, sdrA, and padA in the A. niger genome. Synteny analysis using 30 Aspergillus genomes demonstrated a conserved cinnamic acid decarboxylation gene cluster in most Aspergilli of the Nigri clade. Aspergilli lacking certain genes in the cluster were unable to grow on cinnamic acid, but could still grow on related aromatic compounds, confirming the specific role of these three genes for cinnamic acid metabolism of A. niger.
  • Kajala, Ilkka; Shi, Qiao; Nyyssölä, Antti; Maina, Ndegwa; Hou, Yaxi; Katina, Kati; Tenkanen, Maija; Juvonen, Riikka (2015)
    Wheat bran offers health benefits as a baking ingredient, but is detrimental to bread textural quality. Dextran production by microbial fermentation improves sourdough bread volume and freshness, but extensive acid production during fermentation may negate this effect. Enzymatic production of dextran in wheat bran was tested to determine if dextran-containing bran could be used in baking without disrupting bread texture. The Weissella confusa VTT E-90392 dextransucrase gene was sequenced and His-tagged dextransucrase Wc392-rDSR was produced in Lactococcus lactis. Purified enzyme was characterized using 14C-sucrose radioisotope and reducing value-based assays, the former yielding Km and Vmax values of 14.7 mM and 8.2 μmol/(mg∙min), respectively, at the pH optimum of 5.4. The structure and size of in vitro dextran product was similar to dextran produced in vivo. Dextran (8.1% dry weight) was produced in wheat bran in 6 h using Wc392-rDSR. Bran with and without dextran was used in wheat baking at 20% supplementation level. Dextran presence improved bread softness and neutralized bran-induced volume loss, clearly demonstrating the potential of using dextransucrases in bran bioprocessing for use in baking.
  • Mikkila, Joona; Trogen, Mikaela; Koivu, Klaus A. Y.; Kontro, Jussi; Kuuskeri, Jaana; Maltari, Riku; Dekere, Zane; Kemell, Marianna; Makela, Miia R.; Nousiainen, Paula A.; Hummel, Michael; Sipila, Jussi; Hilden, Kristiina (2020)
    The kraft lignin's low molecular weight and too high hydroxyl content hinder its application in bio-based carbon fibers. In this study, we were able to polymerize kraft lignin and reduce the amount of hydroxyl groups by incubating it with the white-rot fungus Obba rivulosa. Enzymatic radical oxidation reactions were hypothesized to induce condensation of lignin, which increased the amount of aromatic rings connected by carbon-carbon bonds. This modification is assumed to be beneficial when aiming for graphite materials such as carbon fibers. Furthermore, the ratio of remaining aliphatic hydroxyls to phenolic hydroxyls was increased, making the structure more favorable for carbon fiber production. When the modified lignin was mixed together with cellulose, the mixture could be spun into intact precursor fibers by using dry-jet wet spinning. The modified lignin leaked less to the spin bath compared with the unmodified lignin starting material, making the recycling of spin-bath solvents easier. The stronger incorporation of modified lignin in the precursor fibers was confirmed by composition analysis, thermogravimetry, and mechanical testing. This work shows how white-rot fungal treatment can be used to modify the structure of lignin to be more favorable for the production of bio-based fiber materials.
  • Mattila, Hans; Mäkinen, Mari; Lundell, Taina (2020)
    Background Fungal decomposition of wood is considered as a strictly aerobic process. However, recent findings on wood-decaying fungi to produce ethanol from various lignocelluloses under oxygen-depleted conditions lead us to question this. We designed gene expression study of the white rot fungus Phlebia radiata (isolate FBCC0043) by adopting comparative transcriptomics and functional genomics on solid lignocellulose substrates under varying cultivation atmospheric conditions. Results Switch to fermentative conditions was a major regulator for intracellular metabolism and extracellular enzymatic degradation of wood polysaccharides. Changes in the expression profiles of CAZy (carbohydrate-active enzyme) encoding genes upon oxygen depletion, lead into an alternative wood decomposition strategy. Surprisingly, we noticed higher cellulolytic activity under fermentative conditions in comparison to aerobic cultivation. In addition, our results manifest how oxygen depletion affects over 200 genes of fungal primary metabolism including several transcription factors. We present new functions for acetate generating phosphoketolase pathway and its potential regulator, Adr1 transcription factor, in carbon catabolism under oxygen depletion. Conclusions Physiologically resilient wood-decomposing Basidiomycota species P. radiata is capable of thriving under respirative and fermentative conditions utilizing only untreated lignocellulose as carbon source. Hypoxia-response mechanism in the fungus is, however, divergent from the regulation described for Ascomycota fermenting yeasts or animal-pathogenic species of Basidiomycota.
