Phage therapy subjects from Sellano town : Dot plots

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

Dot plots

This a short explanation of Dot plots an easy and powerful means of sequence analysis, useful for searching out regions of similarity in two sequences and repeats within a single sequence.

This the principle:

These are some examples of reading:

By Gepard ("GEnome PAir - Rapid Dotter" is an open source from Helmholtz Zentrum München ) we have two variable parameters:

· Word length - minimum word length for identical subsequences which create a hit in the dotplot.

· Window size - If word length =0 "normal" dotplot mode will be activated where all characters of both sequences are compared against each other.

This parameter specifies the window size over which an average dot value will be calculated.

· Word length is number of bases in a sliding window that is moved along each sequence and compared to generate a single data point on the plot. Word lenght must be an number.

· Mismatch Limit ( is the window size) determines how similar the two sequences in a word lenght must be to "match". For example, if word lenght size is 9 and mismatch limit is 2, then up to 2 mismatches in a 9 base word lenght will still be classified as a match.

If we compare the genomes of My. smegmatis and My. ulcerans by Gepard (two FASTA format sequence files ) and changing the parameters for increasing the sensibility,we have:

This is the best:

Here it is possible to observe common regions, some repeats and palindromic sequences. By the co-ordinate axes it is possible to select a single gene for further evidence.

The next image it doesn't make any difference.

Control: My.smegmatis versus My.smegmatis

Control: My.ulcerans versus My.ulcerans

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 23 August 2014

Dot plots

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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