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Published: 25 May 2024

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1

Aisah, Isah, B. Subartini, and A. Muhaemin. "Endomorphism Representation Matrix From Standard Genetic Code." JURNAL ILMIAH SAINS 20, no. 1 (April 20, 2020): 26. http://dx.doi.org/10.35799/jis.20.1.2020.27787.

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Mutations are changes in genetic material that can occur at the level of genes or chromosomes. Mutations at the gene level are structural changes in the genetic code. In this paper we will investigate the necessary and sufficient conditions for an endomorphism called autumorphism. The method used in this research paper is a review of literature conducted by collecting literature from previous studies in accordance with the study discussed. Mathematically, genetic mutations can be viewed with an endomorphism and automorphism f in the vector space which maps the standard genetic code sequence of wild-type genes into mutant genes. In the endomorphism there is a matrix called the endomorphism representation matrix.Keywords: authomorphism, endomophism, mutation Matriks Representasi Endomorfisma Dari Kode Genetik StandarABSTRAKMutasi merupakan perubahan pada materi genetik yang dapat terjadi pada tingkat gen maupun kromosom. Mutasi pada tingkat gen merupakan perubahan struktur dalam kode genetik. Pada penelitian ini akan dibahas syarat perlu dan syarat cukup sebuah endomorfisma disebut automorfisma. Metode yang digunakan dalam makalah penelitian ini adalah tinjauan literatur yang dilakukan dengan mengumpulkan literatur dari penelitian-penelitian sebelumnya sesuai dengan penelitian yang dibahas. Secara matematis, mutasi genetik dapat ditinjau dengan sebuah endomorfisma dan automorfisma pada ruang vektor yang memetakan barisan kode genetik standar gen wild-type ke dalam gen mutan. Pada endomorfisma tersebut terdapat sebuah matriks yang disebut matriks representasi endomorfisma.Kata kunci: Automorfisma, endomorfisma, mutasi GenetikMutations are changes in genetic material that can occur at the level of genes or chromosomes. Mutations at the gene level are structural changes in the genetic code. In this paper we will investigate the necessary and sufficient conditions for an endomorphism called autumorphism. The method used in this research paper is a review of literature conducted by collecting literature from previous studies in accordance with the study discussed. Mathematically, genetic mutations can be viewed with an endomorphism and automorphism f in the vector space which maps the standard genetic code sequence of wild-type genes into mutant genes. In the endomorphism there is a matrix called the endomorphism representation matrix.Keywords: authomorphism, endomophism, mutation Matriks Representasi Endomorfisma Dari Kode Genetik StandarABSTRAKMutasi merupakan perubahan pada materi genetik yang dapat terjadi pada tingkat gen maupun kromosom. Mutasi pada tingkat gen merupakan perubahan struktur dalam kode genetik. Pada penelitian ini akan dibahas syarat perlu dan syarat cukup sebuah endomorfisma disebut automorfisma. Metode yang digunakan dalam makalah penelitian ini adalah tinjauan literatur yang dilakukan dengan mengumpulkan literatur dari penelitian-penelitian sebelumnya sesuai dengan penelitian yang dibahas. Secara matematis, mutasi genetik dapat ditinjau dengan sebuah endomorfisma dan automorfisma pada ruang vektor yang memetakan barisan kode genetik standar gen wild-type ke dalam gen mutan. Pada endomorfisma tersebut terdapat sebuah matriks yang disebut matriks representasi endomorfisma.Kata kunci: Automorfisma, endomorfisma, mutasi Genetik
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2

Yarus, Michael. "Optimal Evolution of the Standard Genetic Code." Journal of Molecular Evolution 89, no. 1-2 (January 24, 2021): 45–49. http://dx.doi.org/10.1007/s00239-020-09984-8.

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AbstractThe Standard Genetic Code (SGC) exists in every known organism on Earth. SGC evolution via early unique codon assignment, then later wobble, yields coding resembling the near-universal code. Below, later wobble is shown to also create an optimal route to accurate codon assignment. Time of optimal codon assignment matches the previously defined mean time for ordered coding, exhibiting ≥ 90% of SGC order. Accurate evolution is also accessible, sufficiently frequent to appear in populations of 103 to 104 codes. SGC-like coding capacity, code order, and accurate assignments therefore arise together, in one attainable evolutionary intermediate. Examples, which plausibly resemble coding at evolutionary domain separation, are characterized.
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3

Kumar, Balaji, and Supreet Saini. "Analysis of the optimality of the standard genetic code." Molecular BioSystems 12, no. 8 (2016): 2642–51. http://dx.doi.org/10.1039/c6mb00262e.

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Many theories have been proposed attempting to explain the origin of the genetic code. In this work, we compare performance of the standard genetic code against millions of randomly generated codes. On left, ability of genetic codes to encode additional information and their robustness to frameshift mutations.
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4

Yarus, Michael. "Evolution of the Standard Genetic Code." Journal of Molecular Evolution 89, no. 1-2 (January 24, 2021): 19–44. http://dx.doi.org/10.1007/s00239-020-09983-9.

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AbstractA near-universal Standard Genetic Code (SGC) implies a single origin for present Earth life. To study this unique event, I compute paths to the SGC, comparing different plausible histories. Notably, SGC-like coding emerges from traditional evolutionary mechanisms, and a superior route can be identified. To objectively measure evolution, progress values from 0 (random coding) to 1 (SGC-like) are defined: these measure fractions of random-code-to-SGC distance. Progress types are spacing/distance/delta Polar Requirement, detecting space between identical assignments/mutational distance to the SGC/chemical order, respectively. The coding system is based on selected RNAs performing aminoacyl-RNA synthetase reactions. Acceptor RNAs exhibit SGC-like Crick wobble; alternatively, non-wobbling triplets uniquely encode 20 amino acids/start/stop. Triplets acquire 22 functions by stereochemistry, selection, coevolution, or at random. Assignments also propagate to an assigned triplet’s neighborhood via single mutations, but can also decay. A vast code universe makes futile evolutionary paths plentiful. Thus, SGC evolution is critically sensitive to disorder from random assignments. Evolution also inevitably slows near coding completion. The SGC likely avoided these difficulties, and two suitable paths are compared. In late wobble, a majority of non-wobble assignments are made before wobble is adopted. In continuous wobble, a uniquely advantageous early intermediate yields an ordered SGC. Revised coding evolution (limited randomness, late wobble, concentration on amino acid encoding, chemically conservative coevolution with a chemically ordered elite) produces varied full codes with excellent joint progress values. A population of only 600 independent coding tables includes SGC-like members; a Bayesian path toward more accurate SGC evolution is available.
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5

