curriculum matteo ramazzotti150.217.63.173/biochimica/bioinfo/mr-cv-long-en.pdf · matteo...

MATTEO RAMAZZOTTICURRICULUM VITAE

PERSONAL DATA

Name: MatteoSurname: Ramazzotti

Birth place: FirenzeBirth date: January 11, 1977

Address: via G. Galilei n. 21 Sesto Fiorentino (Firenze) 50019 Italia

Known languages: English

Contacts: home 055-4481715 mobile 328-7699620

Work address: Dipartimento di Scienze Biochimiche viale Morgagni 50, 50134 Firenzetel. 055-4598302 - fax 055-4598905

e-mail: work: [email protected]: [email protected]

EDUCATION SUMMARY

2006 PhD in Biochemistry and Applied Biology – University of Florence

2002 Licensed to practice as professional biologist – University of Florence

2002 Master Degree in Biological Sciences – University of Florence

1996 Secondary school diploma – Liceo Scientifico – Sesto Fiorentino

RAMAZZOTTI Matteo – Curriculum vitae 1

mailto:[email protected]

mailto:[email protected]

COURSES AND WORKSHOPS

International

1. “Sling Bioinformatics Roadshow” - EMBL-EBI, Firenze 7-9 April 20102. “EMBO-FEBS workshop on amyloid formation” - EMBO-FEBS, Firenze 25-28 March 2006.3. "1st European Bioinformatics School" - Biosapiens School, Verona 7-13 July 2003.

National

4. “Corso di Ingegneria Enzimatica (dalla ricerca alla bioindustria)” - DBSM Università dell'Insubria - Varese, 11-15 July 2005.

5. “First BioPerl Workshop” - TIGEM, Istituto CEINGE Napoli, 22-23 April 2004.6. “Corso di Bioinformatica” - Società Italiana di Genetica Agraria, Cortona, 8-10 April 2003.7. “IV Workshop Italiano di PCR Quantitativa” - Applied Biosystem, Firenze, 21 November 2001.8. “Scuola di Genetica di Cortona” - Associazione Genetica Italiana, Cortona, 14-16 November 2000.9. “PCR Overview” - Perkin Elmer, Firenze, 3 November 1999.


SCIENTIFIC EXPERIENCES

2011Feb -

Research contract with the Department of Preclinical and Clinical Pharamcology, project title “Bioinformatics approaches for the evaluation of predictive markers for immunotherapy”, supervisor dr. D. Cavalieri.

2010Jul - Oct

EBMO Short Term Fellowship, project title “Analysis of intestinal micro-flora using DNA microarray technology” Computer Laboratory - University of Cambridge UK - 15/07/210- 15/10/2010, supervisor prof. Pietro Liò.

2010Feb - Jun

Research contract with the Interuniversity Center of Marine Biology (CIBM), project title “Evaluation of bioactivities in natural products extracted from marine seaweeds”, supervisor prof. D. Degl’Innocenti.

2010Jan - Dec

Collaboration with Paris CNRS, project title “Molecular mechanisms of Huntingtin aggregation: role of the regions flanking the poly-glutamine stretches”, supervisors prof. R. Melki and prof. D. Degl’Innocenti.

2009Oct - Nov

Research contract with the Department of Biochemical Sceince, project title “Genomic Approaches to the discovery of molecular targets of low molecular weight phophotyrosine protein phospatase (LMW-PTP) in tumorigenisis”, supervisor dr. D. Cavalieri.

2009Apr - Sep

Research contract with the Interuniversity Center of Marine Biology (CIBM), project title “Evaluation of bioactivities in natural products extracted from marine seaweeds”, supervisor prof. D. Degl’Innocenti.

2008 - 2009Jan - Mar

Research fellowship at the Department of Biochemical Sceince, project title “Systematic analysis of the gene expression levels in the pathways involving the acylphosphatase genes”, supervisor prof. G. Manao.

2007Jan - Dec

Research contract with the National Institute of Biostructures and Biosystems (INBB), supervisor prof. F. Chiti.

2006Jan – Nov

Research fellowship at the Department of Biochemical Sceince, project title “Selection of scFv antibodies specific for epitopes in the protein aggregates”, supervisor prof. D. Degl’Innocenti.

2005 Winner of the “CIB fellowship Award” for the best poster at the “International Workshop on Systems Biology”.Winner of the “Zanichelli Prize” for the best poster at the “2005 SIB Congress”.

