Lecture by: Master Student Alberto Ianis Trantea
Title: Synthetic Nanobody Yeast Display Platform for Selecting Allergen-Specific Nanobodies
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Synthetic nanobody libraries combined with yeast display technology, provide a versatile and efficient alternative to immune repertoire libraries, enabling the streamlined selection of allergen-specific nanobodies. In this talk, I will discuss the selection of Api m 1-specific nanobodies and their characterization alongside previously identified nanobodies developed in our lab, providing a foundation for developing targeted diagnostic and therapeutic tools for honeybee allergy treatments.
Master Student
Lecture by: Master Students Marc Marburger & Fie Larsen
Title: FEA and AI of 3D Liver Displacements During pneumoperitoneum and inertial focusing of nanoparticles in vessels of deformable tissue
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Two industrial master theses projects have been launched to improve surgical outcomes in laparoscopic liver surgery. Mathematical models of liver deformations and blood flow is developed and solved using the finite element method. Their geometry is based on segmented 3D image volumes and theoretical vessels.
Marc Marburger’s project:
Fie Larsen’s project:
Master Students
Lecture by: Assistant Professor Vineesh Indira Chandran
Title: A new approach to treating MASH
Place: Gustav Wieds Vej 10A, 8000 Aarhus C, Building 3140, Room 103.
Metabolic dysfunction-associated steatohepatitis (MASH) is a progressive disease of the liver that is currently affecting more than a third of the world’s adult population and is the leading cause of liver transplant, surpassing Hepatitis C-related complications. It is characterized by triglyceride accumulation, severe inflammation, and fibrosis. Due to the high global incidence and prevalence rates of MASH and their substantial economic burden on healthcare systems, early interventions are urgently needed. The exact molecular mechanisms underlying progression of MASH is an active topic of investigation, however a widely held hypothesis is that fat accumulation is the primary driver of the disease. Therefore, drugs targeting fat accumulation in hepatocytes resulting in hepatic steatosis is a topic of active investigation. In this study, we developed a novel antibody-drug conjugate (ADC) targeting asialoglycoprotein receptor 1 (ASGPR1) on liver hepatocytes and characterized the stability, specificity, localization, and biodistribution in liver hepatocytes using in vitro and in vivo models; with potential implications in the treatment of MASH.
Lecture by: Postdoc Tong Tong
Title: The Human Cortex Lab: A Pioneering Human Brain Tissue Platform and Insights into Glioblastoma Cell Excitability
Place: Gustav Wieds Vej 10A, 8000 Aarhus C, Building 3140, Room 103.
Translating basic cancer neuroscience research into clinical applications is challenging, primarily due to the difficulty of bridging the gap between research findings and effective patient treatments. Many therapeutic agents fail in clinical trials, often because preclinical models inadequately replicate human biology. Limited access to patient-derived samples, preservation difficulties, and the lack of integration between biological and clinical data further hinder progress. The Human Cortex Lab addresses these challenges by providing an advanced human brain tissue platform that offers fresh tissue collection, organotypic slice cultures, and viral transduction techniques. This platform links clinical and biological data for comprehensive analyses in collaboration with brain tumor and neuroscience researchers. One research project, using this platform, investigates the excitability of glioblastoma (GBM) cells. Fluorescence-guided whole-cell patch-clamp recordings in human brain slices revealed that 56% of GBM cells at the tumor’s leading edge exhibit neuron-like excitability, generating aberrant action potentials. These findings shed new light on GBM cell behavior and underscore the platform’s critical role in advancing translational research and developing targeted therapies.
Lecture by: Postdoc Pon Ganish Prakash
Title: Comparing the physiological and transcriptional fidelity of 3D organoid models and Native tissue
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Organoids are 3D tissues grown from organ specific adult stem cells, that mimics the functional, structural and biological complexity of human organs. These miniature models can self-organize and differentiate, offering a close approximation to in vivo tissues. Their potential as near-physiological models have led to a surge in research, highlighting their vast applications, particularly in disease modelling and drug discovery. However, their ability to accurately capture transcriptional signatures due to the lack of the in vivo microenvironment, i.e due to the absence of key cell types like stromal and immune cells, remains debated. This presentation will discuss our ongoing research, using single cell sequencing and bioinformatics to evaluate how well patient-derived cervical organoids replicate the cellular diversity and gene expression patterns of actual cervical tissue biopsies.
Lecture by: Guest Researcher Abid Hussain
Title: Identification of a Novel Allergenic Protein from Paper Mulberry Pollen
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Broussonetia papyrifera (Paper Mulberry) is a widely distributed tree and it has a significant impact on public health due to its allergenic potential. In Pakistan, it is a major sensitizer for patients with allergic rhinitis and asthma. Our group recently identified a 12-15 kDa non-specific lipid transfer protein (nsLTP) from Paper Mulberry pollen, now recognized as Bro p 3.0101, which has been accepted by the IUIS/WHO Allergen Nomenclature Sub-Committee. In this seminar, I will discuss the identification and characterization of this newly recognized allergen, its unique immunological reactivity profile, and its implications for advancing allergy diagnostics and targeted therapies.
Guest Researcher
Lecture by: Postdoc Éloïse Marie Mussard
Title: Development and characterization of a piglet intestinal organoid model to study the effects of postbiotics on the intestinal epithelium
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
In piglets, diarrhea is commonly observed after weaning and is associated with a dysfunction of the intestinal epithelial barrier. In the context of the reduction of antibiotics use in farms, new strategies are implemented to preserve the digestive health of piglets at weaning. The use of postbiotics (nutritional products derived from microorganisms) seems to be a promising strategy but their effects on the piglet intestinal epithelium are not well known. The objective of my PhD was to develop and characterize a model of piglet intestinal organoids allowing to test the effects of postbiotics targeting the barrier function of the intestinal epithelium. By culturing piglet intestinal epithelial stem cells in an extracellular matrix protein gel, three-dimensional (3D) structures were formed by a monolayer of polarized epithelial cells and including several cell types. Based on gene expression analyses, we showed that piglet intestinal organoids partially retained the phenotype related to their original digestive segment while they did not maintain the specific gene expression profile of suckling or weaned piglets. Our characterization of 3D organoids confirmed that the apical side of epithelial cells is oriented towards the lumen and is therefore not easily accessible to study the effects of nutritional products. We then developed an organoid cell monolayer culture model that allows access to the apical side of the cells and to study the barrier function of the epithelium. Using this model, the effects of products derived from microorganisms: butyrate, a metabolite produced by the intestinal microbiota, and two postbiotics. We also studied these microorganism-derived products in the context of epithelial barrier dysfunction induced by the mycotoxin deoxynivalenol (DON). Taken together, our results indicate that the piglet intestinal organoid model is useful for studying the physiology of the intestinal epithelium in a gut segment-specific manner. Cell monolayers derived from piglet intestinal organoids allow access to the apical side of the cells and can be used to demonstrate the effects of microorganism-derived products on the epithelial barrier. These new tools can be used in many contexts to study in vitro the porcine digestive epithelium for veterinary and biomedical research.
