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Master Thesis (m/w/d): TUM Campus Straubing for Biotechnology and Sustainability

At TUM Campus Straubing for Biotechnology and Sustainability, the Chair of Chemistry of Biogenic Resources (Prof. Volker Sieber) deals with the development of chemical and biotechnological processes for the conversion of biomass to base chemicals, biofuels, and fine chemicals. For this work, the focus of research is on protein biochemistry (enzyme
engineering), molecular biology (cloning, mutagenesis), microbiology (biotransformation, fermentation), chemical (organic synthesis, heterogenic catalysis), & analytical methods (chromatography, spectroscopy, electrophoreses).

In the field of Multienzyme Cascades: Converging conversion of renewable raw materials to base chemicals via multienzymatic cascades.

– Development of an enzymatic cascade for the converging conversion of various sugar acids into chemicals
– Enzyme and medium engineering
– Production and analysis of enzymes (kcat, Km, Tm, T50)
– Synthesis and analysis of products (HPLC, GC, NMR)

– Majoring in biochemistry, chemistry, biotechnology, biocatalysis or related science majors with prove of above average academic performance in the past
– Having experience working with enzymes
– Experience with the analysis of product mixtures
– Curiosity and interest in scientific problem solving
– Strong dedication, soft skills and creative thinking

We offer:
– Balanced supervision and weekly scientific seminars
– A young and international team of talented scientists
– Working at the new TUM Campus Straubing of Biotechnology and Sustainability
– Possibility of providing a Hiwi position
– Possibility of authorship in publication

I am looking forward to receiving your application via email to luca.schmermund[ät]tum.de. Regarding any inquiries contact me
by email. The application phase starts immediately and ends when a suitable candidate has been found.

Kontakt: Dr. Luca Schmermund; luca.schmermund[ät]tum.de

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Master Thesis: Ultrafast Energy Conversion in Biological Photosystems

Kurzbeschreibung: Do you want use femtosecond laser-spectroscopy to study photosynthetic energy-conversion?

Beschreibung: All forms of higher life on earth rely directly or indirectly on photosynthesis – the biological conversion of light into chemical energy. Substantial attention is being paid to these crucial processes, not only in terms of fundamental principles of nature, but also as inspiration for artificial light-driven systems such as photovoltaics and photocatalysts.

The photosystems of green plants and oxygen-evolving bacteria, whose core functionality is maintained by the two pigment-protein complexes Photosystem I and Photosystem II, are especially privileged due to their direct importance to human life.

In this project, we investigate the processes involved from light capture, via energy transfer, to charge separation in the photosynthetic reaction center of Photosystem I. The tools of choice is temperature-controlled and time-resolved absorption spectroscopies, where we can follow dynamics down to only ~10 femtoseconds.

The successfully completed project will provide important insight into the functionality of this complex system, aiding both in the theoretical modeling of pigment-protein complexes and in the interpretation of data from biochemical experiments.

Kontaktperson: Jürgen Hauer, juergen.hauer[ät]tum.de

Link: https://www.department.ch.tum.de/dynspec/startseite/

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Master’s Thesis: Modification of a testing unit for the gas phase hydrogenation of aldehydes

For students of chemical engineering or chemistry with focus technical chemistry (Professur für Anorganische Chemie, Prof. Dr. K. Köhler & Max Hiller)

Motivation and problem definition:
Hydrogenations belong to the most relevant reactions in industrial practice. Structure-activity relationships and mechanistic investigations are important for catalyst optimization. For that reason, an existing and well-working fixed bed catalyst reactor and the testing unit shall be expanded to gas phase hydrogenations of C3-C4-aldehydes.
A liquid feed pump and a vaporization unit shall be installed for constant feed flow in the gas phase. Both conversion and selectivity shall be monitored online via gas chromatography. Critical reaction parameters for the hydrogenation of aldehydes (p, T, GHSV, feed flow, H2:feed ratio, catalyst bed dilution, …) shall be determined. The hydrogenation of croton aldehyde shall be investigated with focus onto the reaction mechanism.

In addition, copper-zinc catalysts shall be synthesized by various synthesis approaches (precipitation, ligand removal, impregnation, …) to aim catalyst with different copper zinc interfaces. The influence of these interfaces shall be investigated both regarding catalytic activity and selectivity. Characterization techniques shall be used to characterize the catalyst (XRD, BET/BJH, TPR/ TPD, IR, Cu-surface area determination, …). The spent catalyst shall be characterized after transfer under inert conditions.

