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Revision as of 14:32, 30 October 2017
Experiment
The function of dCas9 and gRNA
We first construct the gRNA targeting at OriC and test if it could work as we expected. Through OD measurement we observed an inhibition of growth while dCas9 and gRNA are expressed.
For further description of this synchronization method, we quantifying the number of OriC, dxs and TerC by using qPCR, the results confirms that the initiation of chromosome replication is inhibited.
The flow cytometric is also used to conduct the run-out experiment to quantify the synchronization efficiency.
According our results, we can conclude that the dCas9 and gRNA(OriC) can be used to synchronize the cell cycle of E. Coli.
The light induced CRISPR/dCas9 at transcription level.
The optimization of our CcaS-CcaR system with a higher difference in green and red light is conducted by our advisor.
The result shows the performance of this system. Next we insert the sequence of gRNA(OirC) behind the Pcpcg2, measure the OD performance under green and red light(fig).
The results shows a difference in growth rate when in green or red light. Similarly, next we performed the qPCR and flow cytometric to further demonstrate the synchronization.
But due to time limitation, the result is not so good to see. At last, we test if this system can make reverse regulate, here is our results.
The light induced CRISPR/dCas9 at protein level
We first constructed series of infused pMag-sdCas9 and nMag-sdCas9 with difference split methods, but results of OD measuremen do not shows any difference between them and wild type.
Next we go back to find out where is the problem. First we test the function of pMag and nMag through Luciferase assay.
Results shows that the function of pMag and nMag. Next we test the expression of split dCas9 to check if it is hydrolysis by SDS-PAGE.
After inserting it into pET plasmid, the results turnout that protein is ......
The last reason we want to see if it is because the split method that makes the split dCas9 can’t complement. But due to some reason, we can’t finish constructing the plasmid in time and have no further results.
Material and methods
Plasmid construction
The fragment was PCR amplified with pfu(company) or PrimeSTAR(Takara) according to product length. Product is recycled with gel extraction kit from qiagene after electrophoresis. Golden gate is conducted with total 10 liter containing 100 ng template, 5 liter buffer, 5U BsaI, and 10 U T4 ligase. With 50 cycles with 37 5min and 16 10min finished with 55 5min and deactivate at 98 for 5 min. Then transformed into trans5a using commercial component cell (xxx). homologous recombination to conducted using vyzyme xxxxx kit and operate following the guidebook.
The OD measurement
Cell are cultured overnight in LB broth containing corresponding antibiotics, and diluted into 1% fresh LB broth. When OD is reaching 0.6 add aTc of final concentration 200 ng/ ml to induce expression of dCas9 and inject it into 24 cell culture plate. Culture the plate in 37 and 150 rpm. Every hour put it into a plate reader to measure its OD.
SDS-PAGE is conducted under the following protocol.
The qPCR experiment is conducted using qPCR kit from takara. The sample is collected every 30min and freeze at liquid nitrogen after centrifugal. The genome is for qPCR is extracted using xxxx kit(takara) . Primer used for qPCR is as following.
The flow cytometric is conducted with xxx. A and B are added into culture when the OD is at 0.6. After 2 hours, the riphamaycine and ceph are added to inhibit replication initiation and cell division, and cultured for another 2 hours to let the replication complete. Then the culture is stained with DAPI(roche) for 1 min and send into machine to detect the DNA concentration per cell.
The Agarose Pad Assay
To acquire the growth rate of bacteria for establishing the growth function, an agarose pad assay is conducted. Mix the 0.15g agarose and 10ml LB to reach the concentration of 1.5%,then heat it and add needed matter after cooling slightly.The melted agarose is supposed to be pipetted onto a cover glass(The volume is about 2.5ml.).Then put another clean cover glass on it to get a smooth flat surface after about 3 minutes. The next step is to pipette about 2.5 μL E.coli solution of 0.02 OD and get a new cover glass on it till the solution dries.It’s worth noting that maintain the favorable environment is vital.We used parafilm to avoid the evaporation and tinfoil to keep out the light when observed dCas9 4-1 which was induced by aTc. Observe the agarose pad under microscope to find the optimum bacteria, for instance, which are under the fission.The final thing you do to take and save picture 10 minutes per in 8 to 10 hours.
