Open Thesis Projects

Several research groups have open Master Thesis projects available.

Neuroinflammation research group: Exosomes as mediators of intercellular communication in stroke

Project description: Exosomes are nanosized extracellular vesicles that transfer molecules such as proteins and RNA species between cells, contributing to the cell to cell communication. The aim of the project is to characterise the function of brain derived exosomes after ischemic stroke and to determine the cell specific responses elicited by exosomes.
Skills/requirements needed from the student:  The student should be motivated and precise. Standard laboratory working skills are required but training for specific methods will be provided in the laboratory.
Group leader: Associate Prof. Tarja Malm
Responsible scientist/contact person: Nea Bister
Email address: nea.bister (at) uef.fi; tarja.malm (at) uef.fi
Duration of the project: 3-6 months (negotiable)
Possibility to pay salary or grant: No
Keywords: exosome, stroke

Neurobiology of Disease/Katja Kanninen

Project description: We have several available projects, which can be tailored to fit the specific needs and skills of each student. Most projects focus on Alzheimer’s disease (AD). AD is the most common neurodegenerative disease, yet our understanding of the disease mechanisms is still in its infancy. The purpose of these MSc projects is to decipher the disease mechanisms and test novel approaches for the treatment of AD. We utilize both in vitro and in vivo models and use diverse methodologies including culture of human and murine cells, confocal imaging, gene transfer technologies, protein and gene expression analyses and behavioral testing.
Skills/requirements needed from the student: Basic laboratory skills, enthusiasm, and willingness to learn. Training for specific laboratory skills will be given.
Principal investigator: Academy Research Fellow Katja Kanninen
Responsible scientist/contact person: Katja Kanninen        
Email address: katja.kanninen (at) uef.fi
Duration of the project: 3-6 months (negotiable)
Possibility to pay salary or grant: No
Keywords: Alzheimer’s disease, neurodegeneration

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Molecular brain research laboratory: Mitochondrial Metabolism in Amyotrophic Lateral Sclerosis (ALS)

Project description: We are interested in changes in the astrocytic mitochondrial metabolism seen in ALS. In our studies, we utilize mainly in vitro models and use diverse methodologies including culture of human and murine cells, as well as protein and gene expression analyses. The project can be tailored to fit the specific needs and skills of each student.
Skills/requirements needed from the student: Student should be familiar with standard laboratory practices. Experience in the cultivation of human stem cells and in molecular biology methods are a plus but not necessary. Student will receive a training on how to work aseptically in stem cell laboratory prior to the commencement.
Group leader: Professor Jari Koistinaho
Responsible scientist/contact person: Merja Jaronen, Ph.D.
Email address: merja.jaronen (at) uef.fi
Duration of the project: Negotiable (3-6 months)
Possibility to pay salary or grant: No
Keywords: ALS, mitochondria, induced pluripotent stem cells

Molecular brain research laboratory: Endothelial cells in mitochondrial encephalomyopathy

Skills/requirements needed from the student: Student should be familiar with standard laboratory practices. Experience in the cultivation of human stem cells and in molecular biology methods are a plus but not necessary. Student will receive a training on how to work aseptically in stem cell laboratory prior to the commencement.
Principle investigator: Academy research fellow Riikka Martikainen
Contact person: Riikka Martikainen
Email address: riikka.martikainen (at) uef.fi
Duration of the project: Negotiable (3-6 months)
Possibility to pay salary or grant: No
Keywords: Mitochondria, induced pluripotent stem cells, endothelial cells

Molecular Brain Research Laboratory: Investigating Parkinsonʼs disease using human stem cell-derived astrocytes

Skills/requirements needed from the student: Student should be familiar with standard laboratory practices. Experience in the cultivation of human stem cells and in molecular biology methods are a plus but not necessary. Student will receive a training on how to work aseptically in stem cell laboratory prior to the commencement.
Group leader: Professor Jari Koistinaho
Responsible scientist/contact person: Šárka Lehtonen, Ph.D.
Email address: sarka.lehtonen (at) uef.fi
Duration of the project: Negotiable (3-6 months)
Possibility to pay salary or grant: No
Keywords: Parkinsonʼs disease, induced pluripotent stem cells, astrocytes

