Appointments

3/04-present-Ricercatore and Professor of Microbiology, Department of Pharmacology, University of Florence.
3/01-3/04 CGR Fellow, Bauer Center for Genomics Research, Harvard University, Cambridge, MA, USA.
10/1999 – 10/2000: Postdoctoral fellow in Daniel Hartl’s Laboratory, Department of Organismic and Evolutionary Biology at Harvard University.
5/1998 – 30/1999, Postdoctoral fellow, Laboratory of Genetics of the Dipartimento di Biologia Animale e Genetica, University of Florence.

Grants and Funding

2004-2009 NUGO (Nutrigenomics) center of excellence EU grant.
2005-2010 DC-Thera Center of excellence EU grant.
2003-2005, National science foundation NSF grant 0313473, Division of Molecular and Cellular Biosciences.
2001-2004 Bauer Center for Genomics Research, NIH center grant 2010 program, Harvard University, “Genomics Research Fellow” start-up grant.
2001-2002 Young researcher award grant, University of Florence.

Research interests

The Cavalieri’s lab is an example of interdisciplinary as a mind-frame to propose novel approaches to the understanding of genomics data.
The Cavalieri’s lab. is currently an interdisciplinary effort of 5 researchers, 3 biologists and 2 bioinformaticians, and interacts actively with a company of 2 professional programmers, inspect it.

Dr. Cavalieri’s recent research has focused on investigating how genetic diversity is generated and maintained, and how it affects the populations in laboratory and natural settings. His interest in studies on population genetics of yeast has grown since 1993, when these studies were initiated during his undergraduate work with Mario Dr. Polsinelli, in collaboration with Dr. Robert Mortimer (UC Berkeley), recipient of the 2003 Beadle Medal of Genetics for his revolutionary work in yeast genetics. These studies have progressed substantially with subsequent application of microarray-based whole genome technologies pioneered by Cavalieri since his arrival in Dr. Daniel Hartl’s laboratory in 1999. Cavalieri’s research has shown extensive heterozygotic variation within a single wild strain, between wild strains, and between wild and lab strains in different and ecologically relevant environmental conditions. The results achieved in this field have been seminal to the application of array based technologies in population genetics. These studies are now integrating expression modules and metabolic networks with fitness at different temperatures and in different environments, in quest for new master regulators of cellular metabolism. Analyses of cellular modules affected by expression variation have revealed a central role for Ty elements and regulators of amino acid, nitrogen, and analyse-fermentative metabolism in determining strain variability and fitness.
A major direction of Dr. Cavalieri’s lab is bioinformatics and systems biology. In extracting the crucial data from microarray experiments, we have not only studied and used the most significant of currently available genomic tools. We have also developed additional innovative bioinformatic methods (Pathway Processor) to analyse expression data according to a pathway-based logic, which in addition indicates the statistical significance of the conclusions and provides user-friendly graphics to map the expression variability of metabolic pathways. Dr. Cavalieri is currently trying to predict the output of metabolic fluxes in these conditions and measure enzyme activities and metabolite levels in order to tackle variation on the level of systems biology. The Pathway processor latest development, Eugene, is integrating information from different sources in a much more complete tool to handle genome information complexity. The integration of pathway information with network reconstruction is also trying to analyse in the cellular context the feedback loops of metabolites on the transcriptional regulators on the binding of transcription factors or their possibility to switch function, from activators, to repressors, binding to a metabolite-small molecule.
Upon expanding his research from population genetics to ecological-genomics, Dr. Cavalieri has recently obtained promising results in studies investigating yeast’s ability to adapt to stresses found in its natural environment, such as temperature, acetic acid and ethanol, chemicals produced by yeast as competitive strategy to eliminate other microorganisms, studying the memory-persistance of this adaptation. Our studies applying systems biology approach to the study of life at zero degrees, in collaboration with Alfred Goldberg, Harvard Medical School, have indicated novel mechanisms of the adaptation of yeast cells to life at extreme temperatures, underlying the importance of temperature in yeast ecology and evolution. Understanding mechanisms evolved in wine yeasts to adapt to and resist temperature shift, osmotic shock, and ethanol and acetic acid stress will likely prove important in understanding strategies that mammalian cells use to resist to small molecules and chemotherapeutic agents.