Lecture by: Master Student Matous Najman
Title: Computational Study Of The Immune System Response To Bee Venom
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Development of immune therapy can be aided by computational modelling, helping us to understand mechanisms of sensitivity and allergic reaction, and create predictions for immune system development with and without the therapy. The main hypothesis suggests that a computational model can be developed to model the immune system reaction to bee venom. Moreover, it is hypothesized that such model can be validated and altered using clinical and/or experimental data. He will present findings from his thesis works.
Master Student
Lecture by: Postdoc Anne-Kathrine Kure Larsen
Title: Inka-PAK4 protein crystals as tool to study intracellular mechanobiology
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Cells and tissues are affected by and can respond to physical and biochemical changes of their extracellular environment. Several methods exist to mimic the extracellular environment to study these responses, as well as tools to measure cellular forces from the outside. However, mechanostimulation from the intracellular environment is currently challenging. This presentation will focus on the characterization of a novel tool, inka-PAK4 protein crystals, to physically stretch a cell from the inside, while it also has the potential to assist the measurement of intracellular forces.
Lecture by: Postdoc Naveen Kumar Nirchal
Title: Dietary Modulation of Gastroesophageal Tissue Regeneration Through Organoids and Single-Cell Sequencing
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Gastroesophageal tissues, including the esophagus, gastroesophageal junction, and stomach, are vital for digestive health. Several risk factors, such as male gender, age, smoking, GERD, high-fat diet-related obesity, and Vitamin A deficiency, can disrupt their function and increase the risk of Barrett's esophagus (BE), a condition that elevates the risk of esophageal adenocarcinoma. This presentation will focus on the role of retinoic acid (RA), an active metabolite of Vitamin A, in regulating gastroesophageal tissue homeostasis.
Lecture by: PhD Student Bjarke Krogstrup Jensen
Title: Bi-specific Nanobody-based IgG for Blocking the Major Honeybee Venom Allergen Api m 1
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Hymenoptera venom is the most common cause of anaphylaxis. This occurs due to an allergic reaction, triggered by allergens binding to IgE/receptor complexes located on the surface of effector cells. In this talk, I will characterize different allergen-specific nanobody constructs and show blocking of the binding between the allergen and the IgE/receptor complexes, inhibiting the allergic reaction. These findings provide promising evidence for utilizing nanobody constructs as a passive immunotherapy approach for protection against anaphylaxis in honeybee venom allergy.
Lecture by: PhD Student Catalina Suarez Londoño
Title: Open Foam Characterization for Computer Simulation of Mechanical Cues in Cell Differentiation
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
The stiffness of the extracellular matrix (ECM) plays a significant role in cell differentiation, although the underlying mechanisms remain unclear. Biomaterials composed of different ratios of polycaprolactone (PCL), dioxane, and water, forming open foam structures with macro- and nanopores, are used to investigate these effects. Digital twins of these foams are generated through 3D reconstructions from X-ray tomography and electron microscopy images, enabling the analysis of properties such as porosity, tortuosity and local thickness. Correlating material composition with physical characteristics allows for in silico studies of how mechanical cues influence cell differentiation and motility.
Lecture by: Postdoc Bjarke Nørrehvedde Jensen
Title: Anisotropic Biomaterials with Wireless Electromagnetic Stimulation for Guiding Neural Regeneration
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Nerve injuries affect millions of people worldwide and the current surgical procedures have limited success in repairing damaged tissue. In this presentation I will cover the development of a wireless electromagnetic stimulation system that we have combined with filamentous gelatin-based hydrogels for providing electrical, chemical, and mechanical cues to enhance regeneration after peripheral nerve injuries.
Lecture by: Master Student Lone Hallum
Title: Characterization of Polymeric Scaffold Properties
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Polymeric scaffolds used for tissue regeneration, can be fabricated through thermally induced phase separation. By varying the underlying chemical composition, the resulting scaffolds differ both in morphology and mechanical properties. Through mechanical testing and computational modelling, some of the changes can be quantified and analyzed. In this presentation, I will discuss the utilized methods and some of my findings from the project.
Master Student
Lecture by: Associate Professor Thomas Lykke-Møller Sørensen
Title: X-Ray tomography for imaging organoids
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
X-ray tomography is a tool for the 3D analysis of samples in life sciences. We have used the P-14 beamline at EMBL/DESY in Hamburg to image organoids and develop labelling techniques. I’ll give a short update on progress and challenges and present some recent results.
Lecture by: Master Student Jesper Rosendahl Laursen
Title: ”Cell membrane lipid profiling of bacterial cultures during growth and impact on shelf-life/stability”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
This project delves into the study of the lipid bilayer of Lactic Acid Bacteria, a fundamental component of the dairy and probiotics industry. It focuses on understanding how various environmental stressors influence the evolution of the lipid bilayer and the stability of Lactic Acid Bacteria growth. The project aims to unravel the relationship between growth conditions and membrane composition, thereby contributing to our knowledge of Lactic Acid Bacteria cultures.
Master Student
Lecture by: Master Student Fie Karlskov Larsen
Title: ”R&D to Thesis: Modelling Liver Deformations in Laparoscopic Liver Surgery”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
In collaboration with BK Medical, a GE healthcare company, who specializes in advanced surgical imaging solutions, particularly high-resolution ultrasound systems for real-time imaging, a project has been launched. The aim is to improve surgical outcomes in laparoscopic liver surgery by developing mathematical models of liver deformations to create finite element models based on segmented 3D image volumes. The models will be used to quantify and validate deformations against real data and literature values.
My R&D study focuses on becoming familiar with programs such as 3D Slicer, COMSOL and python, while gaining a better understanding of anatomy, clinical relevance, liver cancer and elasticity theory through a literature study.
Master Student
Lecture by: Postdoc Anne-Sofie Ravn Ballegaard
Title: Is IgE a suitable target in allergy therapy?
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
The antibody isotype IgE is the main player in type I hypersensitivity. Hence, targeting IgE is a major option for therapeutic intervention in allergic diseases. Available treatment forms rely merely on inhibition of the IgE binding to its receptor on effector cells. However, molecular approaches to displace IgE from its receptor on effector cells without risk of activation have been described.
In this presentation, I will give an update on the development of candidate molecules that have the capability of inhibition as well as displacement activity.
