Patterning embryos with genetic oscillations; the mechanisms of vertebrate segmentation

Lead Research Organisation: MRC National Inst for Medical Research

Abstract

The backbone's segmental anatomy forms in the vertebrate embryo by a remarkable process that defines the position of each vertebra with the tick of a genetic clock. When this clock fails, children are born with severe spinal malformation. Using zebrafish embryos to observe this clock ticking in real time, we will investigate the dynamics and the control of its molecular clockworks. We will investigate firstly how each of the cells ticks in isolation, secondly how these cells communicate with their neighbors so that they tick smoothly with a shared rhythm, and finally how the oscillations can be stopped and their time can be recorded to give a signal for the boundary of each newly forming vertebral body segment. These studies will give insight into the way our body axis segments. They will also suggest to us how rapid changes in gene activity are controlled and coordinated in other important contexts such as inflammation and stem cell differentiation, where oscillations have just recently been discovered.

Technical Summary

The segmentation clock is a new paradigm for embryonic patterning in which a rhythmic signal is coordinated with the growth of the tissue to produce a remarkable level of anatomical precision. Thousands of individually noisy oscillating cells are coordinated to give a tissue-level coherence in time and space. Understanding this emergent behavior will give general insight into how biological systems give rise to robust behavior across wide temporal and spatial scales despite being composed of noisy, stochastic components. Signaling pathways of interest in cancer and stem cell regulation such as Delta-Notch, Wnt, and FGF are also involved in regulating the segmentation clock during development. The segmentation clock thus acts as a sensitive model system for understanding the dynamic mechanisms of these key pathways. When the segmentation clock fails in human embryos, the resulting birth defects are severe congenital scoliosis, and this study will provide information about the basic biology of these defects. Our approach uses novel transgenic zebrafish lines carrying real-time reporters of the segmentation clocks rapid gene expression oscillations, combined with advanced imaging and image processing, molecular genetics, and mathematical modeling. The resulting methodological and conceptual frameworks generated by the interdisciplinary sections of this study will help understand other biological processes with fast fluctuating dynamics such as stem cell differentiation and inflammatory responses. Finally, the organizational principles involved will also be of interest to engineers who seek general design rules for constructing reliable control systems using many individually inexpensive and potentially unreliable parts.

Publications

10 25 50
 
Description Teaching Faculty at KITP MORPHO13
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
 
Description Senior Research Fellow in Basic Biomedical Science
Amount £2,166,980 (GBP)
Funding ID WT098025MA 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 09/2012 
End 09/2017
 
Title her1-YFP BAC transgenic zebrafish (Looping1) 
Description We generated a transgenic zebrafish line which shows accurate genetic oscillations in the segmentation clock. 
Type Of Material Model of mechanisms or symptoms - non-mammalian in vivo 
Provided To Others? No  
Impact We have recently published a paper using this line in July this year. We are in the process of transferring the line into the international zebrafish stock centres in Karlsruhe, Germany and in Eugene, USA. Soroldoni D, Jörg DJ, Morelli LG, Richmond DL, Schindelin J, Jülicher F, Oates, AC. A Doppler Effect in Embryonic Pattern Formation. Science. 2014 July 11;345, 222-225 
 
Title zebrafish SPIM 
Description In collaboration with the CIAL of MRC-NIMR, we are constructing a Selective Plane Illumination Microscope to image the fast and faint genetic oscillations of the segmentation clock in the developing zebrafish embryo. 
Type Of Material Technology assay or reagent 
Provided To Others? No  
Impact Still in progress, proof of principle complete. research imaging to start underway in summer 2014. 
 
Description Cell mobility and signalling dynamics 
Organisation RIKEN
Department RIKEN Chief Scientist Laboratories
Country Japan 
Sector Private 
PI Contribution technique and reagent development, experiments and data analysis
Collaborator Contribution theoretical modelling and data analysis
Impact multi-disciplinary: we do the experiments in the discipline of biology, they make theoretical models in the discipline of physics. Uriu K, Morelli LG, Oates AC. Interplay between intercellular signaling and cell movement in development. Seminars in Cell and Developmental Biology. 2014 Jun 2. pii: S1084-9521(14)00157-8. Uriu K, Ares S, Oates AC, Morelli LG. Dynamics of mobile coupled oscillators. Physical Review E, March 2013, 032911.
Start Year 2008
 
