Bio-Molecular Diversity & Evolutionary Biology

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Research Area: 

SCIENTIFIC CATEGORIES: COMPARATIVE BIOLOGY AND CYTOLOGY (BIO/06), GENETICS (BIO/18), MICROBIOLOGY (BIO/19)

Our research activities aim to investigate the molecular, cellular and developmental diversity of organisms at different levels of evolutionary complexity: microorganisms, plants, animals and humans. The relationships among individuals and/or populations, and among them and the environment, are described by means of modern genomic techniques and cellular/morphometric tools. This multidisciplinary approach allows for a much needed and exhaustive description of natural biodiversity, potentially placing the Bio-Molecular Diversity & Evolutionary Biology group in the forefront of both basic and applied research.

SPECIFIC RESEARCH OBJECTIVES:

Microbial ecology and applied microbiology (G. Cenci, E. Federici, S. Covino)
Implementation of bio-molecular approaches to investigate the structural and functional diversity of microbial communities in the environment (e.g., soil, water, host organisms), in biotechnological processes (e.g., bioremediation, waste treatment and valorization) and in human health (e.g., interactions with xenobiotics, probiotic antigenotoxicity).

Conservation genetics and molecular ecology (L. Lucentini)
Mitochondrial and nuclear phylogenetic, phylogeography and DNA variations patterns evaluations  to clarify evolution, dispersal patterns and taxonomic relationships of wild populations and domesticated stocks with theoretical and applied scopes, as pursue forensic and conservation genetics purposes. Application of integrative taxonomy to wild and domesticated stocks.

Development and cell biology vs environment (I. Di Rosa, A. Fagotti)
Biological responses of sentinel organisms to environmental stressors, at different level of biological organization (sub-organismal, individual and population); measurement of biomarkers under natural and controlled conditions. Biological response of developing model organisms to physical and chemical stress: potential applications in pharmacological and bio-medical fields.

Unit: Population genetics and molecular evolution (H. Lancioni)
Genetic analyses of mitochondrial and nuclear DNA sequence variation with the aim of better defining origins, evolution and dispersal patterns of human and livestock populations. Definition of the role played by the human and animal genome variation in association studies and in forensic surveys. 


Members: 

Lecturers:

Giovanni Cenci - Full Professor (BIO/19) – COORDINATOR

Ines Di Rosa - Associate Professor (BIO/06)

Anna Fagotti - Assistant Professor (BIO/06)

Ermanno Federici - Assistant Professor (BIO/19)

Livia Lucentini - Assistant Professor (BIO/06)

Hovirag Lancioni - Assistant Professor (RTD BIO/18)

Stefano Covino – Assistant Professor (RTD BIO/19)

Lab Assistants:

Franco Piccinini

Francesca Simoncelli

PhD Students:

Irene Cardinali

Elisa Ceci

Lab Fellows:

 

Chiara Casagrande


Research Projects: 

2017 - PSR Umbria, sottomisura 16.2.2.  Smarthorse: sviluppo di un sistema di gestione della stalla tramite tecnologia RFID Bluetooth applicato all’allevamento del cavallo TPR in Umbria. H. Lancioni. Research Unit Coordinator.

2017 - BRIC INAIL Projects. Confronto fra tecniche di microbiologia classica e tecniche alternative chimiche, di biologia molecolare, di metagenomica e metaproteomica, per lo studio del bioaerosol negli ambienti di lavoro. E. Federici, Research Unit Coordinator.

2016 - Convenzione con Università degli Studi di Perugia. Monitoraggio della presenza di Legionella spp nel sistema di distribuzione idrica degli edifici dell'Ateneo. E. Federici, Project Coordinator

2015 - Fondazione Cassa di Risparmio di Terni Grants. "Caratterizzazione microbiologica del particolato atmosferico (PM10) nella conca ternana”. E. Federici, Project Coordinator

2015 - BRIC INAIL Projects. Fillobiorisanamento: utilizzo delle interazioni piante-batteri come Strumento INnovativo pER il trattamento bioloGIco di inquinanti volatili per la sicurezzA negli impianti produttivi (SINERGIA). E. Federici, Research Unit Member.

