Responsible: Francesco Paolo Patti

In the laboratory of Integrative taxonomy of benthic organisms (TIOM) one can perform analyses of classical taxonomy, phylogeny and comparative phylogeography of marine organisms using multisciplinary and integrative approaches, such as morphology, biometry, molecular and cellular analyses.

Activities

• Sorting of benthic samples of marine organisms, identification and counting of taxa.
• Taxonomic identification of marine organisms with traditional morphological methods and with more advanced molecular tools (including the preparation of genetic and ecological voucher specimens).
• Extraction and conservation of DNA from different organisms and (algal thalli and invertebrate tissues).
• Extraction of RNA  from different organisms (algal thalli and invertebrate tissues).
• Extraction of secondary metabolites.
• Elettrophoresis in agarose minigel  and digital documentation.
• Amplification of DNA (ss, ds).
• Cloning of DNA target fragments (plasmid preps, restriction and PCR analysis).
• Real-Time fluorescent Polymerase Chain Reaction.
• DNA barcoding.
• Preparation of DNA fragments for sequencing of target markers  (in collaboration with the Unit of Molecular Biology and Bioinformatics of the SZN).

Systems for the experimentation

• Specific laboratory protocol setting
• System of bioinformatics analyses for 1) study of the nucleotidic variability (creation of soft-ware for metadata analyses); 2) study for comparison of morphotypes by mean of morphometric geometry techniques.

Analysis

Analyses of DNA sequences, including the reconstruction of phylogenetic trees.
Analyses of morphological variability  and genetic polymorphism.
Analyses of allelic frequencies and genotypic distribution.
Analyses of polymorphysms of the DNA restriction fragments.
Preparation of samples for morphological analyses (use of fixative for observation at the optical and electron microscopes), and for molecular analyses (cryopreservation, standard fixatives, RNALater).

Instrumentation

• Stereomicroscopes.
• Vibratome.
• Rotavapor.
• Chemical flume.
• Laminar flow flume.
• Apparatus for minigel electrophoreris.
• Laboratory refrigerated centrifuge.
• Spectrophotometer "Genequant Pro Classic".
• Termocyclator PCRs (Techne- Euroclone).
• RTPCR BIO RAD Opticon 2.
• Incubator for cell cultures.
• Analytical balance.
• Thermostatic bath (5l, +30°C/+120°C).
• Laboratory Vortex.
• Autoclave/Sterilizer.
• Granular ice-machine.
• Dewars for liquid nitrogen (5l+30l).
• Vertical ultra-freezer -86°C.
• Vertical freezers  -20°C.
• UVP BioDoc imaging workstations for simple and gel fluorescence image analyses.
• Dedicated computer for phylogenetic analyses and data mining.