Phage therapy subjects from Sellano town : Mycobacterium ulcerans Agy99

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, 19 July 2014

Mycobacterium ulcerans Agy99

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Overview

Project Information
Proposal Name	Mycobacterium ulcerans Agy99
Organism Name	Mycobacterium ulcerans Agy99
Taxon ID	642555140
NCBI Taxon ID	362242
GOLD ID in IMG Database	Project ID: Gc00469
External Links	; NCBI/RefSeq:NC_005916; NCBI/RefSeq:NC_008611; PUBMED:14736915; PUBMED:17210928
Lineage	Bacteria; Actinobacteria; Actinobacteria; Actinomycetales; Mycobacteriaceae; Mycobacterium; ulcerans
Sequencing Status	Finished
IMG Release	IMG/W 2.7
Comment
Release Date	2008-12-01
Add Date	2008-09-20
Modified Date	2011-08-16
Distance Matrix Calc. Date	2014-07-02
High Quality	Yes
Is Public	Yes
Cultured	Yes
Culture Type	Isolate
Geographic Location	ulcerative lesion on the right elbow of a female patient from the Ga district of Ghana in 1999
GOLD ID	Gc00469
Isolation Country	Ghana
Isolation Year	July, 1999
NCBI Project ID	16230
Publication Journal	Genome Res. (17, 192-200)
GOLD Sequencing Status	Complete
Project Sequencing Method	Sanger
Sequencing Center	Institut Pasteur
Metadata
Assembly Method	Phrap, Gap4
Biotic Relationships	Free living
Cell Shape	Rod-shaped
Ecosystem	Host-associated
Ecosystem Category	Human
Ecosystem Type	Unclassified
Ecosystem Subtype	Unclassified
Gram Staining	Gram+
Host Name	Homo sapiens
Host Gender	Female
Host Health	Patient
Isolation	ulcerative lesion on the right elbow of a female patient from the Ga district of Ghana in 1999
Library Method	2-3Kb, 3-5Kb, 5-10Kb
Motility	Nonmotile
Oxygen Requirement	Aerobe
Specific Ecosystem	Unclassified
Sporulation	Nonsporulating
Temperature Range	Mesophile
Temperature Optimum	32
Sample Body Site	Skin
Relevance	Medical, Human Pathogen
Phenotype	Pathogen, Antibiotic resistant
Habitat	Host, Fresh water
Diseases	Buruli ulcer
Cell Arrangement	Singles
Energy Source	Chemoorganotroph
Phenotypes/Metabolism from Pathway Assertion
Metabolism	Auxotroph (L-lysine auxotroph) (IMG_PIPELINE; 2012-10-10)
Metabolism	Prototrophic (L-alanine prototroph) (IMG_PIPELINE; 2012-10-10)
Metabolism	Prototrophic (L-aspartate prototroph) (IMG_PIPELINE; 2012-10-10)
Metabolism	Prototrophic (L-glutamate prototroph) (IMG_PIPELINE; 2012-10-10)
Metabolism	Auxotroph (L-phenylalanine auxotroph) (IMG_PIPELINE; 2012-10-10)
Metabolism	Auxotroph (L-tyrosine auxotroph) (IMG_PIPELINE; 2012-10-10)
Metabolism	Auxotroph (L-tryptophan auxotroph) (IMG_PIPELINE; 2012-10-10)
Metabolism	Auxotroph (L-histidine auxotroph) (IMG_PIPELINE; 2012-10-10)
Metabolism	Auxotroph (Glycine prototroph) (IMG_PIPELINE; 2012-10-10)
Metabolism	Prototrophic (L-arginine prototroph) (IMG_PIPELINE; 2012-10-10)
Metabolism	Prototrophic (L-asparagine prototroph) (IMG_PIPELINE; 2012-10-10)
Metabolism	Prototrophic (L-cysteine prototroph) (IMG_PIPELINE; 2012-10-10)
Metabolism	Prototrophic (L-glutamine prototroph) (IMG_PIPELINE; 2012-10-10)
Metabolism	Prototrophic (L-isoleucine prototroph) (IMG_PIPELINE; 2012-10-10)
Metabolism	Auxotroph (L-leucine auxotroph) (IMG_PIPELINE; 2012-10-10)
Metabolism	Prototrophic (L-proline prototroph) (IMG_PIPELINE; 2012-10-10)
Metabolism	Prototrophic (L-serine prototroph) (IMG_PIPELINE; 2012-10-10)
Metabolism	Prototrophic (L-threonine prototroph) (IMG_PIPELINE; 2012-10-10)
Metabolism	Prototrophic (L-valine prototroph) (IMG_PIPELINE; 2012-10-10)
Metabolism	(Non-selenocysteine synthesizer) (IMG_PIPELINE; 2012-10-10)
Metabolism	Prototrophic (Biotin prototroph) (IMG_PIPELINE; 2012-10-10)
Metabolism	Prototrophic (Coenzyme A prototroph) (IMG_PIPELINE; 2012-10-10)
Metabolism	(Glucose utilizing) (IMG_PIPELINE; 2012-10-10)
Metabolism	Prototrophic (L-methionine synthesis with homocysteine as intermediate) (IMG_PIPELINE; 2012-10-10)
Metabolism	Prototrophic (L-methionine synthesis with methanethiol) (IMG_PIPELINE; 2012-10-10)