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Molecular Brain Research Laboratory: Biomarkers in schizophrenia: A focus on cell-type specific metabolites

Skills/requirements needed from the student: Student should be familiar with standard laboratory practices. Student will receive a training on how to work aseptically in stem cell laboratory prior to the commencement. Training for specific methodologies and data mining will be provided directly in the laboratory.
Group leader: Professor Jari Koistinaho
Responsible scientist/contact person: Šárka Lehtonen, Ph.D.
Email address: sarka.lehtonen (at) uef.fi
Duration of the project: Negotiable (3-6 months)
Possibility to pay salary or grant: No
Keywords: Schizophrenia, induced pluripotent stem cells, metabolomics

Molecular Brain Research Laboratory: Modelling schizophrenia in a 3D cerebral cortex-like structure

Skills/requirements needed from the student: Student should be familiar with standard laboratory practices. Experience in the cultivation of human stem cells and in molecular biology methods are a plus but not necessary. Student will receive a training on how to work aseptically in stem cell laboratory prior to the commencement. Training for specific methodologies (immunohistochemistry) will be provided directly in the laboratory.
Group leader: Professor Jari Koistinaho
Responsible scientist/contact person: Šárka Lehtonen, Ph.D.
Email address: sarka.lehtonen (at) uef.fi
Duration of the project: Negotiable (3-6 months)
Possibility to pay salary or grant: No
Keywords: Schizophrenia, induced pluripotent stem cells, 3D modeling

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Molecular Brain Research Laboratory: The use of hiPSCs derived from both healthy and diseased patients to obtain a physiological or diseased model of the human BBB in vitro

Skills/requirements needed from the student: Student should be familiar with standard laboratory practices. Experience in the cultivation of human stem cells and in molecular biology methods are a plus but not necessary. Student will receive a training on how to work aseptically in stem cell laboratory prior to the commencement.
Group leader: Professor Jari Koistinaho
Responsible scientist/contact person: Šárka Lehtonen, Ph.D.
Email address: sarka.lehtonen (at) uef.fi
Duration of the project: Negotiable (3-6 months)
Possibility to pay salary or grant: No
Keywords: Blood-brain barrier, induced pluripotent stem cells, neural progenitor cells, endothelial cells

Molecular Brain Research Laboratory: Could we study criminal behavior in a dish by induced pluripotent stem cells?

Skills/requirements needed from the student: Student should be familiar with standard laboratory practices. Experience in the cultivation of human stem cells and in molecular biology methods are a plus but not necessary. Student will receive a training on how to work aseptically in stem cell laboratory prior to the commencement.
Group leader: Professor Jari Koistinaho
Responsible scientist/contact person: Šárka Lehtonen, Ph.D.
Email address: sarka.lehtonen (at) uef.fi
Duration of the project: Negotiable (3-6 months)
Possibility to pay salary or grant: No
Keywords: Criminal behavior, induced pluripotent stem cells, neural progenitors cells, astrocytes

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Molecular Neurodegeneration Laboratory: Role of neuroinflammation in frontotemporal dementia

Project description: Frontotemporal dementia (FTD) is a neurodegenerative disorder leading to behavioral changes and dementia. The most common genetic cause of FTD is expansion of a hexanucleotide repeat sequence in C9ORF72 gene. This expansion is exceptionally common in the Finnish FTD patients. Recent studies have shown that C9ORF72 knockout mice show dysregulation of the immune system. In this project, the goal is to investigate the mechanistic role of C9ORF72 proteins in the regulation of neuroinflammation.
Skills/requirements needed from the student: Standard laboratory working skills are required. Experience in cell culture and transfection methods are a plus but not necessary. Hands-on-training for methodology will be given in the laboratory.
Group leader: Annakaisa Haapasalo
Responsible scientist/contact person: Associate Professor Annakaisa Haapasalo
Email address: annakaisa.haapasalo (at) uef.fi
Duration of the project: Negotiable (3-6 months)
Salary: Possibility to pay salary or grant: No

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Epilepsy Research Laboratory: Cortical interneuron network after traumatic brain injury

