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Discussion
Extrapolated pathovar arthropod mechanism in pathogenesis of homo sapiens:
A curious molecular mechanism in interior scaffold and residue matrix.
By Mark McGary
Abstract: The arthropod Anopheles sinensis] XP_006721712.1 Gene residue, is explored with
constraint identity, post identity read .Of particular regard, in the assay, a protospecies premise of passerine homobox donation, multi gene locus to the retroviral assembly. This observation premise impacts oncogene complement of the sarcoma...as well as the EBV co-morbidity.
The assay, progresses forward from the initial summation, below. *as part two.4//14/15
Keywords:
pathovar, Anopheles sinensis, identity scaffold
methods:
Here, the NCBI, NIH, Blast and Cobalt toolbars provision an excellent
view toward arthropod anopheles s.-pathovar...Viral species interface.*Blackberry vine, grape leaf roll. Observationally, the observer should recall the cardiac implication of the arthropod.
The culex, anopheles observation, useful to consider in the known cardiac insult at tissue,
with EBV co morbidity appearance..via unknown molecular pathway.
Results:
A vew to precursor polymorphism is favorable to the premise of insult in homo sapiens.
Why this proceeding conservation is needed is the low scaffold identity in full constraint.
However, the HIV AYY25627 vpu identity set is high in constraint alignment as shown for homo sapiens:
below:
ref|YP_008411010.1|
gb|AFU08344.1|
gb|KFB45370.1|
ref|XP_006721712.1|
aay25627
Centric to pathogen, the blast challenge via AAY25627 at identity: position 33 thru 60 to
blast of Homo sapiens residue component...was productive:
*see 2ACX_A
This intersection study, follows the cobalt view via:
KFA39286
AGA93574
AAV39347
WP_035414988
where the extraction of the identity scaffold viewpoint was: identity read as
LLALLAGIVNSIW
as available to further blast challenge....observationally coherent to the study.
The return to the blackberry, grape leaf roll centric -arthropod *Anopheles s.
extracted from :
YP_008411010.1
AFU08344.1
KFB45370.1
XP_006721712.1
AAY25627.1
Discard to arthropod, blackberry, grape leaf.
Acquire the intersection of Hiv-homo sapiens. And interface the identity sets. Thus, a comparative regard to polymorphism identity at insult.
Several investigational avenues seem useful. Typically, expanded species inquiry toward the arthropod would include culex. Additional homo sapiens regard, also of benefit in contrast and comparative search. But here, the large question might be...how is the mechanism produced?
What is the underlying polymorphism control? As seen in Selkov extrapolated fold data production, HIV demonstrates a proclivity to draft...or produce additive residue to actual host.
This is seen when presenting blast challenge of HIV where the discard at final high mole identifier where previous as blast out to HIV becomes homo sapiens as blast ID. Here, is a much
more singular component is available as molar identity. The identity becomes null in full set, but with discard to
pathovar, available. extracted scaffold read....the exact mechanism of inquiry is observed with a premise of robust data set..
Several variable data are shown when modification of the underlying algorithm is changed,
via pam 30, blossum 62. See results Above.
Very favorable study potential, via the inclusion of multi-species identity extraction, is straightforward....in the regard, HIV, pathovar and homo sapiens are central to observation.
PREDICTED: serine/threonine-protein kinase tousled-like 2 isoform X11 [Homo sapiens]
1.NCBI Reference Sequence: XP_006721712.1 as intersection seen donor to mechanism....a model ..proto species....interesting in the concurrence of pathovar-and primate.
Consideration of morbidity and mortality in HIV-1 insult, suggests the pathovar study excellent to grapple with the precursor dontation...as actual conservation. While the Xanthomonas
study, was productive of insult mechanism, data was sparse towards the intersection of origin.
NCBI, NIH, COBALT Observe as Identity...below
*data:KFA39286 1
The furtherance of that potential view, seems critical to the author. When the arthropod identity is observed, several direct mechanisms of precursor defined insult become available. Within the medical entomology study, I thus urge the inclusion of the specific arthropod residue as KFB45370.1 demonstrated above....as data within any inquiry towards viradiae mechanism.
