Relevant bibliographies by topics / Genetic code

Academic literature on the topic 'Genetic code'

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Published: 4 June 2021
Last updated: 31 July 2024

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Journal articles on the topic "Genetic code"

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Cavalcanti, Andre R. O., and Laura F. Landweber. "Genetic code." Current Biology 14, no. 4 (February 2004): R147. http://dx.doi.org/10.1016/j.cub.2004.01.041.

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Fimmel, Elena, and Lutz Strüngmann. "Linear codes and the mitochondrial genetic code." Biosystems 184 (October 2019): 103990. http://dx.doi.org/10.1016/j.biosystems.2019.103990.

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Habrel, Mykola, and Mykhailo Habrel. "GENETIC CODE OF THE CITY." Current problems of architecture and urban planning, no. 63 (April 14, 2022): 18–41. http://dx.doi.org/10.32347/2077-3455.2022.63.18-41.

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Advances in genetics as a science have led the authors to believe that its methods and approaches can be used in urban research and in justifying decisions on spatial organization and urban development. Using the theoretical and methodological tools of genetics revealed the content of the phenomenon of "genetic top" in urban planning and urban development: understood the key provisions of genetics as a science of heredity – the origin and evolution of organisms, substantiated their feasibility for research on urban history and modern cities; the peculiarities of the genetic method for the study of cities and the role of the phenomenon of heredity for their future are determined. The genetic method is presented as a kind of genetic and aimed at studying the phenomena of development not only in time but also in space, determining the transitions from lower forms of organization of territories (places, settlements) to higher – extremely complex urban systems. It covers: the establishment of initial conditions and the origin of the organism, its main stages, main trends and lines (mutations, modifications) of development. On the example of the city of Lviv the application of certain tools for in-depth understanding of the processes of origin and evolution of the city is revealed. The set of "genes" of the city – spiritual-religious, behavioral-activity and psychological-mental in their various combinations, which form the genotype of the city as connections "man–territory–space–time". It has been confirmed that the city’s genetics (genetic space) is rooted in the past, connected with people, the energy of the Earth and the Universe. "Genetic" research shows that inherited urban differences are a factor that determines urban individuality throughout development, should be taken into account in both research and spatial organization and development of urban systems. The article only initiates certain provisions to substantiate the theory of urban genetics. Future research will determine the evidence in support of the formulated provisions or refute them as false.
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KOJIMA, Tatsuya, Yuuki HAYASHI, and Hiroaki SUGA. "Genetic Code Reprogramming." Seibutsu Butsuri 52, no. 1 (2012): 004–9. http://dx.doi.org/10.2142/biophys.52.004.

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OHAMA, Takeshi, Yuji INAGAKI, Yoshitaka BESSHO, and Syozo OSAWA. "Evolving genetic code." Proceedings of the Japan Academy, Series B 84, no. 2 (2008): 58–74. http://dx.doi.org/10.2183/pjab.84.58.

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Marshall, J. "The genetic code." Proceedings of the National Academy of Sciences 111, no. 16 (April 22, 2014): 5760. http://dx.doi.org/10.1073/pnas.1405652111.

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Helser, Terry L. "Genetic Code Wordsearch." Journal of Chemical Education 80, no. 4 (April 2003): 417. http://dx.doi.org/10.1021/ed080p417.

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YARUS, MICHAEL, and ERIC L. CHRISTIAN. "Genetic code origins." Nature 342, no. 6248 (November 1989): 349–50. http://dx.doi.org/10.1038/342349b0.

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Osawa, S., A. Muto, T. Ohama, Y. Andachi, R. Tanaka, and F. Yamao. "Prokaryotic genetic code." Experientia 46, no. 11-12 (December 1990): 1097–106. http://dx.doi.org/10.1007/bf01936919.

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Giegé, Richard. "Genetic code expansion." Nature Structural & Molecular Biology 10, no. 6 (June 2003): 414–16. http://dx.doi.org/10.1038/nsb0603-414.

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Dissertations / Theses on the topic "Genetic code"

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Nicholls, Felicity K. M. "Genetic analysis of the gene Additional sex combs and interacting loci." Thesis, University of British Columbia, 1990. http://hdl.handle.net/2429/29644.

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In order to recover new mutant alleles of the Polycomb group gene Additional sex combs (Asx), mutagenized chromosomes were screened over the putative Asx allele XT129. Thirteen new mutant strains that fail to complement XT129 were recovered. Unexpectedly, the thirteen strains sorted into four complementation groups. Recombination mapping suggests that each complementation group represents a separate locus. The largest group fails to complement a deletion of Asx and maps in the vicinity of 2-72, the published location of Asx. All new mutant strains enhance the phenotype of Polycomb mutant flies and are not allelic to any previously discovered second chromosome Polycomb group genes. Therefore, the new mutants may be considered putative new members of the Polycomb group. This study suggests that Asx belongs to a sub-group of genes displaying intergenic non-complementation.
Science, Faculty of
Zoology, Department of
Graduate
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Mat, Wai Kin. "Genetic code mutants of bacillus subtilis /." View abstract or full-text, 2007. http://library.ust.hk/cgi/db/thesis.pl?BICH%202007%20MAT.

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Freeland, Stephen J. "Natural selection and the genetic code." Thesis, University of Cambridge, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.313922.

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Gutfraind, Alexander. "Error-Tolerant Coding and the Genetic Code." Thesis, University of Waterloo, 2006. http://hdl.handle.net/10012/2913.

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The following thesis is a project in mathematical biology building upon the so-called "error minimization hypothesis" of the genetic code. After introducing the biological context of this hypothesis, I proceed to develop some relevant information-theoretic ideas, with the overall goal of studying the structure of the genetic code. I then apply the newfound understanding to an important question in the debate about the origin of life, namely, the question of the temperatures in which the genetic code, and life in general, underwent their early evolution.

