Biotechnological and Chemical Sciences in Diagnostics

ANALYTICAL AND STRUCTURAL METHODS IN DIAGNOSTICS

ANALYTICAL AND STRUCTURAL METHODS IN DIAGNOSTICS

Academic year 2024/2025

Sommario del corso

• Course objectives
• Results of learning outcomes
• Program
• Course delivery
• Learning assessment methods
• Support activities
• Notes
• Teaching Modules
• Teaching tools
• Course card

Course objectives

The teaching contributes to the realization of the educational objectives of the physico-chemical and analytical areas of the Master in Biotechnological and Chemical Sciences in Diagnostics. The teaching provides:

(i) the theoretical and practical basis of electronic and atomic force microscopies, colloidal systems and plasmonic nanoparticles.

(ii) learning of the most common statistical tools to conduct multivariate chemometric analyses of large datasets. Ability to develop an original chemometric strategy to tackle complex problems of experimental design, classification, and regression. Ability to use a suitable statistical strategy to obtain grounded decision making policies, based on sound inferential procedures. Ability to apply the acquired theoretical concepts to real cases of diagnostic analysis.

(iii) knowledge of the principles of the analytical methods underlying the common diagnostic devices. Knowledge of the principal detection strategies adopted for the development of in vitro diagnostics. Ability to recognize limits and potential of the different methodological approaches, also as a function of the analytical requirements. Ability to apply the theoretical concepts to examples of applications of in vitro diagnostics.

More details can be found in the description of the specific Modules

Results of learning outcomes

Electron microscopy (Berlier)

Knowledge and understanding

- understand the electronic and optical properties of plasmonic nanoparticles, how these are affected by the environment and how these properties can be exploited for technologically important fields such as nanobiotechnology and diagnostics

- know the principles of electron and atomic force microscopies, their potentiality, limitations and fields of application

- know the basics about crystalline materials and the information that can be obtained by diffraction

- know the basics of Circular Dichroism and its usefulness in the study of biomolecules

Apply knowledge and understanding

- read and interpret SEM, TEM and AFM images

- extract quantitative information from SEM, TEM and AFM images (particle size distribution, surface roughness, etc.)

- correctly interpreting the changes in the optical properties of plasmonic NPs as a function of the environment

- analyse CD spectra and extract information on the secondary structure of biomolecules

Making judgements

- Critically choose the proper technique in relation to the desired information and application

- Be aware of the techniques potentialities and limitations

Communication skills

- Correctly use terms specific to the chemistry of colloids

- Correctly use terms and techincal language specific to electronic and atomic force microscopies

- acquire appropriate skills and tools for processing and presenting experimental data

- know how to work in groups

Learning skills

- To develop autonomous learning skills and self-assessment of their own preparation,
apt to undertake subsequent paths with a high degree of autonomy

Data analysis (Vincenti)

The module recalls fundamental concepts of linear algebra and express the new statistical content with substantial in-depth mathematical abstraction. Therefore, the program explained in classroom should necessarily be integrated by personal and collective thinking over during homework. At the end of this process, the students should exhibit adequate control of the subject and be able to describe the different topics with appropriate terms, following orderly, rational, and consequent sequences of cause and effect. They should also be able to apply the learned concepts to contexts of practical application in diagnostics.

In vitro diagnostics (Anfossi, Di Nardo)

Knowledge and understanding

The students should exhibit adequate knowledge of the principle of the analytical methods, of detection strategies and of the principal platforms of vitro diagnostics

Ability to apply knowledge and understanding

The students should be able to apply the learned concepts to contexts of practical application.

Autonomy of judgment

The students should be able to critically discuss limitations and fields of application of the different analytical approaches and platforms commonly adopted for in vitro diagnostics development

Communication skills

The students should be able to describe the different topics with appropriate terms, following orderly, rational, and consequent sequences of cause and effect

Learning abilities

The students should be able to connect arguments and to propose solutions to simple problems of the application of diagnostics to clinically relevant biomarkers

Program

Electron microscopy (Berlier)

The course aims at providing fundamental knowledge about electronic and atomic force microscopies and about the properties of matter at the nanoscale with a specific focus on the stability of nanoparticles in colloidal systems, and how this is affected by their interaction with (bio)molecules. A class of inorganic nanoparticles (plasmonic NPs) with applications in bioimaging and nanomedicine are specifically addressed.

Data analysis (Vincenti)

The module introduces the most effective statistical and chemometric techniques for multivariate analysis of experimental data and decision making.

Definition and methods to approach complex systems and their multivariate structure. Role of chemometrics in the recognition of holistic effects and macro-properties of complex systems. Data organization in matrices. Mathematical transformation and scaling of data. Concepts of distance between objects, similarity, correlation, and covariance. Analysis of variance. Principal components analysis and its graphical representations. Methods of cluster analysis. Experimental design. Objective function and its modelling as a function of the experimental parameters. Regression techniques and model testing. Analytical methods' validation: calibration, limits-of-detection, accuracy, matrix effect and recovery. Classification analysis and class-modelling. Confusion and loss matrices. Weighted Gini impurity. Receiver operating characteristic curves. Prior odds in Bayesian statistics. Classification methods: SIMCA, K-NN, discriminant analysis, naïve Bayes, decision trees, random forest, logistic regression. Single and multiple ordinary least squares regression.  Examples of real diagnostic applications.

In vitro diagnostics (Anfossi, Di Nardo)

Principle of analytical methods based on molecular recognition properties: immunological, molecular, and enzymatic methods. Formats and methodological approaches: direct and indirect, homogeneous and heterogeneous.

Principle of electrophoresis on solid support and in capillary.

Detection strategies: scattering (turbidimetry and nephelometry), reflectance photometry, luminescence phenomena (chemiluminescence and bioluminescence), electrochemical measurements. Nature and properties of the main probes (enzymes, fluorophores, chemiluminescent molecules, beads, nanoparticles).

Point of care tests: principles, set-up, and operation.

Qualitative and quantitative testing.

Validation of in vitro-diagnostics

Examples of methods used for the measurements of clinically relevant biomarkers (tumor markers, infectious diseases diagnosis, hormones, biomarkers of chronic pathologies, etc).

More details can be found in the description of the specific Modules

Course delivery

Electron microscopy (Berlier)

The theoretical lectures are in English, supported by presentations (ppt) with graphic illustrations in English. Laboratory activities involve the active participation of the student.

Participation to the lab activities is compulsory.

Data analysis (Vincenti)

The module includes 24 hours of classroom teaching (3 CFU). Recap activities in groups of 3 students are promoted. The teaching material plus supporting materials are made available on Moodle.

In vitro diagnostics (Anfossi, Di Nardo)

The module includes 32 hours of classroom teaching (4 CFU). The teaching material (slides), supporting materials and sample exam questions are made available on Moodle.

More details can be found in the description of the specific Modules

Learning assessment methods

The exam will be in oral form.

The final mark is expressed in thirtieths, and will be computed averaging the grade of the different parts, weighted for the number of CFU

Part on Electron microscopy: weight in the final grade = 4/11

Part on Data analysis: weight in the final grade = 3/11

Part on In vitro diagnostics: weight in the final grade = 4/11

Acquisition and understanding of basic knowledge in Chemistry will be evaluated if necessary in relation to the program, as well as the use of a proper scientific/technical language.

Support activities

Teaching materials (lecture slides, in-depth scientific articles, etc.) related to the teaching is made available before the lectures on Moodle platform. Regarding the practical part of the teaching, laboratory protocols are provided during the experiments and uploaded on Moodle at the end of the activity, so as to include the data obtained in the experiences conducted by the different groups of students/students.

Students are reminded to register for teaching on the Moodle platform so that they can consult the teaching materials and receive any timely communications.
In addition, the lecturers make themselves available to answer any doubts related to the topics of the lectures or laboratory activities, during the lessons or by prior appointment via email.

Notes

See specific Modules description for suggested readings and bibliography

Teaching Modules

• Electron Microscopy (BIO0259B)
• In vitro diagnostics and data analysis (BIO0259A)

• Teaching material
• Exams and finals
• Class schedule
• Go to Moodle
• Register for the course
• Enrolled students
• Invia email agli studenti registrati
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