Additional :
1.NP_001158058.1
immunoglobulin-like and fibronectin type III domain-containing protein 1 [Homo sapiens] XP_005245637.1
PREDICTED: immunoglobulin-like and fibronectin type III domain-containing protein 1 isoform X1 [Homo sapiens] XP_006711680.1
PREDICTED: immunoglobulin-like and fibronectin type III domain-containing protein 1 isoform X2 [Homo sapiens] XP_006721712.1
PREDICTED: serine/threonine-protein kinase tousled-like 2 isoform X11 [Homo sapiens] AAY25627.1
vpu protein [Human immunodeficiency virus 1] BAN58185.1
membrane glycoprotein polyprotein [Severe fever with thrombocytopenia syndrome virus] AHE38400.1
glycoprotein [FTLS virus] AFH55149.1
glycoprotein [Huaiyangshan virus]
The above set, prior to the discard potentials of:
2.YP_008411010.1
RNA-dependent RNA polymerase 1b [Blackberry vein banding associated virus] AFU08344.1
RNA dependent RNA polymerase [Grapevine leafroll-associated virus 3m] KFB45370.1
AGAP001406-PA-like protein [Anopheles sinensis] XP_006721712.1
PREDICTED: serine/threonine-protein kinase tousled-like 2 isoform X11 [Homo sapiens] AAY25627.1
vpu protein [Human immunodeficiency virus 1] ...an excellent contrast.
Here, a suggested method is stepwise...singular entry to the yp set, discard to best identity inquiry or corresponding homo sapiens view. As species inquiry centric..
residue, estimated productive. Also, additional species intersection with the starting position of
arthropod, as a forward arm, premised useful.
I should be clear in the choice of NP_000064.1. Effortless productive result in pathogen-homo sapiens inquiry. Fundamental to the study of pathogenesis.
However, as shown in HIV-1 glycoprotein, NP-000064 is not useful in every mechanism study.
I would judge as percentage...above 60% to the NP locus in typical pathogen. Here, the percentage falls to below 10% intersection. Thus, a potential signal of a heavy chain, light chain identity in preliminary. However, the discovery of the locus..at tousled-like isoform, vpu
data, as shown, allows the model to move beyond t cell toward compartment identity...at pathogenesis as mechanism...post pathovar...donation. The available arthropod complement....shown in
Anopheles data, remarkable in the viral inclusion......as extracted scaffold residue. Studholme, et al, Exeter, UK, providing the 2014 upload of pathovar residue...observed to intersect the HIV 1 glycoprotein gene identity in two attached gene ORF read, with many additional glycoprotein elements slightly variant. This suggest rapid mutation, as mechanism...at this envelope observation.
Discussion:
I should be clear, in the introduction of the arthropod residue above, as the preliminary investigational result. Within the larger mutagenic prophensity of virus, a small viewpoint.
But, as evidenced in particular and evidenced intersection as shown for homo sapiens, of a critical regard. The natural development of the set, a research arm of high emphasis for 2015.
I am interested in any comment or inquiry suggestions available from interested observers.
Constraint based inquiry, provides a lessened data. Thus a tight, dense centralization to result identity read as further blast. Addition of species to the cobalt view, productive of refinement in potential interior mechanism. As the inquiry of precursor, proto species donor....data centric to polymorphism specific locus on exemplar ORF site locus.
Interestingly, a library of polymorphism control features is under production as beta model. This comes as the observational fit of dualism in identity, a pairwise complement of orf, is undertaken as control of polymorphism at insult. Problematic in triplet, and identity post pair, the library build is a unique demonstration of blast, cobalt efficiency in sequence assay at beta model. I suggest nomenclature as “Selkov identity scaffold *result”.
Mark McGary
Thyenmed Library
909 Jefferson
Walla Walla, WA
99362
mmcgary44@gmail.com
References:
NCBI, NIH
Blast,
Cobalt
V Cell 5.
