scholarly journals Scaling and Visualization of Nucleotide Sequences

2019 ◽  
Vol 224 ◽  
pp. 03007
Author(s):  
Ivan V. Stepanyan ◽  
Abbakar M. Khussein
Keyword(s):  
Genetic Information ◽  
Visual Representations ◽  
Nucleotide Composition ◽  
Nucleotide Sequences ◽  
Coordinate Systems ◽  
Rna Molecules ◽  
Dna And Rna ◽  
Fractal Clusters ◽  
Living Organisms ◽  
Orthogonal Coordinate Systems

Algorithms for scaling and visualization of nucleotide sequences developed in this study allow identifying relationships between the biochemical parameters of DNA and RNA molecules with scale invariance, fractal clusters, nonlinear ordering and symmetry and noise immunity of visual representations in orthogonal coordinate systems. The algorithms are capable of displaying structures of the nucleotide sequences of living organisms by visualizing them in spaces of various dimensions and scales. Approximately one hundred genes (protozoa, plants, fungi, animals, viruses) were analysed and examples of visualization of the nucleotide composition of genomes of various species have been presented. The developed method contributes to an in-depth understanding of the principles of genetic coding and simplifying the perception of genetic information due to the algorithmic interpretation of the basic properties of polynucleotide fragments with visualization of the final geometric structure of the genetic code.

Investigation of the capabilities of the method of characteristic patterns for graphical presentation of large amounts of information

2021 ◽  
Vol 61 (11) ◽  
pp. 734-739
Author(s):  
I. V. Stepanyan
Keyword(s):  
Genetic Information ◽  
Molecular Genetic ◽  
Nucleotide Composition ◽  
Human Interaction ◽  
Computer Algorithms ◽  
New Methods ◽  
Information Signal ◽  
Analytical Thinking ◽  
Living Organisms ◽  
Graphical Presentation

The author examines new challenges of ergonomics and occupational health, including unknown risks, issues of prevention, and ethics. The author also presents an overview of modern bioinformatics systems and visualization methods in bioinformatics. The researcher analyzed the health risks of human interaction with large volumes of textual information and advanced computational methods to prevent computer syndrome, including overstrain of the visual analyzer and pain in the back, neck, and hands. The study aims to analyze the representations of hereditary molecular genetic information in the form of graphic patterns available for visual perception, characterizing the initial data, and study the possibility of visualizing large amounts of data using the method of characteristic patterns. The author developed new methods of presenting large volumes of hereditary genetic information in bioinformatic systems. The basis of the method is information processing based on computer algorithms. The methods allow us to visually assess the differences in the genetic structure of various species of living organisms and identify the features of their nucleotide composition. The fixation of the internal ordering of the information signal in an individual graphical quasi-fractal structure is a characteristic feature of the methods considered. It makes it possible to expand the possibilities of visual-analytical thinking of a person when interacting with large amounts of information through bioinformatics tools.

scholarly journals Nfeature: A platform for computing features of nucleotide sequences

2021 ◽  
Author(s):  
Megha Mathur ◽  
Sumeet Patiyal ◽  
Anjali Dhall ◽  
Shipra Jain ◽  
Ritu Tomer ◽  
...  
Keyword(s):  
Nucleotide Composition ◽  
Nucleotide Sequences ◽  
Machine Learning Techniques ◽  
Rna Sequences ◽  
Dna And Rna ◽  
Reverse Complement ◽  
Wide Range ◽  
Public Repositories ◽  
Exponential Rates ◽  
And Function

In the past few decades, public repositories on nucleotides have increased with exponential rates. This pose a major challenge to researchers to predict the structure and function of nucleotide sequences. In order to annotate function of nucleotide sequences it is important to compute features/attributes for predicting function of these sequences using machine learning techniques. In last two decades, several software/platforms have been developed to elicit a wide range of features for nucleotide sequences. In order to complement the existing methods, here we present a platform named Nfeature developed for computing wide range of features of DNA and RNA sequences. It comprises of three major modules namely Composition, Correlation, and Binary profiles. Composition module allow to compute different type of compositions that includes mono-/di-tri-nucleotide composition, reverse complement composition, pseudo composition. Correlation module allow to compute various type of correlations that includes auto-correlation, cross-correlation, pseudo-correlation. Similarly, binary profile is developed for computing binary profile based on nucleotides, di-nucleotides, di-/tri-nucleotide properties. Nfeature also allow to compute entropy of sequences, repeats in sequences and distribution of nucleotides in sequences. In addition to compute feature in whole sequence, it also allows to compute features from part of sequence like split-composition, N-terminal, C-terminal. In a nutshell, Nfeature amalgamates existing features as well as number of novel features like nucleotide repeat index, distance distribution, entropy, binary profile, and properties. This tool computes a total of 29217 and 14385 features for DNA and RNA sequence, respectively. In order to provide, a highly efficient and user-friendly tool, we have developed a standalone package and web-based platform (https://webs.iiitd.edu.in/raghava/nfeature).