  • Rizzello, Carlo Giuseppe; Hernandez-Ledesma, Blanca; Fernandez-Tome, Samuel; Curiel, Jose Antonio; Pinto, Daniela; Marzani, Barbara; Coda, Rossana; Gobbetti, Marco (2015)
    Background: There is an increasing interest toward the use of legumes in food industry, mainly due to the quality of their protein fraction. Many legumes are cultivated and consumed around the world, but few data is available regarding the chemical or technological characteristics, and especially on their suitability to be fermented. Nevertheless, sourdough fermentation with selected lactic acid bacteria has been recognized as the most efficient tool to improve some nutritional and functional properties. This study investigated the presence of lunasin-like polypeptides in nineteen traditional Italian legumes, exploiting the potential of the fermentation with selected lactic acid bacteria to increase the native concentration. An integrated approach based on chemical, immunological and ex vivo (human adenocarcinoma Caco-2 cell cultures) analyses was used to show the physiological potential of the lunasin-like polypeptides. Results: Italian legume varieties, belonging to Phaseulus vulgaris, Cicer arietinum, Lathyrus sativus, Lens culinaris and Pisum sativum species, were milled and flours were chemically characterized and subjected to sourdough fermentation with selected Lactobacillus plantarum C48 and Lactobacillus brevis AM7, expressing different peptidase activities. Extracts from legume doughs (unfermented) and sourdoughs were subjected to western blot analysis, using an anti-lunasin primary antibody. Despite the absence of lunasin, different immunoreactive polypeptide bands were found. The number and the intensity of lunasin-like polypeptides increased during sourdough fermentation, as the consequence of the proteolysis of the native proteins carried out by the selected lactic acid bacteria. A marked inhibitory effect on the proliferation of human adenocarcinoma Caco-2 cells was observed using extracts from legume sourdoughs. In particular, sourdoughs from Fagiolo di Lamon, Cece dell'Alta Valle di Misa, and Pisello riccio di Sannicola flours were the most active, showing a decrease of Caco-2 cells viability up to 70 %. The over-expression of Caco-2 filaggrin and involucrin genes was also induced. Nine lunasin-like polypeptides, having similarity to lunasin, were identified. Conclusions: The features of the sourdough fermented legume flours suggested the use for the manufacture of novel functional foods and/or pharmaceuticals preparations.
  • Dilokpimol, Adiphol; Peng, Mao; Di Falco, Marcos; Chin A Woeng, Thomas; Maria Wilhelmina Hegi, Rosa; Granchi, Zoraide; Tsang, Adrian; Hildén, Kristiina S.; Mäkelä, Miia R.; de Vries, Ronald P. (2020)
    Penicillium subrubescens is able to degrade a broad range of plant biomass and it has an expanded set of Carbohydrate Active enzyme (CAZyme)-encoding genes in comparison to other Penicillium species. Here we used exoproteome and transcriptome analysis to demonstrate the versatile plant biomass degradation mechanism by P. subrubescens during growth on wheat bran and sugar beet pulp. On wheat bran P. subrubescens degraded xylan main chain and side residues from the Day 2 of cultivation, whereas it started to degrade side chain of pectin in sugar beet pulp prior to attacking the main chain on Day 3. In addition, on Day 3 the cellulolytic enzymes were highly increased. Our results confirm that P. subrubescens adapts its enzyme production to the available plant biomass and is a promising new fungal cell factory for the production of CAZymes.