The main advance in this thesis is a set of methods for calculating the primordial evolutionary pressures that shaped the genetic code. These pressures are due to genetic errors, and hence the statistical properties of the errors and of the genome are imprinted in the statistical properties of the code. Thus, by studying the code it is possible to reconstruct, to some extent, the primordial error rates and the composition of the primordial genome. In this way, I find evidence that the fixation of the genetic code occurred in organisms which were not thermophiles.
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Mateus, Denisa Daud. "Molecular reconstruction of a genetic code alteration." Doctoral thesis, Universidade de Aveiro, 2011. http://hdl.handle.net/10773/7501.

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Doutoramento em Bioquímica
The genetic code establishes the rules that govern gene translation into proteins. It was established more than 3.5 billion years ago and it is one of the most conserved features of life. Despite this, several alterations to the standard genetic code have been discovered in both prokaryotes and eukaryotes, namely in the fungal CTG clade where a unique seryl transfer RNA (tRNACAG Ser) decodes leucine CUG codons as serine. This tRNACAG Ser appeared 272±25 million years ago through insertion of an adenosine in the middle position of the anticodon of a tRNACGA Ser gene, which changed its anticodon from 5´-CGA-3´ to 5´-CAG-3´. This most dramatic genetic event restructured the proteome of the CTG clade species, but it is not yet clear how and why such deleterious genetic event was selected and became fixed in those fungal genomes. In this study we have attempted to shed new light on the evolution of this fungal genetic code alteration by reconstructing its evolutionary pathway in vivo in the yeast Saccharomyces cerevisiae. For this, we have expressed wild type and mutant versions of the C. albicans tRNACGA Ser gene into S. cerevisiae and evaluated the impact of the mutant tRNACGA Ser on fitness, tRNA stability, translation efficiency and aminoacylation kinetics. Our data demonstrate that these mutants are expressed and misincorporate Ser at CUGs, but their expression is repressed through an unknown molecular mechanism. We further demonstrate, using in vivo forced evolution methodologies, that the tRNACAG Ser can be easily inactivated through natural mutations that prevent its recognition by the seryl-tRNA synthetase. The overall data show that repression of expression of the mistranslating tRNACAG Ser played a critical role on the evolution of CUG reassignment from Leu to Ser. In order to better understand the evolution of natural genetic code alterations, we have also engineered partial reassignment of various codons in yeast. The data confirmed that genetic code ambiguity affects fitness, induces protein aggregation, interferes with the cell cycle and results in nuclear and morphologic alterations, genome instability and gene expression deregulation. Interestingly, it also generates phenotypic variability and phenotypes that confer growth advantages in certain environmental conditions. This study provides strong evidence for direct and critical roles of the environment on the evolution of genetic code alterations.
O código genético regula a correcta descodificação da informação contida nos genes durante a síntese de proteínas. Apresenta um elevado grau de conservação e estima-se que tenha sido originado há mais de 3.5 biliões de anos. Contudo, várias alterações ao código genético foram identificadas em procariotas e eucariotas, nomeadamente nos fungos denominados de “CTG clade”, nos quais um tRNA de serina atípico (tRNACAG Ser) descodifica o codão de leucina CUG como serina. Este tRNACAG Ser foi originado há 272±25 milhões de anos, pela inserção de uma adenosina no centro do anticodão do gene do tRNACGA Ser que alterou a sequência original do anticodão de 5´-CGA-3´ para 5´-CAG-3´. Esta alteração ao código genético promoveu a restruturação do proteoma das espécies denominadas de “CTG clade”. Contudo, permanece por esclarecer o motivo que permitiu que esta alteração atípica fosse preservada no genome destes fungos. Numa tentativa de clarificar os aspectos evolutivos desta alteração ao código genético, procedemos à reconstrução da via evolutiva, proposta para esta alteração, na levedura Saccharomyces cerevisiae. Para tal, induzimos a expressão do gene do tRNACGA Ser de C. albicans, nas versões mutantes e original, em S. cerevisiae e determinámos o impacto das mesmas no crescimento celular, bem como na estabilidade, eficiência na tradução e aminoacilação do tRNA. Os nossos dados, demonstram que as versões mutantes do tRNA, apesar de sua reduzida expressão, induzem a incorporação de serina nos codões CUG de leucina. Observámos ainda, através de uma estratégia de evolução forçada, que o tRNACAG Ser é facilmente inactivado por mutações naturais que impedem o seu reconhecimento pela seryl-tRNA synthetase. O nosso estudo demonstra que a repressão da expressão do tRNACAG Ser, terá desempenhado um papel fundamental na evolução da redefinição do codão CUG de leucina para serina. Com o intuito de compreender a evolução das alterações ao código genético, induzimos redefinições parciais em vários codões de levedura. Os nossos resultados confirmam que a ambiguidade no código genético afecta o crescimento, induz a produção de agregados proteicos, interfere no ciclo celular e promove alterações nucleares, morfológicas, instabilidade genómica e desregulação da expressão genética. Contudo, origina também variedade fenotípica e fenótipos vantajosos em determinadas condições ambientais. Este estudo demonstra o impacto do ambiente na evolução das alterações ao código genético.
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Gomes, Ana Catarina Batista. "Molecular evolution of a genetic code alteration." Doctoral thesis, Universidade de Aveiro, 2008. http://hdl.handle.net/10773/939.

