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- 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.
- ItemDisulfide Bond Engineering of an Endoglucanase from Penicillium verruculosum to Improve Its Thermostability(Basel : Molecular Diversity Preservation International (MDPI), 2019) Bashirova, Anna; Pramanik, Subrata; Volkov, Pavel; Rozhkova, Aleksandra; Nemashkalov, Vitaly; Zorov, Ivan; Gusakov, Alexander; Sinitsyn, Arkady; Schwaneberg, Ulrich; Davari, Mehdi D.Endoglucanases (EGLs) are important components of multienzyme cocktails used in the production of a wide variety of fine and bulk chemicals from lignocellulosic feedstocks. However, a low thermostability and the loss of catalytic performance of EGLs at industrially required temperatures limit their commercial applications. A structure-based disulfide bond (DSB) engineering was carried out in order to improve the thermostability of EGLII from Penicillium verruculosum. Based on in silico prediction, two improved enzyme variants, S127C-A165C (DSB2) and Y171C-L201C (DSB3), were obtained. Both engineered enzymes displayed a 15–21% increase in specific activity against carboxymethylcellulose and β-glucan compared to the wild-type EGLII (EGLII-wt). After incubation at 70 °C for 2 h, they retained 52–58% of their activity, while EGLII-wt retained only 38% of its activity. At 80 °C, the enzyme-engineered forms retained 15–22% of their activity after 2 h, whereas EGLII-wt was completely inactivated after the same incubation time. Molecular dynamics simulations revealed that the introduced DSB rigidified a global structure of DSB2 and DSB3 variants, thus enhancing their thermostability. In conclusion, this work provides an insight into DSB protein engineering as a potential rational design strategy that might be applicable for improving the stability of other enzymes for industrial applications.
- ItemPolymer Brush-Functionalized Chitosan Hydrogels as Antifouling Implant Coatings(Columbus, Ohio : American Chemical Society, 2017) Buzzacchera, Irene; Vorobii, Mariia; Kostina, Nina Yu; de Los Santos Pereira, Andres; Riedel, Tomáš; Bruns, Michael; Ogieglo, Wojciech; Möller, Martin; Wilson, Christopher J.; Rodriguez-Emmenegger, CesarImplantable sensor devices require coatings that efficiently interface with the tissue environment to mediate biochemical analysis. In this regard, bioinspired polymer hydrogels offer an attractive and abundant source of coating materials. However, upon implantation these materials generally elicit inflammation and the foreign body reaction as a consequence of protein fouling on their surface and concomitant poor hemocompatibility. In this report we investigate a strategy to endow chitosan hydrogel coatings with antifouling properties by the grafting of polymer brushes in a "grafting-from" approach. Chitosan coatings were functionalized with polymer brushes of oligo(ethylene glycol) methyl ether methacrylate and 2-hydroxyethyl methacrylate using photoinduced single electron transfer living radical polymerization and the surfaces were thoroughly characterized by XPS, AFM, water contact angle goniometry, and in situ ellipsometry. The antifouling properties of these new bioinspired hydrogel-brush coatings were investigated by surface plasmon resonance. The influence of the modifications to the chitosan on hemocompatibility was assessed by contacting the surfaces with platelets and leukocytes. The coatings were hydrophilic and reached a thickness of up to 180 nm within 30 min of polymerization. The functionalization of the surface with polymer brushes significantly reduced the protein fouling and eliminated platelet activation and leukocyte adhesion. This methodology offers a facile route to functionalizing implantable sensor systems with antifouling coatings that improve hemocompatibility and pave the way for enhanced device integration in tissue.
