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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.
- ItemStatistical Analysis of Scanning Fluorescence Correlation Spectroscopy Data Differentiates Free from Hindered Diffusion(Washington, DC : Soc., 2018-7-20) Schneider, Falk; Waithe, Dominic; Lagerholm, B. Christoffer; Shrestha, Dilip; Sezgin, Erdinc; Eggeling, Christian; Fritzsche, MarcoCells rely on versatile diffusion dynamics in their plasma membrane. Quantification of this often heterogeneous diffusion is essential to the understanding of cell regulation and function. Yet such measurements remain a major challenge in cell biology, usually due to low sampling throughput, a necessity for dedicated equipment, sophisticated fluorescent label strategies, and limited sensitivity. Here, we introduce a robust, broadly applicable statistical analysis pipeline for large scanning fluorescence correlation spectroscopy data sets, which uncovers the nanoscale heterogeneity of the plasma membrane in living cells by differentiating free from hindered diffusion modes of fluorescent lipid and protein analogues.
- Item1D p–n Junction Electronic and Optoelectronic Devices from Transition Metal Dichalcogenide Lateral Heterostructures Grown by One-Pot Chemical Vapor Deposition Synthesis(Weinheim : Wiley-VCH, 2021) Najafidehaghani, Emad; Gan, Ziyang; George, Antony; Lehnert, Tibor; Ngo, Gia Quyet; Neumann, Christof; Bucher, Tobias; Staude, Isabelle; Kaiser, David; Vogl, Tobias; Hübner, Uwe; Kaiser, Ute; Eilenberger, Falk; Turchanin, AndreyLateral heterostructures of dissimilar monolayer transition metal dichalcogenides provide great opportunities to build 1D in-plane p–n junctions for sub-nanometer thin low-power electronic, optoelectronic, optical, and sensing devices. Electronic and optoelectronic applications of such p–n junction devices fabricated using a scalable one-pot chemical vapor deposition process yielding MoSe2-WSe2 lateral heterostructures are reported here. The growth of the monolayer lateral heterostructures is achieved by in situ controlling the partial pressures of the oxide precursors by a two-step heating protocol. The grown lateral heterostructures are characterized structurally and optically using optical microscopy, Raman spectroscopy/microscopy, and photoluminescence spectroscopy/microscopy. High-resolution transmission electron microscopy further confirms the high-quality 1D boundary between MoSe2 and WSe2 in the lateral heterostructure. p–n junction devices are fabricated from these lateral heterostructures and their applicability as rectifiers, solar cells, self-powered photovoltaic photodetectors, ambipolar transistors, and electroluminescent light emitters are demonstrated. © 2021 The Authors. Advanced Functional Materials published by Wiley-VCH GmbH
- ItemBlock Copolymers Featuring Highly Photostable Photoacids Based on Vinylnaphthol: Synthesis and Self-Assembly(Weinheim : Wiley-VCH, 2020) Wendler, Felix; Tom, Jessica C.; Sittig, Maria; Biehl, Philip; Dietzek, Benjamin; Schacher, Felix H.The synthesis of a photoresponsive amphiphilic diblock quarterpolymer containing 5-vinyl-1-naphthol (VN) as a photostable photoacidic comonomer is presented. The preparation is realized via a sequential reversible addition fragmentation chain transfer (RAFT) polymerization starting from a nona(ethylene glycol) methyl ether methacrylate (MEO9MA/“O”) hydrophilic block, which is then used as a macro-RAFT agent in the terpolymerization of styrene (S), 2-vinylpyridine (2VP), and TBS-protected VN (tVN). The terpolymerization proceeds in a controlled fashion and two diblock quarterpolymers, P(Om)-b-P(Sx-co-2VPy-co-VNz), with varying functional comonomer compositions are prepared. These diblock quarterpolymers form spherical core-corona micelles in aqueous media according to dynamic light scattering (DLS) and cryogenic transmission electron microscopy (cryo-TEM). Upon irradiation, the photoacids within the micellar core experience a drastic increase in acidity causing a proton transfer from the photoacid to neighboring 2VP units. As a result, the hydrophilic/hydrophobic balance of the entire assembly is shifted, and the encapsulated cargo is released. © 2020 The Authors. Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
- ItemThe Bouguer-Beer-Lambert Law: Shining Light on the Obscure(Weinheim : Wiley-VCH Verl., 2020) Mayerhöfer, Thomas G.; Pahlow, Susanne; Popp, JürgenThe Beer-Lambert law is unquestionably the most important law in optical spectroscopy and indispensable for the qualitative and quantitative interpretation of spectroscopic data. As such, every spectroscopist should know its limits and potential pitfalls, arising from its application, by heart. It is the goal of this work to review these limits and pitfalls, as well as to provide solutions and explanations to guide the reader. This guidance will allow a deeper understanding of spectral features, which cannot be explained by the Beer-Lambert law, because they arise from electromagnetic effects/the wave nature of light. Those features include band shifts and intensity changes based exclusively upon optical conditions, i. e. the method chosen to record the spectra, the substrate and the form of the sample. As such, the review will be an essential tool towards a full understanding of optical spectra and their quantitative interpretation based not only on oscillator positions, but also on their strengths and damping constants.
