Open Access

This dissertation explores and tries to unravel the fundamental basis of G-quadruplex end-folding as well as G-quadruplex interactions with small molecules by thermodynamic and structural approaches. Selective targeting of G-quadruplexes with ligands remains elusive, either because the ligand has considerable binding affinity for other DNA structures or because it fails to discriminate between different G-quadruplex topologies. Unique structural motifs on the G-quadruplex may enhance or inhibit ligand binding to the G-quadruplex. For such aspects, it is necessary to understand the effect of G-quadruplex motifs or elements on the end-folding in order to better tune certain G-quadruplex topologies as model systems. Importantly for targeting G-quadruplex with ligands, motifs called Quadruplex-duplex (QD) junctions and interfaces are shown to be a binding hotspot for various G-quadruplex ligands containing an intercalator motif. Binding affinity and selectivity of the ligands are discussed with the support of the NMR structures.

In this thesis, new catalysts as well as unprecedented approaches for the valorization of sustainable carbon sources were investigated. The first part deals with the design of catalysts for photocatalytic CO2 reduction (Articles I&II). The promiscuous activity of phenolic acid decarboxylase from Bacillus subtilis (BsPAD) was found to catalyze CO2 reduction (Article I). This cofactor-free enzyme could facilitate the replacement of (noble) metal catalysts regularly employed in CO2 reduction. Based on these findings, additional enzyme catalysts were identified for photocatalytic CO2 reduction. The second part (Articles III-VII) focuses on the valorization of resources obtained from biomass, such as olive mill waste water or lignin, by the promising acyltransferases/hydrolase PestE from Pyrobaculum calidifontis VA1 (Articles IV-VII). The potential of PestE for the valorization of sustainable sources has been demonstrated by enzyme engineering and use in (chemo)enzymatic cascade reactions leading to value-added products.

Marine algae are essential for fixation of carbon dioxide, which they transform into complex polysaccharides. These carbohydrates are degraded e.g., by marine Bacteroidetes and the understanding of their decomposition mechanism can expand our knowledge how marine biomasses can be accessed. This understanding then gains insights into the marine carbon cycle. This thesis summarizes the current knowledge of marine enzymatic polysaccharide degradation in review Article I and extents a previously discovered ulvan degradation pathway in Article II with the description of a novel dehydratase involved in the ulvan degradation pathway. This enlarged ulvan-degradation pathway can be used to generate fermentable sugars from the algal derived polysaccharide ulvan. A potential biorefinery process is proposed in Article III, where B. licheniformis was engineered to degrade ulvan, thus establishing the initial steps for a microbial cell factory development. In addition to ulvan, also plenty of other complex carbohydrate sources are present in the ocean. The enzymatic elucidation principles previously developed were thus adapted towards a new marine carbohydrate. In Article IV a xylan utilization pathway was elucidated, using enzymes present in Flavimarina Hel_I_48 as model bacterium. The Flavimarina genome contains two separated genome clusters which potentially targets xylose containing polymers reflecting the diversity and adaptions towards different marine xylan-like substrates. Besides, marine Bacteroidetes are adapted towards decomposition of methylated polysaccharide, e.g., porphyran, via demethylation catalyzed by cytochrome P450 monooxygenases. This reaction results in the formation of toxic formaldehyde and thus the marine Bacteroidetes require formaldehyde detoxification principles. The analysis of potential formaldehyde detoxification mechanisms revealed a marine RuMP pathway (Article V) and a novel auxiliary activity of an alcohol dehydrogenase of which the encoding gene is adjacent to the demethylase cluster (Article VI).

