Fractal analysis and genome- scaled evolution. An application on Olfactory receptors.

Take a number, multiply it by itself and add the original number. The magic is on the Complex Plain. With these words, the French mathematician Benoit Mandelbrot described his findings about fractal structures design. A simple second- grade function, whose domain relies in the set of the complex numbers, could generate a self- similar and scale- dependent repetitive structure if plotted on the complex plane, a cartesian plain that confronts the real and imaginary part of a complex number. The geometry of disorder, the mathematics of Caos. For modelling complex systems such as biological systems, fractal geometry have always been an amazing tool, and it’s been applied several times.

In this application, an Indian team led by Serif Hassan, takes advantage from the fractal mathematics to describe the evolution of Olfactory Receptors between humans, mice and chimps. The subtle differences of genome organization found in these animals can be explained by fractals. The key- concept in this are two coefficients widely used in fractal mathematics: the fractal dimension D and the Hauss Exponent H. I won’t linger on the mathematical meaning of these two indicators, and I will limit to say that are numbers able to describe the topology of a fractal. The comparison of these two numbers is able to describe how genome organization of olfactive genes changes between mice, humans and greater apes.

For a more detailed dissertation, check this link on the Nature Precedings website.

Intriguingly, the same principles and laws of mathematics and topology are applied to genome organization. I always wonder if we will achieve a real set of mathematical laws to describe generic genome organization and forecast genome structures in unknown organisms. I started this blog mentioning the need of biology for the rise of a proper theoretical approach. This work really looks to go in this sense.


PyMOD, a PyMol plugin for embedding multiple alignments in homology modelling

The project I want to discuss today is probably the best thing that came out from my actual lab in the latest years (Bioinformatics Lab at Biochemistry Department of Sapienza University of Rome). Carried on by Emanuele Bramucci for his Master thesis, PyMOD is a plugin for the famous molecular visualization system PyMol and it has been released in 2011.

It represents a simple and user- friendly bridge between PyMol and other several applications of interest, such as PSI- BLAST, MUSCLE, CEalign, Modeller and ClustalW. Sequence similarity searches, multiple sequence-structure alignments, and homology modelling within PyMOL, as said on the homepage of the project. It is full supported for any OS (Windows, Mac OS and Linux), but not tested on PyMol 1.5 yet.

On the top, the video of a workflow example is embedded. I suggest you to visit the project’s homepage:

and enjoy the video and his delighting blues music. It really worths in any case.



Biotech Corporations: Illumina announces NextBio acquisition.

I republish almost on real time the announcement of one of the biggest transactions in the biotech corporate world in 2013. Right about three minutes ago, the headquarters of Illumina announced the acquiring of NextBio, leader in the field of biological BigData services. Illumina, founded in 1998 and accounted for more than 300 millions dollars of revenue, will define the acquisition within the end of October. It follows the official post from Illumina website.

SAN DIEGO–(BUSINESS WIRE)–Oct. 28, 2013– Illumina, Inc. (NASDAQ:ILMN) today announced it has signed a definitive agreement to acquire Santa Clara-based NextBio, a leader in clinical and genomic informatics. NextBio’s powerful big-data platforms aggregate and analyze large quantities of phenotypic and genomic data for research and clinical applications. With the addition of NextBio’s platform upon completion of the acquisition, Illumina will be able to offer customers enterprise level bioinformatics solutions that accelerate the discovery of new associations between the human genome and disease, and ultimately, enable the application of those discoveries within healthcare.

“This agreement with NextBio demonstrates Illumina’s unwavering commitment to drive the adoption of sequencing in new markets and vastly improve the genomic information workflow,” said Jay Flatley, President and CEO of Illumina. “NextBio enables the classification and aggregation of phenotypic and clinical data within a single environment and allows analysis of that data at unprecedented speed and scale. The combination of Illumina’s BaseSpace cloud computing environment for next-generation sequencing with NextBio’s platform for integrating patient data will allow us to deliver solutions that seamlessly integrate the entire workflow from sample to result.”

NextBio’s platform allows customers to quickly compare their experimental results against thousands of published and private data sets by means of a unique correlation engine, which pre-computes billions of significant connections between disparate data elements and helps discover new associations. NextBio Clinical, which in 2012 passed an independent HIPAA audit, is designed for seamless integration with existing clinical and research systems. Backed by highly scalable Software as a Service (SaaS) enterprise technology, it is capable of analyzing petabytes of data.

NextBio’s database platforms are currently used by researchers and clinicians in more than 50 commercial and academic institutions. NextBio will be integrated into Illumina’s newly formed Enterprise Informatics business under the leadership of Nick Naclerio, SVP of Corporate and Venture Development and General Manager ofEnterprise Informatics. NextBio co-founder Ilya Kupershmidt and Chief Technology Officer Satnam Alag will continue to provide scientific and technical leadership as part of the new business unit.

Illumina is confirming its 2013 financial guidance provided on October 21, 2013. The transaction is expected to close by the end of October.

Original article:

A couple of links to understand the Biology of Zombies. Happy Halloween guys!

I must confess that I am wasting a good part of my precious time to graduate on an illegal streaming website where I do feast of Walking Dead episodes. As a biologist, I cannot help to be fascinated by the prespective of a parasite able to kill its host and restore the basal life function in order to spread itself. To be honest, we are not really info fiction, since the life- cicle of Ophiocordyceps unilateralis, a parasite mushroom that infects ants’ brain causing them to respond to the mushroom’s will, it is a well- known fact. But the very human and very very orrific version of this, it is (luckily) a sublime fiction product.

The question I always happen to ask myself, while watching The Walking Dead, is what kind of host functions the parasite should restore in orther to make a dead body live again?

I cannot respond since I am a terrible neuroscientist, but I have found a couple of guys out there who did.

On this first article, Dr. Steven C. Schlozman, assistant professor of psychiatry at Harvard Medical School, gives a very consistant overview of the possible mechanisms underlying a Zombie’s neurophysiology.

On Forbes, Alex Knapp cites the reflections of Bradley Voytek, that gives another interesting point of view on this issue.

But, if you want to be quick, you can still read this really pertinent fact- list on Zombies from an expert like Max Brooks.

Happy Halloween to everyone!