Cell Model Systems Summer School (CMS3)
|Event Date/Time: Jun 05, 2011||End Date/Time: Jun 10, 2011|
Â· Facilitate an effective sharing and dissemination of new and innovative research ideas, strategies, focal points on cell model systems to promote genomic research and bioinformatics that are starting points for instance of the systems biology and future research in this field.
Â· Promote communication between scientists and allow a network development between scientists and students from several world countries.
Â· Create a platform for discussing research experiences in a very open atmosphere Students have the opportunity to interact with speakers in a full time appointments, during the lessons and afterwards at the accommodation provided at the hotel close to the summer school.
Â· Promote joined and integrated approaches from basic research and new product developments
Â· Provide knowledge in a concentrated form in a planned compendium book for all interested scientists and students as a up to date teaching tool
Â· Make top level equipment and instrumentation (optical and electronic microscopy, Ultra- Vacuum, microsystems and microelectronics, techniques in model membrane, bioinformatics) for characterizing and modelling cells available to a wide interdisciplinary community at European and International level.
* First summer school with theoretical lectures and practical exercises during the 5 days course.
Â· First summer school with an interdisciplinary character in comparison to others at one topic (e.g., â€œBioinformaticaâ€ University of Bologna, â€œGenomic vegetalâ€ European Networking Summer School).
* Training of 70-80 young international post-doc along 5 years in multidiscipline: physic, engineering, chemistry, biology, medicine, mathematics
Â· Developing of new small and medium enterprises at biotechnological level in medicine and biology.
These goals sound very ambitious and idealized. However, the basis for the cooperation is trust in the partner. This trust has to be developed step by step and is mainly founded on personal contacts. The summer school is a stepping-stone towards this. It brings together potential partners and through the personal contact creates an important basis for the future, trust-based cooperation. The developing partnership comprises â€œteachersâ€, â€œstudentsâ€ as well as the group of organizers. This partnership will be expanded step by step.
Models could help speed discovery on new drugs. Modelling predictions are one of the many inputs into the decision making process in the pharmaceutical industry. To develop these goals a synergy among different approaches and models is necessary:
1) Proteomics tools (protein identification and characterization, DNAÂ® Protein, post-translation modification prediction, topology prediction, primary structure analysis, secondary structure prediction, tertiary structure, sequence alignment, phylogenetic analysis, biological test analysis) [E. H. Davidson et al. Science 295: 1669-1677, 2002 â€œA genomic regulatory network for developmentâ€ . Review]
2) Membrane model systems (Since lipid vesicles were first described by the British scientist Bangham in 1964 both industry and academia have had high expectations for their practical application. Drug delivery is one of their main application though recently a vaccination with influenza virosomes has been proposed. However lipid vesicles are powerful tools especially in basic research including topics like lipid biophysics, membrane structure and dynamics, the "raft" concept, lipid-protein interaction, as protocell models, as template for polimerizzation, as biomembrane model systems, etc.)
3) Advanced sensors (micro-electro-mechanical systems, thin film technology used in pattern recognition techniques, detection of chemical, mechanical and physical parameters)
4) Precise analytical methods (high sensitive assays for identifying and quantifying the concentrations, fluxes and interactions of various molecules at high resolution both in space and time, single-molecule measurements, femto-lasers visualization of molecular interactions) [Stochastic gene expression in a single cell. Science 297:1183-1186, 2002]
5) Enhanced imaging capabilities (imaging technology to monitor drug therapy in cancer patients, improve the treatment of addiction, and advance the understanding of inflammation, computer tomography (CT), positron emission tomography (PET), ultrasound and optical imaging, new probes for molecular imaging, computing lab for advanced image analysis, magnetic resonance imaging (MRI), magnetic resonance spectroscopy (MRS), bioluminescence, diffraction advanced imaging (DAI).
