scholarly journals Evolution towards increasing complexity through functional diversification in a protocell model of the RNA world

2021 ◽  
Vol 288 (1963) ◽  
Author(s):  
Suvam Roy ◽  
Supratim Sengupta
Keyword(s):  
Rna World ◽  
Genetic Material ◽  
Lipid Vesicles ◽  
Replication Process ◽  
Rolling Circle ◽  
Rolling Circle Mechanism ◽  
Key Steps ◽  
Functionally Diverse ◽  
Open Question ◽  
The Impact

The encapsulation of genetic material inside compartments together with the creation and sustenance of functionally diverse internal components are likely to have been key steps in the formation of ‘live’, replicating protocells in an RNA world. Several experiments have shown that RNA encapsulated inside lipid vesicles can lead to vesicular growth and division through physical processes alone. Replication of RNA inside such vesicles can produce a large number of RNA strands. Yet, the impact of such replication processes on the emergence of the first ribozymes inside such protocells and on the subsequent evolution of the protocell population remains an open question. In this paper, we present a model for the evolution of protocells with functionally diverse ribozymes. Distinct ribozymes can be created with small probabilities during the error-prone RNA replication process via the rolling circle mechanism. We identify the conditions that can synergistically enhance the number of different ribozymes inside a protocell and allow functionally diverse protocells containing multiple ribozymes to dominate the population. Our work demonstrates the existence of an effective pathway towards increasing complexity of protocells that might have eventually led to the origin of life in an RNA world.

scholarly journals Evolution towards increasing complexity through functional diversification in a protocell model of the RNA world

2021 ◽  
Author(s):  
Suvam Roy ◽  
Supratim Sengupta
Keyword(s):  
Rna World ◽  
Genetic Material ◽  
Lipid Vesicles ◽  
Replication Process ◽  
Rolling Circle ◽  
Rolling Circle Mechanism ◽  
Key Steps ◽  
Functionally Diverse ◽  
Open Question ◽  
The Impact

The encapsulation of genetic material inside compartments together with the creation and sustenance of functionally diverse internal components are likely to have been key steps in the formation of 'live', replicating protocells in an RNA world. Several experiments have shown that RNA encapsulated inside lipid vesicles can lead to vesicular growth and division through physical processes alone. Replication of RNA inside such vesicles can produce a large number of RNA strands. Yet, the impact of such replication processes on the emergence of the first ribozymes inside such protocells and on the subsequent evolution of the protocell population remains an open question. In this paper, we present a model for the evolution of protocells with functionally diverse ribozymes. Distinct ribozymes can be created with small probabilities during the error-prone RNA replication process via the rolling circle mechanism. We identify the conditions that can synergistically enhance the number of different ribozymes inside a protocell and allow functionally diverse protocells containing multiple ribozymes to dominate the population. Our work demonstrates the existence of an effective pathway towards increasing complexity of protocells that might have eventually led to the origin of life in an RNA world.

scholarly journals Viroids and Viroid-like Circular RNAs: Do They Descend from Primordial Replicators?

Life ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 103
Author(s):  
Benjamin D. Lee ◽  
Eugene V. Koonin
Keyword(s):  
Plant Pathogens ◽  
Rna World ◽  
Unit Length ◽  
Circular Rna ◽  
Circular Rnas ◽  
Rolling Circle ◽  
Rna Molecules ◽  
Evolution Of Life ◽  
Rolling Circle Mechanism ◽  
Viral Nucleocapsid

Viroids are a unique class of plant pathogens that consist of small circular RNA molecules, between 220 and 450 nucleotides in size. Viroids encode no proteins and are the smallest known infectious agents. Viroids replicate via the rolling circle mechanism, producing multimeric intermediates which are cleaved to unit length either by ribozymes formed from both polarities of the viroid genomic RNA or by coopted host RNAses. Many viroid-like small circular RNAs are satellites of plant RNA viruses. Ribozyviruses, represented by human hepatitis delta virus, are larger viroid-like circular RNAs that additionally encode the viral nucleocapsid protein. It has been proposed that viroids are direct descendants of primordial RNA replicons that were present in the hypothetical RNA world. We argue, however, that much later origin of viroids, possibly, from recently discovered mobile genetic elements known as retrozymes, is a far more parsimonious evolutionary scenario. Nevertheless, viroids and viroid-like circular RNAs are minimal replicators that are likely to be close to the theoretical lower limit of replicator size and arguably comprise the paradigm for replicator emergence. Thus, although viroid-like replicators are unlikely to be direct descendants of primordial RNA replicators, the study of the diversity and evolution of these ultimate genetic parasites can yield insights into the earliest stages of the evolution of life.

