Master projects at CBMR

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Background: In 2017, 451 million people were estimated to be affected by diabetes worldwide and the number continuously rises. The majority of patients suffer from type 2 diabetes caused by an interplay between genetic predisposition, sedentary lifestyle, and an unhealthy energy-dense diet. Dietary choices and behaviour associated with food intake are influenced by factors such as geographical region, social setting and taste preference. Investigation of the genetics potentially driving taste preference and liking will add to the knowledge of dietary behaviour and aid in future designs of dietary guidelines that are manageable thus increasing compliance levels and positive outcomes for individuals at risk of developing diabetes and related health outcomes.

The project: In the “Taste & DNA” project, we will examine the genetic aspect of taste preference to improve our understanding of dietary habits and the effects of overconsumption on health status. The aim of the project is to survey taste preference and liking in a large cohort using a valid questionnaire adapted to the Danish population. Next, results obtained from the questionnaire will be compared with existing genotypic data from the same individuals in a genome-wide association analysis. The project will provide training in how to handle large data sets as well as genetic statistical analysis.

The student: We are looking for skilled bachelor or Master’s students, who are enthusiastic about research, and have the ability to quickly learn and work independently with data analyses.

Contact: Please contact Postdoc Sara Haydar (sara.haydar@sund.ku.dk) and PhD Student Camilla Cederbye Karlsson (camilla.cederbye@sund.ku.dk) if you would like to know more about the project.

 

 

 

 

 

 

 

 

Background: Adipose tissue’s extracellular matrix plays a role in obesity and metabolic diseases and could be a potential therapeutic target for the treatment of these diseases. Researchers at CBMR recently established the role of the extracellular matrix protein ADAMTS9 in muscle insulin resistance (IR). However, nothing is known about the functions of ADAMTS9 in the adipose tissue, while its expression there implies that it likely has important roles to play.

 

The project: The aim of this project is to characterize the functions of ADAMTS9 in the adipose tissue using genetically modified mouse models. The effect of ADAMTS9 knockdown to metabolic parameters is tested with normal chow and a high fat diet. Tissue samples of different adipose depots will be studied with a range of molecular biology and histological techniques and microscopy. Later, primary adipocytes will be isolated to study the molecular level effects more carefully. This project will increase our understanding of the significance of extracellular matrix in obesity and metabolic diseases, while providing important technological skills and knowledge of adipose tissue metabolism for the student. The project takes place in the lab of associate professor Thomas Frimurer.

 

The student: A motivated and enthusiastic student who is willing to learn a variety of methods and work with laboratory animals. Experience with animal models is appreciated but not essential.

 

Contact: Please contact Post Doc Anna Laitakari (anna.laitakari@sund.ku.dk) if you would like to know more about the project.

 

Background: The effective use of insulin is impaired in type 2 diabetes (T2D), causing failure to transport glucose from the circulation to the cells. Eventually, T2D can lead to circulatory, nervous and immune systems disorders deteriorating the quality of life of its patients. The prevalence of T2D increases rapidly worldwide, together with the global pandemic of obesity and metabolic syndrome. Researchers at CBMR recently established the role of the extracellular matrix protein ADAMTS9 in insulin resistance (IR). These findings suggest that inhibition of ADAMTS9 could be a potential new way of treating IR before it develops into T2D.

 

The project: The aim of this project is to characterize ADAMTS9 inhibitors for the treatment of IR in cell culture and animal models, with inhibitors that are developed at the CBMR. Muscle cells are treated with glucose and insulin to cause IR and treated with the inhibitors. The inhibitors’ potency to prevent IR will be measured with various techniques, also characterizing the mitochondrial function. Next, diabetic mice are treated with the inhibitors. Later, the tissue samples will be studied with a range of molecular biology and histological techniques and microscopy. This project will increase our understanding of diabetes and potentially result in a new drug for its treatment, while providing important technological skills and knowledge of metabolism for the student. The project takes place in the lab of associate professor Thomas Frimurer.

 

The student: A motivated and enthusiastic student who is willing to learn a variety of methods. Experience with cell culture or animal models are appreciated but not essential.

 

Contact: Please contact Postdoc Anna Laitakari (anna.laitakari@sund.ku.dk) if you would like to know more about the project.