This work investigated the enzymatic degradation of polyethylene terephthalate (PET) (ArticlesI and II) and polyvinyl alcohol (PVA) (Article III). Physical or chemical degradation of plastic polymers is often performed under extreme conditions like high temperatures or pressure. In comparison to that, recycling of plastics with enzymes can be carried out at ambient temperatures and neutral pH. Enzymes themselves are non- toxic, environmentally friendly, and have been used successfully in a variety of industrial processes. Enzymatic degradation of polyesters is well studied. Their heteroatomic backbone, which is connecting monomers via ester bonds offers a target for an enzymatic attack. Especially PET, one of the most common polyesters, has been in the focus of research. The first enzyme capable of degrading the polymer was found in 2005. Since then, researchers discovered several enzymes with similar functions and subjected them to enzyme engineering. Improving the enzyme's substrate affinity, activity, and stability aims at making PET recycling more efficient. Article I provides an overview of limitations that enzymatic PET recycling is still facing and the research carried out to overcome them. More precisely, enzyme−substrate interactions, thermostability, catalytic efficiency, and inhibition caused by oligomeric degradation intermediates are summarized and discussed in detail. Article II further addresses one of the above-mentioned limitations, namely product inhibition of PET hydrolyzing enzymes. We elucidated the crystal structure of TfCa, a carboxylesterase from Thermobifida fusca (T. fusca), and applied semi-rational enzyme engineering. The article discusses the structure-function relationship of TfCa based on the apo-structure as well as ligand-soaked structures. Furthermore, it compares the structures of TfCa and MHETase, another PET hydrolase helper enzyme. Lastly, we determined the substrate profile of the carboxylesterase based on terephthalate-based oligo-esters of various lengths and one ortho-phthalate ester. In a dual enzyme system, TfCa degraded intermediate products derived from the PET hydrolysis of a variant of PETase hydrolase from Ideonella sakaiensis (I. sakaiensis). The dual enzyme system utilized PET more efficiently in comparison to solely PETase due to relieved product inhibition. Since TfCa successfully degraded oligomeric intermediates, the reaction not only released terephthalic acid as the sole product but also increased the overall product yield. While PET contains an ester bond that can be attacked and hydrolyzed by esterases or lipases, PVA consists of a homoatomic C-C-backbone with repeating 1,3-diol units. The polymer is water soluble with remarkable physical properties such as thermostability and viscosity. PVA is often described as biodegradable, but microbial degradation is slow and frequently involves cost-intensive cofactors. In this study, we present an improved PVA polymer with derivatized side chains and an enzyme cascade that can degrade not only modified but also unmodified PVA in a one-pot reaction. The enzyme cascade consists of a lipase, an alcohol dehydrogenase (ADH), and a Baeyer-Villiger monooxygenase (BVMO). In comparison to the scarcely published research on PVA degradation with free enzyme, this cascade is not only independent from the frequently required cofactor pyrroloquinoline quinone (PQQ) but, in principle, contains an in vitro cofactor recycling mechanism.

Ziel der Arbeit war es, Mono-Dithiolen-Vanadiumkomplexe zu synthetisieren, die als Katalysatoren in Oxidationsreaktion von prochiralen Sulfiden zu chiralen Sulfoxiden getestet werden sollten. Es konnten verschiedene Ansätze entwickelt werden, die vielversprechend waren, um durch weitere Forschung Mono-Dithiolen-Vanadiumkomplexen erhalten zu können. Insbesondere konnte eine universell anwendbare Syntheseroute für die Verwendung von aliphatischen Dithiolenen in der Komplexsynthese erfolgreich gezeigt werden. Außerdem wurden neue Kristallstrukturen verschiedener Dithiolen-Vanadiumkomplexe erhalten.

In dieser Doktorarbeit konnte in zwei verschiedenen experimentellen Modellen der chronischen Pankreatitis in C57BL/6 Mäusen gezeigt werden, dass die chronische Pankreatitis mit einem Gewichtsverlust und einer Verminderung der muskuloskelettalen Kraft assoziiert sind. Untersuchungen im Kleintier-MRT belegten eine signifikante Verminderung des Durchmessers des Quadrizepsmuskels in beiden Modellen. Auf Proteinebene fanden sich im Skelettmuskel von Mäusen mit chronischer Pankreatitis Expressionssteigerungen von growth differentiation factor 8 (GDF8) und Muscle RING-finger protein-1 (MuRF1). Auf mRNA Ebene konnten wir zeigen, dass Activin A und das transforming growth factor β (TGFβ) in beiden Modellen erhöht waren, wohingegen Follistatin und teilweise auch Inhibin A vermindert waren. Die Anzahl apoptotischer Zellen stieg im Quadrizepsmuskel in beiden Modellen signifikant an, was darauf schließen lässt, dass die Apoptose beim Muskelabbau eine Rolle spielt. Des Weiteren fanden sich in Mäusen mit chronischer Pankreatitis und Sarkopenie Veränderungen des Serummetaboloms und des Stuhlmikrobioms, die jedoch in Abhängigkeit des verwendeten Modells stark variierten. Modellübergreifend war eine Vermehrung von Akkermansia spp. in der chronischen Pankreatitis nachweisbar.

