Tursday lessons

Dear all, the Dept. organized a workshop on RNA world. You’ll attend the seminars as part of the course.

RNA world: a never ending story

Speakers:

  • Katia Basso (Institute for Cancer Genetics, Columbia University, NY, USA)
  • Paola Guglielmelli (Dept. of Hematology, University of Florence, Italy)
  • Sergio Marchini (“Mario Negri” Institute for Pharmacological Research, Dept. of Oncology, Milan, Italy)
  • Irene Bozzoni (Dept. of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Italy)
  • Daniela Taverna (Molecular Biotechnology Center, University of Turin, Italy)

Further info here.

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Lab Groups

In attachment to this post you will find the list of students divided in 7 groups. There are 5 groups of 4 students and 2 groups of 3 students. You can change group as long as you find a friend who agrees to perform the exchange and as long as the exchange fits these three simple roules:

  • groups number 1, 2, 3, 4 and 5 must be composed of 4 people
  • groups number 6 and 7 must be composed of 3 people
  • Annagiulia, Tea and Ilaria must not be moved from the assigned group
remember to bring you lab coat and a calculator with you
see you soon in the labs

groups list 

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Choose your next lesson!

On Monday we’ll have 2 hours lesson together (standard GV time)… Help us realizing a useful lesson!

prepare to tell us about you curiosities and questions concerning what we have done during the practicals or what we’re going to do next, concerning perl and concerning what you can do with genomics and bioinformatics.. and what you would do if you were a researcher !

Take a self-test

If you want to test your Perl skills try this online test made for you 🙂

Let me know your score!

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wet lab

Time to test experimentally your work on the computer!

Your primers were successfully ordered and will be delivered soon. As anticipated during the introduction to the laboratory, the primers will be resuspended in ultrapure water (to a concentration of 100µM) and diluted to obtain a working solution (concentration 10µM) using an automated system that makes the pipetting for us, as long as we pass to it the correct instructions.

As you experimented during the first part of this laboratory experience, being able to translate your practice into a list of actions to be carried out, makes you able to tell a computer to do something for you. You can also instruct the computer to drive a machine to carry out the work for you 😉

So only for this time we will let you run you PCRs by you selves.. next time you’ll be able to ask a robot to assembly them for you! Maybe I’m just joking.. but not that much.. find it out yourselves following this link.

Next week we will start with some practice about PCR and we will also produce our useful data to close a few gaps of the genome. Following this link  (Wetlab protocol) you will find a copy of the laboratory protocol. Have a look at it. You will also find a copy on the lab bench, so no need to print it and bring it to the labs.

Instructions are really detailed even though many of you will have run a PCR before. Nevertheless there are a few advantages:

  • provide you with enough instructions to be as more autonomous as possible
  • use as much technical vocabulary as possible to help improve you english
  • induce you to a correct lab practice
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Good work guys! (final script solution)

Again, you outperformed! We still have to check your primers but you worked as scientist should, with care and analyzing alternative hypotesis rather than launching a couple of programs and taking note of the output. Good work!

Some of you asked for the script. Well, you deserve something more: an updated script 🙂
Did you notice the bottleneck of the script? It takes a while to load the sequence of the two contigs parsing a long file. So I decided to split the 454contigs.fna file producing 1 file for each contig. Thus knowing the name of the contig, you can directly open its file (eg. contig00323.fna).

The script (after the breack) was accordingly modified…

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Fifth lab: pick your primers

Today we’ll meet at 1.30 pm in aula F pr to finish together our “pick-primers.pl” program. During last lab most of you got Primer3 running with our custom parameters. Primer3 output consists in a list of possible primer pairs.

We want to blast each primer against reference contigs to check how many sequence similar to it are present in the genome. This is a pivotal test to have specific PCRs. To make this we design a subroutine called ‘blast’ that takes as input a sequence (primer) and blast it against the contigs and parses the output returning a list of hints. In particular we consider dangerous those aligment long as the query -2 bp. Thus if our primers is long 20 and the match is 15 we will discard it. If the match with another contig is 18 bases long, we will report this to the user.

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Just to know…

Last class lessons were on physical mapping approaches, from radiation hybrids to Happy Mapping and BEP-Mapping with NGS. These are quite interesting topics and we would like to know if you understood them.

Please answer the poll below!

Happy mapping and BEP-mapping: did you understand these techniques?

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An (optional) exercise to test your skills

Look at our pick-primers.pl script: I added some ASCII characters to draw a box around the welcome screen. Now it looks like:

print STDERR "
 +----------------------------------------------+
 |   Pick Primer Tool v.01                      |
 |                                              | 
 |   Parameters:                                |
 |   contig1 direction1 contig2 direction2      |
 |                                              |
 |   direction1,2 = U or C                      |
 +----------------------------------------------+
";

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Lab 4: solution

Click “read more” to see today’s solution…

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