HIV at membrane
Thyenmed Research Text
Continued study with the arthropod view via GENE*
toward homo sapiens sample atextracted scaffold via:
1.AAA87565.1
colon carcinoma kinase-4 [Homo sapiens] XP_011513067.1
PREDICTED: inactive tyrosine-protein kinase 7 isoform X1 [Homo sapiens] BAH12463.1
unnamed protein product [Homo sapiens] AAD22053.1
potassium channel KV4.2 [Homo sapiens] AAC83405.1
unknown [Homo sapiens] CAD38750.2
hypothetical protein [Homo sapiens] AAH17947.1
C19orf55 protein [Homo sapiens] NP_006488.2
hypermethylated in cancer 1 protein isoform 1 [Homo sapiens] XP_011539178.1
PREDICTED: polyhomeotic-like protein 2 isoform X4 [Homo sapiens] EAW88129.1
collagen, type V, alpha 1, isoform CRA_b [Homo sapiens] AAB35900.1
oestrogen receptor [Homo sapiens]
New scaffold & as identity scaffold view:
2.AAA87565.1
colon carcinoma kinase-4 [Homo sapiens] XP_011513067.1
PREDICTED: inactive tyrosine-protein kinase 7 isoform X1 [Homo sapiens] BAH12463.1
unnamed protein product [Homo sapiens] NP_006488.2
hypermethylated in cancer 1 protein isoform 1 [Homo sapiens] XP_011539178.1
PREDICTED: polyhomeotic-like protein 2 isoform X4 [Homo sapiens]
The shortened view, with surprising sparse identity.
3.AAA87565 706 GLS---VGAAVAYIIAVLG[9]KAKRLQKQPEGEEPEMECLNGGPLQNGQPsAEIQEEVA-LTSLGSGPAATNKRHSTSD
4.787 XP_011513067 67GLS---VGAAVAYIIAVLG[9]KAKRLQKQPEGEEPEMECLNGGPLQNGQPsAEIQEEVA-LTSLGSGPAATNKRHSTSD
5.755 BAH12463 714 GLS---VGAAVAYIIAVLG[9]KAKRLQKQPEGEEPEMECLNGGPLRNGQPsAEIQEEVA-LTSLGSGPAATNKRHSTSD
6.795 NP_006488 356 APPpryPGSLDGPGAGGDG -DDYKSSSEETGSSEDPSPPGGHLEGYPC--------PHLAYGEPESFGDNLYVCIPC
7.423 XP_001654799 439 CYTvtlSGANVAEALV--- AKGLATVIKYRQDDDQRSVHYDELRSAET--------QAMKQLKGVHAKDDIPSHRI-
8.503 XP_001848537 438 CYTvtlGGANVAEALV--- SKGLATVIKYRQDDDQRSVHYDELRSAET--------QAAKGLKGVHAKDDIPTHRI-
10.363 XP_006721712 302 SKT---NGA---------- ENETLTLAEYHEQEEIFKLRLGHLKKEE--AEIQAELERLERVRNLHIRELKRIHNED 363
11.Just above, note the potential insertion at gap via the *ANVAEALV, observing line 1 for correspondance
12.in mole weight
Premise of the archecture ofpathogenesis as addative to the homo sapiens touseled gene.
Observation of the mole weight should assess the comparative additive sequence residue.
As to short pattern, here was an astonishing interior pattern, distributed across the protein
interior of the HIV-1,
With the proline *several reference. Topics to the general metastatic envelop in view.... * reading indicated hyper methlyation, methylation
intersection.
