Project descriptions

At the mandatory introductory course the PhD students at DTU Bioengineering write a popular science description of their project. The aim is to train the students in describing complex science to a non scientific audience, which in turn will enhance the students' chances of securing funding in the future and disseminate our research areas to a broader public audience.

Some project descriptions are confidential and therefore only the title, supervisor and PhD student are mentioned. The projects are listed under the introductory course they were written on.

Fall 2018 

PhD Student  Pernille Kjersgaard Bech
Supervisor  Lone Gram
Title  The potention for production of microbial secondary metabolites in marine and soil systems and their influence on microbial diversity

Exploring the true ecological role of microbial secondary metabolites in nature

Microbial secondary metabolites (SMs) have been exploited by mankind for decades, especially as medical drugs. They are complex molecules often produced by biosynthetic genes clusters (BGCs). The predominant thinking is that microbial SMs protect the producer from competitors. However, microbial SMs may display a much broader spectrum of functionalities than currently thought; through their ability to modulate and alter the growth of microorganisms, they may be strong drivers of microbial community assembly and composition and in part be responsible for shaping microbial communities in nature. Recent studies aiming at understanding the role of SMs has focused on laboratory setups investigating the interactions between two microorganisms, or the effect of high concentrations of pure compounds. However, the secondary metabolism of bacteria, and its implications for interactions between microorganisms in natural systems, have remained unexplored and the true ecological roles of SMs in nature have not been elucidated. Hence, we need to examine the microbial ecology through simplified laboratory‐based microbial model systems that allow us to mimic more natural conditions found in nature.

The purpose of my PhD project is to determine the genetic diversity of genes and gene clusters involved in microbial secondary metabolite biosynthesis in natural environments such as soil and marine systems. This will allow us to follow the dynamics of changes in the microbiome composition together with the genetic potential for SM production nature. These findings will provide a foundation for engineering microbial model systems, in order to mimic the natural systems in vitro and follow how the microbiome structure from natural environments is shaped by key SM‐producing microorganisms.


PhD Student  Mikkel Madsen
Supervisor  Birte Svensson
Title Structure and Design of Whey Protein Alginate Complexes

Digging in to the smoothness of yoghurt and softness of bread 

Within food production additives are a strong component to enhance the product, but what is the chemistry behind the additives and how does this influence you?

Protein-hydrocolloid complexes arise when mixing oligosaccharides with whey proteins. These complexes are widely applied in manufactured foods, e.g. yogurts and other fermented milk products to ensure texture, stability, a smooth mouthfeel, shelf life by ambient storage and they might also affect the degradation of food in the digestion tract. 
The most prominent whey protein, β-lactoglobulin has been thoroughly characterized with regard to structure, function, stability and technological properties. It has however not been characterized in the presence of the polysaccharides and oligosaccharides it interacts with in our food production.
 
To characterize, describe and make model protein-hydrocolloid complexes it is necessary to examine the underlying chemistry of the complex formation. To illuminate the subject we are doing a thorough investigation into the binding between protein and oligosaccharides of different degree of polymerisation.
 
To identify structural determinants in whey protein alginate interactions and crosslink whey proteins to obtain better-quality aggregates of complexes with selected alginates we need to undertake the production of recombinant, stable isotope labelled β-lactoglobulin and analysis of sites interacting with defined alginate oligosaccharides using NMR.
Chemical cross-linking of β-lactoglobulin Is pursued by aid of a series of standard bifunctional reagents and transglutaminase followed by identification of cross-linked amino acid residues using mass spectrometry. Evaluation of digestibility in vitro digestion by artificial gastrointestinal tract systems of cross-linked SPC proteins (whey protein mixtures) in complex with alginate will enable validation of functional effects of the complexes.
 
The structural and chemical data that are obtained through this project will lay the foundation for the design of protein hydrocolloid complexes that makes yoghurt smoother, bread softer, have different degradation times and decrease cost in the food production sector.
 

