LABORATORIES
Currently, PhD students in Biochemistry have free access to the 9 Research Facilities and Infrastructures available at the Department of Biochemical Sciences and at the Institute of Molecular Biology and Pathology (IBPM) of the CNR which carries out research in the Department.
These infrastructures are included in the Ricerc@Sapienza portal, and listed below:
ANALYSIS OF RAPID PROCESSES (ARP) ROOM T5
PLATFORM FOR THE HYPOXIC ANALYSIS OF CELL BEHAVIOR (HYP-ACB) ROOM S32
CALORIMETRY LABORATORY ROOM 233 CIRCULAR DYCHROISM ROOM S12
PROTEIN FACTORY TRAINING LAB (ProFacT) ROOM S2 (CU010)
CHROMATOGRAPHY LABORATORY ROOM S15
MASS SPECTROMETRY LABORATORY / CU020 BUILDING
BIOCRYSTAL FACILITY ROOM T7A DETECTION AND IMAGING LABORATORY ROOM 302
SCIENTIFIC EQUIPMENT
In line with the available research lines, these Facilities allow: i) to produce recombinant proteins and characterize their structural, functional and macromolecular interaction aspects; ii) to qualitatively and quantitatively evaluate metabolites and reactions on ex-vivo material; iii) to test the metabolic activities of the cells. Many of these Facilities have a dedicated technical staff unit that ensures that the work chain can be managed with continuity, efficiency and safety. Some facilities have recently undergone renovation of their premises and equipment and others have recently received substantial funding for the modernization of their instruments. The ARP and HYP-ACB infrastructures are currently part of a European H2020 infrastructure network (MOSBRI), while the Biocrystal Facility, recently implemented thanks to the PNRR financing for the ITACA:SB infrastructures, is included in the INSTRUCT Italia infrastructure network, also as a supplier of technologies and know-how in the field of structural biology. This facility brings together the skills and instruments of the Department and the Institute of Molecular Biology and Pathology of the CNR. The possibility of free access to these facilities characterized by a marked international profile represents a unique opportunity for the PhD student in Biochemistry both for the advancement of their research work and for their personal training
In accordance with the research lines supported and viewable at the link https://dsb.uniroma1.it/ricerca/linee-di-ricerca del-dipartimento-di-scienze-biochimiche, Doctoral students have access to available specialist instruments both in individual laboratories and in facilities and infrastructures (https://dsb.uniroma1.it/ricerca/laboratori).
By way of example but not exhaustive, a short list:
Protein factory: 2 INNOVA 44R New Brunswick thermostatic refrigerated incubators for the medium-scale production of prokaryotic biomass; 85 liter autoclave;
Instrumentation for bacterial cultures: biological hoods, preparatory centrifuges for large volumes; 2 sonicators for cell lysis; 1 orbital CO2 incubator for the production of recombinant proteins in eukaryotes.
Rapid Kinetics: Applied Photophysics single-mixing -SX-18; Applied Photophysics Pi-star 180; Applied Photophysics sequential-mixing DX-17MV; Tgk Scientific Hi-Tech PTJ-64 capacitor-discharge T-jump apparatus; in-house built continuous flow (original prototype) based on a capillary mixing methodology (dead-time 50 μs) with a fluorescence CCD camera
Spectrophotometry and image acquisition instruments: ID3x Spectramax plates reader, Tecan Infinite M200, Chemidoc MP Bio-rad equipped with computer and ImageLab program, JASCOJ-710 and J-815 spectropolarimeters, J-760, V730 with Peltier for thermal scanning; Electrophoresis 1-D and 2-D Platform. Various spectrophotometers (with diode array or monochromator) and fluorometers and nanodrops. Fluorescence microscope (Zeiss Axio VertA.1) equipped with computer with specific associated software (ZEN lite) and high resolution camera.
Macromolecular interactions: ITC Microcal iTC200 microcalorimeter; Surface plasmon resonance equipment (SPROCTET SF3). Mass photometry instrument (Refeyne)
Mass spectrometry: MALDI-TOF/TOF Ultraflextreme Bruker
Cell cultures: 4 facilities for cell cultures (each equipped with a 140 l CO2 incubator, optical microscope, BLS2 biological hood, refrigerated benchtop centrifuge); voltmeter for measuring epithelial resistance; Galaxy Eppendorf hypoxia O2 control incubator; HypoxicLab Optronix hypoxic chamber and CO2 incubator;
Metabolism and gene expression: 4 Real-time PCR; Oroboros O2k Respirometer; Free radical analyzer TBR4100 WPI. 2 Seahorse XFe96 Agilent with the possibility of measurements in hypoxia using Hypoxic cabin Don Whitley mod. i2 Workstation;
Chromatography: Gas chromatograph coupled to a quadrupole mass selective detector (Agilent); HPLC apparatus coupled to UV and fluorescent detectors (Agilent); ThermoFisher Vanquish HPLC system; Hplc Knauer Azura with hta300L automated sampler up to 100 samples. 3 AKTA GO and 1 AKTA PURE for protein purification.
