Dottorato in Biologia Evoluzionistica ed Ecologia

People: Giuliana Allegrucci, Gabriele Gentile, Donatella Cesaroni, Marco Mattoccia, Valerio Sbordoni,  Andrea Novelletto, Federica Berrilli, Olga Rickards, Cristina Martinez-Labarga, Antonella Canini 
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• Use of molecular genetics in the species and natural populations conservation. Appropriate analytical tools (phylogenetic and phylogeographic analyses) are used a) to resolve taxonomic conflicts; b) to identify units of evolution significant for the conservation (ESU); c) to estimate parameters of population; d) to evaluate the degree of genetic variability with respect to the maintenance of the evolutionary potential in endangered species. Use of DNA Barcode as taxonomic character in Amphibians and Reptiles and in different taxa of Insects. Phylogenetic methods for estimation of genetic divergence and evolutionary history at different time scales in animal taxa. Population genetics and gene flow patterns in populations of Arthropods, Reptiles and Mammals (Giuliana Allegrucci, Gabriele Gentile, Donatella Cesaroni, Valerio Sbordoni, Marco Mattoccia, Andrea Novelletto, Federica Berrilli).
  
• Use of molecular clocks to reconstruct the biogeographic history in several animal taxa.  (Giuliana Allegrucci, Donatella Cesaroni) 
• Phylogenesis of mitochondrial DNA in Capra hircus. Isolate demography. Modes of selection operated by breeders (Andrea Novelletto).
• Reconstruction of the genetic history of Homo sapiens and its migration routes out of the African cradle towards the other continents, through the analysis of the variation in time and space of the genetic pool of extant human populations from all over the world. Among the various molecules which could be used in unravelling human evolutionary history, mitochondrial DNA (mtDNA) has proved to be useful in studying recent human evolution and in analyzing genetic affinities of populations from different geographical regions so as to delineate major expansions, dispersals and migrations of our species. In particular, the study of the geographic distribution and diversity of genetic variation has been used to reconstruct human expansion into the Mediterranean Basin, Africa and the Americas (Olga Rickards, Cristina Martinez-Labarga).
• Phylogeny of uni- and bi-parentally inherited portions of the human genome. Signals of natural selection. Reconstruction of demography based on genetic data. Genetic dating. Reconstruction of historical processes and migration routes. Genetic signatures of different subsistence modes (Andrea Novelletto).
• Application of DNA barcode technology for the characterization of plant species and for the taxonomic identification of ancient plants (Antonella Canini).

People: Stefano Cataudella, Michele Scardi, Clara Boglione, Eleonora Ciccotti, Tommaso Russo, Federica Berrilli, David Di Cave

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• Study of river fish populations and assemblages aimed at developing biological method useful to assess ecological status of running water ecosystems. Studies on relationship between fish assemblages and abiotic variables in inland waters, also aimed at identifying action plans for fish biodiversity conservation. (Stefano Cataudella, Eleonora Ciccotti)
• Assessment of the ecological status of aquatic ecosystems based on community structure (e.g. according to the Directive 2000/60/EC) and related methods, with special reference  to expert systems and Artificial Intelligence techniques. (Stefano Cataudella, Michele Scardi, Clara Boglione, Eleonora Ciccotti, Tommaso Russo)
• Analysis of the relationship existing among physical, chemical and biotic variables in running waters, with particular attention paid to the biological evaluation of environment quality, to nutrient retention and variations due to antropic alterations.  (Stefano Cataudella,  Clara Boglione, Eleonora Ciccotti)
• Setting up of methodologies able to identify the effects of environmental stress on exposed organisms. (Clara Boglione)
• Study of bone diseases in vertebrates. Anatomy, morphology, histology and epigenetic of skeletal tissues of vertebrates, using fish as a model for studies aimed at extending knowledge about bone diseases. Using skeletal abnormalities in fish as a indicator of the health status of a water body or breeding conditions (density, diet, stress, … ..) in aquaculture. Application of multivariate analysis techniques and artificial intelligence for the integrated analysis of the environmental effects on skeletal remodeling and modeling processes. (Stefano Cataudella, Clara Boglione, Tommaso Russo)
• Macrozoobenthic communities and seagrass meadows analysis in coastal marine ecosystems. Assessment and prediction of phytoplankton primary production based on modeling, both at local and global scale in aquatic (oceanic, transitional and freshwater) ecosystems. Assessment of primary productivity of Posidonia oceanica through lepidocronological analyses and mathematical modeling. Statistical analysis of ecological data and application of Machine Learning techniques to Ecology. (Michele Scardi)
• Analysis of the composition and structure of parasite communities in different hosts. Study of risk factors associated with the spread of parasites, molecular epidemiology of parasitic diseases. (Federica Berrilli, David Di Cave)