2015 - Fondazione Cassa di Risparmio di Perugia Grants. “Tracciabilità genetica di prodotti tipici umbri: lenticchia e capra della Valnerina” H. Lancioni.  Research Unit Coordinator 

2013 - Fondazione Cassa di Risparmio di Perugia Grants. Sviluppo di modelli in vitro per lo studio dello stress cellulare indotto da inquinanti ambientali. A. Fagotti Project Coordinator

2013 - PSR Regione Toscana – Misura 124. ECOPOT, valorizzazione del settore vivaistico incentrata sulla tutela ambientale attuata tramite la sperimentazione di un innovativo prodotto costituito da un contenitore
(vaso) biodegradabile. E. Federici, Research Unit Coordinator.

2012 - Convenzione con DIVA International S.r.l. Studio dell’efficacia antimicrobica di nuove formulazioni per la produzione di salviette umidificate. E. Federici, Project Coordinator.

2012 - Convenzione con Provincia di Perugia. Caratterizzazione Genetica di Materiale da ripopolamento.L. Lucentini, Project Coordinator.

2012 - PSR Regione Toscana – Misura 124. SAN-SOIL, creazione di un nuovo ammendante, sostitutivo della torba utilizzata nel vivaismo, ottenuto dalla trasformazione degli scarti da frantoio oleario. E. Federici, Research Unit Coordinator.

2012 – PRIN. Microrganismi negli alimenti e nell’uomo: studio del microbiota e del relativo metaboloma in funzione della dieta omnivora, vegetariana o vegana. G. Cenci, Research Unit Member.

GRANTS FOR POST-DOCTORAL SCIENTISTS:

2017 Grant National Geographic Society.  Could mitochondrial haplogroup H in the heart of Asia unveil a far echo from the West? Granted to Irene Cardinali (Tutor: H. Lancioni) 

2013 Grant POR UMBRIA FSE 2007-2013. Infezioni da Amphibiocystidium in anfibi anuri: un modello di studio per la rinosporidiosi nell’uomo. Granted to: Dr. R. Rossi (Tutor: A. Fagotti).

2013 Grant POR UMBRIA FSE 2007-2013. Riciclo e valorizzazione dei reflui oleari: approfondimenti degli effetti sul microbiota del suolo. Granted to: Dr S. Scargetta. (Tutor: E. Federici).


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Selected Publications: 

- FULL PAPERS

2017

Federici E., Prete R, Lazzi C., Pellegrini N., Moretti M., Corsetti A., Cenci G. (2017)  Bacterial composition, genotoxicity and cytotoxicity of fecal samples from individuals consuming omnivorous or vegetarian diets.  Front. Microbiol. [28 Feb 2017, 8:300]. doi: 10.3389/fmicb.2017.00300

Federici E., Meniconi S., Ceci E., Mazzetti E., Casagrande C., Montalbani E., Businelli S., Mariani T., Mugnaioli P., Cenci G., Brunone B.(2017) Legionella survey in the plumbing system of a sparse academic campus: A case study at the University of Perugia.  Water  9, 662 – 673. doi:10.3390/w9090662

Ferradini N., Lancioni H., Torricelli R., Russi L., Dalla Ragione I., Cardinali I., Marconi G., Gramaccia M., Concezzi L., Achilli A., Veronesi F., Albertini E. (2017) Characterization and Phylogenetic Analysis of Ancient Italian Landraces of Pear. Frontiers in Plant Science 8:751  doi: 10.3389/fpls.2017.00751

Wang S, Chen N, Capodiferro MR, Zhang T, Lancioni H, Zhang H, Miao Y, Chanthakhoun V, Wanapat M, Yindee M, Zhang Y, Lu H, Dang R, Huang Y, Lan X, Plath M, Chen H, Lenstra JA, Achilli A, Lei C. (2017) Whole Mitogenomes Reveal the History of Swamp Buffalo: Initially Shaped by Glacial Periods and Eventually Modelled by Domestication. Scientific Reports 7: 4708 doi: 10.1038/s41598-017-04830-2.