scholarly journals Assessing the impact of previous experience on lie effects through a transfer paradigm

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Claudia Mazzuca ◽  
Mariagrazia Benassi ◽  
Roberto Nicoletti ◽  
Giuseppe Sartori ◽  
Luisa Lugli
Keyword(s):  
Training Session ◽  
Spatial Task ◽  
Dual Processes ◽  
Transfer Effects ◽  
Transfer Paradigm ◽  
Compatible Condition ◽  
Open Question ◽  
The Impact ◽  
Cognitive Cost ◽  
Spatial Training

AbstractInfluential lines of research propose dual processes-based explanations to account for both the cognitive cost implied in lying and for that entailed in the resolution of the conflict posited by Simon tasks. The emergence and consistency of the Simon effect has been proved to be modulated by both practice effects and transfer effects. Although several studies provided evidence that the lying cognitive demand may vary as a function of practice, whether and how transfer effects could also play a role remains an open question. We addressed this question with one experiment in which participants completed a Differentiation of Deception Paradigm twice (baseline and test sessions). Crucially, between the baseline and the test sessions, participants performed a training session consisting in a spatial compatibility task with incompatible (condition 1) or compatible (condition 2) mapping, a non-spatial task (condition 3) and a no task one (condition 4). Results speak in favour of a modulation of individual performances by means of an immediate prior experience, and specifically with an incompatible spatial training.

scholarly journals Driver Liability Assessment in Vehicle Collisions in Spain

2021 ◽  
Vol 18 (4) ◽  
pp. 1475
Author(s):  
Almudena Sanjurjo-de-No ◽  
Blanca Arenas-Ramírez ◽  
José Mira ◽  
Francisco Aparicio-Izquierdo
Keyword(s):  
Road Safety ◽  
Accurate Estimation ◽  
Main Hypothesis ◽  
Self Organizing Maps ◽  
Safety Measures ◽  
Vehicle Collisions ◽  
Promising Tool ◽  
Visual Clustering ◽  
Open Question ◽  
The Impact

An accurate estimation of exposure is essential for road collision rate estimation, which is key when evaluating the impact of road safety measures. The quasi-induced exposure method was developed to estimate relative exposure for different driver groups based on its main hypothesis: the not-at-fault drivers involved in two-vehicle collisions are taken as a random sample of driver populations. Liability assignment is thus crucial in this method to identify not-at-fault drivers, but often no liability labels are given in collision records, so unsupervised analysis tools are required. To date, most researchers consider only driver and speed offences in liability assignment, but an open question is if more information could be added. To this end, in this paper, the visual clustering technique of self-organizing maps (SOM) has been applied to better understand the multivariate structure in the data, to find out the most important variables for driver liability, analyzing their influence, and to identify relevant liability patterns. The results show that alcohol/drug use could be influential on liability and further analysis is required for disability and sudden illness. More information has been used, given that a larger proportion of the data was considered. SOM thus appears as a promising tool for liability assessment.

scholarly journals Natural 2′,5′-Phosphodiester Bonds Found at the Ligation Sites of Peach Latent Mosaic Viroid

2001 ◽  
Vol 75 (1) ◽  
pp. 19-25 ◽  
Author(s):  
Fabien Côté ◽  
Dominique Lévesque ◽  
Jean-Pierre Perreault
Keyword(s):  
Circular Rna ◽  
Rolling Circle ◽  
Phosphodiester Bonds ◽  
Biological Importance ◽  
Rolling Circle Mechanism ◽  
Ligation Site

ABSTRACT Peach latent mosaic viroid (PLMVd) is a circular RNA pathogen that replicates in a DNA-independent fashion via a rolling circle mechanism. PLMVd has been shown to self-ligate in vitro primarily via the formation of 2′,5′-phosphodiester bonds; however, in vivo the occurrence and necessity of this nonenzymatic mechanism are not evident. Here, we unequivocally report the presence of 2′,5′-phosphodiester bonds at the ligation site of circular PLMVd strands isolated from infected peach leaves. These bonds serve to close the linear conformers (i.e., intermediates), yielding circular ones. Furthermore, these bonds are shown to stabilize the replicational circular templates, resulting in a significant advantage in terms of viroid viability. Although the mechanism responsible for the formation of these 2′,5′-phosphodiester bonds remains to be elucidated, a hypothesis describing in vivo nonenzymatic self-ligation is proposed. Most significantly, our results clearly show that 2′,5′-phosphodiester bonds are still present in nature and that they are of biological importance.

