Tiny Wallaby: Living Link to Giant Kangaroos
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Molecular Insights Into Spider Silk
New Buzz About a Malaria Prevention Drug
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Plants as Antifungal Factories
New Light on Blocking Shiga and Ricin Toxins — And on an Iconic Biological Process
A Code for Reprogramming Immune Sentinels
Scientists to Produce Anti-Cancer Drugs in Yeast
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What Can a Snowflake Teach Us About How Cancer Spreads in the Body?
Parrot Genome Analysis Reveals Insights Into Longevity, Cognition
Breakthrough in Blood Vessel Engineering
An Ancient Strain of Plague May Have Led to the Decline of Neolithic Europeans
- Marine Nitrogen Cycle
- Plants as Antifungal Factories
- Blocking Shiga and Ricin Toxins
- A Code for Reprogramming Immune Sentinels
- Scientists to Produce Anti-Cancer Drugs in Yeast
- News About a Plant Hormone
- How Cancer Spreads: Clues from Snowflakes
- Parrot Genome: Clues to Longevity, Cognition
- Breakthrough in Blood Vessel Engineering
- Decline of Neolithic Europeans: Ancient Plague
Young Aphids Piggyback on Adult Aphids to Get to Safety Faster
Scientists Design Way to Track Steps of Cells’ Development
Sea Invertebrate Sheds Light on Evolution of Human Blood, Immune Systems
Evolution of the Inner Ear: Insights from Jawless Fish
Tuberculosis Survives by Using Host System Against Itself, Study Finds
Scientists Identify ‘Youth Factor’ in Blood Cells That Speeds Fracture Repair
A Bacterial Protein Is Found to Promote Cancer
Novel Approach Improves Understanding of the Formation of New Neurons in the Mammalian Adult Brain
Dynamics of Chromatin During Organ and Tissue Regeneration
Gene That Lets You Eat as Much as You Want Holds Promise Against Obesity
Electrochemical Techniques for Monitoring Microbial Growth Demonstrated
New Technique to Identify Phloem Cells Aids in the Fight Against Citrus Greening
Life Has a New Ingredient
Plant Cells Inherit Knowledge of Where’s Up and Where’s Down from Mother Cell
A New Approach to Studying the Flu
In Death, Lonesome George Reveals Why Giant Tortoises Live So Long
Nanoscale Tweezers Can Perform Single-Molecule ‘Biopsies’ on Individual Cells
Not in the DNA: Epigenetics Discovered in Single-Celled Archaea
Light-Induced Changes in Photosensory Proteins
Researchers Alleviate Schizophrenia Symptoms in New Mouse Models
- Young aphids piggyback on adult aphids to get to safety faster
- Scientists design way to track steps of cells’ development
- Sea invertebrate sheds light on evolution of human blood, immune systems
- Evolution of the inner ear: Insights from jawless fish
- Tuberculosis survives by using host system against itself, study finds
- Scientists identify ‘youth factor’ in blood cells that speeds fracture repair
- A bacterial protein is found to promote cancer
- Novel approach improves understanding of the formation of new neurons in the mammalian adult brain
- Dynamics of chromatin during organ and tissue regeneration
- Gene that lets you eat as much as you want holds promise against obesity
- Electrochemical techniques for monitoring microbial growth demonstrated
- New technique to identify phloem cells aids in the fight against citrus greening
- Life has a new ingredient
- Plant cells inherit knowledge of where’s up and where’s down from mother cell
- A new approach to studying the flu
- In death, Lonesome George reveals why giant tortoises live so long
- Nanoscale tweezers can perform single-molecule ‘biopsies’ on individual cells
- Not in the DNA: Epigenetics discovered in single-celled archaea
- Light-induced changes in photosensory proteins
- Researchers alleviate Schizophrenia symptoms in new mouse models
- A bastard seal from the past reveals the potential for human hybrids
- Focus on resistance to HIV offers insight into how to fight the virus
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- Scientists direct bacteria with expanded genetic code to evolve extreme heat tolerance
- First calf born following IVF embryo breakthrough
- Largest study of CRISPR-Cas9 mutations creates prediction tool for gene editing
- How antibiotics help spread resistance
- DNA with a twist: Discovery could further antibiotic drug development
- Single-cell asymmetries control how groups of cells form 3D shapes together
- The warm and loving tegu lizard becomes a genetic resource
- Newly discovered deep-sea microbes gobble greenhouse gases and perhaps oil spills, too
- A fresh look at winter footprints: Environmental DNA improves tracking of rare carnivores
- Bee gene study sheds light on risks to hives
- Citrate-based biomaterial fuels bone healing with less rejection
- How ancient Mayan shell decor led to a new look at freshwater mussels south of the border
- New biocontainment strategy controls spread of escaped GMOs
- Fine-tuning cell death: New component of death machinery revealed
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- Putting a face on a cell surface
- A Mexican cavefish with a scarred heart
- How a deadly fungal infection shape-shifts into an invasive monster
- Revisiting the hub of protein synthesis
- The taming of the dog, cow, horse, pig and rabbit
- ‘Sneaky’ cancer cells stopped in their tracks
- A toxic bullet involved in bacterial competition
- Freeze-frame microscopy captures molecule’s ‘lock-and-load’ on DNA
- Geneticist solves long-standing finch beak mystery
- New dual-action cancer-killing virus
- Dodging antibiotic resistance by curbing bacterial evolution
- Controlling organ growth with light
- Channels for the supply of energy
- Establishment of the immortalized cell line derived from Okinawa rail (endangered species)
- Solar panels for yeast cell biofactories
- Enzymes in the cross-hairs
- Population of rare Stone’s sheep 20% smaller than previously thought
- Scorpion venom to shuttle drugs into the brain
- Insect antibiotic provides new way to eliminate bacteria
- Mosquito genome opens new avenues for reducing insect-borne disease
- Molecular mechanisms of an African folk medicine
- Researchers discover novel ‘to divide or to differentiate’ switch in plants
- Rainforest vine compound starves pancreatic cancer cells
- Salmon are shrinking and it shows in their genes
- Visualizing ‘unfurling’ microtubule growth
- Synthetic DNA-delivered antibodies protect against Ebola in preclinical studies
- The dawn of a new era for genebanks
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- Microorganisms help production
- How your muscles form
- Stripping the linchpins from the life-making machine reaffirms its seminal evolution
- Sequencing pollen DNA to discover insect migratory routes
- A toast to the proteins in dinosaur bones
- Scientists simplify and accelerate directed evolution bioengineering method
- Moving the motivation meter
- Embryos ‘remember’ the chemicals that they encounter
- Broad genome analysis shows yeasts evolving by subtraction
- Healing kidneys with nanotechnology
- We now know how RNA molecules are organized in cells
- Self-assembling protein filaments designed and built from scratch
- Reducing seafood fraud: Researchers and partners work with sushi restaurants
- Pore size alone does not matter when biological nanopores act as sugar chain biosensors
- Researchers closer to gonorrhea vaccine after exhaustive analysis of proteins
- Breast milk & babies’ saliva shape oral microbiome
- Exploiting epigenetic variation for plant breeding
- Cell behavior, once shrouded in mystery, is revealed in new light
- Exhaustive analysis reveals cell division’s inner timing mechanisms
- Machine-learning algorithm predicts how cells repair broken DNA
- Chlamydia attacks with Frankenstein protein
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In Death, Lonesome George Reveals Why Giant Tortoises Live So Long
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Elena Giulotto: Molecular and Cellular Biology
Elena Raimondi: Molecular Cytogenetics
Solomon Nergadze: Epigenomics and Bioinformatcs
Eleonora Cappelletti (PhD student), Marco Corbo (PhD student), Riccardo Gamba (PhD student), Francesco Gozzo (PhD student), Lela Khoriauli (Post-doctoral fellow), Francesca Piras (Post-doctoral fellow), Annalisa Roberti (PhD student), Marco Santagostino (Post-doctoral fellow)
The complementary competences of the research groups involved allow them to approach the scientific topics described below taking advantage of different experimental procedures encompassing a wide range of cellular, biomolecular (including next generation sequencing), cytogenetic (including the analysis of single chromatin molecules) and bioinformatic methodologies.
The research projects are focused on the molecular mechanisms involved in the maintenance of the integrity of the mammalian genome which play a central role in carcinogenesis and in evolution. The main structures needed for the maintenance of functional and structural chromosome integrity are centromeres and telomeres.
1) The centromere and its epigenetic nature
Centromeres are essential for the separation of chromosomes during cell division. They are enigmatic structures since, contrary to other genetic loci, the function of centromeres is not determined by the underlying DNA sequence, but depends on epigenetic factors. In particular, centromeric chromatin is peculiar for the presence of a modified H3 histone, CENP-A, and of a number of proteins forming a complex named CCAN (Constitutive Centromere Associated Network). Moreover, centrochromatin is characterised by histone modifications whose role in centromere function is still debated.
Mammalian centromeres are typically associated to highly repetitive DNA (satellite DNA); this pattern of organisation hampered a detailed molecular analysis of centromeric chromatin.
The equid model system
Our research group demonstrated, for the first time, the existence in nature of satellite-free centromeres which are stable and fully functional (Wade et al Science 2009). These centromeres are present in a number of chromosomes in the genus Equus (horses, donkeys, zebras), they represent a unique model system for the study of the epigenetic control of centromere function and of its role in karyotype evolution (Piras et al PLoS Genetics 2010; Purgato et al Chromosoma 2015).
It is well known that alterations in chromosome segregation are responsible for the occurrence of numerical chromosomal abnormalities observed in the large majority of tumours.
The equid model system offers the opportunity to investigate the mechanisms involved in the numerical chromosome instability associated to the development and progression of many different types of cancer.
The absence of repetitive DNA at the centromere of a number of equid centromeres makes it possible to study the architectural organisation of centrochromatin and, in particular, the role of DNA methylation, transcription and histone modifications.
Collaborations: Kevin Sullivan (University of Galway, Ireland), Aurora Ruiz-Herrera (Universitat Autonoma de Barcelona, Spain), Giulio Pavesi (Università di Milano), Mariano Rocchi (Università di Bari), Doug Antczak (Cornell University, Ithaca New York), The Horse Genome Project, The Horse FAANG Project.
2) The telomere and its transcription
Telomeres are nucleoproteic structures located at the termini of linear chromosomes. In mammals, telomeric DNA, consisting of the tandem repetition of the hexasanucleotide TTAGGG, is bound to a multiproteic complex named shelterin. Telomeres protect chromosome ends from degradation and from fusion with other telomeres. Telomere malfunctioning causes chromosome rearrangements that can lead to tumorigenesis. Too short telomeres cannot be distinguished from accidental DNA breaks and cause genomic instability. Our group contributed to the demonstration that the telomeres are transcribed in non-coding RNA molecules named TElomeric Repeat-containing RNA (TERRA) (Azzalin et al. Science 2007). We also demonstrated that telomere transcription is strictly regulated (Nergadze et al. RNA 2009) and is probably involved in the maintenance of telomere integrity.
Telomeric transcripts in cancer
It has been demonstrated that telomeric RNA transcription deregulation is deleterious for telomere metabolism and causes genome instability. Therefore, defects in the regulation of telomeric RNA expression may contribute to carcinogenesis and tumour progression. We intend to study the transcriptional state of the telomeres in normal and cancer cells. The analysis of telomeric RNA expression in tissue samples obtained from patients suffering from different forms of cancer will allow us to study the link among the deregulation of telomeric RNA transcription, carcinogenesis and cancer progression.
Interstitial telomeres consist of repetitions of telomeric sequences located in internal chromosome sites. Our previous work demonstrated that, in mammals, interstitial telomeres have been inserted, in the course of evolution, during telomerase mediated repair of double strand breaks or by the capture of double stranded telomeric DNA molecules (Nergadze et al Genome Res. 2004; Nergadze et al Genome Biol. 2007). We have recently demonstrated that some interstitial telomeres play a role in the regulation of gene expression. Our next goal is to analyse the evolution and the function of interstitial telomeres combining molecular, cytogenetic and bioinformantic approaches.
Ionizing radiation induced telomere instability
Ionizing radiations cause severe damages to the DNA double helix, due to the formation of free radicals and to oxidative stress. Telomeres are particularly susceptible to the damages induced by ionising radiations causing an acceleration of their shortening.
We intend to identify the factors involved in telomere metabolism focusing our attention on modifications of the regulation of transcription following the exposure to ionizing radiations.
Collaborations: Claus Azzalin (ETH Zurich, Switzerland), Camillo Porta (IRCCS San Matteo, Pavia), Giovanni Barosi e Vittorio Rosti (IRCCS San Matteo, Pavia), Aurora Ruiz-Herrera (Universitat Autonoma de Barcelona, Spain), Andrea Ottolenghi (Università di Pavia)
3) Production of recombinant proteins in human cells
The production of human recombinant proteins is particularly relevant in various applied fields (drug production, diagnosis) as well as in basic research (biochemical and structural studies). Recombinant proteins can be produced in prokaryotic or eukaryotic expression systems. Prokaryotic expression systems are commonly used for large scale production of some proteic drugs such as insulin. Other molecules, for example erythropoietin, need post-translational modifications that can correctly occur only in mammalian cells.
We developed a vector-host cell system which allows a high production efficiency compared to the mammalian cell systems traditionally employed. With this system we can get hundreds of copies of exogenous genes in human cell lines resulting in overexpression of the encoded protein. The system allows to increase the production efficiency compared to conventional systems thereby decreasing the production costs. The adoption of a production system in human cells opens new prospects for improving the therapeutic efficacy of the protein drugs for human use also reducing side effects. Projects for the construction of human cell lines productive of specific proteins of pharmacological and diagnostic interest are ongoing.
Collaborations: Mark Pepys (University College London), Federico Forneris (Università di Pavia), Vittorio Bellotti e Sofia Giorgetti (Università di Pavia)
Groups leaders: Alessandra Albertini, Cinzia Calvio, Davide Sassera, Claudio Seppi
Collaborators: Giulia Barbieri (Postdoctoral fellow), Paolo Gabrieli (Postdoctoral fellow), Elisabetta Andreoli (technician), Giuliano Gasperi (adjunct professor), Luca Longanesi (assegnista), Francesco Comandatore (Postdoctoral fellow), Stefano Gaiarsa (PhD student), Leone De Marco (PhD student), Emanuela Clementi (technician), Luciano Sacchi (adjunct professor)
REGULATION OF GENE EXPRESSION IN THE GRAM + MODEL ORGANISM Bacillus subtilis
A. Albertini; in collaboration with A.L. Sonenshein and B.R. Belitsky (Department of Molecular Biology and Microbiology Tufts University of Boston MA, USA)
One of our main research interests is the study of regulation of gene expression in Bacillus subtilis. Bacteria can use different strategies to cope with difficult environmental conditions and with scarcity of nutrients. These include the ability to move, the synthesis of degradative enzymes and transporters able to import the products of degradation, and the production of antibiotics. At the onset of stationary phase, Bacillus subtilis is also able to differentiate into competent cells capable of taking up DNA from the environment, or into metabolically dormant spores, highly resistant to external stresses. Our group is interested in the study of the regulatory pathways that control these differentiation processes at the beginning of stationary phase. In collaboration with professors A.L. Sonenshein and B. Belitsky, we recently demonstrated that the global transcriptional regulator CodY, one of the main regulators of the nutritional stress response, is involved in the regulation of four extracellular proteases in B. subtilis.
