Practical course on Animal Diversity and EM sample preparation
By Asli Kilic, Doctoral candidate, Arendt lab-EMBL.
The very first ZooCELL practical course took place at the Centre of Organismal Studies (COS) in Heidelberg, Germany, from February 3rd to 14th, 2025. This hands-on course on “Animal Diversity and EM Sample Preparation” marked the first time all the doctoral candidates and principal investigators of the network came together for an intensive two-week program.
ZooCELL group photo. DCs, PIs and trainers during the practical in Heidelberg.
The course featured insightful lectures on volume electron microscopy (vEM) techniques and sample preparation, alternative imaging methods like X-ray tomography and expansion microscopy (ExM) as well as lectures on evolutionary biology and current research in the field represented by a wide-range of model organisms. As fellows, we had the exciting opportunity to present our research project during a poster session where we shared ideas with the PIs, trainers and other fellows.
The highlight of the event was the hands-on two-week practical training where we learned various sample preparation methods ranging from high-pressure freezing and chemical fixation to sectioning with an ultramicrotome. We also gained hands-on experience in imaging techniques like scanning electron microscopy (SEM) for Array Tomography and FIB-SEM.
DCs at the EMCF at Heidelberg University during the practicals.
Special thanks to Réza Shahidi and Charlotta Funaya from the EMCF at Heidelberg University, to Chandni Bhickta, Paolo Ronchi, and Inés Romero Brey from the EMCF at EMBL Heidelberg for hosting and training us, and to Alexandra Kerbl, Karel Mocaer, Sanja Jasek and Gáspár Jékely from COS for organizing the event and for their commitment to training us.
DCs during the chemical fixation practical session at COS.
ZooCELL Project Launches with Vibrant Kickoff Meeting
The inaugural ZooCELL kick-off meeting convened in the scenic setting of Ischia, Italy, from April 12th to 14th, 2024. This in-person gathering brought together ZooCELL’s Principal Investigators for a series of engaging sessions and discussions.
The meeting started with a training session led by Martina Peskoller-Fuchs, focused on fostering constructive and healthy interactions with PhD candidates. The program also included updates on the project’s implementation status, highlighting milestones, deliverables, and recruitment progress.
Detlev Arendt, the project coordinator, was in charge of giving a scientific introduction to the project and outlining ZooCELL’s objectives and work packages. PIs then presented their laboratories and planned network projects, setting the stage for collaborative research endeavors. The meeting concluded with fruitful discussions on event planning, laying the groundwork for future practical courses and graduate schools.
The kickoff meeting marked a significant milestone in the ZooCELL project. Stay tuned for updates as the project advances towards its goals.
DC12: “Evolution of sensory systems for polychaete larval behaviour and development”
Host and PhD Awarding institution: University of Exeter (UNIEXE)
Primary Supervisor: Dr. Elizabeth Williams
Project duration: 36 months.
Project description: This project will compare the head sensory systems (antennae, cirri, nuchal organ) of closely related nereid polychaete species Platynereis dumerilii and Platynereis massiliensis. Platynereis dumerilii has free-swimming larvae while Platynereis massiliensis shows direct development. Initial studies indicated that sensory structures in P. massiliensis are reduced, for example, they lack antennae. The PhD candidate will analyse an available synapse-resolution serial EM dataset of a Platynereis dumerilii larva and obtain and analyse an EM series of an equivalent stage Platynereis massiliensis larva in collaboration with Professor Gaspar Jekely’s group at the University of Heidelberg. All neurons projecting from sensory head appendages will be reconstructed in both species. Synaptic connectivity maps will be complemented by the comprehensive mapping of conserved proneuropeptides and neurotransmitters and their receptors by a combination of immunostaining and hybridization chain reaction (HCR). The PhD candidate will also generate an atlas of neuroendocrine and nervous system markers in P. massiliensis for comparison with existing data from P. dumerilii. The candidate will compare cellular phenotypes at nanometer resolution between the two species with benthic vs pelagic development and correlate this with neuroendocrine molecular maps. To dissect inter-specific functional differences, the candidate will use neuropeptide pharmacology in both species. By comparing nervous system morphology and signalling in closely related pelagic and direct developing polychaete larval types, this project will contribute to our understanding of the evolution of larval sensory systems for navigation in the sea.
Required applicant profile: Applicants should have a Masters or First Class Honours degree in science, preferably in Biology, or equivalent qualifications. Practical experience in molecular, cell or developmental biology, microscopy (electron microscopy, confocal microscopy), behavioural and/or image analysis will be an advantage, however training for specific techniques will also be provided on the project. Applicants should have a strong enthusiasm for larval biology, sensory systems, evolution, development and/or marine biology and be able to work both independently and as part of a team.