PhD Student Vy Tran Nguyen Ha 
Supervisor  Anne Meyer
Title Kinetics and Technology Functionality of Microbial Fucoidanases


PhD Student Trang Vo Thi Dieu
Supervisor Anne Meyer
Title Aryl sulfatases: Activation, kinetics, mechanism for Technology applications


PhD Student Thuan Nguyen Thi
Supervisor Anne Meyer
Title Enzymatic Fucoidan Extraction and Processing


PhD Student Louise Otterstrøm Martinsen 
Supervisor Gregers Jungersen
Title The local and systemic porcine host response to experimental infection with S. aureus

Time to combat Staphylococcus aureus! 

S. aureus is an opportunistic pathogenic bacterium and one of the most common causes of skin and soft tissue infections on a global scale while also a common harmless colonizer of the human skin. Up to 50% of the human population is colonised with this potential pathogen, either intermittently or permanently. As being colonised with S. aureus can increase the risk of getting an infection, effective treatment and preventive strategies are needed.
Treatment of S. aureus infections are recently being complicated by the emergence of resistant strains, e.g. Methicillin Resistant Staphylococcus aureus (MRSA), causing treatment difficulties or even treatment failure.
Development of effective preventive strategies, such as vaccines, is an obvious alternative to antibiotic treatment. Current vaccine approaches have not demonstrated effective protection against S. aureus infections, increasing the need for engineering new and effective vaccine formulations.
In this project we will test a recently developed vaccine. The antigens in the vaccine are selected by advanced in silico modelling of a predicted outcome of high protection. The selected antigens are conserved across several species of S. aureus, making it possible for this vaccine to protect against several different S. aureus infections including MRSA strains, and have furthermore shown good protection in rodent models.
To further evaluate the efficacy of the vaccine prior to human clinical trials, it will be tested in pigs as these show higher homology to humans in relation to skin anatomy, physiology and immunology compared to other widely used animal models, such as rodent models. Furthermore, the interaction between S. aureus and the porcine host immune response will be characterized, elucidating part of the complex and so far unrevealed interaction between the two organisms. 

PhD Student Morten Lindqvist Hansen 

Supervisor Lars Jelsbak
Title Control of microbial soil communities by Pseudomonas produced secondary metabolites


PhD Student Mathilde Nordgaard Christensen 
Supervisor Ákos Kovács
Title Bacillus subtilis biofilm formation and evolution on Arabidopsis thaliana roots

Towards a more sustainable agriculture by developing Bacillus subtilis strains with enhanced plant protection properties 
 
These days we are facing an increasing demand for a more sustainable and effective agriculture as well as a wish for safer plant-based food. A sustainable solution is biocontrol, which is a method of exploring the ability of microorganisms to control plant diseases, and thereby acts as a replacement of pesticides. For this purpose, Bacillus subtilis is a valuable microorganism since it is naturally found in soil and vegetation, where it colonizes plant roots through biofilm development, and importantly, it is a plant growth-promoting organism.
This project aims to develop B. subtilis strains with enhanced bacteria-plant interactions that benefit the plant. Strain improvement will be accomplished through experimental evolution of B. subtilis on Arabidopsis thaliana roots. In short, an A. thaliana seedling will be exposed to B. subtilis, and every 24 hours the developed colonized root will be transferred to and co-incubated with a non-colonized root, allowing subsequent colonization cycle. The expected result of such serial selection is B. subtilis strains with enhanced root colonization abilities. Whole genome resequencing will allow identification of the genetic alteration(s) responsible for the improved properties. Finally, the improved properties of the evolved isolates will be examined for plant protection of crop species in collaborative field experiments.
The study will result in B. subtilis strains with enhanced benefits on important crop species, and these strains can be used as biocontrol agents in the agriculture, resulting in more productive crops, giving a higher yield and reducing the use of pesticides, thereby contributing to a more sustainable agriculture. 
 