Description of the project: Recent paper described presence of microlesions in the human epileptic cortex. It is not yet known if also TBI can trigger these cellular alterations and are those microlesions present in the rat cortex before seizure onset.  
Specific task is: The aim of this study is to investigate the total numbers of interneurons around the lesion location (perilesional cortex) using unfolded maps after lateral fluid-percussion injury. Additionally, expression of interneuron related genes will be analyzed using existing transcriptome data and bioinformatics approach. Later, their expression in cortex samples will be validated using real-time quantitative PCR.
Skills/requirements needed from the student: Student should have basic laboratory skills. Hands-on-training for methodology will be given in the laboratory by Noora Puhakka, PhD.
Group leader: Asla Pitkänen
Responsible scientist/contact person: Noora Puhakka, PhD
Email address: noora.puhakka (at) uef.fi
Duration of the project: Negotiable (3-6 months)
Salary: Possibility to pay salary or grant: No

Epilepsy Research Laboratory: Localized molecular changes after traumatic brain injury

Description of the project: Traumatic brain injury (TBI) triggers a cascade of molecular and cellular changes that can lead to development of post-traumatic co-morbidies, such as epilepsy and Alzheimer’s disease. The focus of this project is in microRNAs, master regulators of gene expression, and their contribution to pathological changes. Based on our previous bioinformatics and histologic analysis we aim to define localized changes in specific microRNAs and their targets.
Specific task is: The aim of this study is to study localized alteration in miRNA after lateral fluid-percussion injury using Lacer Capture Microscope (LCM) and real-time PCR (RT-PCR).
Skills/requirements needed from the student: Student should have basic laboratory skills. Knowledge in histological techniques is a plus but not necessary. Hands-on-training for specific methodologies will be provided directly in the laboratory.
Group leader: Asla Pitkänen
Responsible scientist/contact person: Noora Puhakka, PhD
Email address: noora.puhakka (at) uef.fi
Duration of the project: Negotiable (3-6 months).
Possibility to pay salary or grant: No

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Neuro-Lymphatic Group: Characterization of pathophysiological role of meningeal lymphatic system after traumatic brain injury

Description of the project: Background: Recent studies (2015) have identified the presence of lymphatic vessels in the meninges that envelop the brain (dura mater). Due to the well-known role of lymphatic system in clearance of macromolecules, resolution of edema and route of immunomodulatory cells, we hypnotize that meningeal lymphatic vessels can play a fundamental role in the pathophysiology of traumatic brain injury.
Specific task is: To study the anatomical and functional alteration of meningeal lymphatic system, and the role of these vessels in the development of post-traumatic brain pathology (neurodegeneration and neuronal circuits alteration). A multimodal approach will be developed, with specific interest into the study of meningeal lymphatic vessels anatomical alterations, and of T-cells parenchyma infiltration, macromolecule accumulation and edema resolution.
Skills/requirements needed from the student:  1) high motivation and availability; 2) knowledge of standard laboratory operational procedures; 3) possibility to work with in vivo mouse models. Immunohistochemistry techniques knowledge is a plus but not necessary. Training for specific methodologies will be provided directly in the laboratory.
Group leader: Academy Research Fellow Francesco M. Noé, PhD
Responsible scientist/contact person: Francesco M. Noé, PhD
Email address: francesco.noe (at) uef.fi
Duration of the project: 6 months - possible to begin immediately
Possibility to pay salary or grant: No
Key words: Meningeal lymphatic system, Traumatic Brain Injury, immunohistochemistry

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Epilepsy Research Laboratory: Mechanisms and consequences of T lymphocyte invasion into the brain after traumatic brain injury

Skills/requirements needed from the student: Knowledge on standard laboratory operational procedures is required. Knowledge on immunohistochemistry is a plus but not necessary. Hands-on-training for methodology will be given in the laboratory by Xavier Ekolle Ndode-Ekane, PhD.
Group leader: Academy Professor Asla Pitkänen
Responsible scientist/contact person: Academy Professor Asla Pitkänen
Email address: asla.pitkanen (at) uef.fi
Duration of the project: Negotiable (3-6 months)
Salary: Possibility to pay salary or grant: No

Epilepsy Research Laboratory: Ethosuximide - a novel treatment for post-traumatic epilepsy?

