Inst. Biotechnologie

464 Items

Recent Submissions
Analytical methods and thermodynamic frameworks for efficient biocatalytic nucleoside synthesis via nucleoside phosphorylases

Kaspar, Felix (2021)

Nucleosides and nucleoside analogs are indispensable biomolecules which serve as buildings blocks of DNA and RNA, pharmaceuticals and molecular biology tools. Sparked by the demand for synthetic access to these compounds, a variety of approaches for nucleoside synthesis has been developed. Among these, biocatalytic nucleoside synthesis via nucleoside phosphorylases promises a solution to the lo...

Retention time prediction using neural networks increases identifications in crosslinking mass spectrometry

Giese, Sven H. ; Sinn, Ludwig R. ; Wegner, Fritz ; Rappsilber, Juri (2021-05-28)

Crosslinking mass spectrometry has developed into a robust technique that is increasingly used to investigate the interactomes of organelles and cells. However, the incomplete and noisy information in the mass spectra of crosslinked peptides limits the numbers of protein–protein interactions that can be confidently identified. Here, we leverage chromatographic retention time information to aid ...

3D bioprinting of tissue-specific osteoblasts and endothelial cells to model the human jawbone

Amler, Anna-Klara ; Thomas, Alexander ; Tüzüner, Selin ; Lam, Tobias ; Geiger, Michel-Andreas ; Kreuder, Anna-Elisabeth ; Palmer, Chris ; Nahles, Susanne ; Lauster, Roland ; Kloke, Lutz (2021-03-01)

Jawbone differs from other bones in many aspects, including its developmental origin and the occurrence of jawbone-specific diseases like MRONJ (medication-related osteonecrosis of the jaw). Although there is a strong need, adequate in vitro models of this unique environment are sparse to date. While previous approaches are reliant e.g. on scaffolds or spheroid culture, 3D bioprinting enables f...

The Nonribosomal Peptide Valinomycin: From Discovery to Bioactivity and Biosynthesis

Huang, Shuhui ; Liu, Yushi ; Liu, Wan-Qiu ; Neubauer, Peter ; Li, Jian (2021-04-08)

Valinomycin is a nonribosomal peptide that was discovered from Streptomyces in 1955. Over the past more than six decades, it has received continuous attention due to its special chemical structure and broad biological activities. Although many research papers have been published on valinomycin, there has not yet been a comprehensive review that summarizes the diverse studies ranging from struct...

Coxsackievirus B3—Its Potential as an Oncolytic Virus

Geisler, Anja ; Hazini, Ahmet ; Heimann, Lisanne ; Kurreck, Jens ; Fechner, Henry (2021-04-21)

Oncolytic virotherapy represents one of the most advanced strategies to treat otherwise untreatable types of cancer. Despite encouraging developments in recent years, the limited fraction of patients responding to therapy has demonstrated the need to search for new suitable viruses. Coxsackievirus B3 (CVB3) is a promising novel candidate with particularly valuable features. Its entry receptor, ...

Clean Bioprinting – Fabrication of 3D Organ Models Devoid of Animal Components

Berg, Johanna ; Kurreck, Jens (2021-04-20)

Bioprinting is a rapidly developing technology that enables the exact positioning of living cells embedded in bio-materials in precise spatial arrangements to fabricate engineered tissues and organs. While the ultimate goal of bio­printing approaches is to produce organs for transplantation purposes, bioprinted organ models also hold great potential for research purposes to serve as alternative...

Developmental Landscape of Potential Vaccine Candidates Based on Viral Vector for Prophylaxis of COVID-19

Bezbaruah, Rajashri ; Borah, Pobitra ; Kakoti, Bibhuti Bhushan ; Al-Shar’I, Nizar A. ; Chandrasekaran, Balakumar ; Jaradat, Da’san M. M. ; Al-Zeer, Munir A. ; Abu-Romman, Saeid (2021-04-15)

Severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, arose at the end of 2019 as a zoonotic virus, which is the causative agent of the novel coronavirus outbreak COVID-19. Without any clear indications of abatement, the disease has become a major healthcare threat across the globe, owing to prolonged incubation period, high prevalence, and absence of existing drugs or vaccines. Developm...

Ten simple rules for hosting artists in a scientific lab

Rillig, Matthias C. ; Bonneval, Karine ; Lutz, Christian de ; Lehmann, Johannes ; Mansour, India ; Rapp, Regine ; Spačal, Saša ; Meyer, Vera (2021-02-25)

Hosting an artist in a scientific lab is likely a new experience for many scientists in the natural and engineering sciences, and perhaps also for many artists, yet it can be a very beneficial experience for both parties [1]. “Art and science are in a tension that is most fruitful when these disciplines observe and penetrate each other and experience how much of the other they themselves still ...

Verbesserung der Zytotoxizität eines TRAIL-exprimierenden onkolytischen Adenovirus in Melanomzellen durch Knockdown des antiapoptotischen Proteins Mcl-1

Tolksdorf, Beatrice Dorothea Friederike (2021)

Die Inzidenz des malignen Melanoms hat in den letzten Jahrzehnten zugenommen. Weltweit wird jedes Jahr bei ungefähr 300.000 Patienten ein Melanom diagnostiziert. Das Melanom gehört damit zu den zehn häufigsten Tumorarten in Nordamerika, Westeuropa und Ozeanien. In den letzten Jahren hat die Zulassung von selektiven Inhibitoren für MAP-Kinasen BRAF und MEK sowie von Immuncheckpoint-Inhibitoren, ...

Histone Deacetylases in the Inflamed Intestinal Epithelium—Promises of New Therapeutic Strategies

Gerbeth, Lorenz ; Glauben, Rainer (2021-03-26)

The intestinal epithelium is a complex, dynamic barrier that separates luminal contents from the immune compartment while mediating nutrient absorption and controlled passage of antigens to convey oral tolerance. A compromised epithelial barrier often leads to inflammation because immune cells in the lamina propria come into direct contact with luminal antigens. Defects in epithelial cell funct...

