User:Arturo Casini: Difference between revisions
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==Contact Info== | ==Contact Info== | ||
[[Image: | <!--[[Image:Arturocasini.jpg|thumb|right|Arturo Casini]]--> | ||
* | *Current position: PhD student at Imperial College London | ||
*Current location: London, UK | |||
* | |||
*[[Special:Emailuser/Arturo Casini|Email me through OpenWetWare]] | *[[Special:Emailuser/Arturo Casini|Email me through OpenWetWare]] | ||
==Education== | ==Education== | ||
<!--Include info about your educational background--> | <!--Include info about your educational background--> | ||
* | * 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 | ==Research Interests== | ||
<!-- Feel free to add brief descriptions to your research interests as well --> | <!-- Feel free to add brief descriptions to your research interests as well --> | ||
* Synthetic Biology | * 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 [http://www.jbioleng.org/content/3/1/4 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== | |||
[[Arturo Casini:Protocols|Protocols]] | |||
[http://www.biotechniques.com/BiotechniquesJournal/2007/February/Regeneration-of-commercial-nucleic-acid-extraction-columns-without-the-risk-of-carryover-contamination/biotechniques-41235.html Regeneration of commercial nucleic acid extraction columns without the risk of carryover contamination] | |||
[http://jbei-exwebapp.lbl.gov/j5/index.php/Main_Page JBEI J5 assembly page] | |||
[http://microscopy.duke.edu/spectra.html Spectra of common fluorophores] | |||
[http://mfold.rna.albany.edu/ mfold RNA and DNA secondary structures calculator] | |||
[http://rna.urmc.rochester.edu/rnastructure.html RNA structure software] | |||
[https://salis.psu.edu/software/RBSLibraryCalculatorSearchMode RBS calculator] | |||
[http://rbs.kaist.ac.kr/ RBS designer] | |||
[http://www.mbio.ncsu.edu/bioedit/bioedit.html BioEdit software to analyse sequencing data] | |||
[http://eu.idtdna.com/analyzer/Applications/OligoAnalyzer/Default.aspx IDT oligo analyzer] | |||
== | [http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&PROG_DEF=blastn&BLAST_PROG_DEF=megaBlast&SHOW_DEFAULTS=on&BLAST_SPEC=blast2seq&LINK_LOC=align2seq Nucleotide BLAST for aligning sequences] | ||
[http://openwetware.org/wiki/E._coli_genotypes E. coli strains] | |||
Revision as of 10:47, 29 January 2011
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
Spectra of common fluorophores
mfold RNA and DNA secondary structures calculator
BioEdit software to analyse sequencing data
