BIOfab seminar

  • Next seminar on tuesday, March 14th (2017) : Lionel Rousseau (ESIEE) "upcoming title"
  • Tuesday, Feb. 7th (2017) : Christoforos Theodorou from IMEP-LAHC "Low-frequency noise phenomena in advanced nano-scale electronic devices"

Abstract. The transistor gate oxide surface miniaturization towards the nanometer scale, the use of new semiconductor or insulator materials, as well as the complex manufacturing process steps, can dramatically increase the device low-frequency noise (LFN) levels. Added to that, individual trapping phenomena can cause the manifestation of high-amplitude random telegraph noise (RTN). On the bright side, LFN and RTN can be used as powerful non-destructive tools for interface quality characterization and trap localization, as well as for sensing purposes.

  • Tuesday, Jan. 10th (2017) : Thibault Honegger from LTM "Microfluidics neuro-engineering for brain on chip applications"

Abstract. Neurodegenerative diseases are now at epidemic proportions in industrialized nations, with Alzheimer’s, Parkinson or Huntington diseases affecting over 7 million people in Europe, and this figure is expected to double every 20 years as the population ages. There are currently no cures for those diseases mainly because of the incapacity of animal model to provide both fundamental insights on the human brain and drug development strategies. This presentation will highlight how brain on chip technologies will provide a new paradigm in neuroscience to better understand the human brain neural circuits and find new cures for Neurodegenerative diseases.

  • Tuesday, Nov. 29th (2016) : Blaise Yvert from BrainTech "Neurotechnology for rehabilitation "

Abstract.Understanding the brain dynamics and finding strategies to overcome disabilities encountered following a trauma or a pathology requires devices to interface the central nervous system and rehabilitation paradigms. Among other means, neural prosthesis and brain-computer interfaces (BCIs) aim at restoring lost functions following lesions or degeneration of the central nervous system. These neurotechnology-based approaches rely on large-scale neural interfacing using arrays of sensors to record and/or elicit activity within large neural populations. Here, I will focus on two research axes that we conduct in this context, one aiming at improving microelectrode arrays for neural sensing and microstimulation, and one aiming at using cortical implants to build a speech BCI to restore communication in locked-in aphasic patients. The presentation will thus be composed of two parts. First, I will insist on the importance of the electrode material when considering dense arrays of small-size microelectrodes, and show how in such case the noise level and stimulation capabilities of a device can be improved using novel nanoporous metal or carbon-based (diamond) electrode materials. Second, I will present our ongoing project aiming at using cortical neural implants to develop a BCI paradigm to restore continuous speech from real-time decoding of cortical activity. For this purpose, we have developed an articulatory speech synthesizer based on deep neural networks mapping the trajectories of the main articulators of the vocal tract (tongue, lips, jaw, velum) onto the acoustic content of speech. Different healthy subjects, in whom we recorded the movements of the main articulators and used these signals as inputs of the synthesizer, could successfully control this synthesizer in real-time. Such closed-loop paradigm will be transposed in a future clinical trial to allow patients implanted with electrode arrays to produce artificial speech from their cortical activity.

  • Tuesday, Nov. 22th (2016) : Clothilde COILHAC from Institut Néel "Thermodynamic of the self-assembly of DNA nanostructures"

Abstract.The self-assembly property of the DNA helix allows the use of DNA as a building block for the assembly of nanostructures. Many 2D or 3D structures have been assembled but little is known about the folding process. This knowledge would enable us to optimize and rationalize the design of such structures. Our approach is to study the folding of model structures (tetrahedron, rectangle origami) to identify the thermodynamically intermediates states. We explore the energy landscape in order to understand the general mechanisms leading these systems towards their minimum free energy. However, these calorimetric measurements require a large amount of DNA. That is why we develop in parallel a calorimetric sensor integrating microfluidic on a membrane to perform ITC experiment (isothermal titration calorimetry) on volume from 1000 to 10000 times smaller.