Engineering cofactor metabolism for improved protein and glucoamylase production in Aspergillus niger

Sui, Yu-fei ; Schütze, Tabea ; Ouyang, Li-ming ; Lu, Hongzhong ; Liu, Peng ; Xiao, Xianzun ; Qi, Jie ; Zhuang, Ying-Ping ; Meyer, Vera (2020-10-23)

Background: Nicotinamide adenine dinucleotide phosphate (NADPH) is an important cofactor ensuring intracellular redox balance, anabolism and cell growth in all living systems. Our recent multi-omics analyses of glucoamylase (GlaA) biosynthesis in the filamentous fungal cell factory Aspergillus niger indicated that low availability of NADPH might be a limiting factor for GlaA overproduction. Res...

Substrate-Flexible Two-Stage Fed-Batch Cultivations for the Production of the PHA Copolymer P(HB-co-HHx) With Cupriavidus necator Re2058/pCB113

Santolin, Lara ; Waldburger, Saskia ; Neubauer, Peter ; Riedel, Sebastian L. (2021-03-22)

Recent studies of the impact and dimension of plastic pollution have drawn the attention to finding more sustainable alternatives to fossil-based plastics. Microbially produced polyhydroxyalkanoates (PHAs) biopolymers are strong candidates to replace conventional plastic materials, due to their true biodegradability and versatile properties. However, widespread use of these polymers is still hi...

Low-quality animal by-product streams for the production of PHA-biopolymers: fats, fat/protein-emulsions and materials with high ash content as low-cost feedstocks

Saad, Victoria ; Gutschmann, Björn ; Grimm, Thomas ; Widmer, Torsten ; Neubauer, Peter ; Riedel, Sebastian L. (2020-12-26)

Objective: The rapid accumulation of crude-oil based plastics in the environment is posing a fundamental threat to the future of mankind. The biodegradable and bio-based polyhydroxyalkanoates (PHAs) can replace conventional plastics, however, their current production costs are not competitive and therefore prohibiting PHAs from fulfilling their potential. Results: Different low-quality animal b...

Wissenschaftsjahr mit „Bio“ — Technologie und Wissen kommunizieren

Lang, Christine (2020-10-14)

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Inspired by the human placenta: a novel 3D bioprinted membrane system to create barrier models

Kreuder, Anna-Elisabeth ; Bolaños-Rosales, Aramis ; Palmer, Christopher ; Thomas, Alexander ; Geiger, Michel-Andreas ; Lam, Tobias ; Amler, Anna-Klara ; Markert, Udo R. ; Lauster, Roland ; Kloke, Lutz (2020-09-24)

Barrier organ models need a scaffold structure to create a two compartment culture. Technical filter membranes used most often as scaffolds may impact cell behaviour and present a barrier themselves, ultimately limiting transferability of test results. In this work we present an alternative for technical filter membrane systems: a 3D bioprinted biological membrane in 24 well format. The biologi...

Route efficiency assessment and review of the synthesis of β-nucleosides via N-glycosylation of nucleobases

Kaspar, Felix ; Stone, M. Rhia L. ; Neubauer, Peter ; Kurreck, Anke (2020-11-19)

Nucleosides and their analogs are biomolecules central to nearly all areas of life science. Consequently, a variety of approaches have been developed to prepare these compounds. These methods typically employ N-glycosylation as a key step which installs a sugar moiety on a heterocyclic nucleobase. However, these methods vary drastically regarding their synthetic strategy, number of steps, yield...

Peptide retention in hydrophilic strong anion exchange chromatography is driven by charged and aromatic residues

Giese, Sven H. ; Ishihama, Yasushi ; Rappsilber, Juri (2018-03-12)

Hydrophilic strong anion exchange chromatography (hSAX) is becoming a popular method for the prefractionation of proteomic samples. However, the use and further development of this approach is affected by the limited understanding of its retention mechanism and the absence of elution time prediction. Using a set of 59 297 confidentially identified peptides, we performed an explorative analysis ...

Noncovalently associated peptides observed during liquid chromatography-mass spectrometry and their effect on cross-link analyses

Giese, Sven H. ; Belsom, Adam ; Sinn, Ludwig ; Fischer, Lutz ; Rappsilber, Juri (2019-01-16)

Cross-linking mass spectrometry draws structural information from covalently linked peptide pairs. When these links do not match to previous structural models, they may indicate changes in protein conformation. Unfortunately, such links can also be the result of experimental error or artifacts. Here, we describe the observation of noncovalently associated peptides during liquid chromatography-m...

Optimized fragmentation regime for diazirine photo-cross-linked peptides

Giese, Sven H. ; Belsom, Adam ; Rappsilber, Juri (2016-07-25)

Cross-linking/mass spectrometry has evolved into a robust technology that reveals structural insights into proteins and protein complexes. We leverage a new tribrid instrument with improved fragmentation capacities in a systematic comparison to identify which fragmentation method would be best for the identification of cross-linked peptides. Specifically, we explored three fragmentation methods...

A study into the Collision-induced Dissociation (CID) behavior of cross-linked peptides

Giese, Sven H. ; Fischer, Lutz ; Rappsilber, Juri (2016-03-01)

Cross-linking/mass spectrometry resolves protein–protein interactions or protein folds by help of distance constraints. Cross-linkers with specific properties such as isotope-labeled or collision-induced dissociation (CID)- cleavable cross-linkers are in frequent use to simplify the identification of cross-linked peptides. Here, we analyzed the mass spectrometric behavior of 910 unique crosslin...