Application deadline: 14th April 2024
How to apply: Applications should be submitted online. Interested candidates may contact Elizabeth Williams (e.williams2@exeter.ac.uk) to discuss the post.
DC 11: “Homology of diverse lophotrochozoan larval types and the characterisation of apical organs”
Host and PhD Awarding institution: University College London (UCL), UK
Primary Supervisor: Prof. Dr. Max Telford
Project duration: 36 months.
Project description: Many marine animal species have indirect development via a larval stage – this is particularly true of the phyla within the major clade of Lophotrochozoa. These larvae are, at least superficially, similar across phyla but their homology is uncertain. The student will compare a distinctive larval feature that is similar across lophotrochozoan larvae – the apical organ. The student will analyse individual component cells of apical organs of multiple animal phyla (with a focus on the flatworm Prostheceraeus crozieri and the phoronid Phoronis mueller) they will characterise gene expression, cellular phenotype and connections between these cells and with other cells (eye spots, ciliary bands etc.). Demonstration of complex similarities would support homology of this larval structure across phyla. Broader comparisons will be made possible by collaboration across the network. The student will also be able to participate in work to resolve the phylogeny of the Lophotrochozoa.
Required applicant profile:
- Experience in molecular biology and embryology methods is essential
- Electron microscopy and bioinformatics are advantageous
- A background in evolutionary biology is beneficial.
- A high motivation and passion for science is essential.
Application deadline: 30th June 2024.
How to apply: To apply for this position, visit the following link.
When applying you will be asked to supply: a cover letter, your Curriculum Vitae and MSc & BSc diploma incl. Grade Transcripts.
DC10: “From transcriptome to morphome: development of a correlative toolbox to perform vEM on targeted cell types”
Host: European Molecular Biology Laboratory (EMBL), DE.
PhD Awarding institution: Heidelberg University (UHEI), DE.
Primary Supervisor: Dr.Yannick Schwab.
Project duration: 36 months.
Project description: The morphome quantitatively describes morphological diversity at multiple scales: At the subcellular level, the set of organelles, their arrangement and associations define functional units that are relevant to cell types (e.g. sarcomeres in muscles, secretory granules in gland cells). The correlation of expression profiles to ultrastructural phenotypes has so far been very difficult. In this project, will focus on the development of tools to bridge scRNAseq to volume Electron Microscopy (vEM), with the specific goal to identify cell types by their expression profile and target these for detailed sub-cellular description by vEM and subsequent image analysis. Within the consortium, collaborations will lead to the investigation of a few model systems (D.Priapulus, Novocrania, and/or Acanthochitona), with a strong focus on the planula larva of the hydrozoan Clytia, in close collaboration with the group of Evelyn Houliston (CNRS-IMEV). The PhD candidate will i) develop correlative in-situ hybridisation and transmission EM workflow to identify cell types and to then ii) further their morphological characterisation by acquiring vEM datasets and iii) performing detailed image analyses (in collaboration the Kreshuk lab). Resulting in a detailed description of the subcellular landscape, iv) parallels will be sought with the corresponding single-cell transcriptomes.
Application deadline: 11th March 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 Yannick Schwab.
DC9: “Orientation in lophophorates”
Host institution: Museum für Naturkunde Berlin (MFN), DE
PhD Awarding institution: Humboldt-University Berlin (HUBER), DE
Primary Supervisor: Prof. Dr. Carsten Lueter
Project duration: 36 months
Project description: The candidate will conduct an in-depth study of the morphology of the frontal nervous system and esp. apical organs based on serial electron microscopy (TEM, FESEM) to 3D-reconstruct (1) the shape of individual neuronal cells in apical organs and the surrounding nervous system inkl. receptor cells, (2) the interconnection between these and the frontal nervous system, and (3) the overall architecture of these sensory structures. Supported by scRNA-seq data partly gathered during the preceding project EvoCELL, immunohistochemistry and new AI-technologies the candidate will characterize developmental stages of the inarticulate brachiopod Novocrania anomala, to be collected at Bergen, Norway, and compare them to data on other lophophorate and lophotrochozoan groups investigated within work packages 1-4 of the ZooCELL network. The goal is to finally decipher interdependencies between nervous system morphology (plasticity) and developmental and environmental cues in these groups. Additionally, as the MfN coordinates the science outreach part of the project, the candidate will be involved in the setup and maintenance of the project’s homepage and activities related to science communication.
Required applicant profile: The candidate preferably has a background in evolutionary morphology of invertebrates and is familiar with high-resolution microscopy techniques, such as TEM, SEM, CLSM etc. Knowledge in molecular biology and a strong interest in science communication are advantageous.
