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RESEARCH TOPICS FOR XXXVIII CYCLE – Main selection procedure

1) Title of the Research Topic: Genomics and Bioinformatics for Unraveling Abiotic Stress Tolerance Mechanisms in Cereals

1 (one) position with grant

Scientific Tutor: Prof. Enrico Francia - co-Tutor: Dr. Justyna Milc

Research topic: In the twenty-first century, after genome knowledge continued to accumulate, bioinformatics in crop plants has evolved tremendously. It has entered into almost all the basic and applied biological research work, and has gained a central role in the field of crop improvement.

The present PhD project attempts to better understand how structural and functional variation of genomes is responsible for the tolerance to an abiotic stresses (mainly low temperature and light) in an economically relevant cereal species (selected at the beginning of the project). The biological information available with the Crop Production research group, mainly in the form of genomic and transcriptomic data, will be analysed with different statistical and bioinformatics tools and techniques to increase the resilience of small grain cereals. Comparison of genomic sequences, identification of structural variants, INDELs and SNPs in candidate genes, transcript profiling in contrasting conditions will be some of the activities carried out by the doctoral fellow.

A period of activity (from 6 to 12 months) is expected to be carried out at a foreign research institution to acquire specific skills regarding the study of copy number variation in plants and how it may have phenotypic effects in crops.

Required skills: Knowledge of plant genetics and genomics, plant breeding, plant ecophysiology, plant biotechnology, basic bioinformatics. PhD student will be supposed to publish one scientific article per year.

 

2) Title of the Research Topic: Innovation in breeding of medical Cannabis

1 (one) position with grant

Scientific Tutor: Prof. Nicola Pecchioni

Research topic: The need to enhance the production of medical Cannabis and to have new genetic sources more suitable for the needs of patients is nowadays of great relevance as well as of considerable scientific interest and strong media impact so as to be a strategic objective of the new National Action Plan for Addictions 2021-25. This research proposal fits into this context with the aim of renewing and expanding the portfolio of Italian Cannabis varieties for medical use, responding to the actual needs of the medical supply chain which requires the availability of an easily standardized product characterized by strong prevalence of one cannabinoid over all the others (primarily THC).

The PhD project will include the detailed chemical (cannabinoid content) and genetic characterization of high-THC genotypes present in the germplasm collection preserved in Rovigo (Year 1). Based on the results, the most promising materials will be crossed, and the progeny will be selected for the content in Δ9-THC> 15% (Year 2). The genotypes with the desired chemical profile will be evaluated for stability, agronomic, and productive aspects to select those most suitable for indoor production for pharmaceutical use (Year 3). The new varieties will be genotyped with NGS technologies to ensure their authenticity. Through all the project, other studies of physiological and genomic regulation of cannabinoid biosynthesis will be carried out.

At the same time, the possibility of further raising THC levels and eliminating the possible presence of CBD and CBC through NBTs (New Breeding Techniques, also named TEA, Tecnologie di Evoluzione Assistita) will be investigated, carefully choosing the target to be edited based on the new genetic knowledge acquired. For a successful realization of the project, the candidate will spend a period of at least 6 months in laboratories where he/she could develop knowledge in NBTs applied to medical Cannabis.

 

3) Title of the Research Topic: Study of Anti-spoilage Activity and Exopolysaccharides Production by selected Lactic Acid Bacteria

1 (one) position with grant

Scientific Tutor: Prof. Andrea Pulvirenti - co-Tutor: Dr. Luciana De Vero

Research topic: Lactic acid bacteria (LAB) have been used, since ancient times, to preserve a wide range of fermented foods, including bread, vegetables and dairy products.

Different LAB strains can produce different types of metabolites, including active amino acids, peptides, sugars and volatile compounds, which also contribute to the final flavor of fermented food products. Some LABs have beneficial technological applications in fermented foods and beverages due to their functional activity. LABs are being studied as preservative agents to control spoilage agents, which are commonly found in cereals and grain-derived food products, causing deterioration in quality and sensoriality. Although chemical preservatives are still widely used, the food industry is forced to provide innovative products by reconsidering the microbial fermentation process and biocompounds as an alternative to meet consumer demands for clean and healthy food.

Therefore, our research is aimed at obtaining new starter cultures capable of guiding the fermentation process and improving microbiological safety and food quality.

The selected candidate will be involved in the following tasks:

- Management of microbial cultures and online databases;

- Polyphasic characterization of microbial cultures;

- Technological screenings for starter culture selection;

- Publication of scientific papers;

- Supervision of master students in executing their research projects.

The project requires the PhD student to spend a period abroad of 6 months, not necessarily consecutive.

 

4) Title of the Research Topic: Exploring the ecology of intestinal microbes and their genetic adaptation to the mammalian gut

1 (one) position with grant

Scientific Tutor: Prof. Maddalena Rossi - co-Tutor: Dr. Stefano Raimondi

Research topic: The mammalian gut is densely inhabited by microorganisms that have coevolved with their host. In this project, we aim to investigate by metagenomic and culturomic approaches the genetic diversity and the ecology of intestinal microorganisms, and to discover how gut microbes colonize and survive in the mammalian gut, so as to facilitate host interactions. Specific functions will be surveyed developing new bioinformatic pipelines, in order to disclose genetic diversity and contributions of gut prokaryotes. The PhD student is expected to spend a period (at least 6 months) of study and research related to this topic at foreign Universities and research bodies.

The project will focus on:

- Metagenome analysis through amplicon sequencing and WGS;

- Functional metagenomics;

- Isolation, physiological characterization, and immunomodulatory properties of gut microbes.

 

5) Title of the Research Topic: Chemometrics and green technologies for a low environmental impact agri-food system

1 (one) position with grant

Scientific Tutor: Prof. Alessandro Ulrici - co-Tutor: Dr. Rosalba Calvini

Research topic: Focused on an efficient and sustainable management of agri-food supply chains, the activity of the PhD student will aim at developing intelligent optical sensors, based on chemometric processing of spectroscopic and of RGB and hyperspectral imaging data; in fact, these sensing systems are a green alternative to the monitoring techniques currently adopted in the agri-food production and processing sectors. The versatility and transversality of these green technologies make it possible to monitor agri-food production along the entire supply chain, "from farm to fork", allowing to react quickly and efficiently to the new challenges posed by climate change.

In particular, the objectives of the research activity will be focused on various aspects related to the evaluation of the quality of food, raw materials and waste products, including for example: i) the development of non-destructive techniques based on NIR-Hyperspectral imaging for the automated detection of fruit defects in the post-harvest phase, useful to reveal damages not visible to the naked eye, increasing product quality and minimizing waste through timely use of damaged products; ii) the automated in-field assessment of the degree of phenolic ripeness of grapes by means of RGB imaging (smartphone), in order to reduce the use of chemical reagents for laboratory analysis, to allow greater timeliness in defining the ripening period of the grapes, and to minimize phytosanitary treatments, with positive repercussions on the environment; iii) the implementation of spectroscopic techniques for real-time evaluation of the chemical composition of agri-food wastes and by-products, for their valorization in the context of circular economy.

The candidate must have knowledge of Chemometrics and of its application to spectra and image analysis. Strong communication attitude in English, autonomous data elaboration and high motivation are highly valued. The project requires the PhD student to spend periods abroad for a total of 6 months.

 

6) Title of the Research Topic: Insight into bacterial cellulose production and scaling up

1 (one) position reserved for employees of BIOWEG UG

Scientific Tutor: Prof. Maria Gullo

Research topic: The PhD research project aim at investigating acetic acid bacteria strains for their ability to produce bacterial cellulose in controlled conditions. The project is based on the integration of microbiological, biotechnological and bioinformatic expertise. Different approaches of strain selection, characterization and processes optimization will be evaluated, at laboratory and prototype scale. Main output obtained at laboratory scale will be transferred to prototype scale for the validation of the best strains/conditions for bacterial cellulose production. Further research activity will be devoted to characterize bacterial cellulose according to the properties required for detected uses.

The applicant should have a strong biological background, motivation to work in national and international research teams, ability to process acquired data and presenting written and oral scientific reports.

 

7) Title of the Research Topic: Microbial Resources and starter culture innovation in the food and beverage field

1 (one) position without grant

Scientific Tutor: Prof. Andrea Pulvirenti - co-Tutor: Dr. Luciana De Vero

Research topic: The selection of new strains, the renewal of management of microbial resources, and new technologies allow continuous improvements in the food and beverage industry. The main topic of this Ph.D. program is to improve microbial-driven fermentation processes and exploit positive innovative impacts of microbial resources on the safety, sensorial and functional properties of different kinds of food and beverage.

The selected candidate will be involved in the following tasks:

- Management of microbial cultures and online databases;

- Polyphasic characterization of microbial cultures;

- Technological screenings for starter culture selection;

- Publication of scientific papers;

- Supervision of master students in executing their research projects.

 

8) Title of the Research Topic: Plants VOCs: how SVs can influence VOC emission, and their role in Forest Medicine

1 (one) position without grant

Scientific Tutor: Dr. Laura Arru - co-Tutor: Prof. Luca Forti

Research topic: Sound Vibration (SV) is an oscillatory pressure wave transmitted through gases, liquids, and solids, and, like many other variables such as light, water, or temperature, it can affect plants. Some physiological growth stages like seed germination, or other molecular level-triggered responses like phenolics content, ATP production, hormone synthesis, etc., can be influenced by SVs. Recent studies show that SVs can enhance stress resistance, root development, flower and fruit number, and chlorophyll content in the leaves and stem. Also, plant-produced Volatile Organic Compounds (VOCs) are expected to be modulated in response to SVs, even if this aspect of research is still quite incomplete.

As well as in the communication used by plants, VOCs are also important for humans. Over the past 40 years in Japan, medical research has deepened behind what is called ‘Shinrin-yoku’ or Forest Bathing. Benefits are not only as a therapy for people who suffer from depression, anxiety, mental health issues and physical complaints such as high blood pressure, but also as preventive medicine. Component of this Shinrin-yoku effect are the compounds that can be inhaled inside a forest.

The Research will investigate VOC emission and other physiological responses under SV stimulus, and the different qualitative and quantitative presence of SVs in different natural and urban environments. The outcome, besides a deeper and better knowledge in this unexplored field of basic research, will add a piece of knowledge about the communication of plants with volatile compounds, and about the nature of these components in forests.

Required skills: the candidate should possess initiative and problem-solving skills, he should be motivated and have a good attitude both to independent work and to teamwork in a highly cross disciplinary environment. The successful candidate must have a Master degree in Biology, Natural Sciences, Agricultural Sciences, Environmental Sciences or closely-related areas.