Combining Microfluidics, Optogenetics and Calcium Imaging to Study Neuronal Communication In Vitro

International audienceIn this paper we report the combination of microfluidics, optogenetics and calcium imaging as a cheap and convenient platform to study synaptic communication between neuronal populations in vitro. We first show that Calcium Orange indicator is compatible in vitro with a commonly used Channelrhodopsine-2 (ChR2) variant, as standard calcium imaging conditions did not alter significantly the activity of transduced cultures of rodent primary neurons. A fast, robust and scalable process for micro-chip fabrication was developed in parallel to build micro-compartmented cultures. Coupling optical fibers to each micro-compartment allowed for the independent control of ChR2 activation in the different populations without crosstalk. By analyzing the post-stimuli activity across the different populations, we finally show how this platform can be used to evaluate quantitatively the effective connectivity between connected neuronal populations

Développement et activité de réseaux de neurones in vitro : enseigner la chimie organique par le jeu

Ma thèse comporte deux grandes parties, la première en biophysique et la seconde en science de l’éducation. La première partie présente des travaux à la frontière entre neurobiologie et microfluidique. Le but de ces travaux est de pouvoir reconstruire et étudier des réseaux complexes de neurones in vitro avec une topologie de connections synaptiques bien contrôlées. Une série de micro-structures mécanique et/ou chimique ont été étudiées pour leur capacité à (i) positionner les corps cellulaires des neurones, (ii) orienter la pousse des neurites, et (iii) différencier les axones des dendrites. Un premier réseau comportant trois populations de neurones connectées en série a été reconstruit à l’intérieur d’un circuit microfluidique. Ce réseau qui mime la voie perforante de l’hippocampe pourra être exploité pour des études en physiologie ou en neuro-dégénerescence. Une méthode entièrement optique de stimulation et d’observation de l’activité neuronal a été mise au point. Elle ouvre de nouvelles portes pour étudier des processus cognitifs complexes dans des systèmes simplifiés in vitro. La seconde partie de mon travail a permis le développement et l’étude de jeux pédagogiques pour l’apprentissage de la chimie en licence. Ces jeux, qui peuvent selon les cas remplacer un cours ou une séance d’exercices, donnent des résultats prometteurs pour l’aide à la compréhension et à la mémorisation de concepts tels que la géométrie des molécules ou la réactivité entre molécules organiques.My PhD is divided in two parts one on biophysic of neuronal networks and one on science of education. The first part present results at the frontier between neurobiology and microfluidic. The overarching goal of this work was to develop tools and methods to build and study complex neuronal networks controlling the topology of synaptic connexions. Micro-patterning techniques with mechanical and/or chemical constraints were explored regarding their capacity to (i) position cell bodies, (ii) orient neurite outgrowth and (iii) polarize neurons. For the first time, a network comprising three different neuronal populations connected in specified directions was reconstructed in a microfluidic device. This network that mimics the perforant pathway of the hippocampus can be used to study physiological rythms or neurodegenerative processes including Alzheimer’s disease. A novel and fully optical method is presented to stimulate and record neuronal activity in vitro. It opens new routes to study complex cognitive processes in simplified in vitro systems. The second part of my work present the development and assessment of educational games in chemistry at the undergraduate level. These games that can either be used to replace courses or exercises, seem promising to improve the understanding and memorization of chemistry concepts og geometries of molecules and organic reactivity

