Difference between revisions of "Team:Pasteur Paris/Experiments/Microflu"

Latest revision as of 03:44, 18 October 2018

General Protocols

PDMS (Polydimethylsiloxane) is a widely used polymer in microfluidics, for its biocompatibility and transparence, among other qualities. Here we show how to prepare PDMS for microfluidic chips, as well as how to demold them and bond them to surfaces.

PDMS Chip Fabrication

PDMS Chip Demolding

PDMS Chip Bonding

Materials

PDMS monomer and curing agent (Sigma-Aldrich, Sylgard 184, 761036-5EA)
Mold (epoxy resin or aluminium)
Isopropanol for cleaning purposes
Scale (Kern PCB 1000-2)
Plastic beaker
Vacuum pump unit (Vacuubrand PC 3 RZ 2.5)
Vacuum bell jar (Kartell desiccator)
Spatula
Stove (Memmert UM 400) at 70 degrees Celsius
Paper (Kimberly-Clark SCOTT Blue)
Gloves (Kimtech Science PFE)

Procedure

According to the Sylgard 184 manual.

Pour PDMS monomer into a beaker.
Pour curing agent into the same beaker (1 g for 10 g of monomer).
Mix with the spatula for 30 seconds. Spatula can be cleaned afterwards with some paper dipped in isopropanol.
Put beaker into the vacuum bell jar connected to the vacuum pump unit in order to extract the air bubbles from the mixture (at least 10 minutes vacuum, look out for overflowings).
Pour mixture onto mold.
Put mold+mixture in stove at 70 degrees Celsius for 3 hours at least.

Materials

Razor blade (OEMTOOLS 25181 Razor Blades, 100 Pack)
Biopsy puncher (Kai Biopsy Punch 4mm )

Procedure

Use a razor blade to cut the borders of the chip and extract the PDMS from its mold. Avoid touching the circuits on your chip to avoid unwanted fingerprints.
Drill input and output holes with the biopsy puncher.

In some cases, before using your chip, you'll need to seal the circuitry. In order to do that, it is common to use plasma bonding to glue the chip to another surface (PDMS or glass).

Materials

Plasma cleaner (Diener Pico PCCE)
Distilled water
Isopropanol for cleaning purposes
Office duct tape
Fume hood (Euroclone aura vertical S.D.4)

Procedure

First, the chip needs to be cleaned in the fume hood. To do so, apply duct tape onto the surface of the chip you want to bond and remove it. Clean the chip with isopropanol.
Put the chip and the surface you want to bond it to into the plasma cleaner. The surfaces you want to bond need to be facing up in the machine in order to be exposed to the plasma.
Expose chip and surface 30 seconds to plasma.
Take the chip and the surface back in the fume hood.
You have 20 minutes to execute this step. Press the microfluidic chip against the surface. The surfaces that need to be glued together need to face each other. If bonding failed, repeat from step 1.

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Membrane Filters

Soon enough we realized that we would need something to confine the bacteria, so that it doesn't attack the neurons during our experiments, or escape the device in a real prosthesis system. The solution came as a nanoporous membrane, that would also be used as the conductive element in our system to transmit the neuron's impulses to an electrode. The goal here is to coat alumina oxide membranes with different types of conductive polymers.

Membrane PEDOT:PSS coating

Membrane PEDOT:Ts and PEDOT:Cl coating

An aqueous solution of PEDOT :PSS can be prepared [1]. We decided to dip the membranes in this solution during the polymerization.

[1] Jikui Wang, Guofeng Cai, Xudong Zhu, Xiaping Zhou, Oxidative Chemical Polymerization of 3,4-Ethylenedioxythiophene and its Applications in Antistatic coatings, Journal of Applied Polymer Science, 2012, Vol. 124, 109-115 .

Materials

EDOT (3,4-Ethylenedioxythiophene, Sigma-Aldrich, 483028-10G)
PSS (Sodium 4-vinylbenzenesulfonate, Sigma-Aldrich, 94904-100G )
Deionised water
Sodium persulfate (Sigma-Aldrich, 216232-500G)
Iron(III) sulfate hydrate (Sigma-Aldrich, F0638-250G)
Alumina Oxide Membrane Filters, 0.2 micron pores, 13 mm (Sterlitech) (figure 1)

Figure 1: White alumina oxide membranes before coating — Figure 1: White alumina oxide membranes
before coating

Stripette (Corning Costar, 5 mL) + pipette filler
Analytical balance (Mettler Toledo NewClassic MF ML204 /01)
Magnetic stirrer with heating plate (yellowline MSH basic)
Fume hood (Delagrave SA OPTIMUM 1500)
Gloves (Kimtech purple nitrile)
Forceps (Bochem art. 1013)
Glass beaker (600 mL)
Petri dish

Procedure

Pour 0.8 g EDOT, 2g PSS and 208 mL water in the glass beaker.
Put the membranes in the solution.
Stir for 10 minutes (figure 2).

Figure 2: Solution after 10 minutes of stirring — Figure 2: Solution and membranes after 10 minutes
of stirring

Add 2 g of sodium persulfate and 0.015 g of iron(III) sulfate hydrate.
Stir for 24 hours (figure 3).

Figure 3: Solution after 24 hours of stirring — Figure 3: Solution after 24 hours
of stirring

Wash membranes with water and let them dry at room temperature in a Petri dish. (figure 4)

Figure 4: PEDOT:PSS coated alumina oxide membranes — Figure 4: PEDOT:PSS coated
alumina oxide membranes

PEDOT :Ts and PEDOT :Cl polymers can be obtained by vapor phase polymerization on alumina oxide membranes [1].

[1] Alexis E. Abelow, Kristin M. Persson, Edwin W.H. Jager, Magnus Berggren, Ilya Zharov, Electroresponsive Nanoporous Membranes by Coating Anodized Alumina with Poly(3,4ethylenedioxythiophene) and Polypyrrole. 2014, 299, 190-197.

Materials

EDOT (3,4-Ethylenedioxythiophene, Sigma-Aldrich, 483028-10G)
Iron(III) p-toluenesulfonate hexahydrate for PEDOT :Ts (Sigma-Aldrich, 462861-25G) or Iron(III) chloride for PEDOT :Cl (Fischer Scientific, 217091000)
1-butanol (Sigma-Aldrich, B7906-500ML)
Deionised water
Alumina Oxide Membrane Filters, 0.2 micron pores, 13 mm (Sterlitech) (figure 1)

Paper masks (figure 2)

Figure 2: Paper mask — Figure 2:
Paper mask

Stripette (Corning Costar, 5 mL) + pipette filler
Analytical balance (Mettler Toledo NewClassic MF ML204 /01)
Magnetic stirrer with heating plate (yellowline MSH basic)
Fume hood (Delagrave SA OPTIMUM 1500)
Gloves (Kimtech purple nitrile)
Forceps (Bochem art. 1013)
Glass beaker (600 mL)
Petri dish

Procedure

Prepare homogenous oxidant solution (1.58 g Iron(III) p-toluenesulfonate hexahydrate and 10 mL butanol for PEDOT:Ts (figure 3) or 1.35 g Iron(III) chloride and 10 mL butanol for PEDOT:Cl (figure 4)

Figure 3: Oxidant solution for PEDOT:Ts — Figure 3: Oxidant solution
for PEDOT:Ts

Figure 4: Oxidant solution for PEDOT:Cl — Figure 4: Oxidant solution
for PEDOT:Cl

Dip membranes in oxydant solution.
Let membranes dry at 40◦C (figure 5).

Figure 5: Membranes after being dipped in oxidant solution — Figure 5: Membranes after being dipped
in oxidant solution

Place membranes in paper masks on Petri dish lids (figure 6) .

Figure 6: Membrane in paper mask — Figure 6:
Membrane in paper mask

Pour 200 µL EDOT in 50 mL beakers.
Place Petri dish lids on top of the 50 mL beakers, membranes facing the inside of the beakers.
Heat the beakers at 40◦C and stop when membranes darken (takes about 6 minutes) (figure 7).

Figure 7: Vapor phase polymerization of PEDOT :Ts — Figure 7: Vapor phase
polymerization of PEDOT :Ts

Wash membranes with butanol and water.
Let membranes dry at room temperature (figures 8 and 9).

Figure 8: PEDOT:Ts coated membranes — Figure 8: PEDOT:Ts
coated membranes

Figure 9: PEDOT:Cl coated membranes — Figure 9: PEDOT:Cl
coated membranes

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Well Chip

The well chip was designed and assembled by our team. It was used to test the biocompatibility of our membranes, as well as the culture of bacteria in the presence of current. Here we show how the molds were made, how the chip itself was assembled, how well's conductivity was measured and how biofilm culture was performed on it.

PDMS Well Chip Mold Fabrication

PDMS Well Chip Fabrication

PDMS Well Chip Conductivity Measurement

Biofilm culture

Molds were made of aluminium according to the following plans. Part 1 Mold's center cylinder part is detachable from the bottom to make the demolding ot PDMS easier.

