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Multiscale Studies of Segmentation in Vertebrate Embryos

Contents

• Contact Information
• Funding Agency 
• Research Emphasis 
• Scales Examined 
• Biomedical, Biological &  Behavioral Areas
• Modeling Methods & Tools  
• Software Development 

Contact Information

Principal Investigator/Contact
James Glazier
Indiana University
Phone:(812) 855-3735
Fax:(812) 855-5533
Email: glazier@indiana.edu 
Project Websites
http://www.biocomplexity.indiana.edu
http://sourceforge.net/projects/compucell/
http://www.informatics.indiana.edu/schnell/research/embryology.asp 

Co-PIs and Collaborators
Santiago Schnell
Indiana University
Phone (812) 856-1833
Fax: (812) 856-1995
Email: schnell@indiana.edu
Web http://www.informatics.indiana.edu/schnell/

Charles Little
University of Kansas Medical Center
Phone: (913) 588-7000
Fax: (913) 588-2710
E-mail: clittle@kumc.edu
Web http://www.kumc.edu/anatomy/little.html

Mark Alber
Notre Dame University
Phone (574) 631-8371
Fax: (574) 631-6579
Email malber@nd.edu
Web http://www.nd.edu/~malber/ 

Grant Number - 1-R01-GM-076692-01

Funding Agency

National Institute of General Medical Sciences (NIH-NIGMS)

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Research Emphasis

In vertebrates, segmentation during early embryogenesis forms somites (paired blocks of mesoderm cells along the vertebrate body axis that form during early vertebrate development.) Segmental structures give rise to the ribs, vertebrae, limbs, associated muscles, and central and peripheral nervous system. Failures in segmentation can be lethal or can cause serious developmental abnormalities.

This project will test the hypothesis that during segmentation, physical forces and biomaterial properties must coordinate with a moving biological oscillator, the segmentation clock, for successful somitogenesis. The software developed will form the core of an open-source, multiscale and general purpose Tissue Simulation Toolkit, which other researchers can apply to various developmental problems.

The proposed research addresses the causes of  significant  developmental malformations which occur in approximately 150,000 infants born each year in the USA (1 out of 28 births). Disturbing somite formation results in Klippel-Feil syndrome, Spondylocostal Dysostosis, Jarcho-Levin syndrome, congenital scoliosis and kyphosis, Goldenhar syndrome, and Spina Bifida, among others disorders. Studying the developmental mechanisms in vertebral patterning will aid in the identification of protective or potentially disruptive factors for normal somitogenesis. This could potentially have an impact on the treatments for the prevention of vertebral patterning disorders. 

Abstract

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Scales Examined 

Time Scales

• Second(s)
• Minutes
• Hours
• Days
• Months

Biological Scales

• Molecular
• Molecular Complexes
• Sub-Cellular
• Cellular
• Multi-Cellular Systems
• Tissue
• Organ
• Organ Systems 

Length Scales 

• Micrometer (μm)
• Millimeter (mm)
• Centimeter (cm)
• Ten centimeter

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Biomedical, Biological and Behavioral (BBB) Areas and Percent Focus

60% - Developmental Biology, Morphogenesis, Gastrulation, Somitogenesis, Cell Tracking, Cell Fate Determination, Cell Differentiation, Biological oscillators, Vertebrate Segmentation, Pattern Formation, Vertebral Precursors, Congenital Vertebral Diseases.

Modeling Methods and Tools (MMT)Areas and Percent Focus

40% - Cellular Potts Model, Ordinary Differential Equation, Boolean Functions, Partial Differential Equation, Finite Elements, Stochastic Modeling.  

Software Development