Description Cell mobility and signalling dynamics 
Organisation University of Buenos Aires
Country Argentina 
Sector Academic/University 
PI Contribution technique and reagent development, experiments and data analysis
Collaborator Contribution theoretical modelling and data analysis
Impact multi-disciplinary: we do the experiments in the discipline of biology, they make theoretical models in the discipline of physics. Uriu K, Morelli LG, Oates AC. Interplay between intercellular signaling and cell movement in development. Seminars in Cell and Developmental Biology. 2014 Jun 2. pii: S1084-9521(14)00157-8. Uriu K, Ares S, Oates AC, Morelli LG. Dynamics of mobile coupled oscillators. Physical Review E, March 2013, 032911.
Start Year 2008
 
Description Mechanics of chevron formation in muscle development 
Organisation Technical University of Dresden
Country Germany 
Sector Academic/University 
PI Contribution We carried out genetics, imaging, small molecular inhibitor experiments, and some data analysis on the dynamics of chevron muscle segment formation in zebrafish.
Collaborator Contribution Data analysis from the time-lapse movies, and the development of a mechanical model of chevron formation.
Impact We have recently published the first paper on quantitative analysis and mathematical modelling of chevron formation in the muscle segments of fish. the paper was multidisciplinary. my group carried out the experimental work in the discipline of biology: imaging, genetics, embryological manipulations, and the group of Lutz Brusch at TUD carried out data analysis and mathematical modelling in the disciples of computer science and physics. Rost F, Eugster C, Schröter C, Oates AC, Brusch L. Chevron formation of the zebrafish muscle segments. Journal of Experimental Biology. 2014 Sept; 217, 3870-3882.
Start Year 2007
 
Description Theoretical analysis of the segmentation clock 
Organisation Max Planck Society
Department Max Planck Institute for the Physics of Complex Systems
Country Germany 
Sector Academic/University 
PI Contribution Experimental data, data analysis
Collaborator Contribution Theoretical models and data analysis
Impact Multidisciplinary: We carry out experiments in the discipline of biology; imaging, genetics, manipulations and data analysis. The Jülicher group carries out data analysis and theoretical modelling in the discipline of physics. Papers since entering into ResearchFish: Soroldoni D, Jörg DJ, Morelli LG, Richmond DL, Schindelin J, Jülicher F, Oates, AC. A Doppler Effect in Embryonic Pattern Formation. Science. 2014 July 11;345, 222-225. Bajard L, Morelli LG, Ares S, Pecreaux J, Jülicher F, Andrew C. Oates AC. Wnt-regulated dynamics of positional information in vertebrate segmentation. Development. 2014 Mar;141(6):1381-91
Start Year 2006
 
Title ROI and LOI interpolators 
Description Simple, easy to use software tools for analysing either regions of interest (ROI) or lines of interest (LOI) in time lapse movies. The user defines a ROI or LOI and modify it's shape and location in a sub-set of frames, then the tool creates a smooth interpolation between them for the entire movie, and exports this in several formats. The tools are open source freely available online as part of Fiji. 
Type Of Technology Webtool/Application 
Year Produced 2014 
Impact two publications: Soroldoni D, Jörg DJ, Morelli LG, Richmond DL, Schindelin J, Jülicher F, Oates, AC. A Doppler Effect in Embryonic Pattern Formation. Science. 2014 July 11;345, 222-225 Webb AB, Soroldoni D, Oswald A, Schindelin J, and Oates AC. Generation of dispersed presomitic mesoderm cell cultures for imaging of the zebrafish segmentation clock in single cells. Journal of Visual Experimentation. 2014 (89), e50307, doi:10.3791/50307. 
URL http://www.fiji.sc/Fiji
 
Description 3rd Ask a Nobel Scientist schools event 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? Yes
Geographic Reach Regional
Primary Audience Schools
Results and Impact Clare Davy, Education Officer at the Francis Crick Institute:
"It was a great opportunity for us at the Crick to listen to what young people think are the important issues of modern science, We hope that the event has inspired them to think deeply about the challenges and possibilities of current biomedical research, and we hope that some of them will join us in the future to address these questions."

I spoke to three students about what it is like to do experiments in a lab, and how to choose a research question.

After the panel and discussion, a head teacher approached the organisers to ask if his school could become affiliated with the Crick in some way
Year(s) Of Engagement Activity 2014
URL http://www.crick.ac.uk/news/cricknews/issue-12/students-quiz-scientists/
 
Description See Fish! 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? Yes
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact These demonstrations are extremely popular. Most people have never seen an embryo in real life, and to realise that they can photograph and make movies with their own cell phones is really stimulating. Several member of the lab are present to demonstrate and aster questions. We had many many questions on development, disease, cancer etc., and many requests for the blueprints of the cell-phone microscopes, which we hand out freely.

Following from the first two events, we have had regular invitations to science fairs/open days.
Year(s) Of Engagement Activity 2013,2014
URL http://thenode.biologists.com/outreach-activity-smartphone-to-microscope-conversion/resources/