scholarly journals The Genetic Code, Algebraic Codes and Double Numbers

2020 ◽  
Author(s):  
Sergey V. Petoukhov
Keyword(s):  
Genetic Code ◽  
Communication Technologies ◽  
Structural Features ◽  
Rna Molecules ◽  
Doubly Stochastic ◽  
Dna And Rna ◽  
Double Numbers ◽  
Algebraic Codes ◽  
Living Organisms ◽  
Algebraic Code

The article shows materials to the question about algebraic features of the genetic code and about the dictatorial influence of the DNA and RNA molecules on the whole organism. Presented results testify in favor that the genetic code is an algebraic code related with a wide class of algebraic codes, which are a basis of noise-immune coding of information in communication technologies. Structural features of the genetic systems are associated with hypercomplex double (or hyperbolic) numbers and with bisymmetric doubly stochastic matrices. The received results confirm that represented matrix approaches are effective for modeling genetic phenomena and revealing the interconnections of structures of biological bodies at various levels of their organization. This allows one to think that living organisms are algebraically encoded entities where structures of genetic molecules have the dictatorial influence on inherited structures of the whole organism. New described algebraic approaches and results are discussed.

scholarly journals Epigenetic Methylations on N6-Adenine and N6-Adenosine with the same Input but Different Output

2019 ◽  
Vol 20 (12) ◽  
pp. 2931 ◽  
Author(s):  
Zhiqing Li ◽  
Ping Zhao ◽  
Qingyou Xia
Keyword(s):  
Genetic Information ◽  
Target Genes ◽  
Technological Development ◽  
Wide Spectrum ◽  
Functional Identification ◽  
Methyl Group ◽  
Cellular Processes ◽  
Dna And Rna ◽  
Future Challenges ◽  
Detection Strategies

Epigenetic modifications on individual bases in DNA and RNA can encode inheritable genetic information beyond the canonical bases. Among the nucleic acid modifications, DNA N6-methadenine (6mA) and RNA N6-methyladenosine (m6A) have recently been well-studied due to the technological development of detection strategies and the functional identification of modification enzymes. The current findings demonstrate a wide spectrum of 6mA and m6A distributions from prokaryotes to eukaryotes and critical roles in multiple cellular processes. It is interesting that the processes of modification in which the methyl group is added to adenine and adenosine are the same, but the outcomes of these modifications in terms of their physiological impacts in organisms are quite different. In this review, we summarize the latest progress in the study of enzymes involved in the 6mA and m6A methylation machinery, including methyltransferases and demethylases, and their functions in various biological pathways. In particular, we focus on the mechanisms by which 6mA and m6A regulate the expression of target genes, and we highlight the future challenges in epigenetic regulation.

scholarly journals Studies on genes expression pattern of antioxidant enzymes and enzymes involved into the genetic information implementation in E.coli cells due to the antibiotic resistance against apramycin and cefatoxime

2020 ◽  
Vol 17 ◽  
pp. 00103
Author(s):  
Oleg Fomenko ◽  
Evgeny Mikhailov ◽  
Nadezhda Pasko ◽  
Svetlana Grin ◽  
Andrey Koshchaev ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Antioxidant Enzymes ◽  
Genetic Information ◽  
Bacterial Resistance ◽  
Resistant Bacteria ◽  
Control Group ◽  
Bacterial Cells ◽  
E Coli ◽  
Antimicrobial Substances ◽  
Dna And Rna

The emergence of antibiotic-resistant bacteria is considered a serious problem. The resistance of bacteria against antimicrobial substances becomes important in the repair systems for damage to DNA and RNA molecules. The role of the antioxidant system in the development of bacterial resistance against antibiotics is not yet practically studied. The article studied the expression regulation of the genes of antioxidant enzymes and enzymes involved in the genetic information in E. coli cells with the antibiotic resistance against apramycin and cefatoxime. The study was conducted on bacterial cells resistant against these two antibiotics. The genes blaOXA-1, blaSHV, blaTEM, mdtK, aadA1, aadA2, sat, strA, blaCTX, blaPER-2, tnpA, tnpR, intC1 and intC1c were identified in bacterial cell case. This indicates the presence of plasmids in bacteria with these genes, which provide bacterial resistance to apramycin and cefatoxime. It was established that during the formation of cefotaxime resistance, there was a sharp increase in the expression of the Cu, Zn superoxide dismutase gene: in comparison with the control group, the representation of its transcripts increased 141.04 times for cefotoxime and 155.42 times for apramycin. It has been established that during the formation of resistance to the studied antibiotics in E. coli, an increase in the expression of the end4 and end3 genes is observed. There is tendency toward an increase in the number of transcripts of the pol3E gene observed in the formation of resistance against cefotaxime and apromycin.

Regulatory aspects of RNAi in plant production.