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Doutoramento em Biologia
Durante os últimos anos, foram descritas alterações ao código genético, quer em procariotas, quer em eucariotas, quebrando o dogma de que o código genético é universal e imutável. Estudos recentes sugerem que a evolução de tais alterações requerem modificações ao nível da estrutura da maquinaria da tradução e são promovidas por mecanismos de descodificação ambígua. Em C. albicans, um organismo que é patogénico para o Homem, a alteração ao código genético é mediada por uma alteração na estrutura de um novo tRNACAG de serina que descodifica o codão CUG de leucina como serina. De forma a determinar se este tRNA, que é aminoacilado pelas Seryl- e Leucyl- tRNA sintetases, promove a descodificação ambígua do codão CUG, foi desenvolvido um sistema para a quantificar in vivo, por espectrometria de massa, os níveis de incorporação de serina e de leucina em codões CUG. Os resultados mostraram que em condições normais de crescimento leucina é incorporada a uma taxa de 3% e que serina é incorporada a uma taxa de 97%. No entanto, o nível de ambiguidade na descodificação de codões CUG aumentou para 5% em células crescidas em condições de stress, indicando que a incorporação de leucina em codões CUG é sensível a factores ambientais e é manipulada durante a tradução do mRNA. Tal, levanta a hipótese de que a incorporação de leucina poderá atingir níveis superiores aos determinados neste estudo. Para testar esta hipótese e determinar os níveis máximos de ambiguidade na descodificação do codão CUG tolerados pelas células, aumentou-se artificialmente a ambiguidade do codão CUG em C. albicans. Surpreendentemente, a incorporação de leucina subiu de 5% para 28%, o que representa um aumento na taxa de erro da tradução de 3500 vezes, relativamente ao descrito para o mecanismo de tradução. Dado existirem 13.000 codões CUG no genoma de C. albicans, a sua descodificação ambígua expande de uma forma exponencial o proteoma deste fungo, criando assim um proteoma estatístico, resultante da síntese de um conjunto de moléculas diferentes para cada proteína a partir de um único RNA mensageiro (mRNA) que contenha codões CUG. Os resultados obtidos demonstraram que o proteoma de C. albicans tem uma dimensão muito superior à prevista pelo seu genoma e demonstram um papel central da descodificação ambígua na evolução do código genético.
Alterations to the standard genetic code have been found in both prokaryotes and eukaryotes, demolishing the dogma of an immutable and universal genetic code. Recent studies suggest that evolution of such alterations require structural change of the translation machinery and are driven through mechanisms that require codon decoding ambiguity. In the human pathogen C. albicans, a structural change in a novel sertRNACAG allows for its recognition by both the LeuRS and SerRS in vitro and in vivo, providing such molecular device. In order to determine whether this tRNA charging ambiguity results in ambiguous CUG decoding, we have developed a system for quantification of the level of serine and leucine at the CUG codon by Mass-Spectrometry. The data showed that 3.0% of leucine and 97.0% of serine are incorporated at CUG codons in vivo under standard growth conditions. Moreover, this ambiguity increases up to 5.0% under stress, indicating that it is sensitive to environmental change and raising the hypothesis that leucine incorporation may be higher than determine experimentally. In order to determine the scope of C. albicans tolerance to CUG ambiguity, we have created highly ambiguous C. albicans cell lines through tRNA engineering. These cell lines tolerated up to 28% leucine incorporation at CUGs, which represents an increase of 3500 fold in decoding error rate. Since there are 13,000 CUG codons in C. albicans such ambiguity expands the proteome exponentially and creates a statistical proteome due to synthesis of arrays of protein molecules from mRNAs containing CUG codons. The overall data showed that the dimension of the C. albicans proteome is far higher than that predicted from its genome and provides important new evidence for a pivotal role for codon ambiguity in the evolution of the genetic code.
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Silva, Raquel Monteiro Marques da. "Molecular reconstruction of a genetic code alteration." Doctoral thesis, Universidade de Aveiro, 2005. http://hdl.handle.net/10773/948.

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Doutoramento em Biologia
Várias espécies de Candida traduzem o codão CUG de leucina como serina. Esta alteração ao código genético é mediada por um novo tRNA (sertRNACAG), que pode ser carregado com serina (97 %) e leucina (3 %) in vivo. Por esta razão o codão CUG é ambíguo, pois pode ser descodificado como serina ou leucina. Para elucidar o impacto da ambiguidade do código genético na expressão génica e na fisiologia da célula, o ser-tRNACAG de C. albicans foi expresso em Saccharomyces cerevisiae. Isto induz a descodificação ambígua do codão CUG, devido à competição entre o tRNA endógeno que traduz o codão CUG como leucina e o C. albicans ser-tRNACAG, que o traduz maioritariamente como serina. A caracterização do transcriptoma e do proteoma das linhas celulares manipuladas de S. cerevisiae mostra que a ambiguidade do código genético induz alterações globais na expressão de genes e proteínas, com alterações na resposta ao stress, metabolismo dos hidratos de carbono e dos aminoácidos, estrutura e função da parede celular, síntese e degradação de proteínas. Adicionalmente, os resultados indicam que a tradução errada do codão CUG regula a expressão génica ao nível da tradução. A ambiguidade do codão CUG gera instabilidade do proteoma e genoma, contudo, estas células não perdem viabilidade. Pelo contrário, os dados sugerem que a resposta ao stress despoletada pela ambiguidade do codão CUG aumenta o potencial de adaptação, como é demonstrado pela tolerância que as células ambíguas têm a várias condições de stress. Por estas razões, a reconstrução da alteração na descodificação do codão CUG providenciou dados importantes sobre o impacto que alterações ao código genético têm na adaptação e evolução das células. Este estudo também trouxe novas ideias acerca dos mecanismos que permitem a tolerância das células eucarióticas a elevados níveis de erro na tradução do mRNA.
Several Candida species translate the standard leucine CUG codon as serine. This genetic code alteration is mediated by a novel tRNA (ser-tRNACAG), which can be charged both with serine (97 %) and leucine (3%) in vivo. Therefore, the CUG codon is ambiguous, since it can be decoded either as serine or leucine. To elucidate the impact of genetic code ambiguity on gene expression and cell physiology, the C. albicans ser-tRNACAG was expressed in Saccharomyces cerevisiae. This induces ambiguous decoding of the CUG codon, due to competition between the endogenous tRNA that decodes the CUG codon as leucine and the C. albicans ser-tRNACAG, which decodes it mainly as serine. Transcriptome and proteome characterization of the engineered S. cerevisiae cell lines show that genetic code ambiguity induces global gene and protein expression changes, with alterations in the stress response, carbohydrate and amino acid metabolism, cell wall structure and function, protein synthesis and protein degradation. Additionally, the results indicate that CUG mistranslation regulates gene expression at the translational level. CUG ambiguity generates proteome and genome instability, however, these cells do not lose viability. Instead, the data suggests that the stress response triggered by CUG ambiguity increases adaptation potential, as shown by the tolerance of ambiguous cells to several stress conditions. Therefore, the reconstruction of the CUG reassignment pathway provided important insight on the impact that genetic code alterations have on cell adaptation and evolution. This study also sheds new light on the mechanisms that allow eukaryotic cells to tolerate high levels of mRNA mistranslation.
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Bezerra, Ana Rita Macedo. "Molecular genomics of a genetic code alteration." Doctoral thesis, Universidade de Aveiro, 2013. http://hdl.handle.net/10773/12499.