- Barbieri G, Albertini AM, Ferrari E, Sonenshein AL, Belitsky BR. Interplay of CodY and ScoC in the Regulation of Major Extracellular Protease Genes of Bacillus subtilis. J Bacteriol. Jan 4;198(6):907-20. doi: 10.1128/JB.00894-15, 2016
- Belitsky BR, Barbieri G, Albertini AM, Ferrari E, Strauch MA, Sonenshein AL. Interactive regulation by the Bacillus subtilis global regulators CodY and ScoC. Mol Microbiol., Aug;97(4):698-716. doi: 10.1111/mmi.13056 4.419, 2015
- Barbieri G, Voigt B, Albrecht D, Hecker M, Albertini AM, Sonenshein AL, Ferrari E, Belitsky BR. CodY regulates expression of the Bacillus subtilis extracellular proteases Vpr and Mpr. J Bacteriol. Apr;197(8):1423-32. doi: 10.1128/JB.02588-14. 2.808, 2015
IDENTIFICATION OF NEW BIOLOGICAL INSECTICIDES BY BACTERIA FOR THE CONTROL OF Aedes albopictus (ASIAN TIGER MOSQUITO)
A. Albertini, G. Gasperi
The project, funded by the Bussolera-Branca Foundation, interests two laboratories with complementary skills of the Department of Biology and Biotechnology, and aims to the identification of new bacterial strains able to produce molecules characterized by specific insecticidal activity for the control of Aedes albopictus. For this purpose, bacteria with larvicidal activity are sought in nature (soil, standing water, etc.) tested and validated on standard tiger mosquito strain larvae of Italian origin, available in the Insects Genomics and Biotechnology Laboratory. Subsequently will be assayed the bacterial strains and the compounds endowed with bio-insecticide activities isolated from soil, for toxicity against other natural populations of Aedes albopictus, as well as for the safety for vertebrates, insects and other animal and plants species of agronomic interest, in view of the validation of a possible field use.
Genomic and metagenomic approaches are employed to identify genes involved in the production of these bacterial secondary metabolites; to improve the level of expression in a bacterium suitable for the production on a commercial scale, such as B. subtilis, will be set up cloning and “genome shuffling” methods.
BACTERIAL CELL FACTORIES FOR CATALYSTS PRODUCTION AND MUTAGENESIS.
A. Albertini and C. Calvio; in collaboration with D. Ubiali and T. Bavaro (Department of Drug Science, University of Pavia) and C. Morelli and G. Speranza (Department of Chemistry, Statale University of Milano)
E. coli is well suited for the expression of foreign genes, due to the vast knowledge of its metabolism and the availability of a large collection of different vectors and strains.
The group of Microbial Genetics and Biotechnology collaborated with the Biocatalysis Laboratory of the Department of Drug Sciences for the production of new biocatalysts, such as PGA (Penicillin G-acylase, catalyst for the production of β lactam nuclei, to be used for the synthesis of semi-synthetic antibiotics), or purine and pyrimidine phosphorylases, catalysts for the transglycosilation reactions between a nucleoside (natural or modified in the sugar moiety) and a natural or modified purine or pyrimidine base.
Aims of these projects are the production of new immobilized catalysts trough the search of new genes for purine and pyrimidine phosphorylases from different bacterial sources, and new strategies coupling in vitro site directed mutagenesis and immobilization for the rational design of more efficient biocatalysts.
Recently, in collaboration with C. Morelli (Department of Chemistry, Statale University of Milano), a CARIPLO research grant is funding studies on the trans-peptidation reactions catalyzed by g-glutamyl transpeptidases (GGTs) of microbial origin to improve through mutagenesis the catalytic properties of the enzymes to produce new g-glutamyl derivatives of interest in the food and pharma industry. The mutagenesis and selection of recombinant GGTs will allow the immobilization for the development of large scales processes.
- Biagiotti M, Borghese G, Francescato P, Morelli C F, Albertini AM, Bavaro T, Ubiali D, Mendichi R and Speranza G. Esterification of poly(γ-glutamic acid) (γ-PGA) mediated by its tetrabutylammonium salt. RSC Adv., 6, 43954-43958. doi: 10.1039/C6RA08567A, 2016
- Ubiali D., Morelli C.F., Rabuffetti M., Cattaneo G., Serra I., Bavaro T., Albertini A.M. and Speranza G. Substrate Specificity of a Purine Nucleoside Phosphorylase from Aeromonas hydrophila Toward 6-Substituted Purines and its Use as a Biocatalyst in the Synthesis of the Corresponding Ribonucleosides, Curr. Org. Chem. 19 (22): 2220 – 2225,. 2.157, 2015
- Serra I., Ubiali D., Cecchini D.A., Calleri E., Albertini A.M., Terreni M., Temporini C. Assessment of immobilized PGA orientation via the LC-MS analysis of tryptic digests of the wild type and its 3K-PGA mutant assists in the rational design of a high-performance biocatalyst. Anal Bioanal Chem. Jan; 405(2-3):745-53. doi: 10.1007/s00216-012-6143-z , 2013
- Serra I., Bavaro T., Cecchini D. A., Daly S., Albertini A.M., Terreni M., Ubiali D., A Comparison between Immobilized Pyrimidine Nucleoside Phosphorylase from Bacillus subtilis and Thymidine Phosphorylase from Escherichia coli in the Synthesis of 5-Substituted Pyrimidine 2′-Deoxyribonucleosides. Journal of Molecular Catalysis B: Enzymatic, 95, 16-22, DOI information: 10.1016/j.molcatb.2013.05.007, 2013
- Serra I., Ubiali D., Piskur J., Christoffersen S., Lewkowicz E., Iribarren A. M.,. Albertini A. M, Terreni M., Developing a Collection of Immobilized Nucleoside Phosphorylases for the preparation of Nucleoside Analogues: Enzymatic Synthesis of Arabinosyladenine and 2′,3′-Dideoxyinosine, Chem Plus Chem, 78 (2), 157-165. DOI: 10.1002/cplu.201200278, 2013
- Serra I., Ubiali D., Cecchini D.A., Calleri E., Albertini A.M., Terreni M., Temporini C. Assessment of immobilized PGA orientation via the LC-MS analysis of tryptic digests of the wild type and its 3K-PGA mutant assists in the rational design of a high-performance biocatalyst. Anal Bioanal Chem., 405(2-3):745-53, DOI: 10.1007/s00216-012-6143-z, 2012
- Ubiali D., Serra C.D., Serra I., Morelli C.F., Terreni M., Albertini A.M., Manitto P. and Speranza G. Production, characterization and synthetic applicatio of a purine nucleoside phosphorylase from Aereomonas hydrophyla. Adv Synth. Catal. 354, 96-1041, 2012
- Serra I, Cecchini DA, Ubiali D, Manazza EM, Albertini AM, Terreni M. Coupling of site-directed mutagenesis and immobilization for the rational design of more efficient biocatalysts. The case of immobilized 3G3K PGA from coli. Eur. J. Org. Chem., 9:1384 -1389, 2009
- Cecchini DA, Serra I, Ubiali D, Terreni M and Albertini AM. New active site oriented glyoxyl-agarose derivatives of Escherichia coli penicillin G acylase. BMC Biotechnol.7: 54, 2007.
Bacillus subtilis STRAIN IMPROVEMENT FOR γ-PGA PRODUCTION
C. Calvio, C. Seppi; in collaboration with P. Mustarelli, Chemistry Dept. and P. Magni, Electrical Computer and Biomedical Engineering (University of Pavia), and G. Mazzini (IGM-CNR, Pavia)
The need of safer raw material, derived from renewable sources is the motor driving the growing interest towards natural biopolymers. γ-PGA is an anionic polymer produced by Bacilli, formed by thousands glutamic acid units. Due to its non-toxicity, the water solubility and biodegradability it finds application in several biotechnological fields as: flocculant for heavy metal removal, cryoprotectant, humectant, thickening additive in cosmetics and food industries, as biological glue, as drug or vaccine carrier or scaffold for biomedical engineering. However, for its full industrial exploitation it is mandatory to reduce production costs, both increasing bacterial productivity and reducing fermentation costs. Our Lab has obtained a producer strain derived from the B. subtilis lab strain, 168, fully characterized. The availability of a well defined strain, which is genetically amendable, offers the opportunity to apply genetic engineering to improve productivity and rationalize metabolic pathways for lowering fermentation costs. By introducing specific mutations we already obtained strains that show high product yield. Now, the aim is to obtain a producer able to ferment organic components contained in some agro-industrial by-products. We plan to take advantage of both rice straw, an abundant biomass currently under-exploited, and raw glycerol, a co-product in the biodiesel industry as bacterial feedstock. The meeting of the above objectives will not only lead to cheaper γ-PGA, but will also contribute to the valorization of the rice and biodiesel production chains and reinforce the development of new bio-economy sectors. This research line is currently funded by two CARIPLO FOUNDATION grants.
γ-PGA-HYDROLASES AS ANTIBACTERIAL TOOLS
- C. Calvio, C. Seppi; in collaboration with C. Morelli form the Dept. of Chemistry (Statale University of Milan) and A. Pastore, Dept. of Molecular Medicine (University of Pavia).
We identified and characterized four new genes of B. subtilis that code for γ-PGA hydrolases. We found that those gene are phage-derived and spread across bacteria through horizontal gene transfer. We also identified γ-PGA coding capacity in several microbial species, among which several pathogens. We are now tryng to analyze the role of γ-PGA in the virulence behavior in some of those species and the possible use of the γ-PGA hydrolase and antibacterial agents.
THE ROLE OF SwrA, A RECENTLY DICOVERED Bacillus subtilis REGULATORY FACTOR
In Bacillus subtilis the two-component system DegS-DegU controls the expression of one hundred of genes involved in the exponential-to stationary phase of growth transition, coordinates single cells differentiation in multicellular communities and in pathogenic species, as Listeria monocytogenes or Bacillus anthracis, is involved in virulence. It has been shown that DegU regulates B. subtilis motility in a complex way. Also SwrA a protein which has no similarity to previously characterized proteins, is involved in such complex regulation. We have shown that there is a functional and molecular interaction between the two proteins, DegU and SwrA, in motility and now would like to extend our analyses to other genetic pathways DegU-regulated.
GENOMIC EPIDEMIOLOGY AND COMPARATIVE GENOMICS OF NOSOCOMIAL PATHOGENS
D. Sassera; in partnership with P. Marone (IRCCS Policlinico S. Matteo in Pavia), S. Brisse (Institut Pasteur, Paris), E. Feil (University of Bath)
This research line is focused on whole-genome sequencing of large numbers of strains of nosocomial pathogens. The genomes thus generated are analyzed using bioinformatics tools, some developed ad-hoc, for the comparative genomic and genomic epidemiology analysis. The genomics of nosocomial pathogens allows to evaluate the genomic variability, the presence and mobility of virulence factors and antibiotic resistance, describe recombination events and overall architecture of genomic variations. This approach leads to applicative outcomes, such as the ability to reconstruct epidemic events and to identify transmission patterns, to characterize strains of interest based on the resistance and virulence profiles, and to approach the objective of using genomics in diagnostic microbiology.
ROLE OF SYMBIOSIS IN PARASITES
D. Sassera; in collaboration with C. Bandi (Statale University of Milan), B. Makepeace (University of Liverpool), O. Plantard (INRA, Nantes), G. Favia (University of Camerino)
Symbiotic microorganisms are widespread in many organisms, where they assume different roles, from parasitism to obligate mutualism. In the context of this research line, we use an interdisciplinary approach to identify new symbionts and to understand their role in the biology of the hosts. Integrating methods of light and electron microscopy, molecular biology, genomics and transcriptomics we are currently working on different microorganisms:
Midichloria mitochondrii: bacterium order Rickettsiales, symbiont of the tick Ixodes ricinus, has the unique ability to localize within the mitochondria of host cells. We are currently working to understand the role of bacteria in the physiology of the tick, through an integrated approach of electron microscopy, transcriptomics and proteomics. In parallel we are looking for bacteria phylogenetically related to M. mitochondrii other host with genomic techniques.
Symbiotic yeasts: yeast strains may have a role of symbionts in different species of arthropods, including vectors of important diseases. With a multidisciplinary project coupling electron microscopy and comparative genomics, we are investigating the presence and role of the yeast species Wickeramomyces anomalus and Meyerozyma guilliermondii in mosquitoes and sandflies.
TRANSCRIPTOMICS OF ARTHROPOD VECTORS
D. Sassera; in collaboration with S. Epis (University of Milan), S. Urbanelli and D. Porretta (University of Rome La Sapienza) , Favia G. and I. Ricci (University of Camerino)
The use of the RNA-seq methodology allows the evaluation of changes in gene expression at the whole transcriptome level. In this line of research we investigate these changes in arthropods that are vectors of diseases of great medical interest, mosquitoes and ticks, during the course of the life cycle or in response to specific stimuli, such as the presence of insecticide molecules. The goal is to understand fundamental aspects of the biology of these vectors, as well as specific responses to treatments, in order to design innovative control strategies.
Group leaders: Prof. Mariangela Bonizzoni, Prof. Ludvik Gomulski, Prof. Lino Ometto, Giuliamo Gasperi (Contract Professor), Anna Rodolfa Malacrida (Contract Professor)
Collaborators: Francesca Scolari (Assistant Professor), Paolo Gabrieli (Postdoc), Patrizia Chiari (Technician), Liliana Marcorio (Technician), Alessandro Di Cosimo (PhD student), Grazia Savini (PhD student)
Climate and demographic change, the increase of trade, urbanization and human travel have facilitated the spread of invasive insect species of economic and sanitary importance. These species include the Asian tiger mosquito, a vector of many viruses pathogenic to humans, and species of fruit flies that are important agricultural pests. The risks due to the invasion of these insects are compounded by the lack of vaccines and treatments for the pathogens that they transmit (i.e. Dengue, Chikungunya and Zika viruses) and the emergence of resistance to insecticides, which are currently the most used tool for their control.
