scholarly journals Searching for signatures of positive selection in cytochrome b gene associated with subterranean lifestyle in fast-evolving arvicolines (Arvicolinae, Cricetidae, Rodentia)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Olga V. Bondareva ◽  
Nadezhda A. Potapova ◽  
Kirill A. Konovalov ◽  
Tatyana V. Petrova ◽  
Natalia I. Abramson
Keyword(s):  
Amino Acid ◽  
Oxidative Phosphorylation ◽  
Adaptive Evolution ◽  
Complex Structure ◽  
Subterranean Rodents ◽  
Amino Acid Sequence Variation ◽  
Tertiary Protein Structure ◽  
Metabolic Performance ◽  
The Impact ◽  
Subterranean Species

Abstract Background Mitochondrial genes encode proteins involved in oxidative phosphorylation. Variations in lifestyle and ecological niche can be directly reflected in metabolic performance. Subterranean rodents represent a good model for testing hypotheses on adaptive evolution driven by important ecological shifts. Voles and lemmings of the subfamily Arvicolinae (Rodentia: Cricetidae) provide a good example for studies of adaptive radiation. This is the youngest group within the order Rodentia showing the fastest rates of diversification, including the transition to the subterranean lifestyle in several phylogenetically independent lineages. Results We evaluated the signatures of selection in the mitochondrial cytochrome b (cytB) gene in 62 Arvicolinae species characterized by either subterranean or surface-dwelling lifestyle by assessing amino acid sequence variation, exploring the functional consequences of the observed variation in the tertiary protein structure, and estimating selection pressure. Our analysis revealed that: (1) three of the convergent amino acid substitutions were found among phylogenetically distant subterranean species and (2) these substitutions may have an influence on the protein complex structure, (3) cytB showed an increased ω and evidence of relaxed selection in subterranean lineages, relative to non-subterranean, and (4) eight protein domains possess increased nonsynonymous substitutions ratio in subterranean species. Conclusions Our study provides insights into the adaptive evolution of the cytochrome b gene in the Arvicolinae subfamily and its potential implications in the molecular mechanism of adaptation. We present a framework for future characterizations of the impact of specific mutations on the function, physiology, and interactions of the mtDNA-encoded proteins involved in oxidative phosphorylation.

scholarly journals The impact of protein architecture on adaptive evolution

2019 ◽  
Author(s):  
Ana Filipa Moutinho ◽  
Fernanda Fontes Trancoso ◽  
Julien Yann Dutheil
Keyword(s):  
Amino Acid ◽  
Adaptive Evolution ◽  
Protein Function ◽  
Population Genomics ◽  
Solvent Accessibility ◽  
Protein Biosynthesis ◽  
Relative Solvent Accessibility ◽  
Adaptive Mutations ◽  
Protein Architecture ◽  
The Impact

AbstractAdaptive mutations play an important role in molecular evolution. However, the frequency and nature of these mutations at the intra-molecular level is poorly understood. To address this, we analysed the impact of protein architecture on the rate of adaptive substitutions, aiming to understand how protein biophysics influences fitness and adaptation. Using Drosophila melanogaster and Arabidopsis thaliana population genomics data, we fitted models of distribution of fitness effects and estimated the rate of adaptive amino-acid substitutions both at the protein and amino-acid residue level. We performed a comprehensive analysis covering genome, gene and protein structure, by exploring a multitude of factors with a plausible impact on the rate of adaptive evolution, such as intron number, protein length, secondary structure, relative solvent accessibility, intrinsic protein disorder, chaperone affinity, gene expression, protein function and protein-protein interactions. We found that the relative solvent accessibility is a major driver of adaptive evolution, with most adaptive mutations occurring at the surface of proteins. Moreover, we observe that the rate of adaptive substitutions differs between protein functional classes, with genes encoding for protein biosynthesis and degradation signalling exhibiting the fastest rates of protein adaptation. Overall, our results suggest that adaptive evolution in proteins is mainly driven by inter-molecular interactions, with host-pathogen coevolution likely playing a major role.

