DNA extraction from environmental

samples & gel electrophoresis

Dr. Eman El Gebaly

Dr. Eman El Gebaly
Dr. Eman El Gebaly
Dr. Eman El Gebaly
• How DNA and RNA are extracted from
environmental matrices?
• 1- in situ cell lysis (thermic and/or chemical
and/or mechanical and/or enzymatic)

• 2-followed by separation/purification of the DNA

from the rest of the environmental matrix
(mineral and organic).

Dr. Eman El Gebaly

• 3- Compared with DNA, RNA is less stable
and more sensitive and partial degradation of
the RNA from environmental samples is often
observed.

• 4- RNA extraction and manipulation is

therefore carried out under much more
stringent conditions (clean room, ribonuclease
treatment of equipment) than for DNA.
Dr. Eman El Gebaly
• 5- The extracted RNA can be converted into
complementary DNA (cDNA) by reverse transcription and,
as cDNA possesses the same degree of stability as DNA, it can
then be analysed with the same molecular tools.

Dr. Eman El Gebaly

Dr. Eman El Gebaly
• Tools for analysing the nucleic acids from
microorganisms can be divided into:
-targeted and non-targeted approaches (Shotgun),
depending on whether they are based on the
analysis of previously selected genes (i.e. genetic
markers) or all the genes.

Dr. Eman El Gebaly

Dr. Eman El Gebaly
Dr. Eman El Gebaly
Dr. Eman El Gebaly
 Shotgun metagenomic sequencing

• is a relatively new environmental sequencing

approach used to examine thousands of
organisms in parallel and sample all genes,
providing insight into community biodiversity
and function.

• Shotgun sequencing allows for the detection

of low abundance members of microbial
communities.

Dr. Eman El Gebaly

Dr. Eman El Gebaly
Environmental proteomics

Dr. Eman El Gebaly

• The metaproteome, by analogy to the
metagenome, is defined as the complete set of
proteins synthesized by the entire microbial
community at a given time.
• The analysis of the metaproteome is described
as metaproteomics

Dr. Eman El Gebaly

• This approach targets the analysis of proteins
at the scale of the microbial organism or
community and provides a functional
complement to studies based on the analysis
of DNA or even RNA.

• It is indeed the functional proteins, not the

genes, which ‘‘act’’. Activity

Dr. Eman El Gebaly

Conclusion

Dr. Eman El Gebaly

Dr. Eman El Gebaly
With All My Best Wishes

Dr. Eman El Gebaly