IRL FuMa

IRL FuMa

French Australian International Research Laboratory in Maths

IRL FuMa

2014 – 2021
Contact:
Filipo Santambrogio
santambrogio(at)math.univ-lyon1.fr

IRL FuMa
Website

Credits: All images of this page come from the paper Joan Licata and Vera Vértesi: “Foliated open books”

Introduction

The IRL “FuMa” for Fundamental Mathematics is a joint CNRS – Australian National University (ANU) initiative in the field of basic and applied mathematics, managed by Prof. Filipo Santambrogio (CNRS) and Stephen Roberts (ANU).

Mission and research themes

This project aims at promoting cooperation between mathematicians from every French university, and mathematicians from the Mathematical Science Institute (Australian National University) in Canberra.

The scientific area that we address is very broad, and has been recently extended (the previous version of this project was called AnGe (“ANalysis and GEometry”) in order to include all mathematical sciences with a priority for fundamental mathematics, but allowing projects on applied mathematics to emerge.

The researchers involved in the project have worked so far on various topics, including, in the latest years,

– differential geometry and topology

– representation theory

– harmonic analysis

– partial differential equations and optimal transport

– biostatistics

Support opportunities

The project is endowed with funds from CNRS and ANU, which are used to support research stays of French mathematicians in Canberra or of mathematicians from ANU in France. Longer stays (3 to 6 months) are preferred but one-month visits are also possible. Applications are done by sending a proposal, with a joint research project and a plan for the visit, to the colleagues in charge of the project (see below). The same colleagues should also be contacted for all practical details about the financial support (reimbursement, bookings, eligible expenses, amount…), which usually covers flight tickets, accommodation, and a small per-diem for local expenses. For French “enseignant-chercheurs” wishing to organize a 6 months visit to ANU the project can also support a request for a CNRS “délégation”.

laboratories involved

France

All labs in mathematics throughout France can take part in this project, but the project itself is hosted by UMR5208 Institut Camille Jordan, which also handles the financial matters The head of the project from the French side, to be contacted for any question is

Filippo Santambrogio, Professor, UMR5208 Institut Camille Jordan, Université Claude Bernard Lyon 1

Australia

Stephen RobertsMathematical Sciences Institute, Australian National University

Construction of a partial open book for a thickened surface.

Construction of a partial open book for a thickened surface.

The pages of a foliated open book near a surface.

The intersection of the pages of a foliated open book with a torus.

The open book foliation of an embedded torus.

The gradient flow lines corresponding to an open book foliation.

IRP REDOCHROME

IRP REDOCHROME

French-Australian International Research Project in Chemistry

IRP REDOCHROME
2015
Contact:

Frederic Paul,
frederic.paul(at)univ-rennes1.fr

IRP REDOCHROME
News

Introduction

The IRP “REDOCHROME” focusing on redox-active and multipolar organometallic assemblies for photonics and molecular electronics is a joint CNRS-ANU and UWA initiative in chemistry. It focuses on molecular photonics and electronics and involves 24 Australian and French researchers. It is the continuation of a Franco-Australian PICS project initiated in 2015 between French researchers at the Institute of Chemical Sciences of Rennes (ISCR), a joint CNRS-University of Rennes 1 unit (UMR CNRS6226), and Australian researchers at ANU.

Missions and research themes

The main research theme concerns the chemical synthesis of redox-active carbon-rich organometallics and related molecular-based materials. These discrete molecular assemblies are often endowed with remarkable electronic and optical properties. Such assemblies are amongst the most complex systems at the nanoscopic scale and are challenging to model theoretically, a situation which calls for more experimental insight into these paradigmatic molecules. The Redochrom LIA involves French researchers from Rennes (UR1) and Toulouse (UPS) universities and Australian partners located at two top-ranking universities, namely the Australian National University (ANU) in Canberra and the University of Western Australia (UWA) in Perth. This group of French and Australian organic and organometallic chemists has additional expertise in spectroscopy, linear and nonlinear optics (LO and NLO) and electron-transfer, and unique instrumentation. The purpose of this LIA is to develop an understanding of these fascinating architectures, so as to permit their use as discrete molecular-based devices in various applications related to photonics and electronics.