Yarus, Michael. "Fitting the standard genetic code into its triplet table." Proceedings of the National Academy of Sciences 118, no. 36 (August 30, 2021): e2021103118. http://dx.doi.org/10.1073/pnas.2021103118.

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Minimally evolved codes are constructed here; these have randomly chosen standard genetic code (SGC) triplets, completed with completely random triplet assignments. Such “genetic codes” have not evolved, but retain SGC qualities. Retained qualities are basic, part of the underpinning of coding. For example, the sensitivity of coding to arbitrary assignments, which must be < ∼10%, is intrinsic. Such sensitivity comes from the elementary combinatorial properties of coding and constrains any SGC evolution hypothesis. Similarly, assignment of last-evolved functions is difficult because of late kinetic phenomena, likely common across codes. Census of minimally evolved code assignments shows that shape and size of wobble domains controls the code’s fit into a coding table, strongly shifting accuracy of codon assignments. Access to the SGC therefore requires a plausible pathway to limited randomness, avoiding difficult completion while fitting a highly ordered, degenerate code into a preset three-dimensional space. Three-dimensional late Crick wobble in a genetic code assembled by lateral transfer between early partial codes satisfies these varied, simultaneous requirements. By allowing parallel evolution of SGC domains, this origin can yield shortened evolution to SGC-level order and allow the code to arise in smaller populations. It effectively yields full codes. Less obviously, it unifies previously studied chemical, biochemical, and wobble order in amino acid assignment, including a stereochemical minority of triplet–amino acid associations. Finally, fusion of intermediates into the final SGC is credible, mirroring broadly accepted later cellular evolution.
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6

Ardell, David H., and Guy Sella. "No accident: genetic codes freeze in error–correcting patterns of the standard genetic code." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 357, no. 1427 (November 29, 2002): 1625–42. http://dx.doi.org/10.1098/rstb.2002.1071.

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The standard genetic code poses a challenge in understanding the evolution of information processing at a fundamental level of biological organization. Genetic codes are generally coadapted with, or ‘frozen‘ by, the protein–coding genes that they translate, and so cannot easily change by natural selection. Yet the standard code has a significantly non–random pattern that corrects common errors in the transmission of information in protein–coding genes. Because of the freezing effect and for other reasons, this pattern has been proposed not to be due to selection but rather to be incidental to other evolutionary forces or even entirely accidental. We present results from a deterministic population genetic model of code–message coevolution. We explicitly represent the freezing effect of genes on genetic codes and the perturbative effect of changes in genetic codes on genes. We incorporate characteristic patterns of mutation and translational error, namely, transition bias and positional asymmetry, respectively. Repeated selection over small successive changes produces genetic codes that are substantially, but not optimally, error correcting. In particular, our model reproduces the error–correcting patterns of the standard genetic code. Aspects of our model and results may be applicable to the general problem of adaptation to error in other natural information–processing systems.
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7

Konjevoda, Paško, and Nikola Štambuk. "Relational model of the standard genetic code." Biosystems 210 (December 2021): 104529. http://dx.doi.org/10.1016/j.biosystems.2021.104529.

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8

Rozhoňová, Hana, Carlos Martí-Gómez, David M. McCandlish, and Joshua L. Payne. "Robust genetic codes enhance protein evolvability." PLOS Biology 22, no. 5 (May 16, 2024): e3002594. http://dx.doi.org/10.1371/journal.pbio.3002594.

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The standard genetic code defines the rules of translation for nearly every life form on Earth. It also determines the amino acid changes accessible via single-nucleotide mutations, thus influencing protein evolvability—the ability of mutation to bring forth adaptive variation in protein function. One of the most striking features of the standard genetic code is its robustness to mutation, yet it remains an open question whether such robustness facilitates or frustrates protein evolvability. To answer this question, we use data from massively parallel sequence-to-function assays to construct and analyze 6 empirical adaptive landscapes under hundreds of thousands of rewired genetic codes, including those of codon compression schemes relevant to protein engineering and synthetic biology. We find that robust genetic codes tend to enhance protein evolvability by rendering smooth adaptive landscapes with few peaks, which are readily accessible from throughout sequence space. However, the standard genetic code is rarely exceptional in this regard, because many alternative codes render smoother landscapes than the standard code. By constructing low-dimensional visualizations of these landscapes, which each comprise more than 16 million mRNA sequences, we show that such alternative codes radically alter the topological features of the network of high-fitness genotypes. Whereas the genetic codes that optimize evolvability depend to some extent on the detailed relationship between amino acid sequence and protein function, we also uncover general design principles for engineering nonstandard genetic codes for enhanced and diminished evolvability, which may facilitate directed protein evolution experiments and the bio-containment of synthetic organisms, respectively.
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9

Massey, Steven E. "The neutral emergence of error minimized genetic codes superior to the standard genetic code." Journal of Theoretical Biology 408 (November 2016): 237–42. http://dx.doi.org/10.1016/j.jtbi.2016.08.022.

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10

Zamudio, Gabriel, and Marco José. "On the Uniqueness of the Standard Genetic Code." Life 7, no. 1 (February 13, 2017): 7. http://dx.doi.org/10.3390/life7010007.

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11

Alvager, T., G. Graham, D. Hutchison, and J. Westgard. "Standard Genetic Code Degeneracies from Maximum Information Calculations." Journal of Chemical Information and Modeling 34, no. 4 (July 1, 1994): 820–21. http://dx.doi.org/10.1021/ci00020a015.

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12

José, Marco V., Gabriel S. Zamudio, and Eberto R. Morgado. "A unified model of the standard genetic code." Royal Society Open Science 4, no. 3 (March 2017): 160908. http://dx.doi.org/10.1098/rsos.160908.

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The Rodin–Ohno (RO) and the Delarue models divide the table of the genetic code into two classes of aminoacyl-tRNA synthetases (aaRSs I and II) with recognition from the minor or major groove sides of the tRNA acceptor stem, respectively. These models are asymmetric but they are biologically meaningful. On the other hand, the standard genetic code (SGC) can be derived from the primeval RNY code (R stands for purines, Y for pyrimidines and N any of them). In this work, the RO-model is derived by means of group actions, namely, symmetries represented by automorphisms, assuming that the SGC originated from a primeval RNY code. It turns out that the RO-model is symmetric in a six-dimensional (6D) hypercube. Conversely, using the same automorphisms, we show that the RO-model can lead to the SGC. In addition, the asymmetric Delarue model becomes symmetric by means of quotient group operations. We formulate isometric functions that convert the class aaRS I into the class aaRS II and vice versa. We show that the four polar requirement categories display a symmetrical arrangement in our 6D hypercube. Altogether these results cannot be attained, neither in two nor in three dimensions. We discuss the present unified 6D algebraic model, which is compatible with both the SGC (based upon the primeval RNY code) and the RO-model.
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13

Hamashima, Kiyofumi, and Akio Kanai. "Alternative genetic code for amino acids and transfer RNA revisited." BioMolecular Concepts 4, no. 3 (June 1, 2013): 309–18. http://dx.doi.org/10.1515/bmc-2013-0002.

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AbstractThe genetic code is highly conserved among all organisms and its evolution is thought to be strictly limited. However, an increasing number of studies have reported non-standard codes in prokaryotic and eukaryotic genomes. Most of these deviations from the standard code are attributable to tRNA changes relating to, for example, codon/anticodon base pairing and tRNA/aminoacyl-tRNA synthetase recognition. In this review, we focus on tRNA, a key molecule in the translation of the genetic code, and summarize the most recently published information on the evolutionary divergence of the tRNAs. Surprisingly, although higher eukaryotes, such as the nematode (worm), utilize the standard genetic code, newly identified nematode-specific tRNAs (nev-tRNAs) translate nucleotides in a manner that transgresses the code. Furthermore, a variety of additional functions of tRNAs, beyond their translation of the genetic code, have emerged rapidly. We also review these intriguing new aspects of tRNA, which have potential impacts on translational control, RNA silencing, antibiotic resistance, RNA biosynthesis, and transcriptional regulation.
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14

Aisah, Isah, Nurul Ula Sayidatunisa, and Edi Kurniadi. "TINJAUAN STRUKTUR ALJABAR PADA KODE GENETIK STANDAR." Sigma-Mu 8, no. 2 (April 12, 2017): 29–34. http://dx.doi.org/10.35313/sigmamu.v8i2.268.

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Genetics is the branch of Biological Sciences that studies about the decline of a living being from parent to the children . Genetics often associated with genes and DNA (deoxyribonucleic acid) which both are one of the genetic material in a living body is very important in terms of inheritance Standard genetic code i as a representation of a gene that is according to needs of the human body protein. Genes in the standard genetic cods presented in the form of code triplet of nitrogen bases and became the language of the gene encoding the living body which produce = 64 different triplet code . All the triplet code of the RNA nucleotide chain translated and produces 20 kinds of amino acids that will be released as a protein in the cell . Set of nitrogen bases in RNA chains compiled and presented in a set N = { C , U , A, G }.This research will be carried out matching N with the cross product Z2 X Z2 {(0,0 ), (0,1 ), (1,0 ), ( 1,1)}. Through this matching then N = { C , U , A, G } forming Klein Group - 4 , the binary vector spaces and The Galois Field . Beside that set of N can be classified into three sets containing partition the set of basic nitrogen based chemical properties of nucleotides that is strong - weak bases, amino - ketonukleotida , and types of bases nitrogen, in the presence of the partition, then N = { C , U , A , G } will form the quotient group. Keywords: DNA, RNA, standard genetic code, quotien group
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15

José, Marco, and Gabriel Zamudio. "Symmetrical Properties of Graph Representations of Genetic Codes: From Genotype to Phenotype." Symmetry 10, no. 9 (September 8, 2018): 388. http://dx.doi.org/10.3390/sym10090388.

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It has long been claimed that the mitochondrial genetic code possesses more symmetries than the Standard Genetic Code (SGC). To test this claim, the symmetrical structure of the SGC is compared with noncanonical genetic codes. We analyzed the symmetries of the graphs of codons and their respective phenotypic graph representation spanned by the RNY (R purines, Y pyrimidines, and N any of them) code, two RNA Extended codes, the SGC, as well as three different mitochondrial genetic codes from yeast, invertebrates, and vertebrates. The symmetry groups of the SGC and their corresponding phenotypic graphs of amino acids expose the evolvability of the SGC. Indeed, the analyzed mitochondrial genetic codes are more symmetrical than the SGC.
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16

Misic, Natasa. "Standard genetic code: p-adic modelling, nucleon balances and selfsimilarity." Facta universitatis - series: Physics, Chemistry and Technology 14, no. 3 (2016): 275–98. http://dx.doi.org/10.2298/fupct1603275m.

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This paper represents the preliminary results and conclusions on the one of fundamental questions of the genetic code related to the underlying selective mechanisms involved in its origin and evolution, in particular their hypothetical different nature, originally considered in [1,2,3]. A novel approach is introduced, based on known arithmetic regularities inside the genetic code, determined by the nucleon balances of amino acids and their divisibility by the decimal number 37 [4]. As a parameter of the genetic code systematization is introduced an aggregate nucleon number of amino acid and cognate codon, while divisibility test is carried out not only by the number 37, but also by 13.7, the selfsimilarity constant of decimal scaling [5]. Relevant nucleon sums were obtained for the most prominent divisions of the standard genetic code (SGC) according to p-adic model of the vertebrate mitochondrial code (VMC) in [6]. The nucleon number divisibility pattern of 37 and 13.7 for the RNA and DNA codon space, as well as for the amino acid space is also analyzed. The obtained results, particularly a general higher divisibility of the nucleon sums by the numbers 37 and 13.7 in SGC than in VMC, as well as a correspondence between the nucleon number divisibility pattern of both the RNA codon space and the amino acid space of SGC, how separately so conjointly, with the code degeneracy pattern, suggest some conclusions: support the hypothesis [1,2,3,7] that the selective driving forces acting during an emergence (an ancient phase) and an evolution (a modern phase) of the genetic code are different, imply the existence of an environmental-dependent stereochemical mechanism throughout the entire period of the genetic code emergence and support a mineral-mediated origin of the genetic code [7,8].
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17

Omachi, Yuji, Nen Saito, and Chikara Furusawa. "Rare-event sampling analysis uncovers the fitness landscape of the genetic code." PLOS Computational Biology 19, no. 4 (April 17, 2023): e1011034. http://dx.doi.org/10.1371/journal.pcbi.1011034.

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The genetic code refers to a rule that maps 64 codons to 20 amino acids. Nearly all organisms, with few exceptions, share the same genetic code, the standard genetic code (SGC). While it remains unclear why this universal code has arisen and been maintained during evolution, it may have been preserved under selection pressure. Theoretical studies comparing the SGC and numerically created hypothetical random genetic codes have suggested that the SGC has been subject to strong selection pressure for being robust against translation errors. However, these prior studies have searched for random genetic codes in only a small subspace of the possible code space due to limitations in computation time. Thus, how the genetic code has evolved, and the characteristics of the genetic code fitness landscape, remain unclear. By applying multicanonical Monte Carlo, an efficient rare-event sampling method, we efficiently sampled random codes from a much broader random ensemble of genetic codes than in previous studies, estimating that only one out of every 1020 random codes is more robust than the SGC. This estimate is significantly smaller than the previous estimate, one in a million. We also characterized the fitness landscape of the genetic code that has four major fitness peaks, one of which includes the SGC. Furthermore, genetic algorithm analysis revealed that evolution under such a multi-peaked fitness landscape could be strongly biased toward a narrow peak, in an evolutionary path-dependent manner.
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18

Zhu, Wen, and Stephen Freeland. "The standard genetic code enhances adaptive evolution of proteins." Journal of Theoretical Biology 239, no. 1 (March 2006): 63–70. http://dx.doi.org/10.1016/j.jtbi.2005.07.012.

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19

Geyer, Regine, and Amir Madany Mamlouk. "On the efficiency of the genetic code after frameshift mutations." PeerJ 6 (May 21, 2018): e4825. http://dx.doi.org/10.7717/peerj.4825.

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Statistical and biochemical studies of the standard genetic code (SGC) have found evidence that the impact of mistranslations is minimized in a way that erroneous codes are either synonymous or code for an amino acid with similar polarity as the originally coded amino acid. It could be quantified that the SGC is optimized to protect this specific chemical property as good as possible. In recent work, it has been speculated that the multilevel optimization of the genetic code stands in the wider context of overlapping codes. This work tries to follow the systematic approach on mistranslations and to extend those analyses to the general effect of frameshift mutations on the polarity conservation of amino acids. We generated one million random codes and compared their average polarity change over all triplets and the whole set of possible frameshift mutations. While the natural code—just as for the point mutations—appears to be competitively robust against frameshift mutations as well, we found that both optimizations appear to be independent of each other. For both, better codes can be found, but it becomes significantly more difficult to find candidates that optimize all of these features—just like the SGC does. We conclude that the SGC is not only very efficient in minimizing the consequences of mistranslations, but rather optimized in amino acid polarity conservation for all three effects of code alteration, namely translational errors, point and frameshift mutations. In other words, our result demonstrates that the SGC appears to be much more than just “one in a million”.
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20

Santos, Manuel A. S., Takuya Ueda, Kimitsuna Watanabe, and Mick F. Tuite. "The non‐standard genetic code of Candida spp.: an evolving genetic code or a novel mechanism for adaptation?" Molecular Microbiology 26, no. 3 (October 1997): 423–31. http://dx.doi.org/10.1046/j.1365-2958.1997.5891961.x.

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21

Kawakami, Takashi, and Hiroshi Murakami. "Genetically Encoded Libraries of Nonstandard Peptides." Journal of Nucleic Acids 2012 (2012): 1–15. http://dx.doi.org/10.1155/2012/713510.

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The presence of a nonproteinogenic moiety in a nonstandard peptide often improves the biological properties of the peptide. Non-standard peptide libraries are therefore used to obtain valuable molecules for biological, therapeutic, and diagnostic applications. Highly diverse non-standard peptide libraries can be generated by chemically or enzymatically modifying standard peptide libraries synthesized by the ribosomal machinery, using posttranslational modifications. Alternatively, strategies for encoding non-proteinogenic amino acids into the genetic code have been developed for the direct ribosomal synthesis of non-standard peptide libraries. In the strategies for genetic code expansion, non-proteinogenic amino acids are assigned to the nonsense codons or 4-base codons in order to add these amino acids to the universal genetic code. In contrast, in the strategies for genetic code reprogramming, some proteinogenic amino acids are erased from the genetic code and non-proteinogenic amino acids are reassigned to the blank codons. Here, we discuss the generation of genetically encoded non-standard peptide libraries using these strategies and also review recent applications of these libraries to the selection of functional non-standard peptides.
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22

Wichmann, Stefan, and Zachary Ardern. "Optimality in the standard genetic code is robust with respect to comparison code sets." Biosystems 185 (November 2019): 104023. http://dx.doi.org/10.1016/j.biosystems.2019.104023.

