Host  institution: Institut de Génomique Fonctionnelle de Lyon (IGFL)- CNRS, FR.

PhD Awarding institution: École Normale Supérieure de Lyon (ENSL), FR. 

Supervisors:  Dr. Michalis Averof and Dr. Mathilde Paris.

Project duration: 36 months.

Project description: Arthropod legs are multi-purpose organs, containing diverse cell types involved in sensing (e.g. sensory organ neurons, glia and accessory cells), locomotion (muscles, tendons, joints), protection and immunity (epidermis, blood cells), as well as numerous cell types with unknown functions. The recruited PhD student will generate a multimodal cell atlas, integrating the molecular profiles of more than 15 distinct cell types that make up the arthropod leg with ultrastructural data, and will identify the functions and evolutionary relationships of these diverse cells.

The student will accomplish this in the crustacean Parhyale hawaiensis, which we have already started to explore using scanning electron microscopy and single-cell transcriptomics. Parhyale legs contain more than 15 cell clusters discovered by single-nucleus RNAseq, corresponding to epidermal, neuronal, muscle and blood cells, as well as several yet unknown/uncharacterized cell types. The student will study the Parhyale leg at subcellular resolution using multi-beam SEM, to identify cell types based on ultrastructure, and will associate each of these with the corresponding transcriptional signatures using correlative light and electron microscopy approaches. Microanatomy and transcriptional profiles will provide a rich set of features for exploring the identities of these cells, their functions, and their relationships to the cells of other animals. Genetic tools such as transgene-mediated cell ablation or CRISPR-mediated gene knock-outs (already established in Parhyale) will be used to test the functions of selected cell types and the role of key regulators that define them.

Required applicant profile: Applicants should have a Masters degree in science, preferably in Biology. Practical experience in molecular, cell or developmental biology, microscopy and/or image analysis will be an advantage. Strongly motivated students from other disciplines should also apply. Applicants should be able to communicate fluently in English.

Application deadline: 15^th March 2024

How to apply: To apply for this position, visit the following link. Applicants should submit a motivation letter and a CV in English.

Host  institution: Institut de la Mer de Villefranche (IMEV), FR

PhD Awarding institution: Sorbonne University (SU), FR 

Primary Supervisor:  Dr. Evelyn Houliston.

Co- Supervisor: Dr. Richard Copley.

Project duration: 36 months.

Project Description: Sensory cells around the aboral pole of the hydrozoan Clytia planula larva mediate responses to environmental cues, but their precise nature and function are unknown. DC4 will relate differences in gene transcription between Clytia planula sensory cell types to morphology, function and developmental history. S/he will characterise the structure and organisation of specific types of Clytia planula neural and neurosensory cell, defining their distinct morphological features by light microscopy techniques in combination with vEM (collaboration with other network fellows/EMBL). S/he will extend scRNA-seq datasets to find drivers and effectors of (i) mature cell type identity, (ii) morphology, and (iii) fate specification, determining the function of specific transcription factors identified by these comparisons, and of the corresponding cell types, using gene knockdown approaches. S/he will collaborate with the other network partners to compare cell type genotype/phenotype across species.

Required applicant profile:   Strong motivation for questioning biological mechanisms and concepts. Training in cell, molecular and developmental biology preferred. Bioinformatics skills would be an advantage

Application deadline:  Provisional deadline is 30^th April 2024, but we will be reviewing and processing applications as they are received.

How to apply: Please send the following documents as a single PDF to evelyn.houliston@imev-mer.fr and richard.copley@imev-mer.fr

• A Cover letter. 
• Your Curriculum Vitae.

Host and PhD Awarding institution: Friedrich Schiller University Jena (FSUJENA), DE.

Primary Supervisor: Prof. Dr. Andreas Hejnol.

Project duration: 36 months.

Project description: The research group, headed by Andreas Hejnol, studies the evolution of animal organ systems using a broad diversity of animal taxa (e.g. nemerteans, priapulids, rotifers, gastrotrichs, acoelomorphs). The group is particularly interested in studying the molecular and cellular basis of organ system development using a comparative approach. The project addresses the question about the evolution of gravitational sensory organs across multicellular animals. Different animal lineages use differently shaped organs and cell types for sensing gravitation. Some of these organs are very prominent (statocyst in Acoelomorpha, Cnidaria and ctenophores) in other lineages the gravitational sense, although present, is not yet discovered. The aim of this project is to use single-cell transcriptomics, in situ hybridization and ultrastructural methods to characterize in detail gravitational sense organs in different animal lineages. The candidate will conduct comparative developmental transcriptomic analyses, detect commonalities and differences in different gravitation-sensing organs in e.g. acoelomorphs, priapulids, brachiopods and hemichordates.

