Teaching activity

Teaching title

N° of hours

Year

Teaching description

Curriculum

Notes

Bioinformatics applications for the study of biological systems

20

first year

This course aims to illustrate the theoretical foundations and tools of bioinformatic analysis applied to the main organisms underlying the development and functioning of biological systems, and in particular: - Development and applications of bioinformatics in biology -omics based on the Next Generation Sequencing (NGS) technologies; - Databases, algorithms and software underlying bioinformatics analysis workflows; - Algorithms for comparative biosequence analysis for the study of molecular evolution and biodiversity: tools for alignment, multi-alignment and similarity searching in databases. Construction of phylogenetic trees; - Bioinformatic tools for analysing NGS data: de novo and reference sequence-driven assembly of new genomes, identification of functional elements in prokaryotic and eukaryotic genomes; - Hints of bioinformatic analysis in metagenomics and DNA metabarcoding approaches; - Algorithms for the bioinformatic study of transcriptomes and proteomes.

Expected learning outcomes: - State of the art of bioinformatics analysis in the light of the recent evolution of NGS technologies; - Basic bioinformatics databases and algorithms for molecular analysis of major biological systems: assembly and annotation of genomes, characterisation of transcriptomes and proteomes; - Tools for the comparative analysis of biosequences; - Algorithms for the evolutionary analysis of biomolecules.

all

Valorisation and dissemination of results, intellectual property and open access to data and research products

20

first year

This course aims to provide the essential knowledge to acquire some of the tools needed to enter the researcher's profession. The objectives of this course are:  - to provide the necessary foundations for effective scientific communication; - to illustrate how to write a scientific publication; - to explain the criteria for evaluating scientific publications; - and to exemplify oral communication techniques.

all

in common with another PhD course

Characterisation of useful and harmful entities through bioinformatics applications

20

first year

Application of the main and most modern bioinformatics tools for omics data and genotyping techniques for the study of noxious (plant pathogens) and beneficial (beneficial components of microbial communities and biocontrol agents) organisms, molecular diagnostics systems, investigations of microbial diversity, population dynamics and evolution, possible ecosystem effects and management of plant adversity, complex interactions between host and pathogen and between microorganisms, and the study of active metabolites produced by plants and microorganisms.

all

in common with another PhD course

Management of research and knowledge of European and international research systems

15

first year

This course will be taught in English by a visiting professor; it is aimed to transfer knowledge and understanding of the principles of research funding systems in the life sciences: how to find funding, an overview of how to plan a project, how to write a high-quality project proposal and how to manage a project during its life cycle. Students will gain knowledge about data management and the protection of intellectual property rights.

all

in common with another PhD course

English

25

first year

In addition to deepening knowledge of grammar and both oral and written communication in English, the aim of the English language course (intermediate and advanced level) is to develop knowledge of formal English and to deepen the English used in everyday life. The course involves students reading and analysing texts and writing short texts, as well as communicative activities in small groups.

all

in common with another PhD course

Advanced informatics

20

first year

The course is aimed to transfer the basic knowledge of programming in R for effective data analysis. The course covers the practical aspects of statistical computing including programming in R, reading data in R, accessing packages and correctly writing, maintaining and executing a script.

all

in common with another PhD course

Advanced English

20

first year

The aim of this course is to provide an overview of the characteristics of English for research purposes, with a focus on both written texts and oral presentations. With regard to written texts, the characteristics of abstracts and research papers will be discussed in order to maximise participants' active reading skills and increase their autonomy in writing texts in English. As far as oral presentations are concerned, the course will also focus on public speaking in order to improve the skills required in presentations at conferences, conventions and workshops and will concentrate on aspects of impact techniques, visual aids, pronunciation and debating skills with moderators and the audience. Participating students will be able to produce a short formal report, orally describe their research activities, and discuss and exchange ideas with colleagues on a variety of scientific topics.

all

in common with another PhD course

Laboratory safety and management

10

first year

The course aims to provide basic skills and tools to work safely and in accordance with current regulations in research laboratories. The course contents cover the general regulatory aspects of safety in the workplace, the organisation and functioning of the protection and prevention system in the university institution, the handling of genetically modified organisms, and the management and handling of research waste in accordance with current regulations. In particular, the topics covered in the frontal activities are: the L.D. 9 April 2008 no. 81 and subsequent amendments and additions; the figures in charge of safety management; the D.V.R.; prevention and protection measures; biological, chemical, physical, ergonomic, accident and behavioural risks; safety data sheets for reagents; PPE and DPC; regulations and procedures for handling genetically modified microorganisms;  L.D. 152/2006 as amended on environmental regulations; waste management; waste coding; special waste, special hazardous waste; regulations and procedures for temporary storage and disposal of special and hazardous waste. In the exercise activities, practical examples are dealt with in relation to: collection, reading and cataloguing of safety data sheets of a chemical reagent; waste coding; simulation of risk assessment procedures in the laboratory.