Lecture by: PhD Student Pon Ganish Prakash
Title: "Single-cell RNA transcriptomics of cervical exfoliated cells during carcinogenesis reveals potential biomarkers”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Cervical cancer is a prevalent gynecological malignancy despite the efficacy of various screening methods. Persistent human papillomavirus (HPV) infection is the primary cause of Cervical cancer. Understanding the multicellular ecosystem and signaling events at different stages in cervical carcinogenesis enables the identification of early detection biomarkers, which is critical for impeding the transition from low-grade cervical intraepithelial lesions to cancer. Here, I will discuss the recent study revealing potential biomarkers and cellular pathogenesis in cervical carcinogenesis using Single-cell RNA sequencing of cervical exfoliated cells.
PhD Student
Lecture by: Master Student Pernille Broch
Title: ”Establishment of selecting artificial immune repertoires via yeast surface display”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
The presentation will focus on the generation of nanobodies with specificity for given target structures from synthetic yeast display libraries. This technology could enable circumvention of time constraints and need of immunization and might have the potential to provide antibodies against immunologically silent epitopes. Benefits and pitfalls of the approach and results obtained in the project so far will be presented.
Master Student
Lecture by: Professor Peter Lindberg Nejsum
Title: Parasite extracellular vesicles show diverse functions in their host
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Helminths are parasitic worms that often cause chronic infection by releasing excretory/secretory products that modulate the host’s immune response. We, and others, have shown that extracellular vesicles (EVs) are released with the excretory/secretory products. To understand the potential role of EVs in host-parasite interaction, we have profiled their content and identified microRNAs and proteins that may be essential for parasite survival. To further understand their role, we have conducted several functional studies, and strikingly, we find that EVs may play a diverse role in host-pathogen interaction depending on parasite species. While we find that Ascaris release EVs that suppress the host immune response and are selectively internalized by monocytes, Trichuris-derived EVs did not modulate the immune response but selectively packed microRNAs in EVs that can suppress cancer genes. Other parasites release highly immunogenic EVs, suggesting a central role in pathogenicity. In conclusion, though we find that EVs are critical in host-parasite interaction their role is context and species-dependent.
Lecture by: Postdoc Kristian Juul-Madsen
Title: Amyloid-β aggregates activate peripheral monocytes in mild cognitive impairment
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
The peripheral immune system is important in neurodegenerative diseases, both in protecting and inflaming the brain, but the underlying mechanisms remain elusive. Alzheimer’s Disease is commonly preceded by a prodromal period. Here, we report the presence of large Aβ aggregates in plasma from patients with mild cognitive impairment (n = 38). The aggregates are associated with low level Alzheimer’s Disease-like brain pathology as observed by 11C-PiB PET and 18F-FTP PET and lowered CD18-rich monocytes. We characterize complement receptor 4 as a strong binder of amyloids and show Aβ aggregates are preferentially phagocytosed and stimulate lysosomal activity through this receptor in stem cell-derived microglia. KIM127 integrin activation in monocytes promotes size selective phagocytosis of Aβ. Hydrodynamic calculations suggest Aβ aggregates associate with vessel walls of the cortical capillaries. In turn, we hypothesize aggregates may provide an adhesion substrate for recruiting CD18-rich monocytes into the cortex. Our results support a role for complement receptor 4 in regulating amyloid homeostasis.
Lecture by: Josephine Baunvig Aagaard (Postdoc in the Immunological Biotechnology group)
Title: Nanobodies for Prevention of Anaphylaxis in Honeybee Venom Allergy
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Insect venom allergy is the most common cause of anaphylaxis. Central in the allergic reaction is the binding of venom allergens to IgE/receptor complexes on the surface of effector cells triggering immediate allergic reactions and potentially anaphylaxis. In this presentation, I will demonstrate how allergen-specific nanobody formats can block the binding of allergens and thereby prevent the subsequent allergic reaction. These findings provide the functional and structural basis for establishing a passive immunotherapy approach for protection against anaphylaxis in honeybee venom allergy.
Lecture by: Mette Steen Toftdal (Industrial Ph.D. student from the group of Nanofiber Technology and Cellular Engineering)
Title: Fighting Diabetes – Combining Beta Cell Therapy with Tissue Engineering
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Diabetes affects over 400 million people worldwide, and while cell therapy holds promise for curing Type 1 diabetes, low retention rates and inadequate cell survival remain ongoing challenges. Combining cell therapy with tissue engineering may provide a solution to these challenges. In this presentation, I will introduce a developed device for beta cell transplantation. The device, consisting of PLCL/GelMA/alginate coaxial nanofibers embedded in an alginate hydrogel, was characterized physically and mechanically, as well as analyzed for its interaction with beta cell clusters. The device shows potential for improving beta cell therapy and overcoming challenges in cell survival.
Lecture by: Postdoc Naveen Kumar Nircha
Title: "From Organoids to Organism: Unraveling the Gastroesophageal Junction Evolution Through Single-Cell and Spatial Transcriptomics”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
The gastroesophageal junction (GEJ) is a key anatomical site prone to stress-induced metaplasia and subsequent esophageal adenocarcinoma (EAC), a cancer with a notably low five-year survival rate. In our study, we utilized single-cell transcriptomics and spatial analysis to identify the cellular and molecular intricacies of the GEJ in healthy mouse tissue, spanning from embryonic to adult stages. We uncovered distinct transcriptional profiles and signaling pathways in epithelial and mesenchymal cells that are pivotal in GEJ development. Through advanced techniques like organoid models, lineage tracing, and single-molecule RNA in situ hybridization, we have further deciphered the regulatory mechanisms of squamo-columnar junctional epithelial cells in the GEJ. Our research illuminates the molecular framework of GEJ development and provides comprehensive insights into the interactions between fibroblasts and epithelial cells, enhancing our understanding of tissue heterogeneity, homeostasis, and regeneration.
Inargural lecture by: Associate Professor Cindrilla Chumduri
Title: "Pathogens, Diet, and Tissue Microenvironment:
A Dynamic Interplay in Regeneration and Carcinogenesis”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
We invite everyone to celebrate the appointment of Cindrilla Chumduri as an Associate Professor in the Medical Biotechnology Section of the Department of Biological and Chemical Engineering with an inaugural lecture.
Sneek Peek:
Cindrilla Chumduri specializes in the study of infection, carcinogenesis, and regeneration. Her research is focused on the intricate connections that exist between the host tissue microenvironment, diet and pathogens during the early stages of cancer development. Her work is at the forefront of developing and using patient-derived 3D organoids and in-vivo models to understand the interplay between host-pathogen interactions, immune responses, tissue homeostasis mechanisms, and disease progression. Using cutting-edge technologies like advanced microscopy, single-cell omics, and spatial analysis, Cindrilla and her interdisciplinary team are working to understand disease mechanisms and to identify biomarkers and therapeutic targets that will benefit early detection and treatment of diseases.
