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	Gel 0,8%		Gel 0,8%
-	<h3>Preparation of tadpole samples for HPLC</h3>
-	'''Aim:''' HPLC test to evaluate the presence of auxin in tadpoles embryos<br>
-	Materiel:<br>
-	- IAA powder (stocked at -20°C)<br>
-	- NAA powder (stocked at room temperature)<br>
-	- Acetonitrile 100% HPLC grade<br>
-	- Methanol 100% HPLC grade<br>
-	- Falcon 15ml<br>
-	- 1,5ml tubes<br>
-	- Pasteur pipettes<br>
-	- Mortar<br>
-	- Centrifuges<br>
-	- Ice<br>
-	- Vortex<br>
-	- P1000, P200 with tips<br>
-	The original protocol from Vastag L, Jorgensen P, Peshkin L, Wei R, Rabinowitz JD, et al. (2011) Remodeling of the Metabolome during Early Frog Development. PLoS ONE 6(2): e16881. doi:10.1371/journal.pone.0016881 article was performed on 1 egg of Xenopus laevis. Because 1 embryo of this species represents 10 embryos of Xenopus tropicalis,  we decided to perform our protocol on 10 Xenopus tropicalis embryos.<br>
-	Prerequisite: To have perform a FIV and the auxin toxicity protocol the day before.<br>
-	Before beginning: Turn on the centrifuge at 4°C<br>
-	1. Preparation of solutions (chemical hood)<br>
-	- Mix for 10 samples<br>
-	2ml acetonitrile<br>
-	2ml methanol<br>
-	1ml H2O<br>
-	Cool mix to -20oC<br>
-	- Preparation of auxin solutions 1mg/ml in 20% acetonitrile/H2O<br>
-	NAA<br>
-	1,8mg NAA<br>
-	360ul acetonitrile<br>
-	1440ul H2O<br>
-	IAA<br>
-	10,4mg IAA<br>
-	2080ul acetonitrile<br>
-	8320ul H2O<br>
-	2. Preparation of the samples<br>
-	Take 10 embryos of each condition in IAA and NAA (0, 125, 250 and 500 uM)<br>
-	Rinse 4 times in H2O:<br>
-	- Fill  4 wells of a 12 wells-plate with ddH2O<br>
-	- Place the embryos of one condition in a well to another, to another…<br>
-	Place the embryos in 1,5ml tubes<br>
-	Add 55ul of cold mix<br>
-	Crush the embryos with a mortar <br>
-	Vortex<br>
-	Place on ice for 20min<br>
-	Centrifuge 5min – 14000 rpm – 4°C (centrifuge eppendorf 5417R)<br>
-	Collect as much as possible of the supernatant and place it in new tubes<br>
-	To extract more:<br>
-	Add 55ul of the mix on the pellet<br>
-	Repeat all steps<br>
Line 185:		Line 137:
	PCR of imperial college BB with these primers to BB IaaH and IaaM.		PCR of imperial college BB with these primers to BB IaaH and IaaM.
	Electrophoresis show that results aren't good.		Electrophoresis show that results aren't good.
		+
		+	<h3>PCR:</h3>
		+
		+	PCR of pCS2+:
		+
		+	<table border="1">
		+	<tr>
		+	<td>Reactants</td>
		+	<td>Volumes (µl)</td>
		+	</tr>
		+	<tr>
		+	<td>GC Buffer</td>
		+	<td>10</td>
		+	</tr>
		+	<tr>
		+	<td>dNTPs</td>
		+	<td>1</td>
		+	</tr>
		+	<tr>
		+	<td>DNA</td>
		+	<td>0,5</td>
		+	</tr>
		+	<tr>
		+	<td>H2O</td>
		+	<td>33</td>
		+	</tr>
		+	<tr>
		+	<td>Primers (FW and RV)</td>
		+	<td>2,5 each</td>
		+	</tr>
		+	<tr>
		+	<td>fusion polymerase</td>
		+	<td>0,5</td>
		+	</tr>
		+	<table/>
		+	<h3>PCR:</h3>
		+	0,8% agarose
	<h2>Thursday, 26th July</h2>		<h2>Thursday, 26th July</h2>

---

Latest revision as of 10:01, 9 August 2012

Weeks:

June			July				August				September				October				November

Week 7: 23rd July - 29th July

Monday, 23rd July

Cloning:

4 different clones pCS2+ RFP => incubation in LB medium overnight at 37 degree celsius.

PCR:

PCR of pCS2+:

Reactants	Volumes (µl)
GC Buffer	10
dNTPs	1
DNA	1
H2O	32,5
Primers (FW and RV)	2,5 each
fusion polymerase	0,5

Xenopus:

Start of auxin's toxicity test on tadpoles: Tadpoles in there growth media + 0/125/250 or 500 µM auxin
We changed this media each days during one week

Tuesday, 24th July

Plasmid Purification:

On the pCS2+ RFP clones incubated the day before:

DNA Concentration

Tube	Concentration (ng.uL-1)
1	144,2
2	161,9
3	184,9
4	120,7

Digestion:

Plasmid digestion

Tube	V DNA (uL)	V SpeI (uL)	V EcoRI (uL)	V buffer (uL)	V H2O (uL)
1	7	1	1	2	9
2	6,2	1	1	2	9,8
3	5,4	1	1	2	10,6
4	8,3	1	1	2	7,7

Gel migration:

Gel 0,8%

Wednesday, 25th July

Reception of primers fo Auxin Enzymes: IaaH FW and Rv and IaaM FW and RV.
PCR of imperial college BB with these primers to BB IaaH and IaaM. Electrophoresis show that results aren't good.

PCR:

PCR of pCS2+:

Reactants	Volumes (µl)
GC Buffer	10
dNTPs	1
DNA	0,5
H2O	33
Primers (FW and RV)	2,5 each
fusion polymerase	0,5

PCR:

0,8% agarose

Thursday, 26th July

Test of auxin toxicity in tadpodes. Retry of IaaH and IaaM BB: Ok for IaaM but not for IaaH.

Friday, 27th July

• PCR of TirI: One PCR with primers TirI FW + Sdm RV / One PCR with primers TirI RV + Sdm FW
• Gel extraction of these PCR
• New PCR with the mix of the two PCR products + primers TirI FW and RV