PhD Student Pernille Neve Myers
Supervisor Susanne Brix Pedersen
Titel Systems Biology of the Infant Gut Microbiome

The gut microbiome in early life and how it affects health later in life
 
During birth, our gastrointestinal tract is colonized by microorganisms from either our mother’s vaginal/intestinal tract or skin, depending on the mode of delivery. As we are exposed to the world, our gut is rapidly colonized by hundreds of different microorganisms, many of which originate from our mother’s gut. Together, the millions of microorganisms, which resides in the gut constitutes the gut microbiome.  Some of the first microorganisms, which are transferred from mother to infant, are specifically adapted towards breaking down the unique sugars found in human breast milk. But, microorganisms do not only help us break down the food we eat, they also produce hundreds of different compounds, which in turn may influence our metabolism and health. I am investigating the importance of the gut microbiome in early life in relation to childhood allergy and obesity by following children and their mother closely from third trimester and early life up until age 5. The goal of my PhD project is to identify early life microbial markers, which determine disease later in life. This is the first step towards developing better strategies in the future for prevention of allergy and obesity in children. Studying the gut microbiome is very challenging because we know very little about the function and role of the majority of the microorganisms found in the gut. I therefore develop new bioinformatics tools for the analysis of DNA sequences from stool (metagenomics). As allergy and obesity is also influenced by many other factors, such as the development of our immune system, I am integrating metagenomics data with multi-omics data from blood and breast milk.
 

Spring 2018


PhD Student Elizabeta Madzharova
Supervisor Ulrich auf dem Keller
Title Functional modification of matrix metalloproteinase (MMP) 9 activity by glycosylation

A new layer of cellular regulation by protein post-translation modifications

Post-translational modifications (PTMs) are essential mechanisms used by eukaryotic cells to coordinate cellular processes. They have been extensively studied and widely characterized individually, however complicated intra- and intermolecular crosstalks of multiple PTMs confer the next level of complexity that we are just beginning to explore.

This project will take a closer look into the regulatory crosstalk between glycosylation, as the most prominent and diverse PTM in the extracellular space, and limited proteolysis, which is by far the most neglected, but an essential additional PTM that irreversibly, modifies bioactive target proteins in- and outside of the cell.

We expect that this project will assess for the first time the fine-tuning of limited proteolysis in the extracellular space by glycosylation and give us more insight of the cellular regulation by revealing a new layer of regulation with substantial implications for basic biology and translation approaches.


PhD Student Simonas Savickas
Supervisor
Ulrich auf dem Keller
Title Interconnected Activities and Functions of Matrix Metalloproteinases at the Wound Edge

Uncovering protease networks in cutaneous wound healing

Protease networks govern pivotal processes in the healing skin wound. By using next generation proteomics/degradomics strategies, we try to understand the multidimensional balance between active and inactive proteases and their disturbance in impaired cutaneous wound healing.


PhD Student Yannick Buijs
Supervisor 
Lone Gram
Title From ecology to technology: Unraveling of the bioactive potention of marine bacteria

From Ecology to Technology: unravelling the bioactive potential of marine bacteria

Between 1962 and 2000, no antibiotics with new structures or activity mechanisms have entered the market. This, in combination with the emergence and rise of various drug-resistantpathogens, has caused a worldwide problem in combating infectious diseases. New antibiotics are necessary in order to remain able to treat illness caused by pathogenic bacteria.

Drug discovery has recently been boosted by the combination of genome sequencing efforts and bioinformatics analyses of the potential for production of biologically active compounds. It wasfound that the large majority of biosynthetic gene clusters, which are clustered genes encoding for the production of so-called secondary metabolites, has not been linked to their correspondingchemical compounds. Marine bacteria are not an exception to this finding. Furthermore, the marine environment harbors a rich and underexplored biodiversity. Marine bacteria are therefore an interesting source for the discovery of new compounds with potentially antimicrobial activities.

The purpose of the project is to design and use smart strategies that help to unravel the bioactive potential in marine bacteria. Genetic reporter systems, adaptive evolution and high throughputscreening methods are examples of the strategies that will be pursued. Furthermore, during the project a look will be taken at the natural roles of antibiotics in the ecosystem. New insights from such studies can be used to speed up the search, so that a fatal antibiotic resistance crisis can be avoided.