Figure 1: PDMS Well Chip Mold Plans — Figure 1:
PDMS Well Chip Mold Plans

Figure 2: PDMS Well Chip Mold — Figure 2:
PDMS Well Chip Mold

Materials

Molds
Syringe (Terumo syringe without needle, 10 mL )
Platinum 24 mm x 2 mm strip (mechanically flattened 24mm long 0.7mm diameter platinum wire)
Polycarbonate gold-coated membrane filters, 0.4 micron, 13mm diameter (Sterlitech) or polymerized membrane see protocol

Refer to sections 1 and 2 of Microfluidics: general protocols for further needed materials.

Procedure

Prepare 20 g of PDMS monomer using section 1 of Microfluidics: general protocols .
Replace step 5 by: Fill the syringe with PDMS. Fill part 1 mold until it's full and part 2 mold until the PDMS layer is more or less 1 cm thick. Keep the PDMS that is left.
Demold the chip following section 2 of Microfluidics: general protocols . Ignore step 2.
Put membrane and platinum strip on PDMS part 1. Refer to figure 1 for their position.

Figure 1: PDMS Parts 1 with platinum strip — Figure 1: PDMS Parts 1
with platinum strip

Refer to section 3 of Microfluidics: general protocols to bond PDMS part 2 to the PDMS part prepared in the previous step. It should look like figure 2.

Figure 2: PDMS Well Chip — Figure 2:
PDMS Well Chip

Apply a small layer of PDMS with the syringe. Refer to figure 3. This way, the well is watertight.

Figure 3: PDMS Deposit Zone — Figure 2:
PDMS deposit
zone in red

Put the chip in the stove for 3 hours.

Materials

Oscilloscope
Function generator
Solderless breadboard assembly
Electric wires with banana connectors
Coaxial cable
Male BCN to 2 female banana connectors converter
BNC Splitter
1 kOhm resistor

Procedure

Reproduce the following electric circuit.

Set function generator on sine, no offset, 4.5 V amplitude.

Figure 2: PDMS well chip on breadboard assembly

Materials

BL21 liquid culture, see Molecular Biology: DNA Assembly and Microbiology
PDMS well chip
Crystal violet (Thermofisher, 0.1 % in water)
Distilled water
Acetone
Ethanol 96%
P1000, P200, P20 (Gilson) + tips
Gloves (Kimtech PFE)
Biochrom WPA CO8000 Cell density meter
Glass jar of bleach
Plastic jar
Falcon tube 15 mL

Procedure

According to Dr Jean-Marc Ghigo.

Biofilm formation

Pour 600 µL of liquid culture in the well.
Incubate well at 37 degrees Celsius for 24 hours.

Well wash

Discard the supernatant in microbiological waste bin. Do not pipet.
Immerse well in the plastic jar with distilled water (let the water softly enter the wells).

Take the well out of the water and discard water sharply over the waste container.
Repeat this operation twice.
Bang on blotter paper to eliminate residual water.

Crystal violet staining

Add 125 µL Crystal violet in the emptied well.
Wait 15 minutes for staining.

Wash 3 times with distilled water as described before.
Bang on blotter paper to eliminate residual water.
Suspend colored biofilm by adding 150 µL ethanol/acetone solution (80 :20).
Transfer 50 µL of the solution in a falcon tube and add 1.5 mL of ethanol/acetone solution (80 :20).

Figure 3: Solution ready for optical density measure

Read optical density of 1 mL of the falcon tube's solution at 600 nm.

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Microchannel Chip

We used the microchannel chip to test the effect of NGF on neuron's growth. Institut Curie allowed us to use their chip design and their molds for our experiments. The microchannel chip is composed of two chambers connected by microchannels of 5 micrometers width and 2 micrometers height, ideal to observe neuron growth. We then proceeded to enhance the chip with a few customizations. We integrated a nanoporous membrane in the chip to prevent our bacteria to come in contact with the neurons.

PDMS Microchannel Chip Mold Fabrication

Basic Microchannel Chip Fabrication

Membrane Microchannel Chip Fabrication

Microchannel Chip Bonding

Double Membrane Microchannel Chip

Chip Sterilization

We were allowed to use the molds made by Institut Curie. We were not involved in the process of their fabrication. Here is a short video we made about how these molds were created.

Materials

Mold

Refer to sections 1 and 2 of Microfluidics: general protocols for further materials.

Procedure

Prepare 80 g of PDMS monomer using section 1 of Microfluidics: general protocols .
Demold the chip following section 2 of Microfluidics: general protocols .

The goal here is to insert a membrane in one of the chambers of the microfluidic chip in order to isolate the neuron's chamber from the bacteria's one.

Materials

Basic microchannel chip
Polycarbonate gold-coated membrane filters, 0.4 micron, 13 mm diameter (Sterlitech)
Razor blade (OEMTOOLS 25181 Razor Blades, 100 Pack)
Scissors
Forceps

Procedure

Make a cut in the basic microchannel chip with a razor blade (see figure below). Do not cut the chip in half!

Figure 1: Make a cut in the microchannel chip along the red line — Figure 1: Make a cut in the microchannel
chip along the red line

Figure 2: Cut microfluidic chip with membrane inserted — Figure 2: Cut microfluidic chip
with membrane inserted

Stretch the cut and insert the membrane using the forceps. Cut with a razor blade the exceeding part of the membrane.

Materials

Basic or membrane microchannel chip
Distilled water
Imaging Dish (Ibidi &mu-dish 35 mm, high glass bottom)
Fridge

Refer to section 3 of Microfluidics: general protocols

Procedure

Bond microfluidic chip to the bottom of an imaging dish using section 3 of Microfluidics: general protocols
Fill the chip with distilled water. If water leaks out of the chip, unstick it from the imaging dish and retry step 1.
Store in fridge.

Here we have to insert a membrane underneath the neuron's chamber of a membrane microchannel chip, in order to be able to expose the neurons to current.

Materials

Membrane microchannel chip
Distilled water
Imaging Dish (Ibidi $mu-dish 35 mm, high glass bottom)
Syringe (Terumo syringe without needle, 10 mL )
Conductive silver paste (MG Chemicals 8330S-21G)
Wooden toothpick
Petri dish
Stove
Fridge

Procedure

Prepare 5g of PDMS following section 1 of Microfluidics: general protocols.
Prepare 1 mL of conductive silver paste following the manufacturer's instructions (Preheat parts A and B in stove at 70 degrees Celsius, put 0.5 mL of part A and 0.5 mL part B in a Petri dish, mix with the toothpick).
See figure below for more information about the position of each element. Deposit a small layer of conductive silver paste on the border of the bottom of the imaging dish. Stick a piece of gold membrane cut with the scissors in the silver paste. Put 10 minutes in the stove at 70 degrees Celsius. Put another small layer of silver paste on top of the previous one.

Figure 1: Bonded double membrane microchannel chip — Figure 1: Bonded double
membrane microchannel chip

Figure 2: Neuron and bacteria chambers — Figure 2: Neuron
and bacteria chambers

Bond membrane microchannel chip to the bottom of the imaging dish following section 3 of Microfluidics: general protocols. The extremity of the gold membrane piece has to be in one of the holes of the neuron's chamber (see figure 3).
Deposit a small layer of PDMS on the side where the membrane sticks out of the chip. Wait 2 minutes. Fill chip with distilled water. If water leaks out, unstick the chip, discard imaging dish and restart from step 3.
Store in fridge.

Unwanted living organisms in microfluidic chips can be a big deal, especially when these chips have to stay for 3 days filled with cultur medium in an incubator. The chips need to be exposed to UV rays in order to eliminate these unwanted organisms. We took extra securitiy measures, because we also needed to transport our chips from Institut Curie's lab at IPGG to Institut Pasteur.

Materials

Bonded (to imaging dish) and water-filled microchannel chips
Big Petri sish (150 mm diameter)
Gloves (Kimtech PFE)
UV curing unit (DWS)
Wrapfilm for food use (Ecopla France film pro)
Parafilm (Bemis parafilm "M")
Fridge

Procedure

Open imaging dishes containing bonded microchannel chips and put them in the UV curing unit with their corresponding lid.

Figure 1: Imaging dishes in UV curing unit — Figure 1: Imaging dishes
in UV curing unit

Expose to UV rays for 20 minutes.
With gloves, put exposed dishes in a big Petri dish.
Seal Petri dish with parafilm.
Cover Petri dish with 3 layers of wrapfilm.
Expose 15 minutes to UV rays.
Cover Petri dish with 2 additional layers of wrapfilm
Store in fridge.

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Vertical Chip

The vertical chip was one of the designs for the support of the final experiment, that would serve as a proof of concept. The idea is to isolate the modified bacteria from the neurons using a membrane. To simplify the membrane's integration in a PDMS chip, a vertical design instead of a microchannel horizontal one was proposed.

PDMS Vertical Chip Mold Fabrication

PDMS Vertical Chip Fabrication

PDMS Chip Sterilization

The mold was made of aluminium according to the following blueprint (figure 1).

Materials

Molds
Polycarbonate gold-coated membrane filters, 0.4 micron, 13mm diameter (Sterlitech) or polymerized membrane ( see protocol )
Biopsy puncher (Kai biopsy puncher 2 mm and 4 mm)
Conductive silver paste (MG Chemicals 8330S-21G)
Tissue culture dish (TPP 93060, 53 mm internal diameter) Refer to Microfluidics: general protocols for further materials.