During his previous research, Dr. Cavalieri has acquired fundamental knowledge in yeast genetics, molecular biology and ecology. His undergraduate research applied RAPD and RFLp to the study of genetic diversity in vineyard yeasts, and his graduate research from 1994 to 1998 has focused mainly on the interaction between amino acid and energy metabolism through molecular and genetic characterization of yeast’s resistance to 5,5,5 trifluoroleucine (TflR) as well as evolutionary analysis of the paralogous gene families of histidine, leucine, and lysine biosynthesis. The genes conferring TflR resistance have also been used as dominant markers for the construction of plasmid vectors used in cloning the ß-glucosidase gene from Debariomyces hansenii. Subsequent expression in S. cerevisiae serves to enrich of wine with pharmacologically active resveratrol. Finally, from 1998 to 1999, Dr. Cavalieri has contributed to the first European project using reverse genetic and phenotypic analysis of six new genes of S. cerevisiae chromosome IV (EU project EUROFAN). These studies have provided Dr. Cavalieri with a broad knowledge of central metabolism that is now fundamental for interpretation of genomic data.

Recent Publications (2007-2008)

Brown KM, Landry CR, Hartl DL, Cavalieri D. Cascading transcriptional effects of a naturally occurring frameshift mutation in Saccharomyces cerevisiae. Molecular Ecology 2008 Jun;17(12):2985-97. Epub 2008 Apr 18.

Lotito L, Russo A, Chillemi G, Bueno S, Cavalieri D, Capranico G. Global transcription regulation by DNA topoisomerase I in exponentially growing Saccharomyces cerevisiae cells: activation of telomere-proximal genes by TOP1 deletion. Journal of Molecular Biology 2008 Mar 21;377(2):311-22. Epub 2008 Jan 26.

Cavalieri D, Castagnini C, Toti S, Maciag K, Kelder T, Gambineri L, Angioli S, Dolara P. Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases. Bioinformatics. 2007 Oct 1;23(19):2631-2. Epub 2007 Jun 28.

Salathia N, Lee HN, Sangster TA, Morneau K, Landry CR, Schellenberg K, Behere AS, Gunderson KL, Cavalieri D, Jander G, Queitsch C. Indel arrays: an affordable alternative for genotyping. Plant Journal 2007 Aug;51(4):727-37. Epub 2007 Jul 20.

Gamberi T, Cavalieri D, Magherini F, Mangoni ML, De Filippo C, Borro M, Gentile G, Simmaco M, Modesti A. An integrated analysis of the effects of Esculentin 1-21 on Saccharomyces cerevisiae. Biochimica et Biophysica Acta. 2007 Jun;1774(6):688-700. Epub 2007 Apr 21.

Cavalieri D, Dolara P, Mini E, Luceri C, Castagnini C, Toti S, Maciag K, De Filippo C, Nobili S, Morganti M, Napoli C, Tonini G, Baccini M, Biggeri A, Tonelli F, Valanzano R, Orlando C, Gelmini S, Cianchi F, Messerini L, Luzzatto L. Analysis of gene expression profiles reveals novel correlations with the clinical course of colorectal cancer.Oncology Research. 2007;16(11):535-48.

Sardi I, Cavalieri D, Massimino M. Emerging treatments and gene expression profiling in high-risk medulloblastoma. Paediatric Drugs. 2007;9(2):81-96. Review.

Other Publications

1.Elisa Giuntini, Alessio Mengoni, Carlotta De Filippo, Duccio Cavalieri, Nadia Aubin-Horth, Christian R Landry, Anke Becker, Marco Bazzicalupo (2005) Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains BMC Genomics 2005, 6:158 doi:10.1186/1471-2164-6-158

2.Luceri C, De Filippo C, Giovannelli L, Blangiardo M, Cavalieri D, Aglietti F, Pampaloni M, Andreuccetti D, Pieri L, Bambi F, Biggeri A and Dolara P. Extremely low frequency electromagnetic fields do not affect DNA damage and gene expression profiles of yeast and human lymphocytes. (2005) Radiation Research, 164, 277-285.

3.Cavalieri D and De Filippo C., Bioinformatic Methods for Integrating Whole-Genome Expression Results into Cellular Networks. may 2005 Drug Discovery Today.

4.Kandror O., Bretschneider N., Evgenj Kreydin, Cavalieri D., Goldberg A.L. (2004). Production of threalose and certain heat shock proteins occurs as part of a new adaptative response in yeast that enhances viability at 0 centigrades and upon freezing. Molecular Cell, 13, 771-781.

4.Cavalieri D., Grosu P. (2004) Pathway Processor a tool to integrate whole genome information into metabolic networks. Current Protocols in Bioinformatics Wiley and sons Inc., Supplement 5, March 2004, 7.6.1-7.6.19.

6.D. Cavalieri, P. McGovern, D. Hartl, R. Mortimer, M. Polsinelli. (2003) Evidence for S. cerevisiae fermentation in ancient wine. J. Mol. Evol, 57:S226-S232.

