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- ItemBatch and continuous lactic acid fermentation based on a multi-substrate approach(Basel : MDPI AG, 2020) Olszewska-Widdrat, Agata; Alexandri, Maria; López-Gómez, José Pablo; Schneider, Roland; Venus, JoachimThe utilisation of waste materials and industrial residues became a priority within the bioeconomy concept and the production of biobased chemicals. The aim of this study was to evaluate the feasibility to continuously produce L-lactic acid from different renewable substrates, in a multi-substrate strategy mode. Based on batch experiments observations, Bacillus coagulans A534 strain was able to continuously metabolise acid whey, sugar beet molasses, sugar bread, alfalfa press green juice and tapioca starch. Additionally, reference experiments showed its behaviour in standard medium. Continuous fermentations indicated that the highest productivity was achieved when molasses was employed with a value of 10.34 g·L−1·h−1, while the lactic acid to sugar conversion yield was 0.86 g·g−1 . This study demonstrated that LA can be efficiently produced in continuous mode regardless the substrate, which is a huge advantage in comparison to other platform chemicals. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.
- ItemSeparation, characterization, and handling of microalgae by dielectrophoresis(Basel : MDPI, 2020) Abt, Vinzenz; Gringel, Fabian; Han, Arum; Neubauer, Peter; Birkholz, MarioMicroalgae biotechnology has a high potential for sustainable bioproduction of diverse highvalue biomolecules. Some of the main bottlenecks in cell-based bioproduction, and more specifically in microalgae-based bioproduction, are due to insufficient methods for rapid and efficient cell characterization, which contributes to having only a few industrially established microalgal species in commercial use. Dielectrophoresis-based microfluidic devices have been long established as promising tools for label-free handling, characterization, and separation of broad ranges of cells. The technique is based on differences in dielectric properties and sizes, which results in different degrees of cell movement under an applied inhomogeneous electrical field. The method has also earned interest for separating microalgae based on their intrinsic properties, since their dielectric properties may significantly change during bioproduction, in particular for lipid-producing species. Here, we provide a comprehensive review of dielectrophoresis-based microfluidic devices that are used for handling, characterization, and separation of microalgae. Additionally, we provide a perspective on related areas of research in cell-based bioproduction that can benefit from dielectrophoresis-based microdevices. This work provides key information that will be useful for microalgae researchers to decide whether dielectrophoresis and which method is most suitable for their particular application. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.
- ItemDegradation Kinetics of Lignocellulolytic Enzymes in a Biogas Reactor Using Quantitative Mass Spectrometry(Basel : MDPI, 2023) Küchler, Jan; Willenbücher, Katharina; Reiß, Elisabeth; Nuß, Lea; Conrady, Marius; Ramm, Patrice; Schimpf, Ulrike; Reichl, Udo; Szewzyk, Ulrich; Benndorf, DirkThe supplementation of lignocellulose-degrading enzymes can be used to enhance the performance of biogas production in industrial biogas plants. Since the structural stability of these enzyme preparations is essential for efficient application, reliable methods for the assessment of enzyme stability are crucial. Here, a mass-spectrometric-based assay was established to monitor the structural stability of enzymes, i.e., the structural integrity of these proteins, in anaerobic digestion (AD). The analysis of extracts of Lentinula edodes revealed the rapid degradation of lignocellulose-degrading enzymes, with an approximate half-life of 1.5 h. The observed low structural stability of lignocellulose-degrading enzymes in AD corresponded with previous results obtained for biogas content. The established workflow can be easily adapted for the monitoring of other enzyme formulations and provides a platform for evaluating the effects of enzyme additions in AD, together with a characterization of the biochemical methane potential used in order to determine the biodegradability of organic substrates.
- ItemGround reaction forces and external hip joint moments predict in vivo hip contact forces during gait(Amsterdam [u.a.] : Elsevier Science, 2022) Alves, Sónia A.; Polzehl, Jörg; Brisson, Nicholas M.; Bender, Alwina; Agres, Alison N.; Damm, Philipp; Duda, Georg N.Younger patients increasingly receive total hip arthroplasty (THA) as therapy for end-stage osteoarthritis. To maintain the long-term success of THA in such patients, avoiding extremely high hip loads, i.e., in vivo hip contact force (HCF), is considered essential. However, in vivo HCFs are difficult to determine and their direct measurement is limited to instrumented joint implants. It remains unclear whether external measurements of ground reaction forces (GRFs), a non-invasive, markerless and clinic-friendly measure can estimate in vivo HCFs. Using data from eight patients with instrumented hip implants, this study determined whether GRF time series data, alone or combined with other scalar variables such as hip joint moments (HJMs) and lean muscle volume (LMV), could predict the resultant HCF (rHCF) impulse using a functional linear modeling approach. Overall, single GRF time series data did not predict in vivo rHCF impulses. However, when GRF time series data were combined with LMV of the gluteus medius or sagittal HJM using a functional linear modeling approach, the in vivo rHCF impulse could be predicted from external measures only. Accordingly, this approach can predict in vivo rHCF impulses, and thus provide patients with useful insight regarding their gait behavior to avoid hip joint overloading.
