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Genetic code expansion as a tool to study regulatory processes of transcription  [PDF]
Moritz J. Schmidt,Daniel Summerer
Frontiers in Chemistry , 2014, DOI: 10.3389/fchem.2014.00007
Abstract: The expansion of the genetic code with non-canonical amino acids (ncAA) enables the chemical and biophysical properties of proteins to be tailored, inside cells, with a previously unattainable level of precision. A wide range of ncAA with functions not found in canonical amino acids have been genetically encoded in recent years and have delivered insights into biological processes that would be difficult to access with traditional approaches of molecular biology. A major field for the development and application of novel ncAA-functions has been transcription and its regulation. This is particularly attractive, since advanced DNA sequencing- and proteomics-techniques continue to deliver vast information on these processes on a global level, but complementing methodologies to study them on a detailed, molecular level and in living cells have been comparably scarce. In a growing number of studies, genetic code expansion has now been applied to precisely control the chemical properties of transcription factors, RNA polymerases and histones, and this has enabled new insights into their interactions, conformational changes, cellular localizations and the functional roles of posttranslational modifications.
Genetic secrets of good wine
Xavier Bosch
Genome Biology , 2003, DOI: 10.1186/gb-spotlight-20040507-01
Abstract: The genetic determinants of grape quality are practically unknown, and how local environmental factors interact at the cellular and molecular levels to cause differences in fruit quality is not understood."Understanding grapevine genomics is now a prerequisite to further improvement of viticultural practices as well as for the development of new varieties through breeding programs and adapting the best clones to the most suitable vineyard environments," José Miguel Martínez-Zapater, the Spanish coordinator of the project at Madrid's National Center of Biotechnology, told us.The grape genomics project, funded by Genome Spain and Genome Canada, is meant to elucidate developmental and metabolic pathways underlying grape development and quality traits and predict how these pathways are modified by microclimate and common viticultural practices as well as by genetic differences among grapevine cultivars.The project, announced last month (April 7) by the University of Navarra, is expected to generate useful tools for genomic analysis, such as full length cDNA libraries."The proposal is highly committed to the development of tools for functional analyses at different organismal levels (i.e., whole plant, organ, and cell), including cell-based assays and whole plants for functional studies as well as detached shoots for greenhouse experiments concerning the environment and berry ripening," notes Martínez-Zapater.Steven Lund, the Canadian coordinator of the project at the University of British Columbia in Vancouver, said that "[this] is a new, exciting project where in more than one way, the Old World meets the New World. Spain, in 'Old World' Europe, is one of the largest grape and wine producers in the world, whereas Canada, in the 'New World,' is one of the very youngest.""Throughout the project," Lund told us, "using complementary areas of expertise, our two countries will together have the opportunity to begin to dissect the traditional practice of viticulture using mod
Simulated evolution applied to study the genetic code optimality using a model of codon reassignments
José Santos, ángel Monteagudo
BMC Bioinformatics , 2011, DOI: 10.1186/1471-2105-12-56
Abstract: Here we used a genetic algorithm to search for better adapted hypothetical codes and as a method to guess the difficulty in finding such alternative codes, allowing to clearly situate the canonical code in the fitness landscape. This novel proposal of the use of evolutionary computing provides a new perspective in the open debate between the use of the statistical approach, which postulates that the genetic code conserves amino acid properties far better than expected from a random code, and the engineering approach, which tends to indicate that the canonical genetic code is still far from optimal. We used two models of hypothetical codes: one that reflects the known examples of codon reassignment and the model most used in the two approaches which reflects the current genetic code translation table. Although the standard code is far from a possible optimum considering both models, when the more realistic model of the codon reassignments was used, the evolutionary algorithm had more difficulty to overcome the efficiency of the canonical genetic code.Simulated evolution clearly reveals that the canonical genetic code is far from optimal regarding its optimization. Nevertheless, the efficiency of the canonical code increases when mistranslations are taken into account with the two models, as indicated by the fact that the best possible codes show the patterns of the standard genetic code. Our results are in accordance with the postulates of the engineering approach and indicate that the main arguments of the statistical approach are not enough to its assertion of the extreme efficiency of the canonical genetic code.The canonical genetic code is not universal although it is present in most complex genomes. Its establishment is still under discussion once the discovery of non-standard genetic codes altered the "frozen accident" [1]. Woese [2] was one of the first to consider the adaptability of the genetic code. He suggested that the patterns within the standard genetic
Stability of the genetic code and optimal parameters of amino acids  [PDF]
V. R. Chechetkin,V. V. Lobzin
Quantitative Biology , 2012, DOI: 10.1016/j.jtbi.2010.10.015
Abstract: The standard genetic code is known to be much more efficient in minimizing adverse effects of misreading errors and one-point mutations in comparison with a random code having the same structure, i.e. the same number of codons coding for each particular amino acid. We study the inverse problem, how the code structure affects the optimal physico-chemical parameters of amino acids ensuring the highest stability of the genetic code. It is shown that the choice of two or more amino acids with given properties determines unambiguously all the others. In this sense the code structure determines strictly the optimal parameters of amino acids. In the code with the structure of the standard genetic code the resulting values for hydrophobicity obtained in the scheme leave one out and in the scheme with fixed maximum and minimum parameters correlate significantly with the natural scale. This indicates the co-evolution of the genetic code and physico-chemical properties of amino acids.
