Project

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EvoDevo and Physics of Skin Colours

English title EvoDevo and Physics of Skin Colours
Applicant Milinkovitch Michel
Number 162743
Funding scheme Interdisciplinary projects
Research institution Département de Génétique et Evolution Faculté des Sciences Université de Genève
Institution of higher education University of Geneva - GE
Main discipline Zoology
Start/End 01.03.2016 - 28.02.2019
Approved amount 522'675.00
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All Disciplines (5)

Discipline
Zoology
Other disciplines of Physics
Condensed Matter Physics
Information Technology
Embryology, Developmental Biology

Keywords (13)

New model organisms; Evo-Devo; Bio-photonics; Modeling; Physics of biology; skin colour; skin appendages; hair; scales; pigments; structural colours; evolution; development

Lay Summary (French)

Lead
La peau et ses appendices (poils, plumes, écailles, épines, glandes) apportent une protection physique à l’individu. Les couleurs de ces structures jouent également des rôles important et variés: thermorégulation, photoprotection, camouflage, signaux comportementaux, etc. Notre projet consiste à combiner de méthodes de physique, de biologie évolutive, de biologie du développement et d’informatique afin d’identifier les mécanismes sous-jacents à la formation des couleurs pigmentaires et structurelles chez les vertébrés. Dans notre projet précédent, nous avons découvert que les caméléons changent de couleur via le réglage actif d’un maillage de nanocristaux présents dans la peau. Ces résultats ont généré un buzz mondial et intéressent diverses industries qui cherchent à capitaliser sur des approches de biomimétisme (développer de nouvelles technologies par imitation de la nature).
Lay summary

Dans notre nouveau projet, nous identifierons les gènes impliqués dans des mutation de la coloration de la peau ainsi que les principes mathématiques et les mécanismes physiques responsables de la formation de patrons de coloration chez les animaux (rayures du zèbre, taches du guépard, etc.). Enfin, nous utiliserons des techniques de pointe (imagerie hyperspectrale, cristallographie photonique, microscopie) pour identifier les mécanismes biochimiques et développementaux qui permettent aux amphibiens et aux reptiles de produire des couleurs structurales, c’est-à-dire des couleurs qui ne sont pas générées par des pigments mais par l’interaction de la lumière avec des matériaux nanoscopiques (exactement comme un CD génère de l’iridescence sur sa face gravée de nano-sillons). Notre projet est à la frontière entre la physique de la biologie et la biologie évolutive du développement.

Direct link to Lay Summary Last update: 10.10.2015

Responsible applicant and co-applicants

Employees

Publications

Publication
Feather arrays are patterned by interacting signalling and cell density waves
Ho William K. W., Freem Lucy, Zhao Debiao, Painter Kevin J., Woolley Thomas E., Gaffney Eamonn A., McGrew Michael J., Tzika Athanasia, Milinkovitch Michel C., Schneider Pascal, Drusko Armin, Matthäus Franziska, Glover James D., Wells Kirsty L., Johansson Jeanette A., Davey Megan G., Sang Helen M., Clinton Michael, Headon Denis J. (2019), Feather arrays are patterned by interacting signalling and cell density waves, in PLOS Biology, 17(2), e3000132-e3000132.
Locally-curved geometry generates bending cracks in the African elephant skin
Martins António F., Bennett Nigel C., Clavel Sylvie, Groenewald Herman, Hensman Sean, Hoby Stefan, Joris Antoine, Manger Paul R., Milinkovitch Michel C. (2018), Locally-curved geometry generates bending cracks in the African elephant skin, in Nature Communications, 9(1), 3865-3865.
Evolution of Cortical Neurogenesis in Amniotes Controlled by Robo Signaling Levels
Cárdenas Adrián, Villalba Ana, de Juan Romero Camino, Picó Esther, Kyrousi Christina, Tzika Athanasia C., Tessier-Lavigne Marc, Ma Le, Drukker Micha, Cappello Silvia, Borrell Víctor (2018), Evolution of Cortical Neurogenesis in Amniotes Controlled by Robo Signaling Levels, in Cell, 174(3), 590-606.e21.
Bifurcation Analysis of Reaction Diffusion Systems on Arbitrary Surfaces
Dhillon Daljit Singh J., Milinkovitch Michel C., Zwicker Matthias (2017), Bifurcation Analysis of Reaction Diffusion Systems on Arbitrary Surfaces, in Bulletin of Mathematical Biology, 79(4), 788-827.
A living mesoscopic cellular automaton made of skin scales
Manukyan Liana, Montandon Sophie A., Fofonjka Anamarija, Smirnov Stanislav, Milinkovitch Michel C. (2017), A living mesoscopic cellular automaton made of skin scales, in Nature, 544(7649), 173-179.
The anatomical placode in reptile scale morphogenesis indicates shared ancestry among skin appendages in amniotes
Di-Poï Nicolas, Milinkovitch Michel C. (2016), The anatomical placode in reptile scale morphogenesis indicates shared ancestry among skin appendages in amniotes, in Science Advances, 2(6), e1600708-e1600708.