The research group deals with genomics, transcriptomics, proteomics and metabolomics of insects of agricultural interest and public health relevance with the aim of developing innovative control strategies that are environmentally sustainable. Additionally, we study their population genetics and evolution in order to understand and prevent their further spread and we use transgenic approaches to study the mechanisms underlying their reproduction in order to improve current genetic control methods.
The insect species currently studied are:
Vectors of disease pathogens:
- Mosquitoes: Aedes albopictus and Aedes aegypti, vectors of viruses including Zika, Dengue and Chikungunya.
- Tsetse fly (Glossina) species, vectors of Trypanosomes that cause Human African Trypanosomiasis (HAT or sleeping sickness) and African Animal Trypanosomiasis (AAT or Nagana).
Fruit flies (Diptera, Tephritidae) of African or Asian origin, that are highly invasive and that have recently been introduced into Southern Europe and the Americas where they have produced significant economic damage:
- Ceratitis capitata, the Mediterranean fruit fly.
- Bactrocera oleae, the Olive fly.
- Bactrocera dorsalis sensu stricto, the Oriental fruit fly.
- Anastrepha fraterculus, the South American fruit fly.
Main Lines of Research
- Genome sequencing targeted at the identification of genes related to reproduction, chemoreception, adaptation, immunity and, consequently, host/parasite interactions. These studies are performed within International scientific consortia:
- Ceratitis capitata (joint project of Baylor College of Medicine Human Genome Sequencing Center, US Department of Agriculture, and the University of Pavia) and the i5K initiative;
- Aedes albopictus (under EC-FP7 Infrastructure – INFRAVEC coordinated by Imperial College London, and an American-Chinese consortium, coordinated by Anthony James and Xiao-Guang Chen);
- 5 Glossina species (IGGI Consortium, coordinated by Yale University).
Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis. Science (2014) 344: 380-6.
Genome sequence of the Asian Tiger mosquito, Aedes albopictus, reveals insights into its biology, genetics, and evolution. Proc Natl Acad Sci USA (2015) 112: E5907-15.
A draft genome sequence of an invasive mosquito: an Italian Aedes albopictus. Pathog Glob Health (2015) 109:207-20.
Presence of extensive Wolbachia symbiont insertions discovered in the genome of its host Glossina morsitans morsitans. PLoS Negl Trop Dis. 2014 Apr 24;8(4):e2728.
- Origin and spread of the tiger mosquito and fruit flies.
We characterized high resolution molecular markers, such as microsatellites and SNPs, in Ae. albopictus, C. capitata and other fruit flies, and we have applied them to study the genetic links between ancestral and derived populations and to characterize the species invasion processes. We also applied mitochondrial markers, in combination with microsatellites, to study the origin of Ae. albopictus in California and, in collaboration with prof. Torroni, to study the variability of ancestral and derived populations.
Relevant genetic differentiation among Brazilian populations of Anastrepha fraterculus (Diptera, Tephritidae). Zookeys. 2015 Nov 26;(540):157-73.
Molecular markers for analyses of intraspecific genetic diversity in the Asian Tiger mosquito, Aedes albopictus. Parasit Vectors. 2015 Mar 28;8:188.
The oriental fruitfly Bactrocera dorsalis s.s. in East Asia: disentangling the different forces promoting the invasion and shaping the genetic make-up of populations. Genetica. 2014 Jun;142(3):201-13.
Microsatellite markers from the ‘South American fruit fly’ Anastrepha fraterculus: a valuable tool for population genetic analysis and SIT applications. BMC Genet. 2014;15 Suppl 2:S13.
Genetic analysis of invasive Aedes albopictus populations in Los Angeles County, California and its potential public health impact. PLoS One (2013) 8:e68586.
A new threat looming over the Mediterranean basin: emergence of viral diseases transmitted by Aedes albopictus mosquitoes. PLoS Negl Trop Dis. 2012;6(9):e1836.
The utility of microsatellite DNA markers for the evaluation of area-wide integrated pest management using SIT for the fruit fly, Bactrocera dorsalis (Hendel), control programs in Thailand. Genetica. 2011 Jan;139(1):129-40.
Uncovering the tracks of a recent and rapid invasion: the case of the fruit fly pest Bactrocera invadens (Diptera: Tephritidae) in Africa. Mol Ecol. 2009 Dec;18(23):4798-810.
Isolation and characterization of microsatellite markers in the newly discovered invasive fruit fly pest in Africa, Bactrocera invadens (Diptera: Tephritidae). Mol Ecol Resour. 2008 Nov;8(6):1509-11.
Globalization and fruitfly invasion and expansion: the medfly paradigm. Genetica. 2007 Sep;131(1):1-9.
- Analyses of reproductive processes using functional genomics, proteomics and metabolomics techniques. RNA-Seq, microarray, proteomics and RNA interference approaches are applied to identify genes and proteins that are related to sexual maturity and mating.
The Spermatophore in Glossina morsitans morsitans: Insights into Male Contributions to Reproduction. Sci Rep. 2016 Feb 5;6:20334.
How functional genomics will impact fruit fly pest control: the example of the Mediterranean fruit fly, Ceratitis capitata. BMC Genet. 2014;15 Suppl 2:S11.
Transcriptome profiling of sexual maturation and mating in the Mediterranean fruit fly, Ceratitis capitata. PLoS One. 2012;7(1):e30857.
Transcriptional profiles of mating-responsive genes from testes and male accessory glands of the Mediterranean fruit fly, Ceratitis capitata. PLoS One. 2012;7(10):e46812.
Gene discovery in an invasive tephritid model pest species, the Mediterranean fruit fly, Ceratitis capitata. BMC Genomics. 2008 May 23;9:243.
- Analysis of reproductive behaviour using molecular and transgenic (GMOs) approaches. Molecular and transgenic markers are used to analyse mating dynamics, sperm competition and sperm use in different species in the laboratory and in nature. These studies are fundamental for the implementation of environmentally friendly control methods such as the Sterile Insect Technique (SIT).
Polyandry in the medfly – shifts in paternity mediated by sperm stratification and mixing. BMC Genet. 2014;15 Suppl 2:S10.
Towards mosquito sterile insect technique programmes: exploring genetic, molecular, mechanical and behavioural methods of sex separation in mosquitoes. Acta Trop. 2014 Apr;132 Suppl:S178-87.
Polyandry is a common event in wild populations of the Tsetse fly Glossina fuscipes fuscipes and may impact population reduction measures. PLoS Negl Trop Dis. 2011 Jun;5(6):e1190.
Safe and fit genetically modified insects for pest control: from lab to field applications. Genetica. 2011 Jan;139(1):41-52.
Sperm storage and use in polyandrous females of the globally invasive fruitfly, Ceratitis capitata. J Insect Physiol. 2010 Nov;56(11):1542-51.
Site-specific recombination for the modification of transgenic strains of the Mediterranean fruit fly Ceratitis capitata. Proc Natl Acad Sci U S A (2009) 106:18171.
Fluorescent sperm marking to improve the fight against the pest insect Ceratitis capitata (Wiedemann; Diptera: Tephritidae). N Biotechnol. 2008 Jun;25(1):76-84.
- Analysis of chemoreception. The genes and the encoded proteins involved in insect-host and insect-insect interactions are being characterised. Specifically we are studying the genes and their encoded proteins that are involved in the perception of: 1) odours emitted by plant hosts, that are involved in attraction/repulsion of insect pests; 2) odours emitted from a vertebrate host, that are involved in the attraction of blood-sucking insects; 3) odours/pheromones involved in mating and oviposition processes. An integrated approach is used involving functional genomics, proteomics, structural biology, electrophysiology coupled to gas chromatography and mass spectrometry. This line of research has significant implications for the development of repellents and attractants.
Sniffing out chemosensory genes from the Mediterranean fruit fly, Ceratitis capitata. PLoS One (2014) 9:e85523.
Identification of pheromone components and their binding affinity to the odorant binding protein CcapOBP83a-2 of the Mediterranean fruit fly, Ceratitis capitata. Insect Biochem Mol Biol (2014) 48:51-62.
- biochemical approaches to study saliva of the tiger mosquito.
The mosquito females require a blood meal for egg development and, when they bite an individual infected with a virus, they can acquire the pathogen. The mosquito saliva contains pharmacologically important proteins, with vasodilatory function, anticoagulants and anti-haemostatic activities that facilitate blood acquisition. The saliva proteins are also known to modulate and enhance viral transmission. In this project, we aim primarily to characterize the components of the saliva of Ae. albopictus and then we will study the biochemical and molecular functions of a subset of these proteins.
- Transcriptomics of resistance to insecticides and development of new bio-insecticides. RNA-seq approaches are used to identify the mechanisms of resistance to insecticides, primarily pyrethroids. Additionally, we are attempting to identify new molecules with bio-insecticide activities produced by soil bacteria.
RNA-seq analyses of changes in the Anopheles gambiae transcriptome associated with resistance to pyrethroids in Kenya: identification of candidate-resistance genes and candidate-resistance SNPs. Parasit Vectors (2015) 8:474.
Comparative transcriptome analyses of deltamethrin-resistant and -susceptible Anopheles gambiae mosquitoes from Kenya by RNA-Seq. PLoS One (2012) 7:e44607.
- Molecular evolution and population genetics (Prof. Lino Ometto). My research activity focuses on the genetic basis of biodiversity, which I investigate with a combination of computational and experimental approaches in both model and non-model systems. I use population genetics to disentangle demographic and selective processes, as well as molecular evolution to identify the genetic basis of phenotypic and adaptive traits in insects and other organisms.
In particular, by merging evolutionary genomics and transcriptomics with ecological, behavioural and morphological data, my research aims at understanding the mechanisms underlying the evolution of invading pest insects and insects of insects of agricultural and medical importance.
- University of Pavia: Andrea Mattevi, Federico Forneris, Antonio Torroni, Alessandra Albertini, Luigi Casella, Enrico Monzani, Eugenio Regazzini, Federico Bassetti, Riccardo Bellazzi, Giovanni Maga, Federico Focher, Daniele Merli, Barbara Mannucci, Antonella Lisa.
- University of Perugia: Andrea Crisanti, Philippos Papathanos
- University Federico II: Francesco Pennacchio, Giuseppe Saccone
- Fondazione Edmund Mach
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, delle Venezie, del Piemonte, Liguria e Valle d’Aosta
- Istituto Superiore di Sanità
- Centro Agricoltura Ambiente
- FAO/IAEA (Vienna, Austria)
- Yale School of Public Health, & Dept. of Ecology and Evolutionary Biology, New Haven, USA
- Institut Pasteur
- Imperial College, London
- European Bioinformatics Institute, Hinxton, UK
- Baylor College of Medicine, Houston, TX, USA
- USDA, US Department of Agriculture
- ICIPE, International Centre of Insect Physiology and Ecology
- University of California, Irvine
- Johns Hopkins University
- Vanderbilt University, Nashville, Tennessee, USA
- Southern Medical University, Guangzhou, China
- Royal Museum for Central Africa, Tervuren, Belgium
- Bioiberica, S.A., Barcelona, Spain
- University of Goettingen, Germany
- University of Giessen, Germany
- Slovak Academy of Sciences, Bratislava, Slovakia
- Institute of Entomology a Ceské Budejovice, Czech Republic
- CNRS di Gif-sur-Yvette, Francia
Active Research Grants
- Biotechnology and Biological Sciences Research Council (BBSRC) (PI Nikolai Windbichler, Malacrida & Scolari collaborators)
- Bioiberica S.A., Barcelona, Research Contract (01/07/2015-current) (PI Scolari)
- ERC Consolidator NIRV_HOST_INT (2016-2021) (PI Bonizzoni)
- FAO/IAEA research CRP project # 17896 (2013-18) (PI Scolari)
- FAO/IAEA Program of the United Nations project #17630 (2013-18) (PI Malacrida)
- FAO/IAEA research CRP project #19049R0 (2015-2020)(PI Gomulski, Gasperi)
- “Fight the mosquito bite” (Universitiamo Crowd-funding initiative, University of Pavia) (2015-present) (PI Gasperi, Malacrida)
- Fondazione Bussolera Branca (2015-17) (PI Gasperi, Albertini)
- NIH R21Al109263-01 (2014-17) (PI Malacrida)
- USDA – University of Pavia – Baylor College “Consortium for genome sequencing of the Medfly, Ceratitis capitata” (2010 – present) (PI Gasperi)
- Vectorbase-NIH Project “Comparative Genomics of 5 Glossina species” (PI Malacrida)
Prof. Daniela Curti, Prof. Maurizia Dossena, Prof. Ornella Pastoris, Prof. Roberto Federico Villa
Collaborators: Sara Arnica, Alice Buzzella, Barbara Balestra, Daniela Buonocore, Federica Ferrari, Silvia Molino, Manuela Verri.
Main research topics
– Neuropharmacology (see “Neurobiology”)
– Pharmacobiochemistry and Toxicology
1) Quest for novel antitumor compounds.
Rational design and evaluation of in vitro and in vivo efficacy of newly synthesized monomeric and dimeric ligands binding sigma-1 and sigma-2 receptors. The research is aimed to identify and optimize new candidate drugs with antitumor activity. In collaboration with: S. Collina and M. Paolillo (Dept. Drug Sciences, UNIPV) (contact: D.Curti).
2) Prevention of oxiplatin-induced peripheral neuropathy
Randomized phase II study on the efficacy of Superoxide Dismutase + Vitamin E supplementation in patients with colorectal cancer. Oxaliplatin, an antineoplastic platinum-derived compound, is the standard drug used for the treatment of colorectal cancer. However, chronic treatment leads to oxaliplatin-induced peripheral neuropathy. The project aims to investigate the efficacy of patients supplementation with Superoxide Dismutase and Vitamin E to prevent/reduce the oxaliplatin-induced neurological complications. The oxidative status of the patients over time and the metabolomic profile will be evaluated to identify the molecules involved in the induction and development of the peripheral neuropathy. In collaboration with: S. Brugnatelli (S.C. Oncologia, Fondazione I.R.C.C.S. Policlinico San Matteo di Pavia); J. Á. Rufián Henares (Dept. Nutrition and Bromatology, University of Granada, Spain (contact: M. Dossena)
3) Assessment of the toxicity, antioxidant, antiradical, antinflammatory, immunomodulatory properties and bioavailability of bioactive compounds extracted from vegetables and microalgae.
The study aims to characterize: 1) naringenin, naringin, as well other polyphenols’ content in grapefruit (C. paradisi) zest, rind, pulp, and juice extract; 2) bioactive compounds extracted from fruit/vegetable waste and microalgae such as Scenedesmus and Aphanizomenon flos-aquae (AFA). AFA, also called Klamath Algae, is a cyanobacterium characterized by a unique nutritional profile, containing specific immunomodulatory, anti-inflammatory and antioxidants molecules. In collaboration with: J. Á. Rufián Henares (Dept. Nutrition and Bromatology, University of Granada, Spain); AOP Unolombardia sacpa and Regione Lombardia (contact: M. Dossena).
