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Class I and II aminoacyl-tRNA synthetase tRNA groove discrimination created the first synthetase-tRNA cognate pairs and was therefore essential to the origin of genetic coding

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IUBMB LIFE 2019年第8期71卷 1088-1098页

作者： Carter, Charles W., Jr. Wills, Peter R. Univ N Carolina Dept Biochem & Biophys Chapel Hill NC 27515 USA Univ Auckland Dept Phys Auckland New Zealand Univ Auckland Te Ao Marama Ctr Fundamental Inquiry Auckland New Zealand

The genetic code likely arose when a bidirectional gene replicating as a quasi-species began to produce ancestral aminoacyl-tRNA synthetases (aaRS) capable of distinguishing between two distinct sets of amino acids. The synthetase class division therefore necessarily implies a mechanism by which the two ancestral synthetases could also discriminate between two different kinds of tRNA substrates. We used regression methods to uncover the possible patterns of base sequences capable of such discrimination and find that they appear to be related to thermodynamic differences in the relative stabilities of a hairpin necessary for recognition of tRNA substrates by Class I aaRS. The thermodynamic differences appear to be exploited by secondary structural differences between models for the ancestral aaRS called synthetase Urzymes and reinforced by packing of aromatic amino acid side chains against the nonpolar face of the ribose of A76 if and only if the tRNA CCA sequence forms a hairpin. The patterns of bases 1, 2, and 73 and stabilization of the hairpin by structural complementarity with Class I, but not Class II, aaRS Urzymes appear to be necessary and sufficient to have enabled the generation of the first two aaRS-tRNA cognate pairs, and the launch of a rudimentary binary genetic coding related recognizably to contemporary cognate pairs. As a consequence, it seems likely that nonrandom aminoacylation of tRNAs preceded the advent of the tRNA anticodon stem-loop. Consistent with this suggestion, coding rules in the acceptor-stem bases also reveal a palimpsest of the codon-anticodon interaction, as previously proposed. (c) 2019 IUBMB Life, 2019 (c) 2019 IUBMB Life, 71(8):1088-1098, 2019

关键词： genetic coding multiple regression molecular reflexivity codon-anticodon pairing reduced alphabets helical stability protein secondary structure

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Underwater Target Classification Based on Feature Fusion and Gene Encoding of CNN-BIGRU-Attention

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IEEE ACCESS 2023年 11卷 139546-139556页

作者： Feng, Ziyi Zhang, Peizhen Huo, Xinze Guangdong Ocean Univ Coll Elect & Informat Engn Zhanjiang 524088 Peoples R China

Towards addressing the issues of poor image quality and limited sample quantity in underwater sonar images. A genetic encoding method for the fusion of image spot and local binary pattern texture features is employed in this study. By encoding the fusion features using genetic algorithms, the dimensionality of the fused features is reduced, thereby enhancing the efficiency of neural network operations while ensuring data transmission confidentiality. Additionally, a deep multi-classifier is introduced, which combines residual units with CNN-BiGRU-Attention. This classifier takes the genetically encoded fused features as input and outputs four predicted probabilities. Through an ensemble learning strategy that evenly assigns weights to the predicted probabilities, the final prediction result is obtained, achieving underwater target recognition. Results demonstrate that the proposed fusion features effectively enlarge inter-class differences among various types of sonar images and improve classifier accuracy. The deep multi-classifier model exhibits stable improvement in prediction accuracy compared to the original model, converging after only 15 training iterations with an average recognition accuracy of 99.1%. The research findings offer an effective approach for target sonar image recognition and classification, with potential applicability to a wider range of underwater target categorization.