PhD Student Liqin Xu
Supervisor
Susanne Brix Petersen
Title The influence of the gut microbiome on anti-cancer therapy

The body produces T cells that, upon activation, are able to kill tumor cells. Tumor cells then evolved to prevent T cell activation. A new class of anticancer drugs, known as immunotherapies including the CTLA‐4, PD‐1 and PD‐L1 blocking antibodies, has been used with great success in patients with many advanced malignancies. The main drawback of immunotherapy is that the great majority of patients do not benefit from the therapy [1]. In the year of 2017, three different studies pointed out that tumor patients’ responses to cancer immunotherapies could depend on their gut bacteria [2,3,4]. However, all these studies were based on dietary and genetic backgrounds of Caucasians, and since dietary habits of different human populations are significantly different, we therefore set-out to carry out an in‐depth study of the gut microbiome of patients that accept the checkpoint inhibitor immunotherapy in the Chinese population. Specifically, we characterize the gut microbiome of non‐small cell lung cancer (NSCLC) and nasopharyngeal carcinoma (NPC) patients that accept the anti‐PD1 immunotherapy, and compare the gut bacteria of patients who are responsive or refractory.

We expect to identify bacteria taxa with the potential to improve the immunotherapeutic effect in our data. Based on these findings, we could help doctors screening the right patients for receiving the immunotherapy. Purification, culture and formulation of selected bacteria should be the topic of future projects with the final goal of administering them as probiotic supplements to patients receiving anti‐PD1 therapy.

Reference:

1. Zhou W, et al. PD‐L1 (B7‐H1) and PD‐1 pathway blockade for cancer therapy: Mechanisms, response biomarkers, and combinations. Sci Transl Med 2016.

2. Matson V, et al. The commensal microbiome is associated with anti–PD‐1 efficacy in metastatic melanoma patients. Science 2017.

3. Gopalakrishnan V, et al. Gut microbiome modulates response to anti‐PD‐1 immunotherapy in melanoma patients. Science 2017.

4. Routy B, et al. Gut microbiome influences efficacy of PD‐1‐based immunotherapy against epithelial tumors, Science 2017.


PhD Student Deniss Petrovs 
Supervisor Birte Svensson
Title Omics-guided Discovery and Characterisation of Enzymes Involved in Utilisation of Xyloglucans and other Plant Dietary Fibres by Probiotic and Gastroin

The answers lie within – understanding the gut flora to improve human health

The human gastrointestinal tract is colonized by a dense microbial ecosystem, which is established shortly after birth and is responsible for the digestion of dietary fibers that we consume from a wide range of foods. Since the human genome does not contain fiber-digesting enzymes, the relationship between the gut microbiota, the host and its diet has a pronounced effect on humanhealth and physiology. However, little is actually known about how our gut bacteria degrade dietary fibres.

Microorganisms that provide us with health benefits are referred to as probiotics and substances that specifically stimulate the growth of these bacteria are prebiotics. Knowledge about the prebiotic digesting enzymes encoded by the genomes of our gut bacteria is expanding and with it the application of probiotics and prebiotics in human health and nutrition. To widen our understanding of the complex microbial interactions in the gut, further research at the molecular level is required.

The main objective of this PhD project is to understand the transport and utilization of ingested fibres by selected commensal and probiotic bacteria and to study the interplay between these microorganisms, the stimulating carbohydrate substrates and the human cells. This will be accomplished through bioinformatical analysis, growth assays, identification, and characterization of candidate carbohydrate-active enzymes (CAZymes). Omics techniques (differential proteomics and transcriptomics) will be used to monitor bacterial gene regulation and protein profile changes when grown on selected glycans and to identify regulated CAZymes and other proteins. Additionally, similar omics analyses upon establishment of symbiotic relationships with other gut microbes and/or host epithelial cells will be conducted.


PhD Student Andreas Møllerhøj Vestergaard
Supervisor Rasmus John Norman Frandsen
Title Food colors cell factory


PhD Student Line Hillerup Kristensen
Supervisor
Uffe Hastrup Mortensen
Title Using Biodiversity to Identify Superior Cell Factories for Secondary Metabolite Production

Imagine that you want to move a heavy rock away from the path you are walking. You ask a big strong person to help you move the rock and not a small person. The small person could possibly be trained to also do the job, but this would take a lot more time and effort. Now imagine if you had an ox or an elephant available to help, they could probably do the job even better. This would be taking advantage of the biodiversity between the different species to find the organism best suited for the task. This is what we want to do with microorganisms in cell factories, choose the best-suited host organism to complete the task at hand e.g. producing a natural food colorant, therapeutic protein or an enzyme for some industrial application.