Procedure

Prepare 15 g of PDMS monomer using section 1 of Microfluidics: general protocols .
Demold the PDMS layer following section 2 of Microfluidics: general protocols . Ignore step 2.
Cut PDMS layer in two halves.
Drill a hole in the center of each half with a 4 mm biopsy puncher. Drill holes in one of the two layer with a 2 mm biopsy puncher (see figure 1).

Figure 1: Two halves of PDMS layer. Left : upper layer. Right : bottom layer — Figure 1: Two halves of PDMS layer.
Left : upper layer. Right : bottom layer

Prepare 2 mL of conductive silver paste following the manufacturer's instructions (Preheat parts A and B in the stove at 70 degrees Celsius, put 0.5 mL of part A and 0.5 mL part B in a Petri dish, mix with the toothpick).
Apply a path of silver paste on bottom layer starting from the center hole and going outwards of the layer (figure 2). Deposit one half of a membrane filter on center hole. Put in the stove at 70 degrees Celsius for 2 hours.

Figure 2: Assembled vertical chip with gold-coated membrane filter — Figure 2: Assembled vertical chip
with gold-coated membrane filter

Bond the two layers together (figure 3) according to section 3 of Microfluidics: general protocols .
Take the bottom of a tissue culture dish and deposit the other half of the membrane filter in the center. Apply silver paste and put in the stove at 70 degrees Celsius for 2 hours (figure 3)

Figure 3: Tissue culture dish with membrane and silver paste — Figure 3: Bonded layers

Bond prepared tissue culture dish with product of step 7 (figure 4), bottom layer (figure 1) facing the dish, refering to section 3 of Microfluidics: general protocols .

Materials

Bonded chip, product of section 2
Big Petri dish (150 mm diameter)
Gloves (Kimtech PFE)
UV curing unit (DWS)
Wrapfilm for food use (Ecopla France film pro)
Parafilm (Bemis parafilm "M")
Fridge

Procedure

Open dishes containing bonded chips and put them in the UV curing unit with their corresponding lid.
Expose to UV rays for 20 minutes.
With gloves, put exposed dishes in a big Petri dish.
Seal Petri dish with parafilm.
Cover Petri dish with 3 layers of wrapfilm.
Expose 15 minutes to UV rays.
Cover Petri dish with 2 additional layers of wrapfilm.
Store in fridge.

