June

Week 1

First week of june we got look arround the laboratory space that we would using and make a list of preparation that we need for wetlab team. We prepare for LB medium, antibiotic optimation and make competent cell using CCMB 80 buffer. We also sterilize all of the equipment needed. We have already choose our idea to engineer bacteria that could degrade plastic. Before choosing that idea we had four main ideas:
1. Microalgae biofuel
2. Synthetic bacteria that could degrade plastic
3. Urine biosensor
4. Sianide biosensor
After competent cells are ready and antibiotic optimation done we have plan to try rehydrated some parts and transform it to our E. coli DH5α competent cell. We also make a design of our construct whic is become the final design after long discussion before so that we will ready to order some synthetic part and order to iGEM Hq for some part that not provided in the 2014 parts.

Week 2

This is our first time to see the iGEM distribution kit plate so exciting. We will make a trial to transform iGEM 2013 distribution kit using our competent cell. That is not work good on first, second and third trial. Then we concluded that we must try the iGEM distribution kit plate 2014. We also try to test our competent cell efficiency and we dont face any problem with our competent cell.

Week 3

Finnaly, we rehydrated parts from iGEM kit plate 2014 which have many twins to make sure our methode is optimal to transform iGEM parts. We have already planed to make four system for our bacteria degrading plastic so that we devided our team into four group that will concerning to each system. We try to transform BBa_K592025, BBa_B0015, BBa_B0034, BBa_I0040. After the transformation still we dont have any colonies.

Week 4

We have target that we must be abble to transform parts from iGEM distribtion kit. Finnaly we can see our red colony from RFP parts. So, we make liquid culture and wait until 16 hours, the medium turn into red. We try to isolation the plasmid using Alkaline Lysis method. Confirmation of the plasmid isolation using electrophoresis, restriction and PCR. The result was positive.

July

Week 1

Finnaly our constructs are already fixed. We ordered our synthetic gene for our main construct and order some parts from iGEM Headquarters. Our competent cell also ready for transforming the other parts that we will use for our construct. We rehydrated BBa_K592025, BBa_J04450, BBa_C0040, BBa_B0017 and BBa_B0015. the colonies was growing well and ready for plasmid isolation. All of the plasmid was confirmed using restriction method and the result was positive. In this first week of July we learn more about 3A assembly since we are ready to make our construct as well.

Week 2

We are ready to construct our building blocks. But first, we make some optimation methode for double digest restriction reaction including for time incubation and reaction compotition. We also receive our parts that we ordered from iGEM headquarter BBa_K103006, BBa_K228004, BBa_K936024, BBa_K339010. We also tried to build our construct using two methods : standard assembly and 3A assembly. Still not work well. In this week we also elaborate and brainstoarming for our next methode after our construct done.

Week 3

We are ready to try 3A assembly again, we make four different ligation compotition to make sure wich one will work well. After transformation, finnaly we got few colony in our petry disc, ready for plasmid isolation. After confirmation for all of the plasmid, we got no right colony yet. Then try again, now we are using PSB1C3 with Rfp for the plasmid bacbone instead of linearized plasmid to make it easier for colony selection using red-white screening. still not got our right construct. Let the challange begin and let’s do the best for it.

Week 4

Challenge accepted, we did our 3A again. We discusse about our failure for the 3A this tw weeks and got some conclussion. We tried to do again and finnaly for this trial we got some collony which the right construct BBa_K1387002. Finnaly we found the optimum ligation compotition and reaction. Ready for another construct for reporter and converter module while waiting for synthetic gene for our main construct.

August

Week 1

We already received our primer to check our construct including universal primer and some primer which is spesific to our gene. First, we optimize our PCR reaction using gradient PCR technique. Some of our construct show a good result. Our problem now is, some of our construct is still in pSB1K3 backbone, so we must make a assembly to make our construct in the pSB1C3 backbone.

Week 2

In this week we are trying to make our 3A assembly again since we still have some gene construct that must be finished before our synthetic gene comes. From the 3A assembly we got several colony that ready for plasmid isolation. After the confirmation through PCR methode, we did not get the right colony yet, so we must try the other compotition in ligation compotition, because we did not face any problem in transformation. After trying any ligation reaction , we got the optimal compotition for some construct, but the other still become our big mystery. In this week, we are also want to try the construct from UC Davis for Lc Cutinase BBa_K936020 and ethylene glycol converter module BBa_K936024. We did plasmid isolation from that part and transform it to the E.coli BL21 (DE3) We try to test the gene expression and test the product through SDS-PAGE method and we can see the protein band from both of the construct but not as the thick band. We also try to sequencing the positive construct in this week.

Week 3

Our target in this third week of august is to finish all of the construct except the construct that need synthetic gene due the parts submission deadline is coming. Restriction, purification gell (if needed), ligation, transformation, plasmid isolation, and confirmation is become our routine activities. In this week, we also learn more about how to express our protein, how to test our construct, how to measure the construct activities and did SDS-PAGE analysis.

Week 4

We focused to make a simple trial for our method to test the protein band of cutinase, and conversion methode, and discuss about our construct characterization especially for OmpA-LcCutinase construct (PET degradation module) as our main construct. We also discuss for synthetic gene cloning method. In this week we also focused on finishing our construct in PSB1C3 backbone and ready for shipment. Brainstoarming also become our routine activities because we found some failure in this week and feel not ready yet facing the parts submision deadline. We also try to elaborate how to make a modeling for our system and discuss with the expert.

September

Week 1

We have to prepare our parts submission form and check all of positive construct to make sure the condition of the construct is still good. In this week, synthetic gene, the thing that we waiting for one and half month finnaly arrived in our campuss. We try to make optimal reaction for our limited stock of synthetic gene. We try to clone our synthetic gene into some backbone including some of commercial clone vector and PSB1C3 of course. No collonies observed, so desperate and we discuss and evaluate our method and take a note of some mistake that we did in this method. Fortunatelly we have primer for our synthetic gene so we could do amplification using PCR for our synthetic gene. We also make new competent cell and trying electhrophoration transformation method instead of common heat shock methode. Still, no colonies observed.

Week 2

We try to clone our synthetic again. We must be succes in this week to step forward finishing our main construct. We try several method and try to use overnight ligation method. Finnaly, we got the positive colony, so happy. We also checked our plasmid again and found that some of our construct disappear but the other is still in good condition. We also make a optimization for PCR using touchdown and temperature gradient method to check the good temperature condition for the primer.

Week 3

We did PCR for construct confirmation for the collonies through crude PCR method using the optimal annealing temperature. We also did plasmid isolation for the positive colonies. We also make the method plan for PET degradation characterization using our construct and compared to UC Davis construct. We make some method for measurement including pH detection, ethylene glycol detection using dichromic acid method, and check the correlation between cell number in PET degradation rate.

Week 4

We submitted some of our parts including BBa_K1387000, BBa_K1387002 and BBa_K1387006 In the 11 days remaining for parts submission, we still try to build our construct and start to think the future development of our system. We also try to help Brawijaya team to cloning some of their parts and synthetic gene. We will start our parts characterization using several method including ethylene glycol assay using chromatic acid, pNPP assay to check the activity, growth curve, SEM, and qualitative assay using tributirin agar method.

October

Week 1

The sending parts week for second term. three parts is ready to send including BBa_K1387001, BBa_K1387006 and BBa_K1387005. Our dry lab team is also ready for modelling. We got some parameter to make the modelling. We also got some idea for our future system.