Primitive selection of the fittest emerging through functional synergy in nucleopeptide networks

Many fundamental cellular and viral functions, including replication and translation, involve complex ensembles hosting synergistic activity between nucleic acids and proteins/peptides. There is ample evidence indicating that the chemical precursors of both nucleic acids and peptides could be efficiently formed in the prebiotic environment. Yet, studies on nonenzymatic replication, a central mechanism driving early chemical evolution, have focused largely on the activity of each class of these molecules separately. We show here that short nucleopeptide chimeras can replicate through autocatalytic and cross-catalytic processes, governed synergistically by the hybridization of the nucleobase motifs and the assembly propensity of the peptide segments. Unequal assembly-dependent replication induces clear selectivity toward the formation of a certain species within small networks of complementary nucleopeptides. The selectivity pattern may be influenced and indeed maximized to the point of almost extinction of the weakest replicator when the system is studied far from equilibrium and manipulated through changes in the physical (flow) and chemical (template and inhibition) conditions. We postulate that similar processes may have led to the emergence of the first functional nucleic-acid–peptide assemblies prior to the origin of life. Furthermore, spontaneous formation of related replicating complexes could potentially mark the initiation point for information transfer and rapid progression in complexity within primitive environments, which would have facilitated the development of a variety of functions found in extant biological assemblies.

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Making Molecules with Clay: Layered Double Hydroxides, Pentopyranose Nucleic Acids and the Origin of Life

Life ◽

10.3390/life9010019 ◽

2019 ◽

Vol 9 (1) ◽

pp. 19 ◽

Cited By ~ 4

Author(s):

Harold Bernhardt

Keyword(s):

Nucleic Acids ◽

Lipid Bilayers ◽

Information Transfer ◽

Prebiotic Synthesis ◽

Base Pairing ◽

Phosphate Backbone ◽

The Origin Of Life ◽

Double Hydroxide ◽

Double Hydroxides ◽

Purine Pyrimidine

A mixture of sugar diphosphates is produced in reactions between small aldehyde phosphates catalysed by layered double hydroxide (LDH) clays under plausibly prebiotic conditions. A subset of these, pentose diphosphates, constitute the backbone subunits of nucleic acids capable of base pairing, which is not the case for the other products of these LDH-catalysed reactions. Not only that, but to date no other polymer found capable of base pairing—and therefore information transfer—has a backbone for which its monomer subunits have a plausible prebiotic synthesis, including the ribose-5-phosphate backbone subunit of RNA. Pentose diphosphates comprise the backbone monomers of pentopyranose nucleic acids, some of the strongest base pairing systems so far discovered. We have previously proposed that the first base pairing interactions were between purine nucleobase precursors, and that these were weaker and less specific than standard purine-pyrimidine interactions. We now propose that the inherently stronger pairing of pentopyranose nucleic acids would have compensated for these weaker interactions, and produced an informational polymer capable of undergoing nonenzymatic replication. LDH clays might also have catalysed the synthesis of the purine nucleobase precursors, and the polymerization of pentopyranose nucleotide monomers into oligonucleotides, as well as the formation of the first lipid bilayers.

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Design, delivery and perception of condition-dependent chemical signals in strepsirrhine primates: implications for human olfactory communication

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2019.0264 ◽

2020 ◽

Vol 375 (1800) ◽

pp. 20190264 ◽

Cited By ~ 6

Author(s):

Christine M. Drea

Keyword(s):

Genetic Diversity ◽

Information Transfer ◽

Dominant Species ◽

Vomeronasal Organ ◽

Olfactory Communication ◽

Scent Mark ◽

Reproductive State ◽

Intended Audience ◽

Evolutionary Trajectories ◽

Selection Of

The study of human chemical communication benefits from comparative perspectives that relate humans, conceptually and empirically, to other primates. All major primate groups rely on intraspecific chemosignals, but strepsirrhines present the greatest diversity and specialization, providing a rich framework for examining design, delivery and perception. Strepsirrhines actively scent mark, possess a functional vomeronasal organ, investigate scents via olfactory and gustatory means, and are exquisitely sensitive to chemically encoded messages. Variation in delivery, scent mixing and multimodality alters signal detection, longevity and intended audience. Based on an integrative, 19-species review, the main scent source used (excretory versus glandular) differentiates nocturnal from diurnal or cathemeral species, reflecting differing socioecological demands and evolutionary trajectories. Condition-dependent signals reflect immutable (species, sex, identity, genetic diversity, immunity and kinship) and transient (health, social status, reproductive state and breeding history) traits, consistent with socio-reproductive functions. Sex reversals in glandular elaboration, marking rates or chemical richness in female-dominant species implicate sexual selection of olfactory ornaments in both sexes. Whereas some compounds may be endogenously produced and modified (e.g. via hormones), microbial analyses of different odorants support the fermentation hypothesis of bacterial contribution. The intimate contexts of information transfer and varied functions provide important parallels applicable to olfactory communication in humans. This article is part of the Theo Murphy meeting issue ‘Olfactory communication in humans’.