– Dimensioning of a catalyst test unit, calculation of useful reaction conditions
– Development of methods for online gas chromatography for product analysis
– Modification of a catalyst test unit, installation of pumps, vaporization of liquids
– Standard synthesis of heterogeneous catalysts (co-precipitation, -impregnation, …)
– Standard characterization techniques (XRD, BET/BJH, TPR/ TPD, elemental analysis)

Contact: Prof. Dr. Klaus Köhler, klaus.koehler[ät]tum.de
Max Hiller, max.hiller[ät]tum.de, 089-289-54224, lab CRC-2042

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Chromatographie: Charakterisierung und Optimierung eines Proteinreinigungs-Prozesses

Kurzbeschreibung: Aufgaben: Protein Herstellung mit E.coli, Chromatographie Methodiken, Auswertung und Validierung experimenteller Daten.

Anforderungen: strukturiertes Arbeiten, Interesse an neuen Technologien, von Vorteil: Kenntnisse im Bereich Chromatographie, Mikrobiologie, Organische Chemie.

Beschreibung: Im Downstream Processing von Proteinen leistet die Chromatographie einen essentiellen Teil, ist jedoch auch wesentlicher Kostentreiber bei der bioprozesstechnischen Herstellung. Es ist daher wichtig, die Unit Operation technologisch und schließlich
wirtschaftlich zu optimieren. Dabei gilt es, die grundlegenden Mechanismen in der Chromatographie Säule besser zu verstehen. Während die Effekte des hydrodynamischen Transports gut beschrieben sind, ist die theoretische Beschreibung des Adsorptionsprozesses von Analyten an das Resin weniger ausgereift. Im Rahmen des Projektes werden die adsorptiven Effekte einer auf Silica basierenden Ion Pairing
Chromatographie untersucht. Dies erfolgt experimentell und theoretisch über die Betrachtung der Oberflächenchemie. Etablierte Modelle und Hypothesen werden dabei dem momentanen Stand der Technik gegenüber gestellt und verglichen. Die dabei resultierende Daten werden verwendet um den Prozess weiter anzupassen und zu verbessern.

Kontaktperson: Tobias Steegmüller, tobias.steegmueller[ät]tum.de

Link: https://www.mw.tum.de/en/stt/bioseparation-engineering/

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Master’s Thesis in Immune Protein Engineering

Short description:
A Master’s thesis project is available in the laboratory for Cellular Protein Biochemistry at the TUM, Chemistry.

Our laboratory aims at understanding how proteins fold, assemble and are scrutinized by the cellular quality control machinery. We are particularly interested in proteins of the secretory pathway that allow cells to interact with their environment. We use an interdisciplinary approach from protein biochemistry to cell biology to analyze the machinery and mechanisms that monitor cellular protein biogenesis. One major model system in our laboratory are interleukins, key signaling molecules in the immune system.

Current projects:
One major interest of our lab is the cellular folding, assembly and quality control of IL- 12 family cytokines. In recent years, we have provided insights into their biogenesis and structural setup (e.g. Müller et al, PNAS, 2019; Meier et al., Nat Commun, 2019). Using these insights, we further seek to understand cellular interactions of IL-12 cytokine subunits and rationally engineer cytokines as potential biopharmaceuticals. The candidate will work on engineering approaches in our lab and have the opportunity to learn and apply a wide variety of state-of-the-art techniques from mammalian cell biology to biophysical protein characterization and work on an exciting project of immediate biomedical relevance. The starting date is flexible upon mutual agreement.

Your profile:
The applicant should hold a BSc in Biochemistry or related fields. Experience in experimental protein biochemistry and cell biology is a benefit.
The application should contain a CV, (degree) certificates and a letter of motivation. Please send your application (single pdf-document) by email to: isabel.aschenbrenner[ät]tum.de

Link: http://www.cell.ch.tum.de

Kontaktperson: Isabel Aschenbrenner, isabel.aschenbrenner[ät]tum.de

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MSc Thesis Position in Functional Genomics: Phase Separation Events in Human Cells

The Jae lab at the Gene Center (Genzentrum) of the Ludwig-Maximilians Universität Munich (LMU) is looking for a highly motivated and skilled master’s student.
Our lab studies the genetic profile of human disease processes with a focus on mitochondrial defects using a combination of CRISPR/Cas9 genome engineering and unbiased genome-wide mutagenesis in haploid human cells (Science, 2013; 2014). High-resolution genetic interaction mapping can be used to discover novel factors in important cellular pathways in an unbiased fashion, annotate the function of ‘orphan genes’ and yield new strategies to therapeutically combat disease (Science, 2015). This approach allows us to directly dissect virtually any cellular phenotype that can be quantified at the single cell level by flow cytometry – previous application include identification of novel factors controlling immune checkpoints (Nature, 2017a), as well as AKT signaling and other key cellular processes (Nature, 2017b). In one of our most recent publications, we deciphered the mitochondrial stress signaling from the organelle to the nucleus in response to a multitude of mitochondrial stressors in human cells (Nature, 2020).