Stella T., Covino S., Čvančarová M., Filipová A., Petruccioli M., D’Annibale A., Cajthaml T. (2017) “Bioremediation of long-term PCB-contaminated soil by white-rot fungi”. J. Hazard. Mater, 324: 701–710. Phylogenetic Analysis of Ancient Italian Landraces of Pear. Frontiers in Plant Science 8:751  doi: 10.3389/fpls.2017.00751

Chiesa S., Lucentini L., Freitas R., Nonnis Marzano F., Breda S., Figueira E., Caill-Milly N., Herbert R., Soares A.M.V.M., Argese E. (2017) A history of invasion: COI phylogeny of Manila clam Ruditapes philippinarum in Europe. Fisheries Research 186, 25-35

Gandolfi A., Crestanello B., Fagotti A., Simoncelli F., Chiesa S., Girardi M., Giovagnoli E., Marangoni C., Di Rosa I., Lucentini L. (2017) New evidences of mitochondrial DNA heteroplasmy by putative paternal leakage between the rock partridge (Alectorisgraeca) and the chukar partridge (Alectoris chukar). PLoS ONE, vol. 12, ISSN: 1932-6203

Gandolfi A., Ferrari C., Crestanello B., Girardi M., Lucentini L., Meraner A. (2017). Population genetics of pike, genus Esox (Actinopterygii, Esocidae), in Northern Italy: evidence formosaic distribution of native, exotic and introgressed populations. Hydrobiologia, vol. 794, p. 1-20,

Chiesa S., Lucentini L., Freitas R., Nonnis Marzano F., Breda S., Figueira E., Caill-Milly N., Herbert R., Soares A.M.V.M., Argese E. Mapping the stranger: genetic diversity of  Manila  clam in European coastal lagoons.  Bulletin of the Fisheries Research Agency of Japan, in press.

2016

Di Lorenzo P., Lancioni H., Ceccobelli S., Curcio L., Panella F., Lasagna E. (2016) Uniparental genetic systems: a male and a female perspective in the domestic cattle origin and evolution. Electronic Journal of Biotechnology 23: 69–78. doi: 10.1016/j.ejbt.2016.07.001.

Cardinali I, Lancioni H, Giontella A, Capodiferro MR, Capomaccio S, Buttazzoni L, Biggio GP, Cherchi R, Albertini E, Olivieri A, Cappelli K, Achilli A, Silvestrelli M (2016) An overview of ten Italian horse breeds through mitochondrial DNA PLoS ONE 11(4):e0153004. doi: 10.1371/journal.pone.0153004. eCollection 2016

Lancioni H, Di Lorenzo P, Cardinali I, Ceccobelli S, Capodiferro MR, Fichera A, Grugni V, Semino O, Ferretti L, Gruppetta A, Attard G,  Achilli A, Lasagna E (2016) Survey of uniparental genetic markers in the Maltese Cattle breed reveals a significant founder effect, but does not indicate local domestication. Animal Genetics 47(2): 267-269 doi: 10.1111/age.12408.

Covino S., Fabianová T., Křesinová Z., Čvančarová M., Burianová E., Filipová A., Vořísková J., Baldrian P., Cajthaml T. (2016) Polycyclic aromatic hydrocarbons degradation and microbial community shifts during co-composting of creosote-treated wood J. Hazard. Mater. 301: 17-26.

Chiesa S., Lucentini L., Freitas R., Nonnis Marzano F., Ferrari C., Filonzi L., Breda S., Minello F., Figueira E., Argese E. (2016) Null alleles of microsatellites for Manila clam Ruditapes philippinarum. Animal Genetics. 47:135-136. doi: 10.1111/age.12382.