Enzymes are well-known for being remarkably selective catalysts. They are often able to catalyse reactions for certain molecules while leaving other similar molecules completely unchanged. Nevertheless, many enzymes are capable of catalysing other reactions and/or transforming other substrates than their physiologically relevant activities. This phenomenon is referred to as enzyme promiscuity and it is thought to play an important role in the emergence of novel functions by providing a starting point for divergent evolution towards different enzymatic activities. It is important for enzymes to be selective to avoid harmful side-products and increase reaction efficiency, but often catalysts are not optimised beyond what is required for their function. Life profits from the cross-reactivity and enzyme promiscuity through accidental discovery of new helpful molecules and pathways, while using regulation to quickly adapt to changing circumstances. Enzymes are grouped together with other similar proteins into structural families and superfamilies. Members of a structural family share significant structural elements and often have similar catalytic mechanisms. However, they often catalyse very different chemical reactions and accept a variety of different substrates. Promiscuous activities are common within superfamilies, where the primary function of one family member is often found as promiscuous activity in other family members. Together with the structural similarities, this prevalent cross-reactivity suggests a common evolutionary origin. One of the largest structural superfamilies is the α/β-hydrolase-fold family. Despite sharing a highly conserved core structure, this superfamily is catalytically diverse and spans several distinct enzyme classes including hydrolases, acyltransferases, oxidoreductases, lyases, and isomerases. Epoxide hydrolases and dehalogenases of the α/β-hydrolase-fold family even share the same Asp/Glu-His-Asp catalytic triad and form similar covalent alkyl-enzyme reaction intermediates, yet they are known for attacking either epoxides or C-X bonds with perfect chemoselectivity. Although promiscuity is often observed within the α/β-hydrolase fold family and despite their mechanistic similarities, no α/β-hydrolases were known that exhibit both epoxide hydrolase and dehalogenase activity simultaneously. The versatility of the catalytic triads used by α/β-hydrolases makes these enzymes attractive targets for the conversion of catalytic activity through protein engineering. Several attempts were made to introduce dehalogenase activity in an epoxide hydrolase, and after several rounds of designing and screening different variants of the epoxide hydrolase PaeCIF from Pseudomonas aeruginosa, minor dehalogenase activity was detected for some of the variants. However, despite promising first results it proved extremely difficult to reliably reproduce the results, primarily due to expression problems and low sensitivity of the halide detection assays that were available at the time. Since the conversion proved to be more difficult than expected (unpublished data), it was decided to investigate other potential protein scaffolds. Considering the prevalence of catalytic promiscuity among members of the α/β-hydrolase-fold superfamily, and the close relationship and catalytic similarities between epoxide hydrolases and dehalogenases, it seemed odd that no enzyme is known to have both epoxide hydrolase and dehalogenase activity. We argued that it is highly probable that a promiscuous epoxide hydrolase-dehalogenase enzyme exists, but it simply has not been found yet due to the absence of sensitive high-throughput halide assays and not screening the right set of enzymes. Although several established assays were available for the determination of dehalogenase activity, these assays suffer major drawbacks. For example, one of the most popular assays, the Iwasaki assay, is not very sensitive and uses extremely toxic chemicals, while pH assays like the phenol red assay are inherently unreliable and insensitive due to the low buffer concentrations employed107,114. Thus, a new assay for the screening of dehalogenase activity through the selective detection of halides was developed115. The halide oxidation assay provides a safer, more reliable, and most importantly, much more sensitive method to detect dehalogenase activity. Using molecular phylogenetics, we studied the evolutionary relationship between epoxide hydrolases and dehalogenases to identify interesting extant epoxide hydrolases. Molecular phylogenetics uses a multiple sequence alignment of the amino acid or nucleotide sequences of extant enzymes to construct a phylogenetic tree. At first, we tried using a large dataset with almost 3,500 putative epoxide hydrolase and dehalogenase sequences, but we quickly realised the resulting phylogenetic tree was impractical. Most of the sequences in this large dataset were not characterised experimentally but annotated automatically based on their sequence similarity to a rather limited number of characterised sequences. Although automated annotations can be used as predictions for catalytic activity, they are often wrong. As we were particularly interested in the interface of both epoxide hydrolase and dehalogenase activities, we needed more certainty and a change in direction was necessary. Instead of trying to filter the α/β-hydrolase fold database, experimentally characterised sequences were collected through literature research. This smaller dataset consisting of characterised sequences resulted in a phylogenetic tree containing 45 epoxide hydrolases, 30 haloalkane dehalogenases and 7 haloacetate dehalogenases from a variety of different organisms. Ancestral sequence reconstruction was attempted for several interesting nodes in this phylogenetic tree. By combining the multiple sequence alignment, the evolutionary relationships from the phylogenetic tree, and evolutionary models, a hypothetical sequence of the theoretical ancestor can be determined. Unfortunately, it was difficult to get good soluble protein expression with the ancestral sequences and despite our best efforts it was not possible to obtain reliable and reproducible screening results. Instead of trying to improve protein expression and purification protocols for the ancestral sequences, we decided to focus on screening extant sequences with the newly developed halide oxidation assay to find a promiscuous epoxide hydrolase-dehalogenase. In addition to reconstructing ancestral sequences, eight extant epoxide hydrolases could be selected for screening towards dehalogenase activity and as promising potential engineering scaffolds from this phylogenetic tree. The eight selected epoxide hydrolases were screened for dehalogenase activity with several haloalkane substrates and the epoxide hydrolase CorEH from Corynebacterium sp. C12 was found to exhibit promiscuous dehalogenase activity. Interestingly, the measured concentrations of bromide for the initial hit with CorEH were only 150-250 nM, well below the lowest detection limit of 20 µM achievable in microtiter plate format with the Iwasaki assay. This means that the dehalogenase activity of CorEH would probably not have been detected were it not for the development of the sensitive halide oxidation assay. CorEH is an epoxide hydrolase that can also catalyse the dehalogenation of haloalkanes, particularly bromoalkanes such as 1-bromobutane and 1-bromohexane. The dehalogenase activity of wild-type CorEH with 1-bromobutane (0.25 nmol·min-1·mg-1) is about 4,000-fold lower than the average activity of several natural dehalogenases with two halide-stabilising residues (1 μmol·min-1·mg-1) and approximately 400-fold lower compared to the dehalogenases with a single halide-stabilising residue. The crystal structure of CorEH was determined to 2.2 Å. Our structure-function studies suggest that the dehalogenase activity of CorEH probably stems from the presence of at least one halide-stabilising residue. Unfortunately, this could not be confirmed experimentally via mutagenesis as the W100A variant lost both the dehalogenase and epoxide hydrolase activity in equal measure, making it difficult to demonstrate that W100 is involved in halide stabilisation. The loss of both activities for variant W100A can possibly be explained by the secondary function of the tryptophan; removal of W100 might lead to the incorrect positioning of the catalytic nucleophile for the nucleophilic attack involved in both epoxide hydrolysis and dehalogenation. Nevertheless, computational modelling of Michaelis-Menten complexes, utilising the crystal structure of CorEH, supports the hypothesis that the tryptophan W100 is involved in halide stabilisation in CorEH. Based on docking studies, the epoxide ring-opening tyrosine is also close enough to form hydrogen bonds to stabilise the substrate. However, it is also possible that like several characterised haloalkane dehalogenases, CorEH only uses a single residue to stabilise the halide. Removal of the tryptophan at the primary halide-stabilising position resulted in the loss of both activities, likely due to the loss of its secondary function to properly position the catalytic nucleophile. Substitution of the uncommon tryptophan in the HGxP-motif with phenylalanine does not completely remove the dehalogenase activity. Nevertheless, it causes a significant drop in both haloalkane dehalogenase and epoxide hydrolase activities, indicating that this residue is important for catalysis or the structural integrity of CorEH. Enzyme promiscuity plays an important role in enzyme evolution and the diversification of enzymes. Several researchers have attempted to interconvert epoxide hydrolase and dehalogenase activity, or to find an enzyme with both activities, without success. It would be hard to maintain the view that promiscuity is a fundamental property crucial to enzyme evolution if we could not observe promiscuity between two enzyme classes with such similar reaction mechanisms. Our findings show that dual epoxide hydrolase and dehalogenase activity can occur in one natural protein scaffold. We believe that we succeeded because we used a phylogenetic analysis of characterised sequences to select the right subset of epoxide hydrolases to investigate and due to the much more sensitive halide assays not available to those before us. The versatility of the catalytic triad in α/β-hydrolases combined with the variety of possible supporting residues found in both epoxide hydrolases and dehalogenases shows that catalytic mechanisms can be flexible. This flexibility allows space for diversification of catalytic residues without loss of function, giving rise to novel (promiscuous) functions and new cross-reactivities.

