Team:Valencia Biocampus/Notebook

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Revision as of 20:43, 18 July 2012

Notebook

18th July: Today, the [yeast sub-team] has made a big digestion of the plasmid for yeast and the first construction. They have left everything ready for the ligation reaction. And,great news for the bacteria sub-team!!!; after glycerining bac1 E.coli transformed cells they have started to measure the fluorescence of the proteins codified by the different inserts constructions in the defined media. They already have achieved good results in 3 out of 5 constructions tests!

17th July: In this sleepy day, the [bacteria sub-team] has picked a colony from a bac1 strain triple groove culture in order to grow it in LB+Amp media. Moreover, they have set up cultures with the other constructions to a selective media to get it grown in exponencial phase.

The [yeast sub-team] has done the minipreps of the second construction. They have run an electrophoresis gel with the maxipreps which were done the previous day, previously digested, and the minipreps of the second construccion, previously digested as well. Maxipreps were great but minipreps were not, so that they will sequence the second construction in order to confirm the integrity of it.

16th July: All the students have had a "wiki meeting" to plan how we want to design our wiki. The [bacteria sub-team] has set up a triple groove of bac1 vector transformed cells.

The [yeast sub-team]has carried on the maxipreps of the expression vectors for yeast. They will be checked tomorrow!

15th July: The [yeast sub-team] transformed E. coli with the second construction. The cell cultures carrying the yeast expresion vector have been incubated in 15 mL of LBA.

13th July: Today, the [bacteria sub-team] members carried on two mini-preps to get Bac1 construction purified. The plasmid with the interest construction was digested using the restriction enzymes EcoRI and PstI and the cell colonies were plated by triple groove. Furthermore, glycerined cultures have been made to keep them in stock.

The [yeast sub-team] did several minipreps to check the integrity of both vectors and the second construction. Unluckily, the last one was damaged, so next week they will start from the beggining with this construction.

12th July: Today, the bacterial cultures made the previous day grew succesfully, the [bacteria sub-team] members stringed several colonies and grew them in LB+Amp liquid media. Last construction (Bac1) arrived so E.coli has been trasnformed with it using the [Transformation Protocol Using Heat Shock]and has been plated in LB+Amp plates.

The [yeast sub-team] checked the 'maxis' done the day before by running an electrophoresis after digestion with EcoRI and PstI. Also, we have grown the strains with the Saccharomyces expression vectors and the yeast second construction for the following day.

11th July: The [bacteria sub-team]has set up some bacterial cultures, they have plated using triple groove in order to get isolated colonies which would be picked and grown in a selective media (37ºC, 200 rpm in a shaking stove) the following day. Moreover, they have made new media: LB and LB-agar.

The [yeast sub-team] has performed the maxipreps of their two constructions and they were stored in the fridge.

10th July: In this sunny day, the [bacteria sub-team] and the [yeast sub-team] have made an electrophoresis using the DNA which has been digested with EcoRV over-night. The results obtained were uneseful because, as the sub-team members discovered, the enzyme EcoRV was used to introduce the insert into the vector pUC57 so the cleavage site wasn't present anymore (the enzyme EcoRV cuts resulting in blunt ends).

9th July: Today, the [bacteria sub-team] and the [yeast sub-team] have made several mini-preps in order to purify the DNA constructions. The next step has been to test if the mini-preps have been successful. To do it, the sub-teams have digested these constructions (using restriction enzymes: EcoRI, PstI) and they have made an agarose gel in order to do an electrophoresis with the digested DNA. After that, they have revealed the gel and they have found out that the results were unexpected, so they have decided to make another digestion, in this case over-night and using only EcoRI, and carry out the subsequent electrophoresis tomorrow.

Moreover, the [poster sub-team] have made a brain-storming to start designing the logo for the team and the have drawn the first sketches.

8th July: Today, the [bacteria sub-team] and the [yeast sub-team] have transfered our transformed E.coli colonies to liquid media to make them grow over-night to manipulate them tomorrow.

6th July: Today, the [bacteria sub-team] and the [yeast sub-team] have transformed E.coli with the different constructions using the [Transformation Protocol Using Heat Shock]and have plated them in LB+Amp plates.

5th July: Today, the [bacteria sub-team] has finished all the culture media (for each construction). The bacteria sub-team has had lunch with the yeast sub-team and we have discussed some aspects about the project. Also, [yeast sub-team] has made the experimental protocol for next week.

4th July: Today, the [bacteria sub-team] has started to make up their bacteria media (L.B. and defined media).

3th July: Today, the [modelling sub-team] has made a meeting in order to share the deduced equations and decide the definitive ones. Later, it has been decided to search information which could be useful to characterize the behavior of E. coli systems and S. cerevisiae system

21th June: Today, the [modelling sub-team] has made a meeting where the advisors have explained the bases of modelling for synthetic biology. After that, the students have been responsible of deducing the equations that characterize our project.

