• Signaling pathways, Hugo Caumon (November 21st 2023)

Cell communication is an omnipresent concept in the study of the regulation of development. Processing of developmental signals by cells is a key step of this communication, and such processing occurs through signaling pathways. In this Back To Basics session, I started by giving a general introduction to the concept of communication, and used the example of spoken communication between two persons as an analogy to define the different steps of cell communication. The definition of "signaling pathway" I chose here englobes three of these steps : signal perception, signaling cascade and cell response.

In the first part of the talk (1), after explaining the functional properties of proteins (the main molecular actors of signaling pathways), I described how these properties allow to convey information within a signaling pathway, via a signaling cascade starting from the receptor and leading to cell response (which can be either gene expression, or the activation of particular effector proteins). In the second part of the talk (2), I presented 3 emergent properties of signaling pathways (amplification, feedback and specificity), and demonstrated their importance in the processing of signals during development.

The take-home message of this Back to Basics is that (1) signaling pathways can be defined as a set of molecular event which bridge signal perception to cell response, and (2) their emergent properties provide complexity in response dynamics, and increase the potentiality of responses, enabling different cells to respond differently to the same signal.

In this respect, signaling pathway are not only a flow of information from the receptor to the targets of the signal, but actively contribute to modulate the information provided by the signal, and to define the nature and dynamics of the cellular response, depending on the developmental context (i.e. which cell receives the signal, in which tissue and at what time during development the signal is received).

• Phylogenetic trees, Marie Monniaux (November 7th 2023)

We often encounter phylogenetic trees in publications, and it is important to know what they are and how we should read them. I briefly explained what is a tree, how we build a tree (using coding or non-coding DNA, depending on the scale we are interested in) and the difference between a species tree and a single-gene tree. The main points to remember are that branches can be flipped around nodes, and that each tree has a focus point (a group that is more thoroughly described than others), which gives the false impression that some clades are "more evolved" than others, although they all reached the same point in evolution. I also listed the wrong terms to use (ancestral, lower plants, primitive, more evolved...), the ok-ish terms to be used with much caution because they depend on how the tree is drawn (basal, early-diverging) and the right terms to use (the actual names of the groups).

• Western blots, Françoise Moneger (October 17th 2023)

• Machine learning, Romain Azaïs (September 26th 2023)

• Random walk and diffusion, Julien Derr (June 13th 2023)

By establishing a link between random walk and diffusion, we have discussed the characteristics of the temporal evolution of a diffusion field. Using orders of magnitude typical of living systems, we have demonstrated the importance of diffusion in biology.

• Dynamical systems, Jeanne Abitbol-Spangaro (May 30th 2023)

• Curvature, Christophe Godin (May 23rd 2023)