How we do it

In the laboratory

We perform experiments with multiple state-of-the art techniques in molecular developmental genetics. Among others, we use in-situ hybridisation and immunostaining of both histological sections and whole-mount tissue samples. In addition, we routinely perform bulk RNA and single-cell sequencing of targeted tissues. Note that we also combine our RNAseq data with whole genome sequencing (Illumina, HiC, PacBio) to assemble and annotate chromosome-quality genomes. These genomes help us to identify the causative mutations of morphological traits on the basis SNP co-segregation in breeding families established with our animal models. Last but not least, we have produced the world’s first transgenic snakes and we now routinely use this approach in snakes and lizards.

Our animal models

The LANE also includes an exceptional, if not one-of-a-kind, animal facility directed by Dr. Athanasia Tzika. Indeed, most of our experiments with animals involve non-classical ‘exotic’ mammalian and reptilian model species that can teach us about unknown and exciting biological and physical processes generating this complex and diverse living world. Below, we succinctly list and introduce our main model species. You can search for our articles associated with each of these species by selecting the corresponding species name(s) in the list of keywords on our ‘Publications’ page.

For two general articles about new models species, please refer to:

Reptilian models

  • Furcifer pardalis (the panther chameleon)
  • Phelsuma grandis (the Madagascar giant day gecko)
  • Timon Lepidus (the ocellated lizard)
  • Salvator merianae (the black & white tegu)
  • Varanus indicus (the mangrove monitor)
  • Heloderma suspectum (the Gila monster)
  • Phelsuma standingi (the Standing's day gecko)
  • Geckolepis maculata (the fish-scale gecko)
  • Pogona vitticeps (the central bearded dragon)
  • Chlamydosaurus kingii (the frilled lizard)
  • Eublepharis macularius (the leopard gecko)
  • Pantherophis guttatus (the corn snake)
  • Lamprophis/Boaedon fuliginosus (the African house snake)
  • Crocodylus niloticus (the Nile crocodile)
  • Gallus gallus domesticus (the chicken)

Learn more…

Mammalian models

  • Acomys dimidiatus (the eastern spiny mouse)
  • Atelerix albiventris (the African pygmy hedgehog)
  • Echinops telfairi (the lesser hedgehog tenrec)

Learn more…

Imaging

Microscopy

Our experimental approach makes extensive use of the latest technologies that facilitate volumetric imaging of biological samples at the cellular and tissue scales. For example, the Photonic Bioimaging Center of the Biology Division provides us with a range of advanced Light sheet fluorescence microscopy (LSFM) and confocal fluorescence microscopy systems.  

LSFM uses a thin sheet of light to excite fluorescent labels within a sample, such as signal from nuclear staining or antibodies. By moving the sample (or the sheet of light) up or down whilst acquiring a series of images, we can generate 3D data that includes multiple different signals. This allows us to precisely capture complex tissue geometries and molecular signalling. One cutting-edge LSFM system — the Ultramicroscope Blaze — is of particular interest to our laboratory because it is adapted to the imaging of samples that can vary dramatically in size and composition, including embryonic crocodile jaws and embryonic elephant trunks.

The Light Sheet Fluorescence Microscope

Feather buds on the wing of the embryonic chicken (E12) stained with TO-PRO-3 Iodide (nuclear staining).

Confocal microscopy uses a highly-focused beam to illuminate the sample that is being imaged. This beam scans across the sample sequentially to illuminate an entire 2D plane. The process is repeated for successive planes to produce a 3D image. By blocking out-of-focus light, confocal microscopy precisely excites fluorescent signals found within our samples, and allows us to capture data at higher resolutions. However, the speed of acquisition is slower than for light-sheet imaging.

Note that we have developed a simple and robust method of whole-mount staining with the ‘Fast Green’ dye that provides unmatched visualisation of 3D collagen network architecture, via confocal or light-sheet microscopy.

R2OBBIE-3D

Phenotypes at larger scales (i.e., larger than those probed with LSFM and confocal microscopy) remain poorly amenable to quantitative analyses. To partially resolve that problem, we have developed R2OBBIE-3D, an integrated system that combines a robotic arm, a high-resolution digital colour camera, an illumination basket of high-intensity light-emitting diodes, and state-of-the-art 3D-reconstruction approaches. R2OBBIE generates accurate 3D models of biological objects between 1 and 100 cm, integrating colour-texture and geometry with a resolution of around 15 to 40 μm without the use of magnifying lenses! We extensively use R2OBBIE to study the dynamics of skin colour patterning in lizards and snakes (e.g., Nature 2017; Nature Communications 2021; Physical Review Letters 2022; Current Biology 2022).

Reference

  • R2OBBIE-3D, a Fast Robotic High-Resolution System for Quantitative Phenotyping of Surface Geometry and Colour-Texture
    Martins A., Bessant M., Manukyan L., M.C. Milinkovitch
    PLOS ONE 10, 6 : e0126740 (2015)

Softwares

  • MetaPIGA v3.1

    MetaPIGA is a versatile and easy-to-use software that implements robust  stochastic heuristics (including the Metapopulation Genetic Algorithm,  metaGA) for large phylogeny inference under maximum likelihood. MetaPIGA  allows analyses of binary and molecular data sets under multiple  substitution models, Gamma rate heterogeneity, and data partitioning.   The software is for all types of users as it can be run through an  extensive and ergonomic graphical interface, or by using batch files and  console interface on your local machine or on distant servers.  MetaPIGA  is platform independent, and easily takes advantage of GPU and  multicore computing.

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  • LANE runner

    A JAVA application developed to facilitate the annotation of de novo  sequenced transcriptomes. It was extensively used for the Reptilian  Brain Transcriptome project (Tzika et al.2011) and for building the  subsequent Reptilian Transcriptomes 2.0 database (Tzika et al. 2015).

    Download…

Resources for students