Specific training activities for the FishMed-PhD program: course units

Marco Candela, University of Bologna (Italy)

The course will be divided into 3 specific areas which involve aspects of a technical, biological and practical nature. The main technical aspects of a metagenomics study will therefore be covered, starting from experimental design, sampling approaches, library preparation and sequencing, up to the basics of bioinformatics and biostatistics. Once the technical aspects have been completed, metagenomics applications in different fields will be discussed, the microbiota-host co-evolutionary trajectories and the implications in eco-evolutionary terms will then be discussed. Furthermore, pioneering applications of metagenomics in the "one health" context will be covered, where microbiomes become central to the health of the planet and the evolutionary history of its inhabitants.

Fréderic Marin, Université de Bourgogne (France)

The course provides a general introduction to biomineralization, the different types, their particularities from phylum to phylum, with particular attention to calcium carbonate-based biomineralization, the most abundant on Earth. In particular, the formation of mollusc shells is analyzed from a molecular and biochemical perspective. The macroevolution of biomineralization from the Archean to the present day is then addressed. A part of the teaching is dedicated to examples of technological applications of biominerals in modern industry. The last part is dedicated to the fossilization of biominerals and how molecular information can be recovered from fossil/subfossil biominerals.

Giovanni Valdrè, University of Bologna (Italy).

The course covers the following topics: Electron Microscopy (EM); Environmental scanning electron microscopy, ESEM (pressure, temperature, type of gas); Electron matter interaction; Information on material properties; Recognitions and prizes for Electron Microscopy; Notes on History; The diffraction limit; Technological frontiers in the development of electron microscopy and other microscopy methods; High resolution spectroscopy; “TEM imaging”; Aberration correction; “Scanning Transmission electron Microscopy”, STEM; “Field Emission Gun” ESEM-STEM; “SEM imaging” and spectroscopy; Sources for electron microscopy; Monte Carlo simulations for X-ray micro and nano-analysis; Limits and problems of conventional SEM; “Gaseous Secondary Electron Detector”; “In-situ dynamic experiments”; X-ray microanalysis (detectors for energy dispersive spectroscopy, signal generation, quantitative analysis methods); Cryo-Electron Microscopy and Cryo-Tomography (“Cryo-Electron Microscopy and Tomography”). At the end of the course the student will be able to know the main and modern methodologies of scanning electron microscopy, SEM, transmission, TEM, and environmental microscopy, the microanalysis conducted within electron microscopy, and the related methods of observation of samples organic and inorganic.

Stefano Goffredo, University of Bologna (Italy)

The course addresses the current problem of climate change, caused by anthropogenic emissions of carbon dioxide into the atmosphere. According to the most accredited hypotheses, such a rapid change would not allow organisms to adapt. In particular, the effects of increasing temperatures and ocean acidification on marine biodiversity will be addressed. Experiments in the laboratory and in the natural environment will be described. Specific topics covered: natural sites with CO2 emissions; ecology of temperate and tropical corals; reproduction, population density; biometrics; sclerochronology; mathematical models of growth and population dynamics.

Jacobus Adrianus (Jaap) Kaandorp, University of Amsterdam (Netherlands)

Rather than being directed by a central control mechanism, embryogenesis can be seen as an emergent behavior resulting from a complex system in which different subprocesses at very different temporal and spatial scales (ranging from nanometers and nanoseconds to cm and days) are connected in a multiscale system. The teaching focuses on the embryogenesis of basal metazoans. Explains methods for analyzing spatio-temporal gene expression patterns and inferring gene regulatory networks, obtainable from gene expression data (qPCR data and in-situ hybridizations). In the last part of the course, a model of calcification physiology that controls biomineralization and a multiscale model of embryogenesis that couples the different levels of organization (gene regulation, cellular mechanics and biomineralization) are illustrated.

