Team ATOMS-Turkiye

atoms2015@googlegroups.com

RESULTS

Here we provide a brief of our project’s results.

ULCER TREATMENT

AcidResistance(GadE-BBa_K1639002)

Our aim in using this part is to have E. Coli acid resistant to make it survive in acidic stomach microenvironment. For this purpose, we planned to make E. Coli overexpressing GadE protein. After we did cloning and some other experiments, we observed that recombinant E. Coli successfully survived in pH 2.0 for 5 to 9 hours. It also was able to showmultiplication function in pH 2.0 for 3-5 hours.Click here to get into deatils..

AcidRepellency(TlpB-BBa_K1639003)

This part is added in order to direct E. coli from acidic gastricjuice to basic stomach mucus layer where H. Pylori lives. To accomplish this, we made E. Coli producing TlpB chemoreseptor. Our cloning results and other experiment results showed that we managed to produce desired protein in the cell.

IncreaseMotilitySpeed: (HNS-BBa_K1639004/HNS-T108I-BBa_K1639005/PotB59-PomA-BBa_K1639006)

We added this part into E. Coli in order to increase votility and torque force of it, thus it expected to penetrate into mucus layer and move freely under that layer. For this purpose, we decided to use HNS-T108I And PotB59/PomA proteins. After cloning and doing some other experiments, we observed both of these parts increased flagellar speed.

SensingH.pylori:(BBa_K1639000,BBa_K1639001, BBa_K1639014)

Our main goal of using this part is sensing Helicobacter Pylori’s presence and report its presence. hence, we decided to sense NH^^ and AI-2 molecules synthesized by H. Pylori. We chose TnrA-pAlsT system for sensing NH3 and Lsr operon for sensing AI-2. To attach these two inputs to one result, we used a novel system called Toehold switch- Trigger RNA system. We used ATOMS 2013 team’s results of Lsr part. Our cloning experiments and other assays showed Toehold swich-Trigger RNA system worked 175 times more efficient. We also observed that system works without any leakage.

Killling H. Pylori (BBa_K1639007, BBa_K1639008)

We aimed to kill H. Pylori with the help of a very efficient antimicrobial peptide called Pexiganan. For this, we designed this process to happen; firstly inactive DAMP-Pex proteins accumulate in cell then they activate with an enzymatic reaction when H. Pylori presence is sensed. After we did cloning and other experiments of this part, we observed that DAMP-Pex and TEV protease were produced successfully. TEV protease is the enzyme responsible for cleavage of DAMP-Pex complex.

GASTRIC CANCER TREATMENT

(BBa_K1639009, BBa_K1639010, BBa_K1639011, BBa_K1639015, BBa_K1639016)

We aimed to kill cancer cells specifically by utilizing their miRNA profiles. Therefore we used a miRNA sensing system which based on pTET off-pTRE and mLacI-LacO systems. We successfully cloned these reporter constructs and got positive results fromother experiments too.