  • Tuesday, June 28th (2016) : Hervé Guillou from Institut Néel "DNA nanostructures: principle and motivations"

Abstract.In this presentation that we plan to be introductory we will present the recent field of DNA origami. We will explain how to assemble by using simple sets of thermodynamic rules 2D and 3D shapes of few nanometers. Interestingly although we exactly know how to program the self-assembly of a given shape and engineer it we know very little on the process itself: what is the pathway ? Our current research focuses on this question and we will present our methodology and recent results on models structures using thermodynamic methods. We will open the field in giving our motivations to explore and design rationally the folding pathways. Beside fundamental thermodynamics, these motivations lies in molecular robotics, information processing and eventually in computing.

  • Tuesday, March 29th (2016) : Manon Guille-Collignon from ENS, Paris "More Transparency in BioAnalysis of Exocytosis: Coupling of Electrochemistry and Fluorescence Microscopy at ITO Electrodes"

Abstract.Vesicular exocytosis is an essential biological mechanism used by cellular organisms to release bioactive molecules (hormones, neurotransmitters…) in their environment. For instance, this is the pathway by which chromaffin cells deliver catecholamines (adrenaline, nor-adrenaline, dopamine…) in blood. During this process, secretory vesicles that initially stored the (bio)chemical messengers dock to the cell membrane. The subsequent fusion of vesicle and cell membranes induces the formation of a fusion pore that initiates the first exchanges between the intravesicular and extracellular media. Its following expansion thus favours a larger release of the vesicular content into the external medium. Several analytical methods have been developed in order to study exocytosis at the single living cell level in real time. Among those techniques, mostly based on electric or optic measurements, amperometry with a carbon-fiber ultramicroelectrode [1], used in the first part of this report, and total internal reflection fluorescence microscopy (TIRFM) appear as the most powerful.[2] Practically, physico-chemical properties of ultramicroelectrodes induce a high detection sensitivity and temporal resolution, thus being particularly well adapted to monitor exocytosis of electroactive molecules in real time. In this work, exocytosis is first studied amperometrically (at carbon fiber ultramicroelectrodes) at adrenal chromaffin cells, which release catecholamines after appropriate stimulation, while testing the effects due to trans-insertion of two exogenous compounds (lysophosphatidylcholine (LPC) and arachidonic acid (AA)) on the kinetics of exocytotic events. Amperometric analyses showed that, under the present conditions (short incubation times and micromolar LPC or AA solutions), LPC favors catecholamine release (rate, event frequency, charge released) while AA disfavors the exocytotic processes. We also observed that the detected amount of neurotransmitters in the presence of LPC was larger than under control conditions, while the opposite trend is observed with AA.[3] Nevertheless, amperometric investigations are obviously limited to the phenomena occurring once the fusion pore onsets. Coupling this technique with fluorescence microscopy would permit to visualize the status of vesicles near the plasma membrane, more particularly their behaviour before and during the fusion as well as the location of the event. In this regard, the combination has to involve a cellular model whose secretory vesicles are both marked by a fluorescent probe and whose content is electroactive. To do so, amperometric and optical investigations have been achieved here to choose a cell model for which the features of the exocytotic events are sufficient to possibly correlate the electrochemical and optical signals. Moreover, the amperometry-microscopy combination also requires the development of specific devices. Thus, semiconducting and transparent ITO (Indium Tin Oxide) is used as an electrode without hindering the optic detection of marked vesicle by a fluorescent probe. Feasibility of this coupling strategy will be demonstrated and results obtained in these conditions on single cell will be described and discussed.[4-7]

[1]. C. Amatore, S. Arbault, M. Guille, F. Lemaître Chem Rev 108, 2585 (2008), [2]. E. Karatekin, V. S. Tran, S. Huet, I. Fanget, S. Cribier, J-P. Henry Biophys. J. 94, 2891 (2008) [3]. L. Chernomordik, A. Chanturiya, J. Green, J. Zimmerberg Biophys. J. 69, 922 (1995) ; C. Amatore, S. Arbault, Y. Bouret, M. Guille, F. Lemaître, Y. Verchier ChemBioChem 7, 1998 (2006) [4]. A. Meunier, O. Jouannot, R. Fulcrand, I. Fanget, M. Bretou, E. Karatekin, S. Arbault, M. Guille, F. Darchen, F. Lemaître, C. Amatore Angew. Chem. 50, 5081 (2011) [5]. A. Meunier, R. Fulcrand, F. Darchen, M. Guille-Collignon, F. Lemaître, C. Amatore Biophys. Chem. 162, 14 (2012) [6]. A. Meunier, M. Bretou, F. Darchen, M. Guille-Collignon, F. Lemaître, C. Amatore Electrochimica Acta 126, 74 (2014) [7]. F. Lemaître, M. Guille-Collignon, C. Amatore Electrochimica Acta 140, 457 (2014)

