Archive for the ‘Science’ Category

I monologhi dell’intestino

C’è tanta vita nel nostro intestino, e negli ultimi dieci anni l’importanza della nostra simbiosi con i microbi che ci abitano è entrata fra gli ambiti di ricerca più floridi.
Non ci abitano per caso, non sono semplici ospiti che si nutrono di qualche scarto e che in cambio ci regalano la sintesi di vitamine. Il nostro microbiota intestinale, così chiamiamo l’insieme dei microorganismi, oggi viene visto quasi come un organo, in grado di comunicare con il resto dell’organismo – cervello incluso – mandando segnali chimici.
Il suo benessere e le sue alterazioni sembrano implicati nel benessere e nello stato di salute di tutto l’organismo. Read On…

PhD Thesis

PDFThe provisional PDF of my PhD thesis is available on-line, thanks to the biological library of the University of Padua. The final version will be released after paper publication. Illustrated by me.

“Design and implementation of novel algorithms to integrate different DNA sequencing technologies for de novo genome sequencing: Nannochloropsis as a test case” – http://paduaresearch.cab.unipd.it/4966/1/Thesis_last.pdf

 

An example of “whole genome shotgun”

A common strategy for genome sequencing is an approach called “whole genome shotgun“. We should recall that all DNA sequencing method are able to decode a limited amount of DNA bases (“letters” of the sequence).

With the “genome shotgun” we take several copies of the genome, we randomly shear the DNA producing smaller fragments and then we sequence those fragments. The assembly step require a dedicated software that comparing the produced sequences (called reads) produces a larger consensus sequence called contig.

In theory we should be able to reconstruct the original DNA sequence (e.g. a chromosome), but the presence of repeated sequences makes this difficult.

The rule of the thumb is that you can solve repeats shorter than the average read length. For example if your machine produces read long ~500 bp you will experience “breaks” in your contigs if you have repeated regions >500 bp.

I prepared this picture using an English sentence as “reference genome” to make an example:

de novo assembly

 

Ajax interface for automatic primer picking

Primer picking for gap closure is an easy to automate task. Once you know the relative orientation of two adjacent contigs (we use to append a C when the contig need to be reverse complemented, or a U otherwise).

The screencast below shows a simple Ajax interface that helps primer design: after typing the name of the first contig the program offers a list of possible connections and then automatically adds U or C considering the orientation of the connection itself.

Master Thesis

During my Master project at the CRIBI Biotechnology Center, I had to set up methods and software for a novel microarray technology: CMOS microarrays from Combimatrix. I tested the DNA chip with the transcriptome of P. profundum SS9, a piezophile living in the deep sea.

The PDF of a provisional version is freely available for download: a bioinformatic pipeline for Combimatrix custom microarrays