MAIN OBJECTIVES OF THE PROJECT

In a continuation of ongoing collaborative projects that link the French and Australian team members, one part of the project is aimed at establishing reliable structure-property relationships for designing (electro-)switchable two-photon absorbers based on redox-active organometallics, which constitute a little-explored class of compounds from the standpoint of their NLO properties. Such materials have potential applied outcomes in all-optical information treatment and other societal uses. A key focus of the Redochrom consortium is to elucidate the role of the metal center(s) on these optical properties.

The second part of the project will progress molecular electronics research beyond two-terminal metal/molecule/metal junctions, based on linearly conjugated organic molecules.

Chemical synthesis, electro- and photo-chemistry and quantum chemical calculations will be deployed to develop understanding of molecular electronic structure as a function of redox state. This highly collaborative research program will create structures in which molecular electronic properties directly impact on the room temperature operating characteristics of the device. By providing both tools and chemical concepts that address the issues of molecule-surface interactions, charge transport across these interfaces, and function, we will advance the field of molecular electronics, increase the critical mass of activity in the area, and improve bilateral research capacity. Furthermore, the synergy between these two complementary facets (molecular photonics and electronics) will facilitate study of each topic in greater detail than in a project concerned with only one of these areas. This synergy is expected to foster more rapid strides towards realization of practical devices made from carbon-rich organometallics.

institutions and laboratories involved

France

  • Frederic Paul (DR CNRS, PI), UMR CNRS 6226 (ISCR-COrInt Team)
  • Jean-François Halet (DR CNRS, co-PI), UMR CNRS 6226 (ISCR- CTI Team)

The consortium of French researchers at Institut des Sciences Chimiques de Rennes (ISCR).led by F. Paul and J.-F. Halet belongs to different groups and teams at ISCR. Besides the strong organic or organometallic chemical synthesis component which is shared by most French participants of ISCR (iron alkynyl complexes; porphyrins; organic chromophores and fluorophores), some team members bring more specific expertise in various physico-chemical fields (silicon surface functionalization and electrochemistry, mixed-valent compounds, second-order and third-order NLO studies). The latter are complemented by ultrafast transient absorption spectroscopic facilities at the Institute of Physics of Rennes (M. Lorenc, IPR). There is also a strong computational component present among the French delegates (led by J.-F. Halet and A. Boucekkine at ISCR), complemented by a specialist in excited-state calculations in Toulouse (I. Dixon, LCPQ-UPS).

Australia

  • M.G. Humphrey (Prof, PI), Research School of Chemistry,  ANU (Canberra)
  • P. J. Low (Prof, co-PI), School of Chemistry and Biochemistry  UWA (Perth)

The group of M. G. Humphrey at ANU in Canberra is fully equipped to study the nonlinear optical properties of molecules with Z-scan experiments for measuring cubic nonlinearities and optical limiting properties recently complemented by a hyper-Rayleigh scattering setup for measuring quadratic nonlinearities.

Laser suite for the study of nonlinear optical properties of molecules (Australian National University).

P. J. Low at UWA (School of Molecular Sciences) has leading expertise in intermolecular electron-transfer processes and molecular electronics. His group is equipped with a spectroscopic and experimental setup to characterize and study eletron-transfer processes through single molecules deposited on surfaces. This complements and extends the long-standing interest and expertise in the synthesis of metal-alkynyl and organometallic derivatives led by G. A. Koutsantonis.

SPM platform for electrochemical AFM/STM experiments (University of Western Australia).

Single molecule electronic studies and spectroelectrochemical facility (University of Western Australia).