all

Challenges and opportunities for PhD students’ career management

10

second year

The course aims to provide PhD students with an opportunity for critical reflection on the relevance of soft skills for the strategic management of their future careers. In particular, the course focuses on the highly challenging role of the academic context in organisational terms and on the need to read this experience as an opportunity to acquire transversal skills (e.g. working in a team, time management, managing symmetrical and asymmetrical relationships) potentially applicable to other contexts. Students will also be urged to consider the theoretical cues offered by the psycho-social perspective and to self-evaluate themselves in a pathway that may offer them relevant indications on career management.

all

Promotion of research

20

second year

The course intends to provide the essential knowledge in the field of copyright, intellectual and industrial property, also including a workshop on the protection and management of copyright and privacy. This activity will be complemented with insights into European, national and local financial programmes and instruments, not forgetting aspects concerning the environment and sustainability of research. A workshop on research design and scientific and cultural enterprise will provide the exercise element.

all

Plant cytogenetics

30

first year

The course aims to provide advanced theoretical and practical elements concerning the structure, number and possible variations in the chromosome structure of plant species of agricultural interest, such as cereals. Topics related to chromatin organisation, mitosis, meiosis and the cell cycle, observation of the karyotype, types of staining and preparation of slides will be covered. Observations and preparation of substrates for optical microscope observations will be carried out.

Plant genetics and bio-technology

Plant pathology clinic

10

first year

Teaching and training activities on the diagnosis of plant diseases and adversities through the observation of the symptoms, their distribution and quantification of damage in the field. The teaching aims to provide knowledge on the most common phytosanitary problems of plants in the field, means and tools necessary to develop the diagnostic pathway through a correct anamnesis and objective examination of plant health status in order to define the laboratory and instrumental analyses required to finalise the diagnostic process.

Crop protection

In vitro culture and micropropagation for the preservation of plant biodiversity

30

first year

In vitro culture is considered to be of great interest for the collection, multiplication and conservation of plant germplasm, providing an efficient solution to the problem of biodiversity erosion under safe and inexpensive conditions. This technique has been extensively studied and developed and is currently applicable for the propagation and upgrading of more than 1000 different rare and endangered plant species of agricultural and medicinal interest. The general teaching content will focus on the preservation of ex situ biodiversity through in vitro culture. The following topics will be analysed and explored in depth: in vitro propagation techniques (micropropagation; organogenesis; somatic embryogenesis); phases of the in vitro propagation cycle and factors influencing its efficiency; synthetic seed; principles and techniques for slow-growth and cryopreservation of cultures. Each process and stage of in vitro culture will be supported by practical laboratory activities.

Sustainable Mediterranean agriculture

Bacterial communities and environment

15

first year

The course will consist of a first part aimed at describing the evolutionary dynamics of bacterial populations structured in communities, with particular reference to: 1) the organisation of bacterial biofilms and their ecological significance; 2) the role of biofilms in bacterial evolution; 3) the role of biofilms in the evolution of mobile and/or mobilisable genetic elements (e.g. plasmids and integrons); 4) CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat) bacterial immune memory systems: structure, functioning and role in bacterial evolution.

The second part will focus on the role of bacteria and horizontal gene transfer in the human-animal-environment circuit and in the context of current issues such as antibiotic resistance and environmental pollution. In particular, reference will be made to: 1) the role of genetic elements in the spread of antimicrobial resistance and the emergence of multi-resistant bacterial strains; 2) anthropogenic activity and selective pressure in the spread of antibiotic resistance; 3) bacterial metabolism as a resource to remove chemical and/or solid pollutants from the environment (bioremediation) and/or to produce biomolecules of interest to humans.

Environmental Sciences

Decision Supporting Systems (DSS) for crop protection (disease and pests)

20

first year

The course aims to provide theoretical and practical knowledge on forecasting models and decision support systems (DSS) for the management of phytosanitary problems and the definition of integrated protection strategies (IPM) of interest for the main plant species and problem solving under complex and uncertain conditions. The main monitoring and risk assessment systems for the presence and spread of pathogens and pests will be examined. Detailed knowledge of the most common currently available decision support systems, data analysis and interpretation, and predictive models will be provided.

Crop protection

Plant in environmental remediation

10

first year

The teaching will provide an understanding of how plant functional processes can form the basis of a sustainable phytoremediation approach. The various phytotechnologies used in environmental remediation and their mechanisms of action will be presented. Aspects of phytotechnology and prevention, phytotechnology and environmental sustainability will be discussed, as well as the factors that may favour or limit the applicability of phytotechnology. The different investigation methodologies including phytoscreening, phytocapping, phytodrying, phytobarriers and rhizorimediation will be described.

