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Potential PhD Projects

An overview with a few of the advertised potential projects that PhD candidates could start in the upcoming winter semester. Please note that this list is not comprehensive and that many projects are arranged individually during the Interview Phase with our 140+ GSN Faculty Members.

How is magnetic information encoded in the pigeon brain?

Supervisor: Prof. David Keayskeays fig. 1

Background. Magnetoreception is the ability to sense the Earth’s magnetic field and use it for orientation and navigation. Behavioural experiments have shown that it is employed by many species; however, our understanding of how magnetic information is encoded within the central nervous system is limited. The Earth’s magnetic field is a vector with three components: (1) a polarity; (2) a intensity; and (3) an inclination. Analogous to the spatial encoding of information by place cells, head direction cells and grid cells in the rodent brain we predict the existence of “magnetic place cells” in the pigeon that encode for defined components of the Earth’s magnetic field.

Preliminary Data. We have undertaken a neuronal activation experiments in pigeons, employing C-fos as a surrogate marker for neuronal activity. We have shown that a rotating magnetic stimulus (3x Earth strength, 72mins) results in a significant upregulation of c-fos positive cells in the pigeon hippocampus (∼30%) (n=23, P<0.01) (Fig. 1).

Proposed experiments. Drawing on our preliminary data we will explore how neurons within the hippocampus encode magnetic information. To undertake these experiments we have built a customised 2-photon microscope. This set up allows the experimenter to deliver magnetic stimuli to head fixed pigeons with a customised double-wrapped coil system that is interfaced with the Matlab software that drives and acquires images from the microscope (Figure 2). keays fig. 2To measure neuronal activity we will quantitate calcium influx employing a genetically encoded calcium indicator (GCaMP6), that will be delivered by an adeno-associated virus (AAV7). This method has already been established. The student will ask whether specific neurons encode for specific components of the magnetic field by delivering a magnetic stimulus with: (a) fixed polarity and inclination but varying intensity; (b) fixed inclination and intensity but with a changing polarity; and (c) constant polarity and intensity but a changing inclination. He/she we will analyze stimulus-response relationships of individual neurons using cross-correlation analysis and specifically explore whether there are spatially restricted neuronal ensembles. As the project advances we anticipate exploiting virtual reality paradigms to ascertain whether magnetically sensitive cells in the hippocampus integrate information from other senses, including vision. This will reveal there a magneto-visual representation of space in the pigeon hippocampus.

Methods: In vivo calcium imaging, magnetic stimulation, surgical procedures, histology, computational analysis.

Website: www.Keayslab.org

Joint PhD Cerebral Organoid Project at LMU and Cambridge University - Avian Cerebral Organoids

Supervisors: Prof. David Keays and Dr. Madeline Lancaster (LMB, Cambridge)

The Project. An opportunity exists for a driven and passionate neuroscientist to undertake a PhD under the supervision of Dr. David Keays and Dr. Madeline Lancaster on avian cerebral organoids. This joint project will exploit the Keays lab’s expertise in Avian biology and the Lancaster Lab’s experience in self-organising neural tissue. The project will aim to generate a library of avian iPSC and ES cells for the generation of three-dimensional neuronal cultures. The latter will then be employed to interrogate Avian specific aspects of neurodevelopment, exploiting CRISPR-Cas9
genome editing, single-cell sequencing, and histological methods. Specifically, we are interested in exploring the shape and type of neuronal progenitors, the modular nature of the avian brain, and the evolution of white matter tracts.

The ideal candidate. This ambitious project requires a candidate with an existing interest in stem cell biology and/or developmental neuroscience. He/she should be diligent, persistent, value quantitative approaches and demonstrate a capacity for scientific excellence. The successful applicant should be prepared to spend time in both Munich and Cambridge. It is envisaged that he/she will be enrolled at LMU through the Graduate School for Neuroscience (GSN), and accordingly the position is open to all nationalities.