International Exchanges

Participants of the Molecular Electronics and Photonics Meeting (MEP 2018), July 10-13, 2018, UR1)

Signing of the first French-Australian SCF-RACI kindred agreement (2018-2022) by the Presidents of SCF (G. Chambaud, left) and RACI (P. Junk, right).

G. A. Koutsantonis at the French-Australian Scientific Day (FASD 2019), April 2019, UR1 (left)

Docteur Honoris Causa nomination of M. G. Humphrey by UR1 (F. Paul left, F. Mongin Right).

Participants of French-Australian MC2R meeting (MCR2 2018), ANU, November 20, 2018.

Program of first French-Australian School on Molecular Electronics and Molecular Photonics (MEMP 2019), ANU, July 4-8, 2019.

IRP APICOLIPID

IRP APICOLIPID

French-Australian International Research Project in Biology

IRP APICOLIPID
2018-2022
Project Coordinator:
Dr Cyrille Botté 
cyrille.botte(at)univ-grenoble-alpes.fr
Twitter: @ApicoLipid 

Coordinator partner: 
Prof Geoff McFadden

IRP APICOLIPID
Website

Apicoplast in malaria

magnetic beads

Zoom basal caps and rigs Full Resolution midlate division 3

Graphical abstract

Toxoplasma ATS2

Introduction

The CNRS-INSERM IRP ApicoLipid (Apicomplexan parasites lipid and membrane biogenesis) is managed by Dr Cyrille Botté (IAB CNRS UMR5309 INSERM U1209, Université Grenoble Alpes) in collaboration with Professor Geoff McFadden (School of Biosciences, University of Melbourne). Our IRP was initiated through a long term and fruitful collaboration between our two laboratories initially supported by a CNRS International Scientific Project (PICS 2013-2017) and through our IRP in 2018. Our consortium aims to better understand the role propagation and pathogenicity of infectious agents causing malaria and toxoplasmosis to identify novel drug targets.

Missions and research themes

Apicomplexan parasites are unicellular eukaryotes responsible for major human infectious and chronic diseases such as malaria and toxoplasmosis, which cause massive social and economic burden. Malaria is caused by Plasmodium spp., via the bite of Anopheles mosquitoes in tropical and sub-tropical areas. Plasmodium infects ±200 million people every year and is responsible for the death of ±450,000, mainly children under the age of 8. Toxoplasma gondii is the causative agent of toxoplasmosis, a global chronic disease that affects ±1/3 of the world population. T. gondii is a lethal threat for the foetus of primo-infected pregnant women and for any immunocompromised patients (HIV, leukemia, chemotherapies, organ transplant…). To date, there is no efficient vaccine against these parasites, and parasite are rapidly developing resistance to most marketed molecules, especially for malaria. Thus, there is a pressing need for the identification of new targets and efficient drugs.

Apicomplexa are obligate intracellular parasites of humans, which means that they have to invade a host cell to survive and propagate. Current evidences strongly support lipid synthesis and membrane biogenesis as crucial pathways for parasite propagation in humans and therefore represent pertinent drug targets.

Our consortium focuses on understanding how this group of infectious parasites can acquire the lipid required for their survival. Our IRP combines a strong expertise, long lasting collaboration and complementary expertise to decipher the complex metabolic pathways sustaining parasite survival in the human hhost. We use a combination of novel genetic edition of the parasite (CrispR-Cas9-based), mass spectrometry-based lipidomics and fluxomics approaches developed in the metabolomic platform developed on the French side (Dr Botté, GEMELI Université Grenoble Alpes) as well as full life cycle analysis of the parasite lipid synthesis via the unique insectarium and mice facility of the Australian partner (Prof McFadden University of Melbourne). Through our interaction, we showed that the parasite can actively scavenge the human host lipid resources, but can also synthesize lipids de novo via a relict non-photosynthetic plastid (i.e. the apicoplast). Importantly, we showed that the parasite has to combine lipids from both host and de novo sources to survive. Recently we also showed that the parasite is also capable to metabolically reprogram both pathways upon the physiological and nutritional environment of their host. We currently focus on understanding how the parasite can sense and adapt to the host and how this is happening in the malaria mosquito vector. Together with our partners (Prof McConville Bio21 University of Melbourne, Dr Christopher Tonkin WEHI Melbourne), we form a taskforce to decipher parasite lipid biology, find the parasite weaknesses that could potentially benefit malaria and toxoplasmosis patients worldwide.