Abstract This work presents the reactivity and dissolution of an as‐polished and electrochemically pre‐treated polycrystalline Au electrode, which is used as a model system. The effect of the electrochemical pre‐treatment in corrosive 0.37 M HCl solutions on the Au surface roughness and dissolution is investigated by varying the number of pre‐treatment steps at 1.16 V against the reversible hydrogen electrode. It is shown that the first 10 s pre‐treatment of the as‐polished Au results in a higher surface roughness and thus higher electrochemically active surface area (ECSA) than that of the as‐polished Au. With the subsequent pre‐treatments, however, the ECSA is gradually decreasing reaching a steady value. The dissolution rate of the pre‐treated Au electrodes upon potential cycling in 0.1 M H2SO4 is determined by in situ inductively coupled plasma mass spectrometry. A non‐linear dependence of Au dissolution amount is found with respect to the number of pre‐treatments. The overall total Au dissolution rate follows a similar trend as ECSA/roughness. However, an important difference in the dissolution behavior is identified with respect to dissolution processes during Au oxidation (anodic dissolution) and Au reduction (cathodic dissolution): the former is more sensitive to the surface roughness. Thus, the ratio between Au anodic and cathodic dissolution amounts decreases substantially with decrease in surface roughness. This finding is explained by the slow and fast dissolution kinetics for anodic and cathodic processes, respectively. Current work further advances our understanding of the complex Au dissolution mechanism.