@@ Line 7: / Line 7: @@
 == '''Notebook''' ==
-'''18th July''': Today, the ['''yeast sub-team'''] has made a big digestion of the plasmid for yeast and the first construction. We left everything prepared for the ligation reaction.
+'''18th July''': Today, the ['''yeast sub-team'''] has made a big digestion of the plasmid for yeast and the first construction. They have left everything ready for the ligation reaction. And,great news for the '''bacteria sub-team!!!'''; after glycerining bac1 E.coli transformed cells they have started to measure the fluorescence of the proteins codified by the different inserts constructions in the defined media. They already have achieved good results in 3 out of 5 constructions tests!
-'''17th July''': In this sleepy day, the ['''bacteria sub-team'''] has picked a colony from a triple groove culture in order to grow it in LB+Amp media (all the cells they will get will be clons). Moreover, the bacteria-members have passed a small volume of E.coli cultures with the other constructions to a selective media. All the falcon tubes containing the cells have been left into the shaking stove (37ºC, 200 rpm). The objetive is to get E.coli cells in exponencial growing in order to start testing the selective media the following day.
+'''17th July''': In this sleepy day, the ['''bacteria sub-team'''] has picked a colony from a bac1 strain triple groove culture in order to grow it in LB+Amp media. Moreover, they have set up cultures with the other constructions to a selective media to get it grown in exponencial phase.
-The ['''yeast sub-team'''] has done the minipreps of the second construcction. We ran a gel of electroforesis with the maxis that we did yesterday, previously digested, and the minipreps of the second construccion, previously digested too. The maxis were great but the minipreps not at all. We will sequence the second construcction in order to confirm the integrity of it.
+The ['''yeast sub-team'''] has done the minipreps of the second construction. They have run an electrophoresis gel with the maxipreps which were done the previous day, previously digested, and the minipreps of the second construccion, previously digested as well. Maxipreps were great but minipreps were not, so that they will sequence the second construction in order to confirm the integrity of it.
 '''16th July''': All the students have had a "wiki meeting" to plan how we want to design our wiki. The [bacteria sub-team] has set up a triple groove of bac1 vector transformed cells.
-The ['''yeast sub-team'''] did the maxis of the expresion vectors for yeast. We will check it tomorrow!
+The ['''yeast sub-team''']has carried on the maxipreps of the expression vectors for yeast. They will be checked tomorrow!
-'''15th July''': The ['''yeast sub-team'''] transformed E. coli with the second construccion. The cultures witch carry the yeast expresion vector were incubated in 15 mL of LBA.
+'''15th July''': The ['''yeast sub-team'''] transformed E. coli with the second construction. The cell cultures carrying the yeast expresion vector have been incubated in 15 mL of LBA.
-'''13th July''': Today, the ['''bacteria sub-team'''] members did two mini-preps in order to get ''Bac1 construction'' purified. After that, they digested the plasmid which contained the construction of interest using the digestion enzymes ''EcoRI'' and ''PstI'' and they made an agarose gel where the samples were put. The picture obtained showed that it was perfect so the bacteria-members decided to plate using triple groove and let the cells divide. Furthemore, they glycerined the cultures with the tested constructions in order to have an stock of cell that the could use if necessary.
+'''13th July''': Today, the ['''bacteria sub-team'''] members carried on two mini-preps to get Bac1 construction purified. The plasmid with the interest construction was digested using the restriction enzymes ''EcoRI'' and ''PstI'' and the cell colonies were plated by triple groove. Furthermore, glycerined cultures have been made to keep them in stock.
-In this day, the ['''yeast sub-team'''] did several minipreps to comprobate the integrity of both vectors and the second construction. Unluckily, the last one was damaged, so the next week will start from the very beggining with this construction.
+The ['''yeast sub-team'''] did several minipreps to check the integrity of both vectors and the second construction. Unluckily, the last one was damaged, so next week  they will start from the beggining with this construction.
-'''12th July''': Today, the bacterial cultures made the previous day grew succesfully, the ['''bacteria sub-team'''] members stringed several colonies and grew them in LB+Amp liquid media. In the afternoon, the last construction (Bac1) arrived so they transformed ''E.coli'' with it using the [Transformation Protocol Using Heat Shock]and have plated ''E.coli'' cells in LB+Amp plates.
+'''12th July''': Today, the bacterial cultures made the previous day grew succesfully, the ['''bacteria sub-team'''] members stringed several colonies and grew them in LB+Amp liquid media. Last construction (Bac1) arrived so ''E.coli'' has been trasnformed with it using the [Transformation Protocol Using Heat Shock]and has been plated in LB+Amp plates.
-The ['''yeast sub-team'''] checked the 'maxis' done the day before by running an electrophoresis after digestion with EcoRI and PstI. Also, we grew the strains with the Saccharomyces expression vectors and the yeast second construction for the next day.
+The ['''yeast sub-team'''] checked the 'maxis' done the day before by running an electrophoresis after digestion with ''EcoRI'' and ''PstI''. Also, we have grown the strains with the ''Saccharomyces'' expression vectors and the yeast second construction for the following day.
-At lunchtime the ['''bacteria sub-team'''] and the ['''yeast sub-team'''] had a nice meeting to discuss some issues related to the project.
-'''11th July''': In this lovely day, the ['''bacteria sub-team'''] set up some bacterial cultures, they plated using triple groove in order to get isolated colonies which would be pick and grown in a selective media (37ºC, 200 rpm in a shaking stove) the following day. Moreover, they  made new media: LB and LB-agar.
+'''11th July''': The ['''bacteria sub-team''']has set up some bacterial cultures, they have plated using triple groove in order to get isolated colonies which would be picked and grown in a selective media (37ºC, 200 rpm in a shaking stove) the following day. Moreover, they have made new media: LB and LB-agar.
-The ['''yeast sub-team'''] has performed the maxipreps of our two constructions and they were stored in the fridge.
+The ['''yeast sub-team'''] has performed the maxipreps of their two constructions and they were stored in the fridge.
 '''10th July''': In this sunny day, the ['''bacteria sub-team'''] and the ['''yeast sub-team'''] have made an electrophoresis using the DNA which has been digested with ''EcoRV'' over-night. The results obtained were uneseful because, as the sub-team members discovered, the enzyme ''EcoRV'' was used to introduce the insert into the vector pUC57 so the cleavage site wasn't present anymore (the enzyme ''EcoRV'' cuts resulting in blunt ends).