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Doutoramento em Biologia
The genetic code is not universal. Alterations to its standard form have been discovered in both prokaryotes and eukaryotes and demolished the dogma of an immutable code. For instance, several Candida species translate the standard leucine CUG codon as serine. In the case of the human pathogen Candida albicans, a serine tRNA (tRNACAGSer) incorporates in vivo 97% of serine and 3% of leucine in proteins at CUG sites. Such ambiguity is flexible and the level of leucine incorporation increases significantly in response to environmental stress. To elucidate the function of such ambiguity and clarify whether the identity of the CUG codon could be reverted from serine back to leucine, we have developed a forced evolution strategy to increase leucine incorporation at CUGs and a fluorescent reporter system to monitor such incorporation in vivo. Leucine misincorporation increased from 3% up to nearly 100%, reverting CUG identity from serine back to leucine. Growth assays showed that increasing leucine incorporation produced impressive arrays of phenotypes of high adaptive potential. In particular, strains with high levels of leucine misincorporation exhibited novel phenotypes and high level of tolerance to antifungals. Whole genome re-sequencing revealed that increasing levels of leucine incorporation were associated with accumulation of single nucleotide polymorphisms (SNPs) and loss of heterozygozity (LOH) in the higher misincorporating strains. SNPs accumulated preferentially in genes involved in cell adhesion, filamentous growth and biofilm formation, indicating that C. albicans uses its natural CUG ambiguity to increase genetic diversity in pathogenesis and drug resistance related processes. The overall data provided evidence for unantecipated flexibility of the C. albicans genetic code and highlighted new roles of codon ambiguity on the evolution of genetic and phenotypic diversity.
O código genético não é universal. Alterações à identidade de vários codões descobertas em procariotas e eucariotas invalidam a hipótese dum código genético universal e imutável. Por exemplo, várias espécies do género Candida traduzem o codão CUG de leucina como serina. Em Candida albicans, um único tRNA de serina (tRNACAGSer) incorpora in vivo 97% de serina e 3% de leucina nas proteínas em resposta a codões CUG presentes nos mRNAs deste fungo patogénico. Esta ambiguidade é flexível e a incorporação de leucina aumenta em condições de stress. De forma a elucidar a função desta ambiguidade e determinar se a identidade dos codões CUG podia ser revertida de serina para leucina, desenvolvemos uma estratégia de evolução forçada e uma proteína recombinante fluorescente cuja actividade depende da incorporação de leucina num codão CUG. Construímos estirpes que incorporam leucina nas proteínas em resposta a codões CUGs em níveis que variam entre 0,64% e 98,46%. Esta reversão de uma alteração ao código genético demostrou de modo inequívoco que o código é flexível e pode evoluir. Testes de crescimento em diferentes meios de cultivo revelaram uma série impressionante de fenótipos com elevado potencial adaptativo nas estirpes mais ambíguas, nomeadamente tolerância a antifúngicos. A sequenciação dos genomas das estirpes que construímos revelou que a ambiguidade do codão CUG resulta na acumulação de polimorfismos de nucleótido únicos (SNP) no genoma. Verificámos também perda de heterozigozidade (LOH) nos cromossomas 5 e R das estirpes que incorporam 80,84% e 98,46% de leucina em locais proteicos codificados por codões CUG. Os SNPs acumularam-se preferencialmente em genes envolvidos na adesão celular, no crescimento filamentoso e na formação de biofilmes, sugerindo que C. albicans utiliza a sua ambiguidade natural para aumentar a diversidade genética dos processos relacionados com a patogénese e resistência a drogas. Estes resultados evidenciam uma notável flexibilidade do código genético de C. albicans e revelam funções inesperadas da ambiguidade do código genético na evolução da diversidade genética e fenotípica.
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Lajoie, Marc Joseph. "Genome Engineering Technologies to Change the Genetic Code." Thesis, Harvard University, 2014. http://dissertations.umi.com/gsas.harvard:11265.

