Phage therapy subjects from Sellano town : Mycobacterium ulcerans Harvey

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 Harvey

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Overview

Project Information
Proposal Name	Mycobacterium ulcerans Harvey
Organism Name	Mycobacterium ulcerans Harvey
Taxon ID	2565956790
IMG Submission ID	36722
NCBI Taxon ID	1299332
GOLD ID in IMG Database	Project ID: Gi0041622
External Links	NCBI/RefSeq:JAOL01000001; NCBI/RefSeq:JAOL01000002; NCBI/RefSeq:JAOL01000003; NCBI/RefSeq:JAOL01000004; NCBI/RefSeq:JAOL01000005; NCBI/RefSeq:JAOL01000006
Lineage	Bacteria; Actinobacteria; Actinobacteria; Actinomycetales; Mycobacteriaceae; Mycobacterium; ulcerans
Sequencing Status	Permanent Draft
IMG Release
Comment
Release Date	2014-04-28
Add Date	2014-04-28
Modified Date
Distance Matrix Calc. Date
High Quality	No
IMG Product Flag	No
Is Public	Yes
Cultured	Yes
Culture Type	Isolate
GOLD ID	Gi0041622
Isolation Country	USA
NCBI Project ID	191796
Publication Journal	Unpublished
GOLD Sequencing Status	Complete
Project Sequencing Method	Pacbio
Sequencing Center	Institute for Genome Sciences
Metadata
Assembly Method	SMRT HGAP v. 2.0.1
Gram Staining	Gram+
Phenotypes/Metabolism from Pathway Assertion
Metabolism	Auxotroph (L-lysine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism	Auxotroph (L-alanine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism	Auxotroph (L-aspartate auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism	Prototrophic (L-glutamate prototroph) (IMG_PIPELINE; 2014-05-01)
Metabolism	Auxotroph (L-phenylalanine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism	Auxotroph (L-tyrosine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism	Auxotroph (L-tryptophan auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism	Auxotroph (L-histidine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism	Auxotroph (Glycine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism	Auxotroph (L-arginine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism	Auxotroph (L-asparagine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism	Auxotroph (L-cysteine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism	Auxotroph (L-glutamine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism	Auxotroph (L-isoleucine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism	Auxotroph (L-leucine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism	Auxotroph (L-proline auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism	Auxotroph (L-serine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism	Auxotroph (L-threonine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism	Auxotroph (L-valine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism	(Non-selenocysteine synthesizer) (IMG_PIPELINE; 2014-05-01)
Metabolism	(Non-biotin synthesizer) (IMG_PIPELINE; 2014-05-01)
Metabolism	Auxotroph (Incomplete Coenyzme A biosynthesis) (IMG_PIPELINE; 2014-05-01)

Genome Statistics

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

	Number	% of Total
DNA, total number of bases	6247430	100.00%
DNA coding number of bases	5084742	81.39%
DNA G+C number of bases	4072505	65.19% ¹

DNA scaffolds	209	100.00%

Genes total number	9228	100.00%
Protein coding genes	9178	99.46%
Pseudo Genes	1	0.01%²
RNA genes	50	0.54%
rRNA genes	2	0.02%
5S rRNA	1	0.01%
23S rRNA	1	0.01%
tRNA genes	48	0.52%
Protein coding genes with function prediction	6911	74.89%
without function prediction	2267	24.57%
Protein coding genes with enzymes	637	6.90%
w/o enzymes but with candidate KO based enzymes	1394	15.11%
Protein coding genes connected to Transporter Classification	363	3.93%
Protein coding genes connected to KEGG pathways³	684	7.41%
not connected to KEGG pathways	8494	92.05%
Protein coding genes connected to KEGG Orthology (KO)	1141	12.36%
not connected to KEGG Orthology (KO)	8037	87.09%
Protein coding genes connected to MetaCyc pathways	625	6.77%
not connected to MetaCyc pathways	8553	92.69%
Protein coding genes with COGs³	1793	19.43%
with KOGs³	2217	24.02%
with Pfam³	5548	60.12%
with TIGRfam³	1028	11.14%
with InterPro	3058	33.14%
with IMG Terms	295	3.20%
with IMG Pathways	117	1.27%
with IMG Parts List	133	1.44%
in paralog clusters	7002	75.88%
in Chromosomal Cassette	9228	100.00%
Chromosomal Cassettes	1159	-
Biosynthetic Clusters	115	-
Genes in Biosynthetic Clusters	1780	19.29%
Fused Protein coding genes	73	0.79%
Protein coding genes coding signal peptides	343	3.72%
Protein coding genes coding transmembrane proteins	1305	14.14%
COG clusters	997	55.61%
KOG clusters	728	40.60%
Pfam clusters	1795	32.35%
TIGRfam clusters	755	73.44%

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 Harvey

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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