People: Donatella Cesaroni, Valerio Sbordoni,  Giuliana Allegrucci, Antonella Canini, Alessandro Travaglini, Roberta Congestri
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• Research directed towards the creation and interoperability of networks linking computerized databases on biodiversity at different geographical scale: regional (Regional Biodiversity Observatory of Latium), national (national network) and international (Life Watch). Cartographic mapping (Web GIS) and elaboration of predictive models of spatial and temporal distribution of animal species. (Donatella Cesaroni, Valerio Sbordoni)
• Taxonomy and phylogeny in several animal taxa. (Giuliana Allegrucci, Donatella Cesaroni, Valerio Sbordoni)
• Conservation of Nature: study of flora and vegetation in M. Simbruini Regional Natural Park in Latium  the and in the SCI Mountains Ruffi and M. Guadagnolo. Study of phenology of Quercus and Cupressus in Rome. Study of urban green. (Alessandro Travaglini)
• Research directed towards the realization of databases for the use of a botanical molecular taxonomy. Constitution of a bank for the germplasm conservation in the Botanical Garden, using systems of seed bank and in vitro culture. (Antonella Canini)
• Microalgal diversity along Latium coasts, long-term dataset implementation; Planktic and benthic microalgal diversity of Latium coasts, collaboration with Regional Environmental Protection Agency in the frame of Marine Strategy Programme, long-term dataset implementation. (Roberta Congestri)

People: Roberta Congestri, Laura Bruno, Cinzia Forni, Luciana Migliore, Maria Cristina Thaller, Antonella Canini, Bianca Gustavino
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• Development of monitoring methods for microalgal and cyanobacterial growth in aquatic ecosystems; selected algal biomass production for biotechnological application in the fields of environment, bioenergy and nanotechnology; integration of optimized biomass production into bioremediation process of wastewaters. Development of monitoring methods for microalgal and cyanobacterial growth in aquatic biofilms and coastal phytoplankton, especially toxic and bloom forming species; image analysis method for automatic cyanobacterial recognition, early warning for phycotoxin release in the environment, Ostreopsis spp. bloom monitoring and biofouling control in industrial systems. (Roberta Congestri)
• Selected algal biomass production for biotechnological application in the fields of environment, bioenergy and nanotechnology; integration of optimized biomass production, pilotscale photobioreactors, into bioremediation process of wastewaters. Phosphorus, nitrogen and heavy metal abatement in effluent waters. Characterization of fatty acid methyl esters (FAMEs) produced by selected microalgae and cyanobacteria. (Laura Bruno, Roberta Congestri)
• Phytoremediation with higher plants. Detection of bioaccumulation of pollutants, tolerance and stress responses by different plant species. Use of aquatic macrophytes in wastewater treatment plant. Utilization of different strategies  for the recovery of salt affected soils. Screening in vitro and in vivo of salt tolerant species, determination of the effects of salt stress on plant metabolism. Preservation of plant gene pools, application of different methodologies to the preservation of biodiversity of crops and trees. In vitro cultures methods , i.e. slow growth and cryopreservation, and biochemical and physiological studies of the mechanisms related to stress response and cryoprotection. Use of natural compounds as elicitors of acquired systemic resistance in crop plants. (Cinzia Forni)
• Development of methods for the identification of the effects of environmental stress in seagrasses: the choice and combination of descriptors (easily measurable, sensitive and responsive to environmental changes) requires the knowledge of organism ecophysiology. In the case of seagrasses, to assess their conservation state, descriptors have been identified based on biochemical approaches (concentration of total phenols, photosynthetic pigments); they can provide timely and reliable information on the ecophysiological state of plants. The metagenomic study of the microbial communities associated with leaves and rhizomes-roots, which is the other partner of the plants in the so-called ‘seagrass holobiont’, has been now added to these descriptors. This integrated approach allows to acquire information on the functional relations between microbial communities and improve the understanding of environmental processes. (Luciana Migliore, Maria Cristina Thaller)
• Characterization of environmental bacterial species, analysis of their potential metabolic activities in environmental biotechnologies and zootechnics; cloning of the related genic determinants. (Luciana Migliore, Maria Cristina Thaller)
• Genotoxic and mutagenic potential monitoring of environmental contamination by physical and chemical pollutants in air, water, soil / sediment through the use of standard test systems (plants, fish, mammalian and human cells), as well as in specimens from natural populations exposed in situ or ex situ. Mechanism of DNA damage induction of the detected mutagenic pollutants. Validation studies for the development of novel bio-indicator organisms of mutagenic / genotoxic effects (both in animal and plant systems) to be employed in bio-monitoring of the different environmental compartments. (Bianca Gustavino)

