
Integrated Laboratory V
Code: 101943Credits: 3
| Degree programme | Type | Course |
|---|---|---|
| Genetics | OB | 3 |
Contact lecturer
- Name :
- María Pilar Garcia Guerreiro
- Email :
- mariapilar.garcia.guerreiro@uab.cat
Teaching staff
- Joaquín Casellas Vidal
- Barbara Negre De Bofarull
- Gemma Armengol Rosell
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 V is the fifth 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 V has as objectives the acquisition of experimental skills in 3 specific modules of content:
- Genomics
- Human Genetics
- Quantitative genetics and improvement
Genomics
The main objective of Genomics module is to understand the process of Assembly, annotation and analysis of genomic sequences. Apart from learning to work with DNA sequences and proteins also will acquire knowledge about the structure and the characteristics of the various functional elements that can be found in a genome.
Human Genetics
The aim of the module of human genetics is know how to identify genetic mutations and polymorphisms related to the generation of diversity and the pathological processes. Through these practices, the student will acquire skills in the application of instrumental, molecular and analytical techniques.
Quantitative genetics and improvement
The aim of this module is to help you understand the principles of Quantitative genetics and its application in the selection, as well as the availability of tools for the identification of individual genes that determine the complex characters.
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 Genomics
The module is organized in 5 sessions of 3 hours each that will take place in the computer room. The work will consist of the Assembly, the annotation and analysis of a sequence. Based on initial data, the practice will be continuing along the 5 sessions so that each of them will be one more step in the process or will examine a different aspect of the secuence. The work will be distributed in the following way:
Session 1. Assembly
Session 2. Scaffolding
Session 3. gene annotation Ab initio and by homology
Session 4. Annotation of genes with RNA-seq
Session 5. Functional analysis and discussion
Module of Human Genetics
The module is organized in 4 sessions of 4 hours each that will be carried out in the laboratory. The students will go through three possible cases occurring in a genetics laboratory: case of prenatal diagnosis, case of leukemia, population screening for a mutation with possible applications (e.g. in the pharmacogenetics or Nutrigenetics). To respond to these three situations several techniques will be used, such as conventional cytogenetics, fluorescence in situ hybridization (FISH), polymerase chain reaction (PCR) combined with restriction fragment length polymorphism (RFLP) analysis, and/or Next-Generation Sequencing (NGS) techniques.
Module of Quantitative genetics and improvement
GQM module is organized in 5 sessions that will take place in the computer room. The sessions will be synchronic with the theory classes (see calendar), so that the student may work and reflect the essential concepts and methodologies of the topic. The sessions are the following:
Session 1. Visit to the UAB Faculty of Veterinary Medicine farm (3 h).
Session 2. Genome-Wide Association Study (GWAS) (3h).
Session 3. BLUP (3h).
Session 4. Response to selection (3 h).
Session 5. Genomic evaluation of breeding stock (3 h).
Learning activities and methodology
| Title | Hours | ECTS | Learning outcomes |
|---|---|---|---|
| Laboratory notebook | 5 | 0.2 | CM18, CM20, SM16, SM18 |
| Quantitative Genetics Module. | 15 | 0.6 | CM18, CM19, CM20, KM13, SM16, SM18 |
| Study | 23 | 0.92 | CM18, CM19, CM20, KM13, KM15, SM17, SM18 |
| Genomics Module | 15 | 0.6 | CM18, CM19, CM20, KM13, SM17, SM18 |
| Human Genetics Module | 16 | 0.64 | CM18, CM19, CM20, KM13, SM16, SM18 |
| Individual tutorials | 1 | 0.04 | CM18, SM17 |
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.
Genomics Module
Self-guided learning guided by the teacher / a by the practitioner. Students will have to elaborate the data, interpret the results obtained, and respond to the different questions raised in the practice guideline.
Human Genetic Module
The student will perform the experimental work independently following the practice guideline and with the help of the practice lecturer. After obtaining the results, these will have to be analysed and interpreted. In the practicals guide, there will be some questions to help with this analysis and interpretation of the results.
Quantitative Genetics Module
Each session begins with an introduction by the teacher and then the student must follow the practice guidelines and obtain their own results, always under the supervision of the teacher.
Assessment
Continuous assessment activities
| Title | Weight | Hours | ECTS | Learning outcomes |
|---|---|---|---|---|
| Human Genetic Module. Continuous evaluation of the results worked | 33.33% | 0 | 0 | CM18, CM19, CM20, KM13, SM16, SM18 |
| Quantitative Genetics Module. Continuous evaluation of the results worked | 33.3% | 0 | 0 | CM18, CM19, CM20, KM13, KM15, SM17, SM18 |
| Genomics module. Continuous evaluation of the results worked | 33.3% | 0 | 0 | CM18, CM19, CM20, KM13, SM17, SM18 |
Attendance at practicals is compulsory and therefore an absence without a justified reason may lead to the non-evaluation of one or more modules.
