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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

Wednesday, 23 March 2011

Virulence factors of Mycobacterium ulcerans

From this web site

Cell wall
Antigen 85
LAM
MmaA4
PDIM
PcaA
Cellular metabolism
FadD33
Isocitrate lyase
LipF
Nitrate reductase
PanC/PanD
Heat-shock protein
HspX
Iron uptake
Mycobactin
Magnesium uptake
MgtC
Regulation
DevRS
HspR
IdeR
MprAB
PhoP
RelA
SigA
SigE
SigF
SigH
WhiB3
Secreted proteins
ESAT-6/CFP-10
Secretion system
ESX-1
ESX-5
Stress protein
AhpC
KatG
SodA
SodC
Toxin
Phospholipase C
Unclassified
Erp
HbhA
PE/PE-PGRS



Mycobacterium ulcerans Agy99



Virulence factors Related genes M. ulcerans Agy99
chromosome NC_008611 (5631606 bp)
Amino acid and purine metabolism
Glutamine synthesis glnA1 MUL_1340
Leucine synthesis leuD MUL_1969
Lysine synthesis lysA MUL_3971
Proline synthesis proC MUL_4570
Purine synthesis purC MUL_0497
Tryptophan synthesis trpD MUL_3549
Anaerobic respiration
Fused nitrate reductase narX
Nitrate reductase narG
narH
narJ
narI
Nitrate/nitrite transporter narK2
Anti-apoptosis factor
NuoG nuoG MUL_2465
Cell surface components
Exported repetitive protein erp MUL_4994
Heparin-binding hemagglutinin hbhA MUL_4543
Laminin-binding protein LBP21/Hlp -
Methyltransferase mma4 MUL_0729
Mycolic acid trans-cyclopropane synthetase cmaA2 MUL_4575
PDIM (phthiocerol dimycocerosate) and PGL (phenolic glycolipid) biosynthesis and transport fadD26 MUL_2020
fadD28 MUL_2008
ppsA MUL_2019
ppsB MUL_2018
ppsC MUL_2017
ppsD MUL_2016
ppsE MUL_2015
papA5 MUL_2011
mas MUL_2010
mmpL7 MUL_2007
ddrA MUL_2014
ddrB MUL_2013
drrC MUL_2012
pks15/1 MUL_2005
-
-
-
- MUL_2377
-
Proximal cyclopropane synthase of alpha mycolates pcaA MUL_4539
Sulfolipid-1 biosynthesis and transport stf0
papA2
papA1
pks2
mmpL8
Lipid and fatty acid metabolism
FAS-II kasB MUL_1303
Isocitrate lyase icl MUL_4536
Lipase lipF
Lipid phosphatase sapM MUL_2676
Pantothenate synthesis panC MUL_4184
panD MUL_4183
Phospholipases C plcA
plcB MUL_2799
plcC
plcD
Mammalian cell entry (mce) operons
Mce1 mce1A MUL_1062
mce1B MUL_1063
mce1C MUL_1064
mce1D MUL_1065
mce1E MUL_1066
mce1F MUL_1067
Mce2 mce2A MUL_0415
mce2B
mce2C
mce2D
mce2E
mce2F
Mce3 mce3A MUL_3918
mce3B MUL_3919
mce3C MUL_3920
mce3D MUL_3921
mce3E MUL_3922
mce3F MUL_3923
Mce4 mce4A MUL_4062
mce4B MUL_4061
mce4C MUL_4060
mce4D MUL_4059
mce4E MUL_4058
mce4F MUL_4057
Mce5 mce5A MUL_3796
mce5B MUL_3797
mce5C MUL_3798
mce5D
mce5E MUL_3800
mce5F MUL_3801
Mce6 mce6A MUL_4919
mce6B MUL_4918
mce6C MUL_4917
mce6D MUL_4916
mce6E MUL_4915
mce6F MUL_4914
Mce7 mce7A
mce7B
mce7C
mce7D
mce7E
mce7F
Mce8 mce8A
mce8B
mce8C
mce8D
mce8E
mce8F
Mce9 mce9A
mce9B
mce9C
mce9D
mce9E
mce9F
Metal uptake
ABC transporter irtA MUL_3902
irtB MUL_3901
Exochelin (smegmatis) -
Iron-dependent regulator ideR MUL_3351
Magnesium transport mgtC MUL_3069
Mycobactin mbtH MUL_3639
mbtG MUL_3640
mbtF MUL_3633
mbtE MUL_3634
mbtD MUL_3638
mbtC MUL_3637
mbtB MUL_3632
mbtA MUL_3641
mbtJ MUL_3642
mbtI MUL_3648
Regulation
(p)ppGpp synthesis and hydrolysis relA MUL_1729
DevR/S devR/dosR MUL_2423
devS MUL_2422
MprA/B mprA MUL_4701
mprB MUL_4700
PhoP/R phoP MUL_0463
phoR MUL_0464
PrrA/B prrA MUL_0248
prrB MUL_0249
Sigma A sigA/rpoV MUL_3341
Sigma E sigE MUL_4519
Sigma F sigF MUL_2640
Sigma H sigH MUL_2545
Sigma M sigM MUL_5064
WhiB3 whiB3 MUL_0895
Secreted proteins
19-kD protein lpqH MUL_4389
Alpha-crystallin hspX
Antigen 85 complex fbpA MUL_4987
fbpB MUL_2970
fbpC MUL_4793
Enhanced intracellular survival protein eis
Protein kinase G pknG MUL_2810
Secretion system
Accessory secretion factor secA2 MUL_3040
ESX-1 (ESAT-6 system-1) -
-
-
-
PE35
-
-
-
mycP1
-
ESX-1 substrates esxA
esxB
-
espA
espB
ESX-5 secretion system - MUL_3077
- MUL_3078
mycP5 MUL_3079
- MUL_3080
- MUL_3081
esxN MUL_3082
esxM MUL_3083
- MUL_3092
- MUL_3092
- MUL_3093
ESX-5 substrates PPE41
Stress adaptation
AhpC ahpC MUL_2999
Catalase-peroxidase katG MUL_2190
Cu,Zn superoxide dismutase sodC MUL_1379
Iron-cofactored SOD sodA MUL_5018