STEBA XL cycle teaching activities
STEBA XL Cycle: topics of the seminars
The teaching activities are in English language and are offered in each of the three years of the course. Each PhD student can attend the teaching activities most relevant to the topics of his/her interest, dividing them over the three years of the doctorate based on his/her specific training needs. In any case, it is required that the PhD students attend a total number of at least 60 hours of teaching activities (30 DFC) over the three years.
Microbial biotechnologies for biorefineries – 4 hours
The seminar will describe fermentation-based processes aiming to exploit biomasses and agro-industrial wastes for the production of value-added metabolites, ranging from biofuels to fine chemicals. The newest trends on the topic will be reported, with particular focus on the exploration of microbial biodiversity, the genetic improvement and selection of microbial strains, and the development/optimization of industrial fermentation processes.
Genetic solutions for sustainable crop production under abiotic stress – 2 hours
Global agriculture faces challenges such as climate change and environmental degradation and a reduction of the agricultural inputs. The prevalence of abiotic stresses such as drought, salinity, extreme temperatures, and nutrient deficiencies significantly reduce crop yields, threatening food security and livelihoods worldwide. The need for sustainable and resilient crop production systems underscores the pivotal role of genetic improvement in addressing these challenges. This seminar explores the intersection of crop production, abiotic stress resilience, and genetic innovation, highlighting breakthroughs in understanding plant responses to environmental constraints. The discussion begins with an overview of key abiotic stresses affecting major crops and their physiological and molecular impacts. We delve into cutting-edge genetic tools such as high-throughput phenotyping, transcriptomic analysis, and bioinformatics technologies to improve our knowledge for abiotic stress tolerance. Through case studies of Triticeae crops such as wheat, barley and rye, we will examine applications of these technologies, including the study of frost resistant, drought-tolerant, salt-resistant cultivars.
Colour and chemical imaging: RGB and hyperspectral image analysis for food monitoring – 4 hours
This seminar aims at introducing the fundamentals of colour and spectral imaging techniques and their application for the analysis of food and agricultural products. In the food industry, image-based systems represent a suitable tool for real-time monitoring, allowing to identify the occurrence of problems directly on the process line. In the last decades, monitoring systems based on RGB colour cameras have found a widespread use for an objective measurement of properties related to colour and appearance of food products. More recently, monitoring systems based on multispectral and hyperspectral imaging have been developed in order to combine the advantages of imaging methods with those of spectroscopic techniques. In this manner, it is possible to investigate surface features of the imaged sample using spectral regions alternative to the visible range (like e.g. the near infrared), thus enabling to visualize the chemical composition of the sample surface in a fast and non-destructive way. In order to highlight the potential of image-based analytical systems, the basic principles of RGB and spectral imaging and the fundamentals of the most common strategies for image analysis will be presented together with some applications in the frame of agri-food sciences.
Introduction to the use of MATLAB environment for the analysis of agri-food data – 8 hours
MATLAB is one of the most widespread programming languages specifically designed for technical and scientific computing. This seminar aims at introducing the basic principles of data handling and programming in MATLAB environment, with a focus on data management and plotting facilities. The seminar is not only designed for students at the very first approach to a programming language, but also to students with expertise on other programming environments and interested in transferring their skills in MATLAB.
Regulation and use of biostimulants in agriculture – 2 hours
Plant biostimulants are sustainable products used in agriculture to improve nutrient use efficiency, tolerance of crops to abiotic stress, availability of nutrients in the soil or rhizosphere and quality traits of agricultural products. These innovative products are ruled by Regulation (EU) 2019/1009. Plant biostimulants may be divided into non-microbial and microbial products. Non-microbial plant biostimulants include humic substances, hydrolysed proteins and amino acids and microalgae and seaweed extracts, whereas microbial plant biostimulants consist of fungi and bacteria.
Food bioactive compounds – 4 hours
The seminar aims to understand how certain bioactive compounds found in food or generated during food processing can contribute to maintain a healthy lifestyle. The main classes of phenolic compounds and their respective bioactivities will be presented, with a mention of their bioavailability during technological processing and gastrointestinal digestion. Afterward, the beneficial effects of phenolic compounds on human health will be discussed. There will also be hints at the interaction between polyphenols and the human microbiota and the mechanisms of action of phenolic compounds on colorectal cancer, cardiovascular, metabolic, and neurodegenerative diseases with examples from recent studies.