People: Olga Rickards, Cristina Martinez-Labarga
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• Forensic Anthropology is a new field of study that deals with the analysis of human skeletal remains in order to extract much information as possible about persons represented by bones (attribution of sex, estimation of age at death, calculation of stature, pathological conditions, occupational stress markers, facial reproduction) and about the circumstances surrounding their death. Since forensic anthropology employs the principles of anthropology to analyze legal problems and/or archaeological context, the researchers involved in this field of study could collaborate with Legal medicine institutes, Soprintendenze, Museums and all the institutions for the human remains safeguard (Olga Rickards, Cristina Martinez-Labarga)

People:Stefano Cataudella, Clara Boglione, Tommaso Russo, Roberta Congestri, Luciana Migliore, Maria Cristina Thaller

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• Analysis of the effects of environmental conditions on development, physiological state and behaviour of Teleost fish (Stefano Cataudella, Clara Boglione)
• Analysis of the pattern of exploitation of life resources in the Mediterranean from the italian commercial fishing fleet by means of Vessel Monitoring System by Satellite: trends, bioeconomical models and spatial statistics. (Stefano Cataudella, Tommaso Russo)

Food safety

• Multidisciplinary evaluation of overall quality of aquatic animal production; setting up of morpho-eco-physiological indicators of products and quality processes aimed at building regulatory models for aquaculture full chain and for environmental quality. Innovative applications to system control of fishery chain: use of immagine analysis for freshness evaluation or for controlling illegal under-size fishes in market boxes. (Stefano Cataudella, Clara Boglione)
• Image analysis method for automatic cyanobacterial recognition in drinking water; early warning, sensor-based, techniques for phycotoxin detection in fish and mussels. (Roberta Congestri)

Microbial Ecology and Ecotoxicology
Effects of increased CO₂:

• Changes in the microbial communities associated with seagrass in experimental conditions (mesocosms) and in naturally acidified sea water; analysis of biochemical markers in plants exposed to sea water acidification. Analysis of the increasing incidence of Vibrionaceae in the Mediterranean, as the consequence of the water-temperature rising which, in turn, is linked to the CO₂ increase and the global warming effect. Molecular identification methods to identify environmental species, including those pathogenic for ‘humans and/or marine animals. (Luciana Migliore, Maria Cristina Thaller)

