Molecular Taxonomy Lab

Coordinator: Francesco Paolo Patti

Activities

In the Laboratory of Integrative Taxonomy of Marine Organisms the activities are based on the analysis of classic taxonomy, phylogeny and comparative phylogeography of marine organisms by means of a multidisciplinary integrated approach (morphological, molecular, cellular and ecological). Following the main activities:

• Sample sorting, identification and counting in ecological and monitoring projects (e.g. Marine Strategy).
• Expert identification of organisms using traditional and advanced morphological and molecular methods (including preparation and deposition of genetic and ecological vouchers).
• Extraction and storage of DNA from different organisms (seaweeds and marine invertebrates tissue).
• RNA extraction from different organisms (seaweeds and marine invertebrates tissue).
• Extraction of secondary metabolites.
• Mini-gel electrophoresis and digital documentation.
• PCR amplification of DNA.
• Molecular cloning of target DNA segments (plasmid preps, restriction and PCR analysis).
• Real-Time fluorescent-based polymerase chain reaction.
• DNA barcoding.
• Terminal Restriction Fragment Length Polymorphism.
• DNA sequencing of fragments (in collaboration with SZN Molecular Biology and Bioinformatics Unit).
• Analysis of DNA sequences including the reconstruction of phylogenetic trees.

Systems for the experimentation

• Dedicated lab protocols.
• Bioinformatic systems analysis: 1) study of nucleotide variability (ad-hoc open source software for metadata analysis); 2) decomposing morphotypes forms into size and shape by geometric morphometric methods.

Analysis

• Analysis of DNA sequences including the reconstruction of phylogenetic trees.
• Analysis of the morphological variability and the genetic polymorphism.
• Analysis of allele frequency and genotype distribution.
• Analysis of terminal restriction Fragment Length Polymorphism.
• Preparation of samples for morphological analysis (using dedicated buffer solutions for microscope observations - Stereomicroscope and Scanning Electron Microscope) and molecular analysis (cryopreservation, standards and RNAlater fixatives for tissue preservation).

Equipment

• Stereomicroscope.
• Vibratome.
• Rotavapor.
• Chemical fume hood.
• Laminar flow hood.
• Mini-Gel horizontal electrophoresis systems.
• Refrigerated Bench-top Centrifuge.
• Spectrophotometer "Genequant Pro Classic".
• PCRs (Techne- Euroclone).
• RTPCR BIO RAD Opticon 2.
• Incubator for cell cultures.
• Analytical balance.
• Temperature controlled water bath (5l, +30°C/+120°C).
• Bench-top vortex mixer with general purpose head.
• Vertical laboratory autoclave and steam sterilizer.
• Laboratory Ice Machine.
• Liquid nitrogen dewars (5l+30l).
• Vertical Ultrafreezer -86°C.
• Vertical Freezers -20°C.
• UVP BioDoc imaging workstations for gel documentation and fluorescent imaging.
• Dedicated computer for phylogenetic reconstruction and data mining.