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The Bangham Lab

Computational Biology

The aim is to understand how patterns of gene activity in biological organs influence the developing shape.

<sgallery width="140" height="200" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="2000"> LabelledCropped_GPT_Snapdragon_2010-000250-0001.png LabelledCropped_GPT_Snapdragon_2010-000340-0001.png LabelledCropped_GPT_Snapdragon_2010-000490-0001.png LabelledCropped_GPT_Snapdragon_2010-000570-0002.png LabelledCropped_GPT_Snapdragon_2010-000570-0003.png LabelledCropped_GPT_Snapdragon_2010-000570-0004.png LabelledCropped_GPT_Snapdragon_2010-000570-0005.png LabelledCropped_GPT_Snapdragon_2010-000570-0007.png LabelledCropped_GPT_Snapdragon_2010-000570-0006.png LabelledCropped_GPT_Snapdragon_2010-000570-0001.png </sgallery>

More on Snapdragon model

Genes and growing shapes

  • Observed: patterns of gene activity regulate tissue growth.
  • Hypothesis: gene activity independently regulates direction of growth.
  • Formalised in the Growing Polarised Tissue Framework (ref).
  • Implemented in GFtbox to make it easy to develop ideas on growth and form.
  • Start with a sheet of tissue (the canvas) with observed, or hypothetical patterns of growth factor activity.
  • Grow the canvas in 3D under constraints of tissue continuity
  • Compare with observed data quantitatively

Downloads and more details on GFtbox

<sgallery width="140" height="200" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="3000"> LabelledCropped GPT Snapdragon 2010-000570-0003 double.png LabelledCropped GPT Snapdragon 2010-000570-0002 triple.png LabelledCropped GPT Snapdragon 2010-000570-0001-Wildtype.png </sgallery>

More on testing models

<sgallery width="160" height="280" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="1500"> Arabidopsis_Leaf_ATH8bbg.png Antirrhinum flower small1.jpg Antirrhinum flower small2.jpg Antirrhinum flower small3.jpg Anthers1.jpg MacroOPTIris1.jpg </sgallery>

More on visualising 3D

Working with 3D volume images

Three dimensional (3D) volume images are key to understanding the development of shape. They are produced by CT X-ray scanners, MRI and PET. However, biological gene activity is monitored using fluorescent probes and so optical methods are used: confocal microscopy and optical projection microscopy. The resulting images are large and are best viewed using software that exploits powerful graphics processors. We implemented VolViewer which is a viewer of choice in the open microscopy environment.

Downloads and more details on VolViewer

<sgallery width="160" height="280" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="4000"> Arabidopsis_Leaf_ATH8bbg.png </sgallery>

More on 3D measurement

Photos, Algorithms and Art

Tools and Demonstrations

About

The Bangham Lab is part of the UEA D’Arcy Thompson Centre for computational biology.