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Integrated Laboratory VI

Code: 101942
Credits: 3
2026/2027
Degree programme Type Course
Genetics OB 3

Contact lecturer

Name :
Jordi Surralles Calonge
Email :
jordi.surralles@uab.cat

Teaching staff

Francisco José Rodriguez-Trelles Astruga
Joan Albiol Sala
Massimo Bogliolo
Ivon Cusco Marti

Group languages

You can consult this information at the end of the document.

Prerequisites

  • It is mandatory to have taken -o being currently taking- the theoretical subjects related to the experimental work developed here. 
  • Biosecurity and security tests at 'campus virtual' need to be passed. The student must prove knowledge and acceptance of the Bioscience laboratory guidelines.
  • It is necessary to go through the theoretical content of each module before the day of the practical classes.
  • Wearing a lab coat is mandatory. It is not possible to enter to the lab without a lab coat.
  • Attendance is mandatory.
  • Students should come to the class following the assigned schedule. Changes in the original schedule need to be approved by the corresponding professor and in all cases before the starting of the classes.

Objectives

The Integrated Laboratory VI is the sixth course in a set of 6 which are distributed along 6 semesters of the first three courses of the degree of genetics. These subjects aim to give a solid foundation of experimental procedures, techniques and skills of genetics and related sciences. The practical work help to reinforce the theoretical concepts acquired in the theory, and allow us to understand the essential dialogue between theory and experimentation that have given rise to the body of knowledge that constitutes the science of genetics.

The Integrated Laboratory VI has as objectives the acquisition of experimental skills in 3 specific modules of content:

  • Molecular genetic diagnostic
  • Evolution
  • Systems Biology

Module of Molecular genetic diagnosis

The practices are structured in 4 sessions of 4 hours each during which different molecular genetics techniques will be performed in order to reach the diagnosis of a genetic disease (we will take as an example the study of Spinal Muscular Atrophy).

The objectives of the practices are:

  1. Consolidate the concepts of molecular genetic diagnosis techniques
  2. Consolidate the technique and interpretation of the direct study by PCR + restriction enzymes
  3. Consolidate the technique and interpretation of the copy number quantification study by MLPA
  4. Consolidate the technique and interpretation of the Sanger sequencing study
  5. Knowing how to interpret the results of indirect studies of STRs markers (microsatellites)

The global analysis of the different results will allow us to reach the molecular diagnosis of a family with Spinal Muscular Atrophy.

 

The four practical sessions are structured as follows:

  1. Introduction of the case
    1. Review of technique
    2. PCR
    3. MLPA (part one)

 

  1. Direct study by PCR+Digestion
    1. Restriction Enzyme Digestion (RFLPs)
    2. MLPA (Part Two)
    3. PCR Sanger sequencing

 

  1. Direct study by MLPA and Sanger
    1. Interpretation of MLPA results
    2. Interpretation of Sanger sequencing results
    3. Introduction to the indirect study using PCR microsatellites

4. Resolution of the case

4.1. Interpretation of microsatellite markers

4.2. Resolution of the case

4.3. Writing final report

Module of Evolution

The main objective of the Evolution module is to help the student to learn to apply the comparative method in evolutionary inference by using molecular sequences.  The module includes the processes of hypothesis formulation and testing, obtention of sequence data for their alignment, modeling of the process of evolutionary change of the sequences, and application of methods of i) phylogenetic reconstruction, ii) characterization of the evolution of gene families, and iii) Identification of footprints of molecular adaptation.  In addition, a perspective on the levels and structure of genetic variation in Homo sapiens will be provided by comparison with what is observed in other closely related living and extinct species. Through these practices the student will acquire skills in the application of analytical techniques to biological and molecular data.

Module of Systems biology

The main objective of the module is to learn how to use the right software in systems biology and better understand the behavior of biological systems. To achieve this the student will conduct simulation exercises with computer to see how the behaviorof a biological system cannot be predicted from the behavior of itsisolated components.