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23

Yarus, Michael. "The Genetic Code Assembles via Division and Fusion, Basic Cellular Events." Life 13, no. 10 (October 17, 2023): 2069. http://dx.doi.org/10.3390/life13102069.

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Standard Genetic Code (SGC) evolution is quantitatively modeled in up to 2000 independent coding ‘environments’. Environments host multiple codes that may fuse or divide, with division yielding identical descendants. Code division may be selected—sophisticated gene products could be required for an orderly separation that preserves the coding. Several unforeseen results emerge: more rapid evolution requires unselective code division rather than its selective form. Combining selective and unselective code division, with/without code fusion, with/without independent environmental coding tables, and with/without wobble defines 25 = 32 possible pathways for SGC evolution. These 32 possible histories are compared, specifically, for evolutionary speed and code accuracy. Pathways differ greatly, for example, by ≈300-fold in time to evolve SGC-like codes. Eight of thirty-two pathways employing code division evolve quickly. Four of these eight that combine fusion and division also unite speed and accuracy. The two most precise, swiftest paths; thus the most likely routes to the SGC are similar, differing only in fusion with independent environmental codes. Code division instead of fusion with unrelated codes implies that exterior codes can be dispensable. Instead, a single ancestral code that divides and fuses can initiate fully encoded peptide biosynthesis. Division and fusion create a ‘crescendo of competent coding’, facilitating the search for the SGC and also assisting the advent of otherwise uniformly disfavored wobble coding. Code fusion can unite multiple codon assignment mechanisms. However, via code division and fusion, an SGC can emerge from a single primary origin via familiar cellular events.
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Yamaguchi, Atsushi, Takayuki Katoh, and Hiroaki Suga. "Drug discovery of non-standard peptide with genetic code reprogramming." Drug Delivery System 26, no. 6 (2011): 584–92. http://dx.doi.org/10.2745/dds.26.584.

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25

Nesterov-Mueller, Alexander, and Roman Popov. "The Combinatorial Fusion Cascade to Generate the Standard Genetic Code." Life 11, no. 9 (September 16, 2021): 975. http://dx.doi.org/10.3390/life11090975.

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Combinatorial fusion cascade was proposed as a transition stage between prebiotic chemistry and early forms of life. The combinatorial fusion cascade consists of three stages: eight initial complimentary pairs of amino acids, four protocodes, and the standard genetic code. The initial complimentary pairs and the protocodes are divided into dominant and recessive entities. The transitions between these stages obey the same combinatorial fusion rules for all amino acids. The combinatorial fusion cascade mathematically describes the codon assignments in the standard genetic code. It explains the availability of amino acids with the even and odd numbers of codons, the appearance of stop codons, inclusion of novel canonical amino acids, exceptional high numbers of codons for amino acids arginine, leucine, and serine, and the temporal order of amino acid inclusion into the genetic code. The temporal order of amino acids within the cascade is congruent with the consensus temporal order previously derived from the similarities between the available hypotheses. The control over the combinatorial fusion cascades would open the road for a novel technology to develop artificial microorganisms.
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26

Sengupta, Supratim, Neha Aggarwal, and Ashutosh Vishwa Bandhu. "Two Perspectives on the Origin of the Standard Genetic Code." Origins of Life and Evolution of Biospheres 44, no. 4 (December 2014): 287–91. http://dx.doi.org/10.1007/s11084-014-9394-1.

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27

Robinson, Richard. "For Arthropod Mitochondria, Variety in the Genetic Code Is Standard." PLoS Biology 4, no. 5 (April 25, 2006): e175. http://dx.doi.org/10.1371/journal.pbio.0040175.

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28

Błażej, Paweł, Małgorzata Wnętrzak, Dorota Mackiewicz, Przemysław Gagat, and Paweł Mackiewicz. "Many alternative and theoretical genetic codes are more robust to amino acid replacements than the standard genetic code." Journal of Theoretical Biology 464 (March 2019): 21–32. http://dx.doi.org/10.1016/j.jtbi.2018.12.030.

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29

Fimmel, Elena, Markus Gumbel, Martin Starman, and Lutz Strüngmann. "Computational Analysis of Genetic Code Variations Optimized for the Robustness against Point Mutations with Wobble-like Effects." Life 11, no. 12 (December 3, 2021): 1338. http://dx.doi.org/10.3390/life11121338.

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It is believed that the codon–amino acid assignments of the standard genetic code (SGC) help to minimize the negative effects caused by point mutations. All possible point mutations of the genetic code can be represented as a weighted graph with weights that correspond to the probabilities of these mutations. The robustness of a code against point mutations can be described then by means of the so-called conductance measure. This paper quantifies the wobble effect, which was investigated previously by applying the weighted graph approach, and seeks optimal weights using an evolutionary optimization algorithm to maximize the code’s robustness. One result of our study is that the robustness of the genetic code is least influenced by mutations in the third position—like with the wobble effect. Moreover, the results clearly demonstrate that point mutations in the first, and even more importantly, in the second base of a codon have a very large influence on the robustness of the genetic code. These results were compared to single nucleotide variants (SNV) in coding sequences which support our findings. Additionally, it was analyzed which structure of a genetic code evolves from random code tables when the robustness is maximized. Our calculations show that the resulting code tables are very close to the standard genetic code. In conclusion, the results illustrate that the robustness against point mutations seems to be an important factor in the evolution of the standard genetic code.
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30

Szymański, Maciej, and Jan Barciszewski. "The genetic code--40 years on." Acta Biochimica Polonica 54, no. 1 (March 20, 2007): 51–54. http://dx.doi.org/10.18388/abp.2007_3268.