Application deadline: 30th November 2024
How to apply: To apply to this position, visit the following link. See “academic staff” section.
**Applications will be accepted from 1st March 2024**
DC8: “Comparative structure and evolution of the ecdysozoan head”
Host institution and PhD Awarding institution: Uppsala University (UU), SE
Primary Supervisor: Dr. Graham Budd
Co- Supervisor: Dr. Ralf Janssen
Project duration: 36 months
Project description: The priapulid worms are a particularly interesting group as they are large and very poorly studied; furthermore, they bear a close resemblance to worms present in the Cambrian fossil record. In order to elucidate the origin of derived ecdysozoan anterior systems, DC8 will therefore study the detailed cellular morphology of the anterior of the priapulid worm Priapulus caudatus, using electron microscopy (array tomography SEM, TEM, DESEM). DC8 will also generate a single-cell transcriptomic dataset for Priapulus. The data on its cellular morphology thus obtained will then be compared to EM data on other ecdysozoans, notably the worm C. elegans, and the onychophoran Euperipatoides. In particular, the structure of the nervous system and any sensory structures, essentially unknown up to now, will be characterised and compared in a phylogenetic context. This project will be placed within an evolutionary framework informed by the excellent fossil record of ecdysozoan evolution in the Cambrian.
Required applicant profile: Applicants should have a Masters degree in science, preferably in Biology. Practical experience in microscopy and/or image analysis will be an advantage. Strongly motivated students from other disciplines (e.g. palaeobiology) are also encouraged to apply. Applicants should be able to communicate fluently in English.
Application deadline: 5th March 2024
How to apply: Interested candidates in the first place should contact Graham Budd (graham.budd@pal.uu.se) who will direct them to the appropriate link when it is available.
DC7: “Application of a high-throughput array tomography vEM pipeline to study the diversity of marine larvae and sensory cell types”
Host institution and PhD Awarding institution: Centre for Organismal Studies (COS) – Heidelberg University, DE.
Primary Supervisor: Prof. Dr. Gaspar Jekely.
Project duration: 36 months.
Project description: The project will offer in-depth training in the volume electron microscopy (vEM) of marine larvae. One goal will be to obtain a high-quality full-body EM volume of a six-day-old Platynereis dumerilii juvenile and analyse the volume in collaboration with other students of the network. The successful candidate will also be instrumental in coordinating other vEM projects in the network. The project will also include extensive data analysis, including skeletonisation, working with volume-segmented data, cell-type and connectome annotation, and network analysis. The project will inform the evolution of larval form and sensory cell types.
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 (e.g. physics, biophysics) are also encouraged to apply. Applicants should be able to communicate fluently in English. German language skills are not required.
Application deadline: Provisional deadline is 31st October 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 gaspar.jekely@cos.uni-heidelberg.de
- A motivation letter describing your research interests and why you apply for the position
- Your Curriculum Vitae
- MSc&BSc diploma incl. Grade Transcripts
- Contact details of two referees
DC6: “Identification of conserved cellular functional modules in sensory neuron evolution”
Host: European Molecular Biology Laboratory (EMBL), DE
PhD Awarding institution: Heidelberg University (UHEI), DE.
Primary Supervisor: Prof. Dr. Detlev Arendt
Project duration: 36 months
Project description: Our aim to elucidate the evolution of the bilaterian brain requires an in-depth understanding of the sensory cell types that innervate the distinct ancient brain parts such as the mechanosensory girdle and the apical nervous system. We will study the evolution of sensory cell types, with a strong emphasis on head mechanosensory cells and chemo-/photosensory-secretory cells of the apical nervous system. We will focus on marine animal model systems that exhibit a differentiated nervous system at life cycle stages composed of relatively few cells so that whole-body cellular resolution can be obtained, as already shown for the annelid P. dumerilii and as also manifest for pre- and postmetamorphic stages of the chiton Acanthochitona crinita and juvenile nemerteans, which together represent a broad range of Lophotrochozoa phyla and will be studied here. For these animals, we will attempt to create whole-body cellular atlases for pre- and postmetamorphic juveniles in P. dumerlii and A. crinita, and for juvenile nemerteans, in collaboration with other ZooCELL doctoral candidates. This effort will combine gene expression and ultrastructural information for the entire body, as a prerequisite for the identification of coregulated gene sets correlating with co-occurring morphofeatures together with DC1 (EMBL). This way the project aims to find and define conserved cellular functional modules characteristic for mechanosensory and sensory-secretory cell types.
*Application closed*
DC5: “Mapping cell type diversity in the arthropod leg”
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: 15th 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.