关键词： Attention BiGRU feature fusion genetic coding sonar image underwater target

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An Optimized Neural Network Prediction Model for Reservoir Porosity Based on Improved Shuffled Frog Leaping Algorithm

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INTERNATIONAL JOURNAL OF COMPUTATIONAL INTELLIGENCE SYSTEMS 2022年第1期15卷 1-19页

作者： Liu, Miaomiao Yao, Dan Guo, Jingfeng Chen, Jing Northeast Petr Univ Sch Comp & Informat Technol Daqing 163318 Peoples R China Key Lab Petr Big Data & Intelligent Anal Heilongj Daqing 163318 Peoples R China Yanshan Univ Coll Informat Sci & Engn Qinhuangdao 066000 Hebei Peoples R China

Efficient and accurate porosity prediction is essential for the fine description of reservoirs, for which an optimized BP neural network (BPNN) prediction model is proposed. Aiming at the problem that the BPNN is sensitive to initialization and converges to local optimum easily, an improved shuffled frog leaping algorithm (ISFLA) is proposed based on roulette and genetic coding. Firstly, a roulette mechanism is introduced to improve the selection probability of elite individuals, thus enhancing the global optimization ability. Secondly, a genetic coding method is carried out by making full use of effective information such as the global and local optimal solutions and the boundary values of subgroups. Subsequently, the ISFLA algorithm is verified on 12 benchmark functions and compared with four intelligent optimization algorithms, and experimental results show its good optimization performance. Finally, the ISFLA algorithm is applied to the optimization of initial weights and thresholds of the BPNN, and a new model named ISFLA_BP is proposed to study the porosity prediction problem. The logging data is preprocessed by grey correlation analysis and deviation normalization, and then the effective prediction of porosity is achieved by natural gamma, density and other relevant parameters. The performance of ISFLA_BP model is compared with the standard three-layer BPNN and four BPNN parameter optimization methods based on swarm intelligence algorithms. Experimental results show that the proposed model has higher training accuracy, stability and faster convergence speed, with a mean square error of 0.02, and its prediction accuracy for porosity is higher than that of the other five methods.

关键词： BP neural network Shuffled frog leaping algorithm Roulette genetic coding Porosity prediction

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Developing a Pareto Front for Thermally Processed Loose Biomass

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Journal of Energy Resources Technology, Part A: Sustainable and Renewable Energy 2025年第3期1卷 031902页

作者： Dhaundiyal, Alok https://***/05wswj918Centre for Energy Research Konkoly-Thege Miklos 1121 Budapest Hungary

This investigation focused on the optimization of pre-treatment conditions of pine waste. The genetic algorithm was applied to determine local Pareto sets of the objective functio... 详细信息

This investigation focused on the optimization of pre-treatment conditions of pine waste. The genetic algorithm was applied to determine local Pareto sets of the objective functions of the ash content obtained after proximate analyses of torrefied samples of pine waste (needles), energy consumption during torrefaction, energy yield, fuel value index, severity factor, and energy-mass co-benefit index. The milled form of pine waste samples underwent torrefaction for 5 min, 10 min, and 15 min at temperatures of 210 °C, 220 °C, 230 °C, 240 °C, and 250 °C. The energy dispersive spectroscopy of pine waste after pretreatment was also considered to evaluate the impact of processing parameters on the elemental composition of organic/inorganic content presented in pine waste. The torrefaction condition to minimize the ash content and maximize the volumetric energy density would occur at 249.98 °C for a residence period of 5 min. The torrefaction of pine waste must be performed at 217.24 °C for 15 min to minimize the electricity consumption of an improvised unit. The energy yield obtained experimentally at 250 °C for 5 min showed a consensus with the corresponding solution obtained through the genetic programming. The Pareto front developed for the selected parameters provided a good consensus with the empirical results. The percentage of Ca and Fe contents dropped by 84% and 50% in thermally processed pine waste, respectively.

关键词： renewable energy sources Pareto frontier machine learning spectroscopy genetic coding processed biomass

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Is BCH Code Useful to DNA Classification as an Alignment-Free Method?