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The genetic code discovered 40 years ago, consists of 64 triplets (codons) of nucleotides. The genetic code is almost universal. The same codons are assigned to the same amino acids and to the same START and STOP signals in the vast majority of genes in animals, plants, and microorganisms. Each codon encodes for one of the 20 amino acids used in the synthesis of proteins. That produces some redundancy in the code and most of the amino acids being encoded by more than one codon. The two cases have been found where selenocysteine or pyrrolysine, that are not one of the standard 20 is inserted by a tRNA into the growing polypeptide.
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31

Park, Ju-Yong, Sung-Kook Lee, and Moon-Ho Lee. "A Standard [UC;AG] Vertical Block Code of Genetic Information 64 Trigram Codon." Journal of the Institute of Internet Broadcasting and Communication 16, no. 6 (December 31, 2016): 135–40. http://dx.doi.org/10.7236/jiibc.2016.16.6.135.

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32

Nesterov-Mueller, Alexander, Roman Popov, and Hervé Seligmann. "Combinatorial Fusion Rules to Describe Codon Assignment in the Standard Genetic Code." Life 11, no. 1 (December 23, 2020): 4. http://dx.doi.org/10.3390/life11010004.

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We propose combinatorial fusion rules that describe the codon assignment in the standard genetic code simply and uniformly for all canonical amino acids. These rules become obvious if the origin of the standard genetic code is considered as a result of a fusion of four protocodes: Two dominant AU and GC protocodes and two recessive AU and GC protocodes. The biochemical meaning of the fusion rules consists of retaining the complementarity between cognate codons of the small hydrophobic amino acids and large charged or polar amino acids within the protocodes. The proto tRNAs were assembled in form of two kissing hairpins with 9-base and 10-base loops in the case of dominant protocodes and two 9-base loops in the case of recessive protocodes. The fusion rules reveal the connection between the stop codons, the non-canonical amino acids, pyrrolysine and selenocysteine, and deviations in the translation of mitochondria. Using fusion rules, we predicted the existence of additional amino acids that are essential for the development of the standard genetic code. The validity of the proposed partition of the genetic code into dominant and recessive protocodes is considered referring to state-of-the-art hypotheses. The formation of two aminoacyl-tRNA synthetase classes is compatible with four-protocode partition.
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33

Aisah, Isah, Eddy Djauhari, and Asep Singgih. "Dihedral Group in The Ancient Genetic." Jurnal Matematika Integratif 16, no. 1 (April 5, 2020): 13. http://dx.doi.org/10.24198/jmi.v16i1.26646.

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The standard genetic code consist of four nucleotide bases which encode genes to produce amino acids needed by living things. The addition of new base (Dummy) causes a sequence of bases to become five nucleotide bases called ancient genetic codes. The five base set is denoted by , where B forms group through matching , , , , and from set . Ancient genetic codes can be reviewed as algebraic structures as a vector spaces and other structures as symmetry groups. In this article, discussed the properties of symmetry groups from ancient genetic codes that will produce dihedral groups. The study began by constructing an expanded nucleotide base isomorphism with . The presence of base causes to have a cardinality of 24, denoted as with . isomorphic with which is denoted by . Group had three clasess of partitions based on strong-weak, purin-pyrimidin types, and amino-keto nucleotide groups which are denoted as , , and . All three classes are subgroups of . By using the rules of rotation and reflection in the four-side plane, it was found that only one group fulfilled the rule was named the dihedral group. Keywords: ancient genetic code, group, subgroup, permutation, symmetry group , dihedral group.
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34

Shenhav, Liat, and David Zeevi. "Resource conservation manifests in the genetic code." Science 370, no. 6517 (November 5, 2020): 683–87. http://dx.doi.org/10.1126/science.aaz9642.

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Nutrient limitation drives competition for resources across organisms. However, much is unknown about how selective pressures resulting from nutrient limitation shape microbial coding sequences. Here, we study this “resource-driven selection” by using metagenomic and single-cell data of marine microbes, alongside environmental measurements. We show that a significant portion of the selection exerted on microbes is explained by the environment and is associated with nitrogen availability. Notably, this resource conservation optimization is encoded in the structure of the standard genetic code, providing robustness against mutations that increase carbon and nitrogen incorporation into protein sequences. This robustness generalizes to codon choices from multiple taxa across all domains of life, including the human genome.
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35

Ardell, David H. "On Error Minimization in a Sequential Origin of the Standard Genetic Code." Journal of Molecular Evolution 47, no. 1 (July 1998): 1–13. http://dx.doi.org/10.1007/pl00006356.

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36

Zamudio, Gabriel S., and Marco V. José. "Phenotypic Graphs and Evolution Unfold the Standard Genetic Code as the Optimal." Origins of Life and Evolution of Biospheres 48, no. 1 (October 29, 2017): 83–91. http://dx.doi.org/10.1007/s11084-017-9552-3.

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37

Struyf, Jef. "The Standard Genetic Code Modeled by the Structure of the Geocentric Cosmos." American Journal of Modeling and Optimization 10, no. 1 (November 15, 2023): 1–8. http://dx.doi.org/10.12691/ajmo-10-1-1.

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38

José, Marco V., Eberto R. Morgado, and Tzipe Govezensky. "An Extended RNA Code and its Relationship to the Standard Genetic Code: An Algebraic and Geometrical Approach." Bulletin of Mathematical Biology 69, no. 1 (November 2, 2006): 215–43. http://dx.doi.org/10.1007/s11538-006-9119-3.

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39

José, Marco V., Eberto R. Morgado, and Tzipe Govezensky. "Genetic Hotels for the Standard Genetic Code: Evolutionary Analysis Based upon Novel Three-Dimensional Algebraic Models." Bulletin of Mathematical Biology 73, no. 7 (August 20, 2010): 1443–76. http://dx.doi.org/10.1007/s11538-010-9571-y.

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40

Kurnaz, Mehmet Levent, Tugce Bilgin, and Isil Aksan Kurnaz. "Certain Non-Standard Coding Tables Appear to be More Robust to Error Than the Standard Genetic Code." Journal of Molecular Evolution 70, no. 1 (December 10, 2009): 13–28. http://dx.doi.org/10.1007/s00239-009-9303-9.