scholarly journals The Impact of Protein Architecture on Adaptive Evolution

2019 ◽  
Vol 36 (9) ◽  
pp. 2013-2028 ◽  
Author(s):  
Ana Filipa Moutinho ◽  
Fernanda Fontes Trancoso ◽  
Julien Yann Dutheil
Keyword(s):  
Amino Acid ◽  
Adaptive Evolution ◽  
Protein Function ◽  
Population Genomics ◽  
Solvent Accessibility ◽  
Protein Biosynthesis ◽  
Relative Solvent Accessibility ◽  
Adaptive Mutations ◽  
Protein Architecture ◽  
The Impact

Abstract Adaptive mutations play an important role in molecular evolution. However, the frequency and nature of these mutations at the intramolecular level are poorly understood. To address this, we analyzed the impact of protein architecture on the rate of adaptive substitutions, aiming to understand how protein biophysics influences fitness and adaptation. Using Drosophila melanogaster and Arabidopsis thaliana population genomics data, we fitted models of distribution of fitness effects and estimated the rate of adaptive amino-acid substitutions both at the protein and amino-acid residue level. We performed a comprehensive analysis covering genome, gene, and protein structure, by exploring a multitude of factors with a plausible impact on the rate of adaptive evolution, such as intron number, protein length, secondary structure, relative solvent accessibility, intrinsic protein disorder, chaperone affinity, gene expression, protein function, and protein–protein interactions. We found that the relative solvent accessibility is a major determinant of adaptive evolution, with most adaptive mutations occurring at the surface of proteins. Moreover, we observe that the rate of adaptive substitutions differs between protein functional classes, with genes encoding for protein biosynthesis and degradation signaling exhibiting the fastest rates of protein adaptation. Overall, our results suggest that adaptive evolution in proteins is mainly driven by intermolecular interactions, with host–pathogen coevolution likely playing a major role.

scholarly journals Recombination facilitates adaptive evolution in rhizobial soil bacteria

2021 ◽  
Author(s):  
Maria Izabel A. Cavassim ◽  
Stig U. Andersen ◽  
Thomas Bataillon ◽  
Mikkel Heide Schierup
Keyword(s):  
Natural Selection ◽  
Amino Acid ◽  
Homologous Recombination ◽  
Adaptive Evolution ◽  
Recombination Rate ◽  
Rhizobium Leguminosarum ◽  
Core Protein ◽  
Bacterial Genome ◽  
Bacterial Populations ◽  
The Impact

AbstractHomologous recombination is expected to increase natural selection efficacy by decoupling the fate of beneficial and deleterious mutations and by readily creating new combinations of beneficial alleles. Here, we investigate how the proportion of amino acid substitutions fixed by adaptive evolution (α) depends on the recombination rate in bacteria. We analyze 3086 core protein-coding sequences from 196 genomes belonging to five closely-related Rhizobium leguminosarum species. We find that α varies from 0.07 to 0.39 across species and is positively correlated with the level of recombination. We then evaluate the impact of recombination within each species by dividing genes into three equally sized recombination classes based on their average level of intragenic linkage disequilibrium. Generally, we found a significant increase in α with an increased recombination rate. This is both due to a higher estimated rate of adaptive evolution and a lower estimated rate of non-adaptive evolution, suggesting that recombination both increases the fixation probability of advantageous variants and decreases the probability of fixation of deleterious variants. Our results demonstrate that recombination facilitates adaptive evolution not only in eukaryotes, but also in prokaryotes. Adaptive evolution could thus be a selective force that universally promotes recombination.Significance statementWhether homologous recombination has a net beneficial or detrimental effect on adaptive evolution is largely unexplored in natural bacterial populations. We address this question by evaluating polymorphism and divergence data across 196 bacterial genome sequences of five closely-related Rhizobium leguminosarum species. We show that the proportion of amino acid changes fixed due to adaptive evolution (α) increases with an increased recombination rate. This correlation is observed both in the interspecies and intraspecific comparisons. These results suggest that homologous recombination directly impacts the efficacy of natural selection in prokaryotes, as it has been shown previously to be in eukaryotes.

scholarly journals HLA-DRB1 Alleles Associated with Lower Leishmaniasis Susceptibility Share Common Amino Acid Polymorphisms and Epitope Binding Repertoires

