PhD Scholarships in Single Cell Dissection of Healthy and Unhealthy Human Adipose Tissue

The Schmidt and Loft groups at the Functional Genomics & Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, invite applications from outstanding candidates who are interested in joining our groups as a PhD student. The positions are available from 1 September 2023, or as soon as possible thereafter. Application deadline: 24 July 2023.

Research projects
Obesity is a major driver of metabolic complications such as type 2 diabetes (T2D), and fatty liver disease. Interestingly, the metabolic consequences of obesity affect individuals to different degrees (i.e. healthy versus unhealthy obesity), opening the possibility of exploiting naturally occurring protective mechanisms for therapy.

1. In an EFSD-funded project in the Schmidt Group, we will investigate mechanisms underlying so-called ‘healthy obesity’ related to human adipose tissue. We will apply advanced single cell sequencing technologies on fat biopsies obtained from patients with T2D, weight-matched healthy obese, and lean subjects combined with a range of mechanistic follow-up studies to determine the cellular and molecular differences between fat biopsies associated with healthy vs unhealthy (T2D-associated) obesity.

2. The project in the Loft Group will investigate how patient-dependent, obesity-induced alterations in human fat tissues affect the progression of metabolic associated fatty liver disease (MAFLD). Here we will analyse patient fat biopsies from different stages of MAFLD using single-cell sequencing technologies and combine this with a range of mechanistic follow-up studies to understand how different cellular and molecular states in the adipose tissue associates with advanced liver dysfunction.

Insight from these projects will help the identification of key transcriptional and signalling mediators as well as genetic variants causally associated with healthy (and unhealthy) adipose tissue that can be explored therapeutically with the aim to prevent development of obesity comorbidities.

The Schmidt Group
Assistant Professor Søren Schmidt is a recipient of an EFSD/Novo Nordisk Foundation Future Leaders Award from 2022. Research in the Schmidt Group focuses on transcriptional coordination of macrophage diversity and plasticity in metabolic health and disease. For this, we combine single cell analyses of clinical samples, cell culture studies, and viral targeting strategies in animal disease models.

The Loft Group
Junior Group Leader Anne Loft is a recipient of a Lundbeck Foundation Fellowship from 2023. Research in the Loft group is particularly focused on understanding how the adipose tissue serves as a critical signaling hub in the context of metabolic diseases, such as MAFLD. For this, we apply single cell genomics technologies on clinical biopsies combined with bioinformatics, and a range of targeting strategies in animal disease models.

As members of the Center of Excellence in Functional Genomics and Tissue Plasticity (ATLAS), a key research focus in both groups, is understanding cellular diversity and communication determining differential interindividual phenotypic outcomes of obesity.

Research environment
The projects will be carried out in close collaboration between the Schmidt and Loft groups and will benefit from the highly interdisciplinary expertise in the ATLAS Center of Excellence. The work will primarily be carried out in the Functional Genomics & Metabolism Research Unit, at Department of Biochemistry and Molecular Biology, SDU, but, depending on the interest of the student, may also involve research exchange to collaborating laboratories, including the Højlund laboratory at Odense University Hospital and the Claussnitzer lab at Broad Institute. The Functional Genomics & Metabolism Research Unit currently hosts eight independent research groups focusing on various aspects of gene regulatory mechanisms controlling cellular identity, differentiation and metabolism. The research unit constitutes an international, ambitious, highly dynamic, and well-equipped working environment. The unit and the department have state-of-the-art facilities for next generation sequencing, single-cell transcriptomics, flow cytometry, mass spectrometry, metabolomics, bioimaging and transgenic mouse work. Strategic research alliances exist with Odense University Hospital (OUH).

PhD scholarship qualifications/requirements
We are looking for highly motivated, dedicated, and ambitious candidates with:

• A Master’s degree in Life Science, preferably Molecular Biology, Biomedicine, or Computational Systems Biology. If you have not yet completed your Master programme, you can apply to be enrolled in our 4+4 PhD programme, which is a way to commence the PhD study whilst concurrently completing the Master programme.
• Experience with cell biology or NGS data analysis. Competence in adipose tissue biology, mouse physiology, immunology, or transcriptional regulation would be an advantage.
• Strong communication and collaborative skills and an interest in working in an interdisciplinary environment.
• Proficiency in spoken and written English.

We offer:

• Two three-year (or four-year for BSc students) PhD positions in a highly stimulating, supportive, international, and interdisciplinary research environment.
• Enrolment in PhD school of Biochemistry and Molecular Biology, which allows the candidate to tailor a flexible individualized course programme.
• Training in a wide range of skills including research management, communication, networking, presentations, writing of manuscripts etc.
• Research exchange to collaborating institution, depending on the interest of the PhD student.
• Mentoring and career development.
• Access to state-of-the-art equipment, facilities, and infrastructure.
• Opportunity to interact with an extensive network of national and international collaborators.
• A competitive salary and social benefits (e.g. health coverage, parental leave, social security etc.).
• Dedicated assistance and support with various practical, social, and legal aspects (housing, visa, administration, tax etc.), especially for international candidates through our international staff office (ISO) and department.
  
  

For further information on the projects and positions, please contact Assistant Professor Søren Fisker Schmidt (e-mail: [email protected]) or Junior Group Leader Anne Loft (e-mail: [email protected]).

Application, salary etc.
Appointment as a PhD Research Fellow is for three (students who have completed their MSc) or four years (students who have not yet completed their
MSc). Employment stops automatically at the end of the period. The holder of the scholarship is not allowed to have other paid employment during the three-year period.

The successful applicant will be employed in accordance with the agreement on salaried PhD scholars between the Ministry of Finance and AC (the Danish Confederation of Professional Associations). Please check links for more information on salary and taxation.

The successful candidate will be enrolled at this university in accordance with faculty regulations and the Danish Ministerial Order on the PhD Programme at the Universities (PhD order).

The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background.

Application must be in English and made in the form of a Declaration of Interest including the following:
• A research proposal/description of your approach to the above project (max one page excluding references).
• A letter stating your specific interests, motivation, and qualifications for the project (max. two pages)(please attach this under box "Application form").
• Detailed CV, including personal contact information, education, work/research experience and skills relevant for the position, publications/manuscripts
• Copies of diplomas, bachelor as well as Master’s degree, including transcript of notes/grades. If awaiting Master’s diploma, provide a written statement from the supervisor.
• At least two signed reference letters. Should your referees wish to send their letters directly to us, please have them use e-mail: [email protected] mentioning your name and the title of the position in the subject line. And please note that these also need to reach us before deadline.

Shortlisting may be used in the assessment process. Applicants will be informed of their assessment by the university. Applications will be evaluated by Centre Director of ATLAS, Professor Susanne Mandrup.

Further information about the PhD-study can be found at the homepage of the University.

Applications must be submitted electronically using the link "Apply online". Attached files must be in Adobe PDF or Word format. Each box can only contain a single file of max. 10 Mb. We strongly recommend that you read How to apply before you apply.

Incomplete applications and applications received after the deadline will neither be considered nor evaluated. This also applies to reference letters.

Further information for international applicants about entering and working in Denmark.