Teaching activity

Teaching title

N° of hours

Year

Teaching description

Curriculum

Notes

Bioinformatics applications for the study of biological systems

20

first year

Application of major and innoivative bioinformatics tools for omics data and genotyping techniques for the study of harmful (plant pathogens) and beneficial (beneficial components of microbial communities and biocontrol agents) organisms, molecular diagnostic systems, investigations of microbial diversity, population dynamics and evolution, possible ecosystem effects and management of plant adversity, complex host-pathogen and microorganism-to-microorganism interactions, and study of active metabolites produced by plants and microorganisms.

all

Challenges and opportunities for PhD students’ career management

10

second year

The teaching aims to provide PhD students with an opportunity to critically reflect 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 organizational terms and the need to read this experience as an opportunity to acquire soft skills (e.g., working in teams, time management, managing symmetrical and asymmetrical relationships) potentially applicable to other contexts. PhD tudents will also be urged to consider the theoretical insights offered by the psycho-social perspective and to self-evaluate themselves in a course of study that may offer them relevant insights into career management. 

all

English

40

first year

In addition to deepening knowledge of both oral and written grammar and communication in English, the aim of teaching is to develop knowledge of formal English used in writing a scientific report so that learners are able to distinguish between formal, impersonal English and English used in everyday life. PhD students also understand the importance of formal text structure. Teaching involves PhD students reading and analyzing texts and writing short texts, as well as communicative activities in small groups. The expected learning outcomes consist of: - being able to use formal, impersonal English; - being able to effectively summarize the content of a text; - being able to produce a short formal report; - being able to express one's opinion in a written test; - being able to describe one's research activity; - being able to discuss and exchange ideas with colleagues on a variety of topics.

all

in common with another PhD course

Exploitation of research products

24

second year

The objective of this teaching activity is to provide doctoral and postgraduate students from all scientific-disciplinary fields with legal notions and tools for the management of the results of their research, both in the academic and business fields. The activities will be structured in seminar-type meetings divided into a theoretical and a practical part, in which, at first, the basic concepts of intellectual property law (copyright and related rights) and industrial property (with specific reference to the patent discipline) will be illustrated, to move on to the study of more complex issues that commonly arise in the exploitation of research products. Issues related to the regime of circulation of copyright and rights “to” and “on” the patent, technology transfer and the new discipline of inventions by university employees (art. 65 c.p.i.) will be explored in depth, examining during the workshop part licensing contracts (also in English) - with the clauses invalid in domestic and international practice -, university regulations and statutes of spin-off companies. Team working activities for the study of practical cases will be proposed, also resorting to the consultation of books and databases.

all

transversal competences

Laboratory safety and management

10

first year

The teaching aims to provide the basic skills and tools to operate safely and according to current regulations in research laboratories. Training activities are carried out through lectures and practical activities. The teaching content covers general regulatory aspects of safety in the workplace, the organization and operation of the protection and prevention system in the university institution, the handling of genetically modified organisms, and the management and handling according to current regulations of waste from research activities. Specifically, the topics covered in the face-to-face activities are: the Legislative Decree No. 81 of April 9, 2008 and s.m.i.; the figures in charge of safety management; the R.V.D.; prevention and protection measures; biological, chemical, physical, ergonomic, accident and behavioral risks; safety data sheets of reagents; PPE and PFD; regulations and procedures for handling genetically modified microorganisms; D. Legislative Decree 152/2006, as amended, on environmental regulations; waste management; waste coding; special waste, special hazardous waste; the regulations and procedures for temporary storage and disposal of special and hazardous waste.

Practical examples related to: collecting, reading and cataloging MSDSs of a chemical reagent; waste coding; and simulating laboratory risk assessment procedures are addressed in the exercise activities.

all

Project management

10

first year

Lo scopo dell’obiettivo è quello di trasferire le conoscenze di base delle tecniche di Project Management utili a progettare efficacemente una attività di ricerca, realizzarla e monitorarla, rendicontarla correttamente e valorizzarne i risultati.  L’insegnamento prevede l’analisi di bandi e call ed esempi applicativi di progetti svolti. I risultati di apprendimento attesi consistono in: - saper cercare, leggere ed esaminare un bando per valutarne la praticabilità; - saper scrivere un abstract di una proposta di ricerca; - saper effettuare una analisi dei costi da sostenere (investimento, gestione, flussi finanziari); - saper gestire e rendicontare un’attività di progetto; - saper comunicare contenuti e risultati di un progetto; - saper valorizzare i risultati nella logica della dissemination.