Justified cause means health problems (you will need to bring the corresponding medical certificate to the internship coordinator) or serious personal problems. In this case, the practice is to recover whenever possible.
If the justified absences exceed 25% of the sessions of any of the modules, the subject will be graded as Not Assessable.
Genomics Module
The practices will be evaluated by delivering the results obtained during the practice that will have to be presented in a clear and understandable way.
The correction of the data obtained will be assessed. The attitude and work of the student in the classroom will also be taken into account.
Human Genetics Module
The practices will be evaluated through the submission of a report on the results obtained during the practical work. The interpretation that is made of the obtained data will be valued especially. The attitude and work of the student in the laboratory will also be taken into account.
Quantitative Genetics Module
At the end of each practical session, students’ level of achievement will be assessed through the completion of exercises, the preparation of a report, or any other form of evidence indicated by the instructor in charge. The assessment will consider the accuracy in solving the proposed questions, the clarity of the comments and conclusions, as well as the formal presentation. The student’s attitude during the practical sessions will also be evaluated.
To pass the course, it is necessary to first approve each module with a mark ≥ 5. Students who do not pass the different modules of the coursewill have the opportunity to retake them on the scheduled resit date.
Any student who has not passed a module after the resit assessment will not pass the course. However, repeat students will not be required to complete the learning activities or assessments for any module already passed, starting from their second enrollment. Repeat students will only need to be assessed on the specific module(s) not yet passed. This exemption will remain valid for up to three additional enrollments.
The final grade is the average of the grades from each module.
Not graded: The Not graded qualification will be obtained when the number of assessment activities performed is less than 50% of the programmed ones.
To be eligible for the retake process, the student should have been previously evaluated in a set of activities equalling at least two thirds of the final score of the course or module.
Thus, the student will be graded as \"No Avaluable\" if the weigh thin of all conducted evaluation activities is less than 67% of the final score.
Attendance to practical sessions is mandatory. Students missing more than 25% of sessions of any of the modules will be graded as \"No Avaluable\".
Students who take the single assessment must do the laboratory practices in face-to-face sessions, as they are teaching activities with compulsory attendance.
This unique assessment system will be applied to modules 1 (Genomics), 2 (Human Genetics) and 3 (Quantitative Genetics and Improvement), and will consist of a unique synthesis test on the contents of the practices plus the delivery of the 'report or report on the practices.
The grade obtained in the synthesis test is 50% of the grade of the corresponding module. The report or memory will be the remaining 50% and can be delivered on the same date set forthe continuous assessment or coinciding with the date of the single synthesis test.If the practice is done with a partner (partner)who is not included in the single assessment, the delivery of the (joint) report will be on the same date set for the continuous assessment.The single assessment test will take place on a date agreed between the students, the subject coordinator and those responsible for each module.
The same criterion will be applied to approve the subject and the same recovery system as for the continuous assessment. The review of the final qualification follows the same procedure as for the continuous assessment.
Any irregularity committed in an assessment activity (academic fraud, plagiarism, or improper use of AI, unless such use is expressly authorized in the study guide) that may lead to a significant alteration of the grade will result in that assessment activity being graded with a 0. If the study guide establishes that obtaining a minimum grade in that assessment activity is an essential requirement for passing the course, or if multiple irregularities occur in the assessment activities of the same course, the final grade for the course will be 0. In addition, disciplinary proceedings may be initiated against any student who engages in any of these irregularities.
Bibliography
Human Genetics Module
Included in the practical manual available to students through the Virtual Campus
Quantitative Genetics Module
Included in the practice guideline that is available to students on the Virtual Campus.
Software
MEGA (https://www.megasoftware.net/)
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PLINK (P2) |
PLINK 1.9 beta
https://www.cog-genomics.org/plink/1.9/ GCTA Windows gcta-1.94.1-Win-x86_64.zip https://yanglab.westlake.edu.cn/software/gcta/#Download The source code are released under GPL v3 R for windows
RStudio
Notepad++
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|
R (P3 y P4)
|
https://cran.r-project.org/bin/windows/base/ |
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Genup (P5) |
http://www-personal.une.edu.au/~bkinghor/genup.htm
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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/Spanish | first semester | morning-mixed |
| (PLABs) Suport a les pràctiques de laboratori | 631 | Catalan/Spanish | first semester | morning-mixed |
| (PLAB) Practical laboratories | 632 | Catalan/Spanish | first semester | afternoon |
| (PLABs) Suport a les pràctiques de laboratori | 632 | Catalan/Spanish | first semester | afternoon |
| (PLAB) Practical laboratories | 633 | Catalan/Spanish | first semester | afternoon |
| (PLABs) Suport a les pràctiques de laboratori | 633 | Catalan/Spanish | first semester | afternoon |