4) Metabolism and physical exercise
The energy demands of the human body depend on energy expenditure and basal metabolic rate. The basal metabolic rate is the minimum energy needed to maintain vital functions. During physical exercise, particularly in sports, our metabolism increases and remains at high level for several hours after the end of the training (up to 12 hours). Exercise increases muscle metabolism indirectly through the secretion of anabolic hormones and the accumulation of muscle mass. However, athletes, in comparison with sedentary people, are more exposed to psychophysical stress that leads to release of cortisol and hormonal imbalance; to the increase of free radicals and to muscle, tendon and ligament damage. Our study will evaluate: 1) energy expenditure associated with various types of physical activities; 2) salivary and blood concentrations of hormones and other molecules related to physical activity or sports (e.g. cortisol, testosterone, growth hormone, inflammatory cytokines, ROS); 3) effects of sport food and supplements on exercise performance and post-exercise muscle recovery; 4) change in body composition by the modulation of diet programs (relationship between macronutrients and glycemic load). In collaboration with: G. D’Antona, M. Negro (Centro di Medicina dello Sport,Voghera, UNIPV); I. Fabbri (FIT e MOTOGPTM) (contact: M. Dossena).
5) Gastrointestinal neurobiopathology
Functional gastrointestinal neurobiopathology is studied by evaluating the neuronal control, and its modulation by neurotransmitters, of intestinal motility. The molecular aspects are investigated by analysing miRNA expression, pharmacogenetics and the influence of the intestinal microbiota in major gastrointestinal disorders such as Celiac disease, Irritable Bowel Syndrome (IBS). Our research interest is also focused on topics related to the pathophysiology of skeletal muscle, especially in the Neuroleptic Malignant Syndrome (NMS). In particular, studies are designed to evaluate the composition of intestinal microbiota in celiac patients using next generation sequencing and to perform genetic and epigenetic analyses in patients with NMS. In collaboration with: Unità di Medicina Interna e Gastroenterologia, Dip. Medicina Interna e Terapia medica UNIPV, Fondazione IRCCS Policlinico San Matteo Unità di Medicina Interna Dip. di Scienze Mediche e Chirurgiche, Università di Bologna, Policlinico S. Orsola-Malpighi; Laboratorio di Tossicologia Clinica e Sperimentale, Centro Antiveleni – IRCCS Fondazione Salvatore Maugeri, Pavia (contact: O.Pastoris).
Physiology is a discipline that covers an extremely wide extension of research fields relevant to the basis and mechanisms of normal cellular and systemic functions of animal organisms, with approaches typically characterized by the application of the highest possible levels of quantitative exactness.
The physiologists of the Dept. of Biological Sciences and Biotechnology “L. Spallanzani” are mainly active in the fields of Neurophysiology, Cellular and molecular Physiology, Cardiovascular Physiololgy, and some other application-directed ones.
Group leaders: Prof. Mauro Toselli, Prof. Gerardo Biella, Prof.ssa Paola Rossi, Prof. Franco Tanzi, Prof.ssa Laura Botta, Prof. Francesco Moccia.
Coworkers: Elisabetta Cesana (postdoc), Claudia Maniezzi (Ph.D. student), Luigi Salvioli (Ph.D. student), Francesca Talpo (postdoc).
Main research topics:
– Neurophysiology (see in the descriction of the research topic “Neurobiology”)
– Cellular and molecular Physiology
(i) Roles of ion channels in tumor cells
It has long been known than ion channels, particularly Ca2+-permeable channels, are involved in the cancer hallmarks described by Hanahan and Weinberg, such as uncontrolled proliferation, apoptosis resistance, and metastasis. The present research project intends to study the role played by intracellular Ca2+ signals in the processes of proliferation, apoptosis resistance and migration in primary cell lines established from patients suffering from two different solid cancers, i.e. renal cellular carcinoma and colorectal carcinoma. Our attention is particularly focused on Orai1-3 and TRPC1-77 channel families.
Research Supervisor: F. Moccia
Collaborations: U. Laforenza, Dipartimento di Medicina Molecolare, UNIPV; D. Montagna, P. Pedrazzoli, C. Porta, IRCCS Policlinico S. Matteo, Pavia
– Cardiovascular Physiology
(i) Role of Ca2+ signaling in physiological and pathological vasculogenesis
Recent studies showed that vasculogenesis, i.e. the formation of blood vessels de novo by endothelial progenitor cells (EPCs), not only takes place during embryonic development, but also during the angiogenic switch in solid tumors. Our group showed for the first time that Ca2+ signals play a key role in the activation of healthy EPCs and EPCs deriving from several types of tumor (renal cellular carcinoma, infantile hemangioma and primary myelofibrosis). The present research project intends to: 1) keep on investigating on the Ca2+ toolkit in healthy EPCs to shed further light on their basic physiological mechanisms; 2) assess whether the Ca2+ toolkit i also dis-regulated in breast cancer-derived patients; 3) investigate whether and how the remodeling of the Ca2+ toolkit underpins tumor EPC resistance to chemotherapeutics and anti-angiogenic drugs; and 4) investigate the molecular mechanisms by which tumor microenvironment alters EPC’s Ca2+ toolkit. The present project takes advantage from the collaboration with IRCCS Policlinico San Matteo in Pavia, which ensures the continuous availability of EPCs deriving from either healthy donors and tumor-affected patients.
Research Supervisor: F. Moccia
Collaborations A. Balduini, U. Laforenza, Dipartimento di Medicina Molecolare, UNIPV; D. Lim, Università del Piemonte Orientale, Novara; G. Guerra, Università del Molise, Campobasso; M. Della Porta, Humanitas Research University, Rozzano; M. Massa, P. Pedrazzoli, C. Porta, V. Rosti, IRCCS Policlinico S. Matteo, Pavia; L. Munaron, Università di Torino
– Other application-directed projects
(i) Antibiofilm profile of Pistacia lentiscus L. Oil. and Lentinula edodes
This research project studies the antioxidant and antimicrobial ability of extracts of Pistacia lentiscus and Lentinula edodes on human (oral) microbiota and, in particular on lingual biofilm. With the antibiotic resistance phenomenon in expansion the search for new antibacterial strategies rises great interest in the clinical context.
The activity will include the isolation of lingual biofilm and the assessment of the extent of oxydative stress with spectrophotometric measurements.
Research Supervisor: P. Rossi
The research activities are focused on the the morphology, physiology, genetics, immunology, pathology, pharmacology of the central nervous system at molecular, cellular and integrated system levels and on the development of innovative strategies to counteract neurodegenerative diseases.
Main research fields:
Group leaders: Prof. Daniela Curti, Prof. Maurizia Dossena, Prof. Ornella Pastoris, Prof. Roberto F. Villa
Coworkers: Sara Arnica (research fellow), A. Buzzella (research fellow), Barbara Balestra (graduated technician), Daniela Buonocore (research fellow), Federica Ferrari (voluntary laboratory attendant)), Silvia Molino (Ph.D. student), Manuela Verri (graduated technician)
(i) Role of Sigma-1 receptor (S1R) isoforms and oligomerisation in motoneuron (MN) survival and death.
S1Rs are ubiquitary proteins, particularly enriched in MNs where they sit on mitochondrial associated endoplasmic reticulum (ER)membranes (MAMs) and in cisternae localized under the post-synaptic densities of cholinergic C-terminals. The physiological role of the enigmatic S1R and its oligomerisation state and the potential as therapeutic target in MN diseases will be studied in cellular and animal models of amyotrophic lateral sclerosis (ALS), in lymphocytes and autoptic spinal cord samples of patients affected by ALS with the aim of developing novel strategies to counteract the disease. In collaboration with M. Peviani (Harvard Medical School, Boston); C. Bendotti (IRCCS M. Negri, Milano); S. Collina (Dip. Scienze del Farmaco, UNIPV); M. Zorzetto, (IRCCS Policlinico San Matteo, Pavia); M. Ceroni (IRCCS C. Mondino e UNIPV) .
Research supervisor: D. Curti
Collaborations: M. Peviani (Harvard Medical School, Boston); C. Bendotti (IRCCS M. Negri, Milano); S. Collina (Dip. Scienze del Farmaco, UNIPV); M. Zorzetto, (IRCCS Policlinico San Matteo, Pavia); M. Ceroni IRCCS C. Mondino e UNIPV.
(ii) Evaluation of metabolic alterations in patients with dementias.
role of insulin-resistance The study aims to evaluate potential alterations of cerebral, liver and skeletal muscle energy metabolism in subjects with dementia, considering blood and cerebrospinal fluid as biological matrices. Potential alterations in the aminoacidic and metabolomic blood profile, in the concentration of plasma acylcarnitines, together with insulin-resistance condition are considered. Pharmacological treatments in combination with nutritional and/or neurological rehabilitation are evaluated. In collaboration with: A. Costa (IRCCS “C. Mondino”, Pavia); A. Navarra (IRCCS, S. Maugeri Pavia, Servizio di Medicina di Laboratorio); M. Daglia (Dip. Scienze del Farmaco, UNIPV); Prof. Luisa Mannina (Dipartimento di Chimica e Tecnologie del Farmaco, Università Sapienza di Roma); Prof. Bruno Solerte (Dipartimento di Medicina Interna e Terapia Medica – IDR S. Margherita, Pavia).
Research supervisor: M. Dossena
Collaborations: A. Costa (IRCCS “C. Mondino”, Pavia); A. Navarra (IRCCS, S. Maugeri Pavia, Servizio di Medicina di Laboratorio); M. Daglia (Dip. Scienze del Farmaco, UNIPV); L. Mannina (Dip. Chimica e Tecnologie del Farmaco, Università Sapienza di Roma); B. Solerte (Dip. Medicina Interna e Terapia Medica – IDR S. Margherita, Pavia).
(iii) Correlation between oxidative stress and cytotoxicity in the progression of Anorexia Nervosa (AN): new biochemical and morphological approaches
Determination of the cytotoxicity of altered lipoproteins and modified amount/activity of hormones in blood of patients with eating disorder and in selected neural cell lines. Investigation of the molecular mechanisms mediating neural damage [In collaboration with MG. Bottone (Dept. Biology and Biotechnology, UNIPV); U. Balottin (IRCCS C. Mondino, UNIPV)].
Research supervisors: M. Dossena, M.G. Bottone
Collaborations: U. Balottin (IRCCS C. Mondino, Pavia).
(iv) Gastrointestinal neurobiopathology
Functional gastrointestinal neurobiopathology is studied by evaluating the neuronal control, and its modulation by neurotransmitters, of intestinal motility. The molecular aspects are investigated by analysing miRNA expression, pharmacogenetics and the influence of the intestinal microbiota. In particular, studies are designed to evaluate: 1) intestinal permeability, glial activation and intestinal microbiota in patients with Parkinson’s disease; 2) the dysfunction of gastrointestinal motility in an animal model of Parkinson’s disease. In collaboration with: F. Blandini (Laboratorio di Neurochimica Funzionale, IRCCS Istituto Neurologico “C. Mondino”, Pavia ).
Research supervisor: O. Pastoris
Collaborations: F. Blandini (Laboratorio di Neurochimica Funzionale, IRCCS Istituto Neurologico “C. Mondino”, Pavia ).
(v) Functional Proteomics and Metabolomics of enzyme bioenergetics
The experimental project regards molecular studies investigating in vivo the mechanisms underlying the biochemical changes in Functional Proteomics of the enzymatic systems linked to energy transduction of cerebral tissue. The analysis of the biochemical connections (Metabolomics) existing between the catalytic properties of some energy linked enzymes during acute or chronic and neurodegenerative Diseases of neurological and psychiatric interest, are examined in the perspective of a neuropharmacological approach for evaluating potential therapies to improve the Central Nervous System functional efficiency.
Research supervisor: R.F. Villa.
National and international collaborations and the outcome of the scientific research carried out so far can be found in R. F. Villa’s curriculum and Publication list, respectively: please refer to these two documents.
– Cellular and integrated Neurophysiology
Group leaders: Prof. Jacopo Magistretti, Prof. Mauro Toselli, Prof. Gerardo Biella, Prof. Paola Rossi, Prof. Franco Tanzi, Prof. Laura Botta, Prof. Francesco Moccia
Coworkers: Elisabetta Cesana (postdoc), Claudia Maniezzi (Ph.D. student), Luigi Salvioli (Ph.D. student), Francesca Talpo (postdoc)
(i) Actions of oxytocin in the central nervous system
Oxytocin, the hormone synthesized in the hypothalamus, acts both peripherally and centrally, thus regulating several behavioral functions. Recently, a correlation between the oxytonergic system and autism has been suggested to exist. Oxytocin receptors are widely distributed throughout the hippocampus, and various electrophysiological studies have been carried out in rodents to identify the oxytonergic circuits and to understand the neurodulatory mechanisms exerted by the neuropeptide in this structure. Oxytocin has turned out to enhance, in the hippocampal CA1 field, inhibitory transmission, by increasing the discharge frequency of a particular class of GABAergic neurons synaptically contacting pyramidal neurons. However, the mechanism through which oxytocin increaseses these interneurons’ discharge frequency has not been clarified yet, neither is it known how this increase influences pyramidal neurons’ excitability. Moreover, the mechanisms through which oxytocin is able to improve the symptoms of the autistic disease are also unknown. Our study focuses on the characterization of oxytocin-operated neuromodulation in the mouse hippocampus, in order to fill the knowledge gaps still existing in this field.
Research supervisors: M. Toselli, G. Biella
Collaborations: B. Chini, Istituto di Neuroscienze – CNR, Milano); M. Parenti, Dip. Medicina Sperimentale Università di Milano Bicocca, Milano
(ii) Analysis of synaptic activity in animal models of Huntington Disease (HD)
HD is a neurodegenerative disease caused by a dominant, autosomal mutation in the IT-15 gene, which codes for a protein named huntingtin (Htt). The normal, functional role(s) of Htt are still unknown. The protein is ubiquitous, it is essential for normal embryogenesis, normal neuronal development and survival, and is also involved in synaptic activity. The expansion of the nucleotidic triplet CAG in exon 1 of the IT-65 gene (with > 36 repetitions) generates a mutated form of Htt (mHtt) which somehow becomes toxic to neurons and causes a wide loss of cerebral neurons, especially in the cortex and the striatum. mHtt brings about, besides neuronal death in the late stages of the disease, also progressive alterations in the morphology, excitability, and synaptic connectivity and function of cortical pyramidal neurons and striatal medium spiny neurons (MSN). Hence, the earliest behavioral and cognitive symptoms of HD anticipate, rather than being a consequence of, neuronal death. Derangements in synaptic connectivity and plasticity at the CPN/MSN synapses, as well as excitotoxicity, mainly mediated by alterations of NMDA receptors, appear to be crucial in HD pathogenesis and progression. By resorting to multidisciplinary experimental approaches (e.g., electrophysiological, behavioral, etc.), we plan to analyze the basis of the progressive de-coupling of excitatory cortico-striatal synapses in knock-in mouse models of HD, both in the pre-symptomatic and symptomatic stages of the disease.
