information

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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: a lytic phages from Italy may be no active on the same bacteria (genus and species) isolated from another country and vice versa.
Chronolability
Mutation rate
Phenotypical delay
Phage cocktail
My point of view

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.

Saturday, 23 August 2014

How to recognize bacterial promoters

Identifying prokaryotic promoter sequences is difficult and for most sequenced bacterial genomes the promoter sequences are still unknown.
Bacterial promoters are generally composed of two elements: one conserved sequence centered at –35 nucleotides and a second conserved sequence centered at –10 nucleotides from the start of the transcript, which is typically a purine nucleotide (A or G).

The terms –35 (TTGACA ) and –10 (Pribnow Box:TATAAT ) refer to the typical location of these sequences, although the number of base pairs separating them can vary among different promoters.

Transcription in bacteria is initiated by a protein complex known as RNA polymerase (RNAP), consisting of five subunits ( core enzyme) and an additional σ factor.
The σ factor is responsible for locating promoters by recognizing two binding sites, typically located at the -10 and -35 positions with respect to the transcription start site (TSS). Once transcription has begun, the σ factor dissociates and transcription continues with core enzyme alone.


Here two examples from two genes of M.ulcerans genome:



MUL 0007



MUL 0010
Practical rule
 
Pribnow Box
: the first positons, TA,in general are preserved but the last T must be present in the promoter.

-35 region:TTG is highly preserved.

-43 region: there are some AT nucleotides.