6) Sophisticated computational tools (development and application of effective algorithms for analysing large sets of often diverse data, for example Raw genomic DNA sequences require analysis to reveal the various functional domains, and protein sequences are most useful when inferences about structure and function can be obtained reliably; expression arrays offer an unprecedented global view of RNAs levels and their dynamics, dynamic molecular simulations, stochastic dynamic to model evolution and reproduction processes, motif recognition of biological networks. Recently some progress has been made in the automated analysis of biomedical information in databases, as an extension of general data miming techniques. In the case of scientific journals context analysis Hoving et al. have presented an interesting technique which enables significant biological relationships to be established on the basis of the content of tens millions articles (Nature Genetics 28:21-8, 2001 see http://www.nature.com/ng/journal/v28/n1/pdf/ng0501_21.pdf). As an example, postulating a functional transitive property of gene names in publications, if names A and B are present in one article and B and C in another, then a functional relationship between A and C is formed. In this way gene relationships, hitherto unknown, have been determined. With the adoption of the more advance context analysis techniques now available, it is likely that many more aspects can be analysed bringing unforeseen knowledge from information already at hand, but whose immense size makes it too difficult to handle.
Expertise at CNR Research Establishment
The research Area of CNR located at Tor Vergata-Rome will provide an unique environment in which top level researchers will training the students in referring specifically to the previous listed points 2, 3, 5 and 6:
Â· Membrane model systems
Lipid vesicles can easily be prepared from a number of different lipids that are present in biological membranes or a number of different non-natural, fully synthetic surfactants. Membrane proteins can be reconstituted in liposomes, allowing the investigation of membrane embedded proteins in a biomimicking environment, outside the living cell. The size of the vesicles prepared can be controlled to some extent, varying between less than 50 nm and more than 10 Î¼m, allowing studies of certain fundamental aspects of organelles and cells as a whole.
Â· Advanced sensors
Development of new chemical and biochemical membranes for advanced sensors (Interdigital Fingers metal-based, Chem-Field Effect Transistors on silico, glass and plastic, Multi-Channel-Quartz-Microbalances). Different applications of sensors based on mimicking natural system. For example, metal-porphyrin, polymeric, glycopeptides, nanobed membranes are developed with technologies on thin film (evaporation under vacuum, dipping, casting and spray casting, self-assembling, electropolimerization). It is equipped with a Clean Room for microfabrication processes and thin film technologies, such as photolithography, evaporation, sputtering, chemical and physical techniques for wafer etching.
Â· Advanced technology and imaging
This include the development and use of Scanning Probe Microscope, especially AFM and SNOM, to material science and life science problems. The increasing prestige of these techniques is due to their ability to provide optical (transmission, fluorescence and reflectivity) and topographical characterization at the nanometer scale of cellular and biomolecular samples that can be performed, in principle, also in physiological environment. Investigation of the biomechanical properties of macromolecules and studies of the dynamical evolution (from minutes to hours) of biological systems can be performed as well. In particular, this latter task includes the capability to perform â€œex vivoâ€ tests of the effect of drugs or environmental agents on suitable model systems. Such tests are to be considered useful tools to be employed after the identification of novel proto-drugs.
Â· Advanced Scientific computer programming
Number crunching computer programming techniques and object oriented languages suited for scientific applications. Implementation of algorithms for efficient data analysis, reduction and storage. Stochastic and probability-based modelling of biological processes and more generally in interactions of complex systems.
The CMS3 summer school will impart the latest theoretical and practical aspects in the field of model systems of the cell and its components.
In order not to limit this knowledge to the circle of participants of the summer school, we have published a book containing all lectures, detailed experimental instructions and computer exercises (bioinformatics) in 2009. Beyond this a website has been create for the initial course in 2008 with its own domain name (i.e. www.cms3.cnr.it) Cell Model System Summer School.
Applicants for a specific course apply with a short scientific CV. Equal consideration will be given to female and male participants. The accommodation at one place close to the summer course location in hotel will provide the possibility to get to know each other better on a personal level.
The number of participants at the summer school will be limited to 15 young investigators, hopefully from many different countries. The limitation is needed to allow the combination of both theoretical lectures and practical exercises during the 5 days course. The summer school is primarily directed to participants from all over the world with a special focus on third countries.
