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Genomics and Transposable Elements

 

Characterization of SChAT family transposases in sugarcane: functional and molecular studies

 

 

The main goals of this project were: identify and characterize hAT-like elements in the sugarcane genome, understand their relation with the genome and possible role in sugarcane genome evolution, as well as, in other grasses like rice, sorghum and brachypodium.    

 

Transposable elements (TEs) have the capacity to mobilize through the genome locus. The mobilization affects the genome structure and evolution by phenomena as genes shuffle and fatten the host genome. Domestication events of the TEs protein domains occur when they are recruitment by the host genome for construct new genes, making the TEs donors of functional protein domains, creators of regulation networks and promoters of genetic variability in all living organism. The hAT transposase superfamily is defined as elements that share dimerization and zinc-finger domains with the previously described hobo (Drosophila melanogaster), Activator (Zea mays) and Tam3 (Antirrhinum majus) transposon elements. For more information see our publication section. 

 

Developer: Edgar Andrés Ochoa C.

Founding: CNPq and FAPESP.

Partners: GaTE-LAB at USP-São Paulo.

                 Genetik AG Kunze at Freie Universitat-Berlin.

 

 

 

 

Metagenomics

 
Can you get the entire DNA from the world?

 

 

There are several microorganisms that can't be, or we haven manage to, culture in the lab. Nevertheless, with Metagenomics you will have access to all the information in your sample, the entire DNA! You just need to take a soil sample, or water, or whatever sample you want. Recover the entire DNA, no matter who this DNA was from. Later, you sequence it. After that, with bioinformatics tools, you can find new genes or important genes that can be used for several purposes. Not so easy as it sound but a lot of people have done it! 

 

 

 

We participated in a metagenomic project at the collecting samples stage. The objective was to take samples of soil and sediment on the Antarctic continent. We were looking for genes related to the biosynthetic pathway of polyketide synthase (PKS). The PKS is a family of enzymes that produce a large class of secondary metabolites (polyketides) in bacteria, fungi and plants. Polyketide synthases are an important source of naturally occurring small molecules used mainly for chemotherapy. There is a long list of industrially important polyketides: many of the commonly used antibiotics, such as tetracycline and erythromycin; molecules as rapamycin (immunosuppressant); lovastatin (anticholesterol drug) and epothilone B (anticancer drug).

 

 

Developer: Edgar Andrés Ochoa C.

Founding:  CNPq.

Partners:  BioProducts-LAB at USP-São Paulo.