all

in common with another PhD course

Science communication and scientific publications

20

first year

The teaching aims to provide the essential knowledge to acquire some of the tools needed to undertake and develop the researcher's profession. Therefore, the objectives of this teaching are: to provide the necessary foundation for effective scientific communication and dissemination; to illustrate how to set up and write a scientific publication and report; to expose the criteria for research and evaluation of scientific publications; to simplify and optimize oral communication techniques.

all

in common with another PhD course

Statistics applied to the biosciences

20

first year

The purpose of the teaching is to transfer the basic knowledge of programming in R for effective data analysis. Teaching covers the practical aspects of statistical computing including programming in R, reading data in R, accessing packages, and properly writing, maintaining, and executing a script. The expected learning outcomes consist of: - Becoming familiar with the interface and language of R; - Manipulating and exploring datasets; - Performing parametric and nonparametric statistical analysis tests; - Correlation and correlation matrices; - Linear, multiple and logistic regression in R; - Graphing with R.

all

in common with another PhD course

Bacterial communities and environment

15

first year

Teaching consists of an initial series of lectures aimed at describing the evolutionary dynamics of community-structured bacterial populations, with particular reference to: (1) organization of bacterial biofilms and their ecological significance; (2) role of biofilms in bacterial evolution; (3) role of biofilms in the evolution of mobile and/or mobilizable genetic elements (e.g., plasmids and integrons); and (4) CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat) bacterial immune memory systems: structure, function and role in bacterial evolution. The second lecture series 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) 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

Bioethology of plant pathogen vectors

15

first year

PhD students will be introduced to the fundamental concepts of plant pathogen transmission by insects and insect-pathogen-host-plant interaction. Special emphasis will be placed on the importance of multidisciplinarity in the study of insect vectors, and how techniques and knowledge from seemingly distant research areas are integrated in order to understand and describe the epidemiology of an insect-borne pathogen and develop sustainable control strategies. Finally, male and female students will have an opportunity to apply the concepts learned by presenting a case of their interest and describing the approach they would follow in studying an insect-borne pathogen.

Crop protection

Biotechnology applications for plant protection

15

first year

The teaching aims to provide theoretical and practical knowledge on molecular host/pathogen interactions and defense technologies based on molecular interference, including through laboratory exercises with application of molecular techniques for the diagnosis and characterization of plant-associated microorganisms. The ultimate goal is to define the laboratory and instrumental analyses required to finalize a diagnostic process in plant pathology.

Crop protection

Chemical monitoring of environment

15

first year

The educational objective of this teaching is to develop knowledge with respect to the natural chemical composition of each environmental matrix and the dynamics of natural and anthropogenic interactions that are triggered in these environmental compartments on local and global scales. For each compartment, the main chemical pollutants of anthropogenic nature will be examined in terms of their sources of origin and the ways in which they are distributed, transformed, accumulated and transferred from one compartment to another. The impacts that these pollutants and, in particular, priority pollutants in terms of persistence and toxicity, cause on the environment and human health will be assessed, and for each of them, the relevant regulatory framework will be explored. Finally, conventional approaches and analytical methodologies used for monitoring, control and containment of pollutant concentrations in ambient air, water and soils will be studied and, also based on case studies, the limitations of these methodologies and the potential of possible innovative and unconventional approaches developed for this purpose will be discussed.

Environmental sciences

Decision Supporting Systems (DSS) for crop protection.

20

first year

The teaching aims to provide theoretical and practical knowledge on predictive models and decision support systems (DSS) for the management of phytosanitary problems and the definition of integrated protection strategies (IPM) of interest for major 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 reviewed. Detailed knowledge of the most common decision support systems currently available, data analysis and interpretation, and predictive models will be provided.

Crop protection

Ecological models applied to ecosystem monitoring

10

first year

The objective of this teaching is to deepen some topics inherent in the use of mathematical models for the analysis of ecological systems, providing basic theoretical conosciences for the analysis and interpretation of ecological data. The following general topics will be covered in the teaching program: - Introduction to data modeling in ecology; - Hypothesis analysis in ecology and experimental design; - Database construction for ecological data analysis and modeling; - Brief overview of univariate statistical tests; - General principles of data sorting techniques and multivariate analysis; - Brief presentation of innovative data modeling techniques (e.g., neural networks).

Basic knowledge for the use of the open source software PAST (PAleontological STatistics) will be introduced, and additional data analysis and modeling software may be illustrated depending on the timing and needs of the teaching program. In addition, some case studies of ecological models applied to the study of community analysis and trophic network modeling will be presented. The expected learning outcomes involve the acquisition of knowledge related to the basic concepts of modeling in ecology, construction of a database, conducting 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

Ecophysiology of tree species.