MAIN PROJECT OF RESEARCH THEMES

  • Understand the pathways of lipid channeling, recycling and combination between the host and the parasite
  • Determine the specificity of lipid synthesis throughout the whole parasite life cycle
  • Contribute to the global knowledge of the intracellular development, lipid synthesis, membrane biogenesis, nutrient acquisition of apicomplexa parasite within their host
  • Identify novel drug targets against malaria and toxoplasmosis
  • Teach and promote novel techniques developed by the consortium: metabolomics/lipidomics/fluxomics; malaria liver and mosquito analysis, molecular approaches in malaria and toxoplasmosis
  • Promote the environment young researcher (PhD, Postdoc, technicians…) to develop their skills and career
  • Promote French and Australian research and knowledge

institutions and laboratories involved

France

Australia

  • Prof McFadden, School of Biosciences, University of Melbourne
  • Prof Malcolm McConville, Bio21 Institute, University of Melbourne
  • Dr Christopher Tonkin, Walter Eliza Health Institute (WEHI) Melbourne

some key publications

Amiar+ S, Katris+ NJ, Berry L, Dass S, Shears MJ, Brunet C, Touquet B, Hakimi MA, McFadden GI, Yamaryo-Botté Y*, Botté CY*. Division and adaptation to host nutritional environment of apicomplexan parasites depend on apicoplast lipid metabolic plasticity and host organelles remodelling, (2020) Cell Rep. 2020 Mar 17;30(11):3778-3792.e9. doi: 10.1016/j.celrep.2020.02.072.

Yang L, Uboldi AD, Seizova S, Wilde ML, Coffey MJ, Katris NJ, Yamaryo-Botté Y, Kocan M, Bathgate RAD, Stewart RJ, McConville MJ, Thompson PE, Botté CY, Tonkin CJ. J Biol Chem. An apically located hybrid guanylate cyclase-ATPase is critical for the initiation of Ca2+ signaling and motility in Toxoplasma gondii. J Biol Chem 2019 May 31;294(22):8959-8972. doi: 10.1074/jbc.RA118.005491

Uboldi AD, Wilde ML, McRae EA, Stewart RJ, Dagley LF, Yang L, Katris NJ, Hapuarachchi SV, Coffey MJ, Lehane AM, Botte CY, Waller RF, Webb AI, McConville MJ, Tonkin CJ. Protein kinase A negatively regulates Ca2+ signalling in Toxoplasma gondii. PLoS Biol. 2018 Sep 12;16(9):e2005642. doi: 10.1371/journal.pbio.2005642.

Shears MJ, MacRae JI, Goodman DG, Mollard VSU, Botté CY *, McFadden GI*. (2017). Characterization of the Plasmodium falciparum and P. berghei glycerol-3-phosphate acyltranferase involved in FASII fatty acid utilization in the malaria parasite apicoplast. Cellular Microbiology 19(1). PMCID:PMC5213128.

Amiar S, MacRae JI, Callahan DL, vanDooren GG, Shears MJ, Dubois D, Cesbron-Delauw MF, Maréchal E, McConville MJ, McFadden GI, Yamaryo-Botté Y*, BOTTÉ CY *.  The Toxoplasma gondii apicoplast is responsible for bulk phospholipid synthesis mainly via a plant-like glycerol 3-phosphate acyltransferase for lysophosphatidic acid precursor assembly. Plos Pathogens 2016 Aug 4;12(8):e1005765. doi: 10.1371/journal.ppat.1005765

BOTTÉ CY*, Yamaryo-Botté Y, Rupasinghe TW, Mullin KA, MacRae JI, Spurck TP, Kalanon M, Shears MJ, Coppel RL, Crellin PK, Maréchal E, McConville MJ, McFadden GI*. Atypical lipid composition in the purified relict plastid (apicoplast) of malaria parasites. (*co-corresponding) Proc Natl Acad Sci U S A. 2013 Apr 30;110(18):7506-11.

