Investigating the functional routes of temporal prediction in audition

In a continuous stream of auditory signals, predicting when certain events will occur (a sound indicating danger or a phoneme important for understanding a sentence) is essential for adaptive behaviour. Temporal predictions help us orient attention in time, which is crucial to protect a cognitive system with limited capacity from overload. Here, we will investigate how temporal predictions benefit hearing, using a psychophysical approach in healthy human adults. Furthermore, we will test the interaction of temporal ('when') and sensory ('what') predictions in audition by investigating their neural signatures in specialised auditory regions of the human brain in an integrative neuroimaging approach. To achieve this goal, we will take advantage of the excellent spatial and temporal resolution of functional magnetic resonance imaging (fMRI) and magnetoencephalography (MEG). This project addresses fundamental research questions in human cognition at the interface of timing and hearing, with the aim to provide a better understanding of the mechanisms supporting the temporal efficiency of auditory processing.

Modeling Traumatic Blast Brain Injury in Human Cerebral Organoids for Pharmacological Evaluation of Drug Candidates

Multiparametric molecular imaging for the prediction and prevention of anxio-depressive symptoms following exposure to organophosphate nerve agents

Organophosphorus (OP) agents such as sarin currently pose a significant threat to both military and civilian populations. While high doses of OP are rapidly fatal in the absence of antidote treatment, it has been demonstrated that exposure to low doses of OP results in a high prevalence of anxious and depressive symptoms in over 40% of subjects, even in the absence of acute toxicity. Early prediction, shortly after exposure, of the risk of developing long-term depressive symptoms could enable monitoring and dedicated intervention, considering the unique neuro-psychiatric disorders induced by OP exposure compared to those typically observed in patients.

This thesis project aims to fully leverage the non-invasive nature of positron emission tomography (PET) neuroimaging techniques to develop predictive assessments of anxious and depressive symptoms and/or their recurrence. Multiparametric molecular imaging approaches will be implemented to allow for longitudinal monitoring of neuronal and neurovascular substrates. Studies will be conducted using a murine model of OP exposure, where an anxio/depressive phenotype has previously been identified. The results will be compared to those obtained in the murine CORT model (chronic exposure to corticosterone), which traditionally mimics the anxious/depressive phenotype observed in humans.

Deciphering the photoactivation mechanism of the orange carotenoid protein by time-resolved serial femtosecond crystallography

The Orange Carotenoid Protein (OCP) is a photoactive protein involved in photoprotection of Cyanobacteria. Recently, a photoactivation mechanism was proposed for OCP, in which the initially excited S2 state yields multiple ps-lived excited states (ICT, S1, S*), but structural evidence is missing. Importantly, only one of these leads to the biologically active OCP-red state on the second timescale. We propose to conduct an ultra-fast time-resolved crystallography experiment at an X-ray free electron laser (XFEL) on OCP to accurately characterize the structures of the short-lived photo-intermediates on the femtosecond to millisecond timescale. In parallel, we will use the new time-resolved crystallography beamline of the ESRF to determine the structures of the later intermediates forming on the millisecond to second timescale. By allowing to visualize protein conformational changes upon photoactivation from the photochemical (hundreds of femtoseconds) to the photobiological timescales (seconds), our integrated structural biology project will allow to (i) test mechanistic hypotheses, (ii) pave the way to a detailed understanding the photophysical properties of OCP, and (iii) open avenues towards its exploitation as an optogenetic component or a regulator of light-uptake in biomimetic photosynthetic systems.

Biosynthesis and functional evaluation of novel antimicrobial peptides from mammalian gut microbiomes

The WHO has identified antibiotic resistance as one of the major threats to human health. According to predictions, the number of deaths related to antibiotic resistance is estimated at 10 million a year by 2050. This situation is prompting scientists to find new molecules, ideally natural ones, whose structures and mode of action differ from those of conventional antibiotics, to overcome the phenomena of resistance. One promising alternative concerns antimicrobial peptides of the RiPPs family (ribosomally synthesized and post-translationally modified peptides) produced by bacteria. Numerous studies show that the intestinal microbiome plays a very important role in the health of the host. Among the mechanisms involved, the production of antimicrobial peptides appears to be of particular importance. Part of our collaborative work aims to identify new antimicrobial peptides from complex biological ecosystems using metagenomic methods. To date, we have identified ten potentially interesting sequences. In this project, we will focus on the biosynthesis as well as the biochemical and structural characterizations of the antimicrobial peptides. An important part of the project will be devoted to the biological activity of these compounds on resistant and multi-resistant pathogens to conventional antibiotics. Moreover, the mode of action and the toxicity of the most effective peptides will be addressed.

Exploring chemotaxis in magnetotactic bacteria

Magnetotactic bacteria (MTB) are a diverse group of bacteria characterized by their capacity to biomineralize magnetite nanoparticles called magnetosomes. The latter allow MTB to passively align along magnetic field lines. This feature makes MTB of great interest to develop magnetic-guided microrobots used for medical applications such as targeted drug delivery. To make the latter efficient, it is not only essential to understand MTB magnetic behavior but also how MTB react to diverse chemical stimuli.
The aim of this internship is to broaden our understanding of chemotaxis in MTB. Several MTB species can be grown in the lab and will be investigated during the thesis. Typically, tethered cells and motility assays involving the use of microfluidics, microscopy and image analysis approaches will be developed to investigate, on a single-cell and population level, the chemotaxis responses of the strains to different chemical stimuli. These responses will be studied with bacteria grown in different growth conditions and in the absence or presence of a magnetic field using a custom-made magnetic microscope. Altogether, the data generated will give first insight into how MTB give an integrated response to chemical and magnetic stimuli and will therefore open new routes for the further development of targeted drug delivery.