Research supervisors: M. Toselli, G. Biella
(iii) Functional evaluation of striatal medium spiny neurons differentiated from embryonal stem cells and re-programmed from fibroblasts of patients with Huntington disease (HD)
This research project focuses on the functional characterization of a specific class of triatal neurons, namely medium spiny neurons (MSN). By means of a specific protocol of differentiation form human embryonal stem cells (hES, H9 strain), 2D or 3D MSN cultures will be obtained. Some cell lines will also exposed to induced over-expression of factors like GSX2 and EBF1 to enhance cell yield and quality. Moreover, given the devastating MSN degeneration typical of HD, our interest is directed towards the electrophysiological characterization of striatal neurons differentiated from induced, pluripotent stem cells (hiPS) obtained from fibroblasts of both normal and HD human subjects. In this way, it becomes possible to model HD in an in vitro system, thus providing a major contribution to understanding of the multiple and still unclear or unknown molecular mechanisms underlying the neurodegeneration occurring in HD. Moreover, the electrophysiological investigations will contribute to validate and consolidate the cell differentiation protocol, in sight of the ultimate aim of generating genuine in vitro MSN, usable for cell therapy, which currently appears to be an excellent candidate in neurodegenerative disease management.
Research supervisors: M. Toselli, G. Biella
Collaborations: E. Cattaneo, Dip. Bioscienze, UNIMI, Milano; M. Onorati , Dept. Neurobiology, Yale School of Medicine, New Haven, Connecticut, USA
(iv) Mechanisms and neuromodulation of membrane excitability in the neurons of parahippocampal cortices and the perirhinal cortex
Parahippocampal cortices (PHCs) establish bidirectional synaptic interactions with the hippocampus that are of fundamental importance for the memory functions and spatial orientation functions typical of the medial-temporal lobe memory system. This project focuses on the study of the mechanisms governing the intrinsic excitable properties of PHC neurons, of their functional implications as far as communications between the parahippocampal region and the hippocampus are concerned, and of the neuromodulatory systems controlling them. In particular, the following aspects are studied: 1) the intrinsic membrane mechanisms which determine the specific discharge properties of medial entorhinal cortex (mEC) neurons; 2) membrane resonance phenomena, their underlying mechanisms, and functional implications in mEC and perirhinal-cortex (PRC) neurons; 3) the control mechanisms by which PRC is able to operate its characteristic function of selecting input signals of cortical origin and directed towards the hippocampus via the mEC, due to the intervention of a complex intrinsic synaptic network in which both projection pyramidal neurons and several different classes of GABAergic interneurons that generate a local inhibitiory action on pyramidal neurons are involved; 4) whether and how various physiological neuromodulatory systems, such as those relying on neurotransmitters like acetylcholine, dopamine, norepinephrine, etc., influence the above mentioned properties of single neurons and local circuits.
Research supervisors: J. Magistretti, M. Toselli, G. Biella
(v) Role of endothelial Ca2+ signals in neurovascular coupling
Neurovascular coupling is the mechanism through which brain blood flux increases or decreases in response to modifications of neural activity of the same sign. The most widely accepted view attributes the ability to release vasoactive mediators, in response to synaptic activity, to neurons and astrocytes. This research project is currently examining, for the first time, the ability of brain vessel endothelium to directly sense the synaptic release of neurotransmitters. Our attention is focusing on the sensitivity of bEND.5 cells, a widely validated model for the study of brain endothelium, to the neurotransmitters, glutamate and acetylcholine, and the neuropeptide, catestatin. Specifically, the present project intends to: 1) study the mechanisms responsible for the generation of the intracellular Ca2+ oscillations which emerge after exposure to each one of the three above-mentioned agonists; 2) to assess whether and how such oscillations trigger the synthesis nitrogen monoxide (NO), the main vasodilating agent of the brain; and 3) evaluating whether and how the NO released by brain endothelial cells can act not only on vascular tone, but also, retroactively, on synaptic activity.
Research supervisor: F. Moccia
Collaborations: T. Angelone, Università della Calabria, Cosenza; E. D’Angelo, Dipartimento di Scienze del Cervello e del Sistema Nervoso, UNIPV; S. Dragoni, University College London, London; G. Guerra, Università del Molise, Campobasso; D. Lim, Università del Piemonte Orientale, Novara
(vi) Study on the effects of oral integration with the medicinal mushroom, Hericium erinaceus (Lion’s mane) on neurogenesis and cognitive functions in wild-type mice
Hericium (Bull.) Pers. Is a medicinal mushroom that is able to modulate the immune system and enhance cognitive functions in humans. In the last decade several in vitro and in vivo studies have been carried out to evaluate the effects Hericium after oral administration. In humans, in particular, the data available in the literature report a neuroprotective effect against brain stroke and effects of partial cognitive recovery in neurodegenerative diseases, such as dementia and Alzheimer disease (AD). In a mouse model of pharmacologically-induced AD development, food supplementation with H. erinaceus prevents impairment of short-term as well as visual recognition memory. No data are available as far as wild-type animals are concerned.
This research line studies the effects of oral administration of this mycotherapic agent in wild-type mice. In particular, two aspects are dealt with: the ability of supplementation to improve some cognitive performances related to memory and the effects on hippocampal neurogenesis.
The patch-clamp technique is applied to hippocampal slice, and in vivo behavioral studies are carried out.
Research supervisor: P. Rossi
Collaborations: F. Brandalise, Brain Research Institute, University of Zurich; A. Gregori, MycoMedica d.o.o., Kranjska Gora, Slovenia; G. Orrù, Dipartimento di Scienze Chirurgiche, Università di Cagliari; M.L. Guglielminetti, M.Rodolfi ed E. Savino, Dipartimento della Terra e dell’Ambiente, Università di Pavia.
(vii) Study on plastic phenotypic modifications and of the neural olfactory network in eggs and tadpole embryos exposed to predation signals
Phenotypic plasticity is the ability of organisms to modify their phenotype in response to environmental changes. In particular, the prey-predator interaction is studied by exposing eggs and tadpole larvae to various chemical signals produced by different kinds of predators (specific, aspecific, indigenous, non-indigenous, etc.), and evaluating the ensuing phenotypic modifications and response changes in the olfactory system’s mitral cells. The physiological mechanisms underlying such changes are studied in the attempt to understand how the information contained in predator-produced signals (kairomones) are coded at the various levels of the prey’s sensory system.
The study exploits the application of the patch-clamp technique to the olfactory system (mitral cells) of in vivo tadpoles as well as the documentation of behavioral changes in tadpoles.
Research supervisor: P. Rossi
Collaborations: P. Galeotti e A. Gazzola, Dipartimento della Terra e dell’Ambiente, Università di Pavia; F. Brandalise, Brain Research Institute, University of Zurich; D. Rubolini, Dipartimento di di Bioscienze, Università di Milano
(viii) Expression of inward-rectifier potassium currents in the vermis and the cerebellar hemispheres of the mouse
Inward-rectifier potassium currents coupled to G proteins (GIRK) play a crucial role during migration and maturation of cerebellar granule cells in the cerebellar vermis. Consistently with such a role, the weaver mouse model, which is characterized by a spontaneous point mutation of a GIRK2-type channel, shows deep alterations in motor function, with a pattern of severe cerebellar ataxia. In cerebellar hemispheres, however, the ontogenesis of GIRK currents during cerebellar granule migration and differentiation shows a completely different pattern. This research line analyzes the regional differences in ontogenetic development of voltage-dependent currents.
The study is based on the application of the patch-clamp technique in mouse cerebellar slices and immunohistochemical measurements with specific antibodies.
Research supervisor: P. Rossi
Collaborations: U. Gerber e F. Brandalise, Brain Research Institute, University of Zurich; R. Lujan, Instituto de Investigaciónen Discapacidades Neurológicas (IDINE), Dept. Ciencias Médicas, Facultad de Medicina, Universidad Castilla-La Mancha, Albacete, Spain
Neuromorphology and Neurogenetics
Group leaders: Prof.ssa Maria Grazia Bottone, Prof. Sergio Comincini, Prof.ssa Rosanna Nano
Collaborators: Violetta Insolia (Ph.D. student), Irene Masiello (Ph.D. student), Marco Biggiogera (full professor)
(i) Study of the development of the central nervous system of mice deficient in prolidase: histochemical alterations in cytoarchitecture areas of NCS
The gene prolidase (PEPD) encodes for the unique Mn (II)-dependent imminodipeptidase responsible for the hydrolysis of dipeptides containing proline or hydroxyproline at the C-terminal. Mutations in this gene cause prolidase deficiency (PD), a rare, autosomal recessive disease. PD patients show reduced or absent enzyme ctivity and a wide spectrum of phenotypes: dermatologic manifestations as incurable leg ulcers; susceptibility to recurrent respiratory infections and varying degrees of mental retardation. In our laboratory, on a mouse model of PD, the dark-like mutant (dal), we assess the correlation between PD and the brain neuroarchitecture and histochemical alterations. In particular, we analyse postnatal alterations in the cerebellum, hippocampus and cerebral cortex. In three different mouse genotypes (wt, dal/+ and dal/dal) we shall evaluate the disorganization of the basement membrane and meninges; the alterations in the migration processes and neuronal differentiation; the imbalance between cell proliferation and cell death; impairment in the major neurotransmitter systems; neurodegeneration and angiogenesis. Morphological, histochemical and microscopic techniques will be utilized together with Western Blotting for quantitative analyses.
Research supervisor: M.G. Bottone
Collaborations: M. Biggiogera, (Dip. Biologia e Biotecnologie, UNIPV); A. Forlino (Dip. Medicina Molecolare, UNIPV)
(i) Astrocytic tumors
ia) Identification of biomarkers to aid in the histopathologic diagnosis of astrocytic tumors, important in the stratification of patients (molecular subtyping) and, in general, for personalized medicine. Development of preclinical protocols for the modulation of autophagic programmed cell death. Translational medicine studies for the development of preclinical therapeutic protocols adjuvant to chemotherapy or radiation treatments.
Research supervisor: S. Comincini
Collaborations: T. Florio (Dept. Internal Medicine and Medical Specialties, University of Genoa) and G. Fossati (ITALFARMACO spa, Milan).
-ib) Development of preclinical anticancer therapeutic strategies based on the use of exosomes and the modification of their molecular content.
Nano-vesicular systems, represented by exosomes, are important systems of communication between the cells and thus may also constitute, given their ability to reach cell districts even very distant, an efficient system for vehicular bioactive molecules to specific target cells, such as cancer cells. Consequently, the isolation and molecular manipulation of exosomial carriers may represent a novel tumor-interference system, useful to improve the effectiveness of current conventional treatment strategies.
Research supervisor: S. Comincini
Collaborations: M. Biggiogera, F. Moccia, G.F. Guidetti (Dept. Biology and Biotechnology, UNIPV).
(iii) Behavioral neurogenetics
In this context, we are focusing on DNA polymorphisms (SNPs) to identify new genetic determinants associated with particular social, psychological, behavioral (behavior genetics). Currently a study is in progress on the identification of polymorphisms of the oxytocin receptor gene associated with the neurological disorder in humans of prosopagnosia (difficulty in recognizing faces).
Research supervisor: S. Comincini
Collaborations: Z. Cattaneo (Dept. Psychiatry, University of Milan Bicocca).
(iv) Study of novel radiopharmaceuticals for the diagnosis of gliomas and of glial cells in physiological and pathological conditions.
The differential diagnosis between tumor recurrence (gliomas and brain metastases) and radiation necrosis phenomena (RN), plays an important role both as a prognostic and therapeutic point of view. Despite significant technological advances of current imaging modalities (PET-CT, MRI, ..) is not yet possible an accurate diagnosis to distinguish areas of active neoplastic proliferation from necrotic or neuro-inflammation areas. Our current research involves the study of new radiopharmaceuticals (18F-FCH, 18F- FET) specific to distinguish low and high grade gliomas. As experimental model various lines of human glioblastoma (T98G, U251, U87) are used to evaluate the in vitro uptake of radiopharmaceuticals mimicking the in vivo situation.
Research supervisor: R. Nano
Collaborations: L. Lodola, M. Persico, F. Buroni (S.C. Medicina Nucleare, IRCCS Policlinico San Matteo, Pavia); F. Corbella, F. Pasi (S.C. Radioterapia Oncologica, IRCCS Policlinico San Matteo, Pavia); A. Facoetti, C. Aprile (Fondazione CNAO, Pavia); E. Giombelli (Divisione Neurochirurgia, Ospedale di Parma); A. Messina (Div. Neurochirurgia, Ospedale di Sondalo); E. Benericetti (Div. Neurochirurgia, Maria Cecilia Hospital GVM, Cotignola, BO).
Group leaders: Prof. Antonio Torroni, Prof. Ornella Semino, Prof. Luca Ferretti, Prof. Anna Olivieri, Prof. Alessandro Achilli
Collaborators: Vincenza Battaglia, Marco Rosario Capodiferro (PhD student), Alessandro Raveane (Postdoc)
One of the main objectives of the research group is the reconstruction, based on genetic and genomic data, of the evolutionary history and demographic events that have involved present and past human populations (at both micro and macro-geographic levels) and some animals (especially domestic animals and those living in close contact with our species). Genetic findings can be easily employed also in multidisciplinary studies involving apparently far away scientific and cultural contexts, from forensics to history, archaeology, linguistics, anthropology, education and public health.
The genetic systems under study are the autosomes as well as the uniparentally transmitted mitochondrial DNA (mtDNA) and male-specific portion of the Y chromosome (MSY). The latter two are not reshuffled by recombination and thus constitute a molecular archive of the history and migration of females and males, respectively, who transmitted them to subsequent generations. Our studies has also implications in biomedicine. For instance, the mitochondrial DNA contains 37 genes that are coding for components of respiratory chain enzyme complexes and are essential for cellular energy production. Thus, one of the aims of the research of this group is also to define the role of the “normal” sequence variation of mtDNA in some diseases (Parkinson’s, Alzheimer’s, diabetes, reduced fertility), in aging and athletic performance.
1) Origin of populations from Europe and the Mediterranean area
The demographic and genetic history of Europe and surrounding regions is extremely complex. The purpose of this research is to investigate, through the analysis of modern and ancient DNA genomes, what aspects of the variability of European populations can be traced back to the first colonization of the continent by modern humans, to post – glacial expansions, the Neolithic diffusion and (or) more recent events of gene flow. Over the years our studies on this general topic have been very productive and have used as the main tool of investigation the two non-recombinant genetic systems (mtDNA and MSY), which we are now integrating with genome-wide analyses.
