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"In silico"


From Wikipedia
If the target host* of a phage therapy treatment is not an animal the term "biocontrol" (as in phage-mediated biocontrol of bacteria) is usually employed, rather than "phage therapy".

In silico
From:"Genomics,Proteomics and Clinical Bacteriology",N.Woodford and Alan P.Johnson

Phrase that emphasizes the fact that many molecular biologists spend increasing amounts of their time in front of a computer screen, generating hypotheses that can subsequently be tested and (hopefully) confirmed in the laboratory.


Phage Therapy is influenced by:

Phage therapy is influenced by:

Country : the epidemiological situation is different from country to country in terms of circulating bacteria and bacteriophages. Example: lytic phages from Italy may be no active on the same bacteria (genus and species) isolated from another country and vice versa.
Temporariness
Mutation rate
Phenotypical delay
Phage cocktail

My point of view

Sunday, 21 February 2010

2.PCR Method for Genotype Analysis of Mycobacterium ulcerans


From:

Development of a PCR Assay for Rapid Diagnosis of Mycobacterium ulcerans Infection

"For the PCR, we isolated an M. ulcerans-specific DNA fragment, 1,109 bp long, which is repeated at least 50 times throughout the genome."



I have verified by "In silico " Restriction Site Analysis the AluI action
on M.ulcerans genome.

By AluI I have found 16975 restriction sites and 16976 restriction fragments.

From M.ulcerans genome the position :228378-229743
is corresponding to IS2404 sequence and
from the restriction Map the position:228599-229707
is corresponding to one restriction fragment by AluI cut.






Restriction Analysis of IS2404 DNA sequence





I have also verified if the indicated primers were effective:

cggcaggctgaagtaactgcc (MU1)

tgtgcagtgaagtaactgcc (MU2)

but
with these primers by FastPCR software I do not have had any results .


On the contrary if I use these primers:

1F2_1_48-69 atctttggtgccgcgctattgg

1R10_1_1135-1156 tcgaaggtgacgtcgcgtatcc

I have had the results:


In silico Primer(s) search for: is2404dnasequenceconsistingof1366bases.

1f2_1_48-69 5'-atctttggtgccgcgctattgg

Position: 48->69 22bp 100% Tm = 60,2°C

5-atctttggtgccgcgctattgg->

||||||||||||||||||||||

actagaaaccacggcgcgataaccccgg

1r10_1_1135-1156 5'-tcgaaggtgacgtcgcgtatcc

Position: 1135<-1156 22bp 100% Tm = 61,8°C

<-cctatgcgctgcagtggaagct-5

||||||||||||||||||||||

ctggatacgcgacgtcaccttcgacgaa

1f2_1_48-69 5'-atctttggtgccgcgctattgg

1r10_1_1135-1156 5'-tcgaaggtgacgtcgcgtatcc

PCR product size: 1109bp