2003-2005Jan - Dec

PhD course in Biochemistry and Applied Biology at the Department of Biochemical Sciences of Florence, thesis title “Advances in acylphosphatase studies: phylogenesis, novel enzymes and amyloid aggregation”, exam commission composed by prof. N. Taddei (University of Firenze), prof. A. Accorsi (University of Bologna) and prof. C.M. Dobson (University of Cambridge UK)


DETAILED SCIENTIFIC AND TECHNICAL SKILLS (WITH PERSONAL BIBLIOGRAPHY)

Bioinformatics

In 2004 it has been published my first project on positional entropy of multi-aligned protein sequences. The software I developed (Entropy Calculator) allowed with a simplified graphical interface to pre-process, align and examine with colour codes the degree of postional entropy [04]. The software was then used to discover and elucidate the role of glycine residues as gatekeepers for amyloid-like aggregation in the acylphosphatase protein family [06].In 2007 I developed and optimized an algorithm (Zagg) for the prediction of the intrinsic amyloid propensity of polypeptide sequences capable of batch-analysing whole proteomes [11]. Thanks to this, in collaboration with dr. E. Monsellier and prof. F. Chiti, a bioinformatics analysis on human proteome was performed. The further integration of data collectors from different data banks allowed to correlate amyloid propension with biological functions, cellular localizations and several other protein features [18].In 2006 I developed a software package (CAIAP) for the prediction of the expressivity level of genes in a fully sequenced genomes based on codon usage and codon optimization strategies. My programs allowed to create a collaboration with dr. M. Brilli and prof. R. Fani for the large scale analysis on all fully sequenced bacteria. The results were exposed in a specifically created web server [http://www.unifi.it/scibio/bioinfo/caiap/html/] with tools for the meta analysis of gene functions in the different ecological niches and for studying the importance of defined metabolic pathways for the different microbial life styles [12]. In 2009 I developed a program (XYLab) for the graphical analysis of multivariate dataset with mixed matrices. The program allowed to visualize up to 5 dimensions 2 of which based on pattern matching, so it offered the unprecedented possibility of adding biological information from annotations to numerical scatters, a fundamental aspect for identifying bi-univocal trends inside a huge number of data points as those emerging from high-throughput techniques such as microarrays and proteomics [16].In the same year I moved my interests to microbial community analysis in collaboration with dr. D. Cavalieri and dr. C. de Filippo. In particular, I developed a set of procedures (popu-probe) for the automated collection of microarray probes based on 16S ribosomal sequences starting from a simple list of bacterial entries. The programs were applied to list of bacteria inhabiting the human GI tract and allowed to produce a microarray chip for the phylogenetic analysis of gut microbial communities, whose experimental validation is currently in progress.In 2010 I moved to the analysis of pyrosequencing data again thanks to the collaboration with dr. D. Cavalieri and dr. C. de Filippo. During this project I set up and optimized several routines for automating the tedious process of large-scale taxonomic assignments and for the rapid collection of informative data from different samples. This work was applied to the comparison of microbial communities in the gut of children from Europe and rural Africa, with exciting results underlining the role of the diet in shaping the human GI microbiota [22]. Within this project I spent some months as an EMBO Short Term fellow in the computer lab of prof. Pietro Lio at the University of Cambridge UK. In this period I focussed on the phylogenetic methods for taxonomy assignment and developed a set of routines for evidencing traces of potential pathogenic species in pyro-sequenced 16S bacterial samples.In the same year I also spent several weeks at the CNRS department of Biochemistry in Paris for setting up a collaboration with researchers in Huntington disease. During the year I developed some new engines for the localization of glutamine-rich / poly-glutamine stretches in genomes and for the analysis of compositional biases in the stretches and in their flanking regions. As an ongoing project, we are investigating the evolution of such peculiar regions in genomes at diverging time from human, trying to map possible relationships between triplet-expansion diseases and the proteins involved in the pathologies. In 2011 I analysed recently sequenced strains of Saccharomyces cerevisiae (both classic Sanger sequencing and Next Generation Sequencing within the European Framework Programme Sybaris) and developed a software for the extraction of gene combinations that, when combined and analysed with phylogenetics techniques, reconstruct pre-determined tree topologies. This work allowed me to identify the a minimal phylogenetic unit composed of three genes that correctly recapitulate the relationships of all the yeast's strains so far available.