Biodata:
Cindrilla is now an Associate Professor at Aarhus University's Medical Biotechnology Section within the Department of Biological and Chemical Engineering with a wealth of international experience. She began her academic journey at the Indian Institute of Science, where she focused on Candida albicans and Salmonella genetics. After that, she earned her Ph.D. in cell biology and cancer from the Max Delbrück Center for Molecular Medicine in Berlin, Germany. In 2010, Cindrilla joined the Max Planck Institute for Infection Biology (MPIIB) and has since been researching how pathogens contribute to diseases, particularly cancers. As a group leader at MPIIB, she discovered crucial host signaling pathways disrupted by pathogens, jeopardizing cellular and genomic stability. In 2018, she was associated with the Charite Medical University, Department of Hepatology and Gastroenterology as a Group Leader. Since 2019, Cindrilla has been leading her research team at the Department of Microbiology, University of Wuerzburg. Currently, she is also holding the position of Visiting Professor at the University of Wuerzburg, Germany.
After the lecture, a reception will take place in front of the lecture hall.
Lecture by: AC-TAP Jonas Karlsen
Title: "Mystery of the bacterial HIRAN domain”
Place: Gustav Wieds Vej 10A, 8000 Aarhus C, Building 3140, Room 103.
A quick search on PubMed for HIRAN domains gives you only 28 articles, and of those only one mentions HIRAN domains found in bacteria. HIRAN domains, as we know them today, are DNA binding proteins which have so far been described as a vital part of the protein complex resolving replication fork stalling in humans. However, new studies have found domain homologs in bacteria with many unknown functions. In this presentation I will go through my thesis work on bacterial HIRAN domains as well as their presumed role in toxin anti-toxin systems.
Lecture by: AC-TAP Cecilie Linneberg Matthiesen
Title: "Investigation of superoxide dismutase 3 in zebrafish and bone”
Place: Gustav Wieds Vej 10A, 8000 Aarhus C, Building 3140, Room 103.
Under this title I will talk about redox biology and how we validated that the predicted zebrafish superoxide dismutase 3 (SOD3) variants, were true functional orthologues to the human SOD3. Furthermore I will talk about how knockout of SOD3 affects both zebrafish and mice bones.
Lecture by: Postdoc Irving Martinez Acosta
Title: "Mathematical modeling and simulation of coronary stents”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Every year approximately 3 million people in the US suffer from atherosclerosis, which is the condition in which one or more arteries get clogged up from excessive cholesterol and other residue build up. In spite of being introduced into the market decades ago, coronary stents remain the most popular solution, given their low surgery risk. However, stents are prone to malfunction after some time, with each type having its own set of complications. The introduction of newer types of stents to resolve the problems of their predecessors comes at the expense of creating different drawbacks. To thwart the improvisational nature of stent development, we attempt to fully understand stents through rigorous mathematical theory and modeling.
In this presentation, we illustrate domain decomposition techniques by taking into account the interplay of distinct meshed domains and lay the theoretical and numerical groundwork to model any type of stent. In particular, we emphasize the understanding and application of PDEs such as Navier-Stokes and advection-diffusion equations in the context of hemodynamics to explore the blood velocity and pressure, the concentration of solutes, and the dissipation of drug across the stented artery system.
Lecture by: PhD student Sif Julie Friis
Title: "Towards in-silico modelling of oral device concepts: novel methods for mechanical characterization of gastrointestinal tissue”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Delivery by oral administration is considered the simplest way to deliver most pharmaceuticals, significantly improving treatment adherence. However, macromolecular drugs cannot survive passage through the gastrointestinal (GI) tract or have limited bioavailability. Oral devices designed to deliver drugs by injection into GI tissues may constitute an interesting solution to this limitation and as an alternative to subcutaneous injection. Conversely, a knowledge gap exists on how these devices will and should interact mechanically with the GI tissue, and there is a lack of understanding of the cellular consequences.
The aim of this PhD project is to answer these questions. It is hypothesized that a reliable virtual model of the mechanics of GI tissues can be built, provided that new test methods are developed to generate mechanical data needed to fit the parameters of the constitutive models. By performing biomechanical tests on GI tissue, necessary information on needle-tissue interaction is established. From the data, constitutive relations describing the tissue behavior under needle penetration in the GI tissue is identified, thereby relating the device design to penetration depth. Further, the experimental data and the virtual model, provide knowledge on the GI tissue strain field, caused by needle penetration and accompanying fractures. From this, it is possible to predict the potential cellular consequences of the mechanical stimuli inflicted by needle penetration. The research towards virtual models is of substantial value in the early screening of device concepts and the parameter evaluation, which may help to move forward with fewer prototype iterations and in-vivo experiments.
Lecture by: Prof. Steffen Goletz
Title: "The Sweet-Spot of Biopharmaceuticals”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Abstract:
Sugar chains play important roles in many biological and disease mechanisms. Glycoengineering is a key tool for elucidating the role of glycans in immunological and disease mechanisms. Optimizing the glycosylation of molecules and cells has a high potential for novel and superior biopharmaceuticals. My research is following my roots as a pioneer and entrepreneur in Biotherapeutic Glycoengineering and antibody engineering. The aim is to establish, expand and elaborate this research area at DTU in order to gain basic insights in the role of carbohydrates in immunological and disease processes and to generate novel biotherapeutic approaches and candidates in immuno-oncology and infectious diseases.
Info:
Steffen Goletz is heading the research group Biotherapeutic Glycoengineering & Immunology at DTU Bioengineering. After early career in academic research, e.g. MDC in Berlin and MRC in Cambridge, he founded, lead and matured Biotech companies successfully as CEO and CSO over 17 years before joining DTU in 2019. Steffen Goletz' research and innovation expertise ranges from molecular protein- and glycoengineering, glycooptimization and humanization of biopharmaceuticals, antibody and protein engineering, over bioprocess technologies, glycol-immunology and cellular glycoengineering to human gut microbiota research and the development of gut bacteria-based nutraceuticals for specific immunological applications, as well as novel glycoengineered GMP manufacturing systems and GMP production, and clinical development.
Department of Biotechnology and Biomedicine, Section for Protein Science and Biotherapeutics, DTU
Lecture by: Prof. Barbara Bohle
Title: "An apple a day keeps the doctor away - new treatment approaches for birch pollen-related food allergy”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Biography:
Barbara Bohle has studied "Food- and Biotechnology" at the University of Natural Resources and Applied Life Sciences in Vienna In 2000 she received her PhD and in 2002 the Venia docendi in Immunology. Since then she leads the research group “Allergy Research” at the Department of Pathophysiology and Allergy Research at the Medical University of Vienna. In 2010 she was appointed a full professor for Cellular Allergology. Since 2011 she is the Head of the Institute of Pathophysiology and Allergy Research and the Division of Experimental Allergology. From 2007-2015 she led the Christian Doppler Laboratory for Immunomodulation.