RI2A – Towards a Responsible Institute Impact Assessment

Recently, there has been a shift in attitudes against improper use of metrics to evaluate research. In our effort to develop alternative approaches to identify relevant measurements for the impact of research at the institute level – beyond simple frequency counts and rankings based on single indicators – we decided to match the publications of a targeted institute to the Web of Science (WoS) database and with the use of machine learning techniques and visualization tools to explore and showcase our results respectively. We present the Responsible Institute Impact Assessment (RI2A) for evaluating the research impact of a targeted institute with a case study. We used the 448 publications retrieved from the University of Southern Denmark’s (SDU) research registration database for the Department of Marketing and Management between 2012-2017. Of these, 170 publications satisfied the criteria of both being peer-reviewed and having a DOI to be matched in the WoS database. We then used the bibliographic coupling algorithm to cluster the articles that cited the work produced at the targeted institute. This algorithm groups data together based on the number of shared references between the identified units for analysis (article, source journal and institution level). Lastly, a co-word analysis was used to identify pair-wise relationships between keywords found in the citing articles. A total of 1195 citing articles without self-citations where identified. The results of RI2A assist the targeted institute by allowing them to discover the researchers who cite their publications and the relationships among them, the journals that cite their publications and the relationships among them, the universities, institutes and organizations that use their publications and the relationships among them, and the main groups of keywords used in the citing articles. Visualizing these results into graphs and making sense of them requires more work than simple publication/citation counts. Although not described in detail here, a collaboration between the SDU library and the university’s research support and policy services has started, where it has been proposed that evaluation should be based on joint work between evaluators and evaluatees focusing on strengths and weaknesses as well as timewise comparison of previous assessments. A straightforward mode would be to compare the results of the mapping exercise with an already known description of the evaluated department’s profile. For instance, by overlaying the targeted department’s research groups on the titles of the citing journals we discovered that the “Strategic Organisation Design” group is referenced a lot in “Organisation Studies”, “Journal of Management Studies”, “Strategic Management Journal” and “Human Relations” journals and that these journals form a distinct cluster based on shared citing practices. Our approach responds to the conditions of keeping the process relatively simple and short for use in the library setting, yet meaningful for a combined quantitative/qualitative evaluation for both management and faculty whose research is affected by the evaluation procedure. Apart from showcasing the academic impact of an institute, RI2A also provides an opportunity to explore remote connections that otherwise might go unnoticed

Développement et activité de réseaux de neurones in vitro (enseigner la chimie organique par le jeu)

Ma thèse comporte deux grandes parties, la première en biophysique et la seconde en science de l éducation. La première partie présente des travaux à la frontière entre neurobiologie et microfluidique. Le but de ces travaux est de pouvoir reconstruire et étudier des réseaux complexes de neurones in vitro avec une topologie de connections synaptiques bien contrôlées. Une série de micro-structures mécanique et/ou chimique ont été étudiées pour leur capacité à (i) positionner les corps cellulaires des neurones, (ii) orienter la pousse des neurites, et (iii) différencier les axones des dendrites. Un premier réseau comportant trois populations de neurones connectées en série a été reconstruit à l intérieur d un circuit microfluidique. Ce réseau qui mime la voie perforante de l hippocampe pourra être exploité pour des études en physiologie ou en neuro-dégénerescence. Une méthode entièrement optique de stimulation et d observation de l activité neuronal a été mise au point. Elle ouvre de nouvelles portes pour étudier des processus cognitifs complexes dans des systèmes simplifiés in vitro. La seconde partie de mon travail a permis le développement et l étude de jeux pédagogiques pour l apprentissage de la chimie en licence. Ces jeux, qui peuvent selon les cas remplacer un cours ou une séance d exercices, donnent des résultats prometteurs pour l aide à la compréhension et à la mémorisation de concepts tels que la géométrie des molécules ou la réactivité entre molécules organiques.My PhD is divided in two parts one on biophysic of neuronal networks and one on science of education. The first part present results at the frontier between neurobiology and microfluidic. The overarching goal of this work was to develop tools and methods to build and study complex neuronal networks controlling the topology of synaptic connexions. Micro-patterning techniques with mechanical and/or chemical constraints were explored regarding their capacity to (i) position cell bodies, (ii) orient neurite outgrowth and (iii) polarize neurons. For the first time, a network comprising three different neuronal populations connected in specified directions was reconstructed in a microfluidic device. This network that mimics the perforant pathway of the hippocampus can be used to study physiological rythms or neurodegenerative processes including Alzheimer s disease. A novel and fully optical method is presented to stimulate and record neuronal activity in vitro. It opens new routes to study complex cognitive processes in simplified in vitro systems. The second part of my work present the development and assessment of educational games in chemistry at the undergraduate level. These games that can either be used to replace courses or exercises, seem promising to improve the understanding and memorization of chemistry concepts og geometries of molecules and organic reactivity.PARIS5-Bibliotheque electronique (751069902) / SudocSudocFranceF