- ItemEnhanced growth of lapine anterior cruciate ligament-derived fibroblasts on scaffolds embroidered from poly(L-lactide-co-ε-caprolactone) and polylactic acid threads functionalized by fluorination and hexamethylene diisocyanate cross-linked collagen foams(Basel : Molecular Diversity Preservation International, 2020) Gögele, Clemens; Hahn, Judith; Elschner, Cindy; Breier, Annette; Schröpfer, Michaela; Prade, Ina; Meyer, Michael; Schulze-Tanzil, GundulaReconstruction of ruptured anterior cruciate ligaments (ACLs) is limited by the availability and donor site morbidity of autografts. Hence, a tissue engineered graft could present an alternative in the future. This study was undertaken to determine the performance of lapine (L) ACL-derived fibroblasts on embroidered poly(l-lactide-co-e-caprolactone) (P(LA-CL)) and polylactic acid (PLA) scaffolds in regard to a tissue engineering approach for ACL reconstruction. Surface modifications of P(LA-CL)/PLA by gas-phase fluorination and cross-linking of a collagen foam using either ethylcarbodiimide (EDC) or hexamethylene diisocyanate (HMDI) were tested regarding their influence on cell adhesion, growth and gene expression. The experiments were performed using embroidered P(LA-CL)/PLA scaffolds that were seeded dynamically or statically with LACL-derived fibroblasts. Scaffold cytocompatibility, cell survival, numbers, metabolic activity, ultrastructure and sulfated glycosaminoglycan (sGAG) synthesis were evaluated. Quantitative real-time polymerase chain reaction (QPCR) revealed gene expression of collagen type I (COL1A1), decorin (DCN), tenascin C (TNC), Mohawk (MKX) and tenomodulin (TNMD). All tested scaffolds were highly cytocompatible. A significantly higher cellularity and larger scaffold surface areas colonized by cells were detected in HMDI cross-linked and fluorinated scaffolds compared to those cross-linked with EDC or without any functionalization. By contrast, sGAG synthesis was higher in controls. Despite the fact that the significance level was not reached, gene expressions of ligament extracellular matrix components and differentiation markers were generally higher in fluorinated scaffolds with cross-linked collagen foams. LACL-derived fibroblasts maintained their differentiated phenotype on fluorinated scaffolds supplemented with a HMDI cross-linked collagen foam, making them a promising tool for ACL tissue engineering. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.
- ItemExchange Bias Effect of Ni@(NiO,Ni(OH)2) Core/Shell Nanowires Synthesized by Electrochemical Deposition in Nanoporous Alumina Membranes(Basel : MDPI, 2023) García, Javier; Gutiérrez, Ruth; González, Ana S.; Jiménez-Ramirez, Ana I.; Álvarez, Yolanda; Vega, Víctor; Reith, Heiko; Leistner, Karin; Luna, Carlos; Nielsch, Kornelius; Prida, Víctor M.Tuning and controlling the magnetic properties of nanomaterials is crucial to implement new and reliable technologies based on magnetic hyperthermia, spintronics, or sensors, among others. Despite variations in the alloy composition as well as the realization of several post material fabrication treatments, magnetic heterostructures as ferromagnetic/antiferromagnetic coupled layers have been widely used to modify or generate unidirectional magnetic anisotropies. In this work, a pure electrochemical approach has been used to fabricate core (FM)/shell (AFM) Ni@(NiO,Ni(OH)2) nanowire arrays, avoiding thermal oxidation procedures incompatible with integrative semiconductor technologies. Besides the morphology and compositional characterization of these core/shell nanowires, their peculiar magnetic properties have been studied by temperature dependent (isothermal) hysteresis loops, thermomagnetic curves and FORC analysis, revealing the existence of two different effects derived from Ni nanowires’ surface oxidation over the magnetic performance of the array. First of all, a magnetic hardening of the nanowires along the parallel direction of the applied magnetic field with respect their long axis (easy magnetization axis) has been found. The increase in coercivity, as an effect of surface oxidation, has been observed to be around 17% (43%) at 300 K (50 K). On the other hand, an increasing exchange bias effect on decreasing temperature has been encountered when field cooling (3T) the oxidized Ni@(NiO,Ni(OH)2) nanowires below 100 K along their parallel lengths.
- ItemInsight into the Impact of Oxidative Stress on the Barrier Properties of Lipid Bilayer Models(Basel : Molecular Diversity Preservation International (MDPI), 2022) Nasri, Zahra; Ahmadi, Mohsen; Striesow, Johanna; Ravandeh, Mehdi; von Woedtke, Thomas; Wende, KristianAs a new field of oxidative stress-based therapy, cold physical plasma is a promising tool for several biomedical applications due to its potential to create a broad diversity of reactive oxygen and nitrogen species (RONS). Although proposed, the impact of plasma-derived RONS on the cell membrane lipids and properties is not fully understood. For this purpose, the changes in the lipid bilayer functionality under oxidative stress generated by an argon plasma jet (kINPen) were investigated by electrochemical techniques. In addition, liquid chromatography-tandem mass spectrometry was employed to analyze the plasma-induced modifications on the model lipids. Various asymmetric bilayers mimicking the structure and properties of the erythrocyte cell membrane were transferred onto a gold electrode surface by Langmuir-Blodgett/Langmuir-Schaefer deposition techniques. A strong impact of cholesterol on membrane permeabilization by plasma-derived species was revealed. Moreover, the maintenance of the barrier properties is influenced by the chemical composition of the head group. Mainly the head group size and its hydrogen bonding capacities are relevant, and phosphatidylcholines are significantly more susceptible than phosphatidylserines and other lipid classes, underlining the high relevance of this lipid class in membrane dynamics and cell physiology.
- ItemFunctional Delineation of a Protein–Membrane Interaction Hotspot Site on the HIV-1 Neutralizing Antibody 10E8(Basel : Molecular Diversity Preservation International (MDPI), 2022) Insausti, Sara; Garcia-Porras, Miguel; Torralba, Johana; Morillo, Izaskun; Ramos-Caballero, Ander; de la Arada, Igor; Apellaniz, Beatriz; Caaveiro, Jose M. M.; Carravilla, Pablo; Eggeling, Christian; Rujas, Edurne; Nieva, Jose L.Antibody engagement with the membrane-proximal external region (MPER) of the envelope glycoprotein (Env) of HIV-1 constitutes a distinctive molecular recognition phenomenon, the full appreciation of which is crucial for understanding the mechanisms that underlie the broad neutralization of the virus. Recognition of the HIV-1 Env antigen seems to depend on two specific features developed by antibodies with MPER specificity: (i) a large cavity at the antigen-binding site that holds the epitope amphipathic helix; and (ii) a membrane-accommodating Fab surface that engages with viral phospholipids. Thus, besides the main Fab–peptide interaction, molecular recognition of MPER depends on semi-specific (electrostatic and hydrophobic) interactions with membranes and, reportedly, on specific binding to the phospholipid head groups. Here, based on available cryo-EM structures of Fab–Env complexes of the anti-MPER antibody 10E8, we sought to delineate the functional antibody–membrane interface using as the defining criterion the neutralization potency and binding affinity improvements induced by Arg substitutions. This rational, Arg-based mutagenesis strategy revealed the position-dependent contribution of electrostatic interactions upon inclusion of Arg-s at the CDR1, CDR2 or FR3 of the Fab light chain. Moreover, the contribution of the most effective Arg-s increased the potency enhancement induced by inclusion of a hydrophobic-at-interface Phe at position 100c of the heavy chain CDR3. In combination, the potency and affinity improvements by Arg residues delineated a protein–membrane interaction site, whose surface and position support a possible mechanism of action for 10E8-induced neutralization. Functional delineation of membrane-interacting patches could open new lines of research to optimize antibodies of therapeutic interest that target integral membrane epitopes.
