Research Assistant: Visualizing Protein Distribution in the Brain

Introduction to the topic:

The Human Protein Atlas aims to visualize protein expression and protein distribution in all major organs and tissues of the human body. The laboratory of Jan Mulder at the Karolinska Institute is responsible for the brain section of the Human Protein Atlas, providing data on protein expression in various regions of the brain of different mammalian species. By using transcriptomics and antibody-based approaches to visualize protein location and transcriptomics approaches to detect protein expression, this research group aims to solve some of the biological mysteries related to (human) brain functions and brain diseases.

Project details:

In our lab, we have generated very complex data with many layers and dimensions that cannot be captured in a single image. These include 3D volumed data on protein distribution in a tissue block that we currently share using Youtube. In collaboration with the startup Atomontage, we explored possibilities to share 3D data and to make this free, explorable, and interactive.

As a research student on this project, you will get a raw 3D image set (stack of >1000 16-bit images) and use image processing tools (ImageJ, Matlab, or your favorite) and Atomontage webtools to generate a 3D model presenting the biological truth. You will then create tools and features to help/guide the users when exploring the data. Your principle mentor will be Jan Mulder, but you are also partnered with other bioinformatic researchers in the lab, the human protein atlas IT group, and developers at Atomontage.

Research Assistantship Hours: You will spend 180 hours directly engaged in research, together with an additional 5 hours in professional workshops and co-curricular activities, during your RAship.

Selected relevant publications:

Gilvesy A; Husen E; Magloczky Z; Mihaly O; Hortobágyi T; Kanatani S; Heinsen H; Renier N; Hökfelt T; Mulder J; Uhlen M; Kovacs GG; Adori C. (2022) Spatiotemporal characterization of cellular tau pathology in the human locus coeruleus-pericoerulear complex by three-dimensional imaging. Acta neuropathologica. 2022 Oct 144(4):651-676.
Sjöstedt, E., Zhong, W., Fagerberg, L., Karlsson, M., Mitsios, N., Adori, C., Oksvold, P.,Edfors, F., Limiszewska, A., Hikmet, F., Huang, J., Du, Y., Lin, L., Dong, Z., Yang, L., Liu, X., Jiang, H., Xu, X., Wang, J., … Mulder, J. (2020). An atlas of the protein-coding genes in the human, pig, and Mouse Brain. Science, 367 (6482)

Prerequisites

One year of biology, programming, bioinformatics, or web design.

Additional application required

You must submit an additional application through the Online Registration portal.

All application materials must be submitted on the following dates by midnight in your time zone:

November 1 for spring semester applicants
May 1 for fall semester applicants

Complete your application through Student Registration.

Recommended experience

Basic knowledge of biology at a university level is recommended.

Faculty

Nicholas Mitsios

Faculty

BSc in Molecular Biology (Liverpool, 1998) and PhD in Molecular Biology of Ischemic Stroke (Manchester, 2005). Currently a researcher at the Department of Neuroscience, Karolinska Institute and the Brain Profiling sub-unit of the Human Protein Atlas (HPA) project since 2011. Research focuses on the central nervous systems of mammals, with an emphasis on the identification of proteins involved in brain normal development and pathophysiology. With DIS since 2020.

Emma Gerrits

Faculty

Bachelor of Science, Life Science and Technology, University of Groningen, 2016 Master of Science, Biology, University of Groningen, 2018 Ph.D., Molecular Neurobiology and Bioinformatics, University of Groningen, 2022 Ph.D. student, University Medical Center Groningen, 2018-2022 Postdoctoral researcher, Karolinska Institutet, 2022-present. With DIS since 2023

Jan Mulder

Faculty

PhD in molecular neurobiology (Rijksuniversiteit Groningen, 2005), MSc in biology (Rijksuniversiteit Groningen, 2000). Senior researcher and group leader at Science for Life laboratory, department of Neuroscience, Karolinska Institute since 2010. Group leader of the brain profiling efforts within the Human Protein Atlas project since 2010. Research in identifying the cellular location of proteins linked to brain function and disease. With DIS since 2017.

Research Assistantship FAQ (this will be replaced by a Pattern Block in the future so all RAships will be linked and updated in one location.

Learn more about research at DIS.

: Earning authorship within the course of a semester is challenging. Exceptional Research Assistants may be considered for co-authorship, subject to evaluation from the supervising Research Mentor.

Though you may not ultimately become an author on a published paper, you will gain many practical skills and insights into the publication process.

: Many research projects last across several semesters, so not all RAs on the same project will conduct the same research.

: On average, students in 3-credit Research Assistantships spend at least 10 hours a week on research tasks. These 10 hours per week consist of a variety of different research-related tasks, including conducting a literature review, data collection, analyses, coding, documentation, and meetings with your mentor. You may decide on a particular block of time (consistent each week) for you to carry out the work, or adjust it on a week-by-week basis.

Students in a 6-credit Research Assistantships spend an average of 20 hours per week with lab and clinically based research tasks. You decide the exact meeting and lab times with your supervisor, but your schedule consists of classes at DIS two days a week, with two days a week in the lab.

There may be peak times in the research process where all Research Assistant students are expected to spend a few more hours, and then possibly fewer hours another week – to reflect the individual research project and process.

: Work for the 3-credit Research Assistantships may take place outside DIS, on your own time at a location of your choosing, or at DIS – this varies from project to project. The 6-credit research assistantships generally take place at labs in Copenhagen or Stockholm outside DIS.

: Students with a variety of academic backgrounds are encouraged to apply for the 3-credit Research Assistant course. While some courses do have prerequisites, many opportunities do not require prior research experience.

The 6-credit Research Assistant opportunity is designed for highly motivated students who have a strong science background within the field of interest and some basic research experience. The student must be willing to commit a large portion of their semester to an engaging opportunity involving hands-on research in universities and medical institutes in Copenhagen or Stockholm.

Introduction to the topic:

Project details:

Prerequisites

Additional application required

Recommended experience

Faculty

Nicholas Mitsios

Emma Gerrits

Jan Mulder

Research Assistantship FAQ (this will be replaced by a Pattern Block in the future so all RAships will be linked and updated in one location.

Will I publish a research paper?

What exactly will I do?

What is the time commitment for a 3-credit or 6-credit Research Assistantship?

Where is the research work carried out?

What type of student applies for the 3- and 6-credit Research Assistant courses?