The main focus of her scientific work is the elucidation of the immune mechanisms underlying the induction, maintenance and therapy of IgE-mediated allergy. Her scientific work markedly contributed to the understanding of the pathophysiology of pollen-related food allergy and was awarded with prestigious national and international prizes. She is the author of >170 peer-reviewed scientific papers published in highly ranked journals in the field of allergy and immunology.
Prof. Barbara Bohle
Lecture by: Postdoc Shivesh Anand
Title: "Breaking the Silence: Biofabrication of Human Eardrum”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
It is estimated that by 2050, one in every ten people will suffer from disabling hearing loss. Perforated eardrums represent the most common injury to the human ear, often resulting in partial or complete hearing loss due to ineffective sound conduction. While microsurgical placement of autologous tissue grafts has long been considered the 'gold standard' for treating damaged eardrums, the inherent properties of these autografts can frequently impede optimal hearing restoration following recovery. Tissue engineering has emerged as a promising approach to address some of these challenges. In this seminar, I will delve into the innovative biofabrication, biomaterial, and bioreactor-driven regenerative therapies that I developed during my PhD on eardrum reconstruction at the MERLN Institute in Maastricht, Netherlands. Join me as we break the silence and explore these cutting-edge technologies!
Lecture by: Postdoc Christoph Alexander Müller
Title: "Graphitic carbon nitride towards multiscale leadless bioelectric modulation”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Materials that allow biomodulation and control of electrophysiological processes hold tremendous therapeutic potential. In my talk, I will present the organic semiconductor graphitic carbon nitride (g-C3N4) with its potential to achieve leadless biomodulation and precise control of biological processes. Particularly, g-C3N4 is incorporated with biomimetic nanostructured fibers or particles, that allow optical modulation of bioelectricity on the subcellular, intercellular, and tissue level.
Lecture by: Bjarke Krogstrup Jensen, PhD student
Title: “Evaluation of the Mechano-Physical Properties and Biocompatibility of Alginate, GelMA, and Alginate-GelMA Hydrogels for Cellular Encapsulation”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
I will present the work performed in my master thesis regarding the evaluation of Alginate, GelMA, and a combination thereof in the field of tissue engineering. The presentation will cover both mechano-physical characterization and assessment of biocompatibility and immunogenicity.
PhD student
Lecture by: Stine Wendelboe Jensen, master student
Title: ”Affinity maturation of nanobodies by yeast display”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
The presentation will focus on the establishment of affinity maturation techniques of antibodies using yeast surface display. The work preformed in the project is within the context of therapeutic single domain antibodies and their expression, mutagenesis and use for library generation and selection.
master student
Lecture by: Postdoc Jesper Guldsmed Madsen
Title: "Comparative Physiology in Biomedical Research”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
The complexity of problems facing biomedical researchers, who try to improve the conditions of human life, can be staggering. However, through evolution, nature has created a vast myriad of physiological solutions to challenges presented to animals by their environment. These animals are invaluable for understanding how certain physiological problems can be overcome.
Lecture by: Associate Professor Edzard Spillner
Title: "Update on structural and functional aspects of IgE”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
IgE is the trigger which is pulled upon exposure to an allergen and its mode of action is crucial for both the development and prevention of disease. In this presentation our basic understanding of this key player of allergic disease and the recent insights will be highlighted and discussed.
Lecture by: Dr. Naveen Kumar Nirchal
Title: "Zooming into the Gastroesophageal Junction: Single-Cell Revelations of histogenesis & Barrett's Esophagus Beginnings"
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Exploring the fascinating world of Gastroesophageal Junction (GEJ) health and disease through the lens of cutting-edge single-cell sequencing and 3D stem cell-derived organoids. Delving into the intricate spatiotemporal cellular dynamics that may hold the key to understanding metaplasia and cancer development at the GEJ.
Lecture by: Master Student Mathias Sønderholm Larsen
Title: "Discovery and characterization of nanobodies for inhibition of Hymenoptera venom allergy"
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Hymenoptera venom allergy is one of the main causes of anaphylaxis and is caused by the binding of venom allergens to receptor-bound IgE on the surface of effector cells. In my master project, I have selected and characterized nanobodies against one of the major wasp venom allergens. The selected nanobodies have the potential to block the binding of IgE to the allergen and thus prevent anaphylaxis upon exposure to the allergen.
Master Student
Lecture by: Professor Peter Korosec
Title: ”Immunological and genetic biomarkers for severity of allergic reactions”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Information about the lecture will follow soon.
Professor, University Clinic of Respiratory and Allergic Diseases Golnik, Slovenia
Lecture by: Business Developer Steen Buchhave Villadsen
Title: "Introduction to The Kitchen and our initiatives”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Steen will talk about the startup hub "The Kitchen" as well as give examples of startups that emerged from the research-world.
Lecture by: Project Coordinator Sara Seidelin Majidi
Title: "An Innoexplorer journey”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Sara will talk about the process of applying for an Innoexplorer grant and how this grant can be used. Furthermore, she will talk about her experience with the journey of going from products in the lab to attempting to bring them into the market.
Lecture by: PhD student Youssif Y. Merhi
Title: "Printed dry electrode for neuromuscular electrical stimulation (NMES) for e-textile”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Muscle atrophy is a well-known consequence of immobilization and critical illness, leading to prolonged rehabilitation and increased mortality. In this study, we develop a solution to preserve muscle mass using customized biocompatible neuromuscular electrical stimulation (NMES) device. We demonstrate the printing of conducting electrodes on a compressive stocking textile that can be used for more than seven days without observing any inflammation. This solution consists of a dry and biocompatible electrode directly integrated into the textile with good mechanical compatibility with the skin.
Lecture by: PhD Student Pon Ganish Prakash
Title: "Modeling uterine cervix infections and disease using patient-derived 3D organoids at single-cell resolution”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Uterine cervix protects the upper reproductive tract from ascending pathogens; however, in some cases, it succumbs to the virulence of pathogens and carcinogenesis. Our study identified regenerative signatures of uterine ecto- and endocervical epithelial niches and their unique defense blueprint against infections at single-cell resolution.
PhD Student
Lecture by: PhD Student Bjarke Nørrehvedde Jensen
Title: "Wireless electromagnetic neural stimulation patch with anisotropic guidance for neural regeneration”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
The human body is limited in healing neurological damage caused by diseases or traumatic injury and advanced neurological therapeutics are required to repair damaged tissue. Electrical stimulation is known to promote neural growth and differentiation. Here, a wireless electromagnetic stimulation scaffold was created for the first time, combining stimulation through electromagnetic induction with physical guiding cues through structural anisotropy. The melt electrowritten polycaprolactone anisotropic structure with 80 nm gold coating directly employed the energy harvesting component (induction coil) as the stimulation delivery interface for direct contact of cells.
Lecture by: Postdoc João Ramos
Title: ”Biophysical studies of SorCS2 interactions required for synaptic plasticity”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
SorCS2 is an important player in the trafficking of neuronal receptors to the synapses. These receptors activate cellular pathways that dictate either cell survival and proliferation or apoptosis. Using biophysical and structural methods we aim to characterize SorCS2 interactions with these receptors to better understand its role in neurological diseases.