Collaborations: Prof. Fulvio Cruciani (Sapienza Univ. di Roma); Dr. Martin Bodner, Prof. Walther Parson (Innsbruck Medical Univ., Austria); Dr. Francesca Gandini, Prof. Maria Pala, Prof. Martin B. Richards (Univ. of Huddersfield, UK); Prof. Vincent Macaulay (Univ. of Glasgow, UK); Prof. Andrea Novelletto (Univ. Tor Vergata, Roma); Prof. Antonio Salas (Univ. of Santiago de Compostela, Spain); Prof. Richard Villems (Estonian Biocentre, Tartu, Estonia).
- Phylogeography of human Y-chromosome haplogroup Q3-L275 from an academic/citizen science collaboration (2017)
- Origin and spread of human mitochondrial DNA haplogroup U7 (2017)
- Reconciling evidence from ancient and contemporary genomes: a major source for the European Neolithic within Mediterranean Europe (2017)
- Genomic insights into the origin of farming in the ancient Near East (2016)
- Mapping human dispersals into the Horn of Africa from Arabian Ice Age refugia using mitogenomes (2016)
- Phylogenetic applications of whole Y-chromosome sequences and the Near Eastern origin of Ashkenazi Levites (2013)
2) The genetic origin of Italian populations
Despite its small geographic area, the Italian peninsula, for geographical, climatic and historical reasons, has occupied for several millennia a central position in the flow of genetic exchange and commercial trades among ancient populations. The objective of this research line is to reconstruct the prehistorical and historical genetics of the early Italy at a very high level of genetic resolution in a very large number of subjects (covering all Italian regions). To accomplish this task, a genome-wide scan on rare and common SNPs as well as analyses of both uniparental genetic systems (MSY and mtDNA) are going to be performed.
Collaborations: Prof. Andrea Angius (Istituto di Ricerca Genetica e Biomedica – CNR, Cagliari); Prof. Cristian Capelli (Univ. of Oxford, UK); Prof. David Caramelli (Univ. di Firenze); Prof. Cristina Cattaneo (Univ. di Milano); Dr. Hovirag Lancioni, Dr. Irene Cardinali (Univ. di Perugia); Prof. Carlo Previderè (Dip. di Medicina Legale, Univ. di Pavia); Prof. Mait Metspalu (Estonian Biocentre, Tartu, Estonia).
- Reconstructing the genetic history of Italians: new insights from a male (Y-chromosome) perspective (2018)
- Genealogical relationships between early medieval and modern inhabitants of Piedmont (2015)
- Small effective population size and genetic homogeneity in the Val Borbera isolate (2013)
- Mitochondrial DNA variation of modern Tuscans supports the near eastern origin of Etruscans (2007)
3) The peopling of Sardinia
Sardinian people are a “genetic outlier” in the European contest. Archaeological data point to a first evidence of modern human presence on the island dating back to about 13,000 years ago (Upper Palaeolithic). Distinctive genetic traits of Sardinians have been retrieved with all genetic systems, due to a combination of founder effects, geographic isolation, and selection. Recent paleo-genomic data based on nuclear genome markers have revealed that, among present-day populations, Sardinians retain the highest levels of genetic similarity with Early Neolithic farmers across Europe. However, this scenario appears in contrast with data provided by uniparentally-transmitted genetic systems. We are currently investigating on this topic, also from an ancient DNA perspective.
Collaborations: Prof. Andrea Angius, Prof. Francesco Cucca, Dr. Carlo Sidore (Istituto di Ricerca Genetica e Biomedica – CNR, Cagliari); Prof. Johannes Krause (Max Planck Institute for the Science of Human History, Germania).
- Mitogenome Diversity in Sardinians: A Genetic Window onto an Island’s Past (2017)
- Mitochondrial haplogroup U5b3: a distant echo of the epipaleolithic in Italy and the legacy of the early Sardinians (2009)
4) The peopling of the Americas: a genetic perspective
The first peopling of the New World is a hot topic in genetics and anthropology. Archaeology, linguistics and genetics agree on the Asian origin of Native Americans. However, the arrival times of the first settlers, the number of migrations / expansions involved in the process and in the subsequent colonization of Central and South America, as well as the genetic consequences of the flourishing of the great Mesoamerican and Andean civilizations are still extensively debated. To clarify these issues, sequence analyses of the two non-recombinant genetic systems (MSY and mtDNA), both at the micro- and macro-geographic levels, are carried out in several modern populations and some ancient samples. In some contexts, these studies are integrated by genome-wide analyses at the nuclear level.
Collaborations: Dr. Martin Bodner, Prof. Walther Parson (Innsbruck Medical Univ., Austria); Prof. Richard Cooke (Smithsonian Tropical Research Institute, Panama); Prof. Ripan Malhi (Univ. of Illinois at Urbana-Champaign, US); Dr. Jorge A. Motta (Secretario Nacional de Ciencia y Tecnología e Innovación, Panama); Dr. Juan Miguel Pascale (Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama); Dr. Ugo A. Perego (Genetic Genealogy Consultant, US).
- Ancient human genomes-keys to understanding our past (2018)
- The peopling of South America and the trans-Andean gene flow of the first settlers (2018)
- The Paleo-Indian Entry into South America According to Mitogenomes (2018)
- Ancient individuals from the North American Northwest Coast reveal 10,000 years of regional genetic continuity (2017)
- The first peopling of South America: new evidence from Y-chromosome haplogroup Q (2013)
- Reconciling migration models to the Americas with the variation of North American native mitogenomes (2013)
5) A comparative analysis of historical-cultural and genetic data: conquest, commerce, crisis, culture and the Panamanian junction (1513-1671) (ERC CoG 648,535 – ArtEmpire)
The narrow Isthmus of Panama was a strategic node of the Spanish Empire and a crucial site for early modern globalization. This project combines analyses of historical documents with archaeological and archaeogenetic approaches to highlight the cultural and biological consequences of encounters between populations and goods from Europe, America, Africa and Asia in the Isthmus of Panama area during the sixteenth and seventeenth centuries.
Collaborations: Dr. Bethany Arhan (Universidad Pablo de Olavide, Spain); Dr. Corina Knipper (Curt-Engelhorn-Zentrum Archäometrie, Mannheim, Germany); Dr. Juan Martin, Dr. Javier Rivera (Universidad del Norte, Colombia).
- Exploring the Y Chromosomal Ancestry of Modern Panamanians (2015)
- Decrypting the mitochondrial gene pool of modern Panamanians (2012)
6 ) Identification of new pathological mtDNA mutations and the roles of mitochondrial background (haplogroups) in the expression of diseases / phenotypes
The mitochondrial ATP production by the oxidative phosphorylation is essential for the maintenance of normal functions of organs and tissues. MtDNA mutations, by interfering with ATP synthesis, can cause serious maternally-transmitted diseases. The search for new disease-causing mtDNA mutations is carried out mainly on Leber’s Optic Neuropathy (LHON). In recent years, an important role of the “neutral” sequence variation of mtDNA has also been postulated for many complex diseases and other phenotypes (aging, athletic performance). To evaluate also these aspects, we are sequencing entire mitogenomes from numerous human populations and building up a database that includes representatives of each mtDNA haplogroup and sub-haplogroup present in our species.
Collaborations: Prof. Valerio Carelli (Univ. di Bologna); Dr. Cristina Cereda (IRCCS Istituto Neurologico Nazionale C. Mondino, Pavia); Prof. Alessandra Montecucco (Istituto di Genetica Molecolare – CNR, Pavia).
- Haplogroup J mitogenomes are the most sensitive to the pesticide rotenone: Relevance for human diseases (2018)
- Peculiar combinations of individually non-pathogenic missense mitochondrial DNA variants cause low penetrance Leber’s hereditary optic neuropathy (2018)
- A missense MT-ND5 mutation in differentiated Parkinson Disease cytoplasmic hybrid induces ROS-dependent DNA Damage Response amplified by DROSHA (2017)
- Association of the mtDNA m.4171C>A/MT-ND1 mutation with both optic neuropathy and bilateral brainstem lesions (2014)
- A novel in-frame 18-bp microdeletion in MT-CYB causes a multisystem disorder with prominent exercise intolerance (2014)
- Cybrid studies establish the causal link between the mtDNA m.3890G>A/MT-ND1 mutation and optic atrophy with bilateral brainstem lesions (2013)
7) The genetics of taste
The ability to perceive flavors is genetically determined and the perception of flavors is the main factor driving the choice of foods, causing their acceptance or rejection. On the other hand, the choice of foods is an important factor that can modulate the risk of common diseases, such as obesity, diabetes, metabolic syndrome, but also cardiovascular diseases and cancer. The aim of our work is to correlate the variations of genes involved in taste perception, and thus in food choices, with diet and health state, in particular with tumors of the digestive system.
Collaborations: Prof. G. Nadia Ranzani (Dip. di Biologia e Biotecnologie, Univ. di Pavia).
8) Origin and spread of the Asian tiger mosquito (Aedes albopictus)
Over the last 40 years, the tiger mosquito Aedes albopictus, indigenous to East Asia, has colonized every continent except Antarctica. Its spread has become a growing public health concern, being a competent vector for many arboviruses including those causing West Nile fever, yellow fever, Dengue fever, Saint Louis encephalitis and the recently emerged Zika fever.
The present study involves the definition and analysis of mitogenome sequence variation in samples from numerous African, European and American populations, in order to identify the ancestral Asian source(s) of Ae. albopictus adventive populations and their possible selective advantages as well as migration routes and expansion times.
- The Worldwide Spread of the Tiger Mosquito as Revealed by Mitogenome Haplogroup Diversity (2016)
Collaborations: Dr. Paolo Gabrieli, Prof. Giuliano Gasperi, Prof. Ludvik Gomulski, Prof. Anna Malacrida (Department of Biology and Biotechnology, Univ. of Pavia).
9) Modes and times of domestication of some mammal species (Bos taurus, Bubalus bubalis, Ovis aeries, Capra hircus, Equus caballus)
Our first phylogeographic studies on the entire mitogenome of cattle, horse, goat and sheep provided new information on the domestication process(es). Most of the domestic species have been involved in a single domestication event that occurred in the Neolithic period (about 10,000 years ago) in the Fertile Crescent. On the contrary, the high number of haplogroups found in modern equine breeds suggests that the domestication of wild horses took place in several centres around Eurasia. The analysis is currently extended to the nuclear genome (in particular to the Y chromosome), focusing on the origin of local breeds (especially in Italy). The overall aim is to highlight parallel genetic histories of humans and domestic animals useful to further extend the current knowledge of human populations.
Collaborations: Dr. Hovirag Lancioni, Dr. Irene Cardinali, Dr. Emiliano Lasagna, Prof. Francesca Maria Sarti, Dr. Katia Cappelli, Prof. Maurizio Silvestrelli and Prof. Emidio Albertini (Univ. di Perugia); Dr. Licia Colli and Prof. Paolo Ajmone Marsan (Univ. Cattolica del S. Cuore, Piacenza).
- Mitochondrial DNA variants of Podolian cattle breeds testify for a dual maternal origin (2018)
- Whole Mitogenomes Reveal the History of Swamp Buffalo: Initially Shaped by Glacial Periods and Eventually Modelled by Domestication (2017)
- An Overview of Ten Italian Horse Breeds through Mitochondrial DNA (2016)
- Survey of uniparental genetic markers in the Maltese cattle breed reveals a significant founder effect but does not indicate local domestication (2016)
- Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability (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 (2015)
10) Genetic origins of Italian wild mammals (Sus scrofa)
The same phylogeographic approach employed to analyze the domestic species is now employed for studying the variability of some wild species that are related or depending on human activities. In particular, virtually all European wild boars belong to only one mtDNA haplogroup, named D1, with the notable exception of the Italian-specific haplogroup D4. A phylogeographic study based on complete mitogenomes is in progress to clarify the origin and spread of this “Italian” lineage.
Collaborations: Dr. Hovirag Lancioni and Dr. Francesca Vercillo (Univ. of Perugia); Dr. Massimo Scandura (Univ. of Sassari).
1) Identification of the cellular target of new antitubercular compounds
Prof. Giovanna Riccardi, Prof. Maria Rosalia Pasca, Dr. Laurent Chiarelli, Dr. José Camilla Sammartino
Mycobacterium tuberculosis, the etiological agent of tuberculosis, (TB) is responsible for an estimated 1.5 million deaths worldwide annually. The emergence and spread of M. tuberculosis multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains and, more recently, totally drug-resistant (TDR) strains is an extremely dangerous threat to public health, in particular to immunocompromised patients. In the new pathway for the discovery of drugs to combat the increasing menace of drug-resistant microorganisms, the crucial first step is to generate a set of target genes, from whole-genome data, that offer the potential for effective therapeutic intervention. Our objectives in the project “More Medicines for Tuberculosis – MM4TB” (VII Framework programme) are to find the molecular targets of prioritized molecules, already available, as well as natural products and synthetic compounds (hits) effective in models of active or latent TB. Among these molecules, we are studying the mechanism of activation of the TP053 prodrug (Albesa-Jove D et al., 2014, ACS Chem. Biol.) and we are searching for its possible cellular target. We have identified the mechanism of inactivation of the Ty38c quinoxaline derivative (Neres J et al., 2014, ACS Chem. Biol.), targeting the DprE1 enzyme identified within the previous “New Medicines for Tuberculosis – NM4TB” (VI Framework programme) as cellular target of Benzothiazinones (BTZ). Recently, a BTZ derivative entered human clinical trials. Lastly, the PyrG CTP synthase enzyme has been identified as the common cellular target of two different prodrugs (Mori G et al., 2015, Chem. Biol.) and it is considered a new promising vulnerable target in M. tuberculosis.
Collaborators: Cole ST (EPFL, Lausanne, Switzerland), Makarov V (Bakh Institute of Biochemistry, Russian Academy of Science, Moscow, Russia), Baltas M (CNRS, Toulouse, France), Mikusova K (Comenius University in Bratislava, Department of Biochemistry, Bratislava, Slovakia), Guerin M (Biophysics Unit, University of the Basque Country, Bilbao, Basque Country, Spain), Marengo E (Università del Piemonte Orientale, Alessandria, Italy).