Ecotoxicity of Nanomaterials

• Development of new ecotoxicological tests and adaptation of already standardized assays for the evaluation of the effects of nanoparticles in freshwater, marine and brackish ecosystems. In particular, a new, rapid and inexpensive test on Vibrio anguillarum has been developed as a model system for the evaluation of the ecotoxicity of metal nanomaterials in marine and brackish ecosystems, where salinity modify the physical state of nanoparticles. Furthermore, other standardized tests on other organisms belonging to other trophic levels (i.e. producer, consumers) have been modifyed, to cope with the needs of nanomaterial evaluation. In accordance with OECD indications, all these assays include the assessment of the physical state and the aggregation of nanomaterials to the different test conditions (i.e. salinity). For this reason the essays include the evaluations by Analytical Centrifugation (Lumisizer ®) and Dynamic light scattering (DLS), to state the relationships between ecotoxicity and physical state of the material in each test (Luciana Migliore). The same tests were utilized to evaluate the effects of microplastics. (Luciana Migliore)

People: Laura Bruno, Olga Rickards, Cristina Martinez-Labarga, Luciana Migliore, Maria Cristina Thaller

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• Assessment and monitoring of the damage from deterioration due to the growth of phototrophic biofilms on frescoes, marble and plaster in archeological hypogea (Roman Catacombs) and on stone monuments (Hindu temples). Microbial diversity assessment by means of a polyphasic approach (LM, CLSM, ecophysiology, exopolymeric secretion characterization, molecular studies). Development of noninvasive and non-destructive techniques against biological colonization of confined environments. (Laura Bruno)
• Extraction methods of DNA and protein from small amounts of tissue were used to obtain information on the genetic background (through the phylogeographic reconstruction of  mtDNA and Y chromosome haplotypes), the diet (by stable isotope analysis and palaeobotanical and palaeozoological studies) and migrations (through high resolution stable isotope analysis of biogenic trace elements preserved in enamel, in particular strontium isotopes ⁸⁷Sr/⁸⁶Sr) of the ancient human populations. These methods will be applied to different fields of the anthropological research –kinship and sex determination, geographical origin, degree of relationships with other ancient and extant populations, and identification of possible pathologies or genetic defects. (Olga Rickards, Cristina Martinez-Labarga)
• Development of an integrated system to assess the biodeterioration of ancient parchments and to identify the model of parchment colonization and the effects on the parchment matrix, through a multidisciplinary approach which includes the metagenomic analysis of the parchment colonizers, the chemical analysis (Raman) of colonization pigment residues and Light Transmitted Analysis to identify the degree of collagen denaturation. (Luciana Migliore, Maria Cristina Thaller)

People: Cinzia Forni, Laura Bruno, Roberta Congestri, Antonella Canini, Stefano Rufini 
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• Production of nutraceutics with antitumor activity in agronomic species. Extraction, purification and identification of secondary metabolites from plant species used in diet and determination of their antitumor activity. Studies of molecular mechanisms involved in the response of cancer cells to the treatment with nutraceutics (Cinzia Forni)
• Microalgal and cyanobacterial biomass production for application in nutra-and pharmaceutics, food and feed additives, antioxidant, antiviral and antinflammatory algal compound. Algal pigments as markers in innovative diagnostic applications Diatom frustule photonics for random lasing and dye trapping applications. (Laura Bruno, Roberta Congestri)
• Selected diatom biomass in photobioreactors for extraction of biosilica (siliceous frustules) and exopolymeric substances (EPS) for innovative application in tissue regeneration (scaffolding) and drug delivery. (Roberta Congestri)
• Nutraceutics and foods: enhancement of bioactive compounds, food and health security. Mechanisms involved in the antitumor response in in vitro and in vivo models. (Antonella Canini)
• Identification and use of toxins for for the development of new diagnostic strategies of dislipidosi human. Many disorder such as Gaucher, Niemann-­‐Pick and Tay Sachs disease, are characterized by an incorrect lipid metabolism that involve the accumulation of different lipid classes in the endo-­‐lysosomal compartment. The analysis of these lipid classes covers a great importance for the diagnosis but is limited by the lack of adequate molecular probes able to distinguish the lipids in whole cells. In this context, some protein toxins represent unique tools to recognize specifically the lipids not only in vitro but also in living cells. (Stefano Rufini)