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New technologies are making it possible to engineer organisms with fundamentally new and useful properties. In vivo genome engineering technologies capable of manipulating genomes from the nucleotide to the megabase scale were developed and applied to reassign the genetic code of Escherichia coli. Such genomically recoded organisms show promise for thwarting horizontal gene transfer with natural organisms, resisting viral infection, and expanding the chemical properties of proteins.
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Jääskelä, E. (Esa). "Genetic algorithm in code coverage guided fuzz testing." Master's thesis, University of Oulu, 2016. http://urn.fi/URN:NBN:fi:oulu-201601151058.

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The security of computers is a growing concern when the amount of devices increases. New and more comprehensive testing methods need to be done to avoid damages to the users and their computers. Fuzzing is a testing method that inserts semi-valid input to the tested system and has before been considered as a good method for the security testing. However, it usually either does not get high code coverage or it requires a long set-up process or a source code analysis to achieve better code coverage. This work presents a genetic algorithm that automatically balances the probabilities of multiple mutators in a fuzzing program. This balancing aims to maximize the code coverage fuzz testing. After fuzzing two different open source libraries it was found that the grey-box approach in fuzzing gives better results than pure black-box fuzzing
Tietokoneiden tietoturva on kasvava huolenaihe, kun laitteiden määrä lisääntyy. Uusia ja kattavampia testauksia täytyy suorittaa, jotta voidaan estää käyttäjille ja heidän laitteilleen tapahtuvat vahingot. Fuzzausta on pidetty hyvänä testausmetodina, mutta yleensä se ei saavuta hyvää koodikattavuutta tai vaatii joko monimutkaisen asennuksen tai lähdekoodianalyysin. Tämä työ esittelee geneettisen algoritmin, joka automaattisesti tasapainottaa fuzzerin eri mutaatiofunktioiden todennäköisyydet. Tämä tasapainotus pyrkii maksimoimaan saavutetun koodikattavuuden ja parantamaan fuzzaamisen tehokkuutta. Kahden avoimen lähdekoodin kirjaston testaamisen perusteella mutatorit koodikattavuuden perusteella tasapainottava työkalu pärjäsi paremmin kuin perinteinen, lisätietoa hyödyntämätön black-box fuzzaus
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Books on the topic "Genetic code"

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National Institutes of Health (U.S.). Clinical Center, ed. Breaking the genetic code. [Bethesda, Md.?]: Clinical Center, National Institutes of Health, 1998.

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National Institutes of Health (U.S.). Clinical Center, ed. Breaking the genetic code. [Bethesda, Md.?]: Clinical Center, National Institutes of Health, 1995.

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Ōsawa, Shōzō. Evolution of the genetic code. Oxford: Oxford University Press, 1995.

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Silverstein, Alvin. The code of life. Mineola, N.Y: Dover Publications, 2004.

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Trifonov, Edward N. Gnomic: A dictionary of genetic codes. [Rehovot, Israel?]: Balaban, 1986.

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Moody, Glyn. Digital Code of Life. New York: John Wiley & Sons, Ltd., 2004.

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Maurel, Marie-Christine. Programme génétique: Concept biologique ou métaphore? Paris: Éditions Kimé, 2001.

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I, Kozlov N. Matematicheskiĭ analiz geneticheskogo koda. Moskva: Binom. Laboratorii︠a︡ znaniĭ, 2010.

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Takeo, Takeyama, ed. Messenger RNA research perspectives. New York: Nova Science Publishers, 2008.

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Farabaugh, Philip J. Programmed Alternative Reading of the Genetic Code. Boston, MA: Springer US, 1997. http://dx.doi.org/10.1007/978-1-4615-5999-3.

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Book chapters on the topic "Genetic code"

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Peck, Stewart B., Carol C. Mapes, Netta Dorchin, John B. Heppner, Eileen A. Buss, Gustavo Moya-Raygoza, Marjorie A. Hoy, et al. "Genetic Code." In Encyclopedia of Entomology, 1595. Dordrecht: Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-6359-6_1055.

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Mierke, Claudia Tanja. "Genetic Code." In Cellular Mechanics and Biophysics, 417–75. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-58532-7_11.

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Nahler, Gerhard. "genetic code." In Dictionary of Pharmaceutical Medicine, 80. Vienna: Springer Vienna, 2009. http://dx.doi.org/10.1007/978-3-211-89836-9_596.

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Freeland, Stephen. "Genetic Code." In Encyclopedia of Astrobiology, 1–5. Berlin, Heidelberg: Springer Berlin Heidelberg, 2014. http://dx.doi.org/10.1007/978-3-642-27833-4_630-2.

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Freeland, Stephen. "Genetic Code." In Encyclopedia of Astrobiology, 933–37. Berlin, Heidelberg: Springer Berlin Heidelberg, 2015. http://dx.doi.org/10.1007/978-3-662-44185-5_630.

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Freeland, Stephen. "Genetic Code." In Encyclopedia of Astrobiology, 639–42. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-11274-4_630.

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Gooch, Jan W. "Genetic Code." In Encyclopedic Dictionary of Polymers, 895. New York, NY: Springer New York, 2011. http://dx.doi.org/10.1007/978-1-4419-6247-8_13816.

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Kumar, Sanjay, and Akanksha Kushwaha. "Genetic Code." In Encyclopedia of Animal Cognition and Behavior, 1–3. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-47829-6_4-1.

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Kumar, Sanjay, and Akanksha Kushwaha. "Genetic Code." In Encyclopedia of Animal Cognition and Behavior, 2903–6. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-319-55065-7_4.

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Freeland, Stephen. "Genetic Code." In Encyclopedia of Astrobiology, 1137–41. Berlin, Heidelberg: Springer Berlin Heidelberg, 2023. http://dx.doi.org/10.1007/978-3-662-65093-6_630.

