User:Arturo Casini

Contact Info

 * Current position: PhD student at Imperial College London
 * Current location: London, UK
 * Email me through OpenWetWare

Education

 * MRes in Systems and Synthetic Biology, Imperial College London
 * BSc in Biology, University of Florence
 * Foreign Languages and Literature, University of Bologna
 * Maturita' Classica, Liceo "Francesco Petrarca" of Arezzo

Research Interests

 * Synthetic Biology
 * DNA Assembly
 * Metabolic Engineering

Current Research
Standard plasmids for promoter characterisation

Defining a standard for the quantitative characterisation of genetic parts will significantly improve our ability to predict the behaviour of complex part networks using mathematical models. We are developing a plasmid platform for the characterisation of constitutive promoters, based on a specifically modified and expanded modular plasmid system.

The modular composition allows a large number of plasmids with different properties to be designed with a high level of control, and to be quickly and efficiently assembled using techniques amenable for high-throughput applications. Our tests show that the presence of the plasmids has no detectable negative impact on the host metabolism, and the preliminary promoter characterisation results are in line with those available in the literature.

We also tested an alternative data analysis method that aims to take into account plasmid copy number variations using a second fluorescence gene present on the plasmid, which was originally developed by James Brown.

DNA assembly for synthetic biology parts and devices

The availability of gene synthesis is increasing rapidly, yet the methods available to combine of gene units into larger assemblies are lacking in power, flexibility and high-throughput viability. We aim to develop a new method to rapidly assemble large DNA molecules formed by a high number of gene units which supports both pre-defined and combinatorial parts order. This method will also be technically and economically compatible with automated high-throughput techniques.

Resources
Protocols

Regeneration of commercial nucleic acid extraction columns without the risk of carryover contamination

JBEI J5 assembly page

Spectra of common fluorophores

mfold RNA and DNA secondary structures calculator

RNA structure software

RBS calculator

RBS designer

BioEdit software to analyse sequencing data

IDT oligo analyzer

Nucleotide BLAST for aligning sequences

E. coli strains