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).
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
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).
Head: Marina Montresor
Activities
The lab contains equipment and infrastructure used for the study of the functional and taxonomic diversity of marine plankton. In particular, in this laboratory analyses are carried out on the taxonomic and molecular diversity of plankton samples collected at the Long Term Ecological Research site MareChiara in the Gulf of Naples as well as elsewhere, in the frame of participation in regional and global projects. Experimental approaches focus on the physiology and life cycles of marine microalgae and on the feeding behaviour of zooplankton.
Systems for experimentation
- Light- and temperature-controlled walk-in incubator and incubators of different volume for in vivo experiments with phyto- and zooplankton.
- Optical system for video footage of zooplankton organisms.
- Plankton wheel for experimentation with phyto-, micro- and mesozooplankton.
Analysis
- Quantitative analysis of marine phytoplankton and zooplankton.
- Preparation of phytoplankton cultures and their morphological and molecular characterization.
- Phylogenetic analysis.
- "Metabarcode" analysis of marine plankton with Next Generation Sequencing approaches.
Instrumentation
- Stereoscopes and optical microscopes
- Microscope with epifluorescence illumination and digital cameras to take photographs and movies.
- Zooscan with related software.
- Camera System for video-registration of zooplankton movement.
- Area equipped for the isolation of cultures and experimentation (laminar flow hood, microscopes for cell isolation, fluorimeter).
- Molecular Laboratory equipped for DNA extraction, PCR, DNA electrophoresis, preparation for NGS sequencing.
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Villa Comunale, 80121 Napoli - Tel.+39 081 5833111 - C.F./P.IVA : IT 04894530635 - PEC: ufficio.protocollo(at)cert.szn.it