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Publikation Definition of the binding specificity of the T7 bacteriophage primase by analysis of a protein binding microarray using a thermodynamic model(Oxford University Press, 10.04.2024) Lipps, GeorgProtein binding microarrays (PBM), SELEX, RNAcompete and chromatin-immunoprecipitation have been intensively used to determine the specificity of nucleic acid binding proteins. While the specificity of proteins with pronounced sequence specificity is straightforward, the determination of the sequence specificity of proteins of modest sequence specificity is more difficult. In this work, an explorative data analysis workflow for nucleic acid binding data was developed that can be used by scientists that want to analyse their binding data. The workflow is based on a regressor realized in scikit-learn, the major machine learning module for the scripting language Python. The regressor is built on a thermodynamic model of nucleic acid binding and describes the sequence specificity with base- and position-specific energies. The regressor was used to determine the binding specificity of the T7 primase. For this, we reanalysed the binding data of the T7 primase obtained with a custom PBM. The binding specificity of the T7 primase agrees with the priming specificity (5′-GTC) and the template (5′-GGGTC) for the preferentially synthesized tetraribonucleotide primer (5′-pppACCC) but is more relaxed. The dominant contribution of two positions in the motif can be explained by the involvement of the initiating and elongating nucleotides for template binding.01A - Beitrag in wissenschaftlicher ZeitschriftPublikation Initial primer synthesis of a DNA primase monitored by real-time NMR spectroscopy(American Chemical Society, 27.03.2024) Wu, Pengzhi; Zehnder, Johannes; Schröder, Nina; Blümmel, Pascal E. W.; Salmon, Loïc; Damberger, Fred. F.; Lipps, Georg; Allain, Frédéric H.-T.; Wiegand, ThomasPrimases are crucial enzymes for DNA replication, as they synthesize a short primer required for initiating DNA replication. We herein present time-resolved nuclear magnetic resonance (NMR) spectroscopy in solution and in the solid state to study the initial dinucleotide formation reaction of archaeal pRN1 primase. Our findings show that the helix-bundle domain (HBD) of pRN1 primase prepares the two substrates and then hands them over to the catalytic domain to initiate the reaction. By using nucleotide triphosphate analogues, the reaction is substantially slowed down, allowing us to study the initial dinucleotide formation in real time. We show that the sedimented protein–DNA complex remains active in the solid-state NMR rotor and that time-resolved 31P-detected cross-polarization experiments allow monitoring the kinetics of dinucleotide formation. The kinetics in the sedimented protein sample are comparable to those determined by solution-state NMR. Protein conformational changes during primer synthesis are observed in time-resolved 1H-detected experiments at fast magic-angle spinning frequencies (100 kHz). A significant number of spectral changes cluster in the HBD pointing to the importance of the HBD for positioning the nucleotides and the dinucleotide.01A - Beitrag in wissenschaftlicher ZeitschriftPublikation Editorial: The RNA revolution and cancer(Frontiers Research Foundation, 20.05.2024) Dlamini, Zodwa; Ladomery, Michael R.; Kahraman, AbdullahRNA biology has revolutionized cancer understanding and treatment, especially in endocrine-related malignancies. This editorial highlights RNA's crucial role in cancer progression, emphasizing its influence on tumor heterogeneity and behavior. Processes like alternative splicing and noncoding RNA regulation shape cancer biology, with microRNAs, long noncoding RNAs, and circular RNAs orchestrating gene expression dynamics. Aberrant RNA signatures hold promise as diagnostic and prognostic biomarkers in endocrine-related cancers. Recent findings, such as aberrant PI3Kδ splice isoforms and epithelial-mesenchymal transition-related lncRNA signatures, unveil potential therapeutic targets for personalized treatments. Insights into m6A-associated lncRNA prognostic models and the function of lncRNA LINC00659 in gastric cancer represents ongoing research in this field. As understanding of RNA's role in cancer expands, personalized therapies offer transformative potential in managing endocrine-related malignancies. This signifies a significant stride towards precision oncology, fostering innovation for more effective cancer care.01A - Beitrag in wissenschaftlicher ZeitschriftPublikation Assessment of the electrolyte heterogeneity of tissues in mandibular bone-infiltrating head and neck cancer using laser-induced breakdown spectroscopy(MDPI, 23.02.2024) Winnand, Philipp; Börnsen, Klaus