Vaccines ◽  
2021 ◽  
Vol 9 (3) ◽  
pp. 270
Author(s):  
Nicky de Vrij ◽  
Pieter Meysman ◽  
Sofie Gielis ◽  
Wim Adriaensen ◽  
Kris Laukens ◽  
...  
Keyword(s):  
Amino Acid ◽  
Cell Epitope ◽  
Human Leukocyte ◽  
Leishmania Species ◽  
Hla Polymorphism ◽  
Common Amino Acid ◽  
Binding Core ◽  
Epitope Discovery ◽  
Epitope Binding ◽  
The Impact

Susceptibility for leishmaniasis is largely dependent on host genetic and immune factors. Despite the previously described association of human leukocyte antigen (HLA) gene cluster variants as genetic susceptibility factors for leishmaniasis, little is known regarding the mechanisms that underpin these associations. To better understand this underlying functionality, we first collected all known leishmaniasis-associated HLA variants in a thorough literature review. Next, we aligned and compared the protection- and risk-associated HLA-DRB1 allele sequences. This identified several amino acid polymorphisms that distinguish protection- from risk-associated HLA-DRB1 alleles. Subsequently, T cell epitope binding predictions were carried out across these alleles to map the impact of these polymorphisms on the epitope binding repertoires. For these predictions, we used epitopes derived from entire proteomes of multiple Leishmania species. Epitopes binding to protection-associated HLA-DRB1 alleles shared common binding core motifs, mapping to the identified HLA-DRB1 amino acid polymorphisms. These results strongly suggest that HLA polymorphism, resulting in differential antigen presentation, affects the association between HLA and leishmaniasis disease development. Finally, we established a valuable open-access resource of putative epitopes. A set of 14 HLA-unrestricted strong-binding epitopes, conserved across species, was prioritized for further epitope discovery in the search for novel subunit-based vaccines.

Assessing the Impact of Secondary Structure and Solvent Accessibility on Protein Evolution

Genetics ◽  
1998 ◽  
Vol 149 (1) ◽  
pp. 445-458 ◽  
Author(s):  
Nick Goldman ◽  
Jeffrey L Thorne ◽  
David T Jones
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Protein Evolution ◽  
Solvent Accessibility ◽  
Strong Association ◽  
Length Distribution ◽  
Parametric Bootstrap ◽  
Amino Acid Replacement ◽  
Physical Constraints ◽  
The Impact

Abstract Empirically derived models of amino acid replacement are employed to study the association between various physical features of proteins and evolution. The strengths of these associations are statistically evaluated by applying the models of protein evolution to 11 diverse sets of protein sequences. Parametric bootstrap tests indicate that the solvent accessibility status of a site has a particularly strong association with the process of amino acid replacement that it experiences. Significant association between secondary structure environment and the amino acid replacement process is also observed. Careful description of the length distribution of secondary structure elements and of the organization of secondary structure and solvent accessibility along a protein did not always significantly improve the fit of the evolutionary models to the data sets that were analyzed. As indicated by the strength of the association of both solvent accessibility and secondary structure with amino acid replacement, the process of protein evolution—both above and below the species level—will not be well understood until the physical constraints that affect protein evolution are identified and characterized.

scholarly journals Deep Neural Network and Polynomial Chaos Expansion-Based Surrogate Models for Sensitivity and Uncertainty Propagation: An Application to a Rockfill Dam

Water ◽  
2021 ◽  
Vol 13 (13) ◽  
pp. 1830
Author(s):  
Gullnaz Shahzadi ◽  
Azzeddine Soulaïmani
Keyword(s):  
Polynomial Chaos ◽  
Complex Structure ◽  
Uncertainty Propagation ◽  
Surrogate Models ◽  
Polynomial Chaos Expansion ◽  
Soil Parameters ◽  
Chaos Expansion ◽  
Rockfill Dam ◽  
Parametric Studies ◽  
The Impact

Computational modeling plays a significant role in the design of rockfill dams. Various constitutive soil parameters are used to design such models, which often involve high uncertainties due to the complex structure of rockfill dams comprising various zones of different soil parameters. This study performs an uncertainty analysis and a global sensitivity analysis to assess the effect of constitutive soil parameters on the behavior of a rockfill dam. A Finite Element code (Plaxis) is utilized for the structure analysis. A database of the computed displacements at inclinometers installed in the dam is generated and compared to in situ measurements. Surrogate models are significant tools for approximating the relationship between input soil parameters and displacements and thereby reducing the computational costs of parametric studies. Polynomial chaos expansion and deep neural networks are used to build surrogate models to compute the Sobol indices required to identify the impact of soil parameters on dam behavior.