Application. We encourage applicants to apply through GSN-LMU at https://www.gsn.uni-muenchen.de/apply/index.html 

Contact:keays@bio.lmu.de and mlancast@mrc-lmb.cam.ac.uk

Related Links:

Cerebrovascular disease and stroke

Supervisor: Prof. Martin Dichgans (Institute for Stroke and Dementia Research)

We invite applications for research projects in the field of cerebrovascular disease and stroke. A major starting point of our work are discoveries from human genetics. We apply GWAS, sequencing and other omics techniques to identify novel targets and pathways relevant to specific mechanistically defined stroke subtypes. Starting from here we dive into mechanistic studies in relevant disease models. We have established novel genetic mouse models for cerebral small vessel disease (SVD) derived from genetic discoveries (e.g. HtrA1, Col4A1, Foxf2) and use these models to identify and characterize key molecular (e.g. receptor-mediated signaling) and physiological (e.g. blood-brain-barrier) pathways as well as cellular targets (in particular vascular endothelial cells and brain pericytes) relevant to the pathogenesis of SVD. We are further pursuing observational and interventional studies in patients with cerebrovascular disease.

For more information see https://www.isd-research.de/dichgans-lab 

PhD-scholarships in Neurophilosophy

In the 2021/22 round, the focus areas of potential projects are:
  • reasoning and decision making (esp. deductive and non-deductive reasoning in science and ordinary life, individual and collective decision making)
  • human agency (esp. mental causation, complex action, multi-tasking, attention, reductive and non-reductive explanation of agency)
  • metacognition (esp. Metacognition in perception, self-evaluation and sense of self)
  • group cognition (group epistemology, collective decisions and group responsibility)

More details at https://www.neuro.philosophie.uni-muenchen.de/students/application_phd/call_applications/index.html

2 PhD positions, Vision circuits lab (Laura Busse), Faculty of Biology, LMU Munich

Two PhD positions are available in Laura Busse’s group at the Faculty of Biology, LMU Munich.

We study the neural circuits of visual perception in awake, behaving mice, where we combine electrophysiological recordings using silicon probes / neuropixels with genetic tools for circuit manipulation. Our aim is to contribute to the understanding of sensory mechanisms of visual information processing and their dependence on visually guided behavior. While the lab is an experimental neuroscience lab, it embraces the systems neuroscience approach and has several fruitful national and international collaborations with computational neuroscientists. The Faculty of Biology at the LMU Munich together with the Graduate School of Systemic Neurosciences (GSN, https://www.gsn.uni-muenchen.de/index.html) offers an outstanding environment for a successful PhD in systems neuroscience, with ample opportunities for collaboration with both experimentalists and computational neuroscientists, both within the department as well as with the neighboring Max-Planck-Institute for Neurobiology. The LMU Munich ranks among the top 10 universities in Europe. Munich, located in the south of Germany, is regularly ranked among the world’s top cities for quality of living.  

The first position is part of an interdisciplinary collaboration with Thomas Euler’s lab at the Center for Integrative Neuroscience in Tübingen within the DFG-funded Collaborative Research Center Robust vision: Inference Principles and neural mechanisms (SFB 1233). In the project, we will explore the visual input received by the mouse visual system under naturalistic conditions and how such input is processed along key stages of the early visual system. The project continues from our publication in Qiu et al. (2021), Current Biology (https://doi.org/10.1016/j.cub.2021.05.017) and will include opportunities for assembling custom camera systems, performing recordings of the visual input and eye tracking in freely moving mice, statistical analysis of the recorded video material, and measurements of neural responses from mouse primary visual cortex. A complementary PhD position based primarily in Tübingen will closely collaborate on the development of the recording hardware and software, and focus on retinal aspects of the project. The ideal starting date will be between July and October 2022.  

The second position is part of funded by the ONE Munich Strategy Forum Project "Next generation Human-Centered Robotics". In a tight collaboration with Simon Jacob (TUM), the project will explore some of the numerous solutions and special adaptations that have evolved in biological nervous systems to provide sparse and efficient representations of our environment and drive our actions. The aim of the project is to quantitatively compare the solutions for energy-efficiency found in different areas of the brain, ranging from early sensory areas to high-level areas related to cognition. We will also test the universality vs. specificity of the solutions by comparing coding principles found in different species, ranging from mouse to human. This project will work with existing data from both the Busse lab and the Jacob lab, and will be supervised jointly by both PIs. This opening will be filled as soon as possible.  