2) New drugs against Burkholderia cenocepacia (FFC 2015)
Prof. Giovanna Riccardi, Dr. Silvia Buroni, Dr. Laurent Chiarelli, Dr. Viola Camilla Scoffone, Dr. Gabriele Trespidi
Burkholderia cenocepacia is a Gram-negative bacterium that infects the airways of patients with cystic fibrosis (CF). Eradication of this infection is complicated by the intrinsic resistance of this microorganism to different antibiotics. In this way, the development of novel antibiotics remains a major issue for the treatment of infectious lung disease, such as that in CF. We are currently pursuing two different ways:
- Synthesis of new molecules effective against cenocepacia. We recently found that a benzothiadiazol compound (10126109) is very active and we identified a mechanism of resistance, which relies on the extrusion of the new drug by RND-9 transporter. The compound is active against clinical isolates and other members of the Bcc, as well as against other Gram-negative and -positive bacteria. We recently identified the mechanism of action and evaluated the toxicity on CF epithelial bronchial cells. New derivatives of 10126109 will be synthesized with the aim to find more active molecules. Moreover, inhalable formulations will be developed in order to administer it to mice to evaluate its in vivo efficacy.
- Characterization of the quorum sensing enzymes, as a target of anti-virulence compounds which could represent a new promising therapeutic approach. The two enzymes CepI and DfsA have been obtained in recombinant form and, for the latter the crystal structure have been resolved. The activity assay of both enzymes have been assessed, allowing the screening of a potential inhibitors. These screen led to new compounds active in vitro against CepI, which are able to dramatically decrease the virulence of the bacteria in an in vivo elegans model.
Collaborations: Makarov V (Bakh Institute of Biochemistry, Russian Academy of Science, Moscow, Russia), Cardona S (University of Manitoba, Winnipeg, Canada), Coenye T (University of Gent, Belgium), Ungaro F (Università di Napoli Federico II), Bragonzi A (Ospedale San Raffaele, Milano), Drevinek P (Motol Hospital, Prague, Czech Republic).
3) Bacterial endophytes from leguminosae seeds for searching new antibacterial molecules, promoting seed germination and phytoremediation of soils
Prof. Edda De Rossi
Endophytic bacteria have been found in virtually every plant studied. Most endophytes appear to originate from the rhizosphere or phyllosphere; however, some may be transmitted through the seed. Endophytic bacteria can promote plant growth and yield and can act as biocontrol agents. Endophytes can also be beneficial to their host by producing a range of natural products that could be harnessed for potential use in medicine, agriculture or industry. In addition, it has been shown that they have the potential to remove soil contaminants by enhancing phytoremediation. So a major reason for the increasing interest in endophytes is the potential for biotechnological applications.
All classes of antibiotics have seen the emergence of resistance compromising their use. The emergence and dissemination of multi-drug-resistant bacteria and the lack of new antibiotics with new modes of action are today one of the major challenges to treat infectious diseases. Endophytes are capable of synthesizing bioactive compounds that are used by plants for defense against pathogens; thus, these microorganisms may represent an underexplored reservoir of novel species of potential interest in the discovery of novel lead compounds. Natural product drug discovery has regained interest due to low production costs, structural diversity, and multiple uses of active compounds to treat various diseases.
Seed germination is a vital phase to plants’ survival and reproduction in either optimal or stressful environmental conditions. Thus, developing methods by which seedling emergence can be enhanced and predicted under the limitations of heat or drought is valuable. The use of endophytic symbionts is a promising method by which seed germination can be enhanced and plants protected from environmental stressors.
The exploitation of plant–endophyte partnerships for the remediation of contaminated soils is a promising area. For example, in the case of phytoremediation of toxic metals, endophytes able to produce natural metal chelators can reduce metal toxicity for their host plant.
The aim of this recently activated project is to isolate the cultivable, endophytic bacteria from the seeds of commercial genotypes of leguminosae belonging to genus Medicago and Trifolium to characterize bacterial strains for the production of new antibacterial agents, germination of seeds and phytoremediation of soils.
Collaborations: Prof.ssa Alma Balestrazzi (Dip. di Biologia e Biotecnologie, Pavia)
4) Study of the membrane protein MmpL3 as cellular target for new antitubercular agents
Prof. Edda De Rossi
The number of multidrug resistant (MDR) strains of Mycobacterium tuberculosis (Mtb) is increasing and without effective treatments; the fear is that the number of infections caused by MDR strains will increase out of control. Therefore, new drugs of different classes against diverse targets are urgently needed. Pyrrole derivatives show a potent activity against Mtb and MDR clinical isolates of Mtb as well as on intracellular bacilli. On the basis of these results, BM212 was considered the lead compound of this new class of derivatives. The Pavia team has identified the membrane protein MmpL3 as target for this compound. MmpL3 is required for the export of mycolic acids in the form of trehalose monomycolates (TMM) to the periplasmic space or outer membrane of Mtb. Recently other researchers have identified seven series of inhibitors that abolish MmpL3-mediated TMM export confirming this essential protein as a novel target for new antitubercular agents. The aim of this project is to characterize the MmpL3 protein for both molecular modeling studies and synthesis of new and more efficient inhibitors.
5) New drugs against Mycobacterium abscessus and other nontuberculous mycobacteria
Prof.ssa Maria Rosalia Pasca
Collaborators: Dr. Laurent Chiarelli, Dr. José Camilla Sammartino
Nontuberculous mycobacteria (NTM) are emerging as important pathogens in cystic fybrosis (CF) lung disease worldwide with an estimated prevalence of about 9%; the Mycobacterium abscessus strains are the most spread in Europe. The M. abscessus treatments are further complicated by the diffusion of strains with inducible macrolide resistance. In these cases, the surgical resection of infected lung tissue could be beneficial in selected patients. Moreover, unsuccessful M. abscessus eradication is considered a contraindication for lung transplantation, being associated with treatment failure and increased mortality.
Consequently, new more active drugs are urgently needed, in particular against M. abscessus. In this project, taking advantage of our experience in tuberculosis research, we would like to move all our knowledge in the new challenging NTM field, by pursuing the following goals:
- Screening of a several compounds (more than 500) synthesized by our collaborator Dr. V. Makarov against abscessus growth.
- Evaluation of the sensitivity of other NTM species and clinical isolates to selected compounds.
- Characterization of the mechanism of action/resistance of the selected compounds.
Collaboration: Makarov V (Bakh Institute of Biochemistry, Russian Academy of Science, Moscow, Russia).
Plant Biotechnology Group
Prof. Alma Balestrazzi, Dr. Anca Macovei, Dr. Susana Araujo, Dr. Andrea Pagano, Dr. Chiara Forti, Dr. Carla Gualtieri
Role of DNA repair in the plant response to abiotic stress. Aim of the research is the molecular characterisazion of genes involved in the response to genotoxic stress (DNA Damage Response-DDR), as useful tools to detect the level of abiotic stress tolerance in crops. The research activity at the Plant Biotechnology Laboratory has led to the isolation and molecular characterisation of novel genes involved in DNA repair processes in planta. This investigation, carried out in the model legume Medicago truncatula, has disclosed for the first time in plants the presence of the small gene family Tdp1 (Tyrosyl-DNA phosphodiesterase) and the TFIIS-like gene. MtTdp1a, MtTdp1b, and MtTFIIS-like genes are up-regulated in response to oxidative/genotoxic stress caused by exposure to heavy metals and osmotic stress, thus confirming their key role in the DDR activated under adverse environmental conditions. These novel gene functions have been investigated using gene silecing approaches, RNA-Seq analysis and genotoxicity tests (Comet Assay-Single Cell Gel Electrophoresis, DNA diffusion).
Molecular profile of seed quality. Aim of the research is the identification of molecular indicators of seed quality (vigor). DNA repair pathways are activated during the early phase of seed germination (imbibition), when the so-called ‘pre-germinative metabolism’ is triggered. A working system has been established, using imbibed seeds from model plants (Legumes, Medicago truncatula; Solanacee, Petunia hybrida) in order to validate the role of novel DNA repair genes during the pre-germinative metabolism. A translational research project has been subsequently started focusing on commercially relevant horticultural species and cereals, in collaboration with Seed Companies (ATLAS srl, APSOVSEMENTI srl, Bejo BV, Hoopmann Group), Breeders (NIRP International), and with the Research Institutes CREA-SCV (S. Angelo Lodigiano, LO), CREA-ORL (Montanaso Lombardo, LO), and CREA-FSO (Sanremo, IM).
DNA repair mechanisms induced by ionizing radiations (IR) in plant cells: basic and applied (in vitro breeding) aspects. DNA repair pathways and the antioxidant response are investigated in plant cells characterised by natural radio-tolerance (Petunia hybrida, Medicago truncatula) irradiated with gamma-rays LDR (Low Dose Rate) and HDR (High Dose Rate) in order to identify the key molecular players of LD(Low Dose)/LDR response in planta. The plant response to IR-induced genotoxic damage results in the activation of different DNA repair mechanisms, some of them are ‘error-prone’. Consequently, there are some DNA repair enzymes which can introduce changes in the original DNA sequence while removing the lesions. This mutagenic effect can be modulated, based on the physical parameters (total dose and dose rate) of irradiation treatments as well as on the qualitative/quantitative features of the DNA damage response (DDR) specific for each plant genotype/variety/cultivar. A deeper understanding of the molecular components of DDR involved in the response to LDR and HDR ionizing radiations is an essential requisite for designing improved breeding protocols of ‘elite’ varieties.
CREA-FSO, Unità di Ricerca per la Floricoltura e le Specie Ornamentali (Sanremo-IM), Dr. Annalisa Giovannini.
CREA-SCV, Unità di Ricerca per la Selezione dei Cereali e la Valorizzazione delle Varietà Vegetali (S. Angelo Lodigiano-LO), Dr. Patrizia Vaccino.
CNR-IPSP, Bari, Dr. Paola Leonetti
Instituto de Tecnologia Quimica e Biologica (ITQB)-Università Nuova di Lisbona (Portogallo). Dr. Susana Araujo, Dr. Pedro Fevereiro.
Institute of Experimental Botany, Praga. Czech Academy of Science. Dr. Karel Angelis.
Institute of Plant Genetics, Poznan. Polish Academy of Science. Dr. Jorge Paiva.
ICGEB, New Delhi (India). Dr. Narendra Tuteja.
National Technical University, Atene (Grecia). Dr. Alexander Georgakilas.
National Institutes for Quantum and Radiological Science and Technology, Gunma (Giappone). Dr. Ayako Sakamoto
Prof. Silvia Garagna, Prof. Valeria Merico, Prof. Carlo Alberto Redi, Prof. Maurizio Zuccotti
The main research objective is the understanding of the factors involved in the differentiation of eggs and sperm, using the house mouse as a model organism. These differentiation processes are also studied when chromosomal or enviromental conditions (e.g. xenobionts) alter both gametogeneses.
We aim at identifying the markers of the ovarian follicle maturation (oocytes and follicle cells), both in vivo and in a 2D or 3D culture system. A Systems Biology approach that associates high throughput methodologies (transcriptomics, genome-wide DNA-methylation, miRNA) with advanced computational approaches is used to bring out the molecular networks that identify and regulate follicle development and the acquisistion of the egg’s developmental competence.
As for the male gamete, our research is focused on the cellular and molecular mechanisms that alterate meiotic progression and sperm differentiation.
Our studies have also an evolutionary perspective. To this regard, both oogenesis and spermatogenesis are studied in the armadillo, pertaining to the ancient ammalian superorder of Xenarthra.
Stem cell biology
Prof. Silvia Garagna, Prof. Valeria Merico, Prof. Carlo Alberto Redi, Prof. Maurizio Zuccotti
To understand the contribution of the environment to the processes of cell differentiation, we study the differentiation of pluripotent stem cells (i.e., embryonic stem cells) into cardiomyocytes. According to the World Heath Organisation, cardio-vascular diseases of environmental origin are a health priority. Recent studies have underlined the contribution of xenobiotics, such as dioxin or arsenic, to induce an alteration of the process of cardiomyocyte differentiation and function. Using cytological and molecular markers, together with systems biology tools, we have developed a differentiation platform to monitor the several steps of cardiomyocyte differentiation with the aim of identifying those signaling pathways that are altered by the presence of environmental contaminants (chemicals: e.g., dioxin, PCBs, arsenic; or physical: e.g., ionising radiations).
The research activity is documented by 140 publications on indexed international scientific journals or chapters in international books.
Modulation of transcription
Prof. Marco Biggiogera
The mechanisms at the basis of the control and modulaiton of transcription are studied at electron microscopy, with particular emphasis on the action of active molecules (drugs, hypometabolizing agents) and an epigenetic control mechanisms (DNA and RNA methylation and posttraslational histone modificaitons). Cell culture systems and tissue models offer physiologicalexamples for studying transcription and splicing by means of immunocytochemical and hybridization techniques at the ultrastructural level. The induction od a hypometabolic stasis in these systems, moreover, is the basis for a study aimed at controlling the metabolism in organs like liver in view of prolonging the survival time of the explanted organ before reimplantation.
Collaborations: Dr. Ansgar Bruning, Dept. of OB/GYN, Molecular Biology Laboratory, University Hospital Munich; Prof. Manuela Malatesta, Dipartimento di Neuroscienze, Biomedicina e Movimento, Università di Verona, Dr. Hiroshi Kimura, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
Study in vivo and in vitro of cytotoxic effects of cisplatin and new platinum compounds: morphological and immunohistochemical study of molecular processes of proliferation and cell death
Prof. Maria Grazia Bottone, Prof. Marco Biggiogera
The action of cisplatin and new compounds, the [Pt (O, O ‘- acac) (γ-acac) (DMS)] and Pt (IV) bis (carboxylato), is evaluated in vitro on cell lines from tumors of neural origin and in vivo on the postnatal development of areas of the central nervous system in rats (hippocampus and cerebellum). The toxicity of treatment is identified with the activation by the cells of cell death with the consequent alteration of the cell cycle and of cell components such as the cytoplasmic organelles.
In the study we are used immunocytochemistry and microscopic techniques, western blotting and cytometric techniques.
Collaborations: Prof. FP. Fanizzi, Dipartimento di Scienze e Tecnologie Biologie ed Ambientali (DiSTeBA) dell’Università del Salento, Lecce; Prof. Domenico Osella, Dipartimento di Scienze e Tecnologie Avanzate, Università del Piemonte Orientale “Amedeo Avogadro”, Alessandria.