Computerized calculation: HPC clusters for advanced calculation and calculation station for cryoEM data processing
Structural biology: 2 Oryx-8 crystallization robots (Douglas Instrument)s with accessory for lipid cubic phase; Phoenix Crystallization Robot - Art Robbins; Liquid handler for the automatic dispensing of liquids; temperature-controlled anti-vibration incubator; Low heating binocular stereomicroscopes for crystal visualization
HARDWARE AND SOFTWARE EQUIPMENT
Each PhD student has a computing and word processing station available to carry out the research project. Many of the featured instruments feature a PC with dedicated software to acquire and analyze measurements. Workstations for advanced cluster computing are available within the bioinformatics research line. Furthermore, the Department of Biochemical Sciences manages both in terms of instrumentation and maintenance, a computerized classroom equipped not only with an IWB and an audio/video system but also with 14 computer stations (14 PCs Newline Trutouch interactive monitor ATLAS 65” Newline OPS PC - Huddly IQ Room Kit; ATEN UE3315 USB3.1; IDATA HDMI2-4K21MH 2-port HDMI Switch 4K HDR 4:4.4; IDATA HDMI-4K2 2-port HDMI Splitter). Units of teaching and technical staff contributed to the multimedia set-up of the classrooms and the management of the computerized classroom, who remain contact persons and manage the relationships with the maintenance company, whose contract is the responsibility of the Department
LIBRARY
The library heritage of the Department of Biochemical Sciences has been merged with the Library of the Department of Chemistry ''Gabriello Illuminati'' (Interdepartmental Library of Chemistry and Biochemistry Gabriello Illuminati BiCB). In the CU27 building of the Department of Biochemical Sciences there is a library room which has no longer been open to the public since 2021 due to lack of staff. The room has been reprogrammed into workstations for doctoral students and research fellows. It is also used for meetings of the Teaching Body and for some doctoral teaching activities (Journal Club, Progress Reports). However, in the library room there are scientific periodicals available to doctoral students.
WORKSTATIONS
Each PhD student has a computing station with fixed and/or portable computers at the laboratory in which he/she is working Furthermore, the doctoral student, if applicable, has a workstation available at the supervisor's laboratory to carry out experimental activities related to the research project. Doctoral students can take advantage of intra- and inter-departmental facilities (see dedicated sections) for shared use. and common spaces for calculation and writing activities: Ex- library room (CU27) where it is possible to use one's own multimedia device or to organize seminar activities thanks to the IWB (interactive multimedia whiteboard) and the connection to the network present in the classroom. It is also used for meetings of the Teaching Board and for some doctoral teaching activities (Journal Club, Progress Report). -Meeting room with IWB (10 seats), where, the Department staff can organize meetings and small meetings and host collaborators, upon reservation,.
READING PLACES RESERVED IN THE LIBRARY
Doctoral students have reserved places in the ex-library rooms at CU027 where there is a large
book heritage available to doctoral students. A reading room is also available and open to doctoral students,
at the CU10 building.
BIBLIOGRAPHIC MATERIAL
A rich collection of books is available in the ex-library room and in the BiCB interdepartmental library
where consultation and specialist texts are available; however, much of the specialized bibliographic material for this scientific sector is available from the authoritative PubMed database, which allows you to consult the scientific literature before publication.
However, all the bibliographic material related to safety training in workplaces, including chemical, biochemical and biological laboratories and the training offered by the teachers in charge of the courses.is made accessible to doctoral students
MAGAZINE SUBSCRIPTIONS
In addition to the book heritage present in the ex-library room, all electronic access is made available to doctoral students of Sapienza University of Rome
DEDICATED FUNDS
List of funding deriving from specific projects with which doctoral students receive additional incentives compared to the provision of the ordinary scholarship:
-FEMS Meeting Organizer Grant (25th European meeting on the nitrogen cycle, FEMS-GO-2021-048)
-PRIN 2022: Nucleotide-based tools to inhibit nanoRNA degradation in cells: Is REXO2 a new target in cancer therapy? 2022KC3X9L
- Pasteur Institute Italy Cenci Bolognetti Foundation. Project title: Sensing of arginine through the Venus Fly Trap domain to control c-di-GMP levels in Pseudomonas aeruginosa: molecular mechanism and metabolic effects of signal transduction.
-PRIN2022 (2022XFFTH5) entitled: Fighting alarming bacterial lung infections through topical administration of new peptide antibiotics
- Pasteur Institute Italy Cenci Bolognetti Foundation: Small multifunctional membrane-active peptides to combat drug-resistant respiratory and wound infections: progress in delivery systems and in vivo efficacy
-Grant Agreement number: 101119633 European Research Executive Agency— IDPro —HORIZON-MSCA-2022-DN-01.
-------------------------------------------------------------------------------------------------------------------------------------------------------------
List of EXTERNAL FUNDERS that contribute to the payment of doctoral student scholarships:
-TAKIS COMPANY AND LAZIO REGION (cycle 36 scholarship funding) Title project. STRUCTURAL BIology for the synergistic development of innovative DRUGS Acronym: BIOSTRUCT-FARM
-SUPERIOR INSTITUTE OF HEALTH AND LAZIO REGION (37th cycle scholarship financing). Project Title: “Development of EPR methods for the study of proteins and radicals in cells”
-SUPERIOR INSTITUTE OF HEALTH AND LAZIO REGION (37th cycle scholarship financing). Project title: “Development of a multi-omics data integration platform for the inference of molecular interaction networks between pathogen and target cell”