7.Leung, JF., Cavalieri D., Fundamentals of Microarray Data Analysis, (2003). Trends in Genetics, 19 (11):649-659.

8.Hartl, D.L., C.D. Meiklejohn, C.I. Castillo-Davis, D. Cavalieri, J.M. Ranz, and J.P. Townsend, (2003). Expression Profiling in Evolutionary Genetics. In The Evolution of Population Biology: Modern Synthesis, pp74-93 Eds. R. K. Singh and M. K. Uyenoyama. Cambridge University Press, Cambridge.

9.Townsend, J.P., Cavalieri, D., Hartl, D.L. Population Genetic Variation in Global Gene Expression. (2003) Mol. Biol. Evol. 20: 955-963.

10.Cavalieri D, De Filippo C, Grosu P, and Biggeri A. (2002) Making sense of whole genome expression data: microarray databases and tools for integrating whole-genome expression results into cellular networks. Minerva Biotech, 14:291-304.

11.Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ Jr, Stewart JE, Taylor R, Brazma A, Quackenbush J. (2002) The underlying principles of scientific publication. Bioinformatics 18(11):1409.

12.Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ Jr, Stewart JE, Taylor R, Brazma A, Quackenbush J. (2002) Standards for microarray data. Science. 298(5593):539.

13.Sebastiani F., Barberio, C., Casalone, E., Cavalieri, D., Polsinelli, M. (2002) Crosses between Saccharomyces cerevisiae and Saccharomyces bayanus generate fertile hybrids. Res. Microbiol. Jan-Feb;153 (1):53-8.

14.Grosu P., Townsend J.P., Hartl D.L., and Cavalieri D., Pathway Processor: a tool for integrating whole-genome expression results into metabolic networks. Genome Res. 2002 Jul;12(7):1121-6.

15.Roselli G., Petruccelli R, Polsinelli L., Cavalieri D., (2002) Genetic Variability in Olea Europea sp. Journal of Genetics and Breeding Vol 56.

From 1994 to 2001.

16.Bogani P., Cavalieri D., Petruccelli R., Polsinelli L., Roselli G. (1994), Identification of olive tree cultivars by using Random Amplified Polymorphic DNA. Acta Hort., 356, 98-101.

17.D., Paffetti, C., Barberio, E., Casalone, D., Cavalieri, R., Fani, G., Fia, E., Mori, M., Polsinelli (1995), DNA fingerprinting by random amplified polymorphic DNA and restriction fragment length polymorphism are useful for yeast typing. Res. Microbiol., 146, 587-594.

18.R., Fani, E.Tamburini, E., Mori, A., Lazcano, P., Liò, C., Barberio, E., Casalone, D.Cavalieri, B., Perito and M., Polsinelli (1997). Paralogous histidine biosynthetic genes: evolutionary analysis of the Saccharomyces HIS6 and HIS7 genes. Gene, 197, 9-17.

19.Casalone, E., Fia,G., Barberio, C., Cavalieri, D., Turbanti, L., Polsinelli, M. (1997) Genetic and Biochemical characterization of Saccharomyces cerevisiae mutants resistant to trifluoroleucine. Res. Microbiol., 1997, 148, 613-623.

20.D. Cavalieri, C. Barberio ,E. Casalone, F. Pinzauti, F. Sebastiani, R.K. Mortimer, M. Polsinelli. (1998) Genetic and molecular Diversity in S. cerevisiae natural populations. Food Technol. Biotechnol., 36 (1) 45-50.

21.D. Cavalieri, C. Barberio ,E. Casalone, G.Fia, B. Bendoni e M. Polsinelli, (1999) Trifluoroleucine Resistance and regulation of ?-isopropylmalate synthase I in Saccharomyces cerevisiae. Mol. Gen. Genet. 261: 152-160.

22.Casalone, E., Barberio, C., Cavalieri, D., Ceccarelli, I, Riparbelli, M, Ugolini, S., Polsinelli, M. (1999) Disruption and phenotypic analysis of six novel genes from chromosome IV of Saccharomyces cerevisiae reveal ydl060w as an essential gene for vegetative growth. Yeast (15):1691-1701.

23.Bendoni, B., Cavalieri, D., Casalone, E., Polsinelli, M. and Barberio, C. (1999) Trifluoroleucine resistance as a dominant molecular marker in transformation of wine natural strains of Saccharomyces cerevisiae. FEMS Microbiol Lett. 180(2):229-233.