1.gag protein [Human immunodeficiency virus 1] 24.4 38.2 75% 30 62% ACU50338.1 Select seq gb|AIA62140.1|
gag protein [Human immunodeficiency virus 1] 24.0 24.0 70% 42 50% AIA62140.1 Select seq gb|ACA49492.1|
envelope glycoprotein [Human immunodeficiency virus 1] 23.5 23.5 55% 60 43% ACA49492.1 Select seq gb|ACU32430.1|
gag protein [Human immunodeficiency virus 1] 23.1 23.1 55% 80 64% ACU32430.1 Select seq gb|AIK02796.1|
nef protein [Human immunodeficiency virus 1] 23.1 23.1 70% 84 67% AIK02796.1 Select seq gb|AAW57324.1|
gag protein [Human immunodeficiency virus 1] 22.7 22.7 75% 109 61% AAW57324.1 Select seq gb|ACP43867.1|
gag protein [Human immunodeficiency virus 1] 22.7 22.7 65% 115 62% ACP43867.1 Select seq gb|ACP43748.1|
gag protein [Human immunodeficiency virus 1] 22.7 22.7 65% 115 62% ACP43748.1 Select seq gb|ACQ42617.1|
gag protein [Human immunodeficiency virus 1] 22.7 22.7 65% 115 62% ACQ42617.1 Select seq gb|AAD19326.1|
pol polyprotein [Human immunodeficiency virus 1] 22.7 68.3 65% 121 88% AAD19326.1
Called up to cobalt identity, the above residue set lost the entire proline viewpoint.
Observed in the blast comparative finding, rather widely mounted on the sequence ORF
as variant locus.
Why is the conservation so variable?
The premise of variable locus conservation, is determined in the donor
precursor.
As xxxxxxxxx PPPPGERxxxxxx Where x locus was cleavage indeterminant.
Mechanism fill in gap insertion.
2.ACU50338 401 EGHIARNCRAPRKRGCWKCGKEGXQMKDctERQAXFLGKLWPSHKGXPGNF----PQSRPEPTAPPP-PAESFRFGEEMT 475 AIA62140 393 EGHIAKNCRAPRKKGCWKCGKEGHQMKDctERQANFLGKIWPSHKGRPGNF----LQNRPDP--PAP-PAES--FGLEGK 463 ACA49492 157 TLAFTQSSGGDPEIVMHSFNXEGEFFYC---NTSQLFNSTWNATTGNNTAT----AAGISAICRIRRiINLMLLLGQAVE 229 ACU32430 1 ---------------------------------------IWPSHKGRPGNFLQSRPE----PPAPPA---ESFRFGEETP 34 AIK02796 90 LSHFLXXXGGLEGLIHSQKRQEILDLWX-yHTQGYFPD--WQNYTPGPGTRXPLTFGWCFKLVPVEPeKVEEANEGENNS 166 AAW57324 1 ---------------------------------------------------------SRPEPTAPPA---ERLGDGGGKI 20 ACP43867 1 ------------------------------ERQANFLGKIWPSHKGRPGNFLQSRPESRPEPSAPPA---ESFRFGEEKA 47 ACP43748 1 ------------------------------ERQANFLGKIWPSHKGRPGNFLQSRPESRPEPSAPPA---ESFRFGEEKA 47 ACQ42617 1 ------------------------------ERQANFLGRIWPSQKGRPGNFLQSRPESRPEPSAPPApPEESFRFGEETI 50 AAD19326 222 SXPLDKDLRKYTAFTIPSINNEPPGIRY----QYNVXPQGW---KGSPAIF-QSSMTKISEPFRKQNpAIVIYQYVDDLY 293
Where, the down codon PPAES, PPAESFGEE CONSERVATION ABOVE:
provides.
Clostridium colicanis. WP_002597881.
When observed at identity, one will appear, the others, down codon bound residue, thus
not in appearance at cobalt, determinant....by blast, indeterminant at idenity via repeat.
The astonishing description, below, of the passerene homobox, histadine-proliene
complex,
as uptake in the Hiv-1, via a curcular mechanism of insertion,
ringlike to mixed insertion,
not well viewed, unless the pattern discovery of the blast complement of tools, as end use.
Provisioning the descriptor.
This view demonstrates well, the nature of the conservation. Multi locus to the pathogen.
The apparent insult potential, via the avian homobox *curious build intersection,
provisioning the wildly insertion productive component as precursor.
In preliminary inspection via pol, I now move to a larger component in the HIV-1
residue as find * goal of assay in all particulars.
