Dipartimento di Medicina e Chirurgia
Università degli Studi di Perugia

PhD Students

Clinical Units/Lab facilities/Research equipment

The Clinical Units where the Curriculum in Pathology and Clinic of Atherosclerosis and Aging is based are the Section of Internal Medicine, Angiology and Arteriosclerosis Diseases (MIAMA) of Perugia, the Section of Internal Medicine of Terni (MIT), the Section of Gerontology and Geriatrics of Perugia, and the Section of Microbiology and Clinical Microbiology of Perugia.

At the healthcare level, MIAMA includes 60 beds, MIT 26 beds, while Gerontology and Geriatrics consists of 24 beds in the Geriatrics SC and 24 beds in the Orthogeriatrics SS. On a clinical level, these sections deal with the main pathologies of internal medicine interest with particular reference to cardiovascular ones with evaluation of heart rate variability, metabolic syndromes, hyperlipemia, arterial hypertension with evaluation of organ damage, geriatric syndromes - such as cognitive deterioration, falls and risk of fractures, delirium-, multimorbidity, and physical and cognitive frailty.

All units carry out clinical research using instruments such as color Doppler ultrasound for the non-invasive evaluation of the arterial and venous vascular system in different body areas, for the evaluation of endothelial function expressed through flow-mediated vasoactivity of the brachial artery, and for the evaluation of cardiac damage; computerized system for quantitative and qualitative analysis of arterial vascular morphological damage, both in the form of measurement of the intima-media thickness and of the atheromatous plaque, also in its aspects qualitative; applanation tonometry for the study of the stiffness of the arterial wall, periungual capillaroscopy and Laser-Doppler flowmetry for the study of the microcirculation, color-Doppler ultrasound for the evaluation of hepatic and renal parenchymal damage, for the distribution and quantification of adiposity, impedance measurement for the anthropometric evaluation , Shear-Wave elastography for the evaluation of parenchymal elasticity, 24-hour blood pressure monitoring (ABPM), electrocardiographic recording according to Holter, measurement of heart rate variability using a computerized system. There is also a computerized web-based system for data collection in the clinical evaluation of subjects with cognitive disorders (Gerico 3.0).

The individual structures, thanks to the multidisciplinarity that characterizes them, have for years been the site of clinical trials with innovative, pharmacological, and non-pharmacological therapies in collaboration with specialized companies or with spontaneous studies supported by international research projects (FP6, FP7, Horizon 2020, IHI) and national (Ministry of Health, Ministry of Research, AIFA, Perugia Foundation, CARIT)

The clinical centers include the following laboratories: 1) Aging Research Center - Gerontology and Geriatrics Laboratory (building C, floor 1) with instruments such as Multiplex Immunoassay System (Bioplex 2000, wash station and software); ELISA analysis system (reader, wash station, software); HPLC system with coularray electrochemical detectors and analysis software; HPLC system with UV detector and analysis software; HPLC system with fluorescence detector; spectrophotometer; optical microscopes; protein electrophoresis systems; 2) MIAMA Laboratory (Building B, Floor 2) with nephelometry instruments; ELISA; RT-PCR; 3) MIT Laboratory (Terni University) Carotid Studio QUIPU Srl system (Pisa); PowerLab, AD Instruments, Sydney.

The Microbiology and Clinical Microbiology Section has valuable experience in the field of innovative diagnostics of time-dependent, multi-drug resistant organisms (MDRO), and emerging viral infections. It represents the leading Regional group for Clinical Microbiology and is the Regional reference laboratory for the surveillance of MDRO and Mycobacterium spp. infections, and for the molecular diagnostics and genome sequencing of respiratory viruses and emerging pathogens, including SARS-CoV-2 virus. The laboratory is fully equipped with advanced molecular technologies for clinical microbiology, molecular biology, cell biology, and bioinformatics research. The Laboratory is also equipped with a biosafety-level 3 section.

All laboratories have instruments for preparing and storing biological samples (centrifuges, refrigerators, ultrafreezers).

Contributing to the activities of the Curriculum in Neurosciences, the Section of Neurology, the Section of Psychiatry, Clinical Psychology and Psychiatric Rehabilitation, the Neurophysiology Laboratory, and experts in Applied Physics.