Evaluating approaches to identifying research supporting the United Nations Sustainable Development Goals

The United Nations (UN) Sustainable Development Goals (SDGs) challenge the global community to build a world where no one is left behind. Recognizing that research plays a fundamental part in supporting these goals, attempts have been made to classify research publications according to their relevance in supporting each of the UN's SDGs. In this paper, we outline the methodology that we followed when mapping research articles to SDGs and which is adopted by Times Higher Education in their Social Impact rankings. We compare our solution with other existing queries and models mapping research papers to SDGs. We also discuss various aspects in which the methodology can be improved and generalized to other types of content apart from research articles. The results presented in this paper are the outcome of the SDG Research Mapping Initiative that was established as a partnership between the University of Southern Denmark, the Aurora European Universities Alliance (represented by Vrije Universiteit Amsterdam), the University of Auckland, and Elsevier to bring together broad expertise and share best practices on identifying research contributions to UN's Sustainable Development Goals.Comment: 12 pages, 3 figures, 7 tables, 19 reference

Design of a simple neuronal device.

<p>A- Scheme showing the neuronal device featuring two micro-wells seeded with hippocampal neurons (DIV 15) and connected by an array of axon diodes. The neurons colored in green correspond to neurons that are transduced by ChR2. Neurons colored in purple are not transduced. B- Image of a neuronal device obtained by confocal fluorescence microscopy showing neurons expressing ChR2-YFP (false color).</p

Local stimulation and burst propagation (DIV15).

<p>A- Picture of a symmetrical two-compartments device with only one side transduced (left). Green and red channels are for ChR2-YFP and Calcium Orange indicator, respectively. This dual marking reveals that 70% of cells are expressing ChR2 inside the transduced compartment. B and C- Averaged response after stimulation of the transduced (B) and non-transduced (C) compartments. The solid colour lines correspond to the peristimulus fluorescence signal averaged over 30 stimulations (0.1 Hz in alternation) while the filled surfaces indicate associated standard deviations. Vertical dashed lines indicate stimulations. Diagrams are presented for clarity, with matching line and population colors. Green neurons are transduced neurons.</p

Optogenetic induction of bursting events.

<p>A- Typical responses of a transduced culture (DIV 13) to different stimulation durations (1, 2, 4, 8, 16, 32, 64, 128, 256, 512 and 1024 ms). Vertical blue bars represent stimulation times and durations. No fluorescence data was recorded during the stimulations as the photodiode, recording directly the stimulated spot, was saturated. B- Same experiment as in A after addition of 10 μM CNQX (AMPA receptor antagonist).</p

Burst transmission in asymmetrical networks (DIV15).

<p>A—Explanatory diagrams for graphs presented on the left and right column respectively, with the same color code as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0120680#pone.0120680.g004" target="_blank">Fig 4</a>. B—Typical example of a device showing unidirectional transmission. C—Results from a device where bursts also propagate in the reverse direction, albeit with a greater delay. Addition of 5 μM CNQX to the latter device yields the typical unidirectional transmission (D). Delays obtained by normalized cross correlation.</p

Compatibility of ChR2 and Calcium Orange.

<p>A- Quantification of background stimulation in ChR2(ET/TC) transduced cultures during calcium imaging with Calcium Orange at DIV12. The abscissa indicates the intensity of excitation light (549 nm) used during imaging relative to the recording conditions used in the rest of the experiments (1x); 2x is twice that level and 4x is 4 times that level. The different bursting rates at 2x and 4x were normalized by the bursting rates recorded at 1x for each culture so as to remove inter-culture variability for initial bursting rates. For information purpose, average absolute bursting rate at 1x was 5.9 ± 2.2 bursts per minute (n = 9 cultures). B- Absorption spectra of two ChR2 variants, including the ChR2(ET/TC) used in this study, as well as those of the commonly used Fluo-4 and its red-shifted counterpart Calcium Orange indicator. The figures of merit of each combination are indicated in % of maximal absorption.</p