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Item Open Access Foam control in biotechnological processes : challenges and opportunities(2024) Tiso, Till; Demling, Philipp; Karmainski, Tobias; Oraby, Amira; Eiken, Jens; Liu, Luo; Bongartz, Patrick; Wessling, Matthias; Desmond, Peter; Schmitz, Simone; Weiser, Sophie; Emde, Frank; Czech, Hannah; Merz, Juliane; Zibek, Susanne; Blank, Lars M.; Regestein, LarsFoam formation is a massive challenge in submerged aerated bioprocesses, e.g., in beer fermentation. While the use of antifoam may easily overcome foaming at laboratory scale, it is often an unattractive solution since the challenge remains in future upscaling, as reduced mass transfer and extra steps in product purification and analytics result in increased costs. Interestingly, the number of studies tackling this challenge is relatively low, although literature suggests a range of alternatives, from avoiding foaming to means of controlling or even using foaming as an in situ product removal. Here we give an overview of the topic in five subsections. (1) We argue that a sound understanding of the molecular origin of foaming can facilitate solutions for overcoming the challenge while introducing some long-known challenges (i.e., in beer fermentation). We then review in (2) the apparent avoidance of foam formation before we in (3) summarize possibilities to reduce and control foam after its formation. Subsequently, in (4), we discuss possible solutions that take advantage of foam formation, for example, via foam fractionation for in situ product removal. Finally, in (5), we provide an overview of microbial strain engineering approaches to cope with some aspects of foaming in fermentations. With this review, we would like to sensitize and inform the interested reader while offering an overview of the current literature for the expert, particularly with regard to the foam special issue in Discover Chemical Engineering.Item Open Access Automation of customizable library preparation for next-generation sequencing into an open microfluidic platform(2024) Hoffmann, Anne; Timm, Anke; Johnson, Christopher; Rupp, Steffen; Grumaz, ChristianNext-generation sequencing (NGS) is becoming more relevant for medical diagnostics, especially for using cell-free DNA to monitor response to therapy in cancer management, as high sensitivity of NGS enables detection of rare events. Sequencing Library preparation is a time-consuming and complex process, and large-scale liquid handlers are often used for automation. However, for smaller labs and low-to-medium throughput samples, these liquid handlers are expensive and need experts for handling. This work presents a proof-of-concept for library preparation on a commercially available and open lab-on-a-chip platform, which provides an alternative automation for low-to-medium throughput requirements. It covers common library preparation steps optimized to a microfluidic environment that include customizable PCR for target enrichment, end-repair, adapter ligation, nucleic acid purification via magnetic beads, and an integrated quantification step. The functionality of the cartridge is demonstrated with reference cfDNA containing different allelic frequencies of seven known mutations. Processing the samples in the cartridge reveals highly comparable results to manual processing (Pearson r = 0.94) based on amplicon sequencing. Summarized, the proposed automated lab-on-a-chip workflow for customizable library preparation could further pave the way for NGS to evolve from a technology used for research purposes to one that is applied in routine cancer management.Item Open Access Discrimination of pancreato-biliary cancer and pancreatitis patients by non-invasive liquid biopsy(2024) Hartwig, Christina; Müller, Jan; Klett, Hagen; Kouhestani, Dina; Mittelstädt, Anke; Anthuber, Anna; David, Paul; Brunner, Maximilian; Jacobsen, Anne; Glanz, Karolina; Swierzy, Izabela; Roßdeutsch, Lotta; Klösch, Bettina; Grützmann, Robert; Wittenberger, Timo; Sohn, Kai; Weber, Georg F.Background. Current diagnostics for the detection of pancreato-biliary cancers (PBCs) need to be optimized. We therefore propose that methylated cell-free DNA (cfDNA) derived from non-invasive liquid biopsies serves as a novel biomarker with the ability to discriminate pancreato-biliary cancers from non-cancer pancreatitis patients. Methods. Differentially methylated regions (DMRs) from plasma cfDNA between PBCs, pancreatitis and clinical control samples conditions were identified by next-generation sequencing after enrichment using methyl-binding domains and database searches to generate a discriminatory panel for a hybridization and capture assay with subsequent targeted high throughput sequencing. Results. The hybridization and capture panel, covering around 74 kb in total, was applied to sequence a cohort of 25 PBCs, 25 pancreatitis patients, 25 clinical controls, and seven cases of Intraductal Papillary Mucinous Neoplasia (IPMN). An unbiased machine learning approach identified the 50 most discriminatory methylation markers for the discrimination of PBC from pancreatitis and controls resulting in an AUROC of 0.85 and 0.88 for a training ( n = 45) and a validation ( n = 37) data set, respectively. The panel was also able to distinguish high grade from low grade IPMN samples. Conclusions. We present a proof of concept for a methylation biomarker panel with better performance and improved discriminatory power than the current clinical marker CA19-9 for the discrimination of pancreato-biliary cancers from non-cancerous pancreatitis patients and clinical controls. This workflow might be used in future diagnostics for the detection of precancerous lesions, e.g. the identification of high grade IPMNs vs. low grade IPMNs.Item Open Access Proton-conducting (blend) membranes based on sulfonated/phosphonated and basic polymers(2024) De Azpiazu Nadal, Ignasi; Tovar, Günter (Prof.)Aiming at new proton-conducting membranes, this thesis deals with the syntheses and characterizations of highly sulfonated poly(arylene sulfides) and other polysulfides for application as polymer electrolytes. The study focuses mainly on the analysis of the polymer structures that would improve the conductivity of current proton conducting membranes while maintaining their mechanical stability. In a first step, several polymers are obtained from which poly(arylene sulfide)s polymers look more promising for further functionalization. They are obtained by using mild reaction conditions of a polycondensation reaction between 4,4 ́-thiobisbenzenethiol (TBBT) and decafluorobiphenyl. Optimization of this reaction allows for the obtainment of higher molecular weights than the ones reported in the literature. In a second step, poly(arylene sulfides) were phosphonated and sulfonated by a nucleophilic aromatic substitution (SNAr) displacement reaction of the fluorine atoms of the fluorinated polymer sub-units using different agents. Highly sulfonated polymers were obtained when using sodium 3-mercapto-1-propanesulfonate and resulted in water soluble ionomers. Kinetic studies of this reaction were performed and several new sulfonated poly(arylene sulfides) were obtained. Finally, stable polymer electrolyte membrane (PEM) with enhanced mechanical and chemical stability were obtained by blending these obtained ionomers with polybenzimidazole (PBIOO). These membranes were further characterized and in the best case a PEM with new sulfonated ionomer showed a conductivity 40 % higher than Nafion 212, used as a golden reference material. The best performing PEM’s obtained were further used in an electrolytic cell being part of eSCALED, a H2020 (MSC-ITN-2017. GA# 765376) European project which aim is to obtain a device that does the artificial photosynthesis in a more efficient way than the current devices.