Both projects require strong experimental skills, an interest in programming, and the ability to work in a distributed team.  

More information about the lab can be found at: https://visioncircuitslab.org.  

Interested candidates are welcome to establish contact via email to busse@bio.lmu.de. Applications should include a CV, a statement of research interests, a cover letter with the expected date of availability, and names and contact information of at least two references. Applications will ideally also go through the LMU Graduate School of Systemic Neuroscience (https://www.gsn.uni-muenchen.de/index.html, deadline 15. February 2022).

Open PhD position in the Laboratory of Experimental Stroke Research, Institute for Stroke and Dementia Research (ISD)

The Laboratory of Experimental Stroke Research (Head: Prof. N. Plesnila) at the Institute for Stroke and Dementia Research, University of Munich, is looking for a PhD student in Neuroscience.

Project. The mechanisms of impaired microvascular perfusion (no-reflow) despite complete pharmacological or surgical thrombectomy in human stroke are unclear. Recently, our laboratory developed an experimental model to study the no-reflow phenomenon by multi-photon imaging in vivo. Using this novel model, we aim of the study the formation of micro-vascular occlusions on the cellular and molecular level after ischemic stroke und to unravel the mechanisms underlying the no-reflow phenomenon. The candidate will learn how to induce ischemic micro-strokes in mice, how to perform intravital 2-photon and/or 3-photon microscopy, and how to design nanoscale drug-delivery systems. The project is funded by the German Research Foundation (DFG).

Candidate. We are looking for a highly motivated and enthusiastic applicant, who has a strong interest in working at the interface of neuroscience, photonics, and nanobiotechnology. Diploma or a M.S. degree in the Life Sciences are required. Experience in animal handling, fluorescent microscopy, and image analysis is welcome. If you are interested in the position please apply through GSN and feel free to contact:

Dr. Igor Khalin, Project Leader, Post-doctoral fellow, Laboratory of Experimental Stroke Research, ISD, igor.khalin@med.uni-muenchen.de

Prof. Dr. med. Nikolaus Plesnila, Head, Laboratory of Experimental Stroke Research, ISD, Nikolaus.Plesnila@med.uni-muenchen.de

Open PhD position at the German Center for Vertigo and Balance Disorders (DSGZ)

Project: Chronic loss of vestibular sensation is linked to impairments in balance, gait and gaze stabilization as well as a reduced capacity for spatial cognition and navigation. Current treatment is limited to physical therapy. Based on the phenomenon of stochastic resonance in sensory processing, our lab has recently established a new approach to treat chronic vestibular hypofunction by means of a non-invasive, low-intensity electrical stimulation of the peripheral vestibular apparatus (e.g., Wuehr et al. Neurology 2016; Brain Stimul 2017). In this project, the therapeutic effects of this treatment approach on vestibular-related perceptual, sensorimotor and behavioral domains will be further explored in patients with chronic vestibular hypofunction (e.g., bilateral vestibulopathy, Parkinson's disease). The candidate will learn a broad spectrum of assessment tools from vestibular psychophysics, video-oculography as well as stance, gait, and daily mobility analysis. The project is funded by the Federal Ministry of Education and Research (BMBF).

Candidate: We are looking for a highly motivated and encouraged candidate, who has a strong interest in working at the interface of sensory neuroscience and clinical neurology and is willing to perform interventional studies in direct contact with patients. A background in medicine, psychology, biology is desirable.

Application: If you are interested in the position, please apply via the GSN-LMU at https://www.gsn.uni-muenchen.de/apply/index.html 

Contact:
Prof. Dr. med. Klaus Jahn (klaus.jahn@med-uni-muenchen.de)
PD Dr. Max Wühr (max.wuehr@med.uni-muenchen.de)