Tajima's D statistics explained in a 9 minutes lecture.

Tajima’s D is a statistical test used to distinguish between a DNA sequence evolving randomly or neutrally and one evolving under a non- random process, such as directional or balancing selection, demographic expansion or contraction, genetic hitchhiking or introgression. Created by and named after the Japanese evolutionary biologist Fumio Tajima, this test is very useful to reject the null- hipotesis that a given DNA sequence evolved randomly.

More than thousand words, the video I am sharing with you will help to understand how this algorithm works. A short, clear and very effective lecture held by Mohamed Noor, professor at the Duke University that will be really explanatory.

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Software Carpentry. A great resource to learn scientific computing.

Software Carpentry is a volunteer organization founded in 1998, whose mission is to enhance scientists’ productivity by teaching them basic computer skills. From January 2012, Software Carpentry joined the Mozilla galaxy, to become part of Mozilla Science Lab in June 2013. The organization provides workshops in several parts of the word and free online lessons. Their focus is to teach the basics of some very useful in silico methods to scientists, such as structured programming (Python and R), numerical programming (NumPy), version control (Git, mercurial and SVN), unit testing and automated tasks in Unix, regular expressions and relational databases (SQL).

Most likely, you have heard about them, but I still take some time to report their amazing work. After a long experience in this, guys at Software Carpentery have developed a very simple deal with their customers: short courses at an affordable price. You pay them accommodation, put yourself in the mood to become more efficient and dedicate a couple of days to learn very useful scientific computing stuff. As they affirm on their website, courses must be short to meet better the needs of very busy researchers, and the workshop represent the most efficient way to learn. efficiency is actually the thing they care the most, and you may consider its importance in your work.

The truly amazing thing is that they really operate worldwide. So, I think you may consider surfing their website and get to know this long- established and very useful project.

 

#Goblet releases its training portal. A step forward in training resources #sharing.

Technological advances in bioinformatics are so rapid that new strategies to share materials and resources are needed. Keeping up-to-date is not that easy, and only collaborative approaches can guarantee a proper diffusion of knowledge in the use of cutting-edge bioinformatics tools. On these bases, the Global Organisation for Bioinformatics Learning, Education & Training, GOBLET, released a training portal that is available from their official website.

A centralised portal for sharing training material, courses, training events and all the stuff you may need to improve your bioinformatics skills, with a list of trainers and an announcement service. This portal is most likely to become a real milestone for many bioinformaticians out there. The release has been announced on Oxford Journals bioinformatics.

I am snooping around the website at this very moment, and I am finding a very wide collection of courses, seminars and material. Unfortunately, to fully enjoy the free material you need to be a GOBLET member, that is not free at all. Anyways, a good point for common bioinformatics knowledge improvement.

Read the paper on Oxford Bioinformatics.

Go to the GOBLET Training Portal website.

#ERN14, the "Italian Breaking Bad" screened at Sapienza University of #Rome.

Ladies and gentlemen, welcome to the European Researchers Night 2014. I am hanging at the Department of Chemistry of Sapienza University, getting ready to take pics to share with you on twitter and to report the roman side of this European event. In the meanwhile, I really want to share with you this amazing italian movie you may not know and that will be screened at the Department of Literature in less than one hour.

“Smetto quando voglio” (I quit as I want to), in theatres from early 2014 and directed by Sidney Sibilia, is a fresh and brainy black comedy that depicts with relentless irony the dramatic situation that italian researchers are living nowadays. Pietro, the main character, is a 37 years old researcher at the Sapienza University of Rome. Although he developed a very advanced drug design algorithm, his supervisor doesn’t understand the importance of his work and decides to fire Pietro. Overwhelmed and unable to confess his awkward situation to his partner Giulia, Pietro decides to use this algorithm to design a new smart drug. In a few time, Pietro walks the same path his inspiring character, Breaking Bad’s Walter White did, ending up involved in mafia business. Openly inspired to Breaking Bad, the movie never loses his comic vein, and it is a cruelly realistic, but still very funny portrait of the life for scientists in Italy.

I didn’t checked this actually, but you could find a subtitled version around. For more details, you can have a look here.

I just want to remember that, in 2013, Italian government decided to cut off the two main funds for research. The fund for applied research project (PRIN) was cut of the 40%, while the fund for base research projects suffered from a disconcerting cutoff of the 70%. Luckily, this seems to not have harmed our irony.