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Conference papers on the topic "Genetic code"

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Browne, Will N. "Code Fragments." In GECCO '16: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2016. http://dx.doi.org/10.1145/2908961.2931737.

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Pantridge, Edward, and Lee Spector. "Code building genetic programming." In GECCO '20: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2020. http://dx.doi.org/10.1145/3377930.3390239.

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Abdullah, Alyasa Gan, and Yap Bee Wah. "Genetic code for sine." In THE 2ND ISM INTERNATIONAL STATISTICAL CONFERENCE 2014 (ISM-II): Empowering the Applications of Statistical and Mathematical Sciences. AIP Publishing LLC, 2015. http://dx.doi.org/10.1063/1.4907519.

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Petke, Justyna. "Genetic Improvement for Code Obfuscation." In GECCO '16: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2016. http://dx.doi.org/10.1145/2908961.2931689.

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Pantridge, Edward, Thomas Helmuth, and Lee Spector. "Functional code building genetic programming." In GECCO '22: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2022. http://dx.doi.org/10.1145/3512290.3528866.

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Reid, Brittany, Christoph Treude, and Markus Wagner. "Optimising the fit of stack overflow code snippets into existing code." In GECCO '20: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2020. http://dx.doi.org/10.1145/3377929.3398087.

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Silva, Maísa de Carvalho, Lariza Laura De Oliveira, and Renato Tinós. "Optimization of Expanded Genetic Codes via Genetic Algorithms." In XV Encontro Nacional de Inteligência Artificial e Computacional. Sociedade Brasileira de Computação - SBC, 2018. http://dx.doi.org/10.5753/eniac.2018.4440.

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In the last decades, researchers have proposed the use of genetically modified organisms that utilize unnatural amino acids, i.e., amino acids other than the 20 amino acids encoded in the standard genetic code. Unnatural amino acids have been incorporated into genetically engineered organisms for the development of new drugs, fuels and chemicals. When new amino acids are incorporated, it is necessary to modify the standard genetic code. Expanded genetic codes have been created without considering the robustness of the code. The objective of this work is the use of genetic algorithms (GAs) for the optimization of expanded genetic codes. The GA indicates which codons of the standard genetic code should be used to encode a new unnatural amino acid. The fitness function has two terms; one for robustness of the new code and another that takes into account the frequency of use of amino acids. Experiments show that, by controlling the weighting between the two terms, it is possible to obtain more or less amino acid substitutions at the same time that the robustness is minimized.
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Sicot, Guillaume, and Ramesh Pyndiah. "Study on the genetic code: comparison with multiplexed codes." In 2007 IEEE International Symposium on Information Theory. IEEE, 2007. http://dx.doi.org/10.1109/isit.2007.4557621.

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Liou, Jhe-Yu, Stephanie Forrest, and Carole-Jean Wu. "Genetic Improvement of GPU Code." In 2019 IEEE/ACM International Workshop on Genetic Improvement (GI). IEEE, 2019. http://dx.doi.org/10.1109/gi.2019.00014.

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Sheikh, Hafiz Fahad, Haroon Atique Babri, and Masood Ahmad. "Genetic code based fractals generation." In 2009 Third International Conference on Electrical Engineering (ICEE). IEEE, 2009. http://dx.doi.org/10.1109/icee.2009.5173171.

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Reports on the topic "Genetic code"

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Rintoul, Mark Daniel, Elebeoba Eni May, William Michael Brown, Anna Marie Johnston, and Jean-Paul Watson. Deciphering the genetic regulatory code using an inverse error control coding framework. Office of Scientific and Technical Information (OSTI), March 2005. http://dx.doi.org/10.2172/922758.

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Woese, Carl R., Nigel Goldenfeld, and Zaida Luthey-Schulten. Role of horizontal gene transfer as a control on the coevolution of ribosomal proteins and the genetic code. Office of Scientific and Technical Information (OSTI), March 2011. http://dx.doi.org/10.2172/1010449.

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Bennett, Alan B., Arthur Schaffer, and David Granot. Genetic and Biochemical Characterization of Fructose Accumulation: A Strategy to Improve Fruit Quality. United States Department of Agriculture, June 2000. http://dx.doi.org/10.32747/2000.7571353.bard.