Braid Group of a Genetic Code  [PDF]
Valerij G. Bardakov
Mathematics , 2006,
Abstract: For every group genetic code with finite number of generating and at most with one defining relation we introduce the braid group of this genetic code. This construction includes the braid group of Euclidean plane, the braid groups of closed orientable surfaces, B type groups of Artin-Brieskorn, and allow us to study all these groups with common point of view. We present some results on the structure of the braid groups of genetic codes, describe normal form of words, torsion, and some results on widths of the verbal subgroups. Also we prove that Scott's system of defining relations for the braid groups of closed surfaces is contradictory.
An Alternative Cracking of The Genetic Code  [PDF]
O. Babatunde Okunoye
Computer Science , 2009,
Abstract: We Propose 22 unique Solutions to the Genetic Code. An Alternative Cracking, from the Perspective of a Mathematician.
Genetic Code and Number Theory  [PDF]
Branko Dragovich
Quantitative Biology , 2009,
Abstract: Living organisms are the most complex, interesting and significant objects regarding all substructures of the universe. Life science is regarded as a science of the 21st century and one can expect great new discoveries in the near futures. This article contains an introductory brief review of genetic information, its coding and translation of genes to proteins through the genetic code. Some theoretical approaches to the modelling of the genetic code are presented. In particular, connection of the genetic code with number theory is considered and the role of $p$-adic numbers is underlined.
Genetic code on the dyadic plane  [PDF]
A. Yu. Khrennikov,S. V. Kozyrev
Quantitative Biology , 2007, DOI: 10.1016/j.physa.2007.03.018
Abstract: We introduce the simple parametrization for the space of codons (triples of nucleotides) by 8\times 8 table. This table (which we call the dyadic plane) possesses the natural 2-adic ultrametric. We show that after this parametrization the genetic code will be a locally constant map of the simple form. The local constancy of this map will describe degeneracy of the genetic code. The map of the genetic code defines 2-adic ultrametric on the space of amino acids. We show that hydrophobic amino acids will be clustered in two balls with respect to this ultrametric. Therefore the introduced parametrization of space of codons exhibits the hidden regularity of the genetic code.
Horizontal symmetry in the algebraic approach of genetic code  [PDF]
J. J. Godina-Nava
Physics , 2013,
Abstract: Using concepts of physics of elementary particles concerning the breaking of symmetry and grannd unified theory we propose to study with the algebraic approximation the degeneracy finded in the genetic code with the incorporation of a horizontal symmetry used in gauge theories to fit the contents of the multiplets of the genetic code. It is used the algebraic approch of Hornos et. al. \cite{main,PRL71,PRE,MPLB}. We propose an example for the incorporation of horizontal symmetry to study mixtures of elements of the multiplets.
The Symmetry of the Genetic Code and a Universal Trend of Amino Acid Gain and Loss  [PDF]
Denis A. Semenov
Quantitative Biology , 2007,
Abstract: Part 1 of the study intends to show that the universal trend of amino acid gain and loss discovered by Jordan et al. (2005) can be accounted for by the spontaneity of DNA typical damages. These damages lead to replacements of guanine and cytosine by thymine. Part 2 proposes a hypothesis of the evolution of the genetic code, the leading mechanism of which is the nucleotide spontaneous damage. The hypothesis accounts for the universal trend of amino acid gain and loss, stability of the genetic code towards point mutations, the presence of code dialects, and the symmetry of the genetic code table.
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