The formation of a wide network and the training of young investigators are the mission of the project. The lectures however are open to all persons interested. The selection of the participants will be made by a steering committee (program board about 6 people). The program board will be renewed by approximately 1/3 of its members on an annual basis after a summer course took place. The renewing of the board will guarantee to incorporate new members, a flexible and living structure, to recognize the latest developments in the field and will keep the board operational all the time.
The CNR Research Establishment at Tor Vergata-Roma, where the School will be held, is located near the University Campus of Tor Vergata. CNR Research Establishment offers a complete range of services to its personnel and to visitors, including library, canteen and a bus service to the Rome Metro Line A. Tor Vergata is one of the largest CNR research establishments and is made up of several Institutes. Four of them are involved in the management of the present project. The organizing committee will be responsible for the local arrangements and the local organization of the summer course and is constituted by the researchers at the following CNR Institutes:
-IFT The Institute of Translational Pharmacology has 40 researchers. Research activities of the IFT focus on mechanisms of insurgence of human disorders, particularly of neoplastic, immuno-degenerative, infective and neurogenetic diseases, and on the development of innovative preventive/therapeutic strategies, also considering the translation to clinic. Particular competence resides within the drug discovery and the study of new chemical entities for different therapeutic areas. The final goal is to apply the scientific knowledge acquired for developing new technological platforms implementing the current diagnostic, preventive and therapeutic tools. Specifically for the scope of the school studies of membrane model systems are developed by the Director of the School Dr. Alfonsina Ramundo-Orlando. IFT provides all equipments and instrumentation for studies on molecular biology, biochemistry and electronic-confocal microscopy.
-IMM The Institute of Microsystems and Microeletronics is devoted to develop of electromechanic microsystems (MEMS) based on semiconductor and magnetic materials. Modelling software, technologies on thin-film. The research group of IMM collaborate with other CNR groups involved on activity R&D on materials and microwave devices.
-ISM The Institute of Structure of Matter is a leader institution in the designing and building of Scanning probe microscopes, namely, Atomic Force, Scanning Near-field Optical, and Scanning Tunneling Microscopes for material science and biology applications. Also application concerning the study of surface and interfaces between molecules deposited in UHV conditions on epitaxial substrates are performed. ISM provides labs for spectroscopy (VIS, NIR, UV, X-rays) and microscopy characterization of life science and material science samples.
-ISC The Institute of Complex Systems aims at achieving a quantitative approach to the study of complex systems, where large multi-component interacting units can give rise to the emergence of many different, counter-intuitive, collective properties. This concerns not only physics, but also even biological, social, economical and informatical systems. The focus is presently on critical and self-organized systems, complex network, and non-linear systems and on the realization and characterization of new superconducting materials. The research activity is both theoretical and experimental, the latter making large use of microscopical and spectroscopical techniques which employ different kind of radiation, like elasticity, light, electrons, neutrons and X rays.
Themes and Speakers
Models of protocells:
-aspects of reactivity among vesicles
-Fabio Mavelli (Chemistry Dep. Univ. Bari, Italy)
-Thomas Gutsmann (Medical Biochemical Research Center, Borstel, Germany)
-Peter Walde (ETH-Zurigo, Switzerland)-Vesicles as biomimetics systems
Models of channel proteins
-Patrica Bassereau (Institute Curie-UMR CNRS,Paris, France)
Enzyme Reaction in Compartments
-Pier Luigi Luisi (UniversitÃ Roma3)
Biomedical applications: nanocapsules & nanocarriers
-Katharina Landfester (Max-Plank, Mainz, Germany)
Novel approaches in drug screening: The case of emulsion w/o
-Christoph Merten (EMBL-Heidelbergh,Germany)
-Krishna Persaud (School of Chemical Engineering and Analytical Science.University of Manchester,UK)
-Ali Eftekhari (Avicenna Institute of Technology, Cleveland, Ohio)
Models of channel proteins: molecular simulation
-Isaiah T. Arkin (Alexander Siberman Inst Jerusalem, Israel)
Magnetic brain activity
-Christopher Braun (University Trento,Italy)