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Team:Newcastle/Project/shape shifting
From 2013.igem.org
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==Our Project== | ==Our Project== | ||
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| + | Unfortunately due to time constraint and our inability to order the high precision master mould for the microfluidics to be made on time we were unable to carry out the experiments we have [https://2013.igem.org/wiki/index.php?title=Team:Newcastle/Project/shape_shifting#Plans planned]. | ||
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| + | ===About Our Project=== | ||
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Most of the bacteria has evolved to have a cell wall - a rigid structure which protects the bacteria from the variety of enviromental hazards such as mechanical stress, osmotic rupture and lysis. The cell wall often sxerves as a docking point to many proteins including various receptors and adherence sites. Along with these properties cell wall provides the cell with a rigid boundary and helps bacteria to acquire and preserve their shape. In ''Bacillus subtilis'' along with other proteins, a group of proteins termed Penicillin Binding Proteins (pbp), usually anchored in the cell wall, is involved in the formation of the rod shape. When the cells lose their cell wall they automatically lose these proteins to the environment as they are being made. The cells lose the support and turn into a sphere as it is the most energetically favourable state (ratio of surface area to volume is minimal, and membrane curvature is more-or-less constant). However it has been previously observed that these cells can become elongated and 'squeeze' into the spaces with a smaller diameter than theirs. | Most of the bacteria has evolved to have a cell wall - a rigid structure which protects the bacteria from the variety of enviromental hazards such as mechanical stress, osmotic rupture and lysis. The cell wall often sxerves as a docking point to many proteins including various receptors and adherence sites. Along with these properties cell wall provides the cell with a rigid boundary and helps bacteria to acquire and preserve their shape. In ''Bacillus subtilis'' along with other proteins, a group of proteins termed Penicillin Binding Proteins (pbp), usually anchored in the cell wall, is involved in the formation of the rod shape. When the cells lose their cell wall they automatically lose these proteins to the environment as they are being made. The cells lose the support and turn into a sphere as it is the most energetically favourable state (ratio of surface area to volume is minimal, and membrane curvature is more-or-less constant). However it has been previously observed that these cells can become elongated and 'squeeze' into the spaces with a smaller diameter than theirs. | ||
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We would also be able to visualise the shape of the cell membrane and confirm our hypothesis by using FM.595 membrane stain to stain the membrane red. This will show that the shape of L-forms can be easily manipulated. | We would also be able to visualise the shape of the cell membrane and confirm our hypothesis by using FM.595 membrane stain to stain the membrane red. This will show that the shape of L-forms can be easily manipulated. | ||
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====30<sup>th</sup> August==== | ====30<sup>th</sup> August==== | ||
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First meeting with Dr.David Swailes, head of fluid mechanics department in the school of Mechanical Engineering at Newcastle University. During the meeting, the underlying physiology of the growth was identified and agreed upon. Based on the physiology, the approach towards the modelling was decided to have three parts: Unrestricted growth, Turning Point and Restricted growth and thus change of the shape. | First meeting with Dr.David Swailes, head of fluid mechanics department in the school of Mechanical Engineering at Newcastle University. During the meeting, the underlying physiology of the growth was identified and agreed upon. Based on the physiology, the approach towards the modelling was decided to have three parts: Unrestricted growth, Turning Point and Restricted growth and thus change of the shape. | ||
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==Modelling== | ==Modelling== | ||
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The full description of the model can be found on this [https://2013.igem.org/Team:Newcastle/Modelling/CellShapeModel page]. | The full description of the model can be found on this [https://2013.igem.org/Team:Newcastle/Modelling/CellShapeModel page]. | ||
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| + | ==Plans== | ||
Revision as of 21:22, 26 September 2013
Contents |
Shape Shifting
Our Project
News
Unfortunately due to time constraint and our inability to order the high precision master mould for the microfluidics to be made on time we were unable to carry out the experiments we have planned.
About Our Project
Most of the bacteria has evolved to have a cell wall - a rigid structure which protects the bacteria from the variety of enviromental hazards such as mechanical stress, osmotic rupture and lysis. The cell wall often sxerves as a docking point to many proteins including various receptors and adherence sites. Along with these properties cell wall provides the cell with a rigid boundary and helps bacteria to acquire and preserve their shape. In Bacillus subtilis along with other proteins, a group of proteins termed Penicillin Binding Proteins (pbp), usually anchored in the cell wall, is involved in the formation of the rod shape. When the cells lose their cell wall they automatically lose these proteins to the environment as they are being made. The cells lose the support and turn into a sphere as it is the most energetically favourable state (ratio of surface area to volume is minimal, and membrane curvature is more-or-less constant). However it has been previously observed that these cells can become elongated and 'squeeze' into the spaces with a smaller diameter than theirs.
This fact has sparked our interest, because the l-form B.subtilis cells can sometimes grow to fairly large sizes before they divide, and we thought it may be possible to fill spaces of various shapes and sizes with them. This ability may be useful to our fellow scientists in many ways such as the following:
L-forms can also be a decent secretory machine, as recombinant proteins which are targeted to the cell will be secreted into the environment. Their flexibility will allow very precise delivery of said proteins to the otherwise hard to reach places ranging from intercellular space to the micro-cracks in solid material.
Microfluidics are a manipulation of fluid in the micro domain. The microfluidics chambers were designed using autoCAD, software used for computer-aided design and drafting, to produce silicon wafer master moulds. Directed flow within the microfluidic wafer will physically maneuver L-form cells into the designed chambers, where they will be maintained by nutrient media. This will enable single cell level analysis for L-forms.
We would also be able to visualise the shape of the cell membrane and confirm our hypothesis by using FM.595 membrane stain to stain the membrane red. This will show that the shape of L-forms can be easily manipulated.
>
News
30th August
The model is working, multiple simulations have been run.
8th August
The rough model outline is now ready. Microfluidics chamber is currently in design.
5th August
Follow-up meeting with Dr.David Swailes. During the meeting, the concepts of the first, and most primitive model were identified. Maths added.
30th July
First meeting with Dr.David Swailes, head of fluid mechanics department in the school of Mechanical Engineering at Newcastle University. During the meeting, the underlying physiology of the growth was identified and agreed upon. Based on the physiology, the approach towards the modelling was decided to have three parts: Unrestricted growth, Turning Point and Restricted growth and thus change of the shape.
<----
Modelling
For the purposes of the study the complex model of the growing cell inside of the confined space can be broken down to simpler models of the system at three phases. The first phase would be a constantly growing cell, followed by a model of the cell gradually adopting the shape of the boundaries.
The full description of the model can be found on this page.