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IEEE ACCESS 2021年 9卷 68552-68560页

作者： Arruda, Milena M. De Assis, Francisco M. De Souza, Taciana A. Univ Fed Campina Grande Dept Elect Engn BR-58429970 Campina Grande Paraiba Brazil Fed Inst Paraiba Dept Math BR-58900000 Cajazeiras Brazil

Similarities between biological and digital communication systems have been investigated since biology also uses a discrete alphabet to represent and transmit information. The genetic information of an organism is encoded in DNA molecules by units called bases. However, there is no a definitive model and the question as what error-correcting code underlies DNA sequences remains an open problem. Recent works show that DNA sequences can be identified as codewords in a class of cyclic error-correcting codes known as BCH codes. We propose improvements regarding the code construction process that resulted in a novel algorithm for searching BCH codes whose codeword differ from a given DNA sequence (mapped to finite field F-4) in up to only one symbol. The most important improvement is to replace brute force decoding with syndrome decoding. In this sense, based on a statistical analysis, we verify whether in a collection of sequences with the same taxonomic rank there is a code that identifies most of these sequences, called dominant code. Furthermore, we check whether the dominant code can provides a biological information to DNA classification being an alignment-free method. Finally, we show that the probability of a DNA sequences with odd-length n be identified by a BCH code tends to analytical probability of the same code identifying a random vector.

关键词： BCH codes DNA sequences error-correcting codes finite field genetic coding genomic signal processing

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Procedure for Identifying Odd-sized Nucleotide Sequences as Codewords of BCH Codes over GF(4)

Procedure for Identifying Odd-sized Nucleotide Sequences as ...

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IEEE International Symposium on Information Theory (ISIT)

作者： Rodriguez-Sarmiento, D. L. Duarte-Gonzalez, M. E. Rodriguez-Quinones, T. Palazzo, Reginaldo, Jr. Antonio Narino Univ FIMEB Bogota Colombia Antonio Narino Univ FIS Bogota Colombia Univ Estadual Campinas FEEC Campinas SP Brazil

ISBN: (纸本)9781538692912

In order to understand how biological information within DNA and RNA biosignals is preserved, several works have proposed that these biosequences can be identified as codewords of BCH error correcting codes over GF(4) (F-4). The current mathematical tool, used to perform such identification, has some limitations: one of them being the need of knowing all binary primitive polynomials and the other one is essentially due to the constraint imposed by the cyclic code construction leading to a restriction regarding the nucleotide sequence lengths. In this work, a novel algorithm for identifying odd-length nucleotide sequences as codewords of BCH codes over GF(4) is presented. As a result more than 270 cDNA sequences of nine different lengths, which could not be considered by the previous algorithm, are identified as codewords of 35 BCH codes.

关键词： BCH codes genetic coding DNA RNA Galois fields

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Reflexivity, coding and quantum biology

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BIOSYSTEMS 2019年 185卷 104027-000页

作者： Wills, Peter R. Univ Auckland Dept Phys PB 92109 Auckland 1142 Aotearoa New Zealand Univ Auckland Te Ao Marama Ctr Fundamental Inquiry PB 92109 Auckland 1142 Aotearoa New Zealand Free Univ Inst Biol Human Biol Konigin Luise Str 1-3 D-14195 Berlin Germany

Biological systems are fundamentally computational in that they process information in an apparently purposeful fashion rather than just transferring bits of it in a purely syntactical manner. Biological information, such has genetic information stored in DNA sequences, has semantic content. It carries meaning that is defined by the molecular context of its cellular environment. Information processing in biological systems displays an inherent reflexivity, a tendency for the computational information-processing to be "about" the behaviour of the molecules that participate in the computational process. This is most evident in the operation of the genetic code, where the specificity of the reactions catalysed by the aminoacyl-tRNA synthetase (aaRS) enzymes is required to be self-sustaining. A cell's suite of aaRS enzymes completes a reflexively autocatalytic set of molecular components capable of making themselves through the operation of the code. This set requires the existence of a body of reflexive information to be stored in an organism's genome. The genetic code is a reflexively self-organised mapping of the chemical properties of amino acid sidechains onto codon "tokens". It is a highly evolved symbolic system of chemical self-description. Although molecular biological coding is generally portrayed in terms of classical bit-transfer events, various biochemical events explicitly require quantum coherence for their occurrence. Whether the implicit transfer of quantum information, qbits, is indicative of wide-ranging quantum computation in living systems is currently the subject of extensive investigation and speculation in the field of Quantum Biology.

