Phage therapy subjects from Sellano town : How to identify Nucleic Acid binding Motifs in Protein Sequences

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 identify Nucleic Acid binding Motifs in Protein Sequences

Mycobacterium phage L5 genome is used as example:

1-download the L5 mycobacterium phage genome (file.gbk from NCBI) or your genome (file.gbk).

2-open this file by Artemis software ( open source) or by another software.

3- each time select from Artemis software one gene and copy the corresponding protein sequence with fasta Aa.

4-paste and filter this sequence in Sequence Manipulation Suite ( open source) if is necessary , copy the filtrate protein sequence .

5- open mJemboss software (open source) and paste the sequence in Helix-Turn-Helix program.

7-safe the result.

8 - in Jemboss by the same sequence open other programs.

9- align the sequences by Strap software (open source) or by Jalview software (open source) and plot the Tree.

L5p46(c31389-30961,142 Aa)

In L5 mycobacterium phage proteome are present for example these Helix-turn-helix motifs :

L5p36 (c26727-26557, 56Aa)

L5p44(c30476-28689, 595Aa)

L5p71(c44882-44331, 183Aa)

TREE

Alignment

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

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Phage therapy is influenced by:

From Wikipedia

Saturday, 23 August 2014

How to identify Nucleic Acid binding Motifs in Protein Sequences

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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