  • Tuesday, March 8th (2016) : Salima RAFAI from the LIPhy "Flowing properties of a microswimmer suspension"

Abstract.Suspensions of motile living organisms represent a non equilibrium system of condensed matter of great interest on a fundamental point of view as well as for industrial applications. These are suspensions composed of self-driven units - active particles- able to convert stored energy into movement. Interactions between active parti cles and the liquid they are swimming in give rise to mechanical stresses and large scale collective motion that have recently attracted a lot of interest in physics and mechanics communities. From the industrial point of view, microalgae are used in many applications ranging from the food industry to the development of new generations of biofuels. The biggest challenges concerning all this applications are the separation, filtration and concentration processes of microalgae. There is thus a real need of a better understanding of the flow of active matter to achieve a optimal control of these systems. I’ll present our recent work on microswimmer suspensions : rheological properties of active suspensions as well as the « microscopic » characteristics of the random walk of the green microalga Chlamydomonas Reinhardtii. We have recently shown that hydrodynamics of a microalgae suspension coupled with phototaxis* leads to a spontaneous concentration of the suspension toward the center of the channel. Experiments as well as simulations will be presented. *Biased movement that occurs when an organism moves in response to the stimulus of light.

  • Tuesday, Jan 12th (2016) : Philippe Marmottant from Liphy - DYnamique des Fluides COmplexes et Morphogénèse "Cavitation of sap in trees and leaves"

Abstract. In this talk, we will present our investigations on the nucleation of bubbles in tree vessels, by showing experiments on wood and on leaves. Such explosive bubbles occur by cavitation, since the liquid sap in trees is under extreme negative pressure. They form an emboly that can affect the hydraulic circulation of sap.

  • Wednesday, June 10th (2015) : Jean-Luc Pellequer from The Institut de Biologie Structurale (IBS) "Microscopie à Force Atomique : de la modélisation moléculaire à l’imagerie"
  • Thursday, April 9th (2015) : Clement Hebert from the Diamond Sensors Laboratory (CEA, LIST) "Diamond for neural interfaces"

Abstract.During this seminar I will present the results obtained in the NEUROCARE project at the Diamond Sensors Lab (CEA Saclay). This project aimed at creating better retinal, cortical and cochlear implantable devices through the use of improved interfacing between the electronic implants and living cells. The NeuroCare concept involves low-cost, carbon-based materials, well-adapted for medical implants, because they (i) offer wide range of electronic properties (metal, semiconductor and insulator), (ii) are bio-inert and (iii) are physically robust. In this context we optimized porous diamond materials toward neural interfaces. The properties of the diamond materials were assessed in vitro and in vivo at Institut de la vision and CEA Clinatec via the use of soft retinal and cortical implants and rigid MicroElectrode Arrays.

  • Thursday, March 19th (2015) : Gregoire Courtine from the Swiss Federal Institute of Technology (EPFL) "Neuroprosthetic technologies to improve locomotion after spinal cord injury"

Abstract.Over the past decade, my team and I developed a pragmatic therapy that restored supraspinal control over refined leg movements after severe spinal cord injury in rodents. Our therapy, termed neuroprosthetic rehabilitation, acts over two time windows. Immediately, electrical and chemical neuromodulation of spinal circuits mediate motor control of the paralysed legs. In the long term, will-powered training regimens enabled by electrochemical neuromodulation and robotic assistance promote neuroplasticity of residual connections—an extensive rewiring that reestablishes voluntary movement. The successful implementation of these interventions required the development of myriad tools, including neural interfaces, computational models, real-time control platforms, robotic systems, and anatomical analyses. Here, I will describe the conceptual framework through which we designed these cutting-edge technologies. I also will reveal some of the mechanisms underlying the immediate and long-term effects of neuroprosthetic rehabilitation on motor control capacities. Finally, I will highlight our current efforts in non-human primates and humans to translate our findings into a viable therapy to improve the recovery of locomotion in paraplegic individuals.

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