30

first year

The teaching aims to provide in-depth knowledge about:

- the eco-physiology of fruiting tree plants and especially the effects of climate change (e.g. water restriction, heat waves, light excesses, failure to meet needs in cold, cold returns, loss of soil fertility) on tree functionality (leaf functionality; water relations within the plant; fruit growth mode; phenology; etc.) on productivity and production quality;

- the methods of monitoring the functional state of an orchard (e.g. Plant Sensing and sensors; multi layer approach; agricultural Decision Support Systems, Internet of Things, etc.).

Sustainable Mediterranean agriculture

In vitro culture and micro-propagation for safeguarding plant biodiversity

20

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, enabling in vitro maintenance of germplasm. This technique has been extensively studied and developed and is currently applicable for the propagation and upgrading of more than 1,000 different rare and endangered plant species of agricultural and medicinal interest. The general teaching content has as its main objective the preservation of ex situ biodiversity through in vitro culture. The following topics will be analyzed and explored in depth: in vitro propagation techniques (micropropagation; organogenesis; somatic embryogenesis); phases of the in vitro propagation cycle and factors affecting its efficiency; synthetic seed; and principles and techniques for slow-growth storage and cryopreservation of cultures. Each process and stage of in vitro culture will be supported by hands-on laboratory activities.

Sustainable Mediterranean agriculture

Management of fruit biodiversity in the context of climate change

10

first year

The objective of the teaching is to provide information, notions and compe-tencies regarding the typical adaptive capacity of some fruit species (many of them defined as minor), in the current context of climate change. The knowledge of these strategies will be necessary for the optimization of cultivation techniques, which will have repercussions on yields and production quality, but also will allow the cultivation of these species in marginal and water-poor environments, while enhancing local varieties.

Sustainable Mediterranean agriculture

Molecular markers in agricultural genetics

30

first year

The teaching aims to provide advanced theoretical knowledge related to the type and use of molecular markers in plant and agricultural genetics. Different types of molecular markers 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 explained, taking care to optimize the applications according to the type of research to be performed.

Plant genetics and bio-technology

Monitoring of habitats and species in the marine environment

10

first year

The proposed teaching aims to provide the main information on the techniques and methodologies used in the marine environment for monitoring habitats and species of relevant ecological and conservation interest within the implementation of the Marine Strategy, with particular reference to coralligenous habitat. The main activities carried out by the Department of Biology of the University of Bari in the framework of the Marine Strategy with the aim of assessing the presence, extent and condition of coralligenous habitat in the Apulia Region will then be illustrated.

Environmental sciences

Phytopathological clinic

10

first year

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

Crop protection

Phytoremediation in environmental remediation

10

first year

Teaching will provide an understanding of how plant functional processes can form the basis of a sustainable phytoremediation approach. Different phytotechnologies used in environmental remediation and their mechanisms of action will be presented. Aspects related to phytotechnology and prevention, phytotechnology and environmental sustainability, and factors that may favor or limit the applicability of phytotechnology will be discussed. Different survey methodologies including phytoscreening, phytocapping, phytodissection, phytobarrier and rhizorimedium will be described.

Environmental sciences

Plant cytogenetics

30

first year

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

Plant genetics and bio-technology

Practice of phytopathological laboratory

10

first year

The teaching aims to provide the organizational and operational skills for proper 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 contextualized application of theoretical knowledge in the practical conduct of research activities, as well as the care and maintenance of equipment available to the researcher.

Crop protection

Zoorimediation in aquatic systems

10

first year

Bioremediation is a set of techniques that exploits the abilities of certain living organisms to mitigate the presence of pollutants in the environment by removing or chemically modifying them through aerobic or anaerobic processes. Historically, during experimentation we first turned to microorganisms, then considered plants and finally animals. The latter is more appropriately referred to as zoorimediation, which is concerned with testing and applying the abilities of certain animals, particularly among aquatic filter-feeding invertebrates, to mitigate or restore aquatic environments by removing pollutant molecules from water. Teaching will illustrate the history of experimentation in the remediation of aquatic environments through the use of animal organisms, from its earliest days to its most recent advances.

Environmental sciences

Seminars

All three years

Seminar activities will be carried out jointly or distinctly by individual curriculum on the basis of the topics addressed, with preference given to visiting speakers at university facilities of the departments involved and leading projects. Particular care will be taken to encourage in-depth study of basic themes, experimental aspects, and cutting-edge research that provide insights for discussion, reflection, and advancement of the themes proper to the PhD course in BAA.

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