Download Q repeat 9 interval amino acid forms in man and pathogen

Q repeat 9 interval amino acid
forms in man and pathogen
Visualization and molecular weight
*Fasta context to graphed data as
process.
Sites:
• http://wit.mcs.anl.gov/WIT2/CGI
http://www.sanger.ac.uk/
• http://www.embl-heidelberg.de/
• http://www.expasy.ch/
• http://protein.toulouse.inra.fr/prodom.html
• http://www-sv.cict.fr/bacterio/
By Mark McGary
This slide presentation is designed to
introduce advanced concepts in assay
of amino acid forms in pathogen and
man.
It includes a repeat set that includes
both TB and man. Those are depicted
among the graphed data shown.
• A note about passion for this subject.
• Nothing has so transformed my view about
the nature of fundamental comparisons
using genomic tools as the task of
translating the German text of Dr. Robert
Koch from the written German to English.
• Among the data of tuberculin
production....and the view of a superb
clinician working to combat disease,
• Koch is available to the reader as a man
who began to medically understand aspects
of TB. At the time of Koch’s inquiry.....
• Tools using genomic functions were
unavailable.
• Dr. Koch reached an impasse within the
technology of his time. Students and
researchers of the year 2000 have available
a formidable advance in conceptual and
comparative data to further assay Homo
sapiens and disease. Ask yourself....”Why is
this important to an understanding of TB,
Public Health Epidemiology and disease?”
• Taking the critical care needed to build
genomic tools is the passage to a larger
understanding of pathogen man interaction.
• In Mycobacterium tuberculosis....and
others...is a formidable set of opponents.
Within this field...must come such
comparisons and the reach for larger impact
on medicine and public health.
•
Goals
• Identify and quantify underlying molecular
chemistry in known amino forms
• Observe similarities available that
demonstrate repeat regions in pathogen and
man in experimental relationships.
• The methods and graphs that follow are
only the opinion of the author...and
represent theory...with “Data” in test
graphs.
These findings are prototypes of a
new form of assay and use graphs
that may be revised.
I invite the student to use similar
...ideas and share those concepts .
WIT 2 : FASTA derived similarity search address:
http://wit.mcs.anl.gov/WIT2/CGI
*
WIT includes a set of over 2900 diagrams
depicting metabolic pathways. This collection is from
the Metabolic
Pathway Database constructed by Evgeni Selkov
and his team. Each pathway diagram includes a set of
functional
roles. The goal of producing a metabolic
reconstruction is to identify which pathways are
present in an organism and
which genes implement the functional roles.
The relational table representing the pathway
collection includes two
columns: a pathway identifier and a
functional role (there will be multiple rows for
each pathway). For each organism, we include
a list of pathways present in the organism.
For each organism, we include a table
connecting genes (ORFs) to hypothesized
functional roles.
“FASTA” ... is a language that describes amino
forms along DNA strands, widely used within
science as a method to quantify amino sequence.
FASTA to underlying amino acid
chemistry:
Mole weight by assigned groupings:
“Quantative assignment”.
As I observe “interval repeats” to occur in other
lesser and greater lengths, I find it compelling that
the 11 region assay is found among man’s critical
tissues of brain stem, bone marrow and hepatic
sites...with amino characters and the repeats among
the pathogens that mirror length. Exploring this issue
among the like regions of Homo sapiens and gram
negative bacilli continues to remain for the
author...an interesting exercise. I continue to remark
on this interesting finding and explore other repeat
contigs that propose method in interval forms.
Method:
Foremost ...among observation...has come the
regard for examining the pattern of Q – nine
interval – Q form.
Typically, this type of domain as a contig is
highly conserved in MTB37Rv.
I provide examples:
with several results graphed.
I want to demonstrate specific aspects of the artifacts I
observe in MTB 37 Rv (Tb.) as regard man as a host.
In comparison with M. bovis, T. pallidum,
Streptococcus, Falciparium, et al and man...MTB 37
Rv’s sequence demonstrates a direct corollary of
sequence length *(contig site variable). I comment
upon this finding and further demonstrate the
availability of the repeat similarity match sets
routinely found at Expasy, EMB, WIT site(s).
The method I have found of most use “routinely
probes contig composition” ...that is...exactly... “the
sequence forms of amino structure toward pathogen
and man”.
As to form and shape..a natural assignment has been
to quantify the underlying chemistries. Thus, the
determining of mole weight of the amino forms is
observed to have good precision and allows
comparative graph.
I include several so that the reader may trace the
development of multiple pathogens ...human contig
intersect
Genetic interval to Mole Weight
• Foremost ...among observation...has come
the regard for examining the pattern of Q –
nine interval – Q form. Examples:
• QKLVSSHKPVQ – Homo sapiens
• QKLVSSHKPVQ – Pathogen and man list:
• QRLAAERDAAQ • Mycobacterium avium: QMIRLATERDQ
• Mycobacterium tuberculosis:
QSVALYLGKGQ
• Mycobacterium bovis: QILASGLTVSQ
DNA in pathogen(s) and Homo sapiens
share common features among the genetic
information available to the student.
Translation of the genetic alphabet to mole
weight form is a critical skill to assay DNA
What is most important to learn?
• FASTA is a language representing amino
forms of DNA. Repeats of these regions
can be identified.
• Identification and subsequent mole weight
mapping follows.
• 119.12 threonine
• 168.0538 selenocysteine
• 117.1474 valine
Fasta forms represent a “shorthand “ of
chemistry as each letter represents a
known amino form. Those forms are
shown here (examples only/ above)with
the accompanying data of mole weight.
Translation of Fasta form to mole
weight number sets can now
occur
• Information from
• QKLVSSHKPVQ
• Can translate to
• Q = 146.1456 glutamine
• ect.
With a table of values....many forms can
be examined to represent amino -subset
comparisions.
A set of similar forms can become a
numerical grid..suitable to graph.
The following slides are a translation
of ten each....amino acid repeat
regions. They include man, TB, and
F.malaria regions of 11 repeat.
Graphs of this data follows.
A comparative view of amino forms of man and pathogen (10
ea) I invite the student to demonstrate further comparative
views. My favorite is shown below. Man and disease share “Q
repeat” regions shown as graphed colors.
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All of the graphs that follow
represent graphed forms of
amino molecular weight.
This represents a concept that the student can
further explore with forms from among
sequences widely published.
Eight slides will follow.
The slides use the same number
sets as shown.... to provide a
computer model for a graphed
form.
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S9
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Here is a graph where amino froms show a depth
in 3-D.
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A graph where peaks are available.
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This form provided a nice overlay. to..amino
comparisions.
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A repeat region graphed for 22 interval.
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A graph allowing a concentric view to
amino forms.
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Excellent /area translation of numbers.
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Notice the peak in amino forms in this view.
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My favorite view of shared amino forms. 11 interval findings!
Notice the species variation....shared endpoints!
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