 

Background: Nanopore sequencing is a third-generation DNA/RNA sequencing technology, that utilises genetically engineered pore-forming proteins subjected to an electrical potential. When nucleic acids pass through the pores, each of the four bases produce a specific electrical signal, enabling high-throughput sequencing in real-time of e.g. DNA and RNA. A number of advantages compared to e.g. Illumina sequencing exists: we can track the sequencing in real-time, we can monitor and stop it anytime and finally, we can easily call methylation patterns and base modifications directly from the recorded electrical signals. The smallest Nanopore sequencing instrument is a true in-field device requiring no advanced lab or setup. It’s smaller than a smartphone, USB powered and it can sequence in remote locations, such as the jungle and even aboard the International Space Station!

 

The project: In this project, the student will learn how sequence cell-free DNA from experimental animals (minipigs) and human blood samples with the Nanopore sequencer. The student will learn to process and analyse high-throughput sequencing data with some of the most advanced bioinformatics tools in a highly supportive and friendly environment. The student will also learn more about the use of experimental animals in metabolic disorders, including visits to our partners facilities. The end goal is to explore the vast potential of cell-free DNA and Nanopore sequencing in the development of a “liquid biopsy” test for use in future clinical settings as new diagnostic or prognostic tools.

 

The student: We are looking for a student to complete a bachelor or master thesis in bioinformatics or a related field.

 

Contact: Markus Hodal Drag, Postdoc (markus.drag@sund.ku.dk)

 

 

Background: Excess energy intake from diet leads to a gain in body weight that consists primarily of fat but also of muscle and bone mass to support the new body weight. Thus, most individuals with obesity not only have higher body fat mass but also higher lean mass than an average person with normal weight. Some individuals, however, show relatively small lean body mass, either due to a low muscle mass (sarcopenia), bone mass (osteopenia) or both. This inclination becomes particularly apparent during aging, when body lean mass is being increasingly replaced by fat mass.

At the moment, the biological mechanisms leading to low lean mass in individuals with obesity are poorly understood. Our aim is to provide exciting new insights into this area using genetic studies.

 

The project: We use genetic association studies, the latest bioinformatics tools, and experimental approaches to identify relevant gene players and understand their functions. The student will learn to analyse large-scale genetic and body composition data and apply advanced bioinformatics tools in a highly supportive and friendly environment.

 

The student: We are looking for a motivated and skilled master student in bioinformatics, computational biology or a related field to complete a research project and/or a bachelor or master thesis. (7.5, 15 or 30 ECTS). If interested, just come and meet us.

 

Contact:

Germán Carrasquilla, MD-PhD (german.carrasquilla@sund.ku.dk)

 

The group
At the Novo Nordisk Foundation Center for Basic Metabolic Research, located in the Maersk Tower, the Hansen Group conducts cross-disciplinary research within genetics and the microbiome field. Our focus is to expand our understanding of metabolic diseases through the use of multi-omics data, in order to design better treatment options and allow for targeted prevention.

The study
In collaboration with Odense University Hospital, we have measured plasma levels of 92 cytokines from thousands of patients with varying stages of liver and metabolic disease, as well as healthy controls. We have also measured the same cytokines after various treatment interventions.

Results
Our preliminary analyses show that many of these cytokines appear to be involved in the pathogenesis of fatty liver disease and may serve as promising diagnostic and prognostic markers, and even indicators of treatment response.

The project
This is why we need you to join us for your Master’s thesis! Your task would be to further analyze these promising data, in order to understand the pathogenic mechanisms underlying liver and metabolic diseases.

Requirements
You are in your final year of bioinformatics, human biology, molecular biomedicine, biology, medicine, or a related degree. We expect you to be interested in metabolic diseases, have basic knowledge of biology, and some experience with coding for data analysis. Understanding of immunology, genetics, statistics, and pathobiology are considered an asset. On a personal level, you are able to work independently, as well as in a team, have good academic standing, and are highly motivated to perform a Master’s thesis project within our group.

More info and contact
If this has spiked your interest, please get in touch with one of our working group members:

Research assistant Rasmus Tanderup Jensen (rasmus.tanderup@sund.ku.dk),

Research assistant Evelina Stankevic (evelina@sund.ku.dk),

PhD student Sara Stinson (sara.stinson@sund.ku.dk),

Postdoc Helene Bæk Juel (helene.baek.juel@sund.ku.dk), or

Professor Torben Hansen

 

Background

Obesity and obesity-related diseases are among the top causes of morbidity and mortality worldwide. One approach to combat obesity is to increase energy expenditure via the activation of brown adipose tissue (BAT). In contrast to white adipose tissue that stores energy, BAT burns energy to produce heat, a process known as thermogenesis. Identifying the molecular pathways that regulate BAT development, activation and function is essential for therapeutic targeting of this tissue to increase whole body energy expenditure for the treatment of obesity.

