We are looking for a talented and enthusiastic PhD student to join the Laboratory of Dr. Panayiota Poirazi at IMBB-FORTH. The PhD will be awarded by the University of Crete and applicants must be accepted in a PhD program at UoC before the start of the contract.

Role of dendritic nonlinearities in V1 network properties after visual learning

Computational Neuroscience
University of Crete
  • Poirazi Lab (www.dendrites.gr), Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology Hellas (FORTH), Heraklion, Greece
  • Vacancy terms:Full Time, Fixed Term starting from 1st April 2021 for 1 year (renewable for 2 more years)
  • Living allowance: 34,800 euro per annum (approximately 22,800 euro Net). Depending on family status, successful candidates will also have a mobility (600 euro per month) and/or family (250 euro per month) allowance, as provided by MSCA grants.
  • Deadline: midnight, 28th February 2021
  • Funding: Marie Curie ETN “Advanced simulation, analysis and interpretation of network structures in biological data”, GA: 860949 — SmartNets

Project description

The successful applicant will build a simulation model of the rodent visual cortex and use it to assess the role of dendritic nonlinearities on the connectivity and activity properties of the resulting memory engrams. Selected model predictions will be tested in headfixed behaving animals performing a visual discrimination task.

Specifically, the successful applicant will build a reduced circuit model of L2/3 V1 neurons, that incorporate dendrites (modeled as linear, sub-linear or supra-linear activation functions) and synaptic plasticity rules (STC-based LTP/LTD, homeostatic plasticity, plasticity of intrinsic excitability etc.). Models will also incorporate key interneuron types such as PV, Somatostatin, calretinin and VIP-expressing cells, modeled as point neurons. The basic biophysical properties of all models will be validated against existing experimental data provided by the literature and ongoing collaborations (e.g. Stelios Smirnakis at Harvard University). The V1 circuit model will be trained with a feature and an integrative learning paradigm. Network analysis will include the size of the neuronal population that responds to stimulus presentation, somatic and dendritic spiking, synaptic weight changes-connectivity, the spatial distribution of modified synapses and the sparsity of the resulting engram. By systematically manipulating dendritic biophysics (i.e. ionic and synaptic conductances) so as to generate linear, sublinear and supralinear dendrites as well as the various synaptic/intrinsic plasticity rules, and interneuron strengths, we will assess the effect of these manipulations on a) learning capacity, b) network connectivity and c) engram size/connectivity/recall stability etc. We will validate our modeling predictions via optogenetic manipulations of pyramidal and/or GABAergic (SST, PV or VIP) neurons in V1, while mice execute a visual discrimination task.

Expected Results

  1. Reduced, biologically relevant model of the L2/3 V1 network with active dendrites and plasticity rules
  2. Implementation of realistic visual learning protocols in the model
  3. Assessment of dendritic contributions to a) learning capacity, b) emergent network connectivity, c) engram size/recall stability etc.

Planned secondments

  1. Radboud University (NL), Fleur Zeldenrust, Tansu Celikel (months 30-32)
  2. Mathworks (DE), Philip Laserstein (months 18-21)

About the lab

The Poirazi Lab investigates how dendrites and their integrative properties contribute to learning and memory related functions, using primarily computational techniques. In close collaboration with experimentalists, models are used to explain findings and predict new roles for dendrites in functions such as spatial navigation/learning, working and associative memory, visual processing etc. The lab has recently expanded its research to include experiments in mice, whereby the role of dendrites in prefrontal functions is investigated via behavioral, electrophysiological and imaging techniques. The laboratory offers a thriving, ambitious research environment which is well funded from several grants.

About you

We seek candidates interested in pursuing a PhD in computational neuroscience, with the possibility of also performing some in vivo experiments in behaving mice. They must be highly motivated and creative individuals who want to work in a dynamic, multi-disciplinary research environment and be willing to interact with both experimental and theoretical neuroscientists. Previous experience should include solid programming skills, ideally including computational simulations of neurons. Experience or familiarity with related experimental procedures/data collection and analysis is desirable.

Characteristics of the ideal candidate

  • BSc in Biology, Neuroscience, Computer Science or Physics
  • MSc in Computational Neuroscience, Neuroscience, Biology or a related subject.
  • Solid programming skills using LINUX (python, NEURON, Matlab, BRIAN)
  • Experience in computational modeling of neurons
  • Experience with processing and analysis of neuronal data.
  • Fluency in spoken and written English.
  • Strong communication and interpersonal skills, being able to work comfortably both in a team and somewhat independently.
  • Demonstrated ability to perform research (eg. publications, conference presentations)

Additional information

IMBB (www.imbb.forth.gr) is part of FORTH (www.forth.gr), one of the leading research foundations worldwide. IMBB is one of the most prominent life science research institutions in Greece, with an outstanding record of scientific achievements, state of the art infrastructure and a broad range of research, innovation and high quality, inspirational educational activities. In addition, IMBB is strongly committed to inclusivity, promoting equality and celebrating diversity among its staff and students.

The wide-range of research activities in the Institute aim at understanding the basic biological processes operating in living organisms. IMBB also hosts interdisciplinary research programs at the interface of biology with informatics, chemistry, physics or medicine and is heavily involved in providing post-graduate students high-level education through joint graduate programs with the University of Crete. An additional standing mandate of IMBB is the exploitation and translation of acquired knowledge to tangible societal benefits, including the development of new technologies, innovative products and services.

IMBB is located close to Heraklion which is the largest city and the administrative capital of the island of Crete, located south of the Greek mainland. It is the fifth largest city in Greece with a population of > 140,000 and is famous for its lively lifestyle and the outstanding outdoors.

Applications (full CV, statement of research interest and name and contact of 2-3 referees) should be sent by e-mail to poirazi@imbb.forth.gr, quoting “SmartNets PhD positions” in the subject line.

The deadline for applications is 28th February 2021. Applications will be examined until the position is filled. Informal enquiries are welcome.