- ItemA Review on Data Fusion of Multidimensional Medical and Biomedical Data(Basel : MDPI, 2022) Azam, Kazi Sultana Farhana; Ryabchykov, Oleg; Bocklitz, ThomasData fusion aims to provide a more accurate description of a sample than any one source of data alone. At the same time, data fusion minimizes the uncertainty of the results by combining data from multiple sources. Both aim to improve the characterization of samples and might improve clinical diagnosis and prognosis. In this paper, we present an overview of the advances achieved over the last decades in data fusion approaches in the context of the medical and biomedical fields. We collected approaches for interpreting multiple sources of data in different combinations: image to image, image to biomarker, spectra to image, spectra to spectra, spectra to biomarker, and others. We found that the most prevalent combination is the image-to-image fusion and that most data fusion approaches were applied together with deep learning or machine learning methods.
- ItemNovel Biobased Self-Healing Ionomers Derived from Itaconic Acid Derivates(Weinheim : Wiley-VCH, 2021) Meurer, Josefine; Hniopek, Julian; Dahlke, Jan; Schmitt, Michael; Popp, Jürgen; Zechel, Stefan; Hager, Martin D.This article presents novel biobased ionomers featuring self-healing abilities. These smart materials are synthesized from itaconic acid derivates. Large quantities of itaconic acid can be produced from diverse biomass like corn, rice, and others. This study presents a comprehensive investigation of their thermal and mechanical properties via differential scanning calorimetry (DSC), thermo gravimetric analysis (TGA), and FT-Raman and FT-IR measurements as well as dynamic mechanic analysis. Within all these measurements, different kinds of structure-property relationships could be derived from these measurements. For example, the proportion of ionic groups enormously influences the self-healing efficiency. The investigation of the self-healing abilities reveals healing efficiencies up to 99% in 2 h at 90 °C for the itaconic acid based ionomer with the lowest ionic content. © 2020 The Authors. Macromolecular Rapid Communications published by Wiley-VCH GmbH
- ItemDetermination of side products in the photocatalytic generation of hydrogen with copper photosensitizers by resonance Raman spectroelectrochemistry(London : RSC Publishing, 2016) Zhang, Ying; Heberle, Martin; Wächtler, Maria; Karnahl, Michael; Dietzek, BenjaminA combination of UV-Vis and resonance Raman spectroscopy in conjunction with electrochemistry is employed to reveal the nature of a side product formed when using heteroleptic Cu(I)-photosensitizers [(P^P)Cu(N^N)]+ for photocatalytic hydrogen generation. It is shown that homoleptic [Cu(N^N)2]+ complexes are formed under oxidative conditions confirming a proposed deactivation pathway.
- ItemExcited-State Dynamics in Borylated Arylisoquinoline Complexes in Solution and in cellulo(Weinheim : Wiley-VCH, 2023) Yang, Tingxiang; Valavalkar, Abha; Romero‐Arenas, Antonio; Dasgupta, Anindita; Then, Patrick; Chettri, Avinash; Eggeling, Christian; Ros, Abel; Pischel, Uwe; Dietzek‐Ivanšić, BenjaminTwo four-coordinate organoboron N,C-chelate complexes with different functional terminals on the PEG chains are studied with respect to their photophysical properties within human MCF-7 cells. Their excited-state properties are characterized by time-resolved pump-probe spectroscopy and fluorescence lifetime microscopy. The excited-state relaxation dynamics of the two complexes are similar when studied in DMSO. Aggregation of the complexes with the carboxylate terminal group is observed in water. When studying the light-driven excited-state dynamics of both complexes in cellulo, i. e., after being taken up into human MCF-7 cells, both complexes show different features depending on the nature of the anchoring PEG chains. The lifetime of a characteristic intramolecular charge-transfer state is significantly shorter when studied in cellulo (360±170 ps) as compared to in DMSO (∼960 ps) at 600 nm for the complexes with an amino group. However, the kinetics of the complexes with the carboxylate group are in line with those recorded in DMSO. On the other hand, the lifetimes of the fluorescent state are almost identical for both complexes in cellulo. These findings underline the importance to evaluate the excited-state properties of fluorophores in a complex biological environment in order to fully account for intra- and intermolecular effects governing the light-induced processes in functional dyes.
- ItemStealth Effect of Short Polyoxazolines in Graft Copolymers: Minor Changes of Backbone End Group Determine Liver Cell-Type Specificity(Washington, DC : ACS Publications, 2021) Muljajew, Irina; Huschke, Sophie; Ramoji, Anuradha; Cseresnyés, Zoltán; Hoeppener, Stephanie; Nischang, Ivo; Foo, Wanling; Popp, Jürgen; Figge, Marc Thilo; Weber, Christine; Bauer, Michael; Schubert, Ulrich S.; Press, Adrian T.Dye-loaded micelles of 10 nm diameter formed from amphiphilic graft copolymers composed of a hydrophobic poly(methyl methacrylate) backbone and hydrophilic poly(2-ethyl-2-oxazoline) side chains with a degree of polymerization of 15 were investigated concerning their cellular interaction and uptake in vitro as well as their interaction with local and circulating cells of the reticuloendothelial system in the liver by intravital microscopy. Despite the high molar mass of the individual macromolecules (Mn ≈ 20 kg mol-1), backbone end group modification by attachment of a hydrophilic anionic fluorescent probe strongly affected the in vivo performance. To understand these effects, the end group was additionally modified by the attachment of four methacrylic acid repeating units. Although various micelles appeared similar in dynamic light scattering and cryo-transmission electron microscopy, changes in the micelles were evident from principal component analysis of the Raman spectra. Whereas an efficient stealth effect was found for micelles formed from polymers with anionically charged or thiol end groups, a hydrophobic end group altered the micelles' structure sufficiently to adapt cell-type specificity and stealth properties in the liver. © 2021 The Authors. Published by American Chemical Society.