Lecture by: Emilie Benedikte Rytter Olesen and Amalie Lykke Olsen
Title: ”Optimizing lipid nanoparticles to include DNA repair template for homology directed repair following mRNA-based CRISPR gene editing”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
CRISPR technology have shown great clinical potential towards neurodegenerative disseases, here amongst muscular dystrophy. A key need that is still unmet is how to efficiently deliver the CRISPR/Cas9 therapeutic complex into the diseased cells. Lipid nanoparticles (LNP) can encapsulate RNA and have shown great potential as a gene and drug delivery system in therapeutic applications.
Master Student
Master Student
Lecture by: AC-TAP Pernille Ommen Andersen and Postdoc Anne-Sofie R. Ballegaard
Title: ”Isolation of antigen-specific nanobodies by combining animal immunization with yeast surface display”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
In our laboratory we engineer and produce nanobodies towards different targets of interest in allergy.
In this presentation we will take you on the journey from animal immunization to in vitro and in vivo testing of identified nanobodies, and we will show how we use yeast surface display in the selection process.
Lecture by: Stephanie Descroix
Title: ”Developing organ on chip for biology and clinics”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
The development of a new generation of in vitro models is of interest in different fields such as basic research in life science to decipher physiological and patho-physiological mechanisms or in pharma companies to drastically improve drug screening process. In the last decade, basic research showed how our understanding of the behavior of physiological and patho-physiological systems can be greatly increased thanks to a rational simplification of the human body in artificial microsystems. Among these different models, organ on chips are considered today as key technologies.
In this talk, we will demonstrate how microfluidics and microfabrication can be used to develop new relevant in vitro models in particular a gut on chip model that allows to the study for the first time he interplay between, stromal and epithelial cells.
As a critical problem in the development and deployment of effective anti-cancer treatments remains the lack of adequate in-vitro model systems, in a second part, I will focus on tumor on chip development recapitulating in vitro the complexity of the tumor-microenvironment.
Doctor, Research Director CNRS, Institut Curie, Paris
Dr. Stéphanie Descroix is team leader of the MMBM team at Institut Curie Paris and Institut Pierre Gilles De Gennes. Her team is worldly renowned for development of microfluidic device and concepts for fundamental biology, biophysics and clinic, with a strong commitment to technology transfer in the field of medicine and life sciences. The MMBM team is cofounder of the Institut Pierre Gilles De Gennes for Microfluidics.
Lecture by: Catalina Suarez
Title: ”In silico study of the transport mechanisms of the blood brain barrier”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
This study presents the modelling of different transport mechanisms of molecules through the blood brain barrier in COMSOL, attempting to replicate experimental results found in literature to create a functional and accurate computational model to predict how particles will behave when crossing from the blood stream to the brain or viceversa.
Master Student
Lecture by: Hekla Liv Mariasdottir
Title: ”Blood-Brain Barrier Models in vitro: Image Analysis of Vesicular Trafficking and 3D Growth Guidance of Brain Endothelial Cells”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
The restrictive properties of the blood brain barrier (BBB) make drug delivery to the brain challenging. Questions related to the exact route of molecular transport across the BBB remain unanswered, however transferrin receptor (TfR)-mediated transcytosis through endothelial cells is believed to be a promising target for delivering therapeutics to the brain. I will present the master thesis I’m currently working on, focusing on super resolution microscopy of vesicular transport in endothelial cells, as well as mechanical studies of human induced pluripotent stem cell-derived brain endothelial cells grown on 3D scaffolds.
Master Student
Lecture by: Jens Vinge Nygaard
Title: ”EMBLs Mathematics for Life”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
I will report on the recent EMBL course Mathematics for Life detailing how biochemetry and pathways is modelled and used to describe cellular behavior. I will then focus on what is wrong with a perspective on cells that is solely based on chemistry and introduce the concept of mechanogeometry that we will explore in a upcoming new project funded by a VILLUM Synergy grant between mathematics and BCE at AU.
Lecture by: Christoph Alexander Müller
Title: ”Optoresponsive particles for intracellular electrical interrogation”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Wireless electrical modulation of cells via opto-stimulation is an emerging approach to trigger and control bioelectric phenomena with high spatiotemporal resolution. In my talk, I will show how optoresponsive materials like graphitic carbon nitride can be used to control neural growth, and act as a tool for intracellular electrical interrogation.
Lecture by: Mikkel Haarslev S. Marqvorsen
Title: ”From Glycosylation to Immunology - A brief tour of miscellaneous projects”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Mikkel Marqvorsen is a newly appointed teaching assistant professor at BCE. In this talk, Mikkel will provide a brief overview of the various fields in which he has worked during the course of a ph.d and two postdoc positions before starting at BCE in June. Mikkel started as a ph.d. student working on glycosylation chemistry at the Dept. of Chemistry (AU) and then worked on the interface between organic chemistry and cell biology (Chemical Biology) in Leiden (NL) for three years before returning to AU at the Dept. of Biomedicine to focus on Immune Cell Biology.
Lecture by: Simon Sutter Rolighed
Title: ”Enriching Synaptosomes for Imaging”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Synaptosomes are isolated synaptic terminals from neurons obtained by homogenization of brain tissue followed by fractionation using Percoll density gradient centrifugation. We have found that these samples contain a variety of vesicular structures, making the search and identification of synaptosomes a challenging and time-consuming task. This presentation will be part two of my master's thesis on the use of immunomagnetic isolation for selective enrichment of synaptosomes.
Lecture by: Josephine Baunvig Aagaard
Title: ”Nanobody-based inhibitors of allergen-mediated anaphylaxis”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Hymenoptera venom allergy is one of the most common causes of anaphylaxis. Central in the allergic reaction is the binding of venom allergens to IgE/receptor complexes on the surface of effector cells triggering immediate allergic reactions and potentially anaphylaxis. In my PhD project, I have developed and characterized nanobodies and nanobody-based formats that block the IgE/allergen interaction and thereby potentially reduce the risk of anaphylaxis during allergen exposure.
Lecture by: Peter Johansen
Title: ”Experimental Cardiovascular Biomechanics”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
This talk gives an overview of ongoing projects in CAVE Lab. Common for all projects are that they are anchored in clinical problems and challenges and therefore conducted in close collaboration with cardiac surgeons and interventional cardiologists. The general approach is to create in vitro models that can mimic the physiology surrounding different devices, implants, and procedures.