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41

Sinnott, Jennifer A., Fiona Cai, Sheng Yu, Boris P. Hejblum, Chuan Hong, Isaac S. Kohane, and Katherine P. Liao. "PheProb: probabilistic phenotyping using diagnosis codes to improve power for genetic association studies." Journal of the American Medical Informatics Association 25, no. 10 (May 17, 2018): 1359–65. http://dx.doi.org/10.1093/jamia/ocy056.

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Abstract Objective Standard approaches for large scale phenotypic screens using electronic health record (EHR) data apply thresholds, such as ≥2 diagnosis codes, to define subjects as having a phenotype. However, the variation in the accuracy of diagnosis codes can impair the power of such screens. Our objective was to develop and evaluate an approach which converts diagnosis codes into a probability of a phenotype (PheProb). We hypothesized that this alternate approach for defining phenotypes would improve power for genetic association studies. Methods The PheProb approach employs unsupervised clustering to separate patients into 2 groups based on diagnosis codes. Subjects are assigned a probability of having the phenotype based on the number of diagnosis codes. This approach was developed using simulated EHR data and tested in a real world EHR cohort. In the latter, we tested the association between low density lipoprotein cholesterol (LDL-C) genetic risk alleles known for association with hyperlipidemia and hyperlipidemia codes (ICD-9 272.x). PheProb and thresholding approaches were compared. Results Among n = 1462 subjects in the real world EHR cohort, the threshold-based p-values for association between the genetic risk score (GRS) and hyperlipidemia were 0.126 (≥1 code), 0.123 (≥2 codes), and 0.142 (≥3 codes). The PheProb approach produced the expected significant association between the GRS and hyperlipidemia: p = .001. Conclusions PheProb improves statistical power for association studies relative to standard thresholding approaches by leveraging information about the phenotype in the billing code counts. The PheProb approach has direct applications where efficient approaches are required, such as in Phenome-Wide Association Studies.
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42

Frank, Alejandro, and Tom Froese. "The Standard Genetic Code can Evolve from a Two-Letter GC Code Without Information Loss or Costly Reassignments." Origins of Life and Evolution of Biospheres 48, no. 2 (June 2018): 259–72. http://dx.doi.org/10.1007/s11084-018-9559-4.

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43

Tripathi, Shubham, and Michael W. Deem. "The Standard Genetic Code Facilitates Exploration of the Space of Functional Nucleotide Sequences." Journal of Molecular Evolution 86, no. 6 (June 29, 2018): 325–39. http://dx.doi.org/10.1007/s00239-018-9852-x.

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44

Hendrickson, Tamara L., Whitney N. Wood, and Udumbara M. Rathnayake. "Did Amino Acid Side Chain Reactivity Dictate the Composition and Timing of Aminoacyl-tRNA Synthetase Evolution?" Genes 12, no. 3 (March 12, 2021): 409. http://dx.doi.org/10.3390/genes12030409.

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The twenty amino acids in the standard genetic code were fixed prior to the last universal common ancestor (LUCA). Factors that guided this selection included establishment of pathways for their metabolic synthesis and the concomitant fixation of substrate specificities in the emerging aminoacyl-tRNA synthetases (aaRSs). In this conceptual paper, we propose that the chemical reactivity of some amino acid side chains (e.g., lysine, cysteine, homocysteine, ornithine, homoserine, and selenocysteine) delayed or prohibited the emergence of the corresponding aaRSs and helped define the amino acids in the standard genetic code. We also consider the possibility that amino acid chemistry delayed the emergence of the glutaminyl- and asparaginyl-tRNA synthetases, neither of which are ubiquitous in extant organisms. We argue that fundamental chemical principles played critical roles in fixation of some aspects of the genetic code pre- and post-LUCA.
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45

ANTONELI, FERNANDO, MICHAEL FORGER, and JOSÉ EDUARDO M. HORNOS. "THE SEARCH FOR SYMMETRIES IN THE GENETIC CODE: FINITE GROUPS." Modern Physics Letters B 18, no. 18 (August 10, 2004): 971–78. http://dx.doi.org/10.1142/s0217984904007499.

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We give a full classification of the possible schemes for obtaining the distribution of multiplets observed in the standard genetic code by symmetry breaking in the context of finite groups, based on an extended notion of partial symmetry breaking that incorporates the intuitive idea of "freezing" first proposed by Francis Crick, which is given a precise mathematical meaning.
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46

Błażej, Paweł, Małgorzata Wnetrzak, Dorota Mackiewicz, and Paweł Mackiewicz. "Basic principles of the genetic code extension." Royal Society Open Science 7, no. 2 (February 2020): 191384. http://dx.doi.org/10.1098/rsos.191384.

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Compounds including non-canonical amino acids (ncAAs) or other artificially designed molecules can find a lot of applications in medicine, industry and biotechnology. They can be produced thanks to the modification or extension of the standard genetic code (SGC). Such peptides or proteins including the ncAAs can be constantly delivered in a stable way by organisms with the customized genetic code. Among several methods of engineering the code, using non-canonical base pairs is especially promising, because it enables generating many new codons, which can be used to encode any new amino acid. Since even one pair of new bases can extend the SGC up to 216 codons generated by a six-letter nucleotide alphabet, the extension of the SGC can be achieved in many ways. Here, we proposed a stepwise procedure of the SGC extension with one pair of non-canonical bases to minimize the consequences of point mutations. We reported relationships between codons in the framework of graph theory. All 216 codons were represented as nodes of the graph, whereas its edges were induced by all possible single nucleotide mutations occurring between codons. Therefore, every set of canonical and newly added codons induces a specific subgraph. We characterized the properties of the induced subgraphs generated by selected sets of codons. Thanks to that, we were able to describe a procedure for incremental addition of the set of meaningful codons up to the full coding system consisting of three pairs of bases. The procedure of gradual extension of the SGC makes the whole system robust to changing genetic information due to mutations and is compatible with the views assuming that codons and amino acids were added successively to the primordial SGC, which evolved minimizing harmful consequences of mutations or mistranslations of encoded proteins.
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47

Rosandić, Marija, and Vladimir Paar. "The Supersymmetry Genetic Code Table and Quadruplet Symmetries of DNA Molecules Are Unchangeable and Synchronized with Codon-Free Energy Mapping during Evolution." Genes 14, no. 12 (December 12, 2023): 2200. http://dx.doi.org/10.3390/genes14122200.