scholarly journals The Impact of O-Glycosylation on Cyanidin Interaction with POPC Membranes: Structure-Activity Relationship

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 2771
Author(s):  
Sylwia Cyboran-Mikołajczyk ◽  
Piotr Jurkiewicz ◽  
Martin Hof ◽  
Halina Kleszczyńska
Keyword(s):  
Biological Activity ◽  
Free Radicals ◽  
Lipid Bilayer ◽  
Lipid Membrane ◽  
Lipid Vesicles ◽  
Structure Activity Relationship ◽  
Activity Relationship ◽  
Beneficial Effects ◽  
Structure Activity ◽  
The Impact

Cyanidin and its O-glycosides have many important physiological functions in plants and beneficial effects on human health. Their biological activity is not entirely clear and depends on the structure of the molecule, in particular, on the number and type of sugar substituents. Therefore, in this study the detailed structure-activity relationship (SARs) of the anthocyanins/anthocyanidins in relation to their interactions with lipid bilayer was determined. On the basis of their antioxidant activity and the changes induced by them in size and Zeta potential of lipid vesicles, and mobility and order of lipid acyl chains, the impact of the number and type of sugar substituents on the biological activity of the compounds was evaluated. The obtained results have shown, that 3-O-glycosylation changes the interaction of cyanidin with lipid bilayer entirely. The 3-O-glycosides containing a monosaccharide induces greater changes in physical properties of the lipid membrane than those containing disaccharides. The presence of additional sugar significantly reduces glycoside interaction with model lipid membrane. Furthermore, O-glycosylation alters the ability of cyanidin to scavenge free radicals. This alteration depends on the type of free radicals and the sensitivity of the method used for their determination.

scholarly journals Intellectual property rights in Brazilian floriculture: innovations for the growth and development of the market

2017 ◽  
Vol 23 (3) ◽  
pp. 296 ◽  
Author(s):  
Antonio Helio Junqueira ◽  
Marcia Peetz
Keyword(s):  
Growth And Development ◽  
Ornamental Plants ◽  
Genetic Material ◽  
The United States ◽  
Consumer Market ◽  
International Trends ◽  
Recent Developments ◽  
Cultivated Species ◽  
The Impact ◽  
Sectoral Policy

One of the most important demands imposed by the consumer market on the Brazilian Productive Chain of Flowers and Ornamental Plants is the constant launching of innovations in cultivated species and varieties. Such innovations include the constant introduction of flowers and plants not yet grown and commercialized, both native and adapted exotic species, as well as transformations and changes in size, shape, coloring and conduction patterns and presentation of these goods to the market. Brazil does not have a relevant breeding and cultivation industry. In this sense, it is highly dependent on imports of genetic material developed by countries such as the Netherlands, Germany, Japan, the United States of America, Thailand, among others. Recent developments in the sectoral policy to protect the rights of genetic developers, in the development of internationally adequate legislation and in the control of the use and trade of cultivars, has allowed Brazil greater access to new genetic materials of high quality and in line with contemporary international trends in the consumption. This article aims to discuss the state of the art of protection of cultivars in Brazil, pointing to the advances that the legislation and the inspection have allowed in relation to the introduction of genetic innovations, evaluating the impact of these measures on the growth and development of the market of consumption of flowers and ornamental plants in the country.

scholarly journals Viroids: unusual small pathogenic RNAs.

2004 ◽  
Vol 51 (3) ◽  
pp. 587-607 ◽  
Author(s):  
Anna Góra-Sochacka
Keyword(s):  
Secondary Structure ◽  
Hammerhead Ribozyme ◽  
Direct Interaction ◽  
Plant Diseases ◽  
Plant Host ◽  
Rolling Circle ◽  
Rna Molecules ◽  
Viroid Replication ◽  
Plant Genes ◽  
Rolling Circle Mechanism