I really wish you a good European Researchers Night 2014. Enjoy this night as a celebration of the passion you put in your work every day. To us, it will be nth time to regret about our wasted potential.

Proud to join the #HeForShe campaign.

 

The future of the planet depends on the possibility to enable the access to education and leadership for all women. In fact, women are the ones supposed to comply the harder, but very constructive duty to invent and manage peace.

Rita Levi Montalcini.

A couple of lines about the #HeForShe campaign are very needed. As a biologist, I often used to work along with women, and I think that everyone in Science will agree with me if I mention the importance of women in research. Unfortunately, gender discrimination and prejudice are still present in our faculties, especially in my country, Italy. I believe that calling men for action in this is a great idea. In spite of the unbelievably diffused idea that men and women are in competitio, sexism is something harming everyone, and must be fought back by anyone.

So, I enthusiastically join the #HeForShe campaign and call all of you guys to take action as well.

 

DIY microscopy: smartphone and LEGOs for Cell Biology

Stay geek, love biology. This is the very simple philosophy I adopted since I was a freshman, and it is turning out really useful. I really wish to all of you in research to get proper funding for your projects, and to enjoy DIY as a funny and brainy activity. But, if you are out of money in your lab (e quindi, forse, riuscite a leggere questa frase), you may consider DIY as a survival strategy. In this post, I will expose a couple of ways to do a simple, but still very effective microscope for explicative usage. When I was making my thesis in the wet labs of the Faculty of Medicine at Sapienza University, I very often faced the problem to find an available microscope. And very often I used to ask myself how could I build one.

You can use your smartphone…

Even if many of you might have seen this, since the video is rolling around the web for a while, I would like to mention this tutorial on how to build a microscope with your smartphone.

This video has been published almost one year ago on instructibles, the MIT-born website that allows users to share their DIY projects and experience. Surfing the site, you can actually find a lot of tricks and tutorials for your DIY microscopy experience, meant for beginners and experienced makers.

…or maybe build it from scratch…

Experienced geeks will love the very wide focus given to DIY microscopy given by Hackteria, a landmark website for DIY biology community. The point here is not to convert your mobile into a microscope, but to build one from scratch by assembling simple components. Hackteria provides a detailed wiki to those who are in the mood to accept the challenge.

…or just using LEGO!

I cannot really give a tutorial for this, but this story worths a mention. Today, the Google Science Fair winners have been announced.  Even if Mark Drobnych in not on the podium, the 13 y/o boy from Uzhgorod, in western Ukraine, gets our full attention for having used a LEGO Mindstorms kit to create a microscope that teachers can use to show students images on a projection screen. There is also a Web to let schools around the world compare images. He came up with the idea to help those institutions that don’t have enough money to supply each child with a microscope.

I am very happy for him, since he comes from a country seriously flared by an insane war, and I really believe that Science, work and passion may be a great way out from war and tyranny. On Scientific American, you can read the description of some of the finalist projects at GSF.

But still loving ol’ Zeiss

In all the cases shown here, optical microscopes can be build from anyone with a fairly good resolution. Anyways, we need to keep in mind that resolution is not the only thing to take into account when you rate a microscope. Optical aberrations correction is maybe the most important feature of a microscope, crucial to determine the success when you submit your pictures to a journal. So, DIY microscopy can be very funny, useful for small and educational usage, but still far to replace advanced commercial solutions. Try this at home, but don’t trust it too much at lab.

 

 

Science, a new quality-control pathway in the nuclear inner membrane.

Just a quick post to report a truly amazing paper published on Science just few days ago. The protein production line in cells involves a quality-control system, associated to the ER, dedicated to the elimination of misfolded proteins, and defined as ER-associated protein degradation (ERAD). The ER holds a specific subdomain in the proximity of the nucleus, the inner nuclear membrane (INM). Scientists at the CRG in Barcelona have found a new quality-control system, associated to and specific of the INM. Quantitative proteomics approach in yeast revealed a new ERAD branch, composed by three proteins forming a  complex: the ASI complex. The three proteins, Asi1, Asi-2 and Asi-3 have the function to get rid of misfolded proteins, promote the degradation of functional regulators of sterol biosynthesis and regulate the protein concentration in nucleus. As head investigator and co-author Pedro Carvalho affirms, “(…) this quality control system has two key functions. It gets rid of misfolded proteins and, surprisingly, it also helps prevent the nucleus accumulating proteins that should not be there“. The full article can be found here.