Virtual laboratories

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Sequence analysis - Direct link to the tools (transcription-translation, sequence pattern search, sequence massager)

General instructions for the use of Cybertory.

Features:

Digestion of DNA with restriction enzymes (81 enzymes available).
PCR amplification by multiplex PCR of DNA segments that include STR polymorphic markers from CODIS (6 available) and a sex marker.
PCR amplification by multiplex PCR of several polymorphic markers and species-specific sequences.
Electrophoresis of DNA fragments on agarose or polyacrylamide gel and ethidium bromide staining.
DNA sequencing using dideoxynucleotides and electrophoresis. Label with either a radioisotope, a fluorochrome or 4 fluorochromes.

Possible applications:

Molecular diagnostics with RFLP or PCR of genetic polymorphism.
Forensic analysis of DNA.
Paternity test using multiplex PCR of polymorphic STR genetic markers.
Molecular analysis of foodstuff adulteration.
Restriction mapping.

Workbooks:

	1A	1B	1C	1D	2A	2B	3	4	5	6	7	8	9
using electrophoresis
using restriction enzymes
using PCR

General instructions for the use of Cybertory.

Genetic diagnosis; β^A/β^S polymorphism in the beta globin gene, responsible for drepanocytosis and drepanocytic anaemia (sickle cell anaemia):

1A		Testing restriction enzymes for the analysis of this polymorphism by RFLP. doi:10.5281/zenodo.1299796
		Some enzyme sets suitable for this practical.
1B		Molecular genetic diagnosis of the polymorphism by RFLP. doi:10.5281/zenodo.1299811
1C		DNA sequencing to analyse this polymorphism (dideoxynucleotides method). doi:10.5281/zenodo.1299816
1D		Introduction to genomic sequence databases and analysis of sequences related to this polymorphism. doi:10.5281/zenodo.1299825

Forensic analysis: genetic identification of individuals:

2A		Using RFLP. doi:10.5281/zenodo.1299843 New v.1.1 after repairing a technical failure (Aug.2024)
2B		Using multiplex PCR on STR markers (CoDIS). doi:10.5281/zenodo.3607339

Paternity test using multiplex PCR on STR markers (CoDIS). https://doi.org/10.5281/zenodo.1299837
Genetic diagnosis, personalised medicine. Identification of polymorphic variants on cytochrome P450 (CYP2C9), using multiplex PCR. doi:10.5281/zenodo.1299846
Genetic diagnosis of celiac disease. Identification of polymorphic variant associated to celaic disease, using multiplex PCR on the DQ2 and DQ8 markers. doi:10.5281/zenodo.1299854
Dairy product analysis. Identification of the source of milk (cow, sheep or goat) by analysis of mitochondrial DNA. doi:10.5281/zenodo.1299860
Vegetable oil analysis. Identification of a poossible adulteration of olive oil with other specis by analysis of chloroplast DNA. (not yet available)
Detection of a plant resistance gene. Detection of the presence or absence of the allele responsible for resistance to nematodes, aphids and whiteflies in tomato plants by analysis ot their DNA. doi:10.5281/zenodo.7997161
Viral infection test. Identification of infection by coronavirus or by common flu virus using multiplex PCR on cDNA obtained from samples. doi:10.5281/zenodo.3730995
Genetic diagnosis. Detection of a mutation in protooncogene RET causing multiple endocrine neoplasia, type 2A (MEN2A). doi:10.5281/zenodo.5168483

Simulation of celulose acetate electrophoresis of proteins

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for serum proteins

for LDH isoenzymes

virtual experiment with LDH isoenzymes

Features:

Electrophoresis of either serum proteins or LDH isoenzymes on cellulose acetate strips.
Only the final result is displayed.
Reveal serum proteins by staining with Coomassie Blue, Amido Black or Ponceau Red, or by autoradiography.
Reveal LDH with an enzyme assay.
A single sample per run.
Predefined profiles, both normal and pathological, or custom profile depending on given proportion of each component.
Automatic plot of both the band pattern on the cellulose acetate strip and its densitogram. Possibility to overlay successive densitograms in the same plot for comparison.

Possible applications:

Clinical interpretation of serum protein profiles.
Differential tissue profile of LDH isoenzymes.
Clinical interpretation of LDH isoenzyme profiles.

Simulation of SDS-PAGE electrophoresis of proteins

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Features:

Electrophoresis of proteins on a polyacrylamide gel with SDS; direct detection.
Several acrylamide concentrations are available: 7.5; 10; 12 and 15%.
4 voltages are available to run the separation.
One lane for standards and another for a sample.
7 standard proteins of known size and 10 unknown samples (with a single protein each).
The progress of the separation is displayed.
Automatic drawing of the calibration line and aided interpolation.

Possible applications:

Estimation of the molecular mass of the unknown proteins.

Workbooks:

These are integrated into the simulation page:

Practice problem 1: influence of the voltage applied.