Learning outcomes

  • CM18 (Integrate experimental techniques and bioinformatics tools for the collection, processing and preliminary analysis of biological data) Integrate experimental techniques and bioinformatics tools for the collection, processing and preliminary analysis of biological data
  • CM19 (Design experimental strategies and data analysis procedures for solving research problems in genetics.) Design experimental strategies and data analysis procedures for solving research problems in genetics.
  • CM20 (Evaluate the relevance, limitations, and biological significance of data obtained using experimental and computational techniques.) Evaluate the relevance, limitations, and biological significance of data obtained using experimental and computational techniques.
  • KM13 (Identify the fundamentals of experimental techniques in molecular genetics, genomics and proteomics, as well as the use of databases and associated bioinformatics tools.) Identify the fundamentals of experimental techniques in molecular genetics, genomics and proteomics, as well as the use of databases and associated bioinformatics tools.
  • KM15 (Identify quantitative and computational simulation methods for modelling and data analysis in population genetics and evolution.) Identify quantitative and computational simulation methods for modelling and data analysis in population genetics and evolution.
  • SM16 (Apply safety, biosafety and waste management protocols in the handling and processing of biological samples.) Apply safety, biosafety and waste management protocols in the handling and processing of biological samples.
  • SM17 (Use bioinformatics tools and databases for the management, analysis and simulation of genetic and genomic data.) Use bioinformatics tools and databases for the management, analysis and simulation of genetic and genomic data.
  • SM18 (Interpret experimental results and genetic data to explain the basis of phenotypes and diseases, evaluating their ethical, social, and gender implications.) Interpret experimental results and genetic data to explain the basis of phenotypes and diseases, evaluating their ethical, social, and gender implications.

Contents

Module of Molecular genetic diagnostic


The four practical sessions are structured as follows:



  1. Introduction of the case

    1. Review of technique

    2. PCR

    3. MLPA (part one)



 



  1. Direct study by PCR+Digestion

    1. Restriction Enzyme Digestion (RFLPs)

    2. MLPA (Part Two)

    3. PCR Sanger sequencing



 



  1. Direct study by MLPA and Sanger

    1. Interpretation of MLPA results

    2. Interpretation of Sanger sequencing results

    3. Introduction to the indirect study using PCR microsatellites



4. Resolution of the case


4.1. Interpretation of microsatellite markers


4.2. Resolution of the case


4.3. Writing final report


Module of Evolution



a) Alignment: obtention, reliability and interpretation.


b) Modeling of molecular evolution: problem of multiple substitutions and selection of optimal models of sequence evolution.


c) Molecular phylogenetic trees: obtention, reliability and interpretation.


d) Distribution of character states. Evolution of gene families.


e) Molecular dating. Human genetic diversity



 


Module of systems biology


The module includes practical exercises corresponding to the theory of the subject ' systems biology' and will consist in the simulation of systems for example corresponding to genetic, metabolic networks, signal transmission or of more complex systems, developed by the student with the recommended software or downloaded from databases of models according to the case.


In general the practices include exercises for the use of software and databases specific to each of the topics. These exercises will allow.


 


 

Learning activities and methodology

Title Hours ECTS Learning outcomes
Module Molecular Systems Biology 15 0.6
Lab booknote 3 0.12
Individual tutorials 1 0.04
Module Molecular genetic diagnosis 16 0.64
Study 23 0.92
Evolution Module 15 0.6

The subject is taught in small groups of students (maximum 20 per session) in the laboratory or computer rooms. Students have a manual or practice guide for each Module. It is necessary to read the corresponding part of each session carefully before starting the practice to obtain the maximum advantage. Students will have to attend the assigned group of internships obligatorily. Only occasional changes will be accepted as long as they are balanced (a student from a group for a student from another group). If a student has not been able to perform a practice session with his group, he can retrieve it by attending another group, as long as the group in question has free spaces.

Molecular genetic diagnosis

The students will have a detailed guideine of the practices with the protocols and the detailed information to be able to carry out them efficiently with the support of the teacher. The guideline will be available on the Virtual Campus of the subject. The students will not only work their data, but will analyze and interpret the set of results obtained.

Evolution

The Practicum will take place in computer rooms using several applications. Data obtained from scientific publications will be used. Different concepts and hypotheses about the evolutionary process will be illustrated through presentation of real problems. A guide to the Practicum will be available on the Virtual Campus of the subject.

Systems biology

Systems biology practices will be carried out in the computerrooms on days and hours defined in the teaching calendar.

For each practice, the student will find the practical guidelines on the virtual campus of the subject 'Systems Biology'.

The student will carry out the practice following the practice guideline and save the files generated in the folder of his personal record provided by the UAB.

When finishing the practice, the student will deliver, through the virtual campus, the files of the exercises as described in each practice.

 

 

Annotation: within the schedule set by the centre or degree programme, 15 minutes of one class will be reserved for students to evaluate their lecturers and their courses or modules through questionnaires.