- ItemDifferent storage conditions influence biocompatibility and physicochemical properties of iron oxide nanoparticles(Basel : Molecular Diversity Preservation International (MDPI), 2015) Zaloga, Jan; Janko, Christina; Agarwal, Rohit; Nowak, Johannes; Müller, Robert; Boccaccini, Aldo R.; Lee, Geoffrey; Odenbach, Stefan; Lyer, Stefan; Alexiou, ChristophSuperparamagnetic iron oxide nanoparticles (SPIONs) have attracted increasing attention in many biomedical fields. In magnetic drug targeting SPIONs are injected into a tumour supplying artery and accumulated inside the tumour with a magnet. The effectiveness of this therapy is thus dependent on magnetic properties, stability and biocompatibility of the particles. A good knowledge of the effect of storage conditions on those parameters is of utmost importance for the translation of the therapy concept into the clinic and for reproducibility in preclinical studies. Here, core shell SPIONs with a hybrid coating consisting of lauric acid and albumin were stored at different temperatures from 4 to 45 °C over twelve weeks and periodically tested for their physicochemical properties over time. Surprisingly, even at the highest storage temperature we did not observe denaturation of the protein or colloidal instability. However, the saturation magnetisation decreased by maximally 28.8% with clear correlation to time and storage temperature. Furthermore, the biocompatibility was clearly affected, as cellular uptake of the SPIONs into human T-lymphoma cells was crucially dependent on the storage conditions. Taken together, the results show that the particle properties undergo significant changes over time depending on the way they are stored.
- ItemA Review on Nano Ti-Based Oxides for Dark and Photocatalysis: From Photoinduced Processes to Bioimplant Applications(Basel : MDPI, 2023) Querebillo, Christine JoyCatalysis on TiO2 nanomaterials in the presence of H2O and oxygen plays a crucial role in the advancement of many different fields, such as clean energy technologies, catalysis, disinfection, and bioimplants. Photocatalysis on TiO2 nanomaterials is well-established and has advanced in the last decades in terms of the understanding of its underlying principles and improvement of its efficiency. Meanwhile, the increasing complexity of modern scientific challenges in disinfection and bioimplants requires a profound mechanistic understanding of both residual and dark catalysis. Here, an overview of the progress made in TiO2 catalysis is given both in the presence and absence of light. It begins with the mechanisms involving reactive oxygen species (ROS) in TiO2 photocatalysis. This is followed by improvements in their photocatalytic efficiency due to their nanomorphology and states by enhancing charge separation and increasing light harvesting. A subsection on black TiO2 nanomaterials and their interesting properties and physics is also included. Progress in residual catalysis and dark catalysis on TiO2 are then presented. Safety, microbicidal effect, and studies on Ti-oxides for bioimplants are also presented. Finally, conclusions and future perspectives in light of disinfection and bioimplant application are given.
- ItemIdentification and molecular analysis of interaction sites in the MtSEO-F1 protein involved in forisome assembly(New York, NY [u.a.] : Elsevier, 2020) Rose, Judith; Visser, Franziska; Müller, Boje; Senft, Matthias; Groscurth, Sira; Sicking, Kevin F.; Twyman, Richard M.; Prüfer, Dirk; Noll, Gundula A.Forisomes are large mechanoprotein complexes found solely in legumes such as Medicago truncatula. They comprise several “sieve element occlusion by forisome” (SEO-F) subunits, with MtSEO-F1 as the major structure-forming component. SEO-F proteins possess three conserved domains –an N-terminal domain (SEO-NTD), a potential thioredoxin fold, and a C-terminal domain (SEO-CTD)– but structural and biochemical data are scarce and little is known about the contribution of these domains to forisome assembly. To identify key amino acids involved in MtSEO-F1 dimerization and complex formation, we investigated protein-protein interactions by bimolecular fluorescence complementation and the analysis of yeast two-hybrid and random mutagenesis libraries. We identified a SEO-NTD core region as the major dimerization site, with abundant hydrophobic residues and rare charged residues suggesting dimerization is driven by the hydrophobic effect. We also found that ~45% of the full-length MtSEO-F1 sequence must be conserved for higher-order protein assembly, indicating that large interaction surfaces facilitate stable interactions, contributing to the high resilience of forisome bodies. Interestingly, the removal of 62 amino acids from the C-terminus did not disrupt forisome assembly. This is the first study unraveling interaction sites and mechanisms within the MtSEO-F1 protein at the level of dimerization and complex formation. © 2018