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+        }
      </style>
-     <div id="banner">
-        <h1>MICROFLUIDICS PROTOCOLS</h1>
-    </div>
      <div id="GeneralContent">
+    <div id="index" class="block">
+        <div id="indexContent">
+            <p><a href="#micro_0" class="link">General protocols</a></p>
+            <p><a href="#micro_3" class="link">Membrane filters</a></p>
+            <p><a href="#micro_1" class="link">Well chip</a></p>
+            <p><a href="#micro_2" class="link">Microchannel chip</a></p>
+            <p><a href="#micro_4" class="link">Vertical chip</a></p>
+        </div>
+        <div id="indexRight">
+            <div id="littleButton">
+            </div>
+        </div>
+    </div>
          <div id="MainContent">
@@ Line 89: / Line 194: @@
          <div class="block full" id="micro_0" style="display:flex;flex-flow: row wrap;justify-content:center;margin:auto;">
-             <h2 style="order:1;">Microfluidics: general protocols</h2>
+             <h2 style="order:1;">General Protocols</h2>
-             <p style="text-indent:0px;order:2;margin:2em;">PDMS (Polydimethylsiloxane) is a widely used polymer in microfluidics, for its biocompatibility and transparence, among other qualities. Here we show how to prepare PDMS for microfluidic chips, as well as how to demold them, bond them to other surfaces and treat them for neuron growth. </p>
+             <p style="text-indent:0px;order:2;margin:2em;">PDMS (Polydimethylsiloxane) is a widely used polymer in microfluidics, for its biocompatibility and transparence, among other qualities. Here we show how to prepare PDMS for microfluidic chips, as well as how to demold them and bond them to surfaces. </p>
@@ Line 130: / Line 235: @@
              </div>
-            <div class="vignette" id="vign_0003">
-                <div class="vignette_for" id="for_0003">
-                </div>
-                <div class="vignette_back" id="back_0003">
-                </div>
-                <div class="vignette_text">
-                    <p>PDMS Chip Treatment for Nerve Growth</p>
-                </div>
-            </div>
@@ Line 150: / Line 244: @@
                  <br>
                  <h3>Materials</h3>
+                <br>
                  <ul>
                      <li> PDMS monomer and curing agent (Sigma-Aldrich, Sylgard 184, 761036-5EA)    </li>
@@ Line 164: / Line 259: @@
                  </ul>
                  <br>
-                 <h3>Protocol</h3>
+                 <h3>Procedure</h3>
-                 <p>According to the <a target="_blank" rel="noopener noreferrer" href="https://static.igem.org/mediawiki/2018/c/c3/T--Pasteur_Paris--Sylgard.pdf">Sylgard 184 manual</a>. <br>
+                 <p>According to the <a rel="noopener noreferrer" href="https://static.igem.org/mediawiki/2018/c/c3/T--Pasteur_Paris--Sylgard.pdf"style="font-weight: bold ; color:#85196a;" target="_blank">Sylgard 184 manual</a>. <br>
                  <ol>
                      <li> Pour PDMS monomer into a beaker.   </li>
-                     <li> Pour curing agent into the same beaker (10:1 proportion: 1g for 10g of monomer). </li>
+                     <li> Pour curing agent into the same beaker (1 g for 10 g of monomer). </li>
                      <li> Mix with the spatula for 30 seconds. Spatula can be cleaned afterwards with some paper dipped in isopropanol.  </li>
                      <li> Put beaker into the vacuum bell jar connected to the vacuum pump unit in order to extract the air bubbles from the mixture (at least 10 minutes vacuum, look out for overflowings).  </li>
@@ Line 175: / Line 270: @@
                  </ol>
                  <br>
-                <div class="protocol_box">
-                    <p> <a href="https://static.igem.org/mediawiki/2018/3/3d/T--Pasteur_Paris--Microfluidics-general-protocols.pdf" target="_blank">Get the PDF version of this protocol</a> </p>
-                </div>
                  <br>
              </div>
@@ Line 186: / Line 278: @@
                  <br>
                  <h3>Materials</h3>
+                <br>
                  <ul>
                      <li> Razor blade (OEMTOOLS 25181 Razor Blades, 100 Pack)    </li>
@@ Line 191: / Line 284: @@
                  </ul>
                  <br>
-                 <h3>Protocol</h3>
+                 <h3>Procedure</h3>
                  <br>
                  <ol>
@@ Line 198: / Line 291: @@
                  </ol>
                  <br>
-                <div class="protocol_box">
-                    <p> <a href="https://static.igem.org/mediawiki/2018/3/3d/T--Pasteur_Paris--Microfluidics-general-protocols.pdf" target="_blank">Get full protocol here</a> </p>
-                </div>
                  <br>
              </div>
@@ Line 207: / Line 297: @@
                  <div class="close_button">
                  </div>
+                <br>
                  <br>
                  <br>
@@ Line 212: / Line 303: @@
                  <br>
                  <h3>Materials</h3>
+                <br>
                  <ul>
                      <li>  Plasma cleaner (Diener Pico PCCE)   </li>
@@ Line 220: / Line 312: @@
                  </ul>
                  <br>
-                 <h3>Protocol</h3>
+                 <h3>Procedure</h3>
                  <br>
                  <ol>
                      <li> First, the chip needs to be cleaned in the fume hood. To do so, apply duct tape onto the surface of the chip you want to bond and remove it. Clean the chip with isopropanol.  </li>
-                     <li> Put the chip and the surface you want to bond it to into the plasma cleaner. The surfaces you want to bond need to be facing up in the machine in order to be exposed to plasma. </li>
+                     <li> Put the chip and the surface you want to bond it to into the plasma cleaner. The surfaces you want to bond need to be facing up in the machine in order to be exposed to the plasma. </li>
                      <li> Expose chip and surface 30 seconds to plasma.  </li>
                      <li> Take the chip and the surface back in the fume hood.  </li>
@@ Line 230: / Line 322: @@
                  </ol>
                  <br>
-                 <div class="protocol_box">
+                 <br>
-                    <p> <a href="https://static.igem.org/mediawiki/2018/3/3d/T--Pasteur_Paris--Microfluidics-general-protocols.pdf" target="_blank">Get full protocol here</a> </p>
-                </div>
-                    <br>
              </div>
-             <div class="panel" id="pan_0003"  style="text-align:left;">
-                 <div class="close_button">
+             <div class="protocol_box">
-                </div>
+                 <p> <a href="https://static.igem.org/mediawiki/2018/3/3d/T--Pasteur_Paris--Microfluidics-general-protocols.pdf" style="font-weight: bold ; color:#85196a;" target="_blank">Get the PDF version of this section</a> </p>
-                <br>
+             </div>
-                <h3>Materials</h3>
-                <ul>
-                    <li>  Poly-D-Lysine (Sigma-Aldrich, Poly-D-Lysine solution, 1.0 mg/mL  ,A-003-E)  </li>
-                    <li>  Laminine (Sigma-Aldrich, Laminin from Engelbreth-Holm-Swarm murine sarcoma basement membrane, L2020-1MG) </li>
-                </ul>
-                <br>
-                <h3>Protocol</h3>
-                <br>
-                <ol>
-                    <li> Pour poly-D-lysine with concentration 10 $\mu$g/mL into the chip and incubate over night.  </li>
-                    <li> Then pour laminine with concentration 4 $\mu$g/mL and incubate for a few hours. </li>
-                </ol>
-                <br>
-                <div class="protocol_box">
-                    <p> <a href="https://static.igem.org/mediawiki/2018/3/3d/T--Pasteur_Paris--Microfluidics-general-protocols.pdf" target="_blank">Get full protocol here</a> </p>
-                </div>
-                    <br>
-             </div>
              <script>
@@ Line 356: / Line 425: @@
          <div class="block full" id="micro_3" style="display:flex;flex-flow: row wrap;justify-content:center;margin:auto;">
-             <h2 style="order:1;width:100%">Microfluidics: membrane filters</h2>
+             <h2 style="order:1;width:100%">Membrane Filters</h2>
+            <p style="text-indent:0px;order:2;margin:2em;width:100%"> Soon enough we realized that we would need something to confine the bacteria, so that it doesn't attack the neurons during our experiments, or escape the device in a real prosthesis system. The solution came as a nanoporous membrane, that would also be used as the conductive element in our system to transmit the neuron's impulses to an electrode. The goal here is to coat alumina oxide membranes with different types of conductive polymers.
+</p>
-            <p style="text-indent:0px;order:2;margin:2em;width:100%"> Soon enough we realized that we would need something to confine the bacteria, so that it doesn't attack the neurons during our experiments. The solution came as a nanoporous membrane, that would also be used as the conductive element in our system to transmit to the neuron's impulse. </p>
              <div class="vignette" id="vign_0300">
@@ Line 396: / Line 468: @@
                  <h3>Materials</h3>
                  <ul>
-                     <li>  3,4-Ethylenedioxythiophene   </li>
+                     <li>  EDOT (3,4-Ethylenedioxythiophene, Sigma-Aldrich, 483028-10G)    </li>
-                     <li>  Sodium 4-vinylbenzenesulfonate   </li>
+                     <li>  PSS (Sodium 4-vinylbenzenesulfonate, Sigma-Aldrich, 94904-100G )    </li>
                      <li>  Deionised water    </li>
-                     <li>  Sodium persulfate  </li>
+                     <li>  Sodium persulfate (Sigma-Aldrich, 216232-500G)  </li>
-                     <li>  Iron(III) sulfate hydrate  </li>
+                     <li>  Iron(III) sulfate hydrate (Sigma-Aldrich, F0638-250G)   </li>
-                     <li>  Alumina Oxide Membrane Filters   </li>
+                     <li>  Alumina Oxide Membrane Filters, 0.2 micron pores, 13 mm (Sterlitech) (figure 1)    </li>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/6/66/T--Pasteur_Paris--Alumina-oxide-membranes.jpg" alt="Figure 1: White alumina oxide membranes before coating">
+                    <figcaption>Figure 1: White alumina oxide membranes <br> before coating</figcaption>
+                </figure>
+                    <li>  Stripette (Corning Costar, 5 mL) + pipette filler </li>
+                    <li>  Analytical balance (Mettler Toledo NewClassic MF ML204 /01)   </li>
+                    <li>  Magnetic stirrer with heating plate (yellowline MSH basic)     </li>
+                    <li>  Fume hood (Delagrave SA OPTIMUM 1500)    </li>
+                    <li>  Gloves  (Kimtech purple nitrile) </li>
+                    <li>  Forceps (Bochem art. 1013)     </li>
+                    <li>  Glass beaker (600 mL)    </li>
+                    <li>  Petri dish   </li>
                  </ul>
                  <br>
-                 <h3>Protocol</h3>
+                 <h3>Procedure</h3>
                  <br>
                  <ol>
                      <li> Pour 0.8 g EDOT, 2g PSS and 208 mL water in the glass beaker.   </li>
