Virtual Laboratories

Access:

Enter the virtual laboratory.

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.

1. 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

2. 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

3. Paternity test using multiplex PCR on STR markers (CoDIS). https://doi.org/10.5281/zenodo.1299837
4. Genetic diagnosis, personalised medicine. Identification of polymorphic variants on cytochrome P450 (CYP2C9), using multiplex PCR. doi:10.5281/zenodo.1299846
5. 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
6. Dairy product analysis. Identification of the source of milk (cow, sheep or goat) by analysis of mitochondrial DNA. doi:10.5281/zenodo.1299860
7. Vegetable oil analysis. Identification of a poossible adulteration of olive oil with other specis by analysis of chloroplast DNA. (not yet available)
8. 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
9. 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
10. Genetic diagnosis. Detection of a mutation in protooncogene RET causing multiple endocrine neoplasia, type 2A (MEN2A). doi:10.5281/zenodo.5168483

Access the simulator:

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.

Acces the simulator.

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).