Histological and histochemical study in situ of the anticancer drugs cytotoxicity locally conveyed by means of fibrin gel or nanoparticles
Prof. Giuseppe Bertone
Surgical removal of neoplastic lesions is often the treatment of choice, but complete eradication is achieved only rarely, with probable recurrence of the primary tumor and / or formation of secondary metastases. Adjuvant systemic chemotherapy becomes mandatory as a complement to surgery. Through systemic therapy, however, it can be problematic to get a good distribution of the drug in the lesion site and, in parallel, the toxic effects due to its accumulation in normal tissues can become so severe as to force to stop the therapy itself. In such conditions the local and targeted release of antineoplastic agents becomes essential, although many technical obstacles must be overcome, especially when the lesions are located in regions difficult to access. With this project in collaboration with an oncology surgeons team we intend to study in a rat experimental model the implementation of alternative methods to convey to the tumor site antineoplastic drugs and/or experimental/in clinical use nanoparticles with antineoplastic activity, avoiding their systemic administration. This method is based on the direct incorporation of chemotherapy drugs into biomatrix implantable on-site and/or by incorporation into sub-microscopic particles (liposomal nanoparticles) able to modulate the release of drugs. It will be implanted experimental breast cancer Walker 256 in Sprague-Dawley rat model. The adopted anticancer drugs will be those of choice in these types of cancer: cisplatin and doxorubicin as such, embedded in fibrin gels ( these matrix are already commonly used by surgeons as healing fast acting undergoing surgical resection of the masses tumor) or in the liposomal nanoparticles. In addition to histological and histochemical verification of differently conveyed anticancer drugs action, it also intends to assess the cytotoxic effects affecting heart, kidney, liver and spleen. In a second step we intend to evaluate with the TUNEL test the percentage of apoptotic cells within the tumor masses.
In collaboration with: Dr. Maurizio Viale, IRCCS Azienda Ospedaliera Universitaria San Martino – Istituto Nazionale per la Ricerca sul Cancro, Dip. Terapie Oncologiche integrate – U.O.C. Bioterapie 16132 Genova, Italy
Team members: Mauro Torti (full professor), Ilaria Canobbio (assistant professor), Gianni Guidetti (assistant professor), Caterina Visconte (PhD student), Marta Zarà (PhD student).
Research activity encompasses fundamental aspects of transmembrane signalling in platelets. Circulating blood platelets have a crucial role in haemostasis, thrombosis, and in many other processes, such as inflammation, neurodegeneration, and cancer metastasis. Understanding the exact contribution of platelets to these events is a big challenge for the future and may provide promising opportunities in biomedicine.
Analysis of platelet signal transduction pathways in thrombosis and haemostasis
The understanding of the mechanisms supporting platelet activation is critical for the identification of novel pharmacological targets for thrombotic diseases, which represent a major cause of death in western countries. In this context, our research is focused on the following aspects:
role of tyrosine kinases (Src, Syk, Pyk2, FAK) and protein phosphorylation in platelet adhesion, activation and aggregation
contribution of different phosphatidylinositol 3-kinase (PI3K) isoforms in platelet activation and analysis of their regulation
signal transduction pathways downstream of integrins, G protein-coupled receptors and ITAM-bearing receptors
mechanisms of platelet activation induced by environmental and engineered nanoparticles
Analysis of amyloid precursor protein (APP) metabolism and function in platelets: a novel link between hemostasis, thrombosis and Alzheimer’s disease
Alzheimer’s disease (AD) is the most invalidating dementia in the elderly and is characterized by the accumulation of amyloid peptides in brain parenchyma and cerebral vessel walls. Amyloid peptides derive from the metabolism of amyloid precursor protein APP. Platelets express high level of APP and release amyloid peptides in the circulation upon stimulation. Our research is mainly focused on:
define the effects of amyloid peptides in plasma. We have demonstrated that amyloid peptides are able to activate platelets and to promote a chronic inflammation state. A collaboration with Pula Lab, University of Bath (UK) is ongoing to study the possible effects of amyloid peptides on endothelial cell activation
define the role of platelet-derived amyloid peptides in AD onset and progression. We will use transgenic mice that overexpress APP and amyloid peptides (3xTgAD) and will evaluate the level of platelet activation and chronic inflammation. In addition, we will analyse the ability of platelet-derived amyloid peptides to cross the brain blood barrier and deposit in the brain
investigate the role of APP in platelet physiology and hemostasis. Using platelets isolated from APPKO mice (that do not express APP) and we have demonstrated that APP plays a crucial role in platelet adhesion and thrombus formation.
Analysis of the contribution of platelets and platelet-derived microparticles to cancer metastasis
Metastasis is strongly influenced by host-cancer interactions and it has been demonstrated that platelets are key players in cancer spread as their depletion, in thrombocytopenic patients or animal models, is associated to reduced metastasis. This suggests that also the pharmacological inhibition of platelet activation could represent a novel approach to control metastatic diffusion.
The goal of our study is the understanding of the molecular mechanisms behind the contribution of platelets to cancer spread. In particular, our attention is focused on the role of platelet-derived microparticles (PMPs), which are small vesicles released upon platelet activation and represent important carriers of biological signals. With this research we aim to:
- analyse the ability of PMPs to alter the invasive potential of cancer cells
- investigate the molecular mechanisms for PMPs modulation of the metastatic properties of cancer cells
- analyse the effect of platelet pharmacological inhibition on the pro-metastatic properties of PMPs
- evaluate the pro-metastatic effects of PMPs in vivo
Research group collaborations
Mitsuhiko Okigaki (Department of Cardiovascular Medicine,Kyoto Prefectural University of Medicine, Kyoto, Japan )
Emilio Hirsch (Molecular Biotechnology Center-MBC, University of Turin, Italy)
Carlo Balduini, Patrizia Noris, Alessandro Pecci (IRCCS Policlinico San Matteo, Pavia, Italy)
Maria Enrica Tira (Department of Biology and Biotechnology, University of Pavia, Italy)
Giampaolo Minetti (Department of Biology and Biotechnology, University of Pavia, Italy)
Giordano Pula (Department of Pharmacy and Pharmacology, University of Bath, UK)
Luciaanna Stivala, Ornella Cazzalini, Paola Perucca (Department of Molecular Medicine, University of Pavia, Italy)
Satya P. Kunapuli (Departments of Physiology and Pharmacology and Sol Sherry Thrombosis Research Center, Temple University, School of Medicine, Philadelphia, Pennsylvania)
Maries Van den Broek (Institute of Experimental Immunology, University of Zurich, Switzerland)
Methods and Techniques
Blood cell purification (platelets and neutrophils). Isolation and characterization of microparticles and microvesicles. Protein analysis (SDS-PAGE, western blotting, chemiluminescence, spectrophotometry, spectrofluorometric analysis, flow cytometry). Adhesion assays under static conditions and under flow. Microscopy (phase contrast and fluorescence microscopy). Molecular biology techniques, DNA and RNA extraction and analysis, PCR. Protein purification (expression, ion-exchange, affinity and size-exclusion chromatography, HPLC, FPLC). Cell culture and transfection, analysis of cell migration, invasion, proliferation, metalloproteinases release. Genetically modified animal models (Mus musculus): Pyk2-KO, PI3Kb-KD, APPKO, 3xTgAD, PLCg2-KO
Red blood cell biochemistry
Group leader: Prof. Giampaolo Minetti
Collaborators: Dr Cesare Achilli, Post-doc; Dr Annarita Ciana, Post-Doc; Anjali Gaur, PhD student of the RELEVANCE project, Marie Skłodowska-Curie Innovative Training Networks, Horizon 2020.
Red blood cell biochemistry
The scientific interests of the research group deal mainly with the basic properties of biological membranes, focusing on the erythrocyte membrane as a classical model. The biochemical properties of normal, pathologic, in vivo aged and stored erythrocytes and of erythrocytes produced under conditions of neocytolysis are investigated. Erythrocyte membrane proteins and lipids are studied using biochemical and biophysical methods (electrophoresis, western blotting, fluorescence microscopy, electron paramagnetic resonance, omega-alkynyl fatty acid analogs and “click” chemistry to study protein acylation) to elucidate the structure and function of various membrane domains, such as the membrane skeleton, lipid rafts, membrane vesicles, and their interplay. High-resolution separation of erythrocytes of different age is implemented in his lab to study in vivo aged erythrocytes.
Methionine sulfoxide reductases
The oxidation of methionine residues often results in the loss of biological activity of the affected protein. Methionine sulfoxide reductase (Msr) enzymes are an important repair system for such oxidative damage. While studying Msr activity in human neutrophils, we observed a stereospecific reduction of only one of the two sulfoxides of L-Met. Our original suspect that two classes of Msr with opposite stereospecificity might exist in nature is now confirmed by several reports in the recent literature. In that study, a new method was proposed to assay Msr activity, which has been successfully adopted by several authors ever since. Neutrophils are cells of the innate immune system that engulf and kill invading pathogens by producing reactive oxygen species (ROS). ROS may induce auto-oxidation of the neutrophil structures. Msr are highly expressed in neutrophils, probably as a protective and/or repair system, in particular the selenoprotein MsrB1 whose activity and properties are actively investigated in his research group.
Blood cells as tools for assessing the toxicology of nanomaterials
A new research line involves the use of blood cells as tools for toxicological studies of nanoparticles.
Proteomics/Metabolomics in the investigation of medical disorders
Group leader: Prof. Paolo Iadarola
With the advent of proteomics, the screening of proteins as potential biomarkers has achieved important progresses. Detection and identification of proteins in different organs/tissues, with the aim of understanding whether they represent an attractive tool for monitoring alterations in these districts, is currently an area of increasing interest.
Clinical proteomics involves the application of proteomic technologies on clinical specimens such as biological fluids. In this context the current work of our laboratory is focused on the identification in biological fluids (sputum, exhaled breath condensate, broncoalveolar lavage fluid), lymphoblastoid cells and cellular extracts of biomarkers of disorders of different origin. In particular the following three lines of investigation are carried out:
- Study of proteomics/metabolomics of lung diseases (chronic obstructive pulmonary diseases, α1-antitrypsin deficiency, sarcoidosis, bronchiolitis obliterans syndrome)
- Proteomic analysis of lymphoblastoid cells from patients affected by a rare neurodegenerative disorder (Nasu-Hakola disease).
- Proteomic analysis of salivary glands and ovaries from the tick Ixodes ricinus.
Genetic predisposition to gastrointestinal cancers
Principal Investigator: Prof. Guglielmina Nadia Ranzani
Collaborators: Raefa Abou Khouzam (PhD student), Gianluca Tedaldi (PhD student), Monica Marabelli (postdoctoral fellow)
The main aim of our research activity is the detection and functional characterization of genetic lesions associated with the development of gastrointestinal tumors in families with hereditary syndromes. These syndromes include HNPCC (hereditary non-polyposis colorectal cancer), FAP/MAP (familial adenomatous polyposis/MUTYH-associated polyposis) and HDGC (hereditary diffuse gastric cancer).
Genetic testing of predisposition genes can establish the presence of cancer predisposing alterations or the absence of any specific changes. However, the finding of variants of uncertain significance (often called VUSs), is another possible result that can complicate rather than improve the risk assessment process. The functional significance of VUSs is investigated by different approaches, including in silico analyses, functional assays, gene expression analysis and characterization of splicing products.
Since genes known to be associated with the above syndromes do not explain all selected families, our research group is part of a collaborative study aimed at searching for new disease-genes by NGS approach (cancer-gene-panel and exome sequencing).
Findings from numerous studies have shown that the genetic component plays a crucial role not only in syndromic and familial cases, but also in the development of the so-called sporadic cancers. Indeed, Genome Wide Association Studies (GWAS) have recently detected genetic variants at different loci that can modulate the risk of colorectal cancer. We are interested in investigating if some low-penetrance alleles that have been associated with colorectal cancer can increase the risk of both pre-neoplastic lesions and cancer also in the Italian population.
Collaborators: Tiziana Venesio (Istituto Oncologico-IRCCS, Candiolo-Torino), Costanza Alvisi (Fondazione IRCCS-Policlinico San Matteo, Pavia); Daniele Calistri e Chiara Molinari (Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori-IRCCS, Meldola-FC); Bernardo Bonanni (IEO-Istituto Europeo di Oncologia, Milano); Natalia Pellegata (Institute for Diabetes and Cancer IDC Helmholtz Center Munich, Germania)
Somatic genetic lesions associated with progression of gastric and colorectal cancers
Principal Investigator: Prof. Guglielmina Nadia Ranzani
Collaborators: Raefa Abou Khouzam (PhD student), Gianluca Tedaldi (PhD student), Monica Marabelli (postdoctoral fellow)
Beside genetic factors predisposing to gastrointestinal cancers, we are analyzing somatic lesions involved in cancer progression.
In particular, we are interested in analyzing: somatic lesions at different loci in sporadic colorectal cancers (with/without epatic metastases) with the aim of identifying prognostic markers that can be used in clinical practice; somatic lesions in cancer samples of patients with MAP syndrome (MUTYH-associated polyposis), in order to characterize the carcinogenic process associated with Base Excision Repair system defects; somatic lesions of CDH1 (E-cadherin) gene in sporadic gastric tumors, with focus on canonical and non-canonical transcripts that can contribute to cancer development.
Collaborators: Tiziana Venesio (Istituto Oncologico-IRCCS, Candiolo-Torino), Costanza Alvisi (Fondazione IRCCS-Policlinico San Matteo, Pavia); Daniele Calistri e Chiara Molinari (Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori-IRCCS, Meldola-FC); Bernardo Bonanni (IEO-Istituto Europeo di Oncologia, Milano); Natalia Pellegata (Institute for Diabetes and Cancer IDC Helmholtz Center Munich, Germania)
Genetics of taste perception
See topic 7 under “Genomics of human and animal populations”
Identification of diagnostic markers and therapeutic preclinical studies in celiac disease
(Group leader: Prof. Sergio Comincini)
The celiac disease is a chronic inflammation of the small intestine, triggered by the ingestion of gluten in genetically predisposed individuals. It is characterized by a clinical picture very variable, ranging from profuse diarrhea with marked weight loss, extra-intestinal symptoms, the association with other autoimmune diseases. Untreated celiac disease can lead to complications too dramatic, such as intestinal lymphoma. Celiac disease can be identified with absolute safety through the serological test and biopsy of the duodenal mucosa during endoscopy. The gluten-free diet is the only currently available therapy and should be carried out rigorously for life.
The theme is divided into two distinct phases: the first, is expected to identify molecular markers isolated from the blood of patients with celiac disease and related pediatric controls that will be collected at the S.C. of Pediatric Surgery of the Fondazione IRCCS Policlinico San Matteo. Among the molecular markers of interest, they will be isolated and quantitatively measured the circulating microRNAs, the particular those able to modulate positively/negatively the degradative processes of the cell functionality, including that autophagic one.
Cellular models are also used for studies in celiac disease, with whom develop preclinical therapeutic protocols based on the possibility of modular molecularly or a pharmacologically degradative right of the cell process, autophagy, can potentially degrade the gluten, in particular by reducing the tendency to form larger molecular aggregates.
External collaborations: Prof. Mauro Bozzola, Dr. Cristina Meazza, Dr. Sara Pagani (Maternal and Child Department, IRCCS San Matteo Pavia); Prof. Gloria Pelizzo (Department of Clinical Surgical, Fondazione IRCCS San Matteo Pavia)