Q repeat 9 interval amino acid forms in man and pathogen

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Q repeat 9 interval amino acidforms in man and
pathogen

• Visualization and molecular weight
• Fasta context to graphed data as process.

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Sites

• http//wit.mcs.anl.gov/WIT2/CGIhttp//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/

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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.

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• 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.

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• 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 Kochs inquiry.....
• Tools using genomic functions were unavailable.

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• 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?

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• 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.
  

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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.

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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 .
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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.
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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.
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FASTA to underlying amino acid chemistry

• Mole weight by assigned groupings
• Quantative assignment.

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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 mans
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.
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MethodForemost ...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 exampleswith several results graphed.
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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 Rvs 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).
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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
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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

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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 DNAWhat 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.

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• 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.
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Translation of Fasta form to mole weight number
sets can now occur

• Can translate to
• Q 146.1456 glutamine
• ect.

• Information from
• QKLVSSHKPVQ

With a table of values....many forms can be
examined to represent amino -subset comparisions.
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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.
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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.
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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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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!