Abstract Amine transaminases (ATAs) are biocatalysts for the synthesis of chiral amines and can be identified in sequence databases by specific sequence motifs. This study shows that the activity level towards the model substrate 1‐phenylethylamine can be predicted solely from the sequence. To demonstrate this, 15 putative ATAs with a different distribution of hydrophobic or hydrophilic amino acid side chains near the active site were characterized. Hydrophobic side chains were associated with a high activity level and were a better predictor of activity than global sequence identity to known ATAs with high or low activities. Enzyme stability investigations revealed that four out of the 15 ATAs showed a good operational stability.

Abstract Azide‐modified nucleosides are important building blocks for RNA and DNA functionalization by click chemistry based on azide‐alkyne cycloaddition. This has put demand on synthetic chemistry to develop approaches for the preparation of azide‐modified nucleoside derivatives. We review here the available methods for the synthesis of various nucleosides decorated with azido groups at the sugar residue or nucleobase, their incorporation into oligonucleotides and cellular RNAs, and their application in azide‐alkyne cycloadditions for labelling and functionalization.

Bradyrhizobium diazoefficiens, a bacterial symbiont of soybean and other leguminous plants, enters a nodulation‐promoting genetic programme in the presence of host‐produced flavonoids and related signalling compounds. Here, we describe the crystal structure of an isoflavonoid‐responsive regulator (FrrA) from Bradyrhizobium, as well as cocrystal structures with inducing and noninducing ligands (genistein and naringenin, respectively). The structures reveal a TetR‐like fold whose DNA‐binding domain is capable of adopting a range of orientations. A single molecule of either genistein or naringenin is asymmetrically bound in a central cavity of the FrrA homodimer, mainly via C–H contacts to the π‐system of the ligands. Strikingly, however, the interaction does not provoke any conformational changes in the repressor. Both the flexible positioning of the DNA‐binding domain and the absence of structural change upon ligand binding are corroborated by small‐angle X‐ray scattering (SAXS) experiments in solution. Together with a model of the promoter‐bound state of FrrA our results suggest that inducers act as a wedge, preventing the DNA‐binding domains from moving close enough together to interact with successive positions of the major groove of the palindromic operator.

Abstract Chiral and enantiopure amines can be produced by enantioselective transaminases via kinetic resolution of amine racemates. This transamination reaction requires stoichiometric amounts of co‐substrate. A dual‐enzyme recycling system overcomes this limitation: l‐amino acid oxidases (LAAO) recycle the accumulating co‐product of (S)‐selective transaminases in the kinetic resolution of racemic amines to produce pure (R)‐amines. However, availability of suitable LAAOs is limited. Here we use the heterologously produced, highly active fungal hcLAAO4 with broad substrate spectrum. H2O2 as byproduct of hcLAAO4 is detoxified by a catalase. The final system allows using sub‐stoichiometric amounts of 1 mol% of the transaminase co‐substrate as well as the initial application of l‐amino acids instead of α‐keto acids. With an optimized protocol, the synthetic potential of this kinetic resolution cascade was proven at the preparative scale (>90 mg) by the synthesis of highly enantiomerically pure (R)‐methylbenzylamine (>99 %ee) at complete conversion (50 %).

