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The course Biological Techniques explain experimental approaches and methodologies of modern biology.
Seminal scientific discoveries from the first three biological lectures of the Science curriculum will be put in context with the particular research approach. Biological Techniques expands understanding of the biological concepts and facts in a practical way necessary for successful research career. The list of covered techniques will correspond to the broad diversity of biological disciplines, with the emphasis to reach state of art achievements. All lecturers are active scientists, specialists in a field they teach. The course Biological Techniques forms the integral unit with three prerequisite courses (From molecules to cells, From cells to organisms and On the Evolution and Ecology). The course is built from topical blocks (see Syllabus) each of them consisting of lecture (3h) and workshop focused on primary literature as a Q&A session (2h). Last update: Půta František, doc. RNDr., CSc. (06.02.2022)
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1. Understanding Light Microscopy (RMS - Royal Microscopical Society) 1st Edition, ISBN-13: 978-0470973752, 2019 Last update: Šebková Nataša, RNDr., Ph.D. (31.05.2022)
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Final mark is based on the oral examination (67%) and results of tests taken during the course (33%). Oral examination takes place during the examination period and students must first obtain the evaluation for Q&A sessions, workshops and take-home exercises. Last update: Půta František, doc. RNDr., CSc. (06.02.2022)
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Introduction to biological research (ethics, observation and experimentation, hypothesis driven research, correct interpretation of the primary data) Seeing is believing - principles of visualisation techniques: limitations, types (AFM, SEM, TEM, light-based), applications, data mining approaches, quantitation, 3D, life imaging, whole-animal imaging, labelling techniques, image analysis Structural biology Computational biology Genetic analysis (sequencing, transcriptomics, epigenomics, study of polymorphisms) Bioinformatics Characterization of protein structure and function - proteomics, NMR, X-ray… Single cell techniques Gene modifications and phenogenomics Application of fluorescent proteins and probes Cladistics Flow cytometry and usage of antibodies Neurophysiological techniques Last update: Půta František, doc. RNDr., CSc. (06.02.2022)
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BIOLOGICAL TECHNIQUES — Learning Outcomes
Foundations of biological research and scientific reasoning After completing the course, the student will be able to: · Differentiate observation, experimentation, and inference, and explain how each contributes to biological discovery. · Formulate a clear, testable hypothesis and derive specific predictions that can be experimentally evaluated. · Identify common pitfalls in data interpretation (confounding, batch effects, overfitting, circular reasoning) and propose strategies to mitigate them. · Justify the choice of experimental controls (positive/negative controls, technical/biological replicates) and define success criteria for an experiment. · Recognise and evaluate ethical issues in experimental biology (human/animal research, dual-use concerns, data integrity, authorship) and apply responsible research practices.
Visualisation and imaging: from molecules to whole organisms After completing the course, the student will be able to: · Compare major imaging modalities (light microscopy, confocal/super-resolution, TEM/SEM, AFM, whole-animal imaging) by resolution, contrast mechanism, sample requirements, throughput, and limitations. · Select an imaging strategy appropriate for a biological question and justify the selection in terms of spatial/temporal resolution and perturbation of the system. · Design a labelling plan (fluorescent proteins, dyes, antibodies, probes) and predict potential artefacts (phototoxicity, overexpression, fixation artefacts, bleed-through). · Quantify image-derived measurements (e.g., colocalisation, morphology, dynamics, intensity-based readouts) and define reproducible analysis steps. · Interpret 3D and time-lapse datasets and communicate imaging results using appropriate figures, annotations, and statistical summaries.
Structural biology and protein characterisation After completing the course, the student will be able to: · Explain what information can be obtained from structural approaches (X-ray crystallography, cryo-EM, NMR, AFM) and contrast strengths/constraints of each. · Propose a workflow to link protein structure to function, including sample preparation, validation, and orthogonal confirmation. · Interpret basic outputs from structural/proteomic analyses (structures, interaction maps, modification profiles) and assess confidence/limitations. · Design an experiment to test a structure–function hypothesis (e.g., mutagenesis + functional assay) and define readouts and controls.
Computational biology and bioinformatics After completing the course, the student will be able to: · Differentiate descriptive vs. predictive computational approaches and state when each is appropriate. · Interpret core concepts behind omics data analysis (normalisation, dimensionality reduction, clustering, differential analysis) at a conceptual level. · Evaluate a bioinformatics pipeline by identifying assumptions, sources of bias, and quality-control checkpoints. · Integrate computational outputs with experimental design by proposing follow-up validation experiments.