Gandolfi A., Fontaneto D., Natali M., Lucentini L. (2016) Mitochondrial genome of Esox flaviae (Southern pike): announcement and comparison with other Esocidae. Mitochondrial DNA 27(4):3037-8

2015

Simoncelli F, Belia S, Di Rosa I, Paracucchi R, Rossi R, La Porta G, Lucentini L, Fagotti A. (2015) Short-term cadmium exposure induces stress responses in frog (Pelophylaxbergeri) skin organ culture. Ecotoxicol. Environ. Saf. 122:221-229

Bocci A., Sebastiani B., Trotta F., Federici E., Cenci G. (2015) In vitro inhibition of 4-nitroquinoline-1-oxide genotoxicity by probiotic Lactobacillus rhamnosus IMC501. J. Microbiol.  Biotechnol. 25(10): 1680-1686.  doi: 10.4014/jmb.1501.01086

Federici E., Rossi R., Fidati L., Paracucchi R., Scargetta S., Montalbani E., Franzetti A., La Porta G., Fagotti A., Simoncelli F., Cenci G., Di Rosa I. (2015). Characterization of the skin microbiota in italian stream frogs (Rana italica) infected and uninfected by cutaneous patasitic disease. Microbes and Environments 30(3): 262-269. doi: 10.1264/jsme2.ME15041

Proietti P., Federici E., Fidati L., Scargetta S., Massacesi L., Nasini L., Regni L., Ricci A., Cenci G., Gigliotti G. (2015) Effects of amendment with oil mill waste and its derived-compost on soil chimica and microbiological characteristics and olive (Olea europea  L.) productivity.  Agriculture, Ecosystems and Environment 207: 51-60.  doi: 10.1016/j.agee.2015.03.028

Colli L, Lancioni H, Cardinali ., Olivier A, Capodiferro MR, Pellecchia M, Rzepus M, Zamani W, Naderi S, Gandini S, Farhad Vahidi SM, Agha S, Randi E, Sardina MT, Portolano B, Rezaei HR, Lymberakis P, Boyer F, Coissac E, Pompanon F, Taberlet P, Ajmone Marsan P and Achilli A (2015) Whole Mitochondrial Genomes Unveil the Impact of Domestication on Goat Matrilineal Variability. BMC Genomics 16(1):1115. doi: 10.1186/s12864-015-2342-2

Grugni V, Battaglia V, Perego UA, Raveane A, Lancioni H, Olivieri A, Ferretti L, Woodward SR, Pascale JM, Cooke R, Myres N, Motta J, Torroni A, Achilli A, Semino O (2015) Exploring the Y chromosomal ancestry of modern Panamanians. PLoS ONE 4;10(12):e0144223. doi: 10.1371/journal.pone.0144223. eCollection 2015

Olivieri A, Gandini F, Achilli A, Fichera A, Rizzi E, Bonfiglio S, Battaglia V, Brandini S, De Gaetano A, El-Beltagi A, Lancioni H, Agha S, Semino O, Ferretti L, Torroni A (2015)  Mitogenomes from Egyptian Cattle Breeds: New Clues on the Origin of Haplogroup Q and the Early Spread of Bos taurus from the Near East. PLoS ONE. 10(10):e0141170. doi: 10.1371/journal.pone.0141170. eCollection 2015

Ceccobelli S, Di Lorenzo P, Lancioni H, Monteagudo Ibáñez LV, Tejedor MT, Castellini C, Landi V, Martínez Martínez A, Delgado Bermejo JV, Vega Pla JL, Leon Jurado JM, García N, Attard G, Grimal A, Stojanovic S, Kume K, Panella F, Weigend S, Lasagna E (2015) Genetic diversity and phylogeographic structure of sixteen Mediterranean chicken breeds assessed with microsatellites and mitochondrial DNA. Livestock Science 175:27-36

Vai S, Ghirotto S, Pilli E, Tassi F, Lari M, Rizzi E, Matas-Lalueza L, Ramirez O, Lalueza-Fox C, Achilli A, Olivieri A, Torroni A, Lancioni H, Giostra C, Bedini E, Baricco LP, Matullo G, Di Gaetano C, Piazza A, Veeramah K, Geary P, Caramelli D, Barbujani G. (2015) Genealogical Relationships between Early Medieval and Modern Inhabitants of Piedmont. PLoS ONE 30;10(1):e0116801

