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IGEM Evry 2014

Biology - Genome Assembly

De novo Genome assembly

Antibiotic resistance

Concerning the antibiotics, we look at specific antibiotics such as kanamycin, erythromycin, tetracycline, ampicillin, and chloramphenicol and other type of resistance gene. For the kanamycin and erythromycin, we found not relevant annotation. However, for the other ones, tetracycline, ampicillin, and chloramphenicol, we found specific annotations.
Regarding the tetracycline, we found that it possessed one Tetracycline repressor protein class H , two Tetracycline resistance protein, class C and nine Bacterial regulatory proteins, tetR family annotated genes. This result are coincident with our experiment where we found that Pseudovibrio is resistant to tetracycline.
About the ampicillin, one Metallo-beta-lactamase superfamily protein, Beta-lactamase, Beta-lactamase type II precursor, two Beta-lactamase precursor, Beta-lactamase hydrolase-like protein HTH-type transcriptional activator AmpR and five Putative beta-lactamase HcpC precursor were predicted by the Prokka software. Also this result is coincident with our experiment.
For the Chloramphenicol antibioctics, we predicted that the chloramphenicol phosphotransferase-like protein, Chloramphenicol 3-O phosphotransferase and Chloramphenicol acetyltransferase are present in our strain. The last one is used as a reporter gene in molecular biology. But in contrary to other antibiotics, the test does not reveal, that our strain is resistant to the Chloramphenicol.
Finally we look at other antibiotic resistance and we see that other antibiotics such as the Bleomycin are predicted. Bleomycin is used as a chemotherapy agents for the Hodgkin's lymphoma. Also it possessed the Multidrug resistance protein, MdtA, MdtA precursor, MdtB, MdtK, MdtN, MdtH, MdtG, which are known to play an important role in antibiotic resistance.

Restriction enzyme

Figure 1: Sequence of the pRhokHi vector and the hightlight of the EcoKI target sequence






Figure2 : Anaerobic pathway degradation for phenol