Skills/requirements needed from the student: Standard laboratory operational procedures. Animal handling, drug dilution and EEG reading are a plus but not necessary. Hands-on-training for methodology will be given in the laboratory by Xavier Ndode-Ekane, PhD
Group leader: Academy Professor Asla Pitkänen
Responsible scientist/contact person: Academy Professor Asla Pitkänen
Email address: asla.pitkanen (at) uef.fi
Duration of the project: Negotiable (3-6 months)
Salary: Possibility to pay salary or grant: No

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Epilepsy Research Laboratory: Characterization of blood exosome profile after traumatic brain injury

Description of the project: Specific task is to study alterations in blood exosome profile after brain insults (traumatic brain injury, status epilepticus) to identify biomarkers specific for epileptogenesis. Developing methods to identify and isolate brain specific exosomes.
Skills/requirements needed from the student: Student should have basic laboratory skills and knowledge about molecular biology. Hands-on-training for methodology will be given in the laboratory by Jenni Karttunen, PhD.
Group leader: Academy Professor Asla Pitkänen
Responsible scientist/contact person: Academy Professor Asla Pitkänen
Email address: asla.pitkanen (at) uef.fi
Duration of the project: Negotiable (3-6 months)
Salary: Possibility to pay salary or grant: No

Epilepsy Research Laboratory: Molecular profiling of post-traumatic epilepsy

Description of the project: Epilepsy is often preceded by brain insult such as traumatic brain injury (TBI). One of the most burning questions in epilepsy research is: can we identify biomarkers that would indicate individuals of risk of epilepsy after brain insults. This project tackles this question by investigating various protein markers in plasma and brain tissue in rats which had experienced TBI in order to identify biomarkers for epileptogenesis.
Specific task is: To study molecular alterations in plasma and brain tissue after brain insults (traumatic brain injury, status epilepticus) to identify biomarkers specific for epileptogenesis.
Skills/requirements needed from the student: Student should have basic laboratory skills. Hands-on-training for methodology will be given in the laboratory by Noora Puhakka, PhD.
Group leader: Academy Professor Asla Pitkänen
Responsible scientist/contact person: Academy Professor Asla Pitkänen
Email address: asla.pitkanen (at) uef.fi
Duration of the project: Negotiable (3-6 months)
Salary: Possibility to pay salary or grant: No

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Biomedical Image Analysis: Predicting cognitive decline using brain imaging

Description of the project: Identifying biomarkers of brain disorders from neuroimaging data is an exciting and rapidly growing research area at the intersection of machine learning, biomedical engineering and neuroscience.  Detecting brain disorders before clinical symptoms appear is projected to be possible by combining brain imaging and advanced computational techniques as minute changes in the brain structure and function precede visible symptoms.
Specific task is: My team develops advanced machine learning approaches for finding patterns that are predictive of disease from brain images. Our major focus is in Alzheimer's disease and there are several possible projects suitable for MSc thesis work. The exact topic and the scope can be decided based on the interests and skills of the student.
Skills/requirements needed from the student: Basic computational skills are required (Matlab/Python/R).
Group leader and contact person: Associate professor Jussi Tohka
Email address: jussi.tohka (at) uef.fi
Duration of the project: Negotiable (3-6 months)
Salary: Possibility to pay salary or grant: No

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Biomedical Image Analysis: Inter-subject correlation based analysis of fMRI

Description of the project: In the inter-subject correlation (ISC) based analysis of the functional magnetic resonance imaging (fMRI) data, the extent of shared processing across subjects during the experiment is determined by calculating correlation coefficients between the fMRI time series of the subjects in the corresponding brain locations. This implies that ISC can be used to analyze fMRI data without explicitly modeling the stimulus and thus ISC is a potential method to analyze fMRI data acquired under complex naturalistic stimuli.
Specific task is: We have developed a graphical user interface (GUI) based software package, ISC Toolbox https://www.nitrc.org/projects/isc-toolbox/, implemented in Matlab for computing various ISC based analyses. Currently, we are preparing the release of the version 3.0 of the toolbox and would welcome a MSc thesis worker to validate new functionalities of the toolbox.
Skills/requirements needed from the student: Familiarity with Matlab is required.
Group leader / contact person: Associate professor Jussi Tohka
Email address: jussi.tohka (at) uef.fi
Duration of the project: Negotiable (3-6 months)
Salary: Possibility to pay salary or grant: No

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