Andrea Luchetti, University of Bologna (Italy)

Teaching revolves around the basics of genome sequencing and analysis, with particular attention to the field of comparative genomics. The first topics focus on the history of sequencing and new technologies, from Sanger methods to pyrosequencing (Roche 454), Next Generation sequencing (mainly Illumina) and very recent methods using long reads (PacBio and ONT technologies), with details on the chemistry used and how the sequencing itself works. The second part of the course concerns the management of sequencing output: strategies and suggestions for sequencing short and long reads, and possible pitfalls. The third part of the teaching concerns the anatomy of the genome (genes, gene families, gene deserts, repetitive DNA, transposable elements) and the analysis of genome sequencing (assembly, gene annotations, functional annotations and genome architecture). The last part is dedicated to the interpretation of genomic variation patterns in light of the biology and evolution of organisms with case studies.

Silvia Franzellitti, University of Bologna (Italy)

Variations in the surface temperature of sea water associated with climate change is pushing scientific research to understand the potential interactive effects between global warming and other sources of physiological stress in marine animals, such as chemical pollution. To predict future scenarios of alteration of marine biodiversity, physiological studies seek to determine the key processes that determine the limits of stress tolerance, how these processes operate under natural conditions, where extremely complex exposure scenarios occur, and whether different species they differ in their acclimatization abilities to change their level of stress tolerance. The course presents a critical analysis of the regulatory mechanisms that govern acclimatatory and stress responses in sentinel marine species, such as mussels and corals. These responses, which occur at the molecular, cellular, and individual levels, can be used as biomarkers of animal-environment interaction and allow an overall assessment of the biological vulnerability of a given environment under the combined action of climate change and chemical pollution.

Antton Albderdi Estibaritz, University of Copenhagen (Denmark)

The course aims to provide an overview of existing opportunities to implement hologenomic methodologies, useful for addressing various scientific questions related to animal-microbiota interactions in marine organisms. The course begins with an introduction on animal-microbiota interactions and focuses on how host organisms shape the biology of microbial communities and how microbial communities shape the biology of hosts The teaching continues with the genomic, microbial and environmental drivers of host-microbiota interactions and how these vary between systems and models.
Next, the generation of multiomic data of both the host and microorganisms is covered, while the final part focuses on the feasibility and challenges of implementing hologenomic techniques. Students gain theoretical knowledge about animal-microbiota interactions and practical knowledge about how to study them through hologenomics.

Damir Kralj, Ruder Boškovic Institute (Croatia)

The aim of the course is to provide basic knowledge of the precipitation (crystallisation) mechanisms of poorly soluble salts in aqueous solutions. Such knowledge can significantly improve the understanding of biomineralization processes and global CO2 exchange by relating it to the speciation of inorganic carbon in seawater and the formation of calcium carbonates. To this end, the concepts of equilibrium in solution, ionic equilibria, supersaturation, polymorphism and solubility of minerals are illustrated, as well as the methodologies for studying the kinetics of the basic processes associated with precipitation (nucleation, crystal growth, dissolution, aging, transformation , and secondary nucleation). The classification of crystal growth mechanisms (bulk diffusion/convection, adsorption, surface diffusion, integration and/or surface nucleation), as well as the role of dissolved impurities (additives), is also illustrated. The experimental approaches used to study crystallization are also explained. Finally, the relationships between the physico-chemical properties of the precipitate (mineralogical composition, grain size distribution of the crystals, morphology) and the mechanisms determining the growth rate are provided.

Jonathan Erez, The Hebrew University of Jerusalem (Israel)

The ocean is the largest active carbon sink on Earth and as such largely controls atmospheric CO2. In this teaching the following topics will be addressed: 1) The global carbon cycle and its disruption due to the combustion of fossil fuels; 2) The physical-chemical response of the oceans to the disturbance caused by anthropogenic CO2 emissions; 3) Biomineralization of CaCO3 in the ocean and the effects of sea acidification; 4) Dissolution of CaCO3 and its potential for CO2 sequestration.