The embryology/development and differentiation of these tissues will be studied using techniques such as Histology, Transmission Electron Microscopy, molecular biology, live-imaging, and single-cell sequencing. The successful candidate will work in close association with the group leader and other lab members with the aim to eventually contribute to the further development of the project in line with his/her interests.

Required applicant profile:

•       Experience in molecular biology and embryology methods is essential while experience in morphology and bioinformatics is highly desirable.
•       A background in evolutionary biology is beneficial.
•       A high motivation and passion for science is essential. 
•       Ability to work both independently and in close collaboration with others in a structured manner.

Application deadline: 20^th March 2024

How to apply: **An application link will soon be provided**

Host  institution: Stazione Zoologica Anton Dohrn (SZN), IT.

PhD Awarding institution: Friedrich Schiller University Jena (FSUJENA), DE. 

Primary Supervisor:  Dr. Maria I. Arnone.

Co- Supervisor: Prof. Dr. Andreas Hejnol.

Project duration: 36 months.

Project description: The sea urchin pluteus larva spends from few to many weeks in the water column, where it is exposed to a complex environment. Therefore, these larvae have evolved mechanisms to adapt to changing, e.g., temperature, light, food conditions. A well-described example is the phenotypic plasticity of larvae depending on food availability that produces plutei with longer arms when food is scarce. Building on the previous knowledge acquired in the Arnone lab, where a pair of photoreceptor cells producing the TRH neuropeptide (TRHergic-PCRs) placed at either side of the Apical Organ (AO) were found to mediate phenotypic plasticity, the project aims at: i) reconstructing the microanatomy and connectome of the Paracentrotus lividus 4 day larva AO using serial vEM;  ii) obtain a single cell transcriptomics atlas of the 4-day larva; iii) placing the transcriptionally identified AO sensory cells and adjacent TRHergic-PCRs onto the 3-D ultrastructural map using correlative microscopy approaches; iv) map the interconnection between the TRHergic-PCRs and the anterior nervous system; v) functionally perturb sensory signalling by pharmacology and/or gene loss of function.

Required applicant profile: Experience in developmental and/or evolutionary biology, electron microscopy, bioinformatics or neurobiology is advantageous.

Application deadline: 28^th June 2024

How to apply: To apply to this position, visit the following link.

Host: European Molecular Biology Laboratory (EMBL), DE.

PhD Awarding institution: Heidelberg University (UHEI), DE.

Primary Supervisor: Dr. Anna Kreshuk.

Project duration: 36 months.

Project description: Morphological analysis of cells in tissues is contingent on our ability to perform cell segmentation in vEM image stacks. While an expert biologist can delineate cell membranes in vEM data manually, this approach does not scale beyond a few cells of interest, making automated cell segmentation algorithms a prerequisite for whole-organism and cross-organism analysis. State-of-the-art segmentation methods, such as the ones used in recent atlas-building efforts or large-scale connectomics studies, operate in the paradigm of supervised machine learning, training the neural networks on densely (manually) annotated reference sub-volumes of the data. The first objective of this project is to significantly relax the requirements to the amount and density of training data, enabling practical use of such methods for multiple datasets from different species acquired on different microscopes. The second objective is to establish a set of unbiased descriptors of the segmented cells, including both shape and ultrastructure features which will allow to group and explore morphologically similar cells across organisms. In addition to cellular-level descriptors, we will develop methods to characterise areas of tissue and enable the search for similar features across datasets. In more detail, we will approach automatic segmentation as both a transfer learning problem from the few available datasets, including the Platynereis dumerilii atlas, and a weakly supervised segmentation problem where manual labels for novel ultrastructural elements will be introduced in a targeted manner. Building on recent success stories for single-cell morphology analysis, our cell descriptors will be based on unsupervised machine learning, exploiting biological priors and targeted manual labels for validation and quality control.

Application deadline: 14^th October 2024

How to apply: Candidates shall apply via the EMBL International PhD program at the following link and express their interest in this position within the group of Anna Kreshuk.