Lecture by: Thomas Lykke-Møller Sørensen
Title: ”Highlight(s) from EMBO/EMBL symposium on Mechanobiology”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Lecture by: Frederik Høbjerg Svejsø
Title: ”Anti-EpCAM Conjugated Melt-Electrowritten Microfibrous Filter for Capturing and Culturing Circulating Tumor Cells”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
This presentation will focus on my Master's thesis, where I am utilizing melt-electrowriting to fabricate porous filters of polycaprolactone (PCL). The fiber surface is subsequently conjugated with an anti-EpCAM antibody to allow for affinity-based capture of rare circulating tumor cells (CTCs) from a liquid biopsy, i.e. a blood sample. Due to the biocompatibility of PCL, the caught CTCs will be cultured ex vivo directly on the filter and the formed clusters may contain information useful for personalized medicine.
Master Student
Lecture by: Pernille Ommen Andersen
Title: ”Development of a targeted drug delivery system for Staphylococcus aureus biofilm infections”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Conventional antibiotic treatment is inadequate for eradication of bacterial biofilm infections as only sublethal concentrations can be administered safely to patients. A potential solution to this challenge is targeted drug delivery.
In my PhD study, we tailored an aptamer-targeted liposomal drug delivery system that accumulates in S. aureus biofilm and delivers a combination of antibiotics locally inside the biofilm. In this presentation I will show the results and discuss what we learned from the study.
Lecture by: Peter Johansen
Title: ”Experimental Cardiovascular Biomechanics”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
This talk gives an overview of ongoing projects in CAVE Lab. Common for all projects are that they are anchored in clinical problems and challenges and therefore conducted in close collaboration with cardiac surgeons and interventional cardiologists. The general approach is to create in vitro models that can mimic the physiology surrounding different devices, implants, and procedures.
Lecture by: Camilla Jessen
Title: ”Establishment and Characterization of Polymicrobial Inter-kingdom three-species biofilm models mimicking the microenvironment of In Vivo Chronic Wounds in Diabetic Foot Ulcers”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Chronic wounds have become a global health problem. Chronic wounds are often infected with polymicrobial biofilms that hinders the normal healing of wounds. Consequently, chronic wounds remain in the inflammatory phase of healing. In vitro studies of chronic wounds often utilizes simple, monocultural models that exhibit unrealistic fast eradication of biofilms, once treated with antimicrobials. Given that these results are not observed in the clinic, there has become a need for more complex in vitro models comprised of multiple microbes. During my thesis, i aim to establish a polymicrobial, inter-kingdom biofilm model comprised of Staphylococcus aureus, Pseudomonas aeruginosa, and Candida albicans.
Master Student
Lecture by: Alice Le Friec
Title: ”Cellularized biomaterials for neural tissue engineering”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
I will first discuss cell and biomaterial co-transplantation for regenerative medicine in the Central Nervous System. I will then introduce my latest research, which aims to design a cryopreservable cellularized scaffold for neural tissue repair.
Lecture by: Anne-Sofie Ravn Ballegaard
Title: ”Food allergy sensitization – knowledge from animal studies”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
The presentation will give an overview of food allergy and different routes of sensitization. This will include results from animal studies with a focus on intestinal permeability and immune responses.
Lecture by: Simon Sutter Rolighed
Title: ”Enriching synaptosomes for imaging”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Synaptosomes are isolated synaptic terminals from neurons which are obtained by homogenization of brain tissue followed by fractionation using Percoll density gradient centrifugation. We have found that these samples contain a variety of vesicular structures making the search and identification of synaptosomes challenging and time-consuming task. I’ll discuss our efforts to selective enrich the sample for synaptosomes.
Lecture by: Naija From Munk-Pedersen
Title: “Development of new mri protocol for knee osteoarthritis”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Speaker: Associate Professor David Bernick from University of California Santa Cruz
Title:
"Engineering the future with Synthetic Bio"
Place: Auditorium 1170-347, Ole Worms Allé 3 , 8000 Aarhus C
David Bernick is an Associate Teaching Professor of Biomolecular Engineering at the University of California Santa Cruz campus, USA. Across both his teaching and research, he explores topics in synthetic biology and bioinformatics, emphasizing opportunities to aid under-resourced communities and the technical challenges in support of those communities. Over the past decade, he has had the pleasure of mentoring undergraduate students in the IGEM program (International Genetically Engineered Machines). Together, they have taken on projects in biofuel development, diabetes management, food insecurity, biotoxicity of water, agricultural plastic waste and access to contraceptives. Each of these areas share the larger goal of supporting our planet while normalizing sustained access to a flourishing life experience.
Dr. Bernick will discuss recently published (view paper) work to produce Exendin-4 with a consumable microbial chassis to improve access to this GLP-1 agonist. This peptide hormone and its derivatives are useful tools in the management of some forms of diabetes caused by insulin regulatory deficiency (link to paper). He will also discuss the IGEM program as a focus for undergraduate education for those interested in bioengineering, bioinformatics and other translational professions.
David Bernick
Associate Teaching Professor
Biomolecular Engineering
University of California
Santa Cruz, Ca
dbernick@ucsc.edu
Speakers: Bekir Engin Eser & Frederik Vig Benfeldt
Titles:
"Expanding the Toolbox of Fatty Acid Hydratases: A Thermostable Hydratase from Marinitoga piezophila with a Low Temperature Optimum and Unique Regioselectivity"
"Multi-enzyme/whole cell catalytic production of short-medium chain diols and diacids"
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
-
1st Speaker : Bekir Engin Eser
Title: Expanding the Toolbox of Fatty Acid Hydratases: A Thermostable Hydratase from Marinitoga piezophila with a Low Temperature Optimum and a Unique Regioselectivity
Abstract: Fatty Acid Hydratases (FAHs) catalyze the addition of water to unsaturated fatty acids to generate hydroxy fatty acids (HFAs) as products. Since HFAs have diverse application areas from materials and cosmetics industries and possess beneficial bioactivities, their benign enzymatic synthesis from abundant oils has attracted a lot of attention in the recent decade. One common challenge with biocatalytic conversions, including FAHs, is the stability of enzymes towards process conditions. Thus, we looked at Nature to find thermostable FAHs and characterized FAH ortholog from the thermostable and piezophilic organism Marinitoga piezophile. As expected, MpFAHY showed high thermostability, retaining over 90 % of its activity even after 30-min incubation at 70 °C. However, interestingly, the enzyme showed the highest activity at a much lower assay temperature of 20 °C, with sharp decreases above and below this temperature. This might indicate a physiological function of the enzyme, e.g. being part of a cold adaptation mechanism of the organism, which normally lives at 45-70 °C. Moreover, the purified enzyme requires NaCl to be active, consistent with the living habitat of its source organism. Another interesting property of the enzyme was its unique regioselectivity. MpFAHY was able to produce a mixture of 10-OH and 13-OH products from linoleic acid, with 13-OH being the preferred product, which is not a common property of wild-type FAHs.