Signature of the LIA APICOLIPID CNRS INSERM at the Australian Science Academy, with CNRS CEO Antoine Petit

Press release medical News 2016

Press release INSB april 2020

Metabolomic day I IAB February 2020

Metabolomic day I IAB February 2020

Journal of lipid Research takeover

IRP GEODESIC

IRP GEODESIC

French-Australian International Research Project in Engineering

IRP (LIA) GEODESIC
2017-2020
Contact:
Dr. Nicolas Le Bihan
nicolas.le-bihan(at)gipsa-lab.fr

Prof. Jonatha H. Manton
jmanton(at)unimelb.edu.au

IRP GEODESIC
News

Non-stationary bivariate signal: geometric and polarization parameters highlight using geometric signal processing approach.

Credits: 

“Time-frequency analysis of bivariate signals”,
J. Flamant, N. Le Bihan and Pierre Chainais
Applied and Computational Harmonic Analysis, Vol. 46, Issue 2, pp. 351-383, 2019

Introduction

The GEODESIC (Geometry-Driven Signal and Image Processing) lab conducts research in the field of data science, with emphasis in signal and image processing applications. Specifically, researchers at GEODESIC develop new methodologies that take into account the geometry of the datasets and of the ambient space they live in.

Missions and research themes

The research themes of GEODESIC are the following:

– Topic 1: Adaptive Signal Processing on Manifolds

This reserach topic focuses on adaptive signal processing on manifolds. Precisely, it aims to
provide a comprehensive framework, describing the complexity and performance of adaptive algo-
rithms on manifolds. Currently, in the field of signal processing, adaptive algorithms on manifolds
are mostly considered heuristically, and on a case-by-case basis. the work at GEODESIC is to provide users with comprehensive guidelines for the design of efficient adaptive algorithms especially designed for processing data belonging to manifolds. Adaptativity is a key ingredient in many applications (pose or attitude estimation, localization, etc.) and manifold valued datasets are numerous. A timely challenge is to propose algorithms which are both adaptive and constrained to live on manifolds.

– Topic 2: Non-Commutative Signal Processing

In recent years, the signal and image processing community, and in a wider sense the engineering
community, has faced an increasing number of problems involving non-commutative algebraic
structures and manifolds. Signals and images taking their values on structures such as spheres
(Cosmic Microwave Background, probability density functions of multiple scattering processes,
…), rotation groups (attitude of rigid-body, polarized signals subject to geometric phase …), Stiefel
manifolds (partially observed attitude, subspace and array processing …) are now encountered on
a daily basis. Firstly approached by adaptation of standard methods, the community soon realized
that new paradigms should be adopted to tackle the non-linear problems faced with the processing
of such signals and images. It is now largely admitted that systematic use of differential geometry
and representation theory should be made, even though this is not exactly the case in practice.
This research topic inside GEODESIC proposes to develop new algorithms dedicated to signal
processing problems strongly related to the geometry of the space in which signals evolve.

– Topic 3: Information processing in sensor networks

The first two topics of GEODESIC are dedicated to signal indexed by (and/or living in) manifolds.
The third topic concentrates on discrete indexation sets: It concerns signals indexed by graphs,
hereafter designated as graph signals.
Graph signals are ubiquitous in our technological world. They are acquired in many applications
ranging from meteorology to neuroscience. They can be obtained from active sensor networks
(meaning that sensors process information and communicate with each other) or from passive
monitoring systems (like ElectroEncephaloGraphy–EEG– recordings). Furthermore, they are at
the heart of massive data sets and high dimensional statistics. For example, high resolution EEG
recordings deliver high temporal resolution signals living in dimension as high as 300. In neuro-
science, next generation imaging systems are likely to deliver high space-time resolution measure-
ments: In a few years, filming the activity of a whole neural networks will be possible.
Researchers at GEODESIC work on the design of inference algorithms for graph signal processing, with targeted applications such as neuroscience.