关键词： genetic coding Reflexivity Quantum biology Information Autocatalysis Aminoacyl-tRRNA synthetase (aaRS)

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Heterogeneity-mediated cellular adaptation and its trade-off: searching for the general principles of diseases

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JOURNAL OF EVALUATION IN CLINICAL PRACTICE 2017年第1期23卷 233-237页

作者： Heng, Henry H. Wayne State Univ Sch Med Ctr Mol Med & Genet Detroit MI 48201 USA Wayne State Univ Sch Med Dept Pathol Detroit MI 48201 USA

Big-data-omics have promised the success of precision medicine. However, most common diseases belong to adaptive systems where the precision is all but difficult to achieve. In this commentary, I propose a heterogeneity-mediated cellular adaptive model to search for the general model of diseases, which also illustrates why in most non-infectious non-Mendelian diseases the involvement of cellular evolution is less predictable when gene profiles are used. This synthesis is based on the following new observations/concepts: 1) the gene only codes parts inheritance while the genome codes system inheritance or the entire blueprint;2) the nature of somatic genetic coding is fuzzy rather than precise, and genetic alterations are not just the results of genetic error but are in fact generated from internal adaptive mechanisms in response to environmental dynamics;3) stress-response is less specific within cellular evolutionary context when compared to known biochemical specificities;and 4) most medical interventions have their unavoidable uncertainties and often can function as negative harmful stresses as trade-offs. The acknowledgment of diseases as adaptive systems calls for the action to integrate genome- (not simply individual gene-) mediated cellular evolution into molecular medicine.

关键词： Adaptive system cellular evolution common mechanism of diseases fuzzy inheritance genetic coding genome theory heterogeneity stress-response system inheritance

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DNA as information

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PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES 2016年第2063期374卷 20150417页

作者： Wills, Peter R. Univ Auckland Dept Phys POB 92019 Auckland 1142 New Zealand Univ Hamburg Inst Biochem & Mol Biol Martin Luther King Pl 6 D-20146 Hamburg Germany Univ N Carolina Dept Biochem & Biophys 120 Mason Farm Rd Chapel Hill NC 27599 USA

This article reviews contributions to this theme issue covering the topic 'DNA as information' in relation to the structure of DNA, the measure of its information content, the role and meaning of information in biology and the origin of genetic coding as a transition from uninformed to meaningful computational processes in physical systems.

关键词： DNA information nominable entities aperiodic crystal meaning genetic coding

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Emergence of coding and its Specificity as a Physico-Informatic Problem

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ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES 2015年第1-2期45卷 249-255页

作者： Wills, Peter R. Nieselt, Kay McCaskill, John S. Univ Auckland Dept Phys Auckland 1142 New Zealand Univ Tubingen Ctr Bioinformat Integrat Transcript D-72076 Tubingen Germany Ruhr Univ Bochum Microsyst Chem & BioIT BioMIP Fac Chem & Biochem D-44801 Bochum Germany

We explore the origin-of-life consequences of the view that biological systems are demarcated from inanimate matter by their possession of referential information, which is processed computationally to control choices of specific physico-chemical events. Cells are cybernetic: they use genetic information in processes of communication and control, subjecting physical events to a system of integrated governance. The genetic code is the most obvious example of how cells use information computationally, but the historical origin of the usefulness of molecular information is not well understood. genetic coding made information useful because it imposed a modular metric on the evolutionary search and thereby offered a general solution to the problem of finding catalysts of any specificity. We use the term "quasispecies symmetry breaking" to describe the iterated process of self-organisation whereby the alphabets of distinguishable codons and amino acids increased, step by step.

关键词： Referential information Computational processes genetic coding General solutions Quasispecies symmetry breaking

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