quinta-feira, 6 de agosto de 2015

Transcription machinery

Transcription is the initial step in gene expression. The number of genes or the genome size are not related to the complexity of an organism, but instead the ability to express a particular set of genes over a specific period of time and in different tissues allows organismal acclimatization to environmental changes. For this reason, it is extremely important the study of transcription machinery to better understand the evolutionary process.

We have sequenced several transcripts involved in the transcription process in all the 16 Loricariidae species investigated so far. The table below shows the sequenced transcripts according to their classification. Note the abundance of transcription factors. 



A fish? A shark? A cat? Or a dog? Just call me Squali


Knock, knock.

Who is there?







Squaliforma emarginata.

Squali who?

Squaliforma emarginata, a fish of the Loricariidae family. Yes, I have this shark-ish name, but I am indeed a fish, more precisely a catfish

OMG, Squalidae is a family of dogfish sharks! What are you?

I am a catfish that looks like a dogfish shark.

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There are around to 13 species of Squaliforma genus, all native from South America. This one was sampled in Manaus, Amazon state, Brazil for our work.

Among the fisherman in Manaus and in portuguese, this fish is known as "bodó de praia", which in a free translation would be "beach suckermouth armoured catfish". The popular name reflect the habit of this to live on sandy beaches along the banks of Solimões river.

The ''bodó de praia'' is trade as ornamental fish.

I hope you enjoyed! 
Bye

First of all, biosafety

Hello!

Biosafety is crucial!

Work in a laboratory frequently involve the use substances that are toxic, flammable, acidic and nasty stuffs. It is very important to be careful and prepared for possible issues. Let's recall some useful steps to avoid accidents in our work environment and always work with security.



Biosecurity is a set of actions to prevent, minimize or eliminate risks to the health of humans, animals and environment that are inherent to laboratory duties. Chief among those actions is the dressing code! Always wear your lab coat, gloves, long pants and closed shoes. The laboratory environment also asks for appropriate behaviour. Do not run, eat, drink or smoke. Always work with careful and attention. These steps will ensure your safety and also the quality of your results.

Be careful with the products, substances, samples, reagents. It is important to know how to handle each of these compounds and to utilize the appropriate safety equipments, like laminar flow cabinets (to volatiles and gases, for instance, since it promotes air recirculation and prevents the person inhale the toxic product). For example, we use TRIzol reagent, which is composed by Phenol and Chloroform, toxic chemicals used for RNA\DNA extraction. We only open Trizol inside laminar flow cabinets. Solvents, infectious substances, mutagenic or carcinogenic chemicals also deserve close attention.  All must be properly disposed of, according to its danger.

Others precautions as in handling fire, laboratory glassware (beaker, graduated cylinder, Erlenmeyer flask), liquid nitrogen and exposure to radiation should be thought. For instance, when we use the ultraviolet light to see the results of our PCRs, we must be careful with the direct exposure to it. U.V. light is a ionising radiation, and can damage the DNA and ultimately lead to cancer development.

To finalize, each laboratory has its particularity and different levels of biosafety are required. Watch out the biosafety level of your laboratory and stay on the safe side. 

Take care!



Don't trust manufacturer and pay attention

Hello!

Today we will give you a friendly advice.

Last month, Maithê and I (Paula) were making some reactions for real-time PCR. As usual, we planned the entire experiment with our advisor. We calculated all reagents that we would to use and we schematised the plate for the real-time PCR. Everything looked fine!

However, one of the necessary primers suddenly vanished when we were pipetting the plate!

This reagent was used just a few times, Maithê and I didn't know what was wrong. There should be plenty of primer left! We went to talk to our advisor and after some thought, the mystery was solved. 

Solution: We followed the manufacturer's instructions!

Yes, that is right, the problem was follow the manufacturer's instructions.

Making a long story short, they recommend to use 50 uL final volume, but use 25 uL to calculate the number of reactions the kit can perform. Easy to compute, if you use the recommended volume, you will be able to do only half of the reactions they advertise. 

At least, they recognised their mistake and are sending a new primer for replacement.

Lesson for the undergrad students: we can prevent these situations and alike by paying attention to the used reagents. We could (and should) have realised this primers was ending just by looking to the remaining volume. This would avoid bigger problems, such as the delay we are experiencing and waste of reagents.

The piece of advice? Do not trust manufacturer and pay close attention to the volume of all reagents you need.

See you.