                      <li> Put the membranes in the solution.  </li>
-                     <li> Stir for 10 minutes.  </li>
+                     <li> Stir for 10 minutes (figure 2).  </li>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/7/7e/T--Pasteur_Paris--PEDOT_PSS_10_minutes_stirring.jpg" alt="Figure 2: Solution after 10 minutes of stirring">
+                    <figcaption>Figure 2: Solution and membranes after 10 minutes <br> of stirring </figcaption>
+                </figure>
                      <li> Add 2 g of sodium persulfate and 0.015 g of iron(III) sulfate hydrate.  </li>
-                     <li> Stir for 24 hours. </li>
+                     <li> Stir for 24 hours (figure 3). </li>
-                     <li> Wash membranes with water and let them dry at room temperature in a Petri dish. </li>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/8/83/T--Pasteur_Paris--PEDOT_PSS_24_hours_stirring.jpg" alt="Figure 3: Solution after 24 hours of stirring">
+                    <figcaption>Figure 3: Solution after 24 hours <br> of stirring</figcaption>
+                </figure>
+                     <li> Wash membranes with water and let them dry at room temperature in a Petri dish. (figure 4) </li>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/8/83/T--Pasteur_Paris--Coated-membranes-1.jpg" alt="Figure 4: PEDOT:PSS coated alumina oxide membranes">
+                    <figcaption>Figure 4: PEDOT:PSS coated <br> alumina oxide membranes</figcaption>
+                </figure>
                  </ol>
                  <br>
-                <div class="protocol_box">
-                    <p> <a href="https://static.igem.org/mediawiki/2018/a/a9/T--Pasteur_Paris--Microfluidics-membranes.pdf" target="_blank">Get full protocol here</a> </p>
-                </div>
                  <br>
+                <br>
+                <br>
              </div>
@@ Line 433: / Line 538: @@
                  <h3>Materials</h3>
                  <ul>
-                     <li>  3,4-Ethylenedioxythiophene   </li>
+                     <li>  EDOT (3,4-Ethylenedioxythiophene, Sigma-Aldrich, 483028-10G)    </li>
-                     <li>  Iron(III) p-toluenesulfonate hexahydrate for PEDOT :Ts or Iron(III) chloride for PEDOT :Cl </li>
+                     <li>  Iron(III) p-toluenesulfonate hexahydrate for PEDOT :Ts (Sigma-Aldrich, 462861-25G) or Iron(III) chloride for PEDOT :Cl (Fischer Scientific, 217091000)  </li>
-                     <li>  1-butanol     </li>
+                     <li>  1-butanol (Sigma-Aldrich, B7906-500ML)     </li>
-                     <li>  Sodium persulfate  </li>
+                     <li>  Deionised water  </li>
-                     <li>  Iron(III) sulfate hydrate  </li>
+                     <li>  Alumina Oxide Membrane Filters, 0.2 micron pores, 13 mm (Sterlitech) (figure 1)  </li>
-                     <li>  Paper masks  </li>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/6/66/T--Pasteur_Paris--Alumina-oxide-membranes.jpg" alt="Figure 1: White alumina oxide membranes before coating">
+                    <figcaption>Figure 1: White alumina oxide membranes <br> before coating</figcaption>
+                </figure>
+                     <li>  Paper masks  (figure 2)  </li>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/b/be/T--Pasteur_Paris--Paper-Mask.jpg" alt="Figure 2: Paper mask">
+                    <figcaption>Figure 2: <br> Paper mask </figcaption>
+                </figure>
+                    <li>  Stripette (Corning Costar, 5 mL) + pipette filler </li>
+                    <li>  Analytical balance (Mettler Toledo NewClassic MF ML204 /01)   </li>
+                    <li>  Magnetic stirrer with heating plate (yellowline MSH basic)     </li>
+                    <li>  Fume hood (Delagrave SA OPTIMUM 1500)    </li>
+                    <li>  Gloves  (Kimtech purple nitrile) </li>
+                    <li>  Forceps (Bochem art. 1013)     </li>
+                    <li>  Glass beaker (600 mL)    </li>
+                    <li>  Petri dish   </li>
                  </ul>
                  <br>
-                 <h3>Protocol</h3>
+                 <h3>Procedure</h3>
                  <br>
                  <ol>
-                     <li> Prepare homogenous oxidant solution (1.58 g Iron(III) p-toluenesulfonate hexahydrate and 10 mL butanol for PEDOT:Ts or 1.35 g Iron(III) chloride and 10 mL butanol
+                     <li> Prepare homogenous oxidant solution (1.58 g Iron(III) p-toluenesulfonate hexahydrate and 10 mL butanol for PEDOT:Ts (figure 3) or 1.35 g Iron(III) chloride and 10 mL butanol for PEDOT:Cl (figure 4)  </li>
- for PEDOT:Cl)   </li>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/8/88/T--Pasteur_Paris--Oxidant-solution-1.jpg" alt="Figure 3: Oxidant solution for PEDOT:Ts">
+                    <figcaption>Figure 3: Oxidant solution <br> for PEDOT:Ts</figcaption>
+                </figure>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/c/c3/T--Pasteur_Paris--Oxidant-solution-2.jpg" alt="Figure 4: Oxidant solution for PEDOT:Cl">
+                    <figcaption>Figure 4: Oxidant solution <br> for PEDOT:Cl</figcaption>
+                </figure>
                      <li> Dip membranes in oxydant solution. </li>
-                     <li> Let membranes dry at 40◦C. </li>
+                     <li> Let membranes dry at 40◦C (figure 5). </li>
-                     <li> Place membranes in paper masks on Petri dish lids.  </li>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/9/9a/T--Pasteur_Paris--Oxidated-membranes.jpg" alt="Figure 5: Membranes after being dipped in oxidant solution">
+                    <figcaption>Figure 5: Membranes after being dipped <br> in oxidant solution</figcaption>
+                </figure>
+                     <li> Place membranes in paper masks on Petri dish lids (figure 6) .  </li>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/5/5e/T--Pasteur_Paris--Membrane-paper-mask.jpg" alt="Figure 6: Membrane in paper mask">
+                    <figcaption>Figure 6: <br> Membrane in paper mask</figcaption>
+                </figure>
                      <li> Pour 200 µL EDOT in 50 mL beakers.  </li>
                      <li> Place Petri dish lids on top of the 50 mL beakers, membranes facing the inside of the beakers.  </li>
-                     <li> Heat the beakers at 40◦C and stop when membranes darken (takes about 6 minutes).  </li>
+                     <li> Heat the beakers at 40◦C and stop when membranes darken (takes about 6 minutes) (figure 7).  </li>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/c/cc/T--Pasteur_Paris--Vapor-phase-polymerization.jpg" alt="Figure 7: Vapor phase polymerization of PEDOT :Ts">
+                    <figcaption>Figure 7: Vapor phase <br> polymerization of PEDOT :Ts</figcaption>
+                </figure>
                      <li> Wash membranes with butanol and water. </li>
-                     <li> Let membranes dry at room temperature. </li>
+                     <li> Let membranes dry at room temperature (figures 8 and 9). </li>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/3/33/T--Pasteur_Paris--Coated-membranes-2.jpg" alt="Figure 8: PEDOT:Ts coated membranes">
+                    <figcaption>Figure 8: PEDOT:Ts <br> coated membranes</figcaption>
+                </figure>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/f/f2/T--Pasteur_Paris--Coated-membranes-3.jpg" alt="Figure 9: PEDOT:Cl coated membranes">
+                    <figcaption>Figure 9: PEDOT:Cl <br> coated membranes</figcaption>
+                </figure>
                  </ol>
                  <br>
-                <div class="protocol_box">
-                    <p> <a href="https://static.igem.org/mediawiki/2018/a/a9/T--Pasteur_Paris--Microfluidics-membranes.pdf" target="_blank">Get full protocol here</a> </p>
-                </div>
-                <br>
              </div>
+            <div class="protocol_box">
+                <p> <a href="https://static.igem.org/mediawiki/2018/a/a9/T--Pasteur_Paris--Microfluidics-membranes.pdf" style="font-weight: bold ; color:#85196a;"target="_blank">Get the PDF version of this section</a> </p>
+            </div>
              <script>
@@ Line 555: / Line 720: @@
          <div class="block full" id="micro_1" style="display:flex;flex-flow: row wrap;justify-content:center;margin:auto;">
-             <h2 style="order:1;width:100%">Microfluidics: well chip</h2>
+             <h2 style="order:1;width:100%">Well Chip</h2>
              <p style="text-indent:0px;order:2;margin:2em;width:100%"> The well chip was designed and assembled by our team. It was used to test the biocompatibility of our membranes, as well as the culture of bacteria in the presence of current. Here we show how the molds were made, how the chip itself was assembled, how well's conductivity was measured and how biofilm culture was performed on it. </p>
@@ Line 592: / Line 757: @@
                  <div class="vignette_text">
                      <p>PDMS Well Chip Conductivity Measurement</p>
+                </div>
+            </div>
+            <div class="vignette" id="vign_0103">
+                <div class="vignette_for" id="for_0103">
+                </div>
+                <div class="vignette_back" id="back_0103">
+                </div>
+                <div class="vignette_text">
+                    <p>Biofilm culture</p>
                  </div>
              </div>
@@ Line 605: / Line 782: @@
                  <p style="text-indent:0px;"> Molds were made of aluminium according to the following plans. Part 1 Mold's center cylinder part is detachable from the bottom to make the demolding ot PDMS easier. </p>
                  <br>
-                 <div style="position:relative;left:13em;">
+                 <figure>
-                     <img src="https://static.igem.org/mediawiki/2018/2/29/T--Pasteur_Paris--PDMS_well_chip_mold_plans.jpg" alt="PDMS Well Chip Mold Plans" style="width:60%;">
+                     <img src="https://static.igem.org/mediawiki/2018/2/29/T--Pasteur_Paris--PDMS_well_chip_mold_plans.jpg" alt="Figure 1: PDMS Well Chip Mold Plans" style="width:500px">
-                 </div>
+                    <figcaption>Figure 1: <br> PDMS Well Chip Mold Plans</figcaption>
+                 </figure>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/c/c7/T--Pasteur_Paris--PDMS-well-chip-molds.jpg" alt="Figure 2: PDMS Well Chip Mold">
+                    <figcaption>Figure 2: <br> PDMS Well Chip Mold</figcaption>
+                </figure>
                  <br>
                  <br>
@@ Line 620: / Line 804: @@
                  <ul>
                      <li>  Molds  </li>
-                     <li>  Syringe without needle </li>
+                     <li>  Syringe (Terumo syringe without needle, 10 mL ) </li>
-                     <li>  Platinum 24mm x 2 mm strip  </li>
+                     <li>  Platinum  24 mm x 2 mm strip  (mechanically flattened 24mm long 0.7mm diameter platinum wire)  </li>
-                     <li>  Circular 13mm diameter membrane </li>
+                     <li>  Polycarbonate gold-coated membrane filters, 0.4 micron, 13mm diameter (Sterlitech) or polymerized membrane
