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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.
- 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.
- 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.
- ItemElucidating the chemistry behind the reduction of graphene oxide using a green approach with polydopamine(Basel : MDPI, 2019) Silva, Cláudia; Simon, Frank; Friedel, Peter; Pötschke, Petra; Zimmerer, CordeliaA new approach using X-ray photoelectron spectroscopy (XPS) was employed to give insight into the reduction of graphene oxide (GO) using a green approach with polydopamine (PDA). In this approach, the number of carbon atoms bonded to OH and to nitrogen in PDA is considered and compared to the total intensity of the signal resulting from OH groups in polydopamine-reduced graphene oxide (PDA-GO) to show the reduction. For this purpose, GO and PDA-GO with different times of reduction were prepared and characterized by Raman Spectroscopy and XPS. The PDA layer was removed to prepare reduced graphene oxide (RGO) and the effect of all chemical treatments on the thermal and electrical properties of the materials was studied. The results show that the complete reduction of the OH groups in GO occurred after 180 min of reaction. It was also concluded that Raman spectroscopy is not well suited to determine if the reduction and restoration of the sp2 structure occurred. Moreover, a significant change in the thermal stability was not observed with the chemical treatments. Finally, the electrical powder conductivity decreased after reduction with PDA, increasing again after its removal. © 2019 by the authors. Licensee MDPI, Basel, Switzerland.
- ItemInteraction of Poly(l-lysine)/Polysaccharide Complex Nanoparticles with Human Vascular Endothelial Cells(Basel : MDPI, 2018) Weber, Dominik; Torger, Bernhard; Richter, Karsten; Nessling, Michelle; Momburg, Frank; Woltmann, Beatrice; Müller, Martin; Schwartz-Albiez, ReinhardAngiogenesis plays an important role in both soft and hard tissue regeneration, which can be modulated by therapeutic drugs. If nanoparticles (NP) are used as vectors for drug delivery, they have to encounter endothelial cells (EC) lining the vascular lumen, if applied intravenously. Herein the interaction of unloaded polyelectrolyte complex nanoparticles (PECNP) composed of cationic poly(l-lysine) (PLL) and various anionic polysaccharides with human vascular endothelial cells (HUVEC) was analyzed. In particular PECNP were tested for their cell adhesive properties, their cellular uptake and intracellular localization considering composition and net charge. PECNP may form a platform for both cell coating and drug delivery. PECNP, composed of PLL in combination with the polysaccharides dextran sulfate (DS), cellulose sulfate (CS) or heparin (HEP), either unlabeled or labeled with fluorescein isothiocyanate (FITC) and either with positive or negative net charge were prepared. PECNP were applied to human umbilical cord vein endothelial cells (HUVEC) in both, the volume phase and immobilized phase at model substrates like tissue culture dishes. The attachment of PECNP to the cell surface, their intracellular uptake, and effects on cell proliferation and growth behavior were determined. Immobilized PECNP reduced attachment of HUVEC, most prominently the systems PLL/HEP and PLL/DS. A small percentage of immobilized PECNP was taken up by cells during adhesion. PECNP in the volume phase showed no effect of the net charge sign and only minor effects of the composition on the binding and uptake of PECNP at HUVEC. PECNP were stored in endosomal vesicles in a cumulative manner without apparent further processing. During mitosis, internalized PECNP were almost equally distributed among the dividing cells. Both, in the volume phase and immobilized at the surface, PECNP composed of PLL/HEP and PLL/DS clearly reduced cell proliferation of HUVEC, however without an apparent cytotoxic effect, while PLL/CS composition showed minor impairment. PECNP have an anti-adhesive effect on HUVEC and are taken up by endothelial cells which may negatively influence the proliferation rate of HUVEC. The negative effects were less obvious with the composition PLL/CS. Since uptake and binding for PLL/HEP was more efficient than for PLL/DS, PECNP of PLL/HEP may be used to deliver growth factors to endothelial cells during vascularization of bone reconstitution material, whereas those of PLL/CS may have an advantage for substituting biomimetic bone scaffold material.
- ItemHeteroepitaxial growth of T-Nb2O5 on SrTiO3(Basel : MDPI, 2018) Boschker, Jos E.; Markurt, Toni; Albrecht, Martin; Schwarzkopf, JuttaThere is a growing interest in exploiting the functional properties of niobium oxides in general and of the T-Nb2O5 polymorph in particular. Fundamental investigations of the properties of niobium oxides are, however, hindered by the availability of materials with sufficient structural perfection. It is expected that high-quality T-Nb2O5 can be made using heteroepitaxial growth. Here, we investigated the epitaxial growth of T-Nb2O5 on a prototype perovskite oxide, SrTiO3. Even though there exists a reasonable lattice mismatch in one crystallographic direction, these materials have a significant difference in crystal structure: SrTiO3 is cubic, whereas T-Nb2O5 is orthorhombic. It is found that this difference in symmetry results in the formation of domains that have the T-Nb2O5 c-axis aligned with the SrTiO3 <001>s in-plane directions. Hence, the number of domain orientations is four and two for the growth on (100)s- and (110)s-oriented substrates, respectively. Interestingly, the out-of-plane growth direction remains the same for both substrate orientations, suggesting a weak interfacial coupling between the two materials. Despite challenges associated with the heteroepitaxial growth of T-Nb2O5, the T-Nb2O5 films presented in this paper are a significant improvement in terms of structural quality compared to their polycrystalline counterparts.