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The goal of the research project was to evaluate the potential to genetically modify or engineer carbohydrate metabolism in tomato fruit to enhance levels of fructose, a sugar with nearly twice the sweetness value of other sugars. The specific research objectives to achieve that goal were to: 1. Establish the inheritance of a fructose-accumulating trait identified in F1 hybrids of an inferspecific cross between L. hirsutum XL. esculentum and identify linked molecular markers to facilitate its introgression into tomato cultivars. This objective was completed with the genetic data indicating a single major gene, termed Fgr (Fructose glucose ratio), that controlled the partitioning of hexose in the mature fruit. Molecular markers for the gene, were developed to aid introgression of this gene into cultivated tomato. In addition, a second major gene encoding fructokinase 2 (FK2) was found to be a determinant of the fructose to glucose ratio in fruit. The relationship between FK2 and Fgr is epistatic with a combined synergistic effect of the two hirsutum-derived genes on fructose/glucose ratios. 2. Characterize the metabolic and transport properties responsible for high fructose/glucose ratios in fructose-accumulating genotypes. The effect of both the Fgr and FK2 genes on the developmental accumulation of hexoses was studied in a wide range of genetic backgrounds. In all backgrounds the trait is a developmental one and that the increase in fructose to glucose ratio occurs at the breaker stage of fruit development. The following enzymes were assayed, none of which showed differences between genotypes, at either the breaker or ripe stage: invertase, sucrose synthase, FK1, FK2, hexokinase, PGI and PGM. The lack of effect of the FK2 gene on fructokinase activity is surprising and at present we have no explanation for the phenomenon. However, the hirsutum derived Fgr allele was associated with significantly lower levels of phosphorylated glucose, G1c-1-P and G1c-6-P and concomitantly higher levels of the phosphorylated fructose, Fru-6-P, in both the breaker and ripe stage. This suggests a significant role for the isomerase reaction. 3. Develop and implement molecular genetic strategies for the production of transgenic plants with altered levels of enzymes that potentially control fructose/glucose ratios in fruit. This objective focused on manipulating hexokinase and fructokinase expression in transgenic plants. Two highly divergent cDNA clones (Frk1 and Frk2), encoding fructokinase (EC 2.7.1.4), were isolated from tomato (Lycopersicon esculentum) and a potato fructokinase cDNA clone was obtained from Dr. Howard Davies. Following expression in yeast, each fructokinase was identified to code for one of the tomato or potato fructokinase isoforms Transgenic tomato plants were generated with the fructokinase cDNA clone in both sense and antisense orientations and the effect of the gene on tomato plants is currently being studied.
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Moneghan, Daniel, Abdalla Abou-Jaoude, Chandrakanth Bolisetti, Ishita Trivedi, D. Lutchenkov, Patrick Ayerle, and Robert Langhans. A Generic Nuclear Code of Accounts for Cost Estimation Standardization. Office of Scientific and Technical Information (OSTI), March 2024. http://dx.doi.org/10.2172/2324771.

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van der Mensbrugghe, Dominique. Using Python for Parallelization. GTAP Working Paper, April 2023. http://dx.doi.org/10.21642/gtap.wp93.

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This short note describes one way of taking advantage of the multiple cores on most desktop computers. It describes running one of the processes in the GTAP build procedure called ’FIT’. The input to ’FIT’ is a balanced input-output table (IOT), which is adjusted to a number of exogenous elements including aggregate domestic absorption and import and export vectors. It is run for each of the countries/regions in the build, but there is no interaction across countries/regions and thus can be run in parallel. The procedure uses a Python script to run the ’FIT’ procedure, either sequentially or in parallel. Most of the code is generic and thus it can be easily adapted to other programs that can take advantage of parallelism, for example Monte Carlo simulations. For the tested ’FIT’ procedure, it reduces the runtime from 75 minutes to 14 minutes on a relatively new desktop with a 12th Generation Intel Core I-9 CPU with 16 physical cores.
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Owcarski, P., K. Burk, J. Ramsdell, and D. Yasuda. FPFP 2: A code for following airborne fission products in generic nuclear plant flow paths. Office of Scientific and Technical Information (OSTI), March 1991. http://dx.doi.org/10.2172/6116361.

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Droby, Samir, Michael Wisniewski, Martin Goldway, Wojciech Janisiewicz, and Charles Wilson. Enhancement of Postharvest Biocontrol Activity of the Yeast Candida oleophila by Overexpression of Lytic Enzymes. United States Department of Agriculture, November 2003. http://dx.doi.org/10.32747/2003.7586481.bard.

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Enhancing the activity of biocontrol agents could be the most important factor in their success in controlling fruit disease and their ultimate acceptance in commercial disease management. Direct manipulation of a biocontrol agent resulting in enhancement of diseases control could be achieved by using recent advances in molecular biology techniques. The objectives of this project were to isolate genes from yeast species that were used as postharvest biocontrol agents against postharvest diseases and to determine their role in biocontrol efficacy. The emphasis was to be placed on the yeast, Candida oleophila, which was jointly discovered and developed in our laboratories, and commercialized as the product, Aspire. The general plan was to develop a transformation system for C . oleophila and either knockout or overexpress particular genes of interest. Additionally, biochemical characterization of the lytic peptides was conducted in the wild-type and transgenic isolates. In addition to developing a better understanding of the mode of action of the yeast biocontrol agents, it was also our intent to demonstrate the feasibility of enhancing biocontrol activity via genetic enhancement of yeast with genes known to code for proteins with antimicrobial activity. Major achievements are: 1) Characterization of extracellular lytic enzymes produced by the yeast biocontrol agent Candida oleophila; 2) Development of a transformation system for Candida oleophila; 3) Cloning and analysis of C.oleophila glucanase gene; 4) Overexpression of and knockout of C. oleophila glucanase gene and evaluating its role in the biocontrol activity of C. oleophila; 5) Characterization of defensin gene and its expression in the yeast Pichiapastoris; 6) Cloning and Analysis of Chitinase and Adhesin Genes; 7) Characterization of the rnase secreted by C . oleophila and its inhibitory activity against P. digitatum. This project has resulted in information that enhanced our understanding of the mode of action of the yeast C . oleophila. This was important step towards enhancing the biocontrol activity of the yeast. Fungal cell wall enzymes produced by the yeast antagonist were characterized. Different substrates were identified to enhance there production in vitro. Exo-b-1, 3 glucanase, chitinase and protease production was stimulated by the presence of cell-wall fragments of Penicillium digitatum in the growing medium, in addition to glucose. A transformation system developed was used to study the role of lytic enzymes in the biocontrol activity of the yeast antagonist and was essential for genetic manipulation of C . oleqphila. After cloning and characterization of the exo-glucanase gene from the yeast, the transformation system was efficiently used to study the role of the enzyme in the biocontrol activity by over-expressing or knocking out the activity of the enzyme. At the last phase of the research (still ongoing) the transformation system is being used to study the role of chitinase gene in the mode of action. Knockout and over expression experiments are underway.
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Paul, Satashree. The Criminal Behavior of Genes. Science Repository OÜ, November 2020. http://dx.doi.org/10.31487/sr.blog.14.