MAIN PROJECTS OF RESEARCH

– Investigation on sensory modalities and their interactions: olfactory recognition and olfactory abilities in air and under water; individual visual recognition, cross-modal recognition.

– Social Network and communication: vocal and olfactory cues to avoid inbreeding; male breeding strategy and vocal assessment; social interaction and vocal recognition in pups.

– PhD funding(s)

– Involvement of French and Australian master students

institutions and laboratories involved

France

  • Grenoble Image Parole Signal Automatique (Gipsa-Lab UMR 5216), Grenoble.
  • Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL UMR 9189), Lille
  • Laboratoire de l’Intégration du Matériau au Système (IMS, UMR 5218), Bordeaux.

Australia

  • The University of Melbourne, Dpt. of Electrical and Electronic Engineering, Melbourne.
  • – The University of Melbourne, Dpt. of Mathematics and Statistics, Melbourne.
  • The University of Melbourne, Dpt. of Physics, Melbourne.

IEA STraS

IEA STraS

French-Australian International Emerging Action on Environment

IEA STraS
2018 – 2020
Contact:

Dr Renard Emmanuelle
Emmanuelle.renard(at)imbe.fr

Dr Bernie Degnan
b.degnan(at)uq.edu.au

IEA (PICS) STraS logo

IEA STraS
Website

IEA STraS
News

Lectin labelling of the pinacocytes of Oscarella lobularis (E. Renard)

Introduction

The International Emerging Action project « Staining and Tracking Sponge Cells to describe morphogenetic processes » (STraS) managed by Dr E. Renard, launched a collaboration between 3 French teams and one Australian team, in order to study and compare the cell biology of 3 sponge species with different features.

Context and objectives

Gene content of sponges was characterized by transcriptomic or genomic approaches. Surprisingly, despite their simplicity sponges contain most of the developmental gene families present in bilaterians. The next step to be reached is now to understand how similar genetic toolboxes can result in widely dissimilar bodyplan organization, dynamics and life histories. To answer this question, three main axes of research have to be undertaken : 1) sequencing more whole genomes ; 2) conducting much more gene expression studies (available data remain sparse) ; 3) developing reproducible knock down protocols ; 4) reinterpreting sponge cell structure and mechanisms with nowadays tools.
The 4 partners are interested and involved in these four aspects, but the present project focuses on point 4. The present knowledge of sponge cell biology mainly relies on classical (static) observations, which fail to provide a dynamical description of cellular behaviors and mechanisms, essential to decipher morphogenetic processes.
Much remains to be tested in terms of cell specific staining and tracking to understand which key cellular processes are involved in sponge morphogenesis and to evaluate the so-called “lability” of sponge cells.

Main OBJECTIVES OF THE PROJECT

We propose to join our efforts and skills to make substantial advances in these techniques to evaluate the implications of three primordial cellular mechanisms : cell death, cell proliferation/differentiation and mesenchymal-epithelial/epithelial-mesenchymal transitions (MET/EMT). We will perform these comparisons in 3 species with different features : 1 filtering Demosponge Amphimedon queenslandica, 1 carnivorous sponge (devoid of aquiferous system) Lycopodina hypogea, 1 Homoscleromorph sponge Oscarella lobularis.

We aim at :
Aim 1 : Evaluating the relative stemness of sponge cell types
Aim 2 : Evaluating the relative involvement of EMT/MET during regeneration
Aim 3 : Evaluating the involvement of apoptotic events during regeneration

institutions and laboratories involved

France

Australia

EDU staining of choanocyte nuclei of Oscarella lobularis (E.

Renard)