Euplotid: A quantized geometric model of the eukaryotic cell

Euplotid: A quantized geometric model of the eukaryotic cell

27 Pages · 2017 · 9.37 MB · English

node.js wrapper to traditional python methods. Here we can pick what cell type and condition we want to investigate. 4.3.2 Pick annotated Insulated Neighborhood. After picking a cell type and condition the list of annotated INs will be populated. A simple dropdown sorted by name is provided. 4 Resu

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Euplotid A quantized geometric model of the eukaryotic cell Author: Diego BorgesRivera November 23, 2017 CCBYNC 40 International license It is made available under a (which was not peerreviewed) is the author/funder, who has granted bi\ oRxiv a license to display the preprint in perpetuity The copyright holder for this preprint http://dxdoiorg/101101/170159 doi: bioRxiv preprint first posted online Jul 31, 2017; Figure 01:Graphical Abstract 2 CCBYNC 40 International license It is made available under a (which was not peerreviewed) is the author/funder, who has granted bi\ oRxiv a license to display the preprint in perpetuity The copyright holder for this preprint http://dxdoiorg/101101/170159 doi: bioRxiv preprint first posted online Jul 31, 2017; 1Epigraph:TheNamingofEuplotid "The cell is a system that is capable of creating and conserving its own code" Marcello Barbieri [1] TheCambrian explosion is responsible for the cementing of animal life on this planet; phylogenetic analysis appears to indicate that all metazoans originated from a single common ?agellated organism, something resembling a Euplotid Darwin has noted that this event does not seem to follow with a traditional evolutionary view, the speed and emergence of metazoans accelerated orders of magnitude when compared to the life that preceded them There have been many attempts to explain this event, from Oxygen concentration to complexity thresholds, but noone has considered that clues may lie within the genetic code itself, after all, this code is fundamental for the evolution of life as we know it A number of patterns have been observed within the codons, but a particularly interesting combination of two rules allows for the writing of the Euplotid genetic code in a contracted manner By combining Rumer ?s Bisection (a) [2] with HisagawaMinata?s [3] ordering by codon redundancy/mass (b) and applying them to the Euplotid genetic code we are able to contract and arrange the codons as ?rst shown in Makukov et al [4] Makukov et al discovered the protacted Euplotid codon arrangement and go well into the arithmetic interpretation, that is to say the part dealing with arithmatic Below is an ideographical interpretation: Figure 11: Contracted codons of the Euplotid Genetic code 1 GGTCGACC: How to number DNA, 0=T, C=1, G=2, A=3 2 GCCCTCTG: What radixnumber system to use CCC = 111 (base 4) = 21 (base 10) = number of amino acids + stop codon TCT = 010 (base 4) = 4 (base 10) = number of nucleotides 3 NNNNNNNN: Is able to complement "GGTCGACC" 4 TATATAGCAGCTATAT: Euplotids remove Internal Eliminated Sequences (IESs) in the process of generating the large vegetative Macronucleus (MAC) from the small sexually produced Micronu cleus (MIC) The Euplote Crassus consensus sequence is 5 0TATrGCRN3 0[5] 5 GTAGTAAAAAATGATG: Translating from left to right starting w/ TAG would produce: Stop StopLysStartStart using the canonical genetic code, but in Euplotids +1 Programmed Ribosomal Frameshifting (+1 PRF) occurs at AAA sites preceding stop codons due to a tRNA recognizing UAAA instead of UAA [6][ 7] So if we perform a +1 PRF and read starting at AGT we get: SerLys LysCys (brief movie showing the process) This is only in Euplotids due to TGA coding for Cys 1 Epigraph: The Naming of Euplotid 3 CCBYNC 40 International license It is made available under a (which was not peerreviewed) is the author/funder, who has granted bi\ oRxiv a license to display the preprint in perpetuity The copyright holder for this preprint http://dxdoiorg/101101/170159 doi: bioRxiv preprint first posted online Jul 31, 2017; instead of stop +1 PRF in Euplotids is used to generate functional proteins from fusing different reading frames in over 3,700 proteins, including the Reverse Transcriptase of LINEelements, ORF2 [8] 6 HHRYRYYRRRYYRYGG: Is able to complement "TATATAGCAGCTATAT" Due to this unique genetic signature, I decided to name this quantized geometric model of the eukaryotic cell, "Euplotid" 1 Epigraph: The Naming of Euplotid4 CCBYNC 40 International license It is made available under a (which was not peerreviewed) is the author/funder, who has granted bi\ oRxiv a license to display the preprint in perpetuity The copyright holder for this preprint http://dxdoiorg/101101/170159 doi: bioRxiv preprint first posted

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