- Structural analysis


During my PhD I’ve extensively used homology modelling and 3D structure analysis of peptides and proteins. One of the model I produced allowed to correctly predict the presence and the localization of a disulfide bridge in the acylphosphatase protein from E.coli, successfully driving experiments for its experimental proof [09,10]. As a second example, during my studies on scFv antibodies, structural analysis allowed to map the region of the epitope (the HypF-N protein used as a model for studying the amyloid aggregation process) constituting the binding site of the antibody, with evident advances in the comprehension of this antigen-antibody interaction system.This kind of approach was also used when I collaborated with the groups of dr. T. Ercolino and prof. S. Giglio for attributing structural roles to newly discovered human mutations in the Von Hippel-Lindau gene (VHL, causing phaeochromocitoma [13]) and ectodisplasin-A gene (EDA, causing ectodermal displasia), leading to a proper description of the effect that the given mutations may have in causing the corresponding diseases.

- Analysis of microarray data

In 2008 I dealt with microarray data analysis for studying the possible co-regulated partners of the human acylphosphatase genes from existing published data. In the first stage of the project I developed a number of tools for the parsing and the coherent mining of data from the NCBI Gene Expression Omnibus (GEO) database. Then a number of expression profiles have been extracted with different degrees of similarity with the AcP genes. The profiles have then been subject to comparison in order to obtain a coherent consensus profile for guiding new experiments aimed at identifying the true expression partners of the Acp genes that, though well studied and characterized in terms of structure and properties of their polypeptide chains, yet retain a substantial lack of information about their true biological role in living cells (importantly, this gene family is ubiquitous in all organisms sequenced so far, apart from fungi).In 2011 I worked with the groups of prof. Carl Figdor and Gerold Shuler to the development of an analysis pipeline for gene expressoin data via Illumina microarrays to the aim of describing maturation process of dendritic cells upon different stimuli and how this affects the outcome of a multicenter (Oncologic Hospital of Nijmegen, The Netherlands and Univeristy) clinical trial Hospital of Erlangen, Erlangen, Germany) on DC vaccination against highly staged melanoma.

Biochemistry

- Enzyme kinetics

My degree and PhD thesis have been focussed on the characterization of novel members of the acylphosphatase family. In particular, I cloned and enzymatically characterized two AcPs from Drosophila melanogaster [01] and Escherichia coli [10], obtaining the main kinetic constants (Km, Kcat, Ki) on different substrates and a newly discovered splicing variant of the human common-type isoform completely devoid of enzymatic activity (for the lack of the proper catalytic AcP signature) but still able to induce apoptosis when over-expressed in cultured cells [03].

- Immuno-enzimatic assays.

During the years I made extensive use of immuno-based techniques for studying the targets of my projects. Techniques such as western-blot and dot-blot have been routinely employed for checking protein purifications and expression levels. In the scFv-based projects the ELISA technique have been deeply used to assist the biopanning procedures and the for the final assessment of affinities and specificities of the selected antibodies. In addition, in collaboration with dr. F. Giansanti, I also set up a new ELISA-based technique for the rapid assessment of the level of the monoclonal antibody infliximab after intravitreal administration [14,20]. Tested and confirmed on rabbits, this technique will allow in a future to drastically reduce the number of animals sacrificed for a single study and hopefully will be of benefit in establishing new antibody-based therapies in human.

- scFv antibody repertoires (phage display)


In 2003 I was involved in a project aimed at isolating from the Nissim Library naïve svFv repertoire the first scFv antibodies able to specifically detect a single secondary structure (an alpha-helix) and to slow the folding process of the protein in which it is present [02]. In 2006 I was enrolled in a second project based on the Tomlinson I+J repertoire and I was able to isolate and characterize a scFv antibody able to identify amyloid-aggregates only when adsorbed on a surface, demonstrating that surfaces may act as a driving force for distorting even solid and highly stabilized protein structures, leading to the idea that surface contacts may act as a denaturing agent and therefore promote aggregation.

Genetic engineering

- Cloning and expression of recombinant proteins

From the very beginning of my work I extensively employed recombinant DNA techniques to produce proteins. In 2003 I cloned AcPDro2, a second Drosophila melanogaster AcP isoform using the pGEX vector series allowing the fusion of the protein with the GST-tag for a convenient purification from bacterial lysates [01]. Similarly, in 2004 I cloned CTsv, a splicing variant of human common type AcP [03]. In 2006 I started using most modern vectors such as the pET vectors to clone EcoAcP, the first bacterial AcP from Escherichia coli, allowing its purification as 6xHIS fusion protein [10]. More recently, I employed the TOPO™-technology for the fast cloning of additional AcP isoforms.