Environmental Sciences

Fruit biodiversity management in the context of climate change

30

first year

The aim of the course is to provide information, knowledge and skills on the typical adaptive capacity of some fruit species (many of which are defined as minor), in the current context of climate change, and the use of agri-voltaic systems as a tool for sustainability, crop protection, safeguarding resources and integrating agricultural income. The knowledge of these strategies will be necessary for the optimisation of cultivation techniques, which will have repercussions on yields and production quality, but will also enable the cultivation of these species in marginal environments with low water availability, allowing them to be accumulated in the winter periods through canalization and at the same time enhancing local varieties. The study of agri-voltaic systems will allow an evaluation, during the design phase, of the crops that are best adapted to the variation of climatic and irradiative parameters typical of cultivation under panels in order to create a productive combination of energy and fruit products.

Sustainable Mediterranean agriculture

Molecular markers in agricultural genetics

30

first year

The course aims to provide advanced theoretical knowledge related to the typology and use of molecular markers in plant and agricultural genetics. Different types of molecular markers will be considered such as: RFLP, RAPD, ISSR, SSR, CAPS, AFLP and SNP. For each type of marker, the functioning, applications, advantages and disadvantages of their application and how to interpret the results obtained will be illustrated, taking care to optimise the applications according to the type of research to be carried out.

Plant genetics and bio-technology

Ecological models applied to ecosystem monitoring

10

first year

The aim of the teaching is to deepen some topics related to the use of mathematical models for the analysis of ecological systems, providing basic theoretical knowledge for the analysis and interpretation of ecological data. The following general topics will be covered in the syllabus: - Introduction to data modelling in ecology; - Hypothesis analysis in ecology and experimental design; - Database construction for ecological data analysis and modelling; - Brief overview of univariate statistical tests; - General principles of data sorting techniques and multivariate analysis; - Brief presentation of innovative data modelling techniques (e.g. neural networks). Basic knowledge for the use of the open source software PAST (PAleontological STatistics) will be introduced and, depending on the timing and requirements of the teaching programme, additional data analysis and modelling software may be presented. In addition, case studies of ecological models applied to the study of community analysis and modelling of trophic networks will be presented. In terms of teaching organisation, lectures with multimedia support and practical activities in the classroom with open source software are planned. Teaching materials will be provided by the lecturer via slides and handouts that can be downloaded online. The expected learning outcomes include the acquisition of knowledge related to the basic concepts of modelling in ecology, the construction of a database, the realisation of an ecological study with the application of an experimental design, the use of discipline-specific language and the ability to expose to a non-expert audience.

Environmental Sciences

Chemical environmental monitoring

15

first year

The course aims to provide students with the theoretical basis for a systemic analysis of the natural environment. The objective of the course is to develop knowledge of the natural chemical composition of each environmental matrix (air, water, soil) and the chemical mechanisms underlying environmental processes and pollution phenomena on a local and global scale. For each compartment, the main anthropogenic pollutants will be examined in terms of their sources and how they are distributed, transformed, accumulated and transferred from one compartment to another. The impacts that these pollutants and, in particular, the priority ones in terms of persistence and toxicity, determine on the environment and human health will be assessed, and for each of them, the reference regulatory framework will be explored. Finally, the conventional approaches and analytical methodologies used to monitor, control and contain pollutant concentrations will be studied, and the limitations of these methodologies and the potential of innovative and unconventional approaches developed for this purpose will be discussed.

Environmental Sciences

Monitoring marine habitats and species

10

first year

The marine environment is a precious heritage that must be protected, safeguarded and, where possible, restored with the ultimate aim of maintaining biodiversity. To address these needs, the European Parliament and the Council of the European Union issued the Marine Strategy Framework Directive 2008/56/EC. The Framework Directive requires Member States to develop a marine strategy based on an initial assessment, definition of good environmental status, identification of environmental targets and establishment of monitoring programmes.

Environmental Sciences

Phytopathology laboratory practice

10

first year

The course aims to provide the organisational and operational skills for the correct use and management of the instrumentation, devices, reagents and digital software accompanying a phytopathology laboratory. The training activity will cover the planning of biological and molecular experiments in the laboratory through the contextualised application of theoretical knowledge in the practical performance of research activities, as well as the care and maintenance of the equipment available to the researcher.

Crop protection

Zooremediation in aquatic systems

10

first year

Bioremediation or bioremediation exploits the capacity of certain living organisms to mitigate the presence of pollutants in the environment by eliminating or chemically modifying them through aerobic or anaerobic processes. Historically, experimentation has first turned to microorganisms, then to plants and finally to animals. In the latter case, we call it more appropriately zooremediation, which deals with experimenting and applying the abilities of certain animals, particularly among filter-feeding aquatic invertebrates, to mitigate or restore aquatic environments by removing polluting molecules from the water. The course will illustrate the history of experimentation in the remediation of aquatic environments through the use of animal organisms, from its beginnings to its most recent advances.

Environmental Sciences

Seminars

during the whole cycle

Seminar activities will be carried out in a joint or separate manner for each curriculum on the basis of the topics addressed, favouring speakers visiting the university facilities of the departments involved and leading projects. Particular care will be taken to encourage the in-depth study of basic themes, special aspects and cutting-edge research that offer opportunities for discussion, reflection and the advancement of the themes of the BAA PhD course.

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