Biology - Laboratory - MB151C06E

• Title: Biology - Laboratory
• Czech title: Biologie -praktické cvičení
• Form of teaching: lecture
• Guaranteed by: Department of Cell Biology (31-151)
• Faculty: Faculty of Science
• Actual: from 2024
• Duration in semesters: 1
• Semester: summer
• E-Credits: 5
• Examination process: summer s.:
• Hours per week, examination: summer s.:0/4, C [HT]
• Capacity: unlimited
• Maximum number of enrolled students: unlimited
• Min. number of students: unlimited
• 4EU+: no
• Virtual mobility / capacity: no
• State of the course: taught
• Language: English
• Note: enabled for web enrollment; priority enrollment if the course is part of the study plan
• Guarantor: Mgr. Aleš Benda, Ph.D.
• Teacher(s): Mgr. Aleš Benda, Ph.D.

Annotation

The practical course Biology – Laboratory is a hands on complement to the Biological Techniques, where selected
methodologies are trained as case projects using advanced instruments located in Faculty of Science core
facilities. Most of the practical are intended to be organized in BIOCEV, where state of art facilities are located,
together with educational lab environment. Practical tasks will be typically performed using mouse models organisms (M. musculus) in collaboration with Czech Center for Phenogenomics, as a problem-oriented exercise reflecting the
real scientific project – implemented with education of basic laboratory skills.

The list of covered techniques will correspond to the broad diversity of biological disciplines, with the emphasis to
apply state of art approaches. All practical tasks are given by active scientists - experts in a field they teach or core
facility specialists.

The course Biology – Laboratory forms the integral unit with Biological Techniques namely and in extenso with
three prerequisite courses (From molecules to cells, From cells to organisms and On the Evolution and Ecology).

The practical course (6 days) is built from topical blocks (see Syllabus) followed by the presentation workshop
focused on data mining strategies and effective presentation skills (1 day) and students own presentation of
acquired data in a poster and oral format (1 day conference-style).

Last update: Benda Aleš, Mgr., Ph.D. (11.03.2026)

Literature

1. Understanding Light Microscopy (RMS - Royal Microscopical Society) 1st Edition, ISBN-13: 978-0470973752, 2019
2. Introduction to Light Microscopy: Tips and Tricks for Beginners, 1st ed. 2019 Edition, ISBN-13: 978-3030053925, 2019
3. Proteomics for Biological Discovery, 2nd Edition, ISBN-13: 978-1118279243, 2019
4. Genome Editing and Engineering: From TALENs, ZFNs and CRISPRs to Molecular Surgery, 1st Edition, ISBN-13: 978-1107170377, 2018
5. Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, 4th Edition, 2002
6. Lecture notes
7. Pre-recorded lectures
8. Problem sets

Last update: Šebková Nataša, RNDr., Ph.D. (31.05.2022)

Course assessment methods and requirements for successful completion, grading scheme

Final mark is based on the presentation of data (67%) and results taken during the course (33%). Presentation conference takes place at the end of the course and students must first obtain the evaluation from the practical sessions, workshops and take-home exercises.

Last update: Půta František, doc. RNDr., CSc. (18.02.2022)

Syllabus

Course Duration:

7-day intensive laboratory course + 1-month data analysis period + final mini-conference

Course Purpose:

To provide hands-on experience with biological methods used in core facilities, focusing on phenotyping and analysis of rare disease mouse models.

Learning Objectives:

• Collect and process biological samples

• Analyze data using core facility instruments

• Perform imaging and physiological tests on mouse models

• Present findings in a scientific format

Course Structure:Week 1: Laboratory Practicals

Day 1 (Monday):

• Orientation in phenotyping barrier

• Introduction to rare disease genes

• Group rotations:

  • Cardio unit: Ultrasound, ECG

  • Metabolism unit: Glucose tolerance test, body composition

  • Hearing unit: Auditory brain stem response

  • Vision unit: Optical coherence tomography

Day 2 (Tuesday):

• Continued group rotations:

  • Metabolism, Vision, Cardio, microCT imaging

Day 3 (Wednesday):

• Sample collection:

  • Sperm collection and imaging

  • Cryo fixation of testis and pancreas

  • Blood collection for flow cytometry, proteomics, metabolomics

  • Teeth collection for SEM

Day 4 (Thursday):

• Sample processing:

  • Flow cytometry

  • Cryosection and islet visualization

  • SEM and TEM sample preparation

Day 5 (Friday):

• Imaging and visualization:

  • SEM and TEM imaging

  • Cryosection of testis

Week 2: Data Handover and Analysis

Day 6 (Monday):

• OMICS excursion

• Proteomics and metabolomics data handover

• Group discussions

Day 7 (Tuesday):

• Microscopy data handover

• Genomics excursion

• Preparation for mini-conference presentation

Final Presentation:

Mini Conference (half a day 2-3 weeks after the practicals):

• Group presentations of results for each rare disease model

Assessment:

• Participation in laboratory activities

• Quality of data collected and analyzed

• Final group presentation

Resources:

• Access to BIOCEV core facilities including CCP

• Support from facility staff and experts

• Instruments for imaging, flow cytometry, genomics, and OMICS analysis

Notes:

• Students are encouraged to consult core facility staff during the analysis phase

• All data must be compiled into a single group presentation per model

Last update: Benda Aleš, Mgr., Ph.D. (28.05.2026)

Learning outcomes

Knowledge and Understanding

1. Describes the principles of systemic phenotyping and the biological relevance of selected rare‑disease mouse models used in the course.

2. Explains the theoretical foundations, capabilities, and limitations of key analytical and imaging methods (e.g., ultrasound, ECG, OCT, microCT, SEM, TEM, flow cytometry, cryosectioning).

3. Summarizes the methodological workflow of omics‑based analyses (proteomics, metabolomics, transcriptomics) and their application in phenotype characterization.

Practical Skills / Application

1. Performs standard laboratory procedures relevant to phenogenomics, including tissue and blood collection, cryo‑fixation, preparation of samples for SEM/TEM, and generation of cell suspensions for flow cytometry.

2. Operates advanced imaging and analytical instruments to acquire phenotyping data from genetically modified mouse models.

3. Applies appropriate bioinformatics tools to process, visualize, and interpret sequencing, proteomics, and metabolomics datasets.

Cognitive Skills / Analysis and Evaluation

1. Analyzes phenotypic differences between wild‑type and genetically modified mouse models using multimodal datasets.

2. Evaluates the quality, reliability, and potential sources of error in imaging, physiological, cytometric, and omics data collected during the practical sessions.

3. Assesses the suitability of selected experimental techniques for addressing defined biological questions related to rare‑disease phenotypes.

Autonomy, Responsibility, and Communication

1. Integrates data from imaging, physiological measurements, and omics analyses to formulate evidence‑based conclusions about the phenotype of a selected gene‑modified mouse model.

2. Prepares a scientifically structured poster and oral presentation that effectively communicates experimental results, methodological approaches, and their interpretation.

3. Collaborates within a research team to plan, execute, and interpret a multi‑day experimental workflow, demonstrating adherence to laboratory safety and research integrity standards.

Last update: Benda Aleš, Mgr., Ph.D. (04.02.2026)