We are seeking a highly motivated and ambitious candidate who shares our dedication to science and enthusiasm for interdisciplinary research with an excellent degree in biochemistry, biomedicine, human biology, biology, or similar. Excellent communication skills and a solid background in molecular and cellular biology techniques, as well as genetics are required.
As part of our young and independent group you are expected to be able to perform challenging experiments, analyze data of high complexity, and work well in a team. A successful candidate will have the chance to employ state-of-the-art techniques ranging from large-scale genome-wide screens to genome engineering and various tools for the mechanistic dissection of candidate gene function.
The project focuses on phase separation events and the formation of stress granules in cells in which proteomic integrity has been challenged, as is frequently observed in human disease. While these events form an important cytoprotective mechanism, aberrant stress granule formation and other phase separation processes are also associated with devastating neurodegenerative defects such as amyotrophic lateral sclerosis (ALS). To dissect composition, kinetics and dynamics of stress granules in response to various stress signals, the successful candidate will employ cutting edge tools in the area of genome editing, cell biology and biochemistry.

Link: Jae Lab – Functional Genomics – Gene Center Munich – LMU Munich (uni-muenchen.de)

Kontaktperson: AG Jae – Genzentrum LMU, eckl[ät]genzentrum.lmu.de

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Bachelor Arbeit – Biozid-Analytik in Kühlschmiermitteln

Es soll eine LC/UV Methode für die quantitative Bestimmung von 3 Bioziden (Pyrithion, BIT, BBIT) in Kühlschmiermitteln (KSS) entwickelt und für unterschiedliche KSS valdidiert werden.

Kühlschmiermittel werden in der Metallverarbeitenden Industrie in vielen Prozessen eingesetzt und bestehen aus einer Öl/Wasser-Mischung. Leider bietet diese Mischung einen guten Nährboden für Mikroorganismen, die für schlechte Gerüche und veränderte Kühl- und Schmiereigenschaften sorgen können, sowie potentielle gesundheitliche Gefahren verursachen können. Um das Wachstum zu der Mikroorganismen zu verhindern, werden meist Biozide in Stoßdosierungen eingesetzt. Durch eine neue Dosierungsstrategie soll eine konstante geringe Dosierung ermöglicht werden, die kontinuierlich das Wachstum verhindern kann. Hierzu soll eine begleitende Analytik mittels Flüssigchromatographie-UV/VIS-Detektion entwickelt und für verschiedene Kühlschmiermittel validiert werden.

Kontaktperson: Dr. Oliver Knoop, oliver.knoop[ät]tum.de

Link: https://www.bgu.tum.de/sww/startseite/

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Bachelorarbeit – Siedlungswasserwirtschaft

Für die Untersuchung verschiedener Fragestellungen wird eine zuverlässige Bestimmungsmethode für volatile Grundwasserschadstoffe der BTEX-Gruppe benötigt. Hier soll im Rahmen einer Bachelorarbeit eine Headspace-GC/FID-Methode etabliert und validiert werden.

BTEX (Benzol, Toluol, Ethylbenzol und p-, o-, und m-Xylol) sind häufig als Schadstoffe im Grundwasser anzutreffen, beispielsweise durch Leckagen an Tankstellen oder Ölförderarbeiten eingetragen. „Advanced Oxidation Processes“ (AOPs), beispielsweise Ozon mit Wasserstoffperoxid (O3/H2O2), ermöglichen eine gute Entfernung, jedoch ist der Transformationsmechanismus teilweise noch unbekannt. Für die Untersuchung verschiedener Fragestellungen wird eine zuverlässige Bestimmungsmethode für volatile Substanzen benötigt. Diese kann im Rahmen einer Bachelor- oder Studienarbeit eigenständig an einem Agilent 7980 GC-FID mit Headspace-Modul entwickelt werden.
Eine umfangreiche Einarbeitung und Betreuung werden gewährleistet. Grundlegende Kenntnisse der Gaschromatographie und ein weitergehendes Interesse an Analytik sind von Vorteil. Die Arbeit kann auf Englisch oder Deutsch abgefasst werden.