Right now, the approach taken when developing new cell factories in many cases resembles the training of the small person. We like him because we know how he reacts in most situations and we can teach him new tricks. This however, does not mean that he will ever be as good at lifting rocks as an elephant, which is simply built completely different. The same is the case for microorganisms, one well known organism may be suited for some applications but definitely not for others. What we want to do in DIVERSIFY is to construct a large library of different yeasts and filamentous fungi to find the best producers of specified products in a much shorter time than would be possible using only traditional host organisms. This way we should end up identifying new superior cell factories ready for greener production of a range of different bio-products. 


PhD Student Katrine Wegener Tams 
Supervisor Anders Folkesson, Mikael Lenz Strube
Title Pig production without the use of antibiotics - impact on the pig resistome and microbiome

Are antibiotic free pigs one of the answers to the resistance crisis?

Antibiotics are widely used in conventional pig farming, which can lead to high amounts of resistant bacteria. Since resistant bacteria are harder to treat than non-resistant bacteria and are known to be transferred from pigs to humans, a rising interest in meat produced without antibiotics has led to an alternative to conventional farming - antibiotic-free (ABF) pigs. Furthermore, antibiotics are known to disrupt the natural microbiome of humans and animals, which might suggest that the ABF pigs healthier and more robust than conventional pigs because they are able to build up a microbiome without antibiotic interruption.

These ABF farms are not completely antibiotic free since sick pigs are individually treated, but these are sold as conventional meat and not as ABF meat. Farmers are also allowed to treat the sows when the ABF pigs are suckling.

This co-rearing case/control setup allows one to ask some interesting questions: Does the microbiome and resistance level changes in the pigs that are treated compared to pen mates? Do the treated pigs affect the microbiome and resistance level of their pen mates? Does a treated sow have an effect on the offspring?

In this project, we want to study the effect of antibiotics on the resistance levels in the pigs as well as their gut microbiome. These ABF pig farms gives us a unique opportunity to study pigs in real life conditions with treated and untreated pigs living in the same environment and with the same genetic background.  We hypothesize that pigs that have not been treated with antibiotics have a healthier microbiome and fewer resistant bacteria. We want to examine this by two methods called 16S rRNA gene sequencing and high-throughput qPCR, which can determine the composition of the microbiome and determine the level of resistant bacteria.

The project is a part of a large national project on ABF pigs. Since improved managerial practices and high animal welfare is necessary for ABF production, these are major overall aims of the larger project.

Hopefully, this project will shed some light on the positive effects of ABF pig farms and maybe on how we can make these farms even better to battle the rising antibiotic resistance in our community.


PhD Student Kyle Rothschild-Mancinelli 
Supervisor  Mikael Rørdam Andersen

Title Genome reduction of a filamentous fungus

A Lean Fungus- A new biofactory for more efficient molecule production

Scientists have been studying the rules of nature for centuries and we are now at a crossroads where we can begin to rewrite the classical rules of biology. One of the problems with engineering biology is the massive complexity and the unpredictability of engineering the cells. This project aims to provide scientists and engineers alike a more efficient system in which to rewrite these rules. We will take Aspergillus niger and strip it down to its bare genetic essentials in order to engineer a biological factory, a synthetic “ideal” host, that can be focused on efficiently producing a desired product, and to be a cost-saving alternative to current resource inefficient engineered production hosts. This genome reduction approach will make bioengineering more predictable, and thus more efficient.

However, industry and academia have until very recently followed the rules of nature, using existing systems in organisms for product production, but now that we better understand the molecular systems behind these production pathways, we can excise them from their original host. Thus, this is advantageous for many reasons, but one of the main ones is that the original organism may be very hard to culture or harness as a production system. Therefore, by inserting the pathway into a pre-adapted host, we can create a controlled environment to produce any product we want.

Fungi have been indispensable staples in biological production ever since the age of fermentation, but only starting in the 1890’s with patents in Aspergillus oryzae did fungi begin to become fully harnessed as biological factories. They are hardy, stable, and produce a large variety of both enzymes and antibiotics naturally. Hopefully, the end of this project will produce a new strain of A. niger that will be adaptable to almost any novel pathway and can be applied across the board in biological industry.

 

Head of PhD School

Bjarke Bak Christensen
Head of Department
DTU Bioengineering
+45 30 66 42 33

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