Difference between revisions of "Team:Paris Bettencourt/Hardware setup"

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<h1>OPTIC MODEL</h1>
 
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<div class=text2left> Medusa aims at controlling bacteria immobilized in a gel thanks to two laser beams. When entering the gel, the laser signal is affected by <b>scattering and absorption <b>. To ensure that the laser kept its adequate properties within the gel, we developed a strategy associating <b> simple light data fitting and modelling </b> to characterize the behaviour of a light beam <b> within a gel. </b> <br>
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Medusa aims at optically controlling bacteria immobilized in a gel. Two questions are important to address to achieve this goal: <br>
  
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We included in our study <b>Agar</b> (the most ubiquitous microbiology gel), <b>Gelrite </b> (which is more transparent than agar) and Alginate (which can be solidified at room temperature by addition of calcium ions). We chose a common working concentration of 1% w/v and studied our with <b>LB nutrient </b>(which surprisingly shows better transmission at most visible wavelengths than the M9 media). refer to our guide to choose the best gel for your optic experiments <br>
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How far can a laser go in a gel? <br>
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What resolution can the laser achieve? <br>
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We present in this page our study of the optical properties of commonly used culture gels. We show that it is possible to obtain a clean light signal even at gel depths greater than 10cm.
  
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The aim of our study is to enable the <b> prediction of the light intensity in all points (x,y,z) of a volume of gel </b> exposed to a laser beam. We employ a simple modelling strategy to represent the absorbance and the diffraction from the laser beam. Once calibrated, our model allows us to predict the <b> light intensity landscape </b> within a gel from a <b>standard cuvette absorbance reading </b>. We compare the predicted landscape to real intensity measurements and demonstrate that our model can accurately predict the resolution of our laser by solidifying light-curing resin particles of the predicted size.
 
  
 
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<div class=text2right>RNA is a light cost nucleotide material in the cell,
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We aim to recreate RNA agglomerations as formed
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<h3> Gel Choice </h3>
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in mammalian cells with triple repeat disorders,
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which show liquid phase separation, forming a
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The optical properties of a gel depends on the gel type, its concentration and the nutrient source. For our study we focused on Agar, Alginate and Gelrite (see table1)
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organelle-like vesicle, where local concentrations of
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enzymes can be created.
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It is best to use a low gel concentration to reduce absorbance. Conveniently some gels have a higher melting point than solidifying point (see fig XX). This hysteresis phenomenon means that the gel concentration can be lowered and still be kept at in a solid state at 37C by pre-cooling them (to 6-8C) prior to warm incubation.
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Alginate gelation is induced by calcium ions which crosslink gelling polymers at room temperature. To get a homogenous gel, calcium ions cannot be mixed with an Alginate solution but must diffuse from an underlying calcium source (1). Since the optical properties of Alginate depends on the amount of crosslinking, they ultimately depend on calcium diffusion which is a difficult parameter  to control. It is important to note that keeping the same diffusion conditions (time, temperature, calcium source concentration etc.) is necessary to maintain identical alginate optical properties between experiments.
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Revision as of 12:52, 31 October 2017

Light Signalling in Gels

OPTIC MODEL

Medusa aims at optically controlling bacteria immobilized in a gel. Two questions are important to address to achieve this goal:
How far can a laser go in a gel?
What resolution can the laser achieve?
We present in this page our study of the optical properties of commonly used culture gels. We show that it is possible to obtain a clean light signal even at gel depths greater than 10cm.

Gel Choice

The optical properties of a gel depends on the gel type, its concentration and the nutrient source. For our study we focused on Agar, Alginate and Gelrite (see table1) It is best to use a low gel concentration to reduce absorbance. Conveniently some gels have a higher melting point than solidifying point (see fig XX). This hysteresis phenomenon means that the gel concentration can be lowered and still be kept at in a solid state at 37C by pre-cooling them (to 6-8C) prior to warm incubation. Alginate gelation is induced by calcium ions which crosslink gelling polymers at room temperature. To get a homogenous gel, calcium ions cannot be mixed with an Alginate solution but must diffuse from an underlying calcium source (1). Since the optical properties of Alginate depends on the amount of crosslinking, they ultimately depend on calcium diffusion which is a difficult parameter to control. It is important to note that keeping the same diffusion conditions (time, temperature, calcium source concentration etc.) is necessary to maintain identical alginate optical properties between experiments.
RNA is a light cost nucleotide material in the cell, We aim to recreate RNA agglomerations as formed in mammalian cells with triple repeat disorders, which show liquid phase separation, forming a organelle-like vesicle, where local concentrations of enzymes can be created.
RNA is a light cost nucleotide material in the cell, We aim to recreate RNA agglomerations as formed in mammalian cells with triple repeat disorders, which show liquid phase separation, forming a organelle-like vesicle, where local concentrations of enzymes can be created.
RNA is a light cost nucleotide material in the cell, We aim to recreate RNA agglomerations as formed in mammalian cells with triple repeat disorders, which show liquid phase separation, forming a organelle-like vesicle, where local concentrations of enzymes can be created.

SECOND MODEL

your text
RNA is a light cost nucleotide material in the cell, We aim to recreate RNA agglomerations as formed in mammalian cells with triple repeat disorders, which show liquid phase separation, forming a organelle-like vesicle, where local concentrations of enzymes can be created.
RNA is a light cost nucleotide material in the cell, We aim to recreate RNA agglomerations as formed in mammalian cells with triple repeat disorders, which show liquid phase separation, forming a organelle-like vesicle, where local concentrations of enzymes can be created.
RNA is a light cost nucleotide material in the cell, We aim to recreate RNA agglomerations as formed in mammalian cells with triple repeat disorders, which show liquid phase separation, forming a organelle-like vesicle, where local concentrations of enzymes can be created.
RNA is a light cost nucleotide material in the cell, We aim to recreate RNA agglomerations as formed in mammalian cells with triple repeat disorders, which show liquid phase separation, forming a organelle-like vesicle, where local concentrations of enzymes can be created.

THIRD MODEL

your text
RNA is a light cost nucleotide material in the cell, We aim to recreate RNA agglomerations as formed in mammalian cells with triple repeat disorders, which show liquid phase separation, forming a organelle-like vesicle, where local concentrations of enzymes can be created.
RNA is a light cost nucleotide material in the cell, We aim to recreate RNA agglomerations as formed in mammalian cells with triple repeat disorders, which show liquid phase separation, forming a organelle-like vesicle, where local concentrations of enzymes can be created.
RNA is a light cost nucleotide material in the cell, We aim to recreate RNA agglomerations as formed in mammalian cells with triple repeat disorders, which show liquid phase separation, forming a organelle-like vesicle, where local concentrations of enzymes can be created.
RNA is a light cost nucleotide material in the cell, We aim to recreate RNA agglomerations as formed in mammalian cells with triple repeat disorders, which show liquid phase separation, forming a organelle-like vesicle, where local concentrations of enzymes can be created.


Centre for Research and Interdisciplinarity (CRI)
Faculty of Medicine Cochin Port-Royal, South wing, 2nd floor
Paris Descartes University
24, rue du Faubourg Saint Jacques
75014 Paris, France
bettencourt.igem2017@gmail.com