2021 ◽  
pp. 154-158
Author(s):  
Werner Schenkel ◽  
Achim Gathmann
Keyword(s):  
Small Rna ◽  
Plant Protection ◽  
Plant Protection Products ◽  
Plant Production ◽  
The European Union ◽  
Relevant Aspect ◽  
Rna Molecules ◽  
Rnai Technology ◽  
Living Organisms ◽  
Intended Use

Abstract Technologies based on RNA interference (RNAi) may be used in plant production in different contexts. With respect to applicable regulations, a major distinction is to be made between plants producing small RNA molecules due to modifications of the genome and topically applied plant protection products (PPPs) based on double-stranded RNA (dsRNA). The first group may be further divided into those using RNAi technology to achieve changes in the plant's metabolism and those where plant-produced RNA molecules are intended to impact other organisms that interact with the plant. For PPPs, relevant aspects are whether the product contains living organisms or only purified molecules. The intended use of the product is another relevant aspect with respect to regulation. It is expected that PPPs will be among the first products utilizing the RNAi mechanism in the European Union. This chapter discusses the regulation of modified RNAi plants and the regulation of PPPs utilizing RNAi mechanisms.

scholarly journals De Novo Nucleic Acids: A Review of Synthetic Alternatives to DNA and RNA That Could Act as Bio-Information Storage Molecules

Life ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 346
Author(s):  
Kevin G Devine ◽  
Sohan Jheeta
Keyword(s):  
Nucleic Acids ◽  
Genetic Information ◽  
De Novo ◽  
Chemical Properties ◽  
Amino Acid Sequences ◽  
Information Storage ◽  
Heterocyclic Base ◽  
Dna And Rna ◽  
Phosphate Backbone ◽  
Physical And Chemical

Modern terran life uses several essential biopolymers like nucleic acids, proteins and polysaccharides. The nucleic acids, DNA and RNA are arguably life’s most important, acting as the stores and translators of genetic information contained in their base sequences, which ultimately manifest themselves in the amino acid sequences of proteins. But just what is it about their structures; an aromatic heterocyclic base appended to a (five-atom ring) sugar-phosphate backbone that enables them to carry out these functions with such high fidelity? In the past three decades, leading chemists have created in their laboratories synthetic analogues of nucleic acids which differ from their natural counterparts in three key areas as follows: (a) replacement of the phosphate moiety with an uncharged analogue, (b) replacement of the pentose sugars ribose and deoxyribose with alternative acyclic, pentose and hexose derivatives and, finally, (c) replacement of the two heterocyclic base pairs adenine/thymine and guanine/cytosine with non-standard analogues that obey the Watson–Crick pairing rules. This manuscript will examine in detail the physical and chemical properties of these synthetic nucleic acid analogues, in particular on their abilities to serve as conveyors of genetic information. If life exists elsewhere in the universe, will it also use DNA and RNA?

scholarly journals Base-pair ambiguity and the kinetics of RNA folding

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Guangyao Zhou ◽  
Jackson Loper ◽  
Stuart Geman
Keyword(s):  
Free Energy ◽  
Secondary Structure ◽  
Thermodynamic Equilibrium ◽  
Secondary Structures ◽  
Minimum Free Energy ◽  
Nucleotide Sequences ◽  
Biologically Relevant ◽  
Rna Molecules ◽  
Comparative Structure ◽  
Kinetic Traps

Abstract Background A folding RNA molecule encounters multiple opportunities to form non-native yet energetically favorable pairings of nucleotide sequences. Given this forbidding free-energy landscape, mechanisms have evolved that contribute to a directed and efficient folding process, including catalytic proteins and error-detecting chaperones. Among structural RNA molecules we make a distinction between “bound” molecules, which are active as part of ribonucleoprotein (RNP) complexes, and “unbound,” with physiological functions performed without necessarily being bound in RNP complexes. We hypothesized that unbound molecules, lacking the partnering structure of a protein, would be more vulnerable than bound molecules to kinetic traps that compete with native stem structures. We defined an “ambiguity index”—a normalized function of the primary and secondary structure of an individual molecule that measures the number of kinetic traps available to nucleotide sequences that are paired in the native structure, presuming that unbound molecules would have lower indexes. The ambiguity index depends on the purported secondary structure, and was computed under both the comparative (“gold standard”) and an equilibrium-based prediction which approximates the minimum free energy (MFE) structure. Arguing that kinetically accessible metastable structures might be more biologically relevant than thermodynamic equilibrium structures, we also hypothesized that MFE-derived ambiguities would be less effective in separating bound and unbound molecules. Results We have introduced an intuitive and easily computed function of primary and secondary structures that measures the availability of complementary sequences that could disrupt the formation of native stems on a given molecule—an ambiguity index. Using comparative secondary structures, the ambiguity index is systematically smaller among unbound than bound molecules, as expected. Furthermore, the effect is lost when the presumably more accurate comparative structure is replaced instead by the MFE structure. Conclusions A statistical analysis of the relationship between the primary and secondary structures of non-coding RNA molecules suggests that stem-disrupting kinetic traps are substantially less prevalent in molecules not participating in RNP complexes. In that this distinction is apparent under the comparative but not the MFE secondary structure, the results highlight a possible deficiency in structure predictions when based upon assumptions of thermodynamic equilibrium.

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