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Identifying the crucial role of genetics in criminal behavior implies there must be something known as a “Crime Gene”. Genes come out as the strongest predictor of whether a person has predisposition towards crime or any criminal behavior.
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Bruce, Bill, Melissa Gould, Tom Bubenik, Chris Alexander, and Michael Rosenfeld. PR-186-204504-R01 PRCI Pipeline Repair Manual 2021 Edition. Chantilly, Virginia: Pipeline Research Council International, Inc. (PRCI), April 2022. http://dx.doi.org/10.55274/r0012221.

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This 2021 Edition of the PRCI Pipeline Repair Manual is an updated version of the original manual that was published 1994 and updated in 2006. The 2021 Edition discusses response to anomaly or defect discovery, reviews repair methods, identifies appropriate repairs for various types of defects, and provides generic guidelines for use of various repair methods. DNV has reviewed existing and emerging pipeline repair technologies and evaluated them in comparison with those in the previous versions of the manual. The review was based on published literature, vendor literature, and industry experience. The 2021 Edition of the Pipeline Repair Manual contains added and updated information on repair technologies gleaned from the literature, vendor publications, and industry experience. Without losing sight of well-established repair methods that have served the industry well, the most recent update focused on repair methods and practices that are commonplace or have emerged and have become commonplace since the previous version of the manual was published. This manual does not identify or prescribe all repair methods for all defects or anomalies. Instead, the manual concentrates on commonly encountered defects and commonly used repair methodologies for those defects. Other repair techniques may be equally valid depending on the specific conditions encountered. This 2021 Edition of the manual does not provide specific guidance on current regulations or on code interpretation. National and international codes and regulations change rapidly, and code interpretation is best left to individual companies. Footnotes identify specific pertinent sections of selected US regulations. Click here for related webinar.
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Gur, Amit, Edward Buckler, Joseph Burger, Yaakov Tadmor, and Iftach Klapp. Characterization of genetic variation and yield heterosis in Cucumis melo. United States Department of Agriculture, January 2016. http://dx.doi.org/10.32747/2016.7600047.bard.

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Project objectives: 1) Characterization of variation for yield heterosis in melon using Half-Diallele (HDA) design. 2) Development and implementation of image-based yield phenotyping in melon. 3) Characterization of genetic, epigenetic and transcriptional variation across 25 founder lines and selected hybrids. The epigentic part of this objective was modified during the course of the project: instead of characterization of chromatin structure in a single melon line through genome-wide mapping of nucleosomes using MNase-seq approach, we took advantage of rapid advancements in single-molecule sequencing and shifted the focus to Nanoporelong-read sequencing of all 25 founder lines. This analysis provides invaluable information on genome-wide structural variation across our diversity 4) Integrated analyses and development of prediction models Agricultural heterosis relates to hybrids that outperform their inbred parents for yield. First generation (F1) hybrids are produced in many crop species and it is estimated that heterosis increases yield by 15-30% globally. Melon (Cucumismelo) is an economically important species of The Cucurbitaceae family and is among the most important fleshy fruits for fresh consumption Worldwide. The major goal of this project was to explore the patterns and magnitude of yield heterosis in melon and link it to whole genome sequence variation. A core subset of 25 diverse lines was selected from the Newe-Yaar melon diversity panel for whole-genome re-sequencing (WGS) and test-crosses, to produce structured half-diallele design of 300 F1 hybrids (MelHDA25). Yield variation was measured in replicated yield trials at the whole-plant and at the rootstock levels (through a common-scion grafted experiments), across the F1s and parental lines. As part of this project we also developed an algorithmic pipeline for detection and yield estimation of melons from aerial-images, towards future implementation of such high throughput, cost-effective method for remote yield evaluation in open-field melons. We found extensive, highly heritable root-derived yield variation across the diallele population that was characterized by prominent best-parent heterosis (BPH), where hybrids rootstocks outperformed their parents by 38% and 56 % under optimal irrigation and drought- stress, respectively. Through integration of the genotypic data (~4,000,000 SNPs) and yield analyses we show that root-derived hybrids yield is independent of parental genetic distance. However, we mapped novel root-derived yield QTLs through genome-wide association (GWA) analysis and a multi-QTLs model explained more than 45% of the hybrids yield variation, providing a potential route for marker-assisted hybrid rootstock breeding. Four selected hybrid rootstocks are further studied under multiple scion varieties and their validated positive effect on yield performance is now leading to ongoing evaluation of their commercial potential. On the genomic level, this project resulted in 3 layers of data: 1) whole-genome short-read Illumina sequencing (30X) of the 25 founder lines provided us with 25 genome alignments and high-density melon HapMap that is already shown to be an effective resource for QTL annotation and candidate gene analysis in melon. 2) fast advancements in long-read single-molecule sequencing allowed us to shift focus towards this technology and generate ~50X Nanoporesequencing of the 25 founders which in combination with the short-read data now enable de novo assembly of the 25 genomes that will soon lead to construction of the first melon pan-genome. 3) Transcriptomic (3' RNA-Seq) analysis of several selected hybrids and their parents provide preliminary information on differentially expressed genes that can be further used to explain the root-derived yield variation. Taken together, this project expanded our view on yield heterosis in melon with novel specific insights on root-derived yield heterosis. To our knowledge, thus far this is the largest systematic genetic analysis of rootstock effects on yield heterosis in cucurbits or any other crop plant, and our results are now translated into potential breeding applications. The genomic resources that were developed as part of this project are putting melon in the forefront of genomic research and will continue to be useful tool for the cucurbits community in years to come.
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