 Stella T., Covino S., Burianová E., Filipová A., Křesinová Z., Voříšková J., Větrovský T., Baldrian P., Cajthaml T. (2015) “Chemical and microbiological characterization of an aged PCB-contaminated soil”. Sci. Total Environ. 533: 177-186

Covino S., D'Annibale A., Stazi S.R., Cajthaml T., Čvančarová M., Stella T., Petruccioli M. (2015) Assessment of degradation potential of aliphatic hydrocarbons by autochthonous filamentous fungi from a historically polluted clay soil. Sci. Total Environ. 505: 545–554.

Simoncelli F., Belia S., Di Rosa I., Paracucchi R., Rossi R., La Porta G., Lucentini L., Fagotti A. (2015) Short-term cadmium exposure induces stress responses in frog (Pelophylax bergeri) skin organ culture. Ecotoxicology and Environmental Safety, 122: 221-229, ISSN 0147-6513, http://dx.doi.org/10.1016/j.ecoenv.2015.08.001.

Chiesa S., Scalici M., Lucentini L., Nonnis Marzano F. (2015) Molecular identification of an alien temnocephalan crayfish parasite in Italian freshwaters. Aquatic Invasions Volume 10, Issue 2: 209–216

2014

Ludovisi A., Rossi R., Paracucchi R., Selvaggi R., Fagotti A., Simoncelli F., Pascolini R., Di Rosa I. (2014) The delayed effects of meteorological changes on the water frogs in Central Italy. Hydrobiologia. 730:139-152

Dominici L., Villarini M., Trotta F., Federici E., Cenci G., Moretti M. (2014)  Protective effects of probiotic Lactobacillus rhamnosus IMC501 in mice treated with PhIP.  J. Microbiol.  Biotechnol. 24(3): 371-378.  doi: 10.4014/jmb.1309.09072

Lladó S., Covino S., Solanas A.M., Petruccioli M., D’Annibale A., Viñas M. (2014) “Pyrosequencing reveals the effect of mobilizing agents and lignocellulosic substrate amendment on microbial community composition in a real industrial PAH-polluted soil” J. Hazard. Mater. 283: 35–43.

Ezechiáš M., Covino S., Cajthaml T. (2014) Ecotoxicity and biodegradability of new brominated flame retardants: A review Ecotox. Environ. Safe. 110: 153–167.

Covino S., Křesinová Z., Čvančarová M., Filipová A., Cajthaml T. (2014). Composting of creosote-impregnated wood via composting with green wastes: Ecotoxicity and microbial community dynamics during polycyclic aromatic hydrocarbons degradation process. New Biotechnol. 31:S136.

Stella T., Covino S., Čvančarová M., Petruccioli M., D’Annibale A., Cajthaml T. (2014). Metagenomics unveils bacterial and fungal communities response to mycoremediation of polychlorinated biphenyl-contaminated soil. New Biotechnol. 31, S69.

Ajmone-Marsan P, Colli L, Han JL, Achilli A, Lancioni H., Joost S, Crepaldi P, Pilla F, Stella A, Taberlet P, Boettcher P, Negrini R, Lenstra JA, Italian Goat Consortium, Econogene Consortium, Econogene Consortium Globaldiv Consortium, Globaldiv Consortium (2014) The characterization of goat genetic diversity: Towards a genomic approach. Small Ruminant Research 121:58-72

Chiesa, S., Lucentini, L., Nonnis-Marzano F. (2014) Genetic data on endangered twaite shad (Clupeidae) assessed in landlocked and anadromous populations: one or more species? Reviews in Fish Biology and Fisheries 24 (2): 659-670

Chiesa S., Lucentini L., Freitas R., Nonnis Marzano F., Minello F., Ferrari C., Filonzi L., Figueira E., Breda S., Baccarani G., Argese E. (2014) Genetic diversity of introduced Manila clam Ruditapes philippinarum populations inferred by 16SrDNA. Biochemical Systematics and Ecology 57: 52-59.