-
2nd Speaker: Frederik Vig Benfeldt
Title: Multi-enzyme/whole cell catalytic production of short-medium chain diols and diacids
Abstract: The rising issue of plastic pollution and the limited motivation for mechanical recycling urges the academia and industry to develop the technologies that enable close- or open- loop recycling and upcycling. To address this, the ACTPAC project seeks to develop a practical method to transform chemically inert C-C backboned plastic waste, specifically polyethylene (PE), into high-value monomers and biochemicals.One of the pivotal challenges in this transformation is the biotransformation of alkanes into α,ω-alkandiols and diacids, particularly due to the difficulty in directing C-H oxy-functionalization at the least reactive terminal positions. The ACTPAC project aims to utilize the unique capabilities of Cytochrome P450 (CYP450) enzymes to overcome this challenge. Our strategy involves screening and characterization of promising CYP153A orthologs capable of hydroxylating and oxidizing medium length alkanes into α, ω-diols and diacids. Engineering of selected CYP153A enzymes to fine-tune their specificity and activity towards targeted substrates through computational methods and machine learning algorithms. Lastly, scale-up is aimed to be conducted in large-scale bioreactors, with a focus on enhancing efficiency, cofactor regeneration, and fine-tuning reaction conditions to maximize yields.
Speakers: Laura Munoz, Susmit Chakraborty & Timothé Philippon
Title: Relevance of H2 consumption characteristics for acetogenic and methanogenic bioelectrochemical CO2 reduction
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Acetogens and methanogens reduce carbon dioxide with H2 as electron donor to obtain energy. This autotrophic metabolism is of interest for CO2 valorization biotechnologies, such as gas fermentation and even more microbial electrosynthesis. Indeed, the ability of those microbes to rapidly consume H2 could enhance electrochemical H2 production, once put near an electrode performing proton reduction. This hypothesis could be important for bio-electrochemical applications if proven to be true. To test our hypothesis, we must first characterize differences in H2 consumption characteristics between available acetogenic and methanogenic strains. Understanding those differences will also aid optimal strain selection for microbial electrosynthesis.
First, we determined the H2 threshold, i.e. the H2 partial pressure at which acetogenesis or methanogenesis halts, for diverse acetogenic (1) and methanogenic strains and observed strong differences. The observed H2 thresholds suggest significant variations in bioenergetics, potentially influencing growth yields and kinetics as well.
Furthermore, we determined the H2 consumption kinetics of different acetogens over a wide range of H2 initial concentrations. Interestingly, we observed that their H2 consumption followed first-order kinetics at under-saturated H2 levels. Our results thus suggest that acetogenic conversion rates can be increased by increasing the H2 partial pressures. In addition, we found strong differences in the first-order H2 consumption coefficient. We hypothesize the kinetic differences can be in part related to different types of hydrogenases of the strains.
In addition, to predict the performance of these strains in bioelectrochemical reactors, we incorporated the H2 threshold and kinetic data into mathematical models. These models simulate the behaviour of the strains under various conditions, such as electric current input, providing useful insights to optimize H2 utilization rates and enhance process efficiency.
Overall, our comprehensive new understanding of H2 dynamics for these hydrogenotrophic strains will guide the selection of suitable biocatalysts for microbial electrosynthesis.
References
1 Munoz, L; Philips, J. No acetogen is equal: Strongly different H2 thresholds reflect diverse bioenergetics in acetogenic bacteria. Environ Microbiol 2023;25:2032–40.
Lecture by: Professor Dr.-Ing. habil. Selin Kara, Department of Biological and Chemical Engineering, Aarhus University, Denmark
Title: "Process intensification for enzymatic decarboxylations: Transitioning from lab to industrial scales”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303
The application of nature’s catalysts, “enzymes,” for the synthesis of chemicals is a crucial emerging field of industrial biotechnology to meet the current and future needs of our society for sustainable manufacturing of chemicals. Nature uses an elegant and efficient synthetic strategy: Coupling enzymes in multi-step pathways without intermediate isolation and purification steps with precise spatial control of catalysis. Inspired by nature, the design of multi-step biotransformations has been attracting significant attention within the biocatalysis community. The talk will introduce enzymatic decarboxylation reactions (in cascading systems), exploring the use of non-conventional media, enzyme immobilization, and different operational modes for enhancing the volumetric productivity of these biocatalytic applications.
Lecture by: Maria Florencia Bambace & Herald Wilson Ambrose
Title: "Reuterin-based biological treatment to mitigate methane emissions from pig slurry storage”
Place: Gustav Wieds Vej 10C, 8000 Aarhus C, Building 3130, Room 303.
Methane (CH4) accounts for more than 90% of farmgate greenhouse gas (GHG) emissions in pig farming, with 80% being produced during manure management. In intensive pig production, slurry is stored in manure pits under the barn floor for short term storage (1 to 6 weeks) and in outside storage tanks for longer storage periods. During this time, CH4 is emitted as a result of microbial degradation of organic substrates present in the pig feces, combined with the anaerobic conditions developed under the slurry surface, which promote the activity of methanogens. Acidification is considered a benchmark technology for mitigating CH4 emissions from stored slurry. However, there are several associated drawbacks such as safety issues in application, soil sensitivity to increased sulphur loads during land application, and inhibitory effects on biogas production. Other chemical additives raise further environmental concerns; hence the need for a biological alternative is highly sought for CH4 mitigation in slurry storage.
Biological treatments studied thus far, utilizing microbial or enzymatic additives have shown little to insignificant potential for CH4 mitigation in pig and cattle slurry storages. In this seminar talk, we will present and discuss the results of a successful biological treatment aimed at inhibiting methanogenic activity in slurry storages, conducted on a laboratory scale headspace emission setup. The biological additive involves the use of Limosilactobacillus reuteri, which in the presence of glycerol produces reuterin, a broad-spectrum antimicrobial agent. We assessed the impact of endogenously produced reuterin on CH4 emissions from pig slurry by initially introducing both L. reuteri and glycerol into the slurry, which was then stored for a period of 26 to 30 days, during which CH4 emissions were measured. We also optimized the dosage combination of L. reuteri and glycerol. Our results showed that endogenously produced reuterin reduced CH4 emissions by 74-90% compared to untreated slurry. The environmental and biological aspect of our study will be further discussed, highlighting this novel approach as a promising alternative to H2SO4 or chemical surfactant treatments for reducing methanogenic activity in pig slurry storages.
Lecture by: Nele Van Dessel, CEO from Ernest Pharmaceuticals (USA)
Title: "The use of Salmonella bacteria to treat cancer”
Place: Zoom, https://aarhusuniversity.zoom.us/j/62375855091
The microbial biotechnology course will host an online guest lecture on the use of Salmonella bacteria to treat cancer.
The guest speaker is Nele Van Dessel, CEO from Ernest Pharmaceuticals (USA), a small startup company, trying to bring this new and intriguing microbial biotechnology to the market.