Abstract Desulfarculus baarsii and Desulfurivibrio alkaliphilus are strictly anaerobic bacteria existing in marine sediments. D. baarsii gains energy through reducing sulphate and D. alkaliphilus is able to reduce elemental sulphur, thiosulphate and polysulphide in seawater. Both organisms were previously identified as key organisms in sediment derived, bidirectional electroactive biofilms. Here, we investigated the electrochemical performance of these two bacteria in bio‐electrochemical systems and their possible involvement in anodic and cathodic reactions. The results show that D. baarsii was unable to donate or accept electrons to/from an electrode, while D. alkaliphilus was able to catalyse both anodic and cathodic reactions and interact with the electrode through direct or potentially indirect electron transfer. Raman spectra of D. alkaliphilus electrode biofilms showed a high similarity to Geobacter sulfurreducens biofilms, including the specific bands of cytochromes b and c, explaining the electroactivity of D. alkaliphilus in bioelectrochemical reactions.

Abstract Rice husk, one of the main side products in the rice production, and its sustainable management represent a challenge in many countries. Herein, we describe the use of this abundant agricultural bio‐waste as feedstock for the preparation of silver‐containing carbon/silica nano composites with antimicrobial properties. The synthesis was performed using a fast and cheap methodology consisting of wet impregnation followed by pyrolysis, yielding C/SiO2 composite materials doped with varying amounts of silver from 28 to 0.001 wt %. The materials were fully characterized and their antimicrobial activity against ESKAPE pathogens, namely E. faecium, S. aureus, K. pneumoniae, A. baumannii, P. aeruginosa, and E. coli, and the pathogenic yeast C. albicans was investigated. Sensitivities of these strains against the prepared materials were demonstrated, even with exceptional low amounts of 0.015 m% silver. Hence, we report a straightforward method for the synthesis of antimicrobial agents from abundant sources which addresses urgent questions like bio‐waste valorization and affordable alternatives to increasingly fewer effective antibiotics.

Introduction Neurofilament light (NfL) can be detected in blood of healthy individuals and at elevated levels in those with different neurological diseases. We investigated if the choice of biological matrix can affect results when using NfL as biomarker in epidemiological studies. Method We obtained paired serum and EDTA-plasma samples of 299 individuals aged 37–67 years (BiDirect study) and serum samples of 373 individuals aged 65–83 years (MEMO study). In BiDirect, Passing–Bablok analyses were performed to assess proportional and systematic differences between biological matrices. Associations between serum or EDTA-plasma NfL and renal function (serum creatinine, serum cystatin C, glomerular filtration rate, and kidney disease) were investigated using linear or logistic regression, respectively. All regression coefficients were estimated (1) per one ng/L increase and (2) per one standard deviation increase (standardization using z-scores). In MEMO, regression coefficients were estimated (1) per one ng/L increase of serum or calculated EDTA-plasma NfL and (2) per one standard deviation increase providing a comparison to the results from BiDirect. Results We found proportional and systematic differences between paired NfL measurements in BiDirect, i.e., serum NfL [ng/L] = −0.33 [ng/L] + 1.11 × EDTA-plasma NfL [ng/L]. Linear regression coefficients for the associations between NfL and renal function did not vary between the different NfL measurements. In MEMO, one standard deviation increase in serum NfL was associated with greater changes in the outcomes than in BiDirect. Conclusion Although there are differences between serum and EDTA-plasma NfL, results can be used interchangeably if standardized values are used.

N6-methyladenosine (m6A) RNA methylation is an emerging epigenetic modification in recent years and epigenetic regulation of the immune response has been demonstrated, but the potential role of m6A modification in GBM tumor microenvironment (TME) cell infiltration and stemness remain unknown. The m6A modification patterns of 310 GBM samples were comprehensively evaluated based on 21 m6A regulators, and we systematically correlated these modification patterns with TME cell infiltration characteristics and stemness characteristics. Construction of m6Ascore to quantify the m6A modification patterns of individual GBM samples using a principal component analysis algorithm. We identified two distinct patterns of m6A modification. The infiltration characteristics of TME cells in these two patterns were highly consistent with the immunophenotype of the GBM, including the immune activation differentiation pattern and the immune desert dedifferentiation pattern. We also identified two modes of regulation of immunity and stemness by m6A methylation. Stromal activation and lack of effective immune infiltration were observed in the high m6Ascore subtype. Pan-cancer analysis results illustrate a significant correlation between m6AScore and tumor clinical outcome, immune infiltration, and stemness. Our work reveals that m6A modifications play an important role in the development of TME and stemness diversity and complexity. Patients with a low m6AScore showed significant therapeutic advantages and clinical benefits. Assessing the m6A modification pattern of individual tumors will help enhance our knowledge of TME infiltration and stemness characteristics, contribute to the development of immunotherapeutic strategies.