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Vulnerability analysis and method of selection of communication protocols for information transfer in Internet of Things systems

RADIOELECTRONIC AND COMPUTER SYSTEMS ◽

10.32620/reks.2021.1.12 ◽

2021 ◽

pp. 133-149

Author(s):

Maryna Kolisnyk

Keyword(s):

Internet Of Things ◽

Initial Data ◽

Information Transfer ◽

System Analysis ◽

Communication Protocols ◽

Critical Systems ◽

Smart Objects ◽

Corporate System ◽

The Given ◽

Selection Of

The subject of study in the paper is the analysis of technologies, architectures, vulnerabilities and cyberattacks, communication patterns of smart objects, messaging models, and Internet of Things (IoT) / Web of Things (WoT) protocols for solving applied problems of critical and non-critical systems. The goal is to develop a method for selecting messaging models and application-level protocols in non-critical and critical multi-level IoT/WoT systems, provided that the type of access to intelligent objects is initially determined by the initial data, as well as analysis of vulnerabilities and attacks using these protocols. Objectives: to formalize the procedure for choosing communication protocols for IoT/WoT systems; analyze possible vulnerabilities of communication protocols; develop a method for selecting communication protocols for given initial data, depending on the selected type of communication template for smart objects; check practically the proposed method. The methods of research are methods of system analysis. The following results were obtained. The analysis of the features of communication protocols is conducted by comparing the main interrelated characteristics of IoT/WoT, the results of which are presented in the form of a table. A method has been developed for selecting communication protocols, depending on the selected type of communication template. The analysis of possible vulnerabilities of communication protocols and possible attacks using these protocols is conducted. The author has tested the method using the example of a corporate system (Smart House) based on the WoT concept. Findings. The scientific novelty of the results obtained is as follows: the analysis conducted in the paper shows that currently there is no unified approach to the choice of a messaging model and application-level protocols for building IoT/WoT, depending on the selected type of communication template for smart objects. The method for selecting communication protocols for the given conditions (for each IoT system its interaction pattern will correspond, depending on which components interact with each other), improved by the authors of the paper, makes it possible to simplify the task of using separate protocols for given IoT systems, considering vulnerabilities of protocols.

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In vitro selection of nucleic acids for diagnostic applications

Reviews in Molecular Biotechnology ◽

10.1016/s1389-0352(99)00005-7 ◽

2000 ◽

Vol 74 (1) ◽

pp. 15-25 ◽

Cited By ~ 50

Author(s):

Jay Hesselberth ◽

Michael P Robertson ◽

Sulay Jhaveri ◽

Andrew D Ellington

Keyword(s):

Nucleic Acids ◽

In Vitro Selection ◽

Diagnostic Applications ◽

Selection Of

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Synergy of Linezolid with Several Antimicrobial Agents against Linezolid-Methicillin-Resistant Staphylococcal Strains

Antibiotics ◽

10.3390/antibiotics9080496 ◽

2020 ◽

Vol 9 (8) ◽

pp. 496

Author(s):

María-José Valderrama ◽

María Alfaro ◽

Icíar Rodríguez-Avial ◽

Elvira Baos ◽

Carmen Rodríguez-Avial ◽

...

Keyword(s):

Antimicrobial Agents ◽

Synergistic Effects ◽

Ribosomal Subunit ◽

Antagonistic Effect ◽

Prolonged Treatment ◽

Synergistic Activity ◽

Methicillin Resistant ◽

Resistant Strains ◽

Time Kill ◽

Selection Of

Linezolid is a synthetic oxazolydinone active against multi-resistant Gram-positive cocci that inhibits proteins synthesis by interacting with the 50S ribosomal subunit. Although linezolid-resistant strains are infrequent, several outbreaks have been recently described, associated with prolonged treatment with the antibiotic. As an alternative to monotherapy, the combination of different antibiotics is a commonly used option to prevent the selection of resistant strains. In this work, we evaluated combinations of linezolid with classic and new aminoglycosides (amikacin, gentamicin and plazomicin), carbapenems (doripenem, imipenem and meropenem) and fosfomycin on several linezolid- and methicillin-resistant strains of Staphylococcus aureus and S. epidermidis, isolated in a hospital intensive care unit in Madrid, Spain. Using checkerboard and time-kill assays, interesting synergistic effects were encountered for the combination of linezolid with imipenem in all the staphylococcal strains, and for linezolid–doripenem in S.epidermidis isolates. The combination of plazomicin seemed to also have a good synergistic or partially synergistic activity against most of the isolates. None of the combinations assayed showed an antagonistic effect.