- Site-directed mutagenesis

The possibility of introducing single point mutations in DNA sequence allows to examine the properties of polypeptide chains with an unprecedented level of detain. I employed site directed mutagenesis to remove cysteine residues from position 5 and 49 from EcoAcP, allowing to eliminate a disulfide bridge that proved to confer an unusual thermodynamic stability to native the protein [10]. A far more extended use of site-directed mutagenesis has been employed in the mapping of the binding site of an scFv on the model protein HypF-N, since I created single point mutants for neutralizing all charged side chains exposed on the surface of the protein.

- Analysis of gene expression levels

In 2003 (when real-time PCR and microarrays were at their early beginning) I analyzed the expression levels of AcPs and CTsv from cultured cell lines with classic techniques such as retro-transcription and PCR coupled to southern-blot and radioactively (32P) labelled probes [03]. In 2006 RT-PCR allowed me to confirm the non-existence of a long N-terminal extended form of AcP in E. coli, therefore cloning the correct version of the gene and to define a set of bioinformatics rules to the correct identification of AcP genes in newly sequenced organisms [10].

Biophysics

- Fluorimetry

During the characterization of AcPDro2 [01] and EcoAcP [10,15] proteins the intrinsic florescence of aromatic residues have been used to study their folding/unfolding kinetics and their thermodynamic properties by means of stopped-flow and equilibrium denaturation techniques after urea- or guanidine-induced denaturation.The ThT and ANS probes have been extensively used during experiments on amyloid aggregation to monitor the aggregation kinetics [06,07,08] and the potential effect of natural inhibitors.

- Spectro-polarimetry (CD)

Spectro-polarimetry have been used during the characterization of AcPDro2 [01] and EcoAcP [10] proteins for preliminary studies on their secondary structure content in response to physical and chemical denaturing agents. Circular dichroism has also been used to document the native state of


AcPDro2 at the early stages of its aggregation, describing the first example of a protein that can undergo amyloid aggregation from its native state [07].

- Dynamic light scattering (DLS)

Since the monitoring of the size of particles is a basic prerequisite for studying the dynamics of amyloid aggregation, it has been extensively employed in all experiments dealing with amyloid. It has been of particular importance for characterizing the early stages of AcPDro2 aggregation [07], allowing a coherent characterization of its native state.


TEACHING EXPERIENCES

Teaching contracts

1. course “General Bioinformatics”, SSD MED/01, 6 CFU, for the Master Degree course in Biology, Faculty of Mathematical Physical and Natural Sciences, University of Ferrara.AA 2009-2010.

2. course “Bioinformatics”, SSD BIO/10, 5 CFU, for the Master Degree course in Biotechnology, Faculty of Pharmacy, University of Florence.AA 2009-2010, 2010-2011.

3. course “Biochemistry of Fermentations”, SSD BIO/10, 5 CFU, for the Master Degree course in Pharmaceutical Biotechnology, Faculty of Pharmacy, University of Florence. AA 2006-2007, 2007-2008, 2008-2009, 2009-2010, 2010-2011.

4. course “Molecular Biology”, SSD BIO/11, 2 CFU, for the Bachelor Degree course in Scientific Information on Drug, of Pharmacy, University of Florence. AA 2009-2010.

5. course “Proteomics”, SSD BIO/10, 2 CFU, for the Master Degree course in Molecular Biotechnology, Faculty of Mathematical Physical and Natural Sciences, University of Florence. AA. 2009-2010, 2010-2011.

6. course “Molecular and Plant Biology”, SSD BIO/13, 2 CFU, for the Master and Bachelor Degree courses in Pharmacy, Pharmaceutical Chemistry and Technology and Scientific Information on Drug, Faculty of Pharmacy, University of Florence AA 2007-2008.

Seminars and Lectures

1. Lecture “Molecular classification of prokaryotes via bioinformatics processing of 16S ribosomal DNA pyrosequencing”, at Istituto Agratrio di San Michele all'Adige, San Michele all'Adige, Trento, 30-06-2011

Partecipations / collaborations

1. course “Protein Bioinformatics“,SSD BIO/10, 3 CFU, for the Master and Bachelor Degree courses in Pharmacy, Pharmaceutical Chemistry and Technology and Scientific Information on Drug, Faculty of Pharmacy, University of Florence AA 2007-2008, legal holder prof. G. Manao.