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The Supersymmetry Genetic code (SSyGC) table is based on five physicochemical symmetries: (1) double mirror symmetry on the principle of the horizontal and vertical mirror symmetry axis between all bases (purines [A, G) and pyrimidines (U, C)] and (2) of bases in the form of codons; (3) direct–complement like codon/anticodon symmetry in the sixteen alternating boxes of the genetic code columns; (4) A + T-rich and C + G-rich alternate codons in the same row between both columns of the genetic code; (5) the same position between divided and undivided codon boxes in relation to horizontal mirror symmetry axes. The SSyGC table has a unique physicochemical purine–pyrimidine symmetry net which is as the core symmetry common for all, with more than thirty different nuclear and mitochondrial genetic codes. This net is present in the SSyGC table of all RNA and DNA living species. None of these symmetries are present in the Standard Genetic Code (SGC) table which is constructed on the alphabetic horizontal and vertical U-C-A-G order of bases. Here, we show that the free energy value of each codon incorporated as fundamentally mapping the “energy code” in the SSyGC table is compatible with mirror symmetry. On the other hand, in the SGC table, the same free energy values of codons are dispersed and a mirror symmetry between them is not recognizable. At the same time, the mirror symmetry of the SSyGC table and the DNA quadruplets together with our classification of codons/trinucleotides are perfectly imbedded in the mirror symmetry energy mapping of codons/trinucleotides and point out in favor of maintaining the integrity of the genetic code and DNA genome. We also argue that physicochemical symmetries of the SSyGC table in the manner of the purine–pyrimidine symmetry net, the quadruplet symmetry of DNA molecule, and the free energy of codons have remined unchanged during all of evolution. The unchangeable and universal symmetry properties of the genetic code, DNA molecules, and the energy code are decreasing disorder between codons/trinucleotides and shed a new light on evolution. Diversity in all living species on Earth is broad, but the symmetries of the Supersymmetry Genetic Code as the code of life and the DNA quadruplets related to the “energy code” are unique, unchangeable, and have the power of natural laws.
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48

Aisah, Isah, Eddy Djauhari, and Asep Singgih. "Dihedral Group in The Ancient Genetic." Jurnal Matematika Integratif 16, no. 1 (April 5, 2020): 13. http://dx.doi.org/10.24198/jmi.v16.n1.26646.13-18.

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The standard genetic code consist of four nucleotide bases which encode genes to produce amino acids needed by living things. The addition of new base (Dummy) causes a sequence of bases to become five nucleotide bases called ancient genetic codes. The five base set is denoted by , where B forms group through matching , , , , and from set . Ancient genetic codes can be reviewed as algebraic structures as a vector spaces and other structures as symmetry groups. In this article, discussed the properties of symmetry groups from ancient genetic codes that will produce dihedral groups. The study began by constructing an expanded nucleotide base isomorphism with . The presence of base causes to have a cardinality of 24, denoted as with . isomorphic with which is denoted by . Group had three clasess of partitions based on strong-weak, purin-pyrimidin types, and amino-keto nucleotide groups which are denoted as , , and . All three classes are subgroups of . By using the rules of rotation and reflection in the four-side plane, it was found that only one group fulfilled the rule was named the dihedral group.
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49

Radványi, Ádám, and Ádám Kun. "The Mutational Robustness of the Genetic Code and Codon Usage in Environmental Context: A Non-Extremophilic Preference?" Life 11, no. 8 (July 30, 2021): 773. http://dx.doi.org/10.3390/life11080773.

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The genetic code was evolved, to some extent, to minimize the effects of mutations. The effects of mutations depend on the amino acid repertoire, the structure of the genetic code and frequencies of amino acids in proteomes. The amino acid compositions of proteins and corresponding codon usages are still under selection, which allows us to ask what kind of environment the standard genetic code is adapted to. Using simple computational models and comprehensive datasets comprising genomic and environmental data from all three domains of Life, we estimate the expected severity of non-synonymous genomic mutations in proteins, measured by the change in amino acid physicochemical properties. We show that the fidelity in these physicochemical properties is expected to deteriorate with extremophilic codon usages, especially in thermophiles. These findings suggest that the genetic code performs better under non-extremophilic conditions, which not only explains the low substitution rates encountered in halophiles and thermophiles but the revealed relationship between the genetic code and habitat allows us to ponder on earlier phases in the history of Life.
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50

Scully, Marc, Turi King, and Steven D. Brown. "Remediating Viking Origins: Genetic Code as Archival Memory of the Remote Past." Sociology 47, no. 5 (October 2013): 921–38. http://dx.doi.org/10.1177/0038038513493538.

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This article introduces some early data from the Leverhulme Trust-funded research programme, ‘The Impact of the Diasporas on the Making of Britain: evidence, memories, inventions’. One of the interdisciplinary foci of the programme, which incorporates insights from genetics, history, archaeology, linguistics and social psychology, is to investigate how genetic evidence of ancestry is incorporated into identity narratives. In particular, we investigate how ‘applied genetic history’ shapes individual and familial narratives, which are then situated within macro-narratives of the nation and collective memories of immigration and indigenism. It is argued that the construction of genetic evidence as a ‘gold standard’ about ‘where you really come from’ involves a remediation of cultural and archival memory, in the construction of a ‘usable past’. This article is based on initial questionnaire data from a preliminary study of those attending DNA collection sessions in northern England. It presents some early indicators of the perceived importance of being of Viking descent among participants, notes some emerging patterns and considers the implications for contemporary debates on migration, belonging and local and national identity.
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