Mass Transfer Modeling in food processing: Fickian diffusion and empirical approaches – 2 hours
The lesson is designed to offer a systematic introduction to mass transfer in food processing with the primary focus on the fundamental principles of Fickian diffusion. As the Fickian diffusion microscopic theory is often not well understood, some researchers use it as an empirical model without realizing the theoretical background. For the students who are planning to start their research careers in this area, it is crucial to gain a proper and concise view of Fickian diffusion as it is used as the basis for many studies in food science and engineering. In addition, the lesson also includes examples of other empirical models that can be used instead of in certain situations. The case studies are based on the processing of muscular and vegetable foods, and the practical applications are illustrated to demonstrate the relevance and generality of these models.
Pollen-pistil interaction. Strategies of flowering plants to promote allogamy – 4 hours
Pollen-pistil interaction represents the first step in seed and fruit development, aspects of unquestionable interest in the reproductive success of wild and domesticated flowering plants. However, the interaction of pollen grains and pistil is itself composed of several steps that, if a failure appears, might interrupt seed and fruit formation. Pollen adhesion, pollen germination, pollen tube growth and ovule fertilization are all aspects strictly regulated. Most recent advances of the factors controlling those steps will be discussed during this short course. In addition, in a second session, we will analyse the different strategies most flowering plants have adopted to limit or completely avoid self-fertilization and promote allogamy. They include self-incompatibility, dichogamy, herkogamy and dicliny.
Role of Culture Collections and exploitation of microbial resources: from strain preservation to industrial starters design – 2 hours
Microorganisms represent most of the biodiversity of living organisms in every ecological habitat. They have profound effects on the functioning of any ecosystem, and therefore on the health of our planet and of human beings. Moreover, microorganisms are the main protagonists in food, medical and biotech industries, so they can be exploited for several applications.
The seminar deals with the roles of the "Culture Collections” and describes the operating methods relating to:
- Staff skills;
- Techniques for short- and long-term storage;
- Quality control and data management.
The seminary describes also the recent Networks of Biological Resource Centers, specifically, the European Infrastructure MIRRI-ERIC (www.mirri.org) and the Italian Network JRU-MIRRI-IT, (www.mirri-it.it) with a focus on their efforts to enhance the availability of bioresources, quality management system and services offered to industries.
Infrared spectroscopy in food analysis – 4 hours
The seminar is focused on infrared spectroscopy, in particular applied to food matrices. Initially the theoretical principles of infrared spectroscopy will be treated, starting from the radiation-matter interaction until the anharmonic potential model. Next, the spectrophotometer will be described, together with the procedures for sample preparation for qualitative and quantitative analysis. In the end, a number of food analysis applications will be explained by way of example.
Functional genomics approaches in crop plants – 4 hours
The ever expanding availability of genomic sequences from plant and animal species allows to study the structural organization and molecular evolution of entire genomes. The vast wealth of data produced by genomic and transcriptomic projects must however be described through functional genomics approaches to interpret gene (and protein) functions and interactions. During the two presented modules students will approach this cutting edge field of knowledge by means of a series of selected examples.
Phytosanitary quality of vegetable seeds in the global market: a challenge for supporting sustainable agriculture and food security – 3 hours
Seeds are the primary basis for human sustenance. One of the major contributory factors to low
productivity is crop loss due to plant health problems: each year, up to 16% of the global harvest is lost due to plant diseases. Limiting or preventing the introduction and dissemination of seed borne
pathogens that harm plants is crucial to ensuring food safety. Therefore, international science-based standards for phytosanitary measures are essential to maintain seed quality and prevent the risk posed by pest and disease dissemination. Among these standards, seed production strategies (e.g., Good Seed and Plant Practices; GSPP), diagnostic protocols and certifications, chemical or physical seed treatments are playing a key role. Concurrently, the actors in these seed systems may involve farmers, seed companies that increasingly operate internationally, as well as governmental regulatory and international bodies like the International Plant Protection Convention (IPPC), International Seed Federation (ISF), European Food Safety Authority (EFSA), European Plant Protection Organisation (EPPO), National Plant Protection Services and research institutions. The biosecurity alert posed by Candidatus Liberibacter solanacearum associated with apiaceous carrot seed will be illustrated as a phytosanitary challenge from the research point of view.