- ItemThe Other Dimension—Tuning Hole Extraction via Nanorod Width(Basel : MDPI, 2022) Rosner, Tal; Pavlopoulos, Nicholas G.; Shoyhet, Hagit; Micheel, Mathias; Wächtler, Maria; Adir, Noam; Amirav, LilacSolar-to-hydrogen generation is a promising approach to generate clean and renewable fuel. Nanohybrid structures such as CdSe@CdS-Pt nanorods were found favorable for this task (attaining 100% photon-to-hydrogen production efficiency); yet the rods cannot support overall water splitting. The key limitation seems to be the rate of hole extraction from the semiconductor, jeopardizing both activity and stability. It is suggested that hole extraction might be improved via tuning the rod’s dimensions, specifically the width of the CdS shell around the CdSe seed in which the holes reside. In this contribution, we successfully attain atomic-scale control over the width of CdSe@CdS nanorods, which enables us to verify this hypothesis and explore the intricate influence of shell diameter over hole quenching and photocatalytic activity towards H2 production. A non-monotonic effect of the rod’s diameter is revealed, and the underlying mechanism for this observation is discussed, alongside implications towards the future design of nanoscale photocatalysts.
- ItemCombined toxicity of gas plasma treatment and nanoparticles exposure in melanoma cells in vitro(Basel : MDPI, 2021) Bekeschus, SanderDespite continuous advances in therapy, cancer remains a deadly disease. Over the past years, gas plasma technology emerged as a novel tool to target tumors, especially skin. Another promising anticancer approach are nanoparticles. Since combination therapies are becoming increas-ingly relevant in oncology, both gas plasma treatment and nanoparticle exposure were combined. A series of nanoparticles were investigated in parallel, namely, silica, silver, iron oxide, cerium oxide, titanium oxide, and iron-doped titanium oxide. For gas plasma treatment, the atmospheric pressure argon plasma jet kINPen was utilized. Using three melanoma cell lines, the two murine non-metastatic B16F0 and metastatic B16F10 cells and the human metastatic B-Raf mutant cell line SK-MEL-28, the combined cytotoxicity of both approaches was identified. The combined cytotoxicity of gas plasma treatment and nanoparticle exposure was consistent across all three cell lines for silica, silver, iron oxide, and cerium oxide. In contrast, for titanium oxide and iron-doped titanium oxide, significantly combined cytotoxicity was only observed in B16F10 cells.
- ItemMorphology, Optical Properties and Photocatalytic Activity of Photo- and Plasma-Deposited Au and Au/Ag Core/Shell Nanoparticles on Titania Layers(Basel : MDPI, 2018-7-6) Müller, Alexander; Peglow, Sandra; Karnahl, Michael; Kruth, Angela; Junge, Henrik; Brüser, Volker; Scheu, ChristinaTitania is a promising material for numerous photocatalytic reactions such as water splitting and the degradation of organic compounds (e.g., methanol, phenol). Its catalytic performance can be significantly increased by the addition of co-catalysts. In this study, Au and Au/Ag nanoparticles were deposited onto mesoporous titania thin films using photo-deposition (Au) and magnetron-sputtering (Au and Au/Ag). All samples underwent comprehensive structural characterization by grazing incidence X-ray diffraction (XRD), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). Nanoparticle distributions and nanoparticle size distributions were correlated to the deposition methods. Light absorption measurements showed features related to diffuse scattering, the band gap of titania and the local surface plasmon resonance of the noble metal nanoparticles. Further, the photocatalytic activities were measured using methanol as a hole scavenger. All nanoparticle-decorated thin films showed significant performance increases in hydrogen evolution under UV illumination compared to pure titania, with an evolution rate of up to 372 μL H2 h−1 cm−2 representing a promising approximately 12-fold increase compared to pure titania.
- ItemNanocomposites with p-and n-type conductivity controlled by type and content of nanotubes in thermosets for thermoelectric applications(Basel : MDPI, 2020) Kröning, Katharina; Krause, Beate; Pötschke, Petra; Fiedler, BodoIn this work, composites based on epoxy resin and various carbon nanotubes (CNTs) were studied regarding their thermoelectric properties. The epoxy composites were prepared by infiltration of preformed CNT buckypapers. The influence of different types of CNTs on the Seebeck coefficient was investigated, namely lab-made and commercially available multi walled carbon nanotubes (MWCNTs), lab-made nitrogen doped MWCNTs (N-MWCNT) and commercially available single walled carbon nanotubes (SWCNTs). It was found that only by varying the lab-made MWCNT content could both n-and p-type composites be produced with Seebeck coefficients between -9.5 and 3.1 µV/K. The incorporation of N-MWCNTs resulted in negative Seebeck coefficients of -11.4 to -17.4 µV/K. Thus, the Seebeck coefficient of pure SWCNT changed from 37.4 to -25.5 µV/K in the epoxy/1 wt. % SWCNT composite. A possible explanation for the shift in the Seebeck coefficient is the change of the CNTs Fermi level depending on the number of epoxy molecules on the CNT surface. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.