: The quality of biospecimens stored in a biobank depends tremendously on the technical personnel responsible for processing, storage, and release of biospecimens. Adequate training of these biobank employees would allow harmonization of correct sample handling and thus ensure a high and comparable quality of samples across biobank locations. However, in Germany there are no specific training opportunities for technical biobank staff. To understand the educational needs of the technical personnel a web-based survey was sent to all national biobanks via established e-mail registers. In total, 79 biobank employees completed the survey, including 43 technicians. The majority of the participating technical personnel stated that they had worked in a biobank for less than three years and had never participated in an advanced training. Three-quarters of the technicians indicated that they were not able to understand English content instantly. Based on these results and the results of a workshop with 16 biobank technicians, 41 learning objectives were formulated. These learning objectives can be used as a basis for advanced training programs for technical personnel in biobanks. Setting up courses based on the identified learning objectives for this group of biobank staff could contribute to harmonization and sustainability of biospecimen quality.

(1) The serine protease inhibitor Kazal type 1 (SPINK1) inhibits trypsin activity in zymogen granules of pancreatic acinar cells. Several mutations in the SPINK1 gene are associated with acute recurrent pancreatitis (ARP) and chronic pancreatitis (CP). The most common variant is SPINK1 p.N34S. Although this mutation was identified two decades ago, the mechanism of action has remained elusive. (2) SPINK1 and human cationic trypsin (TRY1) were expressed in E. coli, and inhibitory activities were determined. Crystals of SPINK1–TRY1 complexes were grown by using the hanging-drop method, and phases were solved by molecular replacement. (3) Both SPINK1 variants show similar inhibitory behavior toward TRY1. The crystal structures are almost identical, with minor differences in the mutated loop. Both complexes show an unexpected rotamer conformation of the His63 residue in TRY1, which is a member of the catalytic triad. (4) The SPINK1 p.N34S mutation does not affect the inhibitory behavior or the overall structure of the protein. Therefore, the pathophysiological mechanism of action of the p.N34S variant cannot be explained mechanistically or structurally at the protein level. The observed histidine conformation is part of a mechanism for SPINK1 that can explain the exceptional proteolytic stability of this inhibitor.

Nucleoredoxin (Nrx) belongs to the Thioredoxin protein family and functions in redox-mediated signal transduction. It contains the dithiol active site motif Cys-Pro-Pro-Cys and interacts and regulates different proteins in distinct cellular pathways. Nrx was shown to be catalytically active in the insulin assay and recent findings indicate that Nrx functions, in fact, as oxidase. Here, we have analyzed Nrx in the mammalian retina exposed to (perinatal) hypoxia-ischemia/reoxygenation, combining ex vivo and in vitro models. Our data show that Nrx regulates cell differentiation, which is important to (i) increase the number of glial cells and (ii) replenish neurons that are lost following the hypoxic insult. Nrx is essential to maintain cell morphology. These regulatory changes are related to VEGF but do not seem to be linked to the Wnt/β-catenin pathway, which is not affected by Nrx knock-down. In conclusion, our results strongly suggest that hypoxia-ischemia could lead to alterations in the organization of the retina, related to changes in RPE cell differentiation. Nrx may play an essential role in the maintenance of the RPE cell differentiation state via the regulation of VEGF release.

Background: Each measurement is subject to measurement uncertainty (MU). Consequently, each measurement of plasma glucose concentration used for diagnosis and monitoring of diabetes mellitus (DM) is affected. Although concepts and methods of MU are well established in many fields of science and technology, they are presently only incompletely implemented by medical laboratories, neglecting MU of target values of internal quality control (IQC) materials. Methods: An empirical and practical approach for the estimation of MU based on the analysis of routine IQC using control samples with assigned target values is presented. Its feasibility is demonstrated exemplarily by analyzing IQC data from one year obtained for glucose employing the hexokinase method with IQC of two different concentrations. Results: Combined relative extended (k = 2) MU comprising bias, coefficient of variation (CV), and MU of the target values assigned to control materials were about 9% with a lower (~ 56 mg/dL; ~3.1 mmol/L) and 8% with a higher (~ 346 mg/dL; ~19.2 mmol/L) concentration sample, analyzing IQC of one year from three different devices. Conclusions: Estimation of MU in this study is quite reliable due to the large number of IQC data from one year. The MU of the target values of the commercial control material in this study was considerably larger than other MU contributions, ie, standard deviation and bias. In the future, the contribution of MU of commercial IQC should be addressed more carefully and technologies to measure glucose should be geared toward smaller MU possible, as needed, especially for glucose concentration measurements in diagnosis and management of DM.