Practice problem 2: influence of the acrylamide concentration.

Practice problem 3: estimation of molecular mass of the unknown proteins.

Practice problem 4: determination of quaternary structure (I).

Practice problem 5: determination of quaternary structure (II).

UV-VIS spectrophotometry laboratories

Simulator of ultraviolet absorption spectra for proteins and nucleic acids

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Features:

Protein and DNA absorption spectrum between 230 and 340 nm.
Absorbance values at 260 and 280 nm, and the ratio between both.
Predefined profiles: proteins, DNA and four mixtures.
Custom profiles based on proportion provided for each type of molecule.
Possible to superimpose sucessive spectra to compare them.

Applications:

Demonstration of the analytical value of the technique for checking DNA contamination with proteins or vice versa.

Virtual UV-VIS spectrophotometer

A) Spectra

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Features:

Absorption spectrum of diverse substances between 200 and 800 nm.
Preparation of dilutions.

Applications:

Relation between absorbance and concentration.
Fundamentals of a protein quantitation assay.
Determination of absorption spectra; search for λ_max

B) Quantitative assays with standard curve

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Features:

Determination of glucose concentration.
Lowry assay for proteins.
Determination of creatinine.

Applications:

Analytical experiments with colorimetric assay, endpoint determination.

C) Kinetic assays

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Features:

Determination of gamma-glutamyltranspeptidase activity.

Applications:

Analytical experiments with colorimetric assay along time.

Colorimetric assay for enzyme activity

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Features:

Enzyme activity assay.
Effect of pH and temperature on the activity of an enzyme.

Applications:

Search for optimal conditions for the enzyme.

Determination of ketone bodies

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Features:

Semiquantitative test on reactive strips.
Intensity of colour obtained depends on acetoacetate concentration in the samples.

Applications:

Diabetes diagnosis.

MTT assay for cell viability

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Features:

Dehydrogenase activity assay as an indicator of cell metabolic viability, using a 24-well plate with adherent cells.

Applications:

Cytotoxicity assay.

Circular dichroism spectrum of proteins

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Features:

CD spectrum between 173 and 250 nm.
Only the final result is displayed.
Predefined profiles: alpha, beta, turn, random and four example proteins.
Custom profiles based on the proportion of each type of secondary structure given by the user.
Posibility to superimpose spectra for comparison.

Applications:

Demostrating the analytical value of the circular dichroism technique to differenciate types of secondary structure in proteins.
Prediction of CD spectra.

Chromatography simulations

Column chromatography of proteins

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Features:

Several types of stationary phase, for:
- molecular exclusion (gel filtration)
- anionic and cationic exchange
- affinity
Analisis of samples made of 3 proteins.
Choose among 13 predefined proteins or proteins with user-provided properties (M_r, pI).
Shows progress of the protein bands along the column as well as así recording of chromatogram (absorbance versus elution volume).

Possible applications:

To illustrate the mechanism of separation on each type of matrix. Effect of pH on ion exchange.
Assay of conditions for resolution of proteins in a sample (for example, for analysis or for purification).

Working plans:

Project: design of problem-solving activities using the simulator.

Ion exchange chromatography to determine glycated haemoglobin

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Features:

Separation of components in a haemoglobin sample to quantify the glycated fraction (HbA_1c).
Diabetes diagnosis.

Thin layer chromatography for the analysis of mixtures

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with amino acids

with lipids

with plant pigments

Features:

Stationary phase is silica gel.
Mobile phase is a mixtrure of organic solvents.
Analysis of mixtures of several amino acids, several types of lipids or several plant pigments, in comparison with standards.
The user must interact to:
- Apply samples and standards.
- Run the chromatography.
- Apply a developing method to detect results (formation of a coloured product either with ninhydrin or iodine, respectively).

Virtual Laboratories

Cybertory: virtual molecular biology lab

Access:

Features:

Possible applications:

Workbooks:

Simulation of celulose acetate electrophoresis of proteins

Features:

Possible applications:

Simulation of SDS-PAGE electrophoresis of proteins

Features:

Possible applications:

Workbooks:

UV-VIS spectrophotometry laboratories

Simulator of ultraviolet absorption spectra for proteins and nucleic acids

Features:

Applications:

Virtual UV-VIS spectrophotometer

A) Spectra

Features:

Applications:

B) Quantitative assays with standard curve

Features:

Applications:

C) Kinetic assays

Features:

Applications:

Colorimetric assay for enzyme activity

Features:

Applications:

Determination of ketone bodies

Features:

Applications:

MTT assay for cell viability

Features:

Applications:

Circular dichroism spectrum of proteins

Features:

Applications:

Chromatography simulations

Column chromatography of proteins

Features:

Possible applications:

Working plans:

Ion exchange chromatography to determine glycated haemoglobin

Features:

Thin layer chromatography for the analysis of mixtures

Features: