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Post by skyship on Mar 31, 2010 13:47:18 GMT -5
www.retrovirology.com/content/5/1/45Origin of Uracil: Uracil produced in the lab NASA"NASA scientists studying the origin of life have reproduced uracil, a key component of our hereditary material, in the laboratory. They discovered that an ice sample containing pyrimidine exposed to ultraviolet radiation under space-like conditions produces this essential ingredient of life. Pyrimidine is a ring-shaped molecule made up of carbon and nitrogen and is the basic structure for uracil, part of a genetic code found in ribonucleic acid (RNA). RNA is central to protein synthesis, but has many other roles. "We have demonstrated for the first time that we can make uracil, a component of RNA, non-biologically in a laboratory under conditions found in space," said Michel Nuevo, research scientist at NASA's Ames Research Center, Moffett Field, Calif. "We are showing that these laboratory processes, which simulate occurrences in outer space, can make a fundamental building block used by living organisms on Earth."".............. www.astrobio.net/pressrelease/3304/uracil-made-in-the-labWOW! simulations of outer space? How was the mimic made? the protocell? possibly from uracil? How get in human body? the spark of life while prion the filament of life? connection between uracil and prions? there is one!!!!!!!!!!!!!!!!!!!!!!!!!!! ure3, ure2 , psi from yeast sup35p, the created cross between inorganic and organic? ? The [URE3] yeast prion is a self-propagating inactive form of the Ure2p protein. We show here that Ure2p from the species Saccharomyces paradoxus (Ure2pSp) can be efficiently converted into a prion form and propagate [URE3] when expressed in Saccharomyces cerevisiae at physiological level. We found however that Ure2pSp overexpression prevents efficient prion propagation. We have compared the aggregation rate and propagon numbers of Ure2pSp and of S. cerevisiae Ure2p (Ure2pSc) in [URE3] cells both at different expression levels. Overexpression of both Ure2p orthologues accelerates formation of large aggregates but Ure2pSp aggregates faster than Ure2pSc. Although the yeast cells that contain these large Ure2p aggregates do not transmit [URE3] to daughter cells, the corresponding crude extract retains the ability to induce [URE3] in wild-type [ure3-0] cells. At low expression level, propagon numbers are higher with Ure2pSc than with Ure2pSp. Overexpression of Ure2p decreases the number of [URE3] propagons with Ure2pSc. Together, our results demonstrate that the concentration of a prion protein is a key factor for prion propagation. We propose a model to explain how prion protein overexpression can produce a detrimental effect on prion propagation and why Ure2pSp might be more sensitive to such effects than Ure2pSc. www.molbiolcell.org/cgi/content/full/20/8/2286;[URE3] propagons seems URE3, as you mentioned AQT, is the propogon. the self replicating uracil? ?? =========== A Promiscuous Prion: Efficient Induction of [URE3] Prion Formation by Heterologous Prion DomainsThe [URE3] and [PSI+] prions are the infections amyloid forms of the Saccharomyces cerevisiae proteins Ure2p and Sup35p, respectively. Randomizing the order of the amino acids in the Ure2 and Sup35 prion domains while retaining amino acid composition does not block prion formation, indicating that amino acid composition, not primary sequence, is the predominant feature driving [URE3] and [PSI+] formation. Here we show that Ure2p promiscuously interacts with various compositionally similar proteins to influence [URE3] levels. Overexpression of scrambled Ure2p prion domains efficiently increases de novo formation of wild-type [URE3] in vivo. In vitro, amyloid aggregates of the scrambled prion domains efficiently seed wild-type Ure2p amyloid formation, suggesting that the wild-type and scrambled prion domains can directly interact to seed prion formation. To test whether interactions between Ure2p and naturally occurring yeast proteins could similarly affect [URE3] formation, we identified yeast proteins with domains that are compositionally similar to the Ure2p prion domain. Remarkably, all but one of these domains were also able to efficiently increase [URE3] formation. These results suggest that a wide variety of proteins could potentially affect [URE3] formation. Key Words: [URE3], amyloid, prion, yeast skyship
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Post by skyship on Mar 31, 2010 13:49:19 GMT -5
Origin of URE3. [URE3] as an Altered URE2 Protein: Evidence for a Prion Analog in Saccharomyces cerevisiae Wickner, Reed B. Science, Volume 264, Issue 5158, pp. 566-569 A cytoplasmically inherited element, [URE3], allows yeast to use ureidosuccinate in the presence of ammonium ion. Chromosomal mutations in the URE2 gene produce the same phenotype. [URE3] depends for its propagation on the URE2 product (Ure2p), a negative regulator of enzymes of nitrogen metabolism. Saccharomyces cerevisiae strains cured of [URE3] with guanidium chloride were shown to return to the [URE3]-carrying state without its introduction from other cells. Overproduction of Ure2p increased the frequency with which a strain became [URE3] by 100-fold. In analogy to mammalian prions, [URE3] may be an altered form of Ure2p that is inactive for its normal function but can convert normal Ure2p to the altered form. The genetic evidence presented here suggests that protein-based inheritance, involving a protein unrelated to the mammalian prion protein, can occur in a microorganism. adsabs.harvard.edu/abs/1994Sci...264..566Wskyship
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Post by skyship on Mar 31, 2010 14:03:12 GMT -5
URE3 and uracil in yeast, even fleischmans? www.pnas.org/content/102/30/10575/T3.expansion.htmlbread and wine, folks................ yeast and fermentation...................... yeast and uracil...................... building blocks of life? uracil building block of artificial life? ======================= PROOF>>>>>>>>>>>>>>>>> "For those who are studying aspects of the origin of life, the question no longer seems to be whether life could have originated by chemical processes involving non-biological components but, rather, what pathway might have been followed. —National Academy of Sciences (1996) It is 1828, a year that encompassed the death of Shaka, the Zulu king, the passage in the United States of the Tariff of Abominations, and the battle of Las Piedras in South America. It is, as well, the year in which the German chemist Friedrich Wöhler announced the synthesis of urea from cyanic acid and ammonia. Discovered by H.M. Roulle in 1773, urea is the chief constituent of urine. Until 1828, chemists had assumed that urea could be produced only by a living organism. Wöhler provided the most convincing refutation imaginable of this thesis. His synthesis of urea was noteworthy, he observed with some understatement, because "it furnishes an example of the artificial production of an organic, indeed a so-called animal substance, from inorganic materials." " www.discovery.org/a/3209skyship
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Post by skyship on Mar 31, 2010 14:08:23 GMT -5
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Post by aqt on Mar 31, 2010 14:13:31 GMT -5
whoa. exposed to ultraviolet radiation under space-like conditions produces this essential ingredient of life.www.retrovirology.com/content/5/1/45didn't I just ask if radiation could have been the spark? vibrating something so fast, it sparks like rubbing 2 sticks together? I think I did. whoa. aqt
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Post by aqt on Mar 31, 2010 14:14:44 GMT -5
sorry, wrote that post after reading the first sentence of first post
now I have seen the rest of the material
we're on it
heavy.
aqt
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Post by aqt on Mar 31, 2010 14:26:49 GMT -5
uracil en.wikipedia.org/wiki/UracilUracil is a common and naturally occurring pyrimidine derivative.[2] Originally discovered in 1900, it was isolated by hydrolysis of yeast nuclein that was found in bovine thymus and spleen, herring sperm, and wheat germ.[3] It is a planar, unsaturated compound that has the ability to absorb light.[4]naturally occurring since 1900 when they introduced it into the human genome? isolated by hydrolysis of yeast neuclein found in pig glands/organs, herring sperm and wheat germ? ? and let us not forget it has the ability to absorb light like we will be able to do before long aqt
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Post by aqt on Mar 31, 2010 14:31:25 GMT -5
Bio-nanocomposites are an emerging group of hybrid materials derived from natural polymers and inorganic solids interacting at the nanometric scale. These nanostructured organic–inorganic materials could be designed and prepared using a wide type of biopolymers and also inorganic solids with different compositions and topologies. Among these last solids, special attention is devoted to layered materials that show the ability to intercalate biopolymers giving hybrids with functional properties. This novel research topic envisages the future development of biomimetic materials to provide novel bio-nanocomposites as multicomponent and multifunctional materialswww.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b505640n&JournalCode=JMBio-nanocomposites are an emerging group of hybrid materials derived from natural polymers ..... thymine and uracil are adsorbed on montmorillonite appreci
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Post by aqt on Mar 31, 2010 14:34:56 GMT -5
Applications of hybrid organic–inorganic nanocomposites, J. Mater. Chem. ... self-organization of adenine- uracil-derived hybrid materialsAlkali cation-ð aromatic conduction pathways in self-organized hybrid membranes tiny.cc/4u3or
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Post by aqt on Mar 31, 2010 14:39:53 GMT -5
Uracil-derivatized monomer 6-undecyl-1-(4-vinylbenzyl)uracil and ... The growth rate of the polymer formation can be derived from the slope of the linear region ... Surprising conversion of nanocomposite hydrogels with high mechanical strength ... and Nanotribomechanical Behavior of POSS/PP Hybrid Nanocompositeswww3.interscience.wiley.com/journal/113390787/issue
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Post by aqt on Mar 31, 2010 16:07:24 GMT -5
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Post by aqt on Mar 31, 2010 16:25:33 GMT -5
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Post by aqt on Mar 31, 2010 16:31:22 GMT -5
carbon-hydrogen bond=organic
inorganics contain metal-organics don't....really? tell that to the person who sent the metal samples that came from her skin
aqt
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Post by skyship on Mar 31, 2010 21:05:50 GMT -5
thymine and uracil are adsorbed on montmorillonite By the chemical reaction ? They are soluble. ah ah .......... uracil the spark of life, has light...... so would light be considered organic, bioilluminescent in fireflies, squid, jelly fish=====yes radiant light, from sun,,,,m,,,,,,,,,,,,,,,,,now is that organic? from out there, sure.......Is a ray of sun organic? mmmmmmmmmmmmmm is photosynthesis organic? mmmmmmmmmm montmorillonite..........natural. yet inorganic natural, not living. but what is it made of? www.webmineral.com/data/Montmorillonite.shtmlSilica? www.galleries.com/minerals/silicate/montmori/montmori.htm======================== nuclein takes us into sy nuclein, which is causing synucleopathies...... "Nuclein Discovery of the mutant alpha synuclein genes raises genetic-testing issues similar to those for such other late-onset diseases as Alzheimer's disease and Huntington's disease.".... more here: en.mimi.hu/biology/nuclein.htmlInclude Morgellons into that group as well.............. So, there is a mutant alpha synuclein we were discussing on other thread.......... the links keep getting closer! ----------- Modeling CNS neurodegeneration by overexpression of disease-causing proteins using viral vectors Deniz Kirik and Anders Björklund Wallenberg Neuroscience Center, Department of Physiological Sciences, Lund University, BMC A11, 22184, Lund, Sweden Abstract Defective handling of proteins is a central feature of major neurodegenerative diseases. The discovery that neuronal dysfunction or degeneration can be caused by mutations in single cellular proteins has given new opportunities to model the underlying disease processes by genetic modification of cells in vitro or by generation of transgenic animals carrying the disease-causing gene. Recent developments in recombinant viral-vector technology have opened up an interesting alternative possibility, based on direct gene transfer to selected subregions or subsets of neurons in the brain. Using the highly efficient adeno-associated virus or lentivirus vectors, recent reports have shown that overexpression of mutated human huntingtin or α-synuclein in neurons in the striatum or substantia nigra induces progressive neuropathology and neurodegeneration, similar to that seen in Huntington's and Parkinson's diseases. Targeted overexpression of disease-causing genes by recombinant viral vectors provides a new and highly flexible approach for in vivo modeling of neurodegenerative diseases, not only in mice and rats but also in primates. www.cell.com/trends/neurosciences/abstract/S0166-2236(03)00164-4create the disease, target it, by using retroviral viruses, thereby creating live models, to measure! How nice! they even seem overjoyed by the overexpression of the mutant. ====================== organic biology organic/inorganic chemistry is chemistry alive? well,,,,,yes! does it have cells, does oxygen have a cell, no but it is molecular........ Is a rock a living thing? does it have cells? organic/inorganic gelology? By symbiosis with living things. organic/inorganic metallurgy? Symbiosis with living things. organic/inorganic physics? mmmmmmm are neutrons, muons, leptons, living things? well,,,,,,,,, are they organic, don't have organs....cells? mmmmm photocell? but not organic. Just thinking here, Jump in aqt anywhere. You got me thinking again........ Molecular level, things become entwined! At Nano level, things begin as a building block. Bottom up can become spontaneous, no shut off. Top down has shut off. Uracil is considered a building block., so what does it symbiosis with to make life? to make molecule, cell? Atom? neutron? Uracil can be natural, but not organic. It is naturally inorganic diatoms, have both shells and organs, or cells, so what diatom would have been used? what makes shell, nacre? mmmmm again symbiosis? a. tamarense? botany.si.edu/references/dinoflag/Taxa/Atamarense.htm------------------------------ How about when seed/spore/filament meets shell? red Algae! is harmful................. diatoms grow on algae. ======================= If we can see where organic and inorganic cross paths, in the Biomineralization, then we can see it. ================== If the humans cells are struggling, why are they struggling? What is destroying them? or spinning them around? Or causing replication or reproduction? What keeps the circular gene that is causing this to keep circling? the circular gene has infiltrated our linear genes? by way of replicating viral viroid or bacteriophage? This makes us symbiotic with all organic things. Homeobox genes, the gene from fly, from the models used, c. elegans, zebra fish, are similar to human. substitution. The protocell, or nanocell, crosses barriers or organic and inorganic. When they say toxic they should be saying gene integration, mutation, aggregation, toxic, can be the mutation itself. So, by introducing an inorganic into the human genome, you have introduced Artificial life, it is not living, but by association with living and chemistry, it can alter functions of native natural organic genes. We are electrical first? Or are we organic first? what is the spark? what is the virus, how are they caused, what is a virus's origin? a virus's job is to mutate. so the filament of life? and the spark of life? example: a virus that forms filaments? Cytoplasmic filaments and associated lucké viruses in the frog renal adenocarcinoma Philip D. Lunger Department of Biological Sciences, University of Delaware, Newark, Delaware Supported in part by research grant (CA 07048) from the United States Public Health Seervice and by a University of Delaware Research Foundation grant. Abstract The morphology and possible functional significance of cytoplasmic filaments associated with herpes-like viruses of the frog renal carcinoma is described. Filaments, invariability arranged in elongated bundles or sheaths, individually measure approximately 30 m in diameter, and are composed of finely granular, proteinaceous material. During the viral maturation sequence, this material is believed to be deposited on the surface of the capsid, thereby possibly providing the virus with a defensive coating prior to ergression from the cell. www3.interscience.wiley.com/journal/109917593/abstractskyship
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Post by lilsissy on Mar 31, 2010 21:52:56 GMT -5
ctbarb imaged Karen's urine and fingernail clipping. Both samples had the branching twig like structures that match the photos I've seen of prions.
I need to learn how to post photos. I think we are beginning to have some proof.
Anyone have a good server for this and and can write me a quick how to, Sky first taught me how to post links remember that Sky?
Great thread. Jen
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Post by lilsissy on Mar 31, 2010 21:55:33 GMT -5
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Post by lilsissy on Mar 31, 2010 22:24:49 GMT -5
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Post by skyship on Mar 31, 2010 22:27:48 GMT -5
lilsissy,
I don't do pictures though!
I think you have download to either a photopage
an then mover link to thread.
Or download into your computer, and then copy to email and then to page.
not sure how to do all that. I just do the words.
==========================
Definite coverup on prions because they were used in labs and release into environment of lab created sup35p, ure2 and ure3, psi,
Prions are from fungi, slugs, in plants, in yeast, cyano, this is in feed. They are in the fungi hanging in the environment created by global dimming. The fungus will dry up if the sun is allowed to shine upon the earth.
Where do they originally come from? usually in soil, in grass, in environment, but, do not effect us, but, if they are used as vectors to unfold proteins, the Prp, and to fold in the artificial dna, then we got em, then we can see what is going on. And human dna is being used in computer to make us symbiotic with the computer, by mere touch on keyboard mouse, and eye contact with screen.
This signal since in us is recognized in computer, since human genes, and other human like genes from other animals, plants, bugs, like antenna of bug, like slugs, movement, genes used in computers, ipods, all touch things. Dna is in fingerprint device recognizes the dna, since human like dna from other organisms are in computers. Signal is there, however, the signal is by way of light, Uracil, related to ure3 from prions?
mmmm when organic meets inorganic a chemical signal evolves by letter, by computer digital, digital............finger! The spark, since we are electrical, computer is, wireless is,
So prion is used to unfold and fold in artificial life.
The calcium, is artificial, nacre, how does the turtle get its shell?
Why does a frog not have a shell?
Turtles like mud. and water. clay and iron enter in the mineral.
Uracil dissolves on montmorillonite - has silica, calcium, ammonia etc.
The stones that form in gall bladder, kidneys, lung, pancreas, are calcium the nacre which is in shells.
But diatoms grow on algae, therein the spore? red algae, cyano........
How do the diatoms get the hard nacre?
mmmmmmm another thing we can look at is the link between red algae prions and uracil.
jump in anyone! everyone! Maybe you all see something I am totally missing!
skyship
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Post by lilsissy on Apr 1, 2010 18:33:34 GMT -5
Could you specify which mineral you are speaking of,
clay and iron enter in the mineral.
Jen
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Post by skyship on Apr 1, 2010 21:44:23 GMT -5
I was thinking calcium, the nacre, but, uracil? and one of the building blocks of life is phosphorus. check this out, getting to the core.....once at the core we can find what was used or substituted. After all, both organic and inorganic matter are made of the same building blocks: atoms of carbon, hydrogen, oxygen, nitrogen and phosphorus. The only difference is how the atoms are arranged in three-dimensional space. vv.arts.ucla.edu/Talks/Barcelona/Arch_Life.htmOf course this is at atomic level. molecular level building blocks. Just found this though, a clay mineral called dickite which absorbs uracil and thymine! Hydrogen bonding of thymine and uracil with surface of dickite: ...... Army Engineer Research and Development Center (ERDC), Vicksburg, MS 39180, USA Abstract The density functional theory (DFT) by means of the B3LYP functional and the 6-31G(d) basis set has been applied to analyze the hydrogen boding of selected nucleic acid bases (thymine and uracil) with the representative cluster models of the clay mineral, dickite. The results obtained from this investigation reveal that the formation of hydrogen bonds accounts for the stabilization of thymine and uracil on the mineral surface. The intermolecular distances and strength of the hydrogen bonds depend on the type of the surface (tetrahedral or octahedral) and on the hydration of the surface. Generally, thymine and uracil are less stable on the tetrahedral surface than on the octahedral surface. The most energetically favorable adsorption is predicted in the case of the system containing hydrated octahedral mineral fragment. The adsorption of thymine on the surface of dickite results in changes in geometry and polarization of thymine. These effects are more significant in the case of the octahedral adsorption than for the tetrahedral adsorption. Keywords: Thymine; Uracil; Hydrogen bonding; Adsorption; Clay tinyurl.com/ybr2gnnskyship
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Post by skyship on Apr 1, 2010 22:23:23 GMT -5
dickite: does refer to nacrite dickite From Wikipedia, the free encyclopedia Jump to: navigation, search dickite General Category Phyllosilicate Chemical formula Al2Si2O5(OH)4 Strunz classification 09.ED.05 Dana classification 71.01.01.01 Identification Color White, with coloration from impurities Crystal habit pseudohexagonal crystals, aggregates of platelets and compact massive Crystal system Monoclinic - domatic, H-M Symbol (m) Space Group: Cc Cleavage Perfect on {001} Tenacity Flexible but inelastic Mohs scale hardness 1.5 - 2 Luster Satiny to pearly Streak White Diaphaneity Transparent Specific gravity 2.6 Optical properties Biaxial (+) Refractive index nα = 1.561 - 1.564 nβ = 1.561 - 1.566 nγ = 1.566 - 1.570 References [1][2][3] dickite (Al2Si2O5(OH)4) has molecular weight of 258.16 grams. It is a phyllosilicate clay mineral chemically composed of aluminium, silicon, hydrogen and oxygen contributing 20.90%, 21.76%, 1.56%, and 55.78% each respectively. It has the same composition as kaolinite, nacrite, and halloysite, but with a different crystal structure (polymorph). dickite sometimes contains impurities such as titanium, iron, magnesium, calcium, sodium and potassium en.wikipedia.org/wiki/dickiteHas the same composition as nacrite: en.wikipedia.org/wiki/Nacritelilsissy, it looks like uracil has been used in recombination, I have been seeing CMV promoter a lot and herepses virus, is in the Lucke virus that was in frogs. But, here this CMV encodes URACIL-DNA glycosylase homolog. So, the viral dna, (uracil is in RNA) has to carry another type of uracil, not the one from human RNA? So this could be the dendrimer(nano artificial induction) smaller than dimer? AND..........in pancreas problems the CYTOSOL is involved! Human cytomegalovirus UL114 encodes a uracil-DNA glycosylase homolog that is highly conserved in all characterized herpesviruses that infect mammals. Previous studies demonstrated that the deletion of this nonessential gene delays significantly the onset of viral DNA synthesis and results in a prolonged replication cycle. The gene product, pUL114, also appears to be important in late phase DNA synthesis presumably by introducing single stranded breaks. www.virologyj.com/content/2/1/55CMV pUL114: So, uracil in the nucleus? Seems there is a relation ship between this and dimers which is base for nano tech, is molecular building blocks from dendrimers. So, could this herpes virus or the cytomegalo vrius, or the murine virus, be mutating ways into the native dna.? dimers running parallel to native dna? then the virus mutates in the artificial strands? However seems uracil is involved? And I found that oligomers, dimers and prions are related. I think oligo's are artificial dna strands possibly from the sup35 mixture of prions, proteins etc. skyship
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Post by skyship on Apr 1, 2010 22:34:34 GMT -5
There is an RNA dimer. The dimeric genome Retroviruses were discovered at the beginning of the 20th century [3,4]. The unique nature of their genome was first discovered in the 1960s [5,6] but the actual dimeric genomes were elucidated, and visualised by electron microscopy, a decade later [7,8]. Bender and colleagues extracted the RNA from several different retroviruses and examined it by electron microscopy under denaturing conditions. The RNA appeared to be joined at a discrete point, termed the dimer linkage site (DLS). Using bromodU to label the RNA at one end, they were able to show that the molecules were joined at their 5' ends [9,10]. Under less stringent conditions the genomes can be demonstrated to interact along their lengths [11] and it is this that probably contributes to confusing reports on the exact location of the primary DLS in different viruses. RNA dimerisation in the primate lentiviruses, predominantly HIV-1, has subsequently been extensively studied [1], yet little has been published on this process in the non-primate lentiviruses. Early studies of rapid harvest virions of the prototype lentivirus, Maedi Visna virus (MVV), identified viral RNA with a Svedberg coefficient of 35S immediately post-budding, which increased with time to 70S. It is possible that weakly interacting dimers formed during RNA encapsidation may have been denatured during purification, however these observations are supportive of a progression from monomeric to dimeric RNA associated with viral maturation [12]. Since 1990 [13] it has been possible to study in vitro the RNA elements involved in the dimer linkage first observed by EM. It was shown that RNA transcripts comprising sequences from the 5' end of the viral genome would migrate as two species of RNA when subjected to electrophoresis. By this means many subsequent studies were able to focus on isolating the elements and structures involved in dimerisation, and to investigate the role of the viral structural proteins in this process. Multiple functions for the dimeric genome? As yet investigators have not been able to agree on a distinct role for the dimer linkage. The fact that it is conserved amongst the retroviridae does not guarantee that its role will be the same in all retroviral families. The following section of the review will endeavour to explore some of the proposed roles, and examine the evidence from different retroviruses. www.retrovirology.com/content/1/1/22===================== By the way, lentivirus is the virus that sickened Becky McLain? am I right? ============================ this is getting veryyyyyy interesting! more from link:next post ======================= skyship
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Post by skyship on Apr 1, 2010 22:49:46 GMT -5
Lil sissy, Here is mention of murine luk virus as well. "his result implies that recombination would occur preferentially at the site where the RNA molecules were in close proximity. In the case of HIV-1, whilst it has been shown that template switching is facilitated by template homology [16], it has also been demonstrated that recombination can occur between viruses of different subtypes which might have different dimer initiation sequences (DIS) [17]. Bearing in mind the fact that the genome is linked at other sites besides the DIS [11], it seems probable that other hot spots for recombination exist. Interestingly, it has been suggested that the nucleocapsid protein (NC) promotes or stimulates the strand transfer reaction. As will be discussed below, NC and the precursor Gag protein both bind the RNA close to the DIS in HIV-1. In addition, there is evidence that the presence of a dimer in the virus particle facilitates the first strand-transfer reaction of reverse transcription [18]. Work in our laboratory has shown that the Maedi Visna Virus DIS is centred on a helix terminating in a GACG tetraloop between positions 281 and 300 in the viral genome; a region which is highly conserved between the ovine and caprine lentiviruses (Monie, personal communication, see Figure 3d). Intriguingly, this structure shows homology with structural motifs in the Alpha- and Gammaretroviruses, but not with DIS regions identified in the primate lentiviruses. Within the Alpha- and Gammaretroviruses GACG tetraloops are involved in the packaging of viral RNA [19,20] and whilst not a component of the core M-MLV DIS motif [21], they may contribute to the process of dimerisation and the stability of the resultant dimer [22]. Importantly, it is possible to form heterodimers between transcripts from these viruses containing the GACG tetraloops and between MVV and M-MLV (personal observations). This raises parallels with recent studies of the dimerisation of murine leukaemia viruses and Harvey Sarcoma virus in which GACG tetraloops were found to regulate inter-species RNA heterodimerisation [23], whilst other linkage elements were postulated to mediate homodimerisation. Recombination, and the genomic variability it confers cannot be the sole function of the dimeric genome, since retroviruses with highly conserved genomes and little sequence variability such as HTLV-1 [24] are also dimeric." ================== check out figure 4: Figure 4. Proposed tertiary structure of the HTLV-1 dimer linkage. 4a Stereoview of 3D molecular modelling of a potential structure of the HTLV-1 DIS from nucleotide A730 to A744 using JUMNA ([61]). 4b. Close up of the terminal loop. Bases are coloured as follows: adenine, grey; cytosine, yellow; guanine, orange; and uracil, cyan. adenine, cytosine, guanine, uracil and cyan..................... www.retrovirology.com/content/1/1/22So, if the viruses are dimeric, then the dimers have been in the body a while. works with all kinds of viruses, and the uracil is present in the dimers it seems. ============= he sequences contained within the palindrome are remarkably conserved. Using an in vitro selection system it has been possible to demonstrate that the DIS has evolved to satisfy both constraints for optimal dimerisation affinity, and the potential to homodimerise [43]. The dimer linkage is found at the terminal end of Stem Loop 1 (SL1) within the packaging signal region of HIV-1 (Figure 2a). The tertiary structure of the whole SL1 RNA has been determined [44,45] and the structures have helped to determine exactly how the RNAs interact with one another. A number of elements appear to be critical for the dimer interaction: flanking purines and central nucleotides in the palindromic sequence [46] and loop B [47-49]. The tertiary structure of the latter has been described (Figure 2c), and there is some debate as to how flexible this internal loop might be. However, work by Borer et al, examining the interaction of NC with elements of the packaging signal, of which loop B is one, showed that, in fact, both structures might exist, the flexible one allowing NC binding at high affinity [50]. There are similar linkages in other retroviruses. The Avian Leukosis Viruses also interact firstly in a kissing hairpin manner, and then form an extended duplex (Figure 3a, [51]). Palindromes remain a theme throughout many of the viruses investigated to-date. As already mentioned, the DIS of HIV-2 is less well defined than that of HIV-1. Whilst there is a palindromic sequence at the top of a stem loop structure that closely resembles the HIV-1 DIS (see Figure 1), there are other regions which have also been demonstrated to be important for dimer formation [25,26]. Other viruses with palindromic sequences as their DLS include HFV (Figure 3c) and MoMLV. In the case of MLV there are other sequences and structures which may play a role in dimer formation, including the GACG tetraloops mentioned previously [52]. The tertiary structure of this stem loop is the only proposed dimer linkage element yet to be determined in a retrovirus other than HIV-1 ([53]). RSV and VL30, also have imperfect repeat sequences in their dimer linkages [54,55] (Figure 3b). ============================= What do they mean by palindrome? ================================= next post..... I think it is here lil sis. skyship =
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Post by skyship on Apr 1, 2010 22:51:06 GMT -5
Palindrome: there is mention of gelatin as well, BUT THE FIRST SENTENCE SAYS IT ALL!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! The retroviral RNA genome is dimeric, consisting of two identical strands of RNA linked near their 5' ends by a dimer linkage structure. Previously it was shown that human foamy virus (HFV) RNA transcribed in vitro contained three sites, designated SI, SII, and SIII, which contributed to the dimerization process (O. Erlwein, D. Cain, N. Fischer, A. Rethwilm, and M. O. McClure, Virology 229:251-258, 1997). To characterize these sites further, a series of mutants were designed and tested for their ability to dimerize in vitro. The primer binding site and a G tetrad in SI were dispensable for dimerization. However, a mutant that changed the 3' end of SI migrated slower on nondenaturing gels than wild-type RNA dimers. The sequence composition of the SII palindrome, consisting of 10 nucleotides, proved to be critical for in vitro dimerization, since mutations within this sequence or replacement of the sequence with a different palindrome of equal length impaired in vitro dimerization. The length of the palindrome also seems to play an important role. A moderate extension to 12 nucleotides was tolerated, whereas an extension to 16 nucleotides or more impaired dimerization. When nucleotides flanking the palindrome were mutated in a random fashion, dimerization was unaffected. Changing the SIII sequence also led to decreased dimer formation, confirming its contribution to the dimerization process. Interesting mutants were cloned into the infectious molecular clone of HFV, HSRV-2, and were transfected into BHK-21 cells.jvi.asm.org/cgi/content/abstract/75/8/3731dimerization process: dimerization is described as " The chemical union of two identical molecules." So, what molecules in the dendrimer and the rna or dna would cause a union, sort of like a mutation caused from a chemical reaction (of uracil) rather than a bio viral mutation. cells can mutate by chemical reaction or electron (physics) or neutron actions. Definitons again; Dimer: Described as: "A dimer is a chemical or biological entity consisting of two structurally similar subunits called monomers, which are joined by bonds, which can be strong or weak." Wiki What is a monomer? "A molecule that can combine with others to form a polymer." from answers.com Now, If building block of atoms, included gases or vapours, then dimers are substituting vapours? for what? dimers: and vapour connection: =================== Vapor phase:en.wikipedia.org/wiki/File:Carboxylic_acid_dimers.png================= what is R? must be for dimer..... commons.wikimedia.org/wiki/File:Carboxylic_acid_dimers.svg================== urease was the the first protein crystallized: Urease Urease (EC 3.5.1.5) is an enzyme that catalyzes the hydrolysis of urea into carbon dioxide and ammonia. The reaction occurs as follows: (NH2)2CO + H2O → CO2 + 2NH3 In 1926 James Sumner showed that urease is a protein. Urease is found in bacteria, yeast and several higher plants. en.wikipedia.org/wiki/Urease========================== s
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Post by skyship on Apr 2, 2010 0:15:05 GMT -5
Dendron:
"Dendrons
Dendrons (Figure 2) are monodisperse wedge-shaped dendrimer sections with multiple terminal groups and a single reactive function at the focal point. In addition to unique properties (i) – (iii) described above, this gives you an option of orthogonal reactions utilizing the distinct focal point and surface groups. For example, it is possible to graft dendrons to a surface, to another dendron,4 or to another macromolecule.5"
Dendrimer Introduction Dendrimers are polymeric macromolecules composed of multiple perfectly-branched monomers radially emanating from a central core (Figure 1). The number of branch points increases upon moving from the dendrimer core to its surface and defines dendrimer generation. The branched topology confers dendrimers with several unique properties for materials applications: image of gneration 2 dendrimer
(i) Compact nm-scale dendrimer structure results in high solubility and low solution viscosity. This property lends dendrimers to applications as rheology (viscosity) modifiers. 1 (ii) Dense presentation of multiple terminal groups on dendrimer surface (multivalency), with number of surface groups increasing with dendrimer generation. Multivalency can be exploited as a means to achieve concentrated payloads of drugs or imaging labels chemically grafted to the dendrimer surface. 2 (iii) Core-shell molecular architecture with chemically distinct interior and surface. The core-shell architecture can be used to encapsulate and release molecules chemically incompatible with the environment external to the dendrimer: for example catalysts, drugs, or chromophores. 3
Sigma-Aldrich offers a wide range of monodisperse dendrimer molecules with four different chemical structures (PAMAM, phosphorous, polypropylenimine, polylysine) and numerous distinct terminal surface groups. To expand the range of dendritic tools for your materials chemistry research, we are pleased to offer two types of dendritic macromolecules: polyester dendrons and hyperbranched polymers based on 2,2-bis(hydroxymethyl)propanoic acid (bis-MPA) monomer. "
Homedimer is describe as "A protein made of paired identical polypeptides. " from answers.com
heterodimer: (according to Webster) ": a protein composed of two polypeptide chains differing in composition in the order, number, or kind of their amino acid residues
Now, we are talking two polypetide chains:
seems we are getting closer to the oligomers.
more later.
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Post by skyship on Apr 2, 2010 12:58:14 GMT -5
Myosin II is a secondary myosin, made with dimers. This is supposed to help heal mysoin issues in diseases. I have had a high count of these, how did these get in me? www.cs.stedwards.edu/chem/Chemistry/CHEM43/CHEM43/Myosin/STRUCT~1.HTMMyosin II's structure The myosin II protein is able to perform functionally and enzymatically because of its dimeric shape. Myosin is a hexamer with a total molecular weight of 520 kD. It is composed of two heavy chains and four light chains. The two heavy chains each weigh 220 kD and begin with a globular head at the N-terminal and end with an alpha-helix at the C-terminal. The tail (C-terminal) region is periodically interspersed with hydrophobic residues to give a "coiled coil" type rod. The amino acids in the C-terminal are non-helical which aids in stabilizing the myosin filament backbone. [1] Furthermore, the backbone contains inter-myosin ionic bonds to assist in stabilization. The tails are connected to the heads at the neck, which is the location of the hinge area. so this alteration in the myosin and most likely actin, almost can be compared to the filament structures in morgellons. I think we are looking at molecular motors: then came the nano motor. By way of dimers, monomers and oligomers? One of the first studies done with wide array of scientists pertaining to muscle actin, myosin, and sliding moving muscle fibers. It does seem that due to thermo changes, enforced or natural climate change the thermodynamics of heat or cold affects the body, and may cause problems with myosin, hence the construction of myosin and actin substitutes by way of molecular motors, may be what is going on. So, if earth is heating up due to sun warming, or earth itself warming from inside, then the issue has been to create dna that would withstand that heat. So, they went into volcano itself and under ocean floor for heat vent dna, dna that could withstand heat. Those Achaean, would become part of the mix. So, to prevent heat shock, or cold shock , heat shock proteins were introduced, and now work on cold shock proteins in case we have a cold shock phenomena going on. this does seem to relate to earth changes. Either way, we should have been informed of this process. Molecular motors would be able to withstand therm conditions. Of course, that would fit nicely into the global warming scheme, but, a change in the environment has taken place. Due to bucky balls which are made of dimers, I believe or clathrin coated iron, to clean up oceans, however this iron mix with ocean bottom is causing other problems, with carbon sequestration, seems methane is now forming. I think in the cytoskeleton cells, actin and myosin are being restructured for durability. Super molecules, super myosin, superhelix, all involved in this. It does appear that energy can be put in these strands, that energy, is involved in atp-adp, and gtp-gdp. This has to do with condensed soft matter physics, and matter itself. So, what is the purpose in this? To conserve what we have? Or to alter us by way of artificial integration? Models used in organic biology probably were released in environment to test and measure the oxygen reactive species, all living matter itself. These models could be why some organisms are dying, they could not handle the models, they may have adjusted naturally if nothing was done. A normal heat trend. But, biogenesis was instigated. a new world of recombined species. Or was this all a scheme to alter humans and the environment to make change happen, to make A NEW WORLD? A New Day, a new dawning? To bring in an Awakening? of A new artificial world? Or is it a real phenomena, that was incorporated to save the planet? Some hard questions, only those who know of this huge venture, know this, and the public is not being made aware. All living things are under scrutiny, mapped, measured, infiltrated, and through the transition, we are falling, are condemned, judged, labeled, and are spitting out the false fibers, as we journey through this experiment called life. Will machines survive the supposed alterations of nature? If the earth is in such dire straits, then how will these machines survive? skyship
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Post by skyship on Apr 2, 2010 13:21:08 GMT -5
This may clarify some of the manner in which this is taking place. Molecular Motor-Induced Instabilities and Cross Linkers Determine Biopolymer Organization D. Smith*, †, F. Ziebert‡, §, D. Humphrey†, C. Duggan†, M. Steinbeck*, W. Zimmermann‡ and J. Käs*, †, Go To Corresponding Author, * Institute for Soft Matter Physics, University of Leipzig, Germany † Center for Nonlinear Dynamics, University of Texas at Austin, Texas ‡ Physikalisches Institut, Universität Bayreuth, Bayreuth, Germany § Materials Science Division, Argonne National Laboratory, Argonne, Illinois Abstract All eukaryotic cells rely on the active self-organization of protein filaments to form a responsive intracellular cytoskeleton. The necessity of motility and reaction to stimuli additionally requires pathways that quickly and reversibly change cytoskeletal organization. While thermally driven order-disorder transitions are, from the viewpoint of physics, the most obvious method for controlling states of organization, the timescales necessary for effective cellular dynamics would require temperatures exceeding the physiologically viable temperature range. We report a mechanism whereby the molecular motor myosin II can cause near-instantaneous order-disorder transitions in reconstituted cytoskeletal actin solutions. When motor-induced filament sliding diminishes, the actin network structure rapidly and reversibly self-organizes into various assemblies. Addition of stable cross linkers was found to alter the architectures of ordered assemblies. These isothermal transitions between dynamic disorder and self-assembled ordered states illustrate that the interplay between passive crosslinking and molecular motor activity plays a substantial role in dynamic cellular organization. www.cell.com/biophysj/abstract/S0006-3495(07)71695-8skyship
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Post by aqt on Apr 5, 2010 12:50:23 GMT -5
The protocell includes two or more RNA replicases which are able to make copies of each other. Concurrent with RNA replication, the vesicle membrane grows through the addition of fatty acids from micelle collisions. This causes the surface area of the protocell to increase while the volume remains constant, resulting in the elongation and increased instability of the protocell membrane. The membrane eventually divides, forming two daughter protocells, with the RNA replicases randomly divided between them. Every once in a while, a replicase will make a mistake, and a mutant replicase RNA is produced. Usually, this mutation will result in a poorer replicase, if catalytic activity is retained at all. Rarely, however, a better replicase could be formed – a replicase that might be able to copy RNAs faster, for example. Even more rarely, a RNA will be introduced to a protocell (by mutations or some other means) that has a new, different catalytic activity, such as the ability to catalyze the formation of fatty acids. These protocells with faster replicases or new functional ribozymes will have an advantage over other protocells by being able to grow and divide faster. Since all protocells in a population will be competing for resources (such as RNA nucleotides and fatty acids), those that can grow and divide more quickly will use up more of the resources, causing the “extinction” of slower-dividing protocell species. exploringorigins.org/protocells.html
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Post by aqt on Apr 5, 2010 12:53:40 GMT -5
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Post by aqt on Apr 5, 2010 12:56:35 GMT -5
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