People: Maria Fuciarelli, Stefano Rufini, Alessandro Travaglini, Bianca Gustavino,  Lina Ghibelli
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• Analysis of human genetic variation to understand health-related issues in order to clarify the interactions between human beings and environment. One part of this topic is focused on complex diseases to evaluate if genetic variation in detoxification enzymes may interact with environmental risk factor increasing the disease risk. Another branch analyzes the evolution of antioxidant genes among human populations. Finally, this topic deals the inter-ethnic differences in the structure of genes related to important health aspects, such as pharmacogenetics and rare disease (Maria Fuciarelli).
• Study of the function of exosomes in intra- and inter-species communication. Exosomes are microvesicles (80-150 nm) bounded by a lipid bilayer that are released from the cells of organisms belonging to all the kingdoms, in response to different stimuli. These microvesciole are synthesized in the interior of multivesicular bodies and released into the extracellular medium, after their fusion with the plasma membrane. The exosomes are characterized by the presence in their inside of numerous proteins and RNA molecules of different type such as mRNA, siRNA and mainly miRNA. While the evidence of their existence has more than ten years, little is known about their real role in cellular communication. Our laboratory is currently involved on two lines of research:
  1) characterization of nuts exosomes and study of their interaction with cells of the human intestinal epithelia. Communication inter-kingdom via exosomes is a promising research field of interest not only theoretical but also for the possible consequence that can open.
  2)Study of exosomes released by human cells in culture challenged with Ionizing Radiation and their interactions with non-stressed cells (Stefano Rufini).
• Aerobiological monitoring and forecasting models for  allergenic pollen spread. Study of pollen back trajectories in the lower layers. Relations between aerospora and flora in the urban area; monitoring of alien flora through monitoring aerobiological. Experience monitoring outdoor and indoor (Alessandro Travaglini).
•  Mutagenic effects and risk evaluation for human exposure to physical (electromagnetic fields at extremely low frequencies: ELF-EMF; radiofrequencies: RF-EMF; radon) and chemical contamination (e.g, drinking water disinfection byproducts) in standard test systems (mammalian and human cells; plants) and bio-indicators. Induction mechanisms of detected genotoxic effects. ( Bianca Gustavino)
• Re-establishing apoptosis competence in cancer cells/tissues via biomodulatory approaches: Apoptosis is generally induced in cancer cells by (DNA) damage inducers (traditional chemotherapy), causing problems of toxicity and cancer repopulation. On the contrary, epigenetic and transcriptional modulator can re-establish apoptosis competence by re-activating cell-integrity check points, eliminating cancer cells with minor side effects. We aim at investigating the molecular mechanisms at the basis of such phenomena. (Lina Ghibelli)
• Nanotechnology Applications in Anticancer Research: nanotechnology is a promising new frontier in anticancer therapy, allowing ideally to target drugs to the tumor site by selective delivery, and exert unprecedented actions in the cancer microenvironment due to the activity of materials in the nanoscale. We aim at linking carrier nanoparticles to natural products of food origin to stabilize them so to increase their bioavailability and exploit their potential anticancer properties; and to exploit the intrinsic ability of redox-active cerium oxide nanoparticles to inhibit the repopulation of cancer tissues after chemotherapy. (Lina Ghibelli)
• Model systems to investigate the mechanisms of the anticancer therapies. We are developing methods to obtain reliable responses anticancer therapies (see above) as a translational approach. Ongoing is the development of “on-chip” models (in collaboration with the Dep. Of Electronic Engineering, Tor Vergata). In preparation are the development of 3D cultures and of zebrafish as an in vivo model.(Lina Ghibelli)