Stylianos Somarakis, Hellenic Centre for Marine Research (Greece)

The course deals with ichthyoplankton biology with emphasis on the reproductive ecology of small pelagics and pelagic food webs. Fisheries ecology and management, ecosystem modeling and aquaculture-fisheries interactions are aspects of applied ecology covered in the course. Hydrographic (temperature and salinity), plankton (chlorophyll a, microzooplankton and mesozooplankton) and fish (somatic condition, sexual maturity) parameters are used to explain seasonal and interannual variability in the feeding periodicity and daily ration of fish.

Michele Casini, University of Bologna (Italy)

The course focuses on the multiple effects of climate change and anthropogenic factors (fishing and nutrient inputs) on commercial fish populations and exploited marine ecosystems in Northern Europe, with particular reference to the Baltic Sea. Particular attention is given to the indirect effects that act on individual populations through the modulation of the structure and functioning of food networks, with specific reference to prey-predator interactions and inter- and intraspecific competition. The management techniques adopted at European level, and potentially usable, are presented and discussed in relation to the objective of achieving an ecosystem approach to fisheries management.

Gian Marco Luna, National Research Council (Italy)

The course presents a general introduction to the teleost microbiome and its role in the physiology, metabolism and nutrition of wild and aquaculture fish and in the safety of fish and fishery products for human health. Explains the role of microbes in global planetary biogeochemical cycles and food webs and the use of nucleic acid-based techniques and omics approaches to study the diversity of marine microbes. The teaching also aims to make students understand how microorganisms influence the general functioning of the marine ecosystem, from the coastal strip to the abyssal depths, with emphasis on the mechanisms that regulate biodiversity and the response of the marine (micro)biota to the impact of man and global change.

Mauro Marini, National Research Council (Italy)

The quality of fish products is increasingly assessed on the traceability of the freshly caught product to the sales counter, defining the geographical fishing area (according to FAO classifications) and the fishing gear used. All this is aimed at promoting fishing techniques that are more respectful of the environment and the protection of biodiversity. To obtain a quality product, we are increasingly trying to identify quality brands for food products that take into account the above factors, but also the ability to bring fresh or semi-finished products of high organoleptic quality onto the market. Furthermore, the content of pollutants that can potentially be contained in seafood for food use is also being increasingly valorised. The course also aims to illustrate the results of the most recent research carried out on these aspects, aimed at defining the impact of contaminating substances on the tissues of food products obtained from the sea.

Jakov Dulcic, Institute of Oceanography and Fisheries (Croatia)

The course deals with ichthyology and fisheries biology, the management and protection of coastal resources, as well as fishing gear and techniques. Topics also include topics on the structure of coastal fish communities and their geographic distribution, the ecology and distribution of juvenile stages, including ichthyoplankton. Particular attention is paid to the species of greatest economic importance, to the state of the ichthyofauna and to the monitoring of variations within communities caused by climate change and the ever-increasing spread of alien species.

Fabio Fiorentino, National Research Council (Italy)

The course provides: i) information on the main sources of data and types of indicators, useful for evaluating the state of resources, ii) guidelines for the use of threshold and trend indicators, iii) indications on the adequacy of each approach depending on the availability of data and the type of fishing, the fleet and the species caught, iv) pros and cons of the different approaches, v) examples of use of the indicators. The dynamics of a fish stock and the cycle of unmanaged fishing are illustrated. The need for stock assessment and management of fishing pressure is highlighted. The main objectives of fisheries management were reviewed and the roles of different types of indicators (biological, ecological, economic and social) in assessing the state of stocks and fisheries performance were described. The main sources of information are then presented (independent and fishing-dependent data) and the main theoretical approaches (surplus production models, catch-by-age models and ecological models) and empirical approaches (trend of population indicators; analysis of abundance by cala, comparison between abundance and biomass in communities). The use of biological reference points (BRPs; Limit Reference Points and Target Reference Points) is then outlined, including the “traffic light” approach for empirical indicators. The approaches presented are framed in the context of the main characteristics of Mediterranean fisheries (use of non-selective gear, early age of first capture, multi-species fishing using different gear, scattered landing sites, high value of small individuals, fishing success mainly due to recruitment). Examples of the use of indicators for the Strait of Sicily area are shown.