Genome Statistics

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and set "Hide Zeroes in Genome Statistics" to "No".

	Number	% of Total
DNA, total number of bases	5805761	100.00%
DNA coding number of bases	4236262	72.97%
DNA G+C number of bases	3796479	65.39% ¹

DNA scaffolds	2	100.00%
Plasmid Count	1

Genes total number	4306	100.00%
Protein coding genes	4241	98.49%
RNA genes	65	1.51%
rRNA genes	3	0.07%
5S rRNA	1	0.02%
16S rRNA	1	0.02%
23S rRNA	1	0.02%
tRNA genes	45	1.05%
Other RNA genes	17	0.39%
Protein coding genes with function prediction	2792	64.84%
without function prediction	1449	33.65%
Protein coding genes connected to SwissProt Protein Product	340	7.90%
not connected to SwissProt Protein Product	3901	90.59%
Protein coding genes with enzymes	1007	23.39%
w/o enzymes but with candidate KO based enzymes	10	0.23%
Protein coding genes connected to Transporter Classification	293	6.80%
Protein coding genes connected to KEGG pathways³	1053	24.45%
not connected to KEGG pathways	3188	74.04%
Protein coding genes connected to KEGG Orthology (KO)	1735	40.29%
not connected to KEGG Orthology (KO)	2506	58.20%
Protein coding genes connected to MetaCyc pathways	988	22.94%
not connected to MetaCyc pathways	3253	75.55%
Protein coding genes with COGs³	2592	60.20%
with KOGs³	1546	35.90%
with Pfam³	3619	84.05%
with TIGRfam³	1074	24.94%
with InterPro	3572	82.95%
with IMG Terms	870	20.20%
with IMG Pathways	336	7.80%
with IMG Parts List	322	7.48%
in paralog clusters	2561	59.48%
in Chromosomal Cassette	4306	100.00%
Chromosomal Cassettes	673	-
Biosynthetic Clusters	69	-
Genes in Biosynthetic Clusters	980	22.76%
Fused Protein coding genes	352	8.17%
Protein coding genes coding signal peptides	298	6.92%
Protein coding genes coding transmembrane proteins	839	19.48%
COG clusters	1326	51.16%
KOG clusters	725	27.97%
Pfam clusters	1778	49.13%
TIGRfam clusters	881	82.03%

Notes:
1 - GC percentage shown as count of G's and C's divided by the total number of bases.
The total number of bases is not necessarily synonymous with a total number of G's, C's, A's, and T's. 2 - Pseudogenes may also be counted as protein coding or RNA genes, so is not additive under total gene count. 3 - Graphical view available.