With the aim to discover and create suitable biocatalysts for the synthesis of chiral amines in a faster and more efficient way, this thesis includes protein engineering studies (Article I), explores transaminase substrate specificities (Articles II and IV), and an ultrahigh-throughput growth system-based for the directed evolution of amine-forming enzymes (Article III). The protein engineering studies described in Article I deal with the creation of a (R)-amine transaminase activity in the α-amino acid transaminase scaffold to expand our knowledge of the evolutionary relationship between amine transaminase and α-amino acid transaminase. Article II describes the broadening of the limited substrate scope of transaminases to enable the conversion of bulky substrates. In Article III, a growth selection system is described for an ultra-high throughput screening strategy to accelerate the identification of desired mutants, which can be widely applied to the directed evolution of amine-forming enzymes.

The hairpin ribozyme is a small Mg2+-dependent catalytic RNA molecule able to catalyze the trans-cleavage of an RNA substrate via a reversible trans-esterification mechanism. In this study, the cleavage activities of several fragmented hairpin ribozyme systems were examined. Due to the complex catalytic structure of the hairpin ribozyme, a new boronic acid ester was used as a covalent linkage to hold the folding of the functional system. It has been demonstrated the possibility of replacing the phosphodiester linkage, at specific positions, with a boronic acid ester to restore or improve the catalytic activity of fragmented hairpin ribozyme.

β-Glucosidases (Bgls) convert cellobiose and other soluble cello-oligomers into glucose and play important roles in fundamental biological processes, providing energy sources in living organisms. Bgls are essential terminal enzymes of cellulose degradation systems and attractive targets for lignocellulose-based biotechnological applications. Characterization of novel Bgls is important for broadening our knowledge of this enzyme class and can provide insights into its further applications. In this study, we report the biochemical and structural analysis of a Bgl from the hemicellulose-degrading thermophilic anaerobe Thermoanaerobacterium saccharolyticum (TsaBgl). TsaBgl exhibited its maximum hydrolase activity on p-nitrophenyl-β-d-glucopyranoside at pH 6.0 and 55 °C. The crystal structure of TsaBgl showed a single (β/α)8 TIM-barrel fold, and a β8-α14 loop, which is located around the substrate-binding pocket entrance, showing a unique conformation compared with other structurally known Bgls. A Tris molecule inhibited enzyme activity and was bound to the active site of TsaBgl coordinated by the catalytic residues Glu163 (proton donor) and Glu351 (nucleophile). Titration experiments showed that TsaBgl belongs to the glucose-tolerant Bgl family. The gatekeeper site of TsaBgl is similar to those of other glucose-tolerant Bgls, whereas Trp323 and Leu170, which are involved in glucose tolerance, show a unique configuration. Our results therefore improve our knowledge about the Tris-mediated inhibition and glucose tolerance of Bgl family members, which is essential for their industrial application.

Ongoing resistance developments against antibiotics that also affect last-resort antibiotics require novel antibacterial compounds. Strategies to discover such novel structures have been dimerization or hybridization of known antibacterial agents. We found novel antibacterial agents by dimerization of indols and hybridization with carbazoles. They were obtained in a simple one-pot reaction as bisindole tetrahydrocarbazoles. Further oxidation led to bisindole carbazoles with varied substitutions of both the indole and the carbazole scaffold. Both the tetrahydrocarbazoles and the carbazoles have been evaluated in various S. aureus strains, including MRSA strains. Those 5-cyano substituted derivatives showed best activities as determined by MIC values. The tetrahydrocarbazoles partly exceed the activity of the carbazole compounds and thus the activity of the used standard antibiotics. Thus, promising lead compounds could be identified for further studies.

Monodithiolenkomplexe des Wolframs und des Molybdäns des Typs [M(CO)2(dt)(PP)] (M= Mo, W; dt= Dithiolen; PP= Bisphosphan) waren bisher nur wenig zugänglich und entsprechend kaum untersucht. Im Rahmen dieser Arbeit wurden diverse Variationen an Dithiolen- und Phosphan-Liganden eingeführt und die erhaltenen Komplexe umfassend charakterisiert. Ein besonderer Fokus wurde hierfür auf die redoxbasierte Reaktivität dieser spannenden Komplexklasse gelegt, sodass eine Aktivierung von molekularem Stickstoff im Rahmen einer Kleinmolekülaktivierung ermöglicht werden sollte. Während der Untersuchungen konnte ein erstes Beispiel für die Generierung eines Dithiolen-Sulfonium-Liganden basierend auf einer Reaktivität gegenüber dem Kleinmolekül Dichlormethan erhalten werden.