Lucentini L., Chiesa S., Giannetto D., Pompei L., Natali M., Sala P., Volta P., Lorenzoni M., Fontaneto D. (2014) Integrative taxonomy does not support the occurrence of two species of the Squalius squalus complex (Actinopterygii, Cypriniformes, Cyprinidae) in Italy. Biochemical Systematics and Ecology 56: 281-288.

2013

Achilli A, Perego UA, Lancioni H, Olivieri A, Gandini F, Hooshiar Kashani B, Battaglia V, Grugni V, Angerhofer N, Rogers MP, Herrera RJ, Woodward SR, Labuda D, Smith DG, Cybulski JS, Semino O, Malhi RS, Torroni A. (2013) Reconciling migration models to the Americas with the variation of North American native mitogenomes. Proc Natl Acad Sci U S A. 110: 14308-13.

Gigliarelli L., Caldelli, A., Morozzi, G., Giannetto, D., Panara, F., Lorenzoni, M., Lucentini, L. (2013) Nuclear PCR-RFLP detects the brook chub, Squalius lucumonis (Leuciscinae: Cyprinidae), and related hybrids with other cyprinid species. Italian Journal of Zoology 80:462-465.

Lancioni H, Di Lorenzo P, Ceccobelli S, Perego UA, Miglio A, Landi V, Antognoni MT, Sarti FM, Lasagna E, Achilli A. Phylogenetic relationships of three Italian merino-derived sheep breeds evaluated through a complete mitogenome analysis. PLoS ONE. 8: e73712. (2013)

Lucentini L., Gigliarelli L., Puletti ME, Palomba A.,Caldelli A., Fontaneto D., Panara F. Spatially explicit genetic structure in the freshwater sponge Ephydatia fluviatilis (Linnaeus, 1759) in the framework of the monopolisation hypothesis. J Limnol 72:172-181. (2013)

Nasini L., Gigliotti G., Balduccini M.A., Federici E., Cenci G., Proietti P. (2013) Effect of solid olive-mill waste amendment on soil fertility and olive (Olea europaea L) tree activity. Agr. Ecosyst. Environ. 164: 292–297.

Pilli E, Modi A, Serpico C, Achilli A, Lancioni H, Lippi B, Bertoldi F, Gelichi S, Lari M, Caramelli D. (2013) Monitoring DNA contamination in handled vs. directly excavated ancient human skeletal remains. PLoS ONE  8: e52524.

Tocchi C., Federici E., Scargetta S., D'Annibale A., Petruccioli M. (2013) Dairy wastewaters polluting load and treatment performances of an aerobic industrial three-cascade-reactor plant. Process Biochemistry 48:941–944.


- BOOK CHAPTERS:

Covino S., Stella T., Cajthaml T. “Mycoremediation of Organic Pollutants: Principles, Opportunities, and Pitfalls”. (Book Chapter) Springer International Publishing Switzerland 2016 D. Purchase (ed.), Fungal Applications in Sustainable Environmenatl Biotechnology, Fungal Biology. [ISBN 978-3-319-42852-9] p. 185-232.

D'Annibale A., Federici E., Petruccioli M. Effect of Mobilising Agents on Mycoremediation of Soils Contaminated by Hydrophobic Persistent Pollutants. In Fungi as Bioremediators, Goltapeh, E. M., Danesh, Y. R., Varma, A. Editors. Soil Biology series 32: 393-417 (2013).

Di Rosa I., Fagotti A., Simoncelli F., Paracucchi R., Rossi R. Declino degli Anfibi: le rane dell’Umbria raccontano... In: Andreone F., et al. (Eds). HerpeThon2013. Herpetological Marathon. Problemi di conservazione della fauna erpetologica nel terzo millennio: estinzioni, introduzioni di specie alloctone, commercio internazionale e programmi di salvaguardia in Italia e nel mondo. Museo Regionale di Scienze Naturali e Societas  Herpetologica Italica, Torino. P. 42. (2013)