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Monitoring

Year 2010 (2011,2012,2013,2014,2015,2016,2017,2018..)

- At present there are Strict rules about Drugs.

Positive and continuous trend in the request of new anti-bacterial drugs.

Year 2025?- Drug regulations changes by a swing in public Opinion and Phage Therapy Units starting inside the Hospitals.

I have read a lot of scientific studies concerning different topics about Phage Therapy and many opinions from the academic world. These comments about the use of Phages in therapy are often sceptical and also sarcastic.
I share some their opinion but the trend of antibiotic resistance is characterising by a relentless advance. In the absence of new antibiotics we are obliged to act with fairness and to weigh the pros and cons of Phage therapy.

Phage Therapy is better than nothing.

Sellano is touched by History

Potential application of Mycobacterium phages in Buruli disease

I have been studying since January 2009 if Phage Therapy could be considered in Buruli ulcer. Patients shed large numbers of bacilli from their wounds.
"In the first stage of disease Mycobacterium ulcerans bacilli are typically found extracellularly, where it might be immediately accessible by phages."
Children under the age of 15 years ( range 2-14 years) are predominantly affected.
After my trip in Ivory Coast it is my personal project and I am exploring if this working hypothesis is possible.

Theory and Practical Applications of Phage Therapy in Human Field.

I must remember that Phage Therapy is not equivalent to the Antibiotic Therapy but in some pathological situations, with well definite circustances and when we have a bacterial infection caused by bacteria resistant to all antibiotics, in that case Phage Therapy would remain the unique and possible treatment with a tangible chance of succes.

A complete and schematized process for working with Phages by Phage Cocktails. Phage Therapy is praticable both in Veterinary Science and in Agricultural and Food Industry. Phage Therapy in Human field is, on the contrary, a demanding job.

I'd like to explain several key points of Phage Therapy, for example:

How to prepare Phages
How to select Phages
How to purify Phages
How to administer Phages

Patenting Issues and Defense of Intellectual Property
One relevant factor in the development of all bacteriophage-based therapies is their intellectual property status, because the idea of using bacteriophages as therapeutic tools is almost a hundred years old, and as such , unpatentable.

Main Obstacles to Phages Therapy

• Pervasive fixation on chemical antibiotics within the clinical establishment.

• Resistance of the pharmaceutical sector, which is heavily invested in chemical antibiotics.

• Physicians' reluctance to forego wide-spectrum antibiotics in favor of the highly specific phages.

• Structural and functional reorganization required for a coordinated and responsive diagnosis-production-administration chain.

• Pervasive aversion within the biotech research establishment to revert to "archaic" microbiology.

• Need to constantly adapt and refresh phage preparations in response to pathogen evolution.

• Delay between clinical presentation and antibacterial administration.

• General disregard for Russian research and clinical practices.

• Concerns with bacterial evolution of resistance to phages.

• Lack of a regulatory reference basis.

Phage therapy subjects from Sellano town

information

Phage therapy is influenced by:

From Wikipedia

Saturday, 19 July 2014

Mycobacterium ulcerans Agy99

Overview

Genome Statistics

Browse Genome

Phylogenetic Distribution of Genes

Putative Horizontally Transferred Genes

Compare Gene Annotations

Scaffold Consistency Check

Export Gene Information

Export Genome Data

Scaffold Search

The authentic Sellano's gonfalon (the year of 1936)

Sellano's gonfalon

The last story from Selllano's castle and its territory.Click on this image:

Phage Therapy Light and Shade

Potential application of Mycobacterium phages in Buruli disease

Plagiarism?No!But,from the Net to the Net!

Sellano's coat of arms.Click on this image:

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