Postharvest disease management of fruits and vegetables: microbial biocontrol as alternative eco-friendly strategy in sustainable agriculture – 3 hours
The human diet should include fruits and vegetables since they provide critical elements such as vitamins and minerals, as well as antioxidant and anticancer compounds. Among the global production of fruit and vegetable crops, postharvest spoilage plays a critical role in food safety, with losses estimated to be over 50%. Here, the infections caused by phytopathogens are currently a major threat for the fresh food production systems: they significantly shorten the shelf life of fruits and vegetables and cause significant deterioration during their postharvest processing, distribution, and storage. Most phytopathogens causing decay are currently controlled by various methods such as physical (refrigeration, controlled atmosphere), chemicals (pre- and postharvest chemical treatments) and biological (using natural plant products or antagonistic microorganisms). A research study on the development and application of a microbiological control agents (MBCAs) against Monilinia fructicola and Monilinia fructigena on stone fruit will be illustrated, as an alternative control method for eco-friendly postharvest disease management.
Innovative applications of acetic acid bacteria: the organism inside the process – 4 hours
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Biotechnology of fermented non-alcoholic beverages
Scientific context of fermented non-alcoholic beverages
Oxidative fermentation by acetic acid bacteria
Significance of selected starter culture in static and submerged fermentations for vinegar production -
Acetic acid bacteria from food to non-food applications, bacterial cellulose as a case study
Biosynthesis of bacterial cellulose by acetic acid bacteria
Selection of acetic acid bacteria for bacterial cellulose production
The industrial era of bacterial cellulose: limits and perspectives
Recovery and valorization of whey proteins for conventional and nonconventional food applications – 3 hours
This seminar explores the recovery and valorization of whey proteins, a valuable byproduct of cheese production. Utilizing membrane technologies like ultrafiltration and diafiltration, whey proteins are separated and concentrated, yielding liquid fractions (LWPC) to be used directly as raw materials or to be dried (WPC) for further applications. These fractions are then applied in both conventional and non-conventional food systems. Conventional applications include the enhancement of well-known dairy products such as fresh cheese, set yogurts, dairy gels, and dairy drinks, improving their nutritional profile and functional properties. Furthermore, the seminar delves into innovative, non-conventional applications, focusing on the development of edible films modified by UV treatment and WPC-based coatings exhibiting antimicrobial activity. This approach not only adds value to whey but also opens new avenues for food preservation and packaging.
Packaging properties related to food quality preservation – 2 hours
Suitable choices of packaging materials and techniques may contribute to the shelf life extension and to the overall sustainability of food chains. The seminar aims at supplying fundamentals on packaging materials and production techniques, and at presenting the packaging properties (diffusional, optical, mechanical) which are crucial for the quality maintenance of food products. Basic knowledge on packaging properties will help increase awareness on the key role of packaging in the modern food industry.
Sustainability-driven innovation in the food industry – 2 hours
The modern food industry is called upon to reduce its impacts on the environment and to supply nutritious and healthy food at a reasonable cost. Some non-conventional processing techniques have recently been adopted, with advantages both in terms of product quality and of environmental sustainability. The seminar will review non-thermal and non-conventional thermal processes with current or potential industrial application. The seminar will also cover innovative packaging materials (biobased and/or biodegradable) which also represent a current sustainability-related issue for the food industry.
Insect farming: sustainable approaches for biowaste valorization and the production of feed and food – 4 hours
In nature there is no waste: the processing waste from the agri-food supply chains can have new life and be enhanced thanks to insects, such as the black soldier flies and some species of mealworms and crickets. These insects are excellent bioconverters that transform organic substrates into substances with high added value (proteins, fats and chitin) that can be used for the production of ingredients to be used for the feed and food industries, as well as for biomedical and agricultural purposes. Even the organic residue that remains after the growth of the insects can be used profitably as a soil conditioner for plants. Thus, insect farming represents an excellent model of circular economy and sustainability in the use and production of resources. The second part of the seminar will focus specifically on the use of insects as food and feed, providing an historical and cultural background of entomophagy, information on the nutritional values and benefits for humans and animals, as well as on safety and regulatory issues (EU regulations on the use of insects as novel foods and for feed production).