3.XP_005532556 1 MSISGTLSNYYVDSIISHESEDSPSSKFPPGQFSSRQSEHLEFPSCSFQPKPAVFGSSWTPLNHHHHHPHPPPPP 75 AAZ91618 1 -------------YFLLKFAGRWPVQIVHTVQLAAISPALQSKQLCWRAGIQQEFGIPYNPQSQGVVESMHKELL 62 ACY70111 1 [804]AEVIPAETGQETAYFLLKLAGRWPVKTIHTDNGSNFTSTTV-KAACWWAGIKQEFGIPYNPQSQGVVESINKELK 878 AAF00687 1 ---IPAETGAETAYFILKLAGSWPVKVIHTDNGSNFTSAAV-KAACWRAGIQQEFGIPYNPQSQGVVESMNKELK 71
The Interior Marker, that is observationally so useful here is the proline *
Histadine-proline procession to multi locus insertion and conservation in the pathogen.
That observation:
driven by the following data. Note the position value, mixed HIV complement:
Envelope #445
232
GAG #14
NEF #20
POL#210
The entirety of gene matrix sharing *PP
modified via:
PPPPA
PPPPAI
PAPPA
DAPPPAPAADGV
PPPALDVG
With the not easily observed proto species value at homo box passerine donor:
*Cobalt below: With T cell, homo sapiens, passerine *
4.XP_005532556 1 MSISGTLSNYYVDSIISHESEDSPSSKFPPGQFSSRQSEHLEFPSCSFQPKPAVF-------GSSWTPLNHHHHHPHPPP 73 NP_000064 1 MEQGKGLAVLILAIILLQGTLAQSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGKMIGFLTEDKKKWNLGSNAKD 80 XP_005532556 74 PPPVFQPFLPQQSSPGEGRFLRAW---IEPRSESIPGSVKTEPL----LPRTSGDAPKNQEYNLEAAGGREGIAPHPFED 146 NP_000064 81 PRGMYQCKGSQNKSKPLQVYYRMCQNCIELNAATISGFLFAEIVSIFVLAVGVYFIAGQDGVRQSRASDKQTLLPNDQLY 160
So valuable in the Histadine-proline marker, so suitable to mine in the multi gene
ORF extraction, to the retro virus.
Excellent, in the transition by scaffold to known intersection in homo sapiens,
a data mine *library marker of superb instance. Vital to grapple with the protospecies,
forward to the mutagenic prophenesity, multi system insult,
with such remarkable oncogene and commens
al intersection as pathogenesis .
This is a difficult pathogen.
What does make this exercise so useful, is the transfer potential towards influenza, and other infectious disease as process, in grappling with underlying precursor insult potential,
observationally coherent to systemic regard in primate.
Discussion specific to HIV-1 protospecies build. The nature of underlying cross species donation to insult...thus.
“My best surmise, then, is the avian contribution to a mixed locus insertion,
insult specific to primate in *both systemic and organ specific mixed
precursor. Viral residue uptake, both pre transcription and post transcription.
As a curcular donation, insertion to all components of the Hiv-1 gene complement.
The homobox, domain, the critical value (as set observation) observed via the scaffold observations,
as a multi species asset, proviiding the toolbar resource to data mine.....the adequate
mutagenic path.
Why this is so useful in the following mole chemistry comes at membrane in the V Cell
5 model, where polymorphism reaction control,
a build of particular useful library viewpoints.”
5.XP_005532556 1 MSISGTLSNYYVDSIISHESEDSPSSKFPPGQFSSRQSEHLEFPSCSFQPKPAVF-------GSSWTPLNHHHHHPHPPP 73 NP_000064 1 MEQGKGLAVLILAIILLQGTLAQSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGKMIGFLTEDKKKWNLGSNAKD 80 XP_005532556 74 PPPVFQPFLPQQSSPGEGRFLRAW---IEPRSESIPGSVKTEPL----LPRTSGDAPKNQEYNLEAAGGREGIAPHPFED 146 NP_000064 81 PRGMYQCKGSQNKSKPLQVYYRMCQNCIELNAATISGFLFAEIVSIFVLAVGVYFIAGQDGVRQSRASDKQTLLPNDQLY 160 XP_005532556 147 NKVCEGSEDKERRDQ------- 161 NP_000064 161 QPLKDREDDQYSHLQGNQLRRN 182
With the adequate histadine -proline vetebral molecular pathway now observationaly coherent to mutagenesis forward premise in HIV-1 viral uptake,
protospecies interior formation.....is in my humble view....within reach. Interestingly,
with non-beta toolbar.