Collaboration

Group / person Country
Types of collaboration
Scientific and Parallel Computing Group / UNIGE Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Research Infrastructure
Quantum Materials Group / UNIGE Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Research Infrastructure

Associated projects

Number Title Start Funding scheme
183529 Multiphoton confocal microscope for multimodal tissue imaging and fluorescence lifetime measurements 01.02.2020 R'EQUIP
179431 Evaluating the roles of geometry and physical processes in the development and evolution of skin appendages and skin colour patterns in reptiles 01.06.2018 Project funding (Div. I-III)

Abstract

A few years ago, I obtained a SINERGIA grant together with Prof. Matthias Zwicker (Computer Science, Bern) and Dirk van der Marel (Condense Matter Physics, Geneva) with the ambition to initiate integration of biological, physical, and computer science approaches for a better understanding of skin colours and patterns of skin appendages and colour in amniotes. The skin appendages and pigmentation systems in vertebrates are promising model systems because species exhibit astonishing variations in skin appendage morphologies, as well as colour and colour patterns generated by pigments (black/brown, yellow and red) and structural elements (photonic crystals) incorporated into various types of chromatophores and iridophores, respectively. This variation is of great ecological importance as scales, feathers, hairs, and spines provide mechanical protection, and colours play critical roles in thermoregulation, photoprotection, camouflage, display, and reproductive isolation (hence, speciation). Our SINERGIA project was a success as we (a) Developed innovative robotics and computer graphics methods for automated phenotyping of skin surface (Martins, et al. 2015), (b) Used these developments for the analysis of scale patterns in crocodiles, a study that allowed us to uncover an entirely new developmental mechanism (Milinkovitch, et al. 2013), (c) Characterised unique multi-sensory micro-organs in the skin of crocodiles (Di-Poi and Milinkovitch 2013), (d) Characterised the development of skin appendages in the spiny mouse (Montandon, et al. 2014), (e) Characterised through histology, mass-spectrometry, photonic methods, and in-silico simulations the interactions between photonic nanostructures and pigmentary elements that generate extensive colour pattern variation in Phelsuma lizards (Saenko, et al. 2013), (f) Used mitochondrial and nuclear DNA data and Support-Vector-Machine (SVM) approaches to characterise the phylogeography of colour pattern variation in panther chameleons (Grbic, et al. 2015), (g) Combined biology and photonics to show that chameleons shift colour through active tuning of a lattice of guanine nanocrystals within a superficial thick layer of dermal iridophores (Teyssier, et al. 2015), (h) Characterised the physical parameters of surface-grating nano-structures (using electron and atomic-force microscopy) that are responsible for iridescence in snakes, and (i) used the knowledge acquired in point h to develop a new technique for computationally-effective and interactive simulation and rendering of diffraction effects produced by such biological nano-structures (Dhillon, et al. 2014). In addition, for linkage-mapping analyses, we have been continuously establishing, these last six years, families of corn snakes and lizards segregating mono-locus skin colour and colour pattern phenotypes.In the present multidisciplinary project, I propose to capitalise on our collaborations and combined expertise in computer science, physics and evolutionary developmental biology for the identification of the physical and biochemical self-organisation mechanisms underlying the formation of skin pigmentation and skin structural colours in squamate reptiles. This will require the development of biological and physical assays as well as new computer science methods, but the project will be greatly facilitated by the equipment, methodologies, and biological material, as well as the close multidisciplinary collaborations, that we have developed in the past. First, we will finalise the linkage mapping analysis of colour pattern mutations in snakes to identify the genes involved in these spectacular phenotypes. Second, we will produce ex-vivo culture of embryonic skin and tissue-disrupted in-vitro cell cultures from reptilian skin and we will treat these samples with pharmacological agents and CRISPR/Cas9 transgenesis to characterise the role of the identified (by linkage mapping) pathways in normal and mutant patterning. In parallel, we will improve and extend our 3D geometry and colour texture acquisition pipeline, perform quantitative analyses of phenotypes, characterise their variation, track changes during their development, and develop mathematical models to simulate pattern formation using Partial-Differential-Equations, Finite-Element and multi-resolution and Cell Automata Methods, all guided by our results on ex-vivo and in-vitro cultures. Third, we will perform hyperspectral imaging and advanced photonic crystallography (using scatterometry and near-field techniques) in chameleons, other lizards and snakes. These analyses will uncover the detailed physical and biological mechanisms explaining how squamate reptiles generate and manipulate structural colours, for example for changing colour during display as shown in our recent article on chameleons (Teyssier et al. 2015). The project is at the frontier between the physics of biology and evolutionary developmental biology. My multidisciplinary team of researchers (including physicists, computer scientists, developmental biologists, and evolutionary biologists), as well as the access to the laboratory equipment and competences in photonics of Prof. Dirk van der Marel’s team, will greatly facilitate our analyses of the evolution and ecological significance of signalling pathways and self-organisational phenomena involved in the determinism of adaptive skin colours and colour patterns.
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