The project

This project will contribute to the identification of novel processes facilitating thermogenesis in brown adipocytes in vitro and in vivo. It is based on preliminary data from the group using eCLIP sequencing and Ribosome sequencing for the identification of novel protein coding and non-coding genes associated with BAT activation. The student will learn how to use downregulation and upregulation systems in order to study the role of specific target genes, using state-of-the-art CRISPR/Cas9 technology to decrease or increase target gene expression. The metabolic function of these genes (protein or ncRNA) in brown adipocytes will be assessed using a range of biochemical and molecular biology techniques. Thus, this project will increase our understanding of BAT function, while providing key technological skills and knowledge of metabolism for the student.

The student

We are looking for skilled Bachelor or Master students who are enthusiastic about research, and have the ability to quickly learn and work independently. You will be mentored by a Postdoc in the lab, who will train and assist you with directing the research project.

Contact

Associate Professor Brice Emanuelli (emanuelli@sund.ku.dk) or Dr. Simone Bossi (simone.bossi@sund.ku.dk).

 

Background: The Clemmensen Group studies the biological regulation of body weight and aims at developing new therapeutic strategies that can correct obesity and protect against weight gain.

The project: You will be taking advantage of genetic and pharmacological tools to study conserved mechanisms of appetite-lowering drugs utilizing two model organisms: a nematode Caenorhabditis elegans (C. elegans) and mice. Your main focus will be exploring the mechanisms of drugs/compounds that have a potential impact on ageing.

The student: we are looking for an ambitious Master student that is willing to learn about the biology of two model organisms: C. elegans and mice. The project duration: one-year

Contact: Vaida Juozaityte, Postdoc, Clemmensen Group, email: vaida@sund.ku.dk

 

Background: Bisulfite sequencing (BS), including reduced representation bisulfite sequencing (RRBS) and whole-genome bisulfite sequencing (WBGS), is an important methodology employed by Barrés Group in order to investigate the methylation state of cells/tissues after various life-style interventions such as diet and exercise. Although BS generates methylation information for millions of CpG sites, the majority of the CpG sites are dropped/filtered-out due to missing values. A common approach to overcome this problem is to impute the missing values. However, there are several missing value imputation algorithms, and a systematic analysis comparing their performance is still lacking.

 

The project: The purpose of the project is to identify the best performing missing value imputation algorithms, build a tool evaluating the performance of the algorithms and potentially develop a novel algorithm that can be used for BS missing value imputation. Addressing this problem will allow us to make better estimations on the methylation status of CpG sites, thereby covering a broader spectrum of epigenetic landscape of the cells/tissues.

The student: You are a MSc student in bioinformatics, computer science, mathematics, biology or similar field. The criteria we seek for:

  • A strong interest in bioinformatics and biological mechanisms
  • Experience in R and/or Python programming languages
  • Familiarity with Linux/UNIX environment and shell scripting
  • Knowledge of next generation sequencing (NGS) techniques
  • Demonstrated capacity for effective teamwork and time management
  • Excellent English communication skills, both written and oral

What you will learn

  • NGS analysis and biological interpretation of RRBS and WGBS data from scratch
  • Project management with GitHub
  • R package development

Contact: Please contact Assistant Professor Ali Altintas (altintas@sund.ku.dk) for details.

 

Background:

In times of food scarcity, internal metabolic cues are vital to ensure survival. Therefore, locomotor activities must be prioritized between foraging for food, reproduction, and escape from predators. 

The project:

Despite locomotion and eating being intertwined and both being essential. behaviors for survival, the mechanisms by which specific motor programs are engaged to maintain energy homeostasis are not well understood. In this project we dissect the neural circuits of the hypothalamic brain regions that encode energy status as well as the mesencephalic locomotor regions.

Techniques: Stereotactic surgery, Anatomical tracing, Data analysis, Immunohistochemistry, Mouse behavior, Optogenetics, Chemogenetics

The student:

We are looking for a student with a keen interest in both metabolism and neuroscience and willingness to learn. It is an advantage if you are familiar with some of the above-mentioned techniques, but not a prerequisite. It is a major advantage if you have a license to work with animals since the project is based on animal experiments.

Contact:

Nathalie Krauth: nathalie.krauth@sund.ku.dk