How we do it

The Lab

As we are interested to decipher processes generating biological complexity and diversity, our research at the LANE is positioned at the interfaces among molecular developmental biology, mathematical modelling and physics of biology. In the wet lab, we adapt existing techniques (and sometimes develop new approaches) to the particularities of the non-classical model species we work on (see below). Besides using basic molecular biology approaches, we have established successful protocols for histological analyses (paraffin and cryosections, immunohistochemistry, laser capture microdissection), whole-mount in-situ hybridisation (fluorescent and chromogenic detection), RT-qPCR, single-cell sequencing, primary cell cultures, ex-vivo tissue cultures, in-ovo drug injections, tissue nanoindentation, and even CRISPR-Cas9 gene-editing in snakes and lizards.

We employ state-of-the-art imaging methods such as bright-field multi-focus imaging, hyperspectral microscopy, fluorescence microscopy, confocal and light-sheet microscopy, scanning and transmission electron microscopy, X-ray and computerised tomography (CT). We also perform 3D surface scanning of skin geometry with structured light as well as with an in-house developed robotic system (R²OBBIE, see below) implementing structure-from-motion and photometric stereo approaches. Most equipments are available in our own lab, in the Genetics & Evolution department or at Bioimaging Centres on campus or at the close-by medical school and hospital.

Our animal models (to be written)

• The corn snake (Pantherophis guttatus):
• ...
• The ocellated lizard (Timon lepidus):
• The panther chameleon: (Furcifer pardalis)
• The  Madagascar giant day gecko (Phelsuma grandis):
• The leopard gecko (Eublepharis macularius):
• ...
• The Nile crocodile (Crocodylus niloticus):
• The chicken (Gallus domesticus):
• The Eastern spiny mouse (Acomys dimidiatus):
• The four-toed pygmy hedgehog (Atelerix albiventris):
• The lesser hedgehog tenrec (Echinops telfairi):
• The greater hedgehog tenrec (Tenrec ecaudatus):

R²OBBIE-3D

R²OBBIE-the-robot is an in-house-developed fast robotic high-resolution system for quantitative phenotyping of surface geometry and colour-texture. R2OBBIE allows us to generate coloured 3D models with a spatial resolution down to 30 microns !  See the video below and check the article for much additional information.

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).

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Softwares for students

• The Evosimulator 2, illustrating how mutations and selection generate complexity.
• The Gray-Scott simulator, illustrating the "complex behaviour from simple model” paradigm using reation-diffusion.