The Section of Neurology of the University of Perugia is a national referral point for the diagnosis and treatment of major neurological disorders such as Alzheimer’s disease, Parkinson’s disease and multiple sclerosis. The section has a longstanding expertise in the context of biomarkers of neurodegenerative diseases being a founding member of the Alzheimer’s Association quality control program for cerebrospinal fluid biomarkers of Alzheimer’s disease and a Center of Excellence of the Parkinson’s Foundation. The Section of Neurology is also included in the Centers authorized to the administration of advanced therapies for the treatment of multiple sclerosis and it is recognized by the Italian Society for the Study of Headaches (SISC) as a center dedicated to the diagnosis and treatment of headache, and by the Italian League against Epilepsy (LICE), as a center dedicated to the treatment of epilepsy in the adulthood.

At Laboratory of Clinical Neurochemistry: •Automated systems for nucleic acid extraction. • qPCR system for APOE determination. • 2 programmable fluorometers for enzymatic activity determinations and seed amplification assays. •  2 ELISA readers. • Multiplex Luminex system. • Automated CLEIA platform Lumipulse G1200. • Biofluid biobank constituted by 4 dedicated ultrafreezers containing with cerebrospinal fluid, whole blood, serum and plasma samples collected from more than 4500 different subjects. • Fluorescence Microscope for cell-based and tissue-based assays to identify autoantibodies. • A biological laminar-flow Hood for human sample processing. • 3 refrigerated centrifuges. • A micro-electrode pH-meter. • Artificial Intelligence for Biomedical Application Center (AIBA) unit.

At Experimental Neurology Laboratories: • 4 workstations for electrophysiological recordings. Each unit is fully equipped to measure neuronal electrical properties, synaptic transmission and plasticity in brain slices. They include a microscope with micromanipulators, a temperature-controlled perfusing system for the maintenance of the slices, one amplifier and a stimulation unit. Each setup for electrophysiological recordings is provided with a PC and a DigiData 1322A interface, for on-line and off-line analysis of the results. In particular, two units are dedicated to electrophysiological recordings with sharp electrodes and extracellular recordings, while two units are configured for patch-clamp experiments. Facilities for animal handling, execution of behavioral tests and surgery are available at the University of Perugia. These include a surgery room equipped with a stereotaxic apparatus, infusion pump and instruments for behavioral tests.

Contributing to the activities of the Curriculum in Biotechnology in Human Bone Marrow Transplantation are the Section of Hematology and Clinical Immunology of Perugia, the Hemopathology of Terni, the Section of Gastroenterology and Hepatology and Digestive Endoscopy, and the Section of Dermatology.

The Hematology clinical department at the Perugia University and General Hospital is one of the referral centers in Italy, particularly for patients with hematological malignancies and includes 38 inpatient beds for intensive chemotherapy, advanced cell therapies (CAR-T), autotransplants and allogeneic hematopoietic stem cell transplants, according to standard and innovative procedures which also include the use of regulatory T cells. In our department, in a multi-disciplinary setting, patients undergo fast-track integrated diagnosis and treatment. As an academic hospital, the Perugia General Hospital has a longstanding experience in managing sponsored and non-commercial, academic initiated, clinical trials, including phase-1 studies thanks to the AIFA-certified hematology phase-1 clinical and laboratories research units.

At Center for Research in hEmato-Oncology (CREO): • Automated systems for nucleic acid extraction, for conventional and molecular cytogenetics analysis. • Affymetrix system for DNA and RNA microarray, DHPLC. • Optical and fluorescence microscopy equipped with automatic systems for capture and analysis, • Cell colture laboratories, various leukemia and tumor cell lines. • Cell biology facility certified for the safe handling of lentivirus and antiblastic in dedicated rooms. • Molecular biology and Next Generation Sequencing (NGS) labs with 9 PCR, a digital droplet PCR, NanoDrop, Agilent Tape Station, Illumina (MiSeq e HiSeq), Ion Torrent, and Tapestri for proteogenomic single cell studies. • Proteomic core for protein immunoprecipitation, separation and immunoblotting. • Flow cytometry facility equipped with 2 6–color FACSCanto II, a 12-color LSRFortessa and 2 FACSAria cell sorter. • High Throughput Screening core with a Tecan D300 high-precision drug dispenser, a PIPETMAX automated pipetting system and a Tecan Spark multimode plate reader. • Microscopy lab equipped with a confocal, an epifluorescent and 4 phase contrast microscopes with high performance CCD cameras and deconvolutiond and 3D software. • Hemopatology - Immunohistochemistry (IHC) fully automated lab for FFPE and frozen samples, and equipped with a laser microdissection microscope. • Cellular Manipulation and Cellular Therapies Laboratory, JACIE-certified, equipped with Clinimax Miltenyi and liquid nitrogen tanks for cell preservation. • Bioinformatic Unit

