scholarly journals Hyperbolic rules of the cooperative organization of eukaryotic and prokaryotic genomes

Biosystems ◽  
2020 ◽  
Vol 198 ◽  
pp. 104273 ◽  
Author(s):  
Sergey V. Petoukhov
Author(s):  
Sergey Petoukhov

The author's method of oligomer sums for analysis of oligomer compositions of eukaryotic and prokaryotic genomes is described. The use of this method revealed the existence of general rules for cooperative oligomeric organization of a wide list of genomes. These rules are called hyperbolic because they are associated with hyperbolic sequences including the harmonic progression 1, 1/2, 1/3, .., 1/n. These rules are demonstrated by examples of quantitative analysis of many genomes from the human genome to the genomes of archaea and bacteria. The hyperbolic (harmonic) rules, speaking about the existence of algebraic invariants in full genomic sequences, are considered as candidates for the role of universal rules for cooperative organization of genomes. The described phenomenological results were obtained as consequences of the previously published author's quantum-information model of long DNA sequences. The oligomer sums method was also applied to the analysis of long genes and viruses including the COVID-19 virus; this revealed, in characteristics of many of them, the phenomenon of rhythmically repeating deviations from model hyperbolic sequences; these deviations are associated with DNA triplets and should be systematically analyzed for a deeper understanding the genetic coding system. The topics of the algebraic harmony in living bodies and of the quantum-information approach in biology are discussed.


Author(s):  
Sergey Petoukhov

The author's method of oligomer sums for analysis of oligomer compositions of eukaryotic and prokaryotic genomes is described. The use of this method revealed the existence of general rules for cooperative oligomeric organization of a wide list of genomes. These rules are called hyperbolic because they are associated with hyperbolic sequences including the harmonic progression 1, 1/2, 1/3, .., 1/n. These rules are demonstrated by examples of quantitative analysis of many genomes from the human genome to the genomes of archaea and bacteria. The hyperbolic (harmonic) rules, speaking about the existence of algebraic invariants in full genomic sequences, are considered as candidates for the role of universal rules for the cooperative organization of genomes. The described phenomenological results were obtained as consequences of the previously published author's quantum-information model of long DNA sequences. The oligomer sums method was also applied to the analysis of long genes and viruses including the COVID-19 virus; this revealed, in characteristics of many of them, the phenomenon of such rhythmically repeating deviations from model hyperbolic sequences, which are associated with DNA triplets. In addition, an application of the oligomer sums method are shown to the analysis of the following long sequences: 1) amino acid sequences in long proteins like the protein Titin; 2) phonetic sequences of long Russan literary texts (for checking of thoughts of many authors that phonetic organization of human languages is deeply connected with the genetic language). The topics of the algebraic harmony in living bodies and of the quantum-information approach in biology are discussed.


2020 ◽  
Vol 36 (Supplement_2) ◽  
pp. i651-i658 ◽  
Author(s):  
Adelme Bazin ◽  
Guillaume Gautreau ◽  
Claudine Médigue ◽  
David Vallenet ◽  
Alexandra Calteau

Abstract Motivation Horizontal gene transfer (HGT) is a major source of variability in prokaryotic genomes. Regions of genome plasticity (RGPs) are clusters of genes located in highly variable genomic regions. Most of them arise from HGT and correspond to genomic islands (GIs). The study of those regions at the species level has become increasingly difficult with the data deluge of genomes. To date, no methods are available to identify GIs using hundreds of genomes to explore their diversity. Results We present here the panRGP method that predicts RGPs using pangenome graphs made of all available genomes for a given species. It allows the study of thousands of genomes in order to access the diversity of RGPs and to predict spots of insertions. It gave the best predictions when benchmarked along other GI detection tools against a reference dataset. In addition, we illustrated its use on metagenome assembled genomes by redefining the borders of the leuX tRNA hotspot, a well-studied spot of insertion in Escherichia coli. panRPG is a scalable and reliable tool to predict GIs and spots making it an ideal approach for large comparative studies. Availability and implementation The methods presented in the current work are available through the following software: https://github.com/labgem/PPanGGOLiN. Detailed results and scripts to compute the benchmark metrics are available at https://github.com/axbazin/panrgp_supdata.


BIOspektrum ◽  
2021 ◽  
Vol 27 (3) ◽  
pp. 274-276
Author(s):  
Morgan S. Sobol ◽  
Anne-Kristin Kaster

AbstractSingle cell genomics (SCG) can provide reliable context for assembled genome fragments on the level of individual prokaryotic genomes and has rapidly emerged as an essential complement to cultivation-based and metagenomics research approaches. Targeted cell sorting approaches, which enable the selection of specific taxa by fluorescent labeling, compatible with subsequent single cell genomics offers an opportunity to access genetic information from rare biosphere members which would have otherwise stayed hidden as microbial dark matter.


2013 ◽  
Vol 110 (9) ◽  
pp. 3287-3292 ◽  
Author(s):  
Yejun Feng ◽  
Jiyang Wang ◽  
D. M. Silevitch ◽  
B. Mihaila ◽  
J. W. Kim ◽  
...  

2013 ◽  
Vol 47 (9) ◽  
pp. 1056-1060 ◽  
Author(s):  
V. V. Suslov ◽  
D. A. Afonnikov ◽  
N. L. Podkolodny ◽  
Yu. L. Orlov

2021 ◽  
Vol 13 (15) ◽  
pp. 8217
Author(s):  
Clea Beatriz Macagnan ◽  
Rosane Maria Seibert

The research aims to identify indicators of representative information on sustainability from the cooperative organizations’ primary stakeholders’ perspective to mitigate information asymmetry. The study develops in seven stages: the primary stakeholders’ selection and training; the evidence survey; the triangulation between stakeholder responses, forming an indicators list; the indicators analysis by specialists; tests for indicators disclosure; and the indicators validation through the disclosure analysis. As a result, a list contains 61 sustainability indicators from the primary stakeholders’ perspective, in four pillars: economic, 20; social, 18; environmental, 13; and cultural, 10. With the cooperative organizations’ websites disclosure analysis, we found that the disclosure policies focus more on information asymmetry mitigating in the pillars: cultural and social, with the environmental and economic being neglected. Therefore, the procedures for disclosing information on sustainability have weaknesses. These policies reduce the primary stakeholders’ reliability about the cooperatives management system respective, limiting the primary stakeholders’ perspective on the cooperative organization value.


Author(s):  
Benjamin Hepp ◽  
Violette Da Cunha ◽  
Florence Lorieux ◽  
Jacques Oberto

Abstract Motivation The retrieval of a single gene sequence and context from completely sequenced bacterial and archaeal genomes constitutes an intimidating task for the wet bench biologist. Existing web-based genome browsers are either too complex for routine use or only provide a subset of the available prokaryotic genomes. Results We have developed BAGET 2.0 (Bacterial and Archaeal Gene Exploration Tool), an updated web service granting access in just three mouse clicks to the sequence and synteny of any gene from completely sequenced bacteria and archaea. User-provided annotated genomes can be processed as well. BAGET 2.0 relies on a local database updated on a daily basis. Availability and implementation BAGET 2.0 befits all current browsers such as Chrome, Firefox, Edge, Opera and Safari. Internet Explorer 11 is supported. BAGET 2.0 is freely accessible at https://archaea.i2bc.paris-saclay.fr/baget/


2018 ◽  
Vol 9 ◽  
Author(s):  
Irina A. Garanina ◽  
Gleb Y. Fisunov ◽  
Vadim M. Govorun
Keyword(s):  

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