Gianna Fabi, National Research Council (Italy)

The course regards the use of ecological engineering, consisting in the design of ecosystems at different levels of complexity for the mutual benefit of man and nature, as a tool for the development of Nature Based Solutions (NBS), i.e. inspired initiatives to nature, aimed at the recovery, protection and implementation of sensitive habitats (e.g. seagrass meadows, coastal areas of reproduction and initial growth of fish species, coral reefs) and at increasing the productivity of the marine environment.

Alessandro Lucchetti, National Research Council (Italy)

The course approaches skills to technologies for sustainable fishing. The responsible use of resources involves biological, technological, economic, social, environmental and commercial aspects. The FAO Code of Conduct for Responsible Fisheries (1995) emphasized that selective and environmentally safe fishing gear and practices should be further developed and applied, in order to maintain biodiversity, conserve aquatic ecosystems and protect quality of the catch; fishing waste, the capture of non-target species, both fish and other organisms (turtles, mammals, seabirds) and impacts on the environment should be reduced to a minimum. Most of the fishing gear used in the Mediterranean involves the use of small mesh and hooks, with the consequence that those landed include small species and juvenile specimens of commercial and non-commercial species. In particular, the mesh sizes of trawl nets appear to be small enough to catch juvenile fish. The weak selectivity implies a large portion of discards. The impact of towed gear on the bottom should be taken into account when defining management measures. The teaching aims to provide information on fishing technology in relation to the following main issues: selectivity, impact, innovation and energy efficiency in fishing activities. Provides an overview of: a) fishing gear used in the Mediterranean; b) European fisheries legislation; c) selectivity and impact of different fishing gears; d) incidental catches of vulnerable species; e) innovations in fishing technology aimed at reducing impacts, discards and fuel consumption.

Donata Luiselli, University of Bologna (Italy)

The course aims to provide basic knowledge on the history and methods of human population, with particular regard to the Mediterranean basin, on the anthropological characteristics of current populations, on the biocultural and adaptive relationships that they have established with their living environments. life, as well as on the biological and demographic dynamics through which their microevolutionary history developed. Man's interaction with the sea is a long history, which began in the most ancient times of our evolutionary history and continued until today with migrations and activities along the coasts to exploit the most accessible marine resources. The Mediterranean Sea has represented for millennia, for the populations that border it, a fundamental resource for the supply of food, through the exploitation of marine resources, and tells a long history of fishing activities, navigation systems, processing and conservation of particular fish products. The course aims to illustrate how communities of traditional fishermen, with a tradition of fishing activities for generations, can constitute peculiar case studies in order to analyze, according to an integrated bio-cultural approach, the complex relationships between man and the coastal environment. Although the beneficial effect of a diet based on fish products is known due to their supply of ω-3, there are numerous contaminants in the marine environment that cause concern from both an environmental and public health point of view. The course specifically illustrates how polymorphisms in genes involved in the synthesis of long-chain fatty acids (PUFA), in relation to different types of diet, and in genes involved in mercury detoxification metabolic pathways (e.g. SEPP1, GSTM1, GCLC ), may constitute susceptibility factors to certain pathologies (developmental mismatch phenomena).

Alessia Cariani, University of Bologna (Italy)

Teaching focuses on the potential of genetic and genomic approaches, their increasingly important role for understanding evolutionary processes, such as adaptation to different habitats within the marine environment, including fishing-induced evolution. Recent advances in genomic technology and their implementation from genome assembly to comparative and population genomics are presented. Examples are provided on how genetic and genomic tools can address multiple challenges to ensure the sustainability and profitability of fisheries management and aquaculture production.