The Bioinformatics Unit provides an interface between the computational infrastructure of the institute and the biology performed within the research groups. The Bioinformatics Unit provides researchers at our Institute and external organizations with services of consultation, organization of next generation sequencing (NGS) and other genomic experiments, NGS data processing, analysis and management, software and database development, bioinformatics training, web-based applications development, secure data storage. The referent of the unit since 2017, Dr. Eng. Giulio Spinozzi has been collaborating for 10 years with the Telethon institute for gene therapy in Milan, and is very careful to nurture talents and transfer knowledge to young people interested in this field.

Contributing to the activities of the Curriculum in Surgical Sciences are the General Thoracic Surgery Section, the General and Oncological Surgery Section, the Oncological Urological Surgery Section, the Clinical Otolaryngology and Head and Neck Surgery Section, and the Diagnostic Imaging Section.

The clinical activities are carried out in the operating block and department/hospital which performs hospitalization and study of the surgical patient of the various specialties. The diagnostic and emergency/urgency department offers spaces dedicated to the instrumental evaluation of the patient. Applied research and hospital diagnostic laboratories collaborate with clinical departments and access/frequency is expected. 

The equipment is: robotic platform with Da Vinci System, hybrid operating room, operating instrumentation for VLS and uni- and multi-portal VATS surgery, 3D printing laboratory and animated simulator, surgical simulator, training laboratory for medical simulation, neuro-sensorial analytical device and program for function recovery, bionic ear, new generation MRI, diagnostic imaging instrumentation with software for multiplanar, 3D imaging reconstruction and radiomics.

Contributing to the activities of the Curriculum in Radiotherapy in Oncology are the Section of Radiotherapy in Oncology, the Section of Ophthalmology, the Section of Clinical, prosthetic, preventive and community dentistry, the Department of Mathematics and Computer Science (University of Perugia), and the Section of Radioterapy in Oncology of University of Pavia.

In particular, the Radiotherapy Unit of the University and General Hospital of Perugia is one of the referral centres in Italy for patients receiving radiotherapy (RT) as a part of the conditioning regimen for allogeneic haematopoietic stem cell transplantation (TBI and TMLI) and as a bridge treatment in patients treated with CAR-T cell therapies. Our Section is also a referral centre for breast and prostate cancer radiation therapy. At our Institution Radiation treatments, systemic therapies concomitant with RT and exclusive medical therapies are prescribed, (e.g. in patients with prostate neoplasia at different stages of disease, castration sensitive or resistant).

All clinical cases are discussed in a multidisciplinary setting. Our Institute regularly hosts physician in training (from European and non-European countries), who wish to improve their knowledge in radiation therapy treatments.

Our Centre is involved in national and international research protocols reagarding both clinical studies and translational research, aimed at investigating the efficacy and toxicity of RT treatments.

The following equipment is available at our Section: CT scan, external beam radiotherapy (EBRT) equipment, such as conventional linear accelerators and tomotherapy; HDR brachytherapy equipment; treatment planning systems; set-up verification systems (Align RT- Vision RT) for breath management.

Other infrastructures available to the PhD students are:

For animal preclinical research activities, a 'Centralized Animal House’ belonging to the University of Perugia is available. It consists of 12 laboratory animal rooms, 5 laboratory animal rooms for indoor breeding, 3 isolation and quarantine rooms and 1 surgical room. It provides high-quality services for basic and translational research in different models of disease including cancer, such as sterile xenografts and maintenance of patient-derived xenografts, efficacy studies, tumor monitoring and imaging, tissue harvesting, animal irradiation. The center, accessible only to users who have received a certification for laboratory animal training courses (academic standard n.18172 of 03/04/07 of the University of Perugia and current law), offers the opportunity to hold and use laboratory animals exclusively for research purposes, use of available equipment and instruments and specific technical and scientific support from the veterinary staff working in the facility.

(https://ceserp.unipg.it/).

The structure of the doctoral school is equipped with a secretariat with staff with IT skills in the various relevant sections and spaces dedicated to training shared with other similar sections (medical simulation centre, animal facility, experimental laboratory on large animal models located at the Department of Veterinary Medicine, etc.).

Doctoral students have access to the Biomedical Library at Medicine Faculty

(https://csb.unipg.it/organizzazione/strutture-bibliotecarie/struttura-medicina/biblioteca-biomedica)