Kontakt: Emil Bein & Oliver Knoop
Email: emil.bein[ät]tum.de
Link: https://www.bgu.tum.de/sww/startseite/

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Masters/PhD projects: Imaging the machines that reshape and remake chromosomes

Master’s thesis and PhD projects in several areas at Max Planck Institute of Biochemistry availabe. We hope to recruit students with a background in physics, biochemistry, or a related field, who have a strong interest in dynamic studies of biological processes using structural and single-molecule approaches. Skills in protein biochemistry, programming, and a basic knowledge of kinetic analysis would be ideal, but are not required. Applicants should have a strong desire to pursue a multidisciplinary collaborative project working closely with others. Creative and independent thinking will be key for the successful completion of the projects.

Imaging the macromolecular complexes that reshape and remake chromosomes

Background: The survival of all organisms depends on the faithful duplication and transfer of genetic material from one generation to the next. In cells, this process is performed by large macromolecular complexes, known as replisomes, which couple the unpackaging of parental DNA with the synthesis of new daughter strands. To ensure genome integrity, these sophisticated molecular machines must coordinate events over a broad range of time and length scales, from the breaking and reformation of chemical bonds within DNA polymerases to the large-scale structural rearrangements of chromosomes. We seek to define the operating principles that guide replisome assembly and function on complex cellular substrates. We are particularly interested in understanding how replication overcomes the numerous structurally diverse obstacles frequently encountered on chromosomes.

Methods: We use a combination of structural, biochemical, and imaging techniques to directly visualize the spatial and conformational dynamics of critical replication intermediates. These efforts range from detailed biophysical investigations of individual complexes and interactions to studies of completely reconstituted replisomes in vitro (E. coli, S. Cerevisiae). We use cutting-edge single-molecule imaging approaches that provide high spatial and temporal resolution to study the dynamics of single replisomes.

We are currently offering Master’s thesis and PhD projects in several areas. First, we are developing single-molecule approaches to directly visualize the disassembly and reassembly of nucleosomes during replication. In the context of this project, we are seeking students to work in a team to purify histone chaperones and remodelers and exploit several chemically diverse fluorophore labeling strategies for single-molecule visualization. Second, we are looking for students to help in our studies of replication and transcription conflicts. Of particular interest are rare events were RNA polymerase bypasses replication factors. Finally, for those interested in software development and biophysics, we are developing ultra-high-throughput approaches to hunt for rare but deadly DNA breaks by topoisomerases.

Please get in touch for further details and to hear about other currently offered projects.

Our lab is located at the Max Planck Institute of Biochemistry. You can find us on the web at http://www.biochem.mpg.de/duderstadt and https://duderstadtlab.org

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Masterarbeit im Fachbereich Onkologie

[english below] Wir bieten ein spannendes Projekt an der Schnittstelle von Zellbiologie und Medizin im Bereich Pankreaskarzinomforschung an. Das duktale Adenokarzinom des Pankreas (PDAC) ist durch ein fibroblastenreiches desmoplastisches Stroma gekennzeichnet, dass eine kritische Rolle bei der Progression und Therapieresistenz des PDAC spielt. Dieses Projekt wird sich auf die Interaktion zwischen CAF (Tumor-assoziierte Fibroblasten) und PDAC-Zellen im humanen Zellkultursystem konzentrieren und aufklären, wie die CAFs die Aggressivität von PDAC-Zellen durch verschiedene Mechanismen fördert und neue Therapiekonzepte abgeleitet werden.

We offer an exciting project at the interface of cell biology and medicine in pancreatic cancer. Pancreatic ductal adenocarcinoma (PDAC) is characterized by a fibroblast-rich desmoplastic stroma which plays a critical role in the progression and therapeutic resistance of PDAC. The stroma is composed of extracellular matrix proteins, mainly deposited by the cancer-associated-fibroblasts (CAFs) and various types of immune cells. Cancer-associated fibroblasts display a high degree of interconvertible states including quiescent, inflammatory and myofibroblastic phenotypes. However, the mechanisms by which this plasticity is achieved are poorly understood.

This project will focus on the CAF – PDAC cell interaction in the human cell culture system and will elucidate how CAF plasticity promotes PDAC cell aggressiveness through multiple mechanism.

Our spectrum of methods we can offer

  • Cell culture
  • Working with primary human and murine cell lines (organoids)
  • Drug screens
  • Co-Culture systems
  • Manipulation of human und murine cell lines (CRISPR Cas9, etc.)
  • Broad spectrum of molecular biology (ELISA, Western Blot, PCR, Cloning of Plasmids)
  • Flow cytometry
  • Orthotopic Implantation (mouse models)
  • Imaging (MRT, PET)


For further details please contact Dr. Karin Feldmann (karin.feldmann[ät]tum.de; AG Reichert | Klinik und Poliklinik für Innere Medizin II, Klinikum rechts der Isar, TUM)