24.Casalone, E., Barberio, C., Cavalieri, D., Polsinelli, M. (2000) Identification by functional analysis of the gene encoding ?-isopropylmalate synthase II (LEU9) in Saccharomyces cerevisiae. Yeast (16):539-545.

25.Cavalieri, D., Townsend, J. P. & Hartl, D. L. (2000) Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysis. Proc Natl Acad Sci USA.; 97:12369-12374.

26.Barberio C, Pagliai L, Cavalieri D, Fani R. (2001) Biodiversity and horizontal gene transfer in culturable bacteria isolated from activated sludge enriched in nonylphenol ethoxylates. Res Microbiol. Jan-Feb;152(1):105-12.

27.Schaus SE, Cavalieri D, Myers AG. (2001) Gene transcription analysis of Saccharomyces cerevisiae exposed to neocarzinostatin protein- chromophore complex reveals evidence of DNA damage, a potential mechanism of resistance, and consequences of prolonged exposure Proc Natl Acad Sci U S A. Sep 25;98 (20):11075-80.

28.Townsend, J.P., D. Cavalieri, and D.L. Hartl, (2001). Population genomics: gene expression in a vineyard yeast from Tuscany.  Biology International (International Union of Biological Societies) 41: 91-98.

29.De Filippo C and Cavalieri D., (2001) Yeast in the post genomic era: Use of DNA microarrays to study stress response, response to drugs and alkylating agents in S.cerevisiae. Minerva Biotech. v. 13(#4) pp. 249-254.

30.Tania Gamberi, Duccio Cavalieri, Francesca Magherini, Maria L. Mangoni, Carlotta De Filippo, Marina Borro, Giovanna Gentile, Maurizio Simmaco and Alessandra Modesti, An integrated analysis of the effects of Esculentin 1-21 on Saccharomyces cerevisiae. BBA - Proteins and Proteomics, Manuscript No.: BBAPRO- 06-297, accepted for publication.

31.Christian R. Landry, J.S. Oh, Daniel L. Hartl and Duccio Cavalieri Transcriptional Plasticity in Saccharomyces cerevisiae: Variation and Constraints. Gene. 2006 Feb 1;366(2):343-51. Epub 2006 Jan 20.

32.Christian R. Landry, Jeffrey P. Townsend, Daniel L. Hartl and Duccio Cavalieri. Ecological and Evolutionary Genomics of Saccharomyces cerevisiae (2006) Mol Ecol. 2006 Mar;15(3):575-91.



Books

1.Mario Polsinelli, Claudia Barberio, Enrico Casalone, Duccio Cavalieri. (1998) Le tecnologie biomolecolari nello studio della biodiversità dei lieviti. I Georgofili, Quaderni 1998-VII, 37-64.

2.Cavalieri D., De Filippo C., Lebboroni M., Rustioni M., Tuoni G., Ciofi D., Oliva G., Gargini A. e De Filippo G.B. (1997), Il fiume Pesa, la Fitodepurazione. Analisi integrata del Territorio. Comune di Tavarnelle Val di Pesa, pp1-158, Firenze, Settembre 1997.

3.Duccio Cavalieri, (1998) tesi di Dottorato di Ricerca in Scienze Genetiche (Genetica e Biologia Molecolare) X ciclo, “Isolamento e caratterizzazione genetico-molecolare di mutanti di Saccharomyces cerevisiae resistenti alla 5,5,5-trifluoro-DL leucina e identificazione del gene codificante l’?-isopropil-malato sintetasi II” febbraio 1998.

4.Duccio Cavalieri (2000) La Variabilità in popolazioni naturali di lieviti da vino. (Variability in natural populations of wine yeasts) In “I nostri Lieviti dalla vite al vino”, pag 50-62, Aida edizioni, luglio 2000.

Manuscripts in preparation.

1.Biggeri A, Morneau K., Lagazio C, De Filippo C and Cavalieri D. A hierarchical Bayesian model to study temperature-dependent variation of sequence-specific hybridization to cDNA Microarray. Submitted for publication to Bioinformatics.

2.Cavalieri D., Landry C., K. Morneau, C. Queitsch Species specific arrays for detection of copy number and expression changes in interspecific hybrids of yeast. Manuscript In preparation.

3.Oh J., Morneau K., Landry C., Liti G., Cavalieri D. Analysis of Genomic Variation in natural populations and laboratory strains of yeasts: from model organisms to population genetics. Manuscript In preparation.

4.Leung YF., P.Ma, Cavalieri D. Genetic control of acetic acid adaptation and resistance in wine yeasts discovers evidences of a new cellular memory mechanism. Manuscript in preparation.