Genetic analysis and genomics (sequencing, transcriptomics, epigenomics, polymorphisms) After completing the course, the student will be able to: · Compare common sequencing strategies (targeted, whole-genome, RNA-seq, single-cell RNA-seq, epigenomics) and justify an appropriate choice for a given question. · Explain how genetic variation (SNPs, CNVs, structural variants) can be studied and predict its potential functional consequences. · Design an experiment that connects genotype to phenotype using genomics + functional validation. · Assess limitations of genetic association vs. causal inference and propose approaches to strengthen causal claims.
Single-cell and spatially resolved approaches After completing the course, the student will be able to: · Explain why single-cell approaches are needed (heterogeneity, rare populations, dynamic trajectories) and identify suitable single-cell modalities (scRNA-seq, CITE-seq/conceptually, spatial transcriptomics—if covered). · Design a sampling strategy that preserves biological meaning (tissue handling, dissociation bias, viability, batch effects) and define quality criteria. · Interpret single-cell results conceptually (cell states vs. cell types, trajectories, markers) and propose validation steps (imaging, flow cytometry, perturbations).
Gene modification and phenogenomics After completing the course, the student will be able to: · Compare gene perturbation strategies (CRISPR knock-out/knock-in, CRISPRi/a conceptually, RNAi, transgenesis) and select an approach appropriate to the biological model and goal. · Design a gene-editing experiment including guide strategy, delivery, genotyping/verification, off-target risk management, and phenotypic readouts. · Propose a phenogenomic workflow to connect engineered changes to organismal or cellular phenotypes, including prioritisation of assays and controls.
Fluorescent proteins and molecular probes After completing the course, the student will be able to: · Select fluorescent proteins/probes appropriate for an experiment (spectra, brightness, maturation, photostability, toxicity) and justify trade-offs. · Design multiplex experiments and predict technical issues (spectral overlap, compensation needs, cross-reactivity) and mitigation strategies. · Interpret probe-based readouts (localisation, dynamics, biosensors) and distinguish signal from artefact.
Antibodies, flow cytometry, and quantitative cell profiling After completing the course, the student will be able to: · Explain core principles of antibody-based detection (specificity, affinity/avidity, validation) and propose a validation plan (controls, knock-out/knock-down, isotypes where relevant). · Design a flow cytometry panel at a conceptual level (marker choice, gating logic, controls, compensation needs) and define what constitutes a robust interpretation. · Interpret flow cytometry outputs by constructing a gating strategy and explaining how populations relate to the biological hypothesis. · Propose how flow cytometry can be integrated with sorting and downstream assays (omics, functional assays, imaging) to strengthen conclusions.
Cladistics and evolutionary reasoning as a “technique” After completing the course, the student will be able to: · Construct a basic cladistic argument (characters, homology vs. analogy, parsimony logic) and use it to generate testable biological hypotheses. · Explain how comparative approaches guide experimental design (choosing model systems, identifying conserved vs. derived mechanisms).
Neurophysiological techniques After completing the course, the student will be able to: · Differentiate major neurophysiological readouts (electrical activity, imaging-based activity proxies, stimulation/perturbation concepts) and select a method appropriate for a defined question. · Design a basic neurophysiology experiment including stimulus/perturbation, recording strategy, controls, and interpretation boundaries. · Evaluate whether a reported neurophysiological effect supports causation or correlation and propose stronger causal tests.
Assignment-specific learning outcomes: Visionary grant proposal + peer review After completing the course, the student will be able to: · Formulate a visionary but scientifically grounded biological hypothesis and justify its significance and broader impact. · Design an integrated methodological strategy that combines at least four distinct techniques taught in the course, explaining how they complement each other. · Anticipate major technical and conceptual risks (feasibility, artefacts, confounders, scalability) and propose contingency plans and alternative approaches. · Define clear milestones, decision points, and measurable success criteria for the proposed project. · Write a structured grant proposal (intro + methods + ethics) using clear scientific argumentation and appropriate primary-literature support. · Analyse and critique an anonymised peer proposal by identifying strengths, weaknesses, missing controls, and feasibility issues, and provide constructive, actionable feedback. · Discuss ethical, societal, environmental, and dual-use implications of advanced biological techniques, and propose mitigation strategies where relevant.
Last update: Šebková Nataša, RNDr., Ph.D. (27.01.2026)
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