All beta aspects of inquiry are discarded with the full description of a suitable start position.
Making further ...forward inquiry....a full value of known robust
intersection.
*References:
part two mirror to text: references above.
McGary
additional : Thyenmed Research text: passerine observation 4/14/2015
extract via:http://en.wikipedia.org/wiki/Ground_tit
The ground tit was traditionally considered a relative of the
1.ground jays (Podoces), based on its voice and habits. Its autapomorphies have certainly puzzled 20th century ornithologists, but due to its remote range and nondescript appearance, it was little studied and not suspected to be anything but an aberrant ground jay for more than 100 years after its description by Hume.[5] In 1978[6] and 1989[7] however, two studies of its anatomy determined that – although at that time unassignable to any family due to its peculiar adaptations, it appeared that it was not a corvid but a more advanced songbird of the infraorder today known as Passerida.[1]
From 2003 onwards, osteological, mtDNA and nDNA sequence and other biochemical data[8] has firmly allied it with the tits and chickadees (Paridae). In fact, genetic evidence suggests that it is a closer relative of the great tit and its relatives in the genus Parus sensu stricto than the chickadees and their relatives of the genus Poecile.[9]
It occurs across the
2.Tibetan Plateau of China and the neighboring areas of western Sichuan and Gansu. The Tibetan ground-tit inhabits open alpine steppe and sometimes more arid regions with small scattered shrubs, rarely if ever occurring lower than 3,000 meters above sea level. It is not found anywhere where dense vegetation (especially trees) predominates. The flight of this bird is not strong and it flies low over the ground preferring to run or jump out of the way if approached which it does very quickly. It moves on the ground in unpredictable hops and bounces which can be quite long – jumps of three times the bird's length are achieved without assistance by the wings – rather than striding or running like Podoces ground jays. Observers have compared the sight of a Tibetan ground-tit moving along to a small greyish-brown rubber ball.[2]
It obtains food on the ground, eating a wide range of arthropod prey, often obtained by probing yak (Bos grunniens) dung and turning it over to flush the prey out. It also peers into rock crevices and into holes in the ground in its search for food. Individuals have been observed to poke mud in and near puddles like hoopoes (Upupa epops); in general the bill is extensively used for digging, much like the similarly-shaped one of the red-billed chough (Pyrrhocorax pyrrhocorax). If chased by a bird of prey or other predator, it will bolt straight down the nearest hole like a rodent until the danger has passed. They are frequently found near colonies of pikas (Ochotona). Though the birds and the mammals probably benefit from each other's vigilance, their association is probably less due to a strong mutualism but rather because both prefer habitat with similar ground cover and soil.[2]
The nest is rather unusual for that of a passerine, being built inside a burrow which the birds excavate themselves. It is usually dug horizontally into a bank or wall of earth, and can reach a depth of 1.8 meters. The nest is placed at the end of this in a small chamber and consists usually just of bit of wool placed onto a grass base. The 4–6 eggs are pure white and the young stay with their parents for some time after fledging; half-grown young are still fed by their parents on occasion as late as August.[10]
The ground tit is not a migratory bird but may descend to lower altitudes in valleys during the winter. In addition to digging nesting burrows, ground-tits frequently dig roosting burrows to use during the coldest months.[11
*Authors note:
as the proximity to *Ochotona is observed, the passerine-mammalian insult potential of
viral uptake as mutagenic forward conservation seems cohrent.
As to the mutation specific to HIV-1, a complete research arm, thus suggested productive.
In particular, exacture in species sample, needed.
McGary