Olaf; Ooms, Mark; Heitzer, Marius; Vohl, Nils; Lammert, Matthias; Hölzle, Frank; Modabber, AliLaser-induced breakdown spectroscopy (LIBS) was recently introduced as a rapid bone analysis technique in bone-infiltrating head and neck cancers. Research efforts on laser surgery systems with controlled tissue feedback are currently limited to animal specimens and the use of nontumorous tissues. Accordingly, this study aimed to characterize the electrolyte composition of tissues in human mandibular bone-infiltrating head and neck cancer. Mandible cross-sections from 12 patients with bone-invasive head and neck cancers were natively investigated with LIBS. Representative LIBS spectra (n = 3049) of the inferior alveolar nerve, fibrosis, tumor stroma, and cell-rich tumor areas were acquired and histologically validated. Tissue-specific differences in the LIBS spectra were determined by receiver operating characteristics analysis and visualized by principal component analysis. The electrolyte emission values of calcium (Ca) and potassium (K) significantly (p < 0.0001) differed in fibrosis, nerve tissue, tumor stroma, and cell-rich tumor areas. Based on the intracellular detection of Ca and K, LIBS ensures the discrimination between the inferior alveolar nerve and cell-rich tumor tissue with a sensitivity of ≥95.2% and a specificity of ≥87.2%. The heterogeneity of electrolyte emission values within tumorous and nontumorous tissue areas enables LIBS-based tissue recognition in mandibular bone-infiltrating head and neck cancer.01A - Beitrag in wissenschaftlicher ZeitschriftPublikation Atomically precise surface chemistry of zirconium and hafnium metal oxo clusters beyond carboxylate ligands(Royal Society of Chemistry, 2024) Unniram, Ajmal; Pokratath, Rohan; Parammal, Muhammed Jibin; Dhaene, Evert; Van den Eynden, Dietger; Balog, Sandor; Prescimone, Alessandro; Infante, Ivan; Shahgaldian, Patrick; De Roo, JonathanThe effectiveness of nanocrystals in many applications depends on their surface chemistry. Here, we leverage the atomically precise nature of zirconium and hafnium oxo clusters to gain fundamental insight into the thermodynamics of ligand binding. Through a combination of theoretical calculations and experimental spectroscopic techniques, we determine the interaction between the M6O88+ (M = Zr, Hf) cluster surface and various ligands: carboxylates, phosphonates, dialkylphosphinates, and monosubstituted phosphinates. We refute the common assumption that the adsorption energy of an adsorbate remains unaffected by the surrounding adsorbates. For example, dialkylphosphinic acids are too sterically hindered to yield complete ligand exchange, even though a single dialkylphosphinate has a high binding affinity. Monoalkyl or monoaryl phosphinic acids do replace carboxylates quantitatively and we obtained the crystal structure of M6O8H4(O2P(H)Ph)12 (M = Zr, Hf), giving insight into the binding mode of monosubstituted phosphinates. Phosphonic acids cause a partial structural reorganization of the metal oxo cluster into amorphous metal phosphonate as indicated by pair distribution function analysis. These results rationalize the absence of phosphonate-capped M6O8 clusters and the challenge in preparing Zr phosphonate metal–organic frameworks. We thus further reinforce the notion that monoalkylphosphinates are carboxylate mimics with superior binding affinity.01A - Beitrag in wissenschaftlicher ZeitschriftPublikation Manganese reductive dissolution coupled to Sb mobilization in contaminated shooting range soil(Springer, 10.04.2024) Costa, Lara; Martinez, Mathieu; Suleiman, Marcel; Keiser, Rolf; Lehmann, Moritz; Lenz, MarkusA “redox-stat” RMnR bioreactor was employed to simulate moderately reducing conditions (+ 420 mV) in Sb-contaminated shooting range soils for approximately 3 months, thermodynamically favoring Mn(IV) reduction. The impact of moderately reducing conditions on elemental mobilization (Mn, Sb, Fe) and speciation [Sb(III) versus Sb(V); Fe2+/Fe3+] was compared to a control bioreactor RCTRL without a fixed redox potential. In both bioreactors, reducing conditions were accompanied by an increase in effluent Sb(V) and Mn(II) concentrations, suggesting that Sb(V) was released through microbial reduction of Mn oxyhydroxide minerals. This was underlined by multiple linear regression analysis showing a significant (p < 0.05) relationship between Mn and Sb effluent concentrations. Mn concentration was the sole variable exhibiting a statistically significant effect on Sb in RMnR, while under the more reducing conditions in RCTRL, pH and redox potential were also significant. Analysis of the bacterial community composition revealed an increase in the genera Azoarcus, Flavisolibacter, Luteimonas, and Mesorhizobium concerning the initial soil, some of which are