- ItemInfluence of redox stress on crosstalk between fibroblasts and keratinocytes(Basel : MDPI, 2021) Bhartiya, Pradeep; Masur, Kai; Shome, Debarati; Kaushik, Neha; Nguyen, Linh N.; Kaushik, Nagendra Kumar; Choi, Eun HaAlthough the skin is constantly subjected to endogenous and exogenous stress, it maintains a homeostatic state through wound repair and regeneration pathways. Treatment for skin diseases and injury requires a significant understanding of the various mechanisms and interactions that occur within skin cells. Keratinocytes and fibroblasts interact with each other and act as key players in the repair process. Although fibroblasts and keratinocytes are widely studied in wound healing and skin remodeling under different conditions, the influence of redox stress on keratinocyte-fibroblast crosstalk has not been thoroughly investigated. In this study, we used cold atmospheric plasma (CAP) to generate and deliver oxidative stress to keratinocytes and fibroblasts and to assess its impact on their interactions. To this end, we used a well-established in vitro 3D co-culture model imitating a realistic scenario. Our study shows that low CAP exposure is biocompatible and does not affect the viability or energetics of fibroblasts and keratinocytes. Exposure to low doses of CAP enhanced the proliferation rate of cells and stimulated the expression of key genes (KGF, MMP2, GMCSF, IL-6, and IL-8) in fibroblasts, indicating the activation and initiation of the skin repair process. Additionally, enhanced migration was observed under co-culture conditions under the given redox stress conditions, and expression of the upstream regulator and the effectors of the Hippo pathway (YAP and CYR61, respectively), which are associated with enhanced migration, were elevated. Overall, this study reinforces the application of CAP and redox stress in skin repair physiology.
- ItemConsensusPrime—A Bioinformatic Pipeline for Ideal Consensus Primer Design(Basel : MDPI, 2022) Collatz, Maximilian; Braun, Sascha D.; Monecke, Stefan; Ehricht, RalfBackground: High-quality oligonucleotides for molecular amplification and detection procedures of diverse target sequences depend on sequence homology. Processing input sequences and identifying homogeneous regions in alignments can be carried out by hand only if they are small and contain sequences of high similarity. Finding the best regions for large and inhomogeneous alignments needs to be automated. Results: The ConsensusPrime pipeline was developed to sort out redundant and technical interfering data in multiple sequence alignments and detect the most homologous regions from multiple sequences. It automates the prediction of optimal consensus primers for molecular analytical and sequence-based procedures/assays. Conclusion: ConsensusPrime is a fast and easy-to-use pipeline for predicting optimal consensus primers that is executable on local systems without depending on external resources and web services. An implementation in a Docker image ensures platform-independent executability and installability despite the combination of multiple programs. The source code and installation instructions are publicly available on GitHub.
- ItemMolecular monitoring of the poplar wood chip microbiome as a function of storage strategy(Barking : Elsevier, 2021) Zöhrer, Julia; Probst, Maraike; Dumfort, Sabrina; Lenz, Hannes; Pecenka, Ralf; Insam, Heribert; Ascher-Jenull, JudithOne of the most challenging aspects of using wood chips as renewable energy source is the loss of biomass related to storage. Therefore, we installed three outdoor industrial-scale piles (250 m³) of poplar wood chips and monitored the bacterial and fungal communities by next-generation sequencing over a storage period of 120 d. Two of the three piles were supplemented with calcium dihydroxide (Ca(OH)2) (1.5%, 3% w/w) in order to test its potential as alkaline stabilization agent to preserve woody biomass during storage. Shifts in the microbial community composition occurred almost entirely in the beginning of the storage experiment, which we attribute to the temperature rise of up to 60 °C within the first week of storage. Later, however, we found little changes. Independent of Ca(OH)2 concentration, a consortium of lignocellulolytic and thermotolerant microorganisms dominated the stored wood chip microbiota emphasizing their role as key players during wood decomposition. Although the addition of Ca(OH)2 altered the physicochemical properties of wood chips, it did not prevent loss of biomass. Especially the pH was increased in Ca(OH)2 treated piles. However, only minor differences in the microbial communities’ composition were detected following Ca(OH)2 addition, highlighting the microbes tolerance towards and adaptation to changing environmental conditions.
