Principles of Physiological and Metabolic Processes in Agriculture

A.Y. 2023/2024
10
Max ECTS
88
Overall hours
SSD
AGR/13 AGR/16
Language
Italian
Learning objectives
The course will provide students the basic knowledge of the fundamental biochemical and physiological processes of plants, with the general objective of understanding mechanisms most involved in the determination of crop plant yield, also in unfavourable environments. The course also proposes to provide the fundamental notions concerning General and Agro-Food Microbiology and basic microbiological techniques for the analysis of food samples. These skills will be acquired both through lectures and classroom exercises concerning the resolution of biochemistry problems and through laboratory exercises related to biochemical and microbiological analyses aimed at defining the quality of agricultural-food products.
Expected learning outcomes
The student will acquire the knowledge of the mechanisms regulating energy transfer and carbon metabolism in plants and in microorganisms, and of the biochemical and physiological factors underlying the productivity in the agro-food sector, even in unfavorable environments. At course completion, the acquired knowledge will be useful to face practical problems in agricultural contexts, also through the application of basic biochemical and microbiological techniques for the analysis of agro-food samples. Participation in classroom exercises, laboratory activities, and oral or written assessment methods will contribute to the development of communication skills. Furthermore, the use of diversified study tools (manuals, on-line material made available by the Teachers, personal notes, on line resources) will help to develop the ability to find independently information and useful ideas for future job activities.
Single course

This course can be attended as a single course.

Course syllabus and organization

Single session

Responsible
Lesson period
Second semester
Course syllabus
T.U. 1 - BIOCHEMISTRY AND PLANT PHYSIOLOGY - GIAN ATTILIO SACCHI - FRONTAL LESSONS 6 CFU
The Course describes the fundamental biochemical and physiological processes of higher plants, whose knowledge is mandatory for understanding the main mechanisms involved in determining crop yield, also in unfavourable environments.

COURSE SYLLABUS - SYNTHESIS
In synthesis, the Course syllabus foresees the topics following listed.
BIOENERGETICS AND BIOCHEMISTRY: 1) Thermodynamics and Bioenergetics (0.75 CFU); 2) Enzyme catalysis (0.75 CFU); 3) Energy metabolism: Glycolysis, fermentation, TCA cycle, and other pathways of carbon metabolism; Oxidative phosphorylation (1.5 CFU).
PLANT PHYSIOLOGY; 1) Photosynthesis: light reactions and assimilation reactions, ecophysiology of photosynthesis (1.5 CFU); 2) Plant-water relations; transpiration, stomata regulation, water transport in the xylem; translocation of photosynthates and sink-source relationships (1 CFU): 7) Mineral nutrition: chemical and electrochemical potentials, solute absorption and assimilation (0.5 CFU).
COURSE SYLLABUS
BIOENERGETICS AND BIOCHEMISTRY
Principles of bioenergetics and thermodynamics (0.75 CFU): thermodynamic systems and their environments; I and II thermodynamics laws; entropy and free energy; exo- and endo-ergonic reactions; energetically coupled reactions; ATP and phosphor group transfer; other high-energy compounds; carbon redox states in compounds of biological interest; oxy-reduction potential; relationship between delta E and delta G; oxy-reduction coenzymes; redox reactions of biological interest
Thermodynamic and kinetic aspects of enzymatic catalysis. (0.75 CFU): Michaelis-Menten's equation; Inhibition and regulation of enzyme-catalyzed reactions
Metabolic reactions: the concepts of catabolism and anabolism (1.5 CFU): carbon metabolism: degradation of storage polysaccharides (starch); glycolysis and lactic and alcoholic fermentation; energy yield of anaerobic glucose degradation; the Krebs cycle; electron flux and oxidative phosphorylation; Mitchell's chemiosmosis theory; energy yield of glucose aerobic degradation; other mechanisms of O2 consumption in plants; other pathways of glucose degradation: the pentose-P pathway; basic aspects of the metabolism of storage lipids: energy yield of fatty acids degradation; basic aspects of storage lipid degradation in plants.
PLANT PHYSIOLOGY
Photosynthesis: (1.5 CFU): the electromagnetic spectrum; energy content of different wavelength radiations; photosynthetically active radiation; absorption and action spectra; photosynthetic pigments: excitation and de-excitation phenomena; Photosystems, light-harvesting complexes, reaction centers; energy transfer from the light-harvesting complexes to the reaction center; accessory pigments; photosynthetic electron flow and phosphorylation: the Z scheme; non-cyclic and cyclic photophosphorylation; herbicides disrupting the photosynthetic electron transport; photooxidative damage; carbon assimilation: C3 and C4 cycles, CAM metabolism; photorespiration; responses to light and temperature: light compensation point, CO2 compensation point.
Plants and water (1 CFU): definition of water potential and factors contributing to it in the plant cell: pressure, temperature, presence of solutes; components of water potential in the plant cell: solute potential, matric potential, pressure potential; osmotic phenomena: Van't Hoff's law. Isotonic, hypotonic, and hypertonic solutions; plasmolysis, cell turgor; Expansion growth; the soil-plant-atmosphere continuum; water absorption by roots: the apoplastic and symplastic pathways; transpiration; the driving force for the ascent of the xylem sap in the xylem; loss of water through the stomata, regulation of stomata opening; photosynthate translocation in the phloem: osmotically generated pressure flow; role of active transport of H+ in sucrose loading and unloading; sink-sources relationships.

Mineral nutrition (0.5 CFU): plant nutrient requirements (micro- and macronutrients); nutrient availability and plant growth; solute transport in plant cells; cell membranes and the plasmalemma: their role in cell physiology; selective permeability; chemical and electrochemical potentials and their role in determining the direction of solute flux; diffusion, active and passive transport; the Nernst's equation; carriers and ion channels; role of the PM H+-ATPase in generating the transmembrane electrochemical proton gradient and its role in secondary active transport; absorption and assimilation of N, S and P; micronutrient absorption: the case of Fe; heavy metal toxicity: the case of Al; mechanism of resistance to heavy metals: exclusion and detoxification.
Specific topics will be broadened by exercises in the classroom.

T.U.2 - GENERAL AND AGRO-FOOD MICROBIOLOGY - MANUELA SILVIA ROLLINI - FRONTAL LESSONS 3 CFU, LABORATORY ACTIVITIESI 1 CFU
The course provides fundamental notions regarding morphology, physiology, metabolism and function of micro-organisms in nature, with reference to their use in agricultural biotechnologies concerning environmental protection, animal and plant production, food processing.

COURSE SYLLABUS - SYNTHESIS
In summary, the Course syllabus includes the presentation and the discussion of the following topics:
1) Morphology and cytology of prokaryotes and eukaryotes (0.25 CFU). 2) Microbial growth, its evaluation and control (0.35 CFU). 3) Bacterial viruses (0.15 CFU). 4) Microbial metabolism (0.5 CFU). 5) Genetics of prokaryotes (0.5 CFU); 6) Microbial ecosystems: interactions between microorganisms, animals and plants (0.75 CFU). between microorganisms, animals and plants (0.5 CFU). 7) Microbial groups involved in the main food trasnsformations (0.75 CFU). 8) Laboratory (1 CFU): bacterial cultures, microscopy, and microbiological analysis.
COURSE SYLLABUS
GENERAL MICROBIOLOGY
The Microbial world (prokaryotic cell): structure, functions; comparison with eukaryotic cell; morphology of prokaryotic cell and of eumycetes.
Microorganisms nutritional requirements: factors influencing microbial growth: pH, temperature, free water availability, oxygen availability.
Bacterial growth control: antimicrobial (physical and chemical) treatments and factors influencing their effectiveness; antibiotic resistance.
Bacteriophages: lytic and lysogenic cycle.
Microbial metabolism: catabolism and anabolism relationships; the main energetic metabolic pathways (aerobic respiration, anaerobic respiration, fermentation).
The genetic recombination: transformation, conjugation and transduction; principles of mutations.
Main concepts of microbial phylogenesis and classification: definition of genera, specie and strain. Identification criteria.

AGRO-FOOD MICROBIOLOGY
Interactions between micro-organisms in microbial ecosystems: nneutralism, competition, amensalism, predation, commensalism, parasitism, mutualism.
Interactions between micro-organisms and plants: mutualistic symbiosis.
The main microbial groups involved in food production and storage.
Identification and classification of the main eumycetes involved in the food sector.

LABORATORY ACTIVITIES
Work in sterility, sterilization techniques. Bacterial growth and culture media. Transplantation, isolation in pure culture, research of specific microbial groups in environmental and food samples.
Prerequisites for admission
Complete understanding of the Course contents strictly depends on the knowledge from previous courses of fundamentals of Plant Biology, Physics, Inorganic Chemistry and Organic Chemistry. Such prerequisites apply to all students, whether attending the Course or not.
Teaching methods
The Course uses e-learning teaching tools present in the Ariel 2.0 platform (Power Point slides, video recordings of the lectures).
Teachers will use: a) frontal lessons; b) classroom exercise; c) laboratory practices (Microbiology). All the activities will contribute to gaining the Expected Learning Outcomes (see dedicated paragraph).
Attending the lectures is strongly recommended.
Teaching Resources
T.U.1
Nelson D., Cox M. "Introduzione alla biochimica di Lehninger", ed. Zanichelli (T.U. 1, Biochemistry).
Pinton et al., Fondamenti di Biochimica Agraria, Patron Editore, Bologna (T.U. 1, Biochemistry).
D'Andrea G. Biochimica Essenziale EdiSES (T.U. 1, Biochemistry).
N. Rascio, "Elementi di Fisiologia Vegetale", Edises (T.U. 1, Plant Physiology).
R.F Evert, S.E Eichhorn, Biologia delle piante di Raven, Zanichelli (T.U. 1, Biochemistry and Plant Physiology).
Notes from the course lectures. Copy of the slides shown during the lectures will be made available to the students of the Degree Course on the website http://ariel.unimi.it. (Prof. Gian Attilio Sacchi).

T.U.2
B. Biavati e C. Sorlini, 2012: Microbiologia generale e Agraria. Vol. 1, Casa Editrice Ambrosiana, Milano.
On http://ariel.unimi.it (Prof. Manulea Silvia Rollini) the material for the laboratory practices and the files with all the slides showed during the lessons are available; moreover it is present additional and integrative material about the topics covered.
Assessment methods and Criteria
The student should demonstrate the ability to elaborate the Course contents by integrating them with those of the prior Courses. There is no mandatory prerequisite concerning other Courses of the Study Course. Nevertheless, successfully getting through the First Year Courses (Plant and Animal Biology, Physics, General and Inorganic Chemistry and Organic Chemistry) is strongly recommended before starting to study the topics inherent to the exam.

Knowledge and understanding of the topics of the first part of the course (first 3 CFUs of T.U. 1) are imperative to understand the topics that will be considered subsequently concerning both Plant physiology (last 3 CFUs of T.U. 1) and Microbiology (4 credits, T.U. 2) issues.
In this framework, and to facilitate the exam preparation, an assessment of the student's knowledge about the first 3 CFU of T.U.1 will take place as a first written test. This test consists of 4/5 open-ended questions concerning principles of Thermodynamics and Biochemistry. The questions can also include figures and tables that must be described and discussed.
Moreover, concerning T.U.1, at the end of the lessons concerning the last 3 CFUs (Plant Physiology), a second written test will be scheduled. This test consists of 4/5 open-ended questions concerning principles of Plant physiology. The questions can also include figures and tables that must be described and discussed. Only the students who have passed the first test can take part in the second test.
Finally, for those who passed both the written tests, a colloquium will be planned to briefly discuss and deepen some issues of the T.U.1. Whenever only the first test was passed, this colloquium will consist of 2/3 questions concerning the issues of the second test. At the end of the colloquium, an overall score, considering also the results of the written tests, will be proposed.
In general, the answers in both the written tests and in the colloquium will be evaluated on the basis of the student's capability to organize his/her knowledge of the topics, speech quality, and use of proper terms.
For the students who have not passed or have decided to not address both the written tests, starting from the end of the lessons, an oral exam will be scheduled. This exam will consist of at least three questions covering all the topics of T.U.1. Also, this exam will be evaluated on the basis of the student's capability to organize his/her knowledge of the issues, speech quality, and use of proper terms. At the end of this oral exam, an overall score for the whole T.U.1 will be proposed.
In the case of T.U.2 (Microbiology), the assessment of learning is carried out through a written test, which typically includes four questions: two concerning General Microbiology (also dealing with microbiological analysis techniques) and two concerning agricultural and food microbiology, which the student will demonstrate the ability to use the knowledge gained in the course to solve agro-environmental problems in an interdisciplinary way.

Both in the case of T.U1 and T.U.2, the assessment methods and criteria of evaluation will be identical for attending and non-attending students.

The final score of the course exam (10 CUFs) will be obtained from the weighted mean, with respect to the relative CFUs, of the two Teaching Units.

Examinations will take place at Edolo with a minimum number of students equal to 5; otherwise, at the sole discretion of the commission, they will take place at the Facoltà di Scienze Agrarie ed Alimentari, via Celoria 2, Milano. The location will be, therefore, communicated to the students (online registration) by e-mail after the deadline of the registration time, i.e., 2 d before the test date. Students are therefore prompted to check regularly their institutional e-mail boxes ([email protected]) and the Ariel 2.0 notice boards.
Students enrolled on an exam session who no longer wish to take the exam are therefore required, if access to the online system is already closed, to promptly notify the teachers. If not, the student will not be allowed to take the next exam session.

Students with Specific Learning Disorders (DSA): in order to take advantage of the foreseen dispensatory and compensatory tools, it is mandatory to have delivered the appropriate certification to the UniMI DSA Service (https://www.unimi.it/en/ugov/ou-structure/cosp-disability-and-sld-services). The DSA contact for the Study Course is Prof. Fulvia Tambone ([email protected]). Furthermore, DSA students are required to agree with the Teacher(s), in due advance, the methods of examination and the eligible supporting material (logical schemes, tables, etc.), provided their specific situation has been certified.
In one solar year, six examination dates for each of the three parts of the whole exam are foreseen, scheduled according to the teaching calendar and to the week of teaching interruption. During the periods of teaching activity, examinations are NOT foreseen. Only for Off-Course students, on the basis of specific and documented requirements and upon agreement with the Teacher(s) additional exam sessions may be planned at the Faculty of Agriculture in Milan.
Any additional information about the examination procedures will be illustrated by the Teachers during the course.
AGR/13 - AGRICULTURAL CHEMISTRY
AGR/16 - AGRICULTURAL MICROBIOLOGY
Laboratories: 16 hours
Lessons: 72 hours
Professor(s)
Reception:
to be defined via email