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Solvent viscosity facilitates replication and ribozyme catalysis from an RNA duplex in a model prebiotic process

Nucleic Acids Research ◽

10.1093/nar/gkz496 ◽

2019 ◽

Vol 47 (13) ◽

pp. 6569-6577 ◽

Cited By ~ 4

Author(s):

Christine He ◽

Adriana Lozoya-Colinas ◽

Isaac Gállego ◽

Martha A Grover ◽

Nicholas V Hud

Keyword(s):

Information Transfer ◽

Rna World ◽

Hammerhead Ribozyme ◽

Information Storage ◽

Additional Challenge ◽

The Origin Of Life ◽

World Hypothesis ◽

Synthesis Reactions ◽

Rna World Hypothesis ◽

Single Sequence

Abstract The RNA World hypothesis posits that RNA was once responsible for genetic information storage and catalysis. However, a prebiotic mechanism has yet to be reported for the replication of duplex RNA that could have operated before the emergence of polymerase ribozymes. Previously, we showed that a viscous solvent enables information transfer from one strand of long RNA duplex templates, overcoming ‘the strand inhibition problem'. Here, we demonstrate that the same approach allows simultaneous information transfer from both strands of long duplex templates. An additional challenge for the RNA World is that structured RNAs (like those with catalytic activity) function poorly as templates in model prebiotic RNA synthesis reactions, raising the question of how a single sequence could serve as both a catalyst and as a replication template. Here, we show that a viscous solvent also facilitates the transition of a newly synthesized hammerhead ribozyme sequence from its inactive, duplex state to its active, folded state. These results demonstrate how fluctuating environmental conditions can allow a ribozyme sequence to alternate between acting as a template for replication and functioning as a catalyst, and illustrate the potential for temporally changing environments to enable molecular processes necessary for the origin of life.

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Determination of interactions between structured nucleic acids by fluorescence resonance energy transfer (FRET): selection of target sites for functional nucleic acids

Nucleic Acids Research ◽

10.1093/nar/26.3.735 ◽

1998 ◽

Vol 26 (3) ◽

pp. 735-743 ◽

Cited By ~ 26

Author(s):

N Ota

Keyword(s):

Energy Transfer ◽

Nucleic Acids ◽

Fluorescence Resonance Energy Transfer ◽

Resonance Energy Transfer ◽

Resonance Energy ◽

Target Sites ◽

Fluorescence Resonance ◽

Functional Nucleic Acids ◽

Selection Of

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Nucleic acids and information transfer

Journal of Cellular and Comparative Physiology ◽

10.1002/jcp.1030620411 ◽

1963 ◽

Vol 62 (S1) ◽

pp. 111-122 ◽

Cited By ~ 4

Author(s):

Liebe F. Cavalieri

Keyword(s):

Nucleic Acids ◽

Information Transfer

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The Use of Magnetostrictive Cores for the Vibrations Generation and Energy Harvesting from Vibration, in the Selected Frequencies of Work

Key Engineering Materials ◽

10.4028/www.scientific.net/kem.598.75 ◽

2014 ◽

Vol 598 ◽

pp. 75-80 ◽

Cited By ~ 6

Author(s):

Jerzy Kaleta ◽

Krzysztof Kot ◽

Rafał Mech ◽

Przemyslaw Wiewiorski

Keyword(s):

Energy Transfer ◽

Information Transfer ◽

Wide Frequency Range ◽

Frequency Range ◽

Mechanical Vibrations ◽

Energy Transportation ◽

To Receive ◽

Low Power Electronics ◽

Time Selection ◽

Selection Of

The paper presents research on use of magnetostrictive cores for the recovery of energy from vibrations and its use to power low-power electronics. To achieve this goal a test stand was constructed to generate and to receive the vibrations in the measurement system at the same time. Selection of an appropriate magnetomechanical parameters of the system was an important element influencing end results. The most important were values of the prestress and magnetising field for actuators and harvesters. As a result of the investigation the device operating in a wide frequency range (up to 40 KHz) and a system for energy transportation through mechanical vibrations were developed. Moreover it was shown that the proposed solution allow information transfer in a short bursts over the same system as energy transfer.

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