Pest risk analysis and management of alien pests – 4 hours
This is a two-parts seminar, each part being held by a different lecturer
- Introduction to Pest Risk Analysis (PRA)
Globalisation of markets and climate changes may favor the worldwide movement of alien species (microorganisms, plants, animals) and their establishment into new areas. But not any living organism, accidentally imported into an area where it was absent, may pose a phytosanitary risk. The process of evaluation of such aliens as possible threat for agriculture is called Pest Risk Analysis (PRA). Therefore, a PRA is necessary in order to qualify an alien species as deserving specific phytosanitary measures or regulation.
- Management of alien pests
When the introduction and/or spread of alien species threatens or adversely impact upon biodiversity and related ecosystem services, this ultimately may result in interference with human health and economy. In order to minimize these effects it is therefore necessary to undertake a proper and prompt management of the introduced population, with actions and strategies aimed at its eradication, control and containment. Early detection and prevention are therefore of crucial importance. Appropriate methods to track the spread in the territory and for field monitoring must be chosen according to the species biological features. The seminar focuses on the management of some invasive agricultural pests that recently became of worldwide importance.
Model Plants – 2 hours
- Model plant concept
- Arabidopsis (genome sequence/transformation/mutagenesis/ TILLING/ natural variation/Arabidopsis community/bioinformatic resources)
- Brachypodium (genome sequence; germplasm & mutant collections; natural diversity; bioinformatic resource; case study: transcriptional profiling of Brachypodium – pathogen interaction)
Speed and precision for present and future Plant Breeding – 2 hours
The seminar will give a general overview of the innovations in plant breeding, that in the last few years revolutionized the entire process of plant improvement.
a. Speed breeding. Technological innovations leading to shorten the plant growth cycles, and the time of release of new plant varieties.
b. Precision Breeding. Technological innovations that by the use of image analysis and processing, together with machine learning algorithms, increase the precision and depth of phenotyping, as the number of traits under selection.
Metagenomic analysis – 2 hours
Next-generation sequencing technologies revolutionized the study of microbial biodiversity that now can be investigated at a much greater scale and detail than in the past.
The seminar introduces the metagenomic approach to the study of genetic material recovered directly from complex ecosystems (environmental, food, human samples), describing its principle, the NGS technology, the bioinformatic pipeline, and proposing examples of taxonomic profiling as well as functional analysis.
R statistical language: an introduction to data management, plotting, image analysis and modelling for agri-food applications – 4 hours
An introduction to R and the R studio environment. Examples of reading and modifying a dataset; plotting; analyze and elaborate satellite images; build and apply simple models. The class is organized to allow students to read and execute the code of the provided R examples independently.
Table olives: nutritional, production, hygienic, chemical and sensory aspects. Valorization of by-products from the olive oil processing industry – 3 hours
- Nutritional aspects of table olives
- General principles of table olive production according to the International Olive Council (IOC)
- Debittering process of table olives and importance of microbial populations
- Abnormal fermentations and defects in table olives
- Microbiological and chemical analyses: methods
- Sensory analysis according to IOC
- Extraction and recovery of bioactive substances from olive mill wastewater, leaves and pomace. Case studies and results.
The model organism Saccharomyces cerevisiae through the lens of the biotechnologist – 4 hours
Saccharomyces cerevisiae is one of the best-understood and most powerful genetic model systems to study fundamental aspects of eukaryotic cell biology, such as aging, cell development and human disease. The seminary will move from a brief historical perspective on the model system concept in the era of high-throughput sequencing, highlighting strength and weakness points in using model organisms to study complex biological problems. History on the emergence of S. cerevisiae as a premier experimental system over the course of the past century will be delineated. Then, central features of the S. cerevisiae genome will be introduced, including the nature of its genetic elements and general organization. The most common experimental tools, mutant strains collections and resources available to yeast geneticists will be presented to challenge PhD students to learn more about the experimental amenability of this budding yeast.