+                          <a href="https://static.igem.org/mediawiki/2018/a/a9/T--Pasteur_Paris--Microfluidics-membranes.pdf"style="font-weight: bold ; color:#85196a;" target="_blank"> see protocol </a>  </li>
                  </ul>
+                Refer to sections 1 and 2 of <a href="https://static.igem.org/mediawiki/2018/3/3d/T--Pasteur_Paris--Microfluidics-general-protocols.pdf" style="font-weight: bold ; color:#85196a;"target="_blank"> Microfluidics: general protocols </a> for further needed materials.
                  <br>
-                 <h3>Protocol</h3>
+                 <h3>Procedure</h3>
                  <br>
                  <ol>
-                     <li> Prepare 15g of PDMS monomer using our protocol, section 1. Replace step 5 by : Fill the syringe with PDMS. Fill part 1 mold until it's full and part 2 mold until the PDMS layer is more or less 1 cm thick.  </li>
+                     <li> Prepare 20 g of PDMS monomer using section 1 of <a href="https://static.igem.org/mediawiki/2018/3/3d/T--Pasteur_Paris--Microfluidics-general-protocols.pdf" target="_blank"style="font-weight: bold ; color:#85196a;"> Microfluidics: general protocols </a>. <br>Replace step 5 by: Fill the syringe with PDMS. Fill part 1 mold until it's full and part 2 mold until the PDMS layer is more or less 1 cm thick.
-                     <li> Demold the chip following our protocol, section 2. Ignore step 2. </li>
+                    Keep the PDMS that is left. </li>
-                     <li> Put membrane and platinum strip on PDMS part 1. </li>
+                     <li> Demold the chip following section 2 of <a href="https://static.igem.org/mediawiki/2018/3/3d/T--Pasteur_Paris--Microfluidics-general-protocols.pdf" style="font-weight: bold ; color:#85196a;"target="_blank"> Microfluidics: general protocols </a>. Ignore step 2. </li>
-                     <li> Refer to our protocol, section 3 to bond PDMS part 2 to the PDMS part prepared in the previous step.</li>
+                     <li> Put membrane and platinum strip on PDMS part 1. Refer to figure 1 for their position. </li>
-                     <li> Apply a small layer of PDMS with the syringe on the contact zone of the PDMS part 2 and the platinum strip. </li>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/7/74/T--Pasteur_Paris--PDMS-well-chip-part-1.jpg" alt="Figure 1: PDMS Parts 1 with platinum strip">
+                    <figcaption>Figure 1: PDMS Parts 1 <br> with platinum strip</figcaption>
+                </figure>
+                     <li> Refer to section 3 of <a href="https://static.igem.org/mediawiki/2018/3/3d/T--Pasteur_Paris--Microfluidics-general-protocols.pdf" style="font-weight: bold ; color:#85196a;"target="_blank"> Microfluidics: general protocols </a> to bond PDMS part 2 to the PDMS part prepared in the previous step. It should look like figure 2.</li>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/4/42/T--Pasteur_Paris--PDMS-well-chip.jpg" alt="Figure 2: PDMS Well Chip">
+                    <figcaption>Figure 2: <br> PDMS Well Chip</figcaption>
+                </figure>
+                     <li> Apply a small layer of PDMS with the syringe. Refer to figure 3. This way, the well is watertight. </li>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/a/a7/T--Pasteur_Paris--PDMS-deposit-zone.pdf" alt="Figure 3: PDMS Deposit Zone" style="width:100px;">
+                    <figcaption>Figure 2: <br> PDMS deposit <br> zone in red</figcaption>
+                </figure>
                      <li> Put the chip in the stove for 3 hours. </li>
                  </ol>
                  <br>
-                <div class="protocol_box">
-                    <p> Get full protocol here </p>
-                </div>
                  <br>
              </div>
@@ Line 657: / Line 859: @@
                      <li>  Male BCN to 2 female banana connectors converter   </li>
                      <li>  BNC Splitter    </li>
-                     <li>  1 kOhm resistor
+                     <li>  1 kOhm resistor </li>
- </li>
                  </ul>
                  <br>
-                 <h3>Protocol</h3>
+                 <h3>Procedure</h3>
                  <br>
                  <ol>
                      <li> Reproduce the following electric circuit.  </li>
-                    <br>
-                    <div style="position:relative;left:13em;">
+                <figure>
-                        <img src="https://static.igem.org/mediawiki/2018/b/bb/T--Pasteur_Paris--Electrical_circuit_1.pdf" alt="Electric circuit 1" style="width:50%;">
+                    <img src="https://static.igem.org/mediawiki/2018/b/bb/T--Pasteur_Paris--Electrical_circuit_1.pdf" alt="Figure 1: Electric circuit">
-                     </div>
+                     <figcaption>Figure 1: Electric circuit</figcaption>
-                    <br>
+                </figure>
                      <li> Set function generator on sine, no offset, 4.5 V amplitude. </li>
-                    <li> Measure Y2 peak-to-peak amplitude and Y2's phase relative to Y1.</li>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/7/79/T--Pasteur_Paris--Breadboard-assembly.jpg" alt="Figure 2: PDMS well chip on breadboard assembly">
+                    <figcaption>Figure 2: PDMS well chip on breadboard assembly</figcaption>
+                </figure>
                  </ol>
                  <br>
-                 <div class="protocol_box">
+                 <br>
-                    <p> Get full protocol here </p>
+            </div>
+           <div class="panel" id="pan_0103"  style="text-align:left;">
+                <div class="close_button">
                  </div>
+                <br>
+                <h3>Materials</h3>
+                <ul>
+                    <li> BL21 liquid culture, see <a href="https://static.igem.org/mediawiki/2018/a/a6/T--Pasteur_Paris--DNA-Assembly-and-Microbiology.pdf"style="font-weight: bold ; color:#85196a;"target="_blank"> Molecular Biology: DNA Assembly and Microbiology  </a> </li>
+                    <li> PDMS well chip </li>
+                    <li> Crystal violet (Thermofisher, 0.1 % in water)  </li>
+                    <li>  Distilled water  </li>
+                    <li>  Acetone </li>
+                    <li> Ethanol 96%  </li>
+                    <li>  P1000, P200, P20 (Gilson) + tips  </li>
+                    <li> Gloves (Kimtech PFE)  </li>
+                    <li> Biochrom WPA CO8000 Cell density meter  </li>
+                    <li>  Glass jar of bleach  </li>
+                    <li>  Plastic jar  </li>
+                    <li> Falcon tube 15 mL </li>
+                </ul>
+                <br>
+                <h3>Procedure</h3>
+                <br>
+                <p> According to Dr Jean-Marc Ghigo. </p>
+                <br>
+                <h4>Biofilm formation </h4>
+                <ol>
+                    <li> Pour 600 µL of liquid culture in the well.  </li>
+                    <li> Incubate well at 37 degrees Celsius for 24 hours. </li>
+                </ol>
+                <br>
+                <h4>Well wash </h4>
+                <ol>
+                    <li>  Discard the supernatant in microbiological waste bin. Do not pipet.   </li>
+                    <li>  Immerse well in the plastic jar with distilled water (let the water softly enter the wells).</li>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/1/14/T--Pasteur_Paris--Immersed-well-chip.jpg" alt="Figure 1: Immersed well">
+                    <figcaption>Figure 1: Immersed well</figcaption>
+                </figure>
+                    <li> Take the well out of the water and discard water sharply over the waste container. </li>
+                    <li> Repeat this operation twice.  </li>
+                    <li>  Bang on blotter paper to eliminate residual water. </li>
+                </ol>
+                <br>
+                <h4> Crystal violet staining </h4>
+                <ol>
+                    <li> Add 125 µL Crystal violet in the emptied well. </li>
+                    <li> Wait 15 minutes for staining.</li>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/b/bf/T--Pasteur_Paris--Crystal-violet-well-chip.jpg" alt="Figure 2: Wells with crystal violet">
+                    <figcaption>Figure 2: Wells with crystal violet</figcaption>
+                </figure>
+                    <li> Wash 3 times with distilled water as described before. </li>
+                    <li> Bang on blotter paper to eliminate residual water.  </li>
+                    <li> Suspend colored biofilm by adding 150 µL ethanol/acetone solution (80 :20). </li>
+                    <li> Transfer 50 µL of the solution in a falcon tube and add 1.5 mL of ethanol/acetone solution (80 :20). </li>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/d/da/T--Pasteur_Paris--PDMS-well-optical-density.jpg" alt="Figure 3: Solution ready for optical density measure">
+                    <figcaption>Figure 3: Solution ready for optical density measure</figcaption>
+                </figure>
+                    <li> Read optical density of 1 mL of the falcon tube's solution at 600 nm. </li>
+                </ol>
+                <br>
                  <br>
              </div>
+            <div class="protocol_box">
+                <p> <a href="https://static.igem.org/mediawiki/2018/b/b5/T--Pasteur_Paris--PDMS-well-chip.pdf"style="font-weight: bold ; color:#85196a;"target="_blank">  Get the PDF version of this section </a> </p>
+            </div>
@@ Line 777: / Line 1,059: @@
          <div class="block full" id="micro_2" style="display:flex;flex-flow: row wrap;justify-content:center;margin:auto;">
-             <h2 style="order:1;width:100%">Microfluidics: microchannel chip</h2>
+             <h2 style="order:1;width:100%">Microchannel Chip</h2>
+            <p style="text-indent:0px;order:2;margin:2em;width:100%"> We used the microchannel chip to test the effect of NGF on neuron's growth. Institut Curie allowed us to use their chip design and their molds for our experiments. The microchannel chip is composed of two chambers connected by microchannels of 5 micrometers width and 2 micrometers height, ideal to observe neuron growth. We then proceeded to enhance the chip with a few customizations. We integrated a nanoporous membrane in the chip to prevent our bacteria to come in contact with the neurons. </p>
-            <p style="text-indent:0px;order:2;margin:2em;width:100%"> We used the microchannel chip to test the effect of NGF on the neuron's growth. </p>
              <div class="vignette" id="vign_0200">
@@ Line 792: / Line 1,075: @@
                  </div>
              </div>
+            <div class="vignette" id="vign_0201">
+                <div class="vignette_for" id="for_0201">
+                </div>
+                <div class="vignette_back" id="back_0201">
+                </div>
+                <div class="vignette_text">
+                    <p>Basic Microchannel Chip Fabrication</p>
+                </div>
+            </div>
+            <div class="vignette" id="vign_0202">
+                <div class="vignette_for" id="for_0202">
+                </div>
+                <div class="vignette_back" id="back_0202">
+                </div>
+                <div class="vignette_text">