2. course “Protein structures” , SSD BIO/10, 3 CFU, for the Master Degree course in Pharmaceutical Biotechnology, Faculty of Pharmacy, University of Florence, legal holder prof. G. Manao

3. course “Biological Modelling” , SSD BIO/10, 3 CFU, for the Bachelor Degree in Cellular and Molecular Biology, Faculty of Mathematical Physical and Natural Sciences, University of Florence, legal holders prof. L.Pazzagli and G. Cappugi.

4. course “Laboratory of Molecular Biology”, SSD BIO/11 for the Bachelor Degree in Biotechnology, Faculty of Mathematical Physical and Natural Sciences, University of Florence, legal holder prof. G. Raugei.

Honours

1. Declared “Expert in the field of Biochemistry” by the Faculty of Pharmacy, University of Florence on March 24, 2004

Other experiences

1. Assistant supervisor in theses development for thee courses in Biotechnology and Pharmacy.2. Exam sessions for the courses of Animal and Vegetal Biology (prof. D. Degl’Innocenti), Biochemistry

(prof. G. Manao) e Engineering of Antibodies (prof. D. Degl’Innocenti).


3. Member in Thesis Commission for degree courses in Pharmaceutical Biotechnology, Molecular Biotechnology and Pharmacy.


CONGRESS ACTIVITY

Talks

O1. “Cortona Prokaryotes Meeting” – Italia Genetics Association, Cortona, April 4-6 2007 – Talk title: “The CAI Analyser Package: studying gene expressivity with genomic data and Codon Adaptation Index”.

O2. “Convegno congiunto AGI-SIBV-SIGA” - Assisi 19-22 Settmbre 2011 - Comunicazione orale dal titolo “Phylogenomics applied to saccharomyces cerevisiae reveals genes with high evolutionary resolution”

Partecipations

C1. “L’immunologia e il suo contributo nel laboratorio biologico” - Ordine Nazionale dei Biologi, Firenze, 28 ottobre 2000.

C2. “Incontro Cortona Procarioti” - Associazione Genetica Italiana, Cortona, 27-28 Aprile 2000.C3. “Proteine 2002 XVI Meeting of Protein Workgroup” - L’Aquila, 6-8 Giugno 2002.C4. “Fifth European Symposium of The Protein Society” - Firenze, 29 Marzo - 2 Aprile 2003. C5. “SIB 2003 Joint Symposia with the British Biochemical Society” - Ferrara, 15-18 Settembre 2003.C6. “1° Congresso Nazionale IHUPO” - Napoli, 26-27 Settembre 2003.C7. “Proteine 2004 XVII Meeting of Protein Workgroup” - Viterbo, 20-22 Maggio 2004.C8. "From Structural Genomics to Drug Discovery" – Parma, Settembre 2004. C9. “49° Congresso Nazionale SIB” - Riccione, Settembre 2004.C10. “Workshop On System Biology” - CEBIB, Università della Bicocca, Milano, 15-16 Giugno 2005.C11. “18° Riunione Nazionale dei Dottorandi di Biochimica” – Comunicazione orale - Brallo di Pregola, 7

-10 Giugno 2005 Pavia.C12. “50° Congresso Nazionale SIB” - Riccione, 27-30 Settembre 2005.C13. “Second Meting of Italian Evolutionary Biologists - First SIBE-ISEB congress” – Firenze, 4-7

Settembre 2006.C14. “Incontro Cortona Procarioti” Associazione Genetica Italiana, Cortona, 4-6 Aprile 2007.

Posters and abstracts

G1. D. Degl’Innocenti, M. Ramazzotti, R. Marzocchini, G. Raugei and G.Ramponi “Identification and molecular characterization of a novel acylphosphatase from D.melanogaster”, Ital. J. Biochem (2002) n° 51, pag. 58 abstract from “Proteine 2002 XVI Meeting of Protein Workgroup, L’Aquila, June 6-8, 2002”.

G2. D. Degl’Innocenti, M. Ramazzotti and G. Ramponi “Cloning and characterization of a novel acylphosphatase gene from Escherichia coli”, Protein Science (2003) n° 12 suppl.1, pag. 148-149 abstract from “Fifth European Symposium of The Protein Society, Florence, March 29-April 2, 2003”.