Viroids are small (about 300 nucleotides), single-stranded, circular, non-encapsidated pathogenic RNA molecules. They do not code for proteins and thus depend on plant host enzymes for their replication and other functions. They induce plant diseases by direct interaction with host factors but the mechanism of pathogenicity is still unknown. They can alter the expression of selected plant genes important for growth and development. Viroids belong to two families, the Avsunviroidae and the Pospiviroidae. Viroids of the Avsunviroidae family adopt a branched or quasi rod-like secondary structure in their native state. Members of the Pospiviroidae family adopt a rod-like secondary structure. In such native structures five structural/functional domains have been identified: central (C), pathogenicity, variable and two terminal domains. The central conserved region (CCR) within the C domain characterizes viroids of the Pospiviroidae. Specific secondary structures of this region play an important role in viroid replication and processing. Viroids of the Avsunviroidae family lack a CCR but possess self-cleaving properties by forming hammerhead ribozyme structures; they accumulate and replicate in chloroplasts, whereas members of the Pospiviroidae family have a nuclear localization. Viroid replication occurs via a rolling circle mechanism using either a symmetric or asymmetric pathway in three steps, RNA transcription, processing and ligation.

scholarly journals Autonomous Replication of the Conjugative Transposon Tn916

2016 ◽  
Vol 198 (24) ◽  
pp. 3355-3366 ◽  
Author(s):  
Laurel D. Wright ◽  
Alan D. Grossman
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Origin Of Replication ◽  
Rolling Circle Replication ◽  
Conjugative Transposon ◽  
Rolling Circle ◽  
Autonomous Replication ◽  
Integrative And Conjugative Elements ◽  
Rolling Circle Mechanism ◽  
Origin Of Transfer

ABSTRACTIntegrative and conjugative elements (ICEs), also known as conjugative transposons, are self-transferable elements that are widely distributed among bacterial phyla and are important drivers of horizontal gene transfer. Many ICEs carry genes that confer antibiotic resistances to their host cells and are involved in the dissemination of these resistance genes. ICEs reside in host chromosomes but under certain conditions can excise to form a plasmid that is typically the substrate for transfer. A few ICEs are known to undergo autonomous replication following activation. However, it is not clear if autonomous replication is a general property of many ICEs. We found that Tn916, the first conjugative transposon identified, replicates autonomously via a rolling-circle mechanism. Replication of Tn916was dependent on the relaxase encoded byorf20of Tn916. The origin of transfer of Tn916,oriT(916), also functioned as an origin of replication. Using immunoprecipitation and mass spectrometry, we found that the relaxase (Orf20) and the two putative helicase processivity factors (Orf22 and Orf23) encoded by Tn916likely interact in a complex and that the Tn916relaxase contains a previously unidentified conserved helix-turn-helix domain in its N-terminal region that is required for relaxase function and replication. Lastly, we identified a functional single-strand origin of replication (sso) in Tn916that we predict primes second-strand synthesis during rolling-circle replication. Together these results add to the emerging data that show that several ICEs replicate via a conserved, rolling-circle mechanism.IMPORTANCEIntegrative and conjugative elements (ICEs) drive horizontal gene transfer and the spread of antibiotic resistances in bacteria. ICEs reside integrated in a host genome but can excise to create a plasmid that is the substrate for transfer to other cells. Here we show that Tn916, an ICE with broad host range, undergoes autonomous rolling-circle replication when in the plasmid form. We found that the origin of transfer functions as a double-stranded origin of replication and identified a single-stranded origin of replication. It was long thought that ICEs do not undergo autonomous replication. Our work adds to the evidence that ICEs replicate autonomously as part of their normal life cycle and indicates that diverse ICEs use the same replicative mechanism.

REACTION OF SPRING WHEAT LINES WITH FOREIGN GENETIC MATERIAL TO THE IMPACT OF ARTIFICIALLY CREATED STRESSES

2021 ◽  
Author(s):  
O. V. Pavlova ◽  
◽  
L. A. Marchenkova ◽  
R. F. Chavdar ◽  
T. G. Orlova ◽  
...  
Keyword(s):  
Sodium Chloride ◽  
Environmental Factors ◽  
Spring Wheat ◽  
Genetic Material ◽  
Growth Processes ◽  
Genetic Characteristics ◽  
Early Stages ◽  
Inhibition Of Growth ◽  
Wheat Lines ◽  
The Impact

The adaptive properties of spring wheat lines with foreign genetic material at the early stages of ontogenesis on the backgrounds of salinization with sodium chloride and prolonged flooding of seeds in water were evaluated. In the course of the work, different degrees of inhibition of growth processes were revealed, depending on the factor used and the genetic characteristics of the studied forms, a comprehensive (summary) assessment of the index of stability characterizing adaptability to adverse environmental factors was shown.

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