+                    <p>Membrane Microchannel Chip Fabrication</p>
+                </div>
+            </div>
+            <div class="vignette" id="vign_0203">
+                <div class="vignette_for" id="for_0203">
+                </div>
+                <div class="vignette_back" id="back_0203">
+                </div>
+                <div class="vignette_text">
+                    <p>Microchannel Chip Bonding</p>
+                </div>
+            </div>
+            <div class="vignette" id="vign_0204">
+                <div class="vignette_for" id="for_0204">
+                </div>
+                <div class="vignette_back" id="back_0204">
+                </div>
+                <div class="vignette_text">
+                    <p>Double Membrane Microchannel Chip</p>
+                </div>
+            </div>
+            <div class="vignette" id="vign_0205">
+                <div class="vignette_for" id="for_0205">
+                </div>
+                <div class="vignette_back" id="back_0205">
+                </div>
+                <div class="vignette_text">
+                    <p>Chip Sterilization</p>
+                </div>
+            </div>
              <div class="panel" id="pan_0200"  style="text-align:left;">
-                 <div class="close_button">
+                 <div class="close_button" >
                  </div>
                  <br>
@@ Line 812: / Line 1,159: @@
                  <br>
              </div>
+            <div class="panel" id="pan_0201" style="text-align:left;">
+                <div class="close_button">
+                </div>
+                <br>
+                <h3>Materials</h3>
+                <br>
+                <ul>
+                    <li>  Mold  </li>
+                </ul>
+                <br>
+                <p> Refer to sections 1 and 2 of <a href="https://static.igem.org/mediawiki/2018/3/3d/T--Pasteur_Paris--Microfluidics-general-protocols.pdf" style="font-weight: bold ; color:#85196a;"target="_blank"> Microfluidics: general protocols </a> for further materials. </p>
+                <br>
+                <h3>Procedure</h3>
+                <br>
+                <ol>
+                    <li> Prepare 80 g of PDMS monomer using section 1 of <a href="https://static.igem.org/mediawiki/2018/3/3d/T--Pasteur_Paris--Microfluidics-general-protocols.pdf" style="font-weight: bold ; color:#85196a;"target="_blank"> Microfluidics: general protocols </a>.  </li>
+                    <li> Demold the chip following section 2 of <a href="https://static.igem.org/mediawiki/2018/3/3d/T--Pasteur_Paris--Microfluidics-general-protocols.pdf" style="font-weight: bold ; color:#85196a;"target="_blank"> Microfluidics: general protocols </a>. </li>
+                </ol>
+                <br>
+                <br>
+            </div>
+            <div class="panel" id="pan_0202" style="text-align:left;">
+                <div class="close_button">
+                </div>
+                <br>
+                <br>
+                <p> The goal here is to insert a membrane in one of the chambers of the microfluidic chip in order to isolate the neuron's chamber from the bacteria's one.  </p>
+                <br>
+                <h3>Materials</h3>
+                <br>
+                <ul>
+                    <li> Basic microchannel chip </li>
+                    <li> Polycarbonate gold-coated membrane filters, 0.4 micron, 13 mm diameter (Sterlitech)  </li>
+                    <li> Razor blade (OEMTOOLS 25181 Razor Blades, 100 Pack) </li>
+                    <li> Scissors </li>
+                    <li> Forceps </li>
+                </ul>
+                <br>
+                <h3>Procedure</h3>
+                <br>
+                <ol>
+                    <li> Make a cut in the basic microchannel chip with a razor blade (see figure below). Do not cut the chip in half! </li>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/4/40/T--Pasteur_Paris--Microchannel-cut.png" alt="Figure 1: Make a cut in the microchannel chip along the red line" style="width:200px;">
+                    <figcaption>Figure 1: Make a cut in the microchannel <br> chip along the red line</figcaption>
+                </figure>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/f/f9/T--Pasteur_Paris--Microchannel-chip-cut.jpg" alt="Figure 2: Cut microfluidic chip with membrane inserted
+" style="width:200px;">
+                    <figcaption>Figure 2: Cut microfluidic chip <br> with membrane inserted</figcaption>
+                </figure>
+                    <li> Stretch the cut and insert the membrane using the forceps. Cut with a razor blade the exceeding part of the membrane.  </li>
+                </ol>
+                <br>
+                <br>
+            </div>
+            <div class="panel" id="pan_0203" style="text-align:left;">
+                <div class="close_button">
+                </div>
+                <br>
+                <h3>Materials</h3>
+                <br>
+                <ul>
+                    <li>  Basic or membrane microchannel chip  </li>
+                    <li>  Distilled water  </li>
+                    <li>  Imaging Dish (Ibidi &mu-dish 35 mm, high glass bottom)  </li>
+                    <li>  Fridge </li>
+                </ul>
+                <br>
+                <p> Refer to section 3 of <a href="https://static.igem.org/mediawiki/2018/3/3d/T--Pasteur_Paris--Microfluidics-general-protocols.pdf" style="font-weight: bold ; color:#85196a;"target="_blank"> Microfluidics: general protocols </a>  </p>
+                <br>
+                <h3>Procedure</h3>
+                <br>
+                <ol>
+                    <li> Bond microfluidic chip to the bottom of an imaging dish using section 3 of <a href="https://static.igem.org/mediawiki/2018/3/3d/T--Pasteur_Paris--Microfluidics-general-protocols.pdf"style="font-weight: bold ; color:#85196a;"target="_blank"> Microfluidics: general protocols </a>  </li>
+                    <li> Fill the chip with distilled water. If water leaks out of the chip, unstick it from the imaging dish and retry step 1. </li>
+                    <li> Store in fridge. </li>
+                </ol>
+                <br>
+                <br>
+            </div>
+            <div class="panel" id="pan_0204" style="text-align:left;">
+                <div class="close_button">
+                </div>
+                <br>
+                <br>
+                <br>
+                <p> Here we have to insert a membrane underneath the neuron's chamber of a membrane microchannel chip, in order to be able to expose the neurons to current. </p>
+                <br>
+                <h3>Materials</h3>
+                <br>
+                <ul>
+                    <li> Membrane microchannel chip   </li>
+                    <li> Distilled water   </li>
+                    <li> Imaging Dish (Ibidi $mu-dish 35 mm, high glass bottom)   </li>
+                    <li> Syringe (Terumo syringe without needle, 10 mL )   </li>
+                    <li> Conductive silver paste (MG Chemicals 8330S-21G)   </li>
+                    <li>  Wooden toothpick  </li>
+                    <li>  Petri dish  </li>
+                    <li> Stove   </li>
+                    <li>  Fridge </li>
+                </ul>
+                <br>
+                <h3>Procedure</h3>
+                <br>
+                <ol>
+                    <li> Prepare 5g of PDMS following section 1 of Microfluidics: general protocols. </li>
+                    <li> Prepare 1 mL of conductive silver paste following the manufacturer's instructions (Preheat parts A and B in stove at 70 degrees Celsius, put 0.5 mL of part A and 0.5 mL part B in a Petri dish, mix with the toothpick). </li>
+                    <li> See figure below for more information about the position of each element.
+Deposit a small layer of conductive silver paste on the border of the bottom of the imaging dish. Stick a piece of gold membrane cut with the scissors in the silver paste. Put 10 minutes in the stove at 70 degrees Celsius. Put another small layer of silver paste on top of the previous one.  </li>
+               <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/3/37/T--Pasteur_Paris--Double-membrane-chip.jpg" alt="Figure 1: Bonded double membrane microchannel chip">
+                    <figcaption>Figure 1: Bonded double <br> membrane microchannel chip</figcaption>
+                </figure>
+               <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/a/af/T--Pasteur_Paris--Microchannel-chambers.png" alt="Figure 2: Neuron and bacteria chambers">
+                    <figcaption>Figure 2: Neuron <br> and bacteria chambers</figcaption>
+                </figure>
+                    <li> Bond membrane microchannel chip to the bottom of the imaging dish following section 3 of Microfluidics: general protocols. The extremity of the gold membrane piece has to be in one of the holes of the neuron's chamber (see figure 3). </li>
+                    <li> Deposit a small layer of PDMS on the side where the membrane sticks out of the chip. Wait 2 minutes. Fill chip with distilled water. If water leaks out, unstick the chip, discard imaging dish and restart from step 3. </li>
+                    <li> Store in fridge. </li>
+                </ol>
+                <br>
+                <br>
+            </div>
+            <div class="panel" id="pan_0205" style="text-align:left;">
+                <div class="close_button">
+                </div>
+                <br>
+                <br>
+                <br>
+                <p> Unwanted living organisms in microfluidic chips can be a big deal, especially when these chips have to stay for 3 days filled with cultur medium in an incubator. The chips need to be exposed to UV rays in order to eliminate these unwanted organisms. We took extra securitiy measures, because we also needed to transport our chips from Institut Curie's lab at IPGG to Institut Pasteur. </p>
+                <br>
+                <h3>Materials</h3>
+                <br>
+                <ul>
+                    <li>   Bonded (to imaging dish) and water-filled microchannel chips  </li>
+                    <li>   Big Petri sish (150 mm diameter)  </li>
+                    <li>   Gloves (Kimtech PFE)   </li>
+                    <li>  UV curing unit (DWS) </li>
+                    <li>  Wrapfilm for food use (Ecopla France film pro)  </li>
+                    <li>   Parafilm (Bemis parafilm "M")  </li>
+                    <li>  Fridge </li>
+                </ul>
+                <br>
+                <br>
+                <h3>Procedure</h3>
+                <br>
+                <ol>
+                    <li> Open imaging dishes containing bonded microchannel chips and put them in the UV curing unit with their corresponding lid.  </li>
+               <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/3/31/T--Pasteur_Paris--Chip-sterilization.jpg" alt="Figure 1: Imaging dishes in UV curing unit">
+                    <figcaption>Figure 1: Imaging dishes <br> in UV curing unit</figcaption>
+                </figure>
+                    <li> Expose to UV rays for 20 minutes.  </li>
