Methods in Cell Biology and Biochemistry

METHODS IN CELL BIOLOGY (2 CFU)
This part aims to provide the basis for methods for obtaining, growing and manipulating cellular models. The following topics will be covered in the course:

Frontal education
-Mammalian cell cultures
Advantages and disadvantages of cell cultures. Primary cell lines: achievement and maintenance. Disaggregation of primary tissues and cultures. Separation and characterization of specific cell types present in a tissue. Stabilized and / or immortalized cell lines: obtaining and maintaining. The transformation factors, the oncogene-mediated immortalization of cells, the hybrid systems obtained from cell fusions. Specific immortalization with transforming agents: direct tumorigenesis. Stem cells and pluripotent induced stem cells (iPSC).
-The laboratory for mammalian cell cultures
Sterility, personal protective equipment and collective protection, biological safety hoods, incubators, small instruments and cell culture supports. Safety measures and associated risks.
Dry heat and wet heat sterilization techniques, filtrations.
-Cell cultures maintenance. The culture environment: substrates, culture medium, temperature, growth factors, serum types and chemical additives. Culture methods (suspension, adhesion, monolayer and 3D culture), substrates for cell culture in adhesion, analysis of cell culture morphology. Analysis of growth curves of a cell culture, subculture, mechanical or enzymatic detachment, cell counting and seeding, freezing of cell lines. Cell viability and mortality assays: trypan blue staining, calcein-acetoxy methyl staining, propidium iodide staining, lactate dehydrogenase enzyme release, alamar-blue assay, MTT assay, ATP test.
-Cellular engineering. Genetic cargoes for protein overexpression or gene silencing: DNA plasmids, antisense oligonulceotides, siRNA, micro-RNA, mRNA, cosmids and lambda phage. Cell transfection techniques for gene expression study and for proteins analysis.
Non-viral transfection vectors: chemical methods (calcium chloride, DEAE-dextran, lipofection) and physical methods (electroporation, microinjection and gene gun). Viral vectors: advantages and disadvantages. Adenoviral, lentiviral, AAV vectors. Production of viral vectors: modification of the viral genome, packaging cells, titration and analysis of the relevant replication revertants, main safety standards for working with viruses. Transient, stable (trasposase and Flp-in) and stable-inducible transfections (tet on / tet off). Reporter systems. Genome editing: zinc-finger systems, TALENs and CRISPR / Cas9 technology.
-Fluorescence and its applications for the study of cell cultures.
Basic principles of fluorescence. Fluorochromes, fluorescent proteins and fluorescent chimeras. The fluorescence microscope. Immunofluorescence: cell fixation, permeabilization, detection using primary and secondary fluorescent antibodies. Examples of applications of using fluorescent proteins/compounds to mark organelles, to measure cellular activity.
Fluorescence microscopy techniques: FRET and FRAP.

Laboratory practice
During laboratory, students will be taught how to work under sterile conditions in a biological safety hood, introducing them to basic mammalian cell culture handling techniques. Students will learn how to assess the health of a cell culture, detach cells by trypsinization, count them, and perform cell seeding. On the seeded cells, each student will experiment with different methods outlined in the frontal lectures, including: transfection, a cell viability assay, a cell death assay, evaluation of transfection efficiency using beta-galactosidase enzyme activity assay. In addition, students will learn to process the data obtained using MS Excel. At the end of the laboratory, each student will have to present the data obtained in a written report, which will contribute to the final evaluation.


METHODS IIN BIOCHEMISTRY
Frontal education (including seminars and classroom exercises):
- Quantitative analysis of gene expression: definition and methodologies, basic PCR concepts, qRT-PCR operating scheme, approaches for real-time amplification detection, methods for quantitative data analysis; qRT-PCR applied to miRNAs.
- Techniques for the study of macromolecule interactions: co-(immuno)precipitation with native or fusion proteins, GST-pull down and related approaches, study of interactions by FRET (in vitro and in vivo); analysis of interactions between proteins and nucleic acids by Electrophoretic mobility shift assay, analysis of interactions between proteins and DNA in the context of chromatin (Chromatin immunoprecipitation), analysis of proteins interacting with RNA (RNA immunoprecipitation).
- Approaches for the study of the proteome: general definition of proteome, proteomic analysis and related methodological approaches; application of mass spectrometry for the determination of the molecular weight of proteins (MALDI-TOF, ionization by electrospray); approaches for protein identification: 2D-gel electrophoresis, enzymatic digestion, sequencing by tandem mass spectrometry, peptide fragmentation pattern, quantitative analysis in mass spectrometry.
- Approaches for the study of the metabolome: general definition of metabolome, metabolomic analysis and related methodological approaches; targeted metabolomics: sample preparation, instrumentation, application examples; untargeted metabolomics: sample preparation, instrumentation, application examples; statistical analysis of metabolomic data.
- Approaches for the study of energy metabolism: methods for the analysis of mitochondrial morphology, methods for the analysis of mitochondrial density and biogenesis, methods for the analysis of respiration in cell cultures and animal models, measurement of ATP synthesis, membrane potential, reactive oxygen species, and main mitochondrial metabolic pathways.
- Next generation nucleic acid sequencing techniques: introduction to next generation sequencing techniques; technologies based on the principle "sequencing by synthesis": applications (DNA-protein interactions, RNA-seq, RNA-protein interactions, DNA methylation, whole genome sequencing, de novo sequencing); libraries preparation;; data analysis.

Laboratory practice
- Design of primers and probes for Real time PCR, quantitative analysis of qRT-PCR data and targeted metabolomics data, introduction to secondary and tertiary analysis of Next generation sequencing data (computer laboratory)
- Isolation of nucleic acids from cell cultures, preparation for the PCR reaction and analysis of amplification products by agarose gel electrophoresis; cell fractionation, analysis of the protein profile of the cell fractions by SDS-PAGE, determination of the protein concentration of the cell fractions by colorimetric method, analysis of mitochondrial metabolism (bio-laboratory).
The contents of the lab activities will be the subject of individual tests that will contribute to the final evaluation.