  • Chroumpi, Tania; Peng, Mao; Markillie, Lye Meng; Mitchell, Hugh D.; Nicora, Carrie D.; Hutchinson, Chelsea M.; Paurus, Vanessa; Tolic, Nikola; Clendinen, Chaevien S.; Orr, Galya; Baker, Scott E.; Makela, Miia R.; de Vries, Ronald P. (2021)
    The filamentous ascomycete Aspergillus niger has received increasing interest as a cell factory, being able to efficiently degrade plant cell wall polysaccharides as well as having an extensive metabolism to convert the released monosaccharides into value added compounds. The pentoses D-xylose and L-arabinose are the most abundant monosaccharides in plant biomass after the hexose D-glucose, being major constituents of xylan, pectin and xyloglucan. In this study, the influence of selected pentose catabolic pathway (PCP) deletion strains on growth on plant biomass and re-routing of sugar catabolism was addressed to gain a better understanding of the flexibility of this fungus in using plant biomass-derived monomers. The transcriptome, metabolome and proteome response of three PCP mutant strains, Delta larA Delta xyrA Delta xyrB, Delta ladA Delta xdhA Delta sdhA and Delta xkiA, grown on wheat bran (WB) and sugar beet pulp (SBP), was evaluated. Our results showed that despite the absolute impact of these PCP mutations on pure pentose sugars, they are not as critical for growth of A. niger on more complex biomass substrates, such as WB and SBP. However, significant phenotypic variation was observed between the two biomass substrates, but also between the different PCP mutants. This shows that the high sugar heterogeneity of these substrates in combination with the high complexity and adaptability of the fungal sugar metabolism allow for activation of alternative strategies to support growth.
  • Mattila, Hans Kristian; Kuuskeri, Jaana Tuulia; Lundell, Taina Kristina (2017)
    Ethanol production from non-pretreated lignocellulose was carried out in a consolidated bioprocess with wood-decay fungi of phlebioid Polyporales. Ethanol production was attempted on glucose, spruce wood sawdust and waste core board. Substantial quantities of ethanol were achieved, and isolate Phlebia radiata 0043 produced 5.9 g/L of ethanol reaching the yield of 10.4% ethanol from core board lignocellulose substrate. Acidic initial culture conditions (pH 3) induced ethanol fermentation compared to the more neutral environment. Together with bioethanol, the fungi were able to produce organic acids such as oxalate and fumarate, thus broadening their capacity and applicability as efficient organisms to be utilized for bioconversion of various lignocelluloses. In conclusion, fungi of Phlebia grow on, convert and saccharify solid lignocellulose waste materials without pre-treatments resulting in accumulation of ethanol and organic acids. These findings will aid in applying fungal biotechnology for production of biofuels and biocompounds.
  • Lucenius, Jessica; Valle-Delgado, Juan José; Parikka, Kirsti; Österberg, Monika (2019)
    Plant-based polysaccharides (cellulose and hemicellulose) are a very interesting option for the preparation of sustainable composite materials to replace fossil plastics, but the optimum bonding mechanism between the hard and soft components is still not well known. In this work, composite films made of cellulose nanofibrils (CNF) and various modified and unmodified polysaccharides (galactoglucomannan, GGM; hydrolyzed and oxidized guar gum, GGhydHox; and guar gum grafted with polyethylene glycol, GG-g-PEG) were characterized from the nano- to macroscopic level to better understand how the interactions between the composite components at nano/microscale affect macroscopic mechanical properties, like toughness and strength. All the polysaccharides studied adsorbed well on CNF, although with different adsorption rates, as measured by quartz crystal microbalance with dissipation monitoring (QCM-D). Direct surface and friction force experiments using the colloidal probe technique revealed that the adsorbed polysaccharides provided repulsive forces–well described by a polyelectrolyte brush model – and a moderate reduction in friction between cellulose surfaces, which may prevent CNF aggregates during composite formation and, consequently, enhance the strength of dry films. High affinity for cellulose and moderate hydration were found to be important requirements for polysaccharides to improve the mechanical properties of CNF-based composites in wet conditions. The results of this work provide fundamental information on hemicellulose-cellulose interactions and can support the development of polysaccharide-based materials for different packaging and medical applications.
  • Castillo, Sandra; Barth, Dorothee; Arvas, Mikko; Pakula, Tiina M.; Pitkänen, Esa; Blomberg, Peter; Seppanen-Laakso, Tuulikki; Nygren, Heli; Sivasiddarthan, Dhinakaran; Penttila, Merja; Oja, Merja (2016)
    Background: Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis. Results: A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model. Conclusions: The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1on-strate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes.