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BIOANALYTICAL CHEMISTRY

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BIOANALYTICAL CHEMISTRY

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Academic year 2023/2024

Course ID
BIO0227
Teachers
Laura Anfossi
Federica Dal Bello
Marco Vincenti
Fabio Di Nardo
Year
1st year
Teaching period
Annual
Type
Distinctive
Credits/Recognition
12
Course disciplinary sector (SSD)
CHIM/01 - analytical chemistry
Delivery
Formal authority
Language
English
Attendance
Obligatory
Type of examination
Written and oral
Prerequisites
Knowledge of the basic principles of (1) vector and matrix algebra, (2) analytical, physical, organic, and inorganic chemistry, and (3) biochemistry immunology and molecular biology.
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Sommario del corso

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Course objectives

Module: Bioanalytical Chemistry (Dal Bello, 1st semester)

The teaching, which is distinctive, offers as principal objective the learning of the basic principles of the bioanalytical chemistry and of the techniques used in bioanalytical laboratory. In particular the objectives to be reached are: learning the role of bioanalytical chemistry; detailed knowledge of sampling and extractive procedures of bioanalytical samples analysis; detailed knowledge of the separation techniques and their applications; learning the main instrumental techniques used in the biochemical, biopharmaceutical and biomedical fields; learning the validation of bioanalytical techniques.

The aim of the course is to provide students with the tools for understanding and solving bioanalytical problems using the appropriate techniques of samples pre-treatment and analysis.  applicability in the biochemical and biopharmaceutical fields.

Module: Chemometrics (Vincenti, 2nd semester)

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 (including calibration), by means of the correct choice of statistical approaches. 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.

Module: In vitro diagnostics (Anfossi, Di Nardo, 2nd semester)

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.

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Results of learning outcomes

Module: Bioanalytical Chemistry (Dal Bello, 1st semester)

At the end of the course, students will be able to:

  • understand the use and importance of bioanalytical chemistry for the analysis of samples in the biochemical, biopharmaceutical and biomedical fields.
  • know the sampling methods for bioanalytical chemistry analysis
  • know when to use the illustrated bioanalytical techniques
  • understand the importance of analytical techniques to address biochemical, biotechnological and biopharmaceutical problems
  • critically evaluate the experimental results reported in the literature and discussed during the exercises (independent judgment)
  • use the correct bioanalytical terminology (communication skills)

Module: Chemometrics (Vincenti, 2nd semester)

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.

Module: In vitro diagnostics (Anfossi, Di Nardo, 2nd semester)

  1. 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
  2. Ability to apply knowledge and understanding: The students should be able to apply the learned concepts to contexts of practical application.
  3. 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
  4. 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
  5. 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
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Program

Module: Bioanalytical Chemistry (Dal Bello, 1st semester)

  • introduction to bioanalytical chemistry: what is it and the role of the science
  • sampling and sample extraction, preparation, and purification
  • separation techniques (GC, LC, TLC): principles of chromatographic separations. Liquid chromatography: partition, adsorption, ion exchange, size exclusion and affinity chromatography. Gas chromatography. Thin layer chromatography
  • techniques of analysis of biosamples: basic principles and applications of the techniques. UV-Vis, fluorescence and phosphorescence, atomic and emission spectrometry, vibrational spectroscopy (infrared, raman, sers), NMR, electroanalysis, mass spectrometry, ICP-MS, microchip and microarray (in-depth analysis in the module of In vitro diagnostics).
  • calibration and validation of bioanalytical methods (in-depth analysis in the module of Chemometrics)

Module: Chemometrics (Vincenti, 2nd semester)

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.

Module: In vitro diagnostics (Anfossi, Di Nardo, 2nd semester)

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

Detection strategies: absorption, scattering (turbidimetry and nephelometry), reflectance photometry, luminescence phenomena (fluorescence, 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).

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Course delivery

Module: Bioanalytical Chemistry (Dal Bello, 1st semester)

The module includes 40 hours of classroom teaching lessons (5 CFU), which involve interaction between students and the professor. Bibliography articles to be read at home will be assigned to critically comment in the classroom the obtained results and the methods used. The analysis of the articles in question will be: corrected by the professor, self-assessed by the student following the correction keys provided by the professor, and evaluated among colleagues with the aforementioned correction keys. For the discussion of the bibliographic articles, small groups of students will be formed.

During the lectures, students will be encouraged to use apps such as Mentimeter, Kahoot or similar, to answer short questions proposed by the professor. Using this method, any learning problems can be highlighted and solved together.

The platform course contains the material of the lessons (slides and videos when present) and the bibliography articles with the analysis proposed during the lessons.

Module: Chemometrics (Vincenti, 2nd semester)

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.

Module: In vitro diagnostics (Anfossi, Di Nardo, 2nd semester)

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.

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Learning assessment methods

Module: Bioanalytical Chemistry (Dal Bello, 1st semester)

The exam consists of a written test lasting 1 hour. The test contains 20 specific short open questions and 2 general open-ended questions aimed at verifying the learning and mastery of a specific analytical language. Each of the 20 short questions is assigned a score of 0, 0.5 or 1 point; each of the 2 general open questions is assigned a maximum score of 7. Scores > 32 might be cum laude.

Student can request an oral examination (optional) to increase the score acquired in the written test. If, following the oral examination, the score is lower than that obtained during the written test, the student can: accept the previous grade of the written test, or take the oral examination again (two opportunities) within 12 months of the written test, or refuse the score and take the written test again.

Module: Chemometrics (Vincenti, 2nd semester)

An oral examination of the candidate is conducted along 45-60 minutes, and represents a significant stage of individualized teaching. The student is asked to illustrate theroretical concepts in a logical sequence, to express definitions using appropriate nomenclature, to answer to specific questions, to logically deduce consequences and/or practical operating conditions from the learned theoretical concepts. The aspects of narrative coherence, phenomenology understanding, and deducing proficiency are considered at the highest grade. In order to develop this expertise, it is strongly recommended to study in groups (not individually), so as to allow wide discussion of concepts, comparison of interpretations, and reciprocal explanation of content and ideas. Ultimate objective of the assessment is to make evident to the student how deep is its theoretical knowledge, how this knowledge has been translated into real expertise, and how much he/she is capable of transferring this competence to somebody else.

Module: In vitro diagnostics (Anfossi, Di Nardo, 2nd semester)

An oral examination of the candidate is conducted along 30-40 minutes. The student is asked to illustrate concepts by using appropriate language, to answer to specific questions, and to logically connect concepts.

The final grade will be assessed based on the weighted average of the grades of three tests.

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Support activities

Module: Bioanalytical Chemistry (Dal Bello, 1st semester)

Professor is available to receive students by appointment for the clarification of individual doubts. On the platform it is possible to ask questions (even anonymously) directly to the professor using the forum section.

Suggested readings and bibliography



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Book
Title:  
Chemometrics: Statistics and Computer Application in Analytical Chemistry, 3rd Edition
Year of publication:  
2016
Publisher:  
Wiley-VCH Verlag, Germany
Author:  
Mathias Otto
ISBN  
Required:  
No


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Book
Title:  
Grokking Machine Learning
Year of publication:  
2021
Publisher:  
Manning Publications
Author:  
Luis G. Serrano
ISBN  
Required:  
No


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Book
Title:  
Applied Chemometrics for Scientists
Year of publication:  
2007
Publisher:  
John Wiley & Sons Ltd., England
Author:  
Richard G. Brereton
ISBN  
Required:  
No


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Book
Title:  
Chemometrics: Data Analysis for the Laboratory and Chemical Plant
Year of publication:  
2003
Publisher:  
John Wiley & Sons Ltd., England
Author:  
Richard G. Brereton
ISBN  
Required:  
No


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Book
Title:  
Tools and trends in bioanalytical analysis
Year of publication:  
2022
Publisher:  
Springer
Author:  
Lauro Tatsuo Kubota, José Alberto Fracassi da Silva, Marcelo Martins Sena, Wendel Andrade Alves
ISBN  
Required:  
No


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Book
Title:  
Biomolecular and Bioanalytical Techniques: Theory, Methodology and Applications
Year of publication:  
2019
Publisher:  
John Wiley & Sons Ltd
Author:  
Vasudevan Ramesh
ISBN  
Required:  
No


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Book
Title:  
Fundamentals of Analytical Chemistry
Year of publication:  
2022
Publisher:  
Cengage
Author:  
Douglas A. Skoog, Donald M. West, F. James Holler, Stanley R. Crouch,
ISBN  
Required:  
No


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Book
Title:  
The Immunoassay Handbook Theory and Applications of Ligand Binding, ELISA and Related Techniques, 4th ed
Year of publication:  
2013
Publisher:  
Elsevier LTD
Author:  
David Wild
ISBN  
Required:  
No
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The presentations slides together with depth study papers are available in the e-learnig UniTO moodle website



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