RAIC - FIOCRUZ

Hey guys,

This week we (me and Paula) are participating of the RAIC (Annual Meeting of Undergraduate Students) at FIOCRUZ. It is the first time we take part on a meeting like that, in which undergrad students introduce their project to a committee that evaluate the 10 minutes student talk.

Last Friday (May 22), we attended the opening section. It was an interesting lecture about the differences of applied and basic research, and how importante it is to connect both.

We presented our work in the morning of May 28. I spoke about our sub-project with the endangered species Hypancistrus zebra (learn more about this species in our previous post), and Paula spoke about our work with the transcription machinery of Pterygoplichthys anisitsi (you will learn more about this in a near future post). Nonetheless, as in our section there was other three undergrads presenting their work, it was fantastic to hear about their projects, to know a little more about others areas, and what people think over our research.
We realised that not many researchers in our Institution are aware of the NGS potentialities. It is indeed an expensive method that demand a knowledge of bioinformatic that many people do not have (and, by the way, that we are learning). Two professors at our evaluation committee got interesting in this method and asked for our advisor email to exchange ideas. It was a nice and enriching experience.

Do you know what are Catalases?

Hi there,

Do you know what are Catalases? Where are they found? What does they do?

I will talk a little bit about them.

When we sequenced the Pterygoplichthys transcriptome, we found a lot of genes which were classified into many different families. After a primary separation, we obtained a big group of defensome genes, and among these, we have found one coding for a catalase enzyme.

Ok, but what is the importance them?

Catalase is an enzyme found in most aerobic organisms. In eukaryotic cells, it is located in the peroxisomes and it has the role of protecting the cell against the toxic effects of hydrogen peroxide (H2O2), a product from cellular metabolism. Catalase is an important enzyme for the prevention of oxidative damage, which is related to several diseases and ageing.

As any enzyme, catalase accelerate a chemical reaction; in this case, the conversion of a molecule of hydrogen peroxide to water and oxygen. It is important because converts the reactive oxygen species of H2O2 that causes oxidative stress in cells, compromising the health of the cell. So, it must be done quickly.

Simple reaction

Its structure is well know. Its active form is being compound for four polypeptide chains in a quaternary structure, so it's a tetrameric enzyme, with four heme groups. Interestingly, we found just a single transcript coding for catalase, specially because the active form of the enzyme is a tetramer. This is probably due to the very essencial and conserved function of this enzyme in aerobic organisms. You can see a diversity of crystallographic structures that are known in Protein Data Bank.

I hope you enjoyed.
See you later.

Hypancistrus zebra, the Zebra pleco

Hypancistrus zebra, or Zebra pleco, is just one of the 34 species of which we sequenced the liver transcriptome, but a good example of all the current threatens against Loricariidae fish. 

The Zebra pleco is endemic to a stretch of Xingu River of only 100km. This region, known as the “big bend”, is impacted by the construction of the Belo Monte dam, the world's third-largest hydroelectric dam. Fish ecologists say that the habitat changes caused by the dam construction puts this species at risk of extinction. This is among the main reasons why the Zebra pleco is at the list of endangered species from the Brazilian Ministry of the Environment and its capture is forbidden. Another major cause of concern is the Zebra pleco being extremely valuable in the international aquarium trade and, therefore, the traffic of this species is a regular practice that has challenged the Brazilian Environmental Authorities and the Federal Police. Sequencing and annotating the transcriptome of H. zebra and other endemic loricariids are effective ways to catalog and preserve the genetic biodiversity of these species. This genetic information provide environmental police-makers and the Federal Police unique ways to prevent and combat the traffic of the Zebra pleco and several other Loricariidae fishes popular in in the aquarium trade. Moreover, the genetic information that will be produced can also be useful to subsidize strategies for the conservation of these species, including their reproduction in captivity. 

By the way, the Zebra pleco we used were a kind donation from Dr. Jansen Zuanon, a fish taxonomy and ecology at the Brazilian National Institute for Amazonian Research who serve as the trustee for all H. zebra apprehended by Brazilian authorities.

ATP-binding cassette (ABC) family

Hello!

It is time to learn about one more gene superfamily.

Today, we will briefly introduce ATP-binding cassette (ABC) family, a very important group of proteins in our metabolism.

ATP-binding cassette proteins, or just ABCs, are present in cells from prokaryotes (bacterias) to eukaryotes (including mammals). Most ABCs are transmembrane proteins responsible for the transport of many substrates across cellular membrane, putting chemical compounds in and out the cell. Examples of ABCs substrates vary at length, but include amino acids, peptides, ions and others molecules that are usually hydrophilic (polar).

The transport of substrates carried out by ABCs occurs at an energy cost. ATP molecules must be   hydrolysed, realising the energy used to bind and move the substrate across the membrane. In other words, ABC proteins perform active transport (expend energy). The ABC proteins has an  hydrophilic portion in its structure and also an lipophilic portion, which is embedded inside the cellular membrane.

ABC proteins consist principally in two distinct domains, the transmembrane domain (TMD) and the nucleotide-binding domain (NBD). The first is compound for alpha helix in membrane bilayer. When transport a substrate, the TMD change its conformation and adapts to it. And the NBD is responsible for interact with ATP molecule and make the hydrolysis to produce energy for the protein action.

There are many differents types of ATP-binding cassette, its diversity is big. In the transcriptome we have analysed so far, we found 24 differentes subfamilies of ABC!

More exciting news are about to come.

See you soon!