possible key players in the process of Sb mobilization. The overall amount of Sb released in the RMnR (10.40%) was virtually the same as in the RCTRL (10.37%), which underlines a subordinate role of anoxic processes, such as Fe-reductive dissolution, in Sb mobilization. This research underscores the central role of relatively low concentrations of Mn oxyhydroxides in influencing the fate of trace elements. Our study also demonstrates that bioreactors operated as redox-stats represent versatile tools that allow quantifying the contribution of specific mechanisms determining the fate of trace elements in contaminated soils. Key points • “Redox-stat” reactors elucidate Sb mobilization mechanisms • Mn oxyhydroxides microbial reductive dissolution has a major role in Sb mobilization in soils under moderately reducing conditions • Despite aging the soil exhibited significant Sb mobilization potential, emphasizing persistent environmental effects01A - Beitrag in wissenschaftlicher ZeitschriftPublikation Cell invasive amyloid assemblies from SARS-CoV-2 peptides can form multiple polymorphs with varying neurotoxicity(Royal Society of Chemistry, 2024) Sanislav, Oana; Tetaj, Rina; Ratcliffe, Julian; Phillips, William; Klein, Annaleise R.; Sethi, Ashish; Zhou, Jiangtao; Mezzenga, Raffaele; Saxer, Sina; Charnley, Mirren; Annesley, Sarah J.; Reynolds, Nicholas P.The neurological symptoms of COVID-19, often referred to as neuro-COVID include neurological pain, memory loss, cognitive and sensory disruption. These neurological symptoms can persist for months and are known as Post-Acute Sequalae of COVID-19 (PASC). The molecular origins of neuro-COVID, and how it contributes to PASC are unknown, however a growing body of research highlights that the self-assembly of protein fragments from SARS-CoV-2 into amyloid nanofibrils may play a causative role. Previously, we identified two fragments from the SARS-CoV-2 proteins, Open Reading Frame (ORF) 6 and ORF10, that self-assemble into neurotoxic amyloid assemblies. Here we further our understanding of the self-assembly mechanisms and nano-architectures formed by these fragments and their biological responses. By solubilising the peptides in a fluorinated solvent, we eliminate insoluble aggregates in the starting materials (seeds) that change the polymorphic landscape of the assemblies. The resultant assemblies are dominated by structures with higher free energies (e.g. ribbons and amorphous aggregates) that are less toxic to cultured neurons but do affect their mitochondrial respiration. We also show the first direct evidence of cellular uptake of viral amyloids. This work highlights the importance of understanding the polymorphic behaviour of amyloids and the correlation to neurotoxicity, particularly in the context of neuro-COVID and PASC.01A - Beitrag in wissenschaftlicher ZeitschriftPublikation Neoantigen vaccine nanoformulations based on chemically synthesized minimal mRNA (CmRNA): small molecules, big impact(Nature, 18.01.2024) Imani, Saber; Tagit, Oya; Pichon, ChantalRecently, chemically synthesized minimal mRNA (CmRNA) has emerged as a promising alternative to in vitro transcribed mRNA (IVT-mRNA) for cancer therapy and immunotherapy. CmRNA lacking the untranslated regions and polyadenylation exhibits enhanced stability and efficiency. Encapsulation of CmRNA within lipid-polymer hybrid nanoparticles (LPPs) offers an effective approach for personalized neoantigen mRNA vaccines with improved control over tumor growth. LPP-based delivery systems provide superior pharmacokinetics, stability, and lower toxicity compared to viral vectors, naked mRNA, or lipid nanoparticles that are commonly used for mRNA delivery. Precise customization of LPPs in terms of size, surface charge, and composition allows for optimized cellular uptake, target specificity, and immune stimulation. CmRNA-encoded neo-antigens demonstrate high translational efficiency, enabling immune recognition by CD8+ T cells upon processing and presentation. This perspective highlights the potential benefits, challenges, and future directions of CmRNA neoantigen vaccines in cancer therapy compared to Circular RNAs and IVT-mRNA. Further research is needed to optimize vaccine design, delivery, and safety assessment in clinical trials. Nevertheless, personalized LPP-CmRNA vaccines hold great potential for advancing cancer immunotherapy, paving the way for personalized medicine.01A - Beitrag in wissenschaftlicher ZeitschriftPublikation Investigation of factors influencing seed load analysis results(Hochschule für Life Sciences FHNW, 2023) Baumann, Patrick; Tagit, Oya11 - Studentische ArbeitPublikation Elucidating the Mechanism of Action of STING Degradation(Hochschule für Life Sciences FHNW, 2023) Schürch, Stefanie; Lipps, Georg; Novartis11 - Studentische Arbeit