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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

Saturday, 21 February 2009

Methods for Typing Staphylococcus aureus strains


From " Complete genomes of two clinical Staphylococcus aureus strains: Evidence for the rapid evolution of virulence and drug resistance"


The size of the sequenced S. aureus genomes varies from 2.800 Mbp to 2.903 Mbp, encoding 2565–2721 proteins.
It has been calculated that approx. 75% of the genome is conserved among all S. aureus isolates representing the core genome.


Comparative Genomics of Staphylococcus aureus

Genes of Staphylococcus aureus Genome subsp.aureus Col


Genome
Staphylococcus aureus NCTC 8325

Staphylococcus aureus genome sequence

Staphylococcus aureus strain NCTC 8325 annotation list of ORFs

Gene assigned a role category



Harmony


From "Harmony
Goals"


Pulsed-Field Gel Electrophoresis

Harmony PFGE protocol



Multilocus Sequence Typing


PFGE method

Organism-------Staphylococcus aureus

Recommended lysis
enzyme:lysozyme,lysostaphin,proteinase K

Restriction enzyme----------------SmaI, CspI

Approximate no. of-----------10–15, 15–20
restriction Fragments

Fragments size-------------10–700, 30–500
range (kb)




Organism-------Staphylococcus(coagulase negative)

Recommended lysis
enzyme:lysozyme,lysostaphin,proteinase K

Restriction enzyme----------------SmaI

Approximate no. of----------- 1520
restriction Fragments

Fragments size-------------5400
range (kb)




Identification of Staphylococcus species


Staphylococcus species



Staphylococci belong to the family Micrococcaceae, which includes the genus Micrococcus in addition to Staphylococcus.

Staphylococci grow rapidly on multiple culture media, in a wide range of environments, including up to 10 percent sodium chloride, and in a broad range of temperatures. Staphylococcus aureus is a nonmotile, nonspore forming, facultative anaerobic grampositive coccus that commonly colonizes healthy humans and is a frequent cause of disease.

It is frequently identified as growing in clusters or clumps.
This is a result of the effect of bound coagulase (“clumping factor”), which binds fibrinogen, converts it to insoluble fibrin, and results in aggregation.

Staphylococcus aureus is the only Staphylococcus found in humans which produces coagulase; other staphylococcal species are commonly identified as coagulase-negative staphylocci.

Staphylococcus aureus produces at least five cytolytic toxins, two exfoliative toxins, eight enterotoxins, and toxic shock syndrome toxin. Some of these toxins act as superantigens, which recruit host defense cells that liberate cytokines and, therefore, produce systemic effects.

Heating will kill the S. aureus organisms, but not inactivate the enterotoxins, because they are stable to heating at 100°C (112°F) for 30 minutes and are resistant to breakdown by gastric acids.

Of growing public health concern is the rapid spread of antibiotic resistance within S. aureus isolates.
Some S. aureus isolates have been identified recently with reduced sensitivity to vancomycin. The mechanism of this resistance is unknown.

Genes
that confer resistance can be transferred between organisms by plasmid transfer, transduction and cell-to-cell contact.