Projects
Name
Analysis of collective phenomena in pancreatic islets in normal and pathophysiological conditions
University
Austria (AMSA) - University of Vienna, Vienna
Domain
Physiology
Departement
Center for Physiology and Pharmacology, Schwarzspanierstr. 17, 1090 Vienna, Austria
Head
Prof. Dr. Michael Freissmuth
Tutor
Dr. Marjan Slak Rupnik
Languages
English
Duration
4 weeks
Availability
Cities/Months Jan Feb Mar Apr May Jun Jul Augt Sep Oct Nov Dec
Yes No No No No No Yes Yes Yes No No No
Type of Research Project
- Basic science
What is the background of the project?
Pancreatic islet is composed of several types of endocrine cells. Collectives of beta cells that secrete insulin, a key hormone regulating influx of nutrients into all cells in a vertebrate organism to support nutrition, house-keeping or energy storage, form the largest part of the islet. The behavior of these collectives has been well described using methodologies from the armamentarium of complexity science. However, the role of these cell collectives under different pathophysiological conditions has not yet been included into these collective analyses.
What is the aim of the project?
The goal of this project is to assess the interactions between different endocrine cell types in pancreatic islets to gain better understanding on the function and dysfunction of pancreatic islets.
What techniques and methods are used?
A substantial part of the candidates’ work will be devoted to the analyses of the already recorded data. The recorded calcium signals will be assessed with tools from the realms of the time series analysis, such as detrending, Fourier Analysis and Filtering (FFT) band-pass filtration and other denoising procedures, wavelet analysis, and empirical mode decompositions. The extracted signals will then be subjected to a peak-detection algorithm, which serves as a basis for the detection of the classical parameters, such as frequency, durations, relative active time, interspike intervals, and synchronicity. Furthermore, to investigate the collective behavior of cell populations, methodologies from the armamentarium of complexity science will be used, such as complex network theory, phase-flipping mechanism, spin glass model or random matrix theory.
What is the role of the student?
- The student will observe the practical experiments but will be highly involved in the analysis of the results
What are the tasks expected to be accomplished by the student?
Practically, the candidate will engage with the semi-automated scripts for data analysis already developed by the laboratory. It is also expected that s/he will upgrade the algorithms and adjust them in accordance with the aims of the project. Most of the theoretical work will be conducted in Python or similar environments (MatLab, etc).
Will there be any theoretical teaching provided (preliminary readings, lectures, courses, seminars etc)
We will provide the theoretical teaching for the students in the form of preliminary readings and in depth discussions.
What is expected from the student at the end of the research exchange? What will be the general outcome of the student?
- The student will prepare a scientific report
- The student’s name will be mentioned in a future publication
What skills are required of the student? Is there any special knowledge or a certain level of studies needed?
Being able to work with computer. Python and data analysis
Are there any legal limitations in the student’s involvement
No
Hours
8
Type of students accepted
This project accepts:
- Medical students
- Graduated students (less than 6 months)
- Pre-Medical students from the American-British system
- Students in biomedical fields
Articles
- Korošak D; Slak Rupnik M (2018) Collective sensing of beta-cells generates the metabolic code. 9:31. doi.org/10.3389/fphys.2018.00031.
- Gosak M; Markovič R; Dolenšek J; Slak Rupnik M; Marhl M; Stožer A; Perc M. (2017) Network science of biological systems at different scales: a review. Physics of life reviews. doi.org/10.1016/j.plrev.2017.11.003.
- Gosak M; Stozer A; Markovic R; Dolensek J; Perc M; Slak Rupnik M; Marhl M (2017) Critical and Supercritical Spatiotemporal Calcium Dynamics in Beta Cells. Frontiers in Physiology. doi.org/10.3389/fphys.2017.01106
- Markovič R; Stožer A; Gosak M; Dolenšek J; Marhl M; Slak Rupnik M. (2015) Progressive glucose stimulation of islet beta cells reveals a transition from segregated to integrated modular functional connectivity patterns. Sci Rep. 19;5:7845. doi: 10.1038/srep07845.