Assessment

Continuous assessment activities

Title Weight Hours ECTS Learning outcomes
Module Molecular genetic diagnosis. Continuous evaluation of the results worked 33% 0.65 0.026 CM18, CM19, CM20, KM13, KM15, SM16, SM17, SM18
Module Molecular biology of systems. Continuous evaluation of the results worked 33% 0.65 0.026 CM18, CM19, CM20, KM13, KM15, SM16, SM17, SM18
Evolution Module 33% 0.7 0.028 CM18, CM19, CM20, KM13, KM15, SM16, SM17, SM18

Attendance to practical sessions is mandatory. Students missing more than 20% of programmed sessions will be graded as \"No Avaluable\".

Attendance to the practices is mandatory and therefore an absence without justification may entail the non-evaluation of one or more modules. Missing a session implies a reduction of the grade equal to% of this session in the whole module. Thus, in a module of 4 sessions, missing a day involved a reduction of 25% of the note in this module. Those students who can not attend the session of their group for just cause are exempt from this penalty. Health problems are deemed justified (the corresponding medical certificate must be carried out by the practice coordinator) or serious personal problems. In this case the practice will be recovered whenever possible.

Notwithstanding other disciplinary measures deemed appropriate, and in accordance with the current academic regulations, the irregularities committed by the student who can lead to a variation in the qualification of an act of self- evaluation. Therefore, copying or letting copy a practice or any other evaluation activity will imply suspending it with a zero, and if it is necessary to pass it to pass it, the entire subject will be suspended. Qualified assessment activities will not be recovered in this way and by this procedure, and therefore the subject will be suspended directly without opportunity to recover it in the same academic year.

Module Molecular genetic diagnosis

This module will be evaluated by means of a final exam about the experimental procedure of the practices, that will take place the last day of the practices and will count 40% of the note. The other 60% of the mark will be evaluated by delivering a practical script. In the event that the student suspends the examination, the exam may be recovered, but the maximum grade that can be obtained in the recovery will be 5. The possibility of notifying notes is contemplated. The delivery note can not be recovered in any case.

Evolution Module

The module will be evaluated with a practical test of the contents included in the module. The final qualification of the module will take into account the attitude and work of the student in the classroom.

Systems Biology

Grading of the Systems Biology module will be calculated as follows:

First part of the grade (40%) will be obtained from practical sessions 1 to 4. It will be obtained from the responses to the proposed questionnaire as well as from the proposed exercises as described in each guide for the practical work.

The second part of the grade (60%) will be obtained from the 5th practical class (last one) from the delivered simulator files and the answers provided to the proposed questions, delivered in the summary document for the 5th practical class.

In case the weighted average obtained using the above procedure would not be equal or higher to 5, the student can take a remedial exam.

For the written reports, the use of Artificial Intelligence (AI) technologies is permitted exclusively in support tasks, such as bibliographic or information searches, text correction or translations. The student must clearly identify which parts have been generated with this technology, specify the tools used and include a critical reflection on how these have influenced the process and the final result of the activity. The lack of transparency in the use of AI in this assessable activity will be considered a lack of academic honesty and may lead to a partial or total penalty in the grade of the activity, or greater sanctions in serious cases.

The final grade is the average of the notes of each module.

The commission of any irregularity in an assessment act (academic fraud, plagiarism or improper use of AI, unless this use is expressly authorized in the teaching guide), which may lead to a significant variation in the grade, means that this act will be graded with a 0. In the event that the teaching guide provides that to pass the subject it is an essential requirement to have obtained a minimum grade in this assessment act or that several irregularities occur in the assessment acts of the same subject, the final grade for this subject is 0. Apart from this, a disciplinary process may be initiated against the student who incurs any of these irregularities.

Bibliography

The scripts of the different practices will contain the specific bibliography of each one of them.

Software

- COPASI (http://copasi.org/)

Course groups and languages

The information provided is provisional until November 30. After this date, you will be able to consult the language of each group through this link. To access the information, you will need to enter the course CODE

Type of teaching Group Language Semester Shift
(PLAB) Practical laboratories 631 Catalan second semester morning-mixed
(PLABs) Suport a les pràctiques de laboratori 631 Catalan second semester morning-mixed
(PLAB) Practical laboratories 632 Catalan second semester morning-mixed
(PLABs) Suport a les pràctiques de laboratori 632 Catalan second semester morning-mixed
(PLAB) Practical laboratories 633 Catalan second semester morning-mixed
(PLABs) Suport a les pràctiques de laboratori 633 Catalan second semester morning-mixed