For further description of this synchronization method, we quantifying the number of OriC, dxs and TerC by using qPCR, the results confirms that the initiation of chromosome replication is inhibited.
The flow cytometric is also used to conduct the run-out experiment to quantify the synchronization efficiency.
According our results, we can conclude that the dCas9 and gRNA(OriC) can be used to synchronize the cell cycle of E. Coli.
The light induced CRISPR/dCas9 at transcription level.
The optimization of our CcaS-CcaR system with a higher difference in green and red light is conducted by our advisor.
The result shows the performance of this system. Next we insert the sequence of gRNA(OirC) behind the Pcpcg2, measure the OD performance under green and red light(fig).
The results shows a difference in growth rate when in green or red light. Similarly, next we performed the qPCR and flow cytometric to further demonstrate the synchronization.
But due to time limitation, the result is not so good to see. At last, we test if this system can make reverse regulate, here is our results.
The light induced CRISPR/dCas9 at protein level
We first constructed series of infused pMag-sdCas9 and nMag-sdCas9 with difference split methods, but results of OD measuremen do not shows any difference between them and wild type.
Next we go back to find out where is the problem. First we test the function of pMag and nMag through Luciferase assay.
Results shows that the function of pMag and nMag. Next we test the expression of split dCas9 to check if it is hydrolysis by SDS-PAGE.
After inserting it into pET plasmid, the results turnout that protein is ......
The last reason we want to see if it is because the split method that makes the split dCas9 can’t complement. But due to some reason, we can’t finish constructing the plasmid in time and have no further results.
Material and methods
Plasmid construction
The fragment was PCR amplified with pfu(company) or PrimeSTAR(Takara) according to product length. Product is recycled with gel extraction kit from qiagene after electrophoresis. Golden gate is conducted with total 10 liter containing 100 ng template, 5 liter buffer, 5U BsaI, and 10 U T4 ligase. With 50 cycles with 37 5min and 16 10min finished with 55 5min and deactivate at 98 for 5 min. Then transformed into trans5a using commercial component cell (xxx). homologous recombination to conducted using vyzyme xxxxx kit and operate following the guidebook.
The OD measurement
Cell are cultured overnight in LB broth containing corresponding antibiotics, and diluted into 1% fresh LB broth. When OD is reaching 0.6 add aTc of final concentration 200 ng/ ml to induce expression of dCas9 and inject it into 24 cell culture plate. Culture the plate in 37 and 150 rpm. Every hour put it into a plate reader to measure its OD.
SDS-PAGE is conducted under the following protocol.
The qPCR experiment is conducted using qPCR kit from takara. The sample is collected every 30min and freeze at liquid nitrogen after centrifugal. The genome is for qPCR is extracted using xxxx kit(takara) . Primer used for qPCR is as following.
The flow cytometric is conducted with xxx. A and B are added into culture when the OD is at 0.6. After 2 hours, the riphamaycine and ceph are added to inhibit replication initiation and cell division, and cultured for another 2 hours to let the replication complete. Then the culture is stained with DAPI(roche) for 1 min and send into machine to detect the DNA concentration per cell.
The Agarose Pad Assay
To acquire the growth rate of bacteria for establishing the growth function, an agarose pad assay is conducted. Mix the 0.15g agarose and 10ml LB to reach the concentration of 1.5%,then heat it and add needed matter after cooling slightly.The melted agarose is supposed to be pipetted onto a cover glass(The volume is about 2.5ml.).Then put another clean cover glass on it to get a smooth flat surface after about 3 minutes. The next step is to pipette about 2.5 μL E.coli solution of 0.02 OD and get a new cover glass on it till the solution dries.It’s worth noting that maintain the favorable environment is vital.We used parafilm to avoid the evaporation and tinfoil to keep out the light when observed dCas9 4-1 which was induced by aTc. Observe the agarose pad under microscope to find the optimum bacteria, for instance, which are under the fission.The final thing you do to take and save picture 10 minutes per in 8 to 10 hours.