G3. M. Ramazzotti, D. Degl’Innocenti, G. Manao and G. Ramponi “Entropy Calculator: scorer for multiple sequence alignments”, Ital. J. Biochem (2003) n° 52, pag. 151 abstract from “Proteine 2003 XVII Meeting of Protein Workgroup, Ferrara, September 15-18, 2003”.

G4. M. Ramazzotti, D. Degl’Innocenti, G. Manao and G. Ramponi “Analysis of acylphosphatases in Drosophila melanogaster”, abstract from “Book of abstracts” of “1° Congersso nazionale IHUPO”, Napoli, 26-27 september 2003.

G5. M. Ramazzotti, G. Manao, G. Ramponi and D. Degl’Innocenti “Expressivity of protein families by codon adapatation index analysis: the FAMiCOD Analyser”, Ital. J. Biochem (2002) n° 53, pag. 128 abstract from “Proteine 2004 XVII Meeting of Protein Workgroup, Viterbo, May 20-22, 2004”.

G6. M. Ramazzotti, G. Manao, M. Stefani, G. Ramponi and D. Degl’Innocenti “Expression and kinetic properties of E.coli acylphosphatase”, Ital. J. Biochem (2004) n° 53, pag. 96 abstract from “Proteine 2004 XVII Meeting of Protein Workgroup, Viterbo, May 20-22, 2004”.

G7. C. Parrini, M. Ramazzotti, D. Degl’Innocenti, G. Ramponi, C. M. Dobson, N. Taddei and F. Chiti “Glycine residues appear to be evolutionary conserved for their ability to inhibit aggregation”, Ital. J. Biochem (2002) n° 53, pag. 38, abstract from “Proteine 2004 XVII Meeting of Protein Workgroup, Viterbo, May 20-22, 2004”.


G8. M. Ramazzotti, N. Mulinacci, F. F. Vincieri, G. Manao and D. Degl'Innocenti “Protein extraction from refined oils and allergenic potency”, Ital. J. Biochem (2004) n° 53, pag. 219, abstract from “SIB 2004 Riccione, September 28-October 1, 2004”.

G9. M. Ramazzotti, G. Manao, M. Stefani, G. Ramponi and D. Degl'Innocenti “Uncommon behaviour of E. coli acylphosphatase: a new perspective on AcP family”, Ital. J. Biochem (2004) n° 53, pag. 336, abstract from “SIB 2004 Riccione, September 28-October 1, 2004”.

G10. M. Ramazzotti, G. Manao, G. Ramponi and D. Degl'Innocenti “Studying gene expression with genomic data and Codon Adaptation Index – The FAMiCOD analyser package”, abstract del workshop “System Biology” - CEBIB, Università della Bicocca, Milano, June 15-16 2005

G11. M. Ramazzotti, N. Mulinacci, F. F. Vincieri, G. Manao and D. Degl’Innocenti “Determination of protein content in refined oil and allergenic potency”, abstract Poster 542 from “International Congress and 53rd Annual Meeting of The Society for Medical Plants Research – GA”, Firenze 21-25 Agosto 2005

G12. M. Ramazzotti, M. Stefani, F. Chiti, G. Ramponi, G. Manao and D. Degl'Innocenti “Cell membrane contact drives a conformational change in epitope of HypF-N amyloid early aggregates”, Ital. J. Biochem (2005) n° 54, pag. 188, abstract from “SIB 2005 Riccione, September 27-30, 2005”.

G13. M. Ramazzotti, M. Brilli, R. Fani, G. Manao and D.Degl’Innocenti “Studying gene expression with genomic data and Codon Adaptation Index” abstract from “Congresso SIBE - Firenze 4-7 Settembre 2006” Aracne ed.

G14. M. Ramazzotti, G. Calloni, M. Stefani, F. Chiti, G. Manao and D. Degl’Innocenti “Selection of scFv against cytotoxic protein aggregates”, abstract from “SIB 2006 Riccione, September 28-30, 2006”.

G15. S. Gestri, M. Ramazzotti, N. Mulinacci, F.F. Vincieri, M. Innocenti, G. Manao and D. Degl’Innocenti “Anti-amyloidogenic effect of some vegetal compounds: preliminary studies”, abstract from “SIB 2006 Riccione, September 28-30, 2006”.

G16. S. Gestri, M. Ramazzotti, N. Mulinacci, F.F. Vincieri, M. Innocenti, B. Tiribilli, G. Manao and D. Degl'Innocenti “Amyloidosis inhibition by polyphenols” Phytotherapy Food & Health - 2° Verona Meeting, Verona, September 29-30, 2007.

G17. M. Ramazzotti, F. Niccheri and D. Degl’Innocenti Donatella “Biochemical characterization of extracts from tyrrhenian seaweeds”, abstract from “BMA annual meeting 2010”, San Benedetto del Tronto, May 20-21 2010

G18. M. Ramazzotti, B. Tiribilli, F. Niccheri and D. Degl’Innocenti Donatella “The effects of tyrrenian seaweeds extracts on amyloid aggregation assessed by atomic force microscopy”, abstract from “BMA annual meeting 2010”, San Benedetto del Tronto, May 20-21 2010

G19. M. Ramazzotti, F. Niccheri and D. Degl’Innocenti Donatella “Biochemical characterization of the Tyrrhenian seaweed Halopithys incurva”, abstract from “ISMAR Ecotoxicology Congres 2010”, Livorno, October 20-22 2010


LIST OF PUBLICATIONS (2003-2012), H-INDEX 8

P1. D. Degl’Innocenti, M. Ramazzotti, R. Marzocchini, F. Chiti, G. Raugei and G. Ramponi “Characterization of a novel Drosophila melanogaster acylphosphatase”, FEBS Letters (2003) 26930:1-4. (pmid 12560098).

P2. D. Degl’Innocenti, N. Taddei, M. Ramazzotti, M. Stefani, F. Chiti and G. Ramponi “Selection of antibody fragments specific for an -helix region of acylphosphatase protein” Journal of Molecular Recognition, (2004) 17:62-66. (pmid 14872538).

P3. D. Degl’Innocenti, R. Marzocchini, F. Malentacchi, M. Ramazzotti, G. Raugei and G. Ramponi “ACYP1 gene possesses two alternative splicing forms that induce apoptosis”, IUMBM Life (2004) 56:29-33. (pmid 14992377).

P4. M. Ramazzotti, D. Degl’Innocenti, G. Manao, G. Ramponi “Entropy Calculator: getting the best from your multiple protein alignments”, Italian. Journal of Biochemistry (2004) 53: 136-142. (pmid 15356957).

P5. S. Zuccotti, C. Rosano, M. Ramazzotti, D. Degl’Innocenti, M. Stefani, G. Manao and M. Bolognesi “Three-dimensional structural characterization of a novel Drosophila melanogaster acylphosphatase”, Acta Crystallographica. (2004) D60: 1177-1179. (pmid 15159593).

P6. C. Parrini, N. Taddei, M. Ramazzotti, D. Degl'Innocenti, G. Ramponi, C.M. Dobson and F.Chiti “Glycine residues appear to be evolutionarily conserved for their ability to inhibit aggregation”, Structure (2005) 13:1143-1151. (pmid 16084386).

P7. G. Soldi, F. Bemporad, S. Torassa, A. Relini, M. Ramazzotti, N. Taddei and F.Chiti “Amyloid formation of a protein in the absence of unfolding and destabilization of the native state” Biophysical Journal (2005) 89(6):4234-4244. (pmid 16169977).

P8. M. Calamai, J. Kumita, J. Misfud, C. Parrini, M. Ramazzotti, G. Ramponi, N. Taddei, F. Chiti and C.M. Dobson “Nature and significance of the interactions between amyloid fibrils and biological polyelectrolytes” Biochemistry (2006) 45(42):12806-12815 (pmid 17042499).

P9. K. Pagano, M. Ramazzotti, P. Viglino, G. Esposito, D. Degl'innocenti, N. Taddei, and A. Corazza “NMR solution structure of the acylphosphatase from Escherichia coli” Journal of Biomolecular NMR. (2006) 36:199-204 (pmid 17021943).

P10. M. Ramazzotti, C. Parrini, M. Stefani, G. Manao, D. Degl’Innocenti “The intrachain disulfide bridge is responsible of the unusual stability properties of novel acylphosphatase from Escherichia coli” FEBS Letters (2006) 580(30):6763-6768 (pmid 17134700).

P11. E. Monsellier, M. Ramazzotti, P. Polverino de Laureto, G.G. Tartaglia, N. Taddei, M. Vendruscolo and F. Chiti “The distribution of the amino acid residues of a polipeptide sequence is a fundamental determinant of the aggregation rate that has been optimized by evolution” Biophys. Journal (2007) 93:4382-4391 (pmid: 17766358).

