Reference: Filomena Ristoratore
Laboratory equipped for the study of molecular aspects of physiological responses of marine organisms at various stages of life cycle.
Includes areas equipped for electrophysiology and molecular biology, cell culture and basic laboratory equipments.
Systems for experimentation
- Genomic amplification and gene expression.
- Electrophysiology.
Analysis
- Physiological responses of marine organisms to stimuli.
- Membrane potential during fertilization events of marine organisms.
- Electrophysiology and Neurophysiology.
- Physiological analysis of immune responses in marine invertebrates.
Equipments
- Eletrophysiological Set-ups.
- Cell culture apparata.
- Molecular biology (nucleic acids and proteins).
Coordinator: Gabriele Procaccini
Scientific activities
Strumentazione di base per la biologia molecolare (PCR, centrifughe, apparati elettroforetici, transilluminatore, bagni termostatici, spettrofotometro, fluorimetro, pH-metro, bilancia di precisione)
Gene gun (apparecchio per la trasformazione biolistica)
In the laboratory of Molecular Ecology and Functional Genomics we carry out studies addressing ecological questions, using molecular approaches. The laboratory covers research activities ranging from molecular phylogeny and taxonomy to phylogeography and population genetics, using sequence analysis and analysis of polymorphic markers, such as microsatellites and SNPs. It also deals with the study of gene function through functional genomics approaches and reverse genetics (mainly production of transgenic lines of diatoms). We also makes use of analysis of environmental genomics and comparative transcriptomics, and we carry out gene expression studies in natural and controlled conditions (RNA-Seq, RT-qPCR).
Experimental systems
- Mesocosms for maintaining benthic organisms under controlled conditions.
- Walk-in chamber for microalgal cultures.
Analysis
- DNA extraction, purification and quantification.
- RNA extraction, purification, quantification and reverse transcription.
- Protein extraction and quantification.
- Sample preparation for RT-qPCR in plates.
- Samples preparation for massive sequencing.
- Samples preparation for sequence analysis.
- Samples preparation for fragments analysis.
- single and multiplex PCR.
- Electrophoresis on agarose and acrylamide gel.
- Statistical analysis of population genetics and molecular phylogeny.
- Primers design, analysis of electropherograms.
- Cloning and bacterial transformation.
- Preparation of plasmid DNA (mini and maxi prep).
- Biolistic transformation and cultivation of GM crops.
- Algal cultures.
- Colorimetric assays with fluorescent vital dyes and microscopic analysis.
- Southern blot, Northern blot.
- Western blot and enzyme assays (colorimetric, ELISA).
- Use of specialized software for the analysis of protein and nucleotide databases and for the exploration of genomes.
Equipments
- Basic equipment for molecular biology (PCR, centrifuges, electrophoresis apparatus, transilluminator, thermostatic baths, spectrophotometer, fluorometer, pH meter, balance).
- Gene gun (apparatus for biolistic transformation).
- Hoods for algal cultures.
- Microscopes.
- Mixer Mill (Tissue Lyser).
- PC and software for molecular analysis.
- Fume hood.
- TurboGen (equipment for generating marine turbulence).
Coordinator: Daniele Iudicone
Activities
The aim of the laboratory is to support the study of the ecology of marine plankton and of the ocean physics that is relevant for the plankton ecology. The laboratory of ecological modeling has as main activity the preparation and realization of numerical simulations of the ocean circulation at microscale (DNS), mesoscale (ROMS) and at global scale (NEMO) and of the associated plankton dynamics. The activities are integrated with statistical analysis of environmental (physicochemical) data, ecological (populations) data and biological (metagenomics, functional parameters) data.
Experimental systems
- In-house configurations of numerical codes for simulating the ocean circulation, the fluid dynamics at the microscale (turbulence) and the impact on microorganisms.
- In-house configurations of numerical codes for simulating planktonic populations at different levels of complexity.
- Turbulence Profiler.
- Devices for the production of marine turbulence in lab (TurboGen).
Analysis
- Analysis of the variability of the ocean physics (including thermodynamics) and biochemistry at various spatial and temporal scales at basin and sub-basin scales.
- Statistical analysis of environmental data and ecological.
- Water mass thermodynamic budgets.
Instrumentation
- Servers and computers for numerical simulations.
- Software for data analysis.
- Software for the simulation of the physics and biology of marine organisms (produced in-house or by external collaborators).
Reference: Remo Sanges
Laboratory equipped for studies of computational genomics throughout bioinformatics approaches.
Systems for experimentation
Databases, high throughput functional genomics.
Analysis
Computational approaches, bioinformatics, comparative genomics, data-mining (genomics and transcriptomics in marine organisms).
Strumentazioni
- Personal computers.
- Workstations and servers.
Turtle Point
Stazione Zoologica Anton Dohrn
For emergencies: 334 6424670
Tel. +39 081 5833602
e-mail: andrea.affuso(at)szn.it