- ItemEEG biomarkers of activation of the lymphatic drainage system of the brain during sleep and opening of the blood-brain barrier(Gotenburg : Research Network of Computational and Structural Biotechnology (RNCSB), 2022) Semyachkina-Glushkovskaya, O.V.; Karavaev, A.S.; Prokhorov, M.D.; Runnova, A.E.; Borovkova, E.I.; Ishbulatov, Yu.M.; Hramkov, A.N.; Kulminskiy, D.D.; Semenova, N.I.; Sergeev, K.S.; Slepnev, A.V.; Sitnikova, E.Yu.; Zhuravlev, M.O.; Fedosov, I.V.; Shirokov, A.A.; Blokhina, I.A.; Dubrovski, A.I.; Terskov, A.V.; Khorovodov, A.P.; Ageev, V.B.; Elovenko, D.A.; Evsukova, A.S.; Adushkina, V.V.; Telnova, V.V.; Postnov, D.E.; Penzel, T.U.; Kurths, J.G.The lymphatic drainage system of the brain (LDSB) is the removal of metabolites and wastes from its tissues. A dysfunction of LDSB is an important sign of aging, brain oncology, the Alzheimer's and Parkinson's diseases. The development of new strategies for diagnosis of LDSB injuries can improve prevention of age-related cerebral amyloid angiopathy, neurodegenerative and cerebrovascular diseases. There are two conditions, such as deep sleep and opening of the blood-brain-barrier (OBBB) associated with the LDSB activation. A promising candidate for measurement of LDSB could be electroencephalography (EEG). In this pilot study on rats, we tested the hypothesis, whether deep sleep and OBBB can be an informative platform for an effective extracting of information about the LDSB functions. Using the nonlinear analysis of EEG dynamics and machine learning technology, we discovered that the LDSB activation during OBBB and sleep is associated with similar changes in the EEG θ-activity. The OBBB causes the higher LDSB activation vs. sleep that is accompanied by specific changes in the low frequency EEG activity extracted by the power spectra analysis of the EEG dynamics combined with the coherence function. Thus, our findings demonstrate a link between neural activity associated with the LDSB activation during sleep and OBBB that is an important informative platform for extraction of the EEG-biomarkers of the LDSB activity. These results open new perspectives for the development of technology for the LDSB diagnostics that would open a novel era in the prognosis of brain diseases caused by the LDSB disorders, including OBBB.
- ItemIntegrating Biophysics in Toxicology(Basel : MDPI, 2020) Del Favero, G.; Kraegeloh, A.Integration of biophysical stimulation in test systems is established in diverse branches of biomedical sciences including toxicology. This is largely motivated by the need to create novel experimental setups capable of reproducing more closely in vivo physiological conditions. Indeed, we face the need to increase predictive power and experimental output, albeit reducing the use of animals in toxicity testing. In vivo, mechanical stimulation is essential for cellular homeostasis. In vitro, diverse strategies can be used to model this crucial component. The compliance of the extracellular matrix can be tuned by modifying the stiffness or through the deformation of substrates hosting the cells via static or dynamic strain. Moreover, cells can be cultivated under shear stress deriving from the movement of the extracellular fluids. In turn, introduction of physical cues in the cell culture environment modulates differentiation, functional properties, and metabolic competence, thus influencing cellular capability to cope with toxic insults. This review summarizes the state of the art of integration of biophysical stimuli in model systems for toxicity testing, discusses future challenges, and provides perspectives for the further advancement of in vitro cytotoxicity studies.
- ItemSurface cleaning and sample carrier for complementary high-resolution imaging techniques(Melville, NY : AIP, 2020) Benettoni, Pietro; Ye, Jia-Yu; Holbrook, Timothy R.; Calabrese, Federica; Wagner, Stephan; Zarejousheghani, Mashaalah; Griebe, Jan; Ullrich, Maria K.; Musat, Niculina; Schmidt, Matthias; Flyunt, Roman; Reemtsma, Thorsten; Richnow, Hans-Hermann; Stryhanyuk, HryhoriyNowadays, high-resolution imaging techniques are extensively applied in a complementary way to gain insights into complex phenomena. For a truly complementary analytical approach, a common sample carrier is required that is suitable for the different preparation methods necessary for each analytical technique. This sample carrier should be capable of accommodating diverse analytes and maintaining their pristine composition and arrangement during deposition and preparation. In this work, a new type of sample carrier consisting of a silicon wafer with a hydrophilic polymer coating was developed. The robustness of the polymer coating toward solvents was strengthened by cross-linking and stoving. Furthermore, a new method of UV-ozone cleaning was developed that enhances the adhesion of the polymer coating to the wafer and ensures reproducible surface-properties of the resulting sample carrier. The hydrophilicity of the sample carrier was recovered applying the new method of UV-ozone cleaning, while avoiding UV-induced damages to the polymer. Noncontact 3D optical profilometry and contact angle measurements were used to monitor the hydrophilicity of the coating. The hydrophilicity of the polymer coating ensures its spongelike behavior so that upon the deposition of an analyte suspension, the solvent and solutes are separated from the analyte by absorption into the polymer. This feature is essential to limit the coffee-ring effect and preserve the native identity of an analyte upon deposition. The suitability of the sample carrier for various sample types was tested using nanoparticles from suspension, bacterial cells, and tissue sections. To assess the homogeneity of the analyte distribution and preservation of sample integrity, optical and scanning electron microscopy, helium ion microscopy, laser ablation inductively coupled plasma mass spectrometry, and time-of-flight secondary ion mass spectrometry were used. This demonstrates the broad applicability of the newly developed sample carrier and its value for complementary imaging. © 2020 Author(s).