P12. M. Ramazzotti, M. Brilli, R. Fani, G. Manao and D. Degl’Innocenti “The CAI Analyser Package: studying gene expressivity with genomic data and Codon Adaptation Index” In Silico Biology (2007) online: 7-0035, printed: 7:507-526 (pmid: 18391240).

P13. T. Ercolino, L. Becherini, A. Valeri, M. Maiello, M.S. Gaglianò, G. Parenti, M. Ramazzotti, E. Piscitelli, L. Simi, P. Pinzani, G. Nesi, D. Degl’Innocenti, N. Console, C. Bergamini, M. Mannelli “Uncommon clinical presentation of pheochromocytoma and paraganglioma in two different patients affected by two distinct novel VHL germline mutations” Clinical endocrinology (2008), 68(5):762-768 (pmid: 18031321).

P14. F. Giansanti, M. Ramazzotti, L. Vannozzi, E. Rapizzi, T. Fiore, B. Iaccheri, D. Degl’Innocenti, D. Moncini and U. Meschini “A Pilot Study on Ocular Safety of Intravitreal Infliximab in a Rabbit Model” Investigative Ophthalmology and Visual Science (2008), 49(3):1151-1156 (pmid:18326743).

P15. C. Parrini, F. Bemporad, A. Baroncelli, S. Gianni, C. Travaglini-Allocatelli, J.E. Kohn, M. Ramazzotti, F. Chiti and N. Taddei “The folding process of acylphosphatase from E.coli is remarkably accelerated by the presence of a disulfide bond” Journal of Molecular Biology (2008) 379:1107-1118 (pmid: 18495159).

P16. M. Ramazzotti, E. Monsellier and D. Degl’Innocenti “XYLab: an interactive plotting tool for mixed multivariate data observation and interpretation” Bioinformation (2008), 2(9):392-394 (pmid: 18795112).

P17. M. Ramazzotti, N. Mulinacci, L. Pazzagli, M. Moriondo, G. Manao, F.F. Vincieri and D. Degl’Innocenti “Analytic investigations on protein content in refined seed oils: implications in food allergy” Food and Chemical Toxicology (2008), 46(11):3383-3388 (pmid: 18768153).


P18. E. Monsellier*, M. Ramazzotti*, N. Taddei and F. Chiti “Aggregation propensity of the human proteome”, PLoS Computational Biology (2008), 4(10):e1000199 (pmid: 18927604). *equal contribution

P19. M. Coppo, M. Boddi, M. Bandinelli, D. Degl’Innocenti, M. Ramazzotti, F. Marra, S. Galastri, R. Abbate, G.F. Gensini and L. Poggesi “Angiotensin II upregulates renin-angiotensin system in human isolated T-lymphocytes” Regulatory Peptides (2008), 151(1-3):1-6 (pmid: 18723052).

P20. F. Giansanti*, M. Ramazzotti*, M. Giuntoli, G. Virgili, L. Vannozzi, D. Degl'innocenti and U. Menchini “Intravitreal Infliximab Clearance in a Rabbit Model: different sampling methods and assay techniques” Investigative Ophthalmology and Visual Science (2009), 50 (11):5328-35 (pmid: 19474407). *equal contribution

P21. E. Monsellier, M. Ramazzotti, N. Taddei and F. Chiti “A computational approach for identifying the chemical factors involved in the glycosaminoglycans-mediated acceleration of amyloid fibril formation” PLoS ONE (2010), 5(6): e11363 (pmid: 20613870).

P22. C. De Filippo, D. Cavalieri, M. Di Paola, M. Ramazzotti, J.B. Poullet, S. Massart, S. Collini and P. Lionetti “Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa” Proc Natl Acad Sci USA. (2010) 107(33):14691-6 (pmid: 20679230).

P23. M. Belli, M.Ramazzotti and F. Chiti “Prediction of amyloid aggregation in vivo.” EMBO Reports (2011) 12(7):657-63 (pmid: 21681200).

P24. M. Ramazzotti, L. Berná, I. Stefanini, D. Cavalieri “A computational pipeline to discover highly phylogenetically informative genes in sequenced genomes: application to S. cerevisiae natural strains” Nucleic Acids Research (2012) , epub ahead of print, (pmid: 22266652).

P25. M. Ramazzotti, E. Monsellier, C. Kamoun, D. Degl’Innocenti, R. Melki “Polyglutamine Repeats Are Associated to Specific Sequence Biases That Are Conserved among Eukaryotes” PLoS ONE (2012) 7(2): e30824. (pmid:NA).


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