+                    <li> With gloves, put exposed dishes in a big Petri dish.  </li>
+                    <li> Seal Petri dish with parafilm. </li>
+                    <li> Cover Petri dish with 3 layers of wrapfilm. </li>
+                    <li>  Expose 15 minutes to UV rays.  </li>
+                    <li> Cover Petri dish with 2 additional layers of wrapfilm</li>
+                    <li> Store in fridge. </li>
+                </ol>
+                <br>
+                <br>
+            </div>
+            <div class="protocol_box">
+                <p> <a href="https://static.igem.org/mediawiki/2018/4/46/T--Pasteur_Paris--Microfluidics-microchannel-chip.pdf" style="font-weight: bold ; color:#85196a;"target="_blank">Get the PDF version of this section</a> </p>
+            </div>
              <script>
@@ Line 885: / Line 1,419: @@
          </div>
+        <div class="block separator-mark">
+        </div>
+        <div class="block full" id="micro_4" style="display:flex;flex-flow: row wrap;justify-content:center;margin:auto;">
+            <h2 style="order:1;">Vertical Chip</h2>
+            <p style="text-indent:0px;order:2;margin:2em;">The vertical chip was one of the designs for the support of the final experiment, that would serve as a proof of concept. The idea is to isolate the modified bacteria from the neurons using a membrane. To simplify the membrane's integration in a PDMS chip, a vertical design instead of a microchannel horizontal one was proposed. </p>
+            <div class="vignette" id="vign_0400">
+                <div class="vignette_for" id="for_0400">
+                </div>
+                <div class="vignette_back" id="back_0400">
+                </div>
+                <div class="vignette_text">
+                    <p>PDMS Vertical Chip Mold Fabrication</p>
+                </div>
+            </div>
+            <div class="vignette" id="vign_0401">
+                <div class="vignette_for" id="for_0401">
+                </div>
+                <div class="vignette_back" id="back_0401">
+                </div>
+                <div class="vignette_text">
+                    <p>PDMS Vertical Chip Fabrication</p>
+                </div>
+            </div>
+            <div class="vignette" id="vign_0402">
+                <div class="vignette_for" id="for_0402">
+                </div>
+                <div class="vignette_back" id="back_0402">
+                </div>
+                <div class="vignette_text">
+                    <p>PDMS Chip Sterilization</p>
+                </div>
+            </div>
+            <div class="panel" id="pan_0400" style="text-align:left;">
+                <div class="close_button">
+                </div>
+                <br>
+                <br>
+                <p> The mold was made of aluminium according to the following blueprint (figure 1). </p>
+                <br>
+                <br>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/b/b6/T--Pasteur_Paris--Vertical-Chip-Blueprint.jpg" alt="Figure 1: Vertical chip mold blueprint">
+                    <figcaption>Figure 1: Vertical chip mold blueprint</figcaption>
+                </figure>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/5/5b/T--Pasteur_Paris--Vertical-Chip-Mold.jpg" alt="Figure 2: Vertical chip mold" style="width:400px">
+                    <figcaption>Figure 2: Vertical chip mold</figcaption>
+                </figure>
+                <br>
+                <br>
+            </div>
+            <div class="panel" id="pan_0401" style="text-align:left;">
+                <div class="close_button">
+                </div>
+                <br>
+                <h3>Materials</h3>
+                <br>
+                <ul>
+                    <li> Molds  </li>
+                    <li> Polycarbonate gold-coated membrane filters, 0.4 micron, 13mm diameter (Sterlitech) or polymerized membrane (<a href="https://static.igem.org/mediawiki/2018/a/a9/T--Pasteur_Paris--Microfluidics-membranes.pdf"style="font-weight: bold ; color:#85196a;"target="_blank"> see protocol </a>)  </li>
+                    <li> Biopsy puncher (Kai biopsy puncher 2 mm and 4 mm)  </li>
+                    <li> Conductive silver paste (MG Chemicals 8330S-21G)   </li>
+                    <li> Tissue culture dish (TPP 93060, 53 mm internal diameter) Refer to <a href="https://static.igem.org/mediawiki/2018/3/3d/T--Pasteur_Paris--Microfluidics-general-protocols.pdf" style="font-weight: bold ; color:#85196a;"target="_blank"> Microfluidics: general protocols </a> for further materials.  </li>
+                </ul>
+                <br>
+                <h3>Procedure</h3>
+                <br>
+                <ol>
+                    <li>  Prepare 15 g of PDMS monomer using section 1 of <a href="https://static.igem.org/mediawiki/2018/3/3d/T--Pasteur_Paris--Microfluidics-general-protocols.pdf" style="font-weight: bold ; color:#85196a;"target="_blank"> Microfluidics: general protocols </a>. </li>
+                    <li> Demold the PDMS layer following section 2 of <a href="https://static.igem.org/mediawiki/2018/3/3d/T--Pasteur_Paris--Microfluidics-general-protocols.pdf" style="font-weight: bold ; color:#85196a;"target="_blank"> Microfluidics: general protocols </a>. Ignore step 2.</li>
+                    <li> Cut PDMS layer in two halves. </li>
+                    <li> Drill a hole in the center of each half with a 4 mm biopsy puncher. Drill holes in one of the two layer with a 2 mm biopsy puncher (see figure 1).</li>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/c/c6/T--Pasteur_Paris--Vertical-Chip-Layers.jpg" alt="Figure 1: Two halves of PDMS layer. Left : upper layer. Right : bottom layer">
+                    <figcaption> Figure 1: Two halves of PDMS layer. <br> Left : upper layer. Right : bottom layer
+</figcaption>
+                </figure>
+                    <li>Prepare 2 mL of conductive silver paste following the manufacturer's instructions (Preheat parts A and B in the stove at 70 degrees Celsius, put 0.5 mL of part A and 0.5 mL part B in a Petri dish, mix with the toothpick). </li>
+                    <li> Apply a path of silver paste on bottom layer starting from the center hole and going outwards of the layer (figure 2). Deposit one half of a membrane filter on center hole. Put in the stove at 70 degrees Celsius for 2 hours.</li>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/d/d6/T--Pasteur_Paris--Vertical-Chip.jpg" alt="Figure 2: Assembled vertical chip with gold-coated membrane filter" >
+                    <figcaption> Figure 2: Assembled vertical chip <br> with gold-coated membrane filter </figcaption>
+                </figure>
+                    <li>  Bond the two layers together (figure 3) according to section 3 of <a href="https://static.igem.org/mediawiki/2018/3/3d/T--Pasteur_Paris--Microfluidics-general-protocols.pdf" style="font-weight: bold ; color:#85196a;"target="_blank"> Microfluidics: general protocols </a>.</li>
+                    <li> Take the bottom of a tissue culture dish and deposit the other half of the membrane filter in the center. Apply silver paste and put in the stove at 70 degrees Celsius for 2 hours (figure 3) </li>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/d/d5/T--Pasteur_Paris--Vertical-Chip-Dish.jpg" alt="Figure 3: Tissue culture dish with membrane and silver paste" >
+                    <figcaption> Figure 3: Bonded layers </figcaption>
+                </figure>
+                    <li>Bond prepared tissue culture dish with product of step 7 (figure 4), bottom layer (figure 1) facing the dish, refering to section 3 of <a href="https://static.igem.org/mediawiki/2018/3/3d/T--Pasteur_Paris--Microfluidics-general-protocols.pdf" style="font-weight: bold ; color:#85196a;"target="_blank"> Microfluidics: general protocols </a>. </li>
+                <figure>
+                    <img src="https://static.igem.org/mediawiki/2018/4/42/T--Pasteur_Paris--Vertical-Chip-Bonded.jpg" alt=" Figure 4: Bonded vertical chip" >
+                    <figcaption> Figure 4: Bonded vertical chip </figcaption>
+                </figure>
+                </ol>
+                <br>
+                <br>
+            </div>
+            <div class="panel" id="pan_0402" style="text-align:left;">
+                <div class="close_button">
+                </div>
+                <br>
+                <h3>Materials</h3>
+                <br>
+                <ul>
+                    <li> Bonded chip, product of section 2  </li>
+                    <li> Big Petri dish (150 mm diameter) </li>
+                    <li>  Gloves (Kimtech PFE)   </li>
+                    <li>  UV curing unit (DWS)  </li>
+                    <li>  Wrapfilm for food use (Ecopla France film pro)   </li>
+                    <li>  Parafilm (Bemis parafilm "M")   </li>
+                    <li>  Fridge  </li>
+                </ul>
+                <br>
+                <h3>Procedure</h3>
+                <br>
+                <ol>
+                    <li> Open dishes containing bonded chips and put them in the UV curing unit with their corresponding lid. </li>
+                    <li>Expose to UV rays for 20 minutes. </li>
+                    <li> With gloves, put exposed dishes in a big Petri dish. </li>
+                    <li>  Seal Petri dish with parafilm. </li>
+                    <li>  Cover Petri dish with 3 layers of wrapfilm. </li>
+                    <li> Expose 15 minutes to UV rays. </li>
+                    <li> Cover Petri dish with 2 additional layers of wrapfilm. </li>
+                    <li> Store in fridge.</li>
+                </ol>
+                <br>
+                <br>
+            </div>
+            <div class="protocol_box">
+                <p> <a href="https://static.igem.org/mediawiki/2018/d/da/T--Pasteur_Paris--Vertical-chip.pdf" style="font-weight: bold ; color:#85196a;"target="_blank">Get the PDF version of this section</a> </p>
+            </div>
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+                                    }
+                                }
+                            }
+                            if (index_act != -1) {
+                                /*close active element*/
+                                var panel_act = document.getElementById("pan_"+cont_index+index_act);
+                                var back_act = document.getElementById("back_"+cont_index+index_act);
+                                var for_act=back_act.previousElementSibling;
+                                var text_act=back_act.nextElementSibling;
+                                panel_act.style.maxHeight = null;
+                                for_act.style.opacity = 1;
+                                text_act.style.opacity = 0.8;
+                                text_act.style.top = "4em";
+                            }
+                            /*open clicked element*/
+                            panel.style.maxHeight = panel.scrollHeight + "px";
+                            vignFor.style.opacity = 0;
+                            vignText.style.opacity = 1;
+                            vignText.style.top = "15em";
+                        }
+                    });
+                }
+            </script>
+        </div>