Giulio Antonio Malorgio, University of Bologna (Italy)

The course is organized into three sections: 1) Fishing in the framework of the economy of renewable resources (fishing and the functions of the environment; analysis of prices, costs and market forms; natural resources: renewable and non-renewable resources ; the sustainable development of the fishing sector; stocks, catches and fishing effort; the bio-economic balance); 2) Externalities and property rights (collective natural resources; excludability and rivalry of collective natural resources; fish resources as common goods; technical and pecuniary externalities; property rights in the management of fish resources); 3) Regulatory policies for fishing activity (green deal and marine environment; blue growth and ecosystem services; blue growth and marine spatial planning; multifunctionality of the fishing sector; output and input control measures: catch limits , limitation of licenses, technical measures; effectiveness of subsidies and taxes; the reform of the common fisheries policy).

Simona Fermani, University of Bologna (Italy)

The teaching aims to give a complete vision of the strategies for valorising waste materials from fishing and aquaculture. Two main materials are taken into consideration: polysaccharides and biominerals. The first part of the teaching is dedicated to the weight and geographical distribution of these waste materials. The difficulty of collection and storage is then illustrated. The teaching continues with the illustration of the fundamental characteristics of biominerals, demonstrating that they are in all respects biomaterials with a high potential for use. Examples involving both calcium phosphate and calcium carbonate are presented. These find application in many fields ranging from agriculture to biomedical. The use of polysaccharides is focused on chitin. First of all, the distribution among the different organisms and the quantity available in nature are illustrated. Subsequently, the structure of chitin, its polymorphs and possible chemical modifications are illustrated. The teaching continues with the illustration of some research aimed at valorising chitin from waste materials. The course ends with perspectives on the future uses of waste materials from fishing and aquaculture.

Felice Adinolfi, University of Bologna (Italy)

The essential elements of the Blue Economy and the Common Fisheries Policy are introduced in the teaching. In the first part, the macroeconomic dimension of the fishing sector is analyzed in order to understand its structure and value and the microeconomic dimension, examining the peculiarities of the fishing company through company evaluation tools. In the second part, the historical path of the Common Fisheries Policy is reconstructed, analyzing the historical reasons for its birth and evolution to arrive at the establishment of the FEAMPA (European Maritime Affairs, Fisheries and Aquaculture Fund). The two parts will be analyzed synergistically in order to understand the influence of policy support in the transformation of companies in the fishing sector in terms of economic and environmental sustainability.

Giulio Zanaroli, University of Bologna (Italy)

The teaching discusses the main types of persistent organic pollutants, their sources and their distribution in the marine environment, the potential of marine microorganisms with regards to their biotransformation and/or biodegradation and the strategies for exploiting them for the purposes of bioremediation of contaminated marine environments. The metabolic strategies used by microorganisms to biodegrade halogenated and non-halogenated pollutants in aerobic and anaerobic conditions are explored in depth, as well as the factors that limit their effectiveness in the field and the approaches and technologies to stimulate them and promote the bioremediation of sediments and/or the column. of contaminated water.

Antonella Penna, University of Urbino Carlo Bo (Italy)

The course aims to provide students with information on the ecology of marine phytoplankton. Topics will be covered on: the main phytoplankton groups, size, seasonal cycles, mechanisms relating to primary productivity, irradiance and photosynthesis, compensation curves, harmful algal blooms (HAB), eutrophication, sampling methodologies, analysis techniques. Some case studies: Adriatic Sea and Mediterranean Sea.

Invited speakers

Seminars/lessons by invitation. The seminars will focus on issues related to the economics of renewable resources with particular reference to the problems related to the economic system of fishing, the main phenomena relating to the structural, environmental and market conditions of fish products and the application of tools for the analysis of economic management and forms of intervention of fisheries policies. The circular economy will be treated as a production and consumption model with specific insights into its implications: sharing, lending, reusing, repairing, reconditioning and recycling existing materials and products for as long as possible, to extend the life cycle of the products , help reduce waste to a minimum and generate additional value. Finally, the interventions necessary to eliminate the sources of pollution or polluting substances, or to reduce their concentrations, will be discussed, with the aim of bringing them below the risk threshold concentrations (CSR)/Contamination (CSC), in order to recover areas compromised by contamination phenomena; eliminate potential risks for the environment and human health; redevelop a territorial area.