Development of new antidote formulations based on chitosan-coated bilosome with active targeting, against intoxications by organophosphorus neurotoxins for nasal administration

The aim of this innovative project is to develop and validate the biological efficacy of new formulations including original and patented reactivators (CNRS/IRBA). These molecules present a large spectrum of action against acetylcholinesterase (AChE) inhibited by Organophosphorus Neurotoxins (NOPs), hence the interest in developing centrally effective antidotes for nose-to-brain administration. The novel bilosome-based formulations designed at CEA will be administered via the non-invasive nasal route, which could enable delivery to the brain either after passage into the systemic circulation, or by absorption through the olfactory nerves which provides direct access to cerebrospinal fluid and brain parenchyma, bypassing the blood-brain barrier (BBB). The approval by health authorities of Nyxoïd (naloxone) and Valtoco (diazepam) demonstrates the relevance of nasal therapeutic approaches to emergency situations (e.g. overdose, epilepsy) in subjects who may be unconscious or in respiratory distress. The project's innovations could ultimately interest the recently-created french company OPGS Pharmaceuticals, for the valorization of the work with the preclinical development (toxicity, selectivity...) and a possible industrialization of this medical countermeasures.
The thesis will take place in TOULOUSE.

In vitro fertilization technology: microfluidic platform for non-invasive embryo reception and characterization

Infertility affects 17.5% of couples of childbearing age. Assisted reproductive technologies (ART), such as in vitro fertilization (IVF), are costly and complex procedures requiring advanced equipments and a highly skilled workforce. Successive embryo manipulations are a source of stress that can impact on embryo quality and viability. But developmental abnormalities and miscarriages are mainly caused by chromosomal number anomalies or aneuploidies. These can be detected by pre-implantation diagnosis of aneuploidies (PGD-A) followed by high-throughput sequencing (NGS). However, PGD-A remains complex and invasive, with embryo biopsy potentially having implications for embryo development.
The question the PhD student will have to answer is: can we design a technological alternative that enables both automated culture of in vitro fertilization (IVF) embryos and their selection by non-invasive methods? The project will focus on automating embryo handling, while minimizing mechanical stress, and on extracting the extra-embryonic medium for circulating DNA analysis.
Expected results include an automated microfluidic platform for handling embryos without human intervention, extraction of extra-embryonic medium for aneuploidy analysis by sequencing, and building the program basis for microfluidic technologies applied to IVF.

Role of excited state vibrational modes of chlorophylls in photosynthesis

Photosynthesis empowers the entire biosphere and is arguably the most important biological process on earth. The quantum efficiency of excitation energy transfer (EET) in photosynthetic light-harvesting complexes can reach almost unity. This high efficiency is even more puzzling if we take into account that the high excitation energy transfer through hundreds of pigments in a disordered energetic landscape cannot be explained with the current models. Currently, there are two main hypotheses to explain the ultrafast energy transfer: “quantumness” and “vibrational assistance” (see context section). To validate these hypotheses, it is necessary to characterize the electronic and vibrational properties of the excited states of the cofactors involved in the ETT process. We have designed an interdisciplinary project, in which the student will be trained in biochemical techniques for protein purification and ultrafast photophysics techniques to analisys of the excitation energy transfer. The use of different detergents for purifying light-harvesting complexes leads to disturbed systems with differences in the excitation energy pathways. The differences between light-harvesting complexes from each purification will be characterized by resonance Raman and time-resolved fluorescence. Then, we will use ultrafast techniques such as fs-transient absorption, 2-D electronic spectroscopy (2DES) and femtosecond stimulated Raman Spectroscopy (FSRS). This data will be employed to develop new models for photosynthetic energy transfer. The student will be involved in the analysis and discussions for the theoretical modeling of this process but learning modeling techniques is out of the scope of the thesis.

Involvement of Rad51 paralogs in Rad51 filament formation in DNA repair

Homologous recombination (HR) is a major repair mechanism for DNA double-strand breaks induced by ionizing radiation. A key step in HR is the formation of Rad51 nucleoprotein filaments on the single-stranded DNA generated from these breaks. We have shown that strict control of these filaments is essential, so that HR does not itself induce chromosomal rearrangements (eLife 2018, Cells 2021). In humans, functional homologs of control proteins are tumor suppressors. Thus, the control of HR appears to be as important as the HR mechanism itself. Our project involves the use of new molecular tools enabling a real breakthrough in the study of these controls. We will be using a functional fluorescent version of the Rad51 protein developed for the first time by our collaborators A. Taddei (Institut Curie), R. Guérois and F. Ochsenbein (I2BC, Joliot, CEA). This major advance will enable us to observe the influence of control proteins on DNA repair by microscopy in living cells. We have also developed highly accurate structural models of control protein megacomplexes in association with Rad51 filaments. This study also led to the identification of specific domains for each paralog protein, outside the structurally conserved Rad51-like core, that might define the specificity of each paralog proteins. We will use a multidisciplinary approach based on genetic, molecular biology, biochemistry, protein structure and live microscopy methods and yeast as model organism to study the consequences of the ablation of these specific domains. We will also search for proteins specifically binding these domains. Their identification would be crucial to understand the function of Rad51 paralog complexes and help to develop new therapeutic approaches.