Innovation in food yeasts: current state, perspectives, and limits – 4 hours
Yeast is the workhouse for the production of many food products and biotechnological commodities. Selection and genetic manipulation of this powerful cell factory increase yield and predictability of fermentative transformations and enhance the overall food quality and safety. The seminary will describe the main strategies and genetic tools to manipulate yeast cell, with a special attention to non-OGM techniques used to develop novel food bio-catalysers. A flow-chart for decision making will be provided to Ph.D. students in order to choose the most reasonable manipulation strategy based on the genetics of the desired phenotype.
Lactic acid bacteria for healthy and sustainable food systems: starter cultures, probiotics, and food waste valorization – 2 hours
Lactic acid bacteria (LAB) have been widely exploited in food fermentation worldwide. LAB convert sugars into lactic acid and many flavourful secondary metabolites, impacting the final food safety and quality. LAB also include the many probiotic strains and can be used in sustainable production of functional food. New developments in systems biology and biotechnology to harness LAB for food waste valorisation and environmental regeneration. The present lecture will introduce the PhD students to the following topics: i) the role of LAB as starter in food fermentation; ii) the potential of food LABs as health-promoting agents iii) LAB as cell factories for food waste valorisation.
How microbes could help save the planet – 2 hours
This seminary will describe the role of microbiology in sustainable development, taking into account three main case studies: 1) microbes harvest energy in the form of electricity: the case of microbial fuel cell; 2) microbes fix carbon and turn it into fuels: integrated bioprocess for conversion of gaseous substrates to liquids; 3) plastic eating bacteria for pollution reduction; 4) hydrogenotrophs bacteria can transform CO2 into proteins suitable for human consumption.
Contamination and health risks posed by pesticide residues in vegetable products: assessment and management – 4 hours
The seminar intends to tackle the issues posed by pesticide residues in food as a possible threat for human health. The PhD students will be introduced to the basic concepts on the nature of a pesticide, the evaluation of their toxicological nature (including hints of environmental toxicology), on which basis a risk assessment (single or cumulative) should be done, the definition of a risk matrix, and how possible risks posed by pesticides should be communicated to the consumers.
Mass spectrometry application in food science – 4 hours
Mass spectrometry is an emerging and constantly evolving technique with a plenty of application in food analysis. Recently different types of mass spectrometry analysis (e.g., liquid chromatography-electrospray ionization-mass spectrometry, matrix-assisted laser desorption/ionization-time of flight-mass spectrometry) have been successfully applied in different fields of food science such as food safety, food authentication and bioactive compounds analysis. The present seminar will give a brief introduction on the most recent high-resolution mass spectrometry instruments to then analyze the different applications of mass spectrometry-based techniques (proteomics, peptidomics and metabolomics) to the analysis of foods with particular emphasis to the most recent scientific studies. The recent advances in food authentication, food quality, food safety and bioactive compounds analysis will be discussed.
Applications of multivariate analysis in the agri-food context – 8 hours
This seminar is aimed at introducing the basic techniques of multivariate statistics, with examples of applications to the analysis of experimental data in the frame of agricultural and food science. In recent decades, the number of analytical techniques available for the study of agricultural and food matrices underwent an exponential growth, as well as the amount of experimental data that can be acquired in short times. As a result, it is often difficult - if not impossible - to effectively manage large datasets by means of the "traditional" univariate methods, in order to extract and interpret the useful information therein contained. On the other hand, thanks to the spread of increasingly powerful and versatile computers and software, huge amounts of data can be easily processed. In this context, the chemometric techniques of multivariate analysis are reaching an increasing spread in the agro-food sector not only in research labs, but also in the industry. In order to present the benefits of multivariate statistical approaches, a brief description of the theoretical principles will be followed by the presentation of some applications for the solution of different problems related to various types of agricultural food matrices.
Academic English: Writing and presenting with and without the support of LLMs – 20 hours
The lessons integrate the traditional elements of a course on writing and presenting in English with insights and strategies on the way Large Language Models (LLMs), such as ChatGPT, Poe, Gemini and Curie can be used as a support, but highlighting that they also have serious deficiencies.