scholarly journals Codon harmonization reduces amino acid misincorporation in bacterially expressed P. falciparum proteins and improves their immunogenicity

AMB Express ◽  
2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Neeraja Punde ◽  
Jennifer Kooken ◽  
Dagmar Leary ◽  
Patricia M. Legler ◽  
Evelina Angov
Keyword(s):  
Protein Structure ◽  
Amino Acid ◽  
Codon Usage ◽  
Dna Sequences ◽  
Structural Integrity ◽  
Host Cells ◽  
Loss Of Function ◽  
Species Specific ◽  
And Function ◽  
The Impact

Abstract Codon usage frequency influences protein structure and function. The frequency with which codons are used potentially impacts primary, secondary and tertiary protein structure. Poor expression, loss of function, insolubility, or truncation can result from species-specific differences in codon usage. “Codon harmonization” more closely aligns native codon usage frequencies with those of the expression host particularly within putative inter-domain segments where slower rates of translation may play a role in protein folding. Heterologous expression of Plasmodium falciparum genes in Escherichia coli has been a challenge due to their AT-rich codon bias and the highly repetitive DNA sequences. Here, codon harmonization was applied to the malarial antigen, CelTOS (Cell-traversal protein for ookinetes and sporozoites). CelTOS is a highly conserved P. falciparum protein involved in cellular traversal through mosquito and vertebrate host cells. It reversibly refolds after thermal denaturation making it a desirable malarial vaccine candidate. Protein expressed in E. coli from a codon harmonized sequence of P. falciparum CelTOS (CH-PfCelTOS) was compared with protein expressed from the native codon sequence (N-PfCelTOS) to assess the impact of codon usage on protein expression levels, solubility, yield, stability, structural integrity, recognition with CelTOS-specific mAbs and immunogenicity in mice. While the translated proteins were expected to be identical, the translated products produced from the codon-harmonized sequence differed in helical content and showed a smaller distribution of polypeptides in mass spectra indicating lower heterogeneity of the codon harmonized version and fewer amino acid misincorporations. Substitutions of hydrophobic-to-hydrophobic amino acid were observed more commonly than any other. CH-PfCelTOS induced significantly higher antibody levels compared with N-PfCelTOS; however, no significant differences in either IFN-γ or IL-4 cellular responses were detected between the two antigens.

scholarly journals A Study of the Effects of Rain, Snow and Hail on the Atmospheric Electric Field near Ground

Atmosphere ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 996
Author(s):  
Athanasios Karagioras ◽  
Konstantinos Kourtidis
Keyword(s):  
Frequency Distribution ◽  
Complex Structure ◽  
Potential Gradient ◽  
Weather Conditions ◽  
The Other ◽  
Fair Weather ◽  
Northern Greece ◽  
Rain Events ◽  
The Impact ◽  
Bounce Back

The purpose of the present study is to investigate the impact of rain, snow and hail on potential gradient (PG), as observed in a period of ten years in Xanthi, northern Greece. An anticorrelation between PG and rainfall was observed for rain events that lasted several hours. When the precipitation rate was up to 2 mm/h, the decrease in PG was between 200 and 1300 V/m, in most cases being around 500 V/m. An event with rainfall rates up to 11 mm/h produced the largest drop in PG, of 2 kV/m. Shortly after rain, PG appeared to bounce back to somewhat higher values than the ones of fair-weather conditions. A decrease in mean hourly PG was observed, which was around 2–4 kV/m during the hail events which occurred concurrently with rain and from 0 to 3.5 kV/m for hail events with no rain. In the case of no drop, no concurrent drop in temperature was observed, while, for the other cases, it appeared that, for each degree drop in temperature, the drop in hourly mean PG was 1000 V/m; hence, we assume that the intensity of the hail event regulates the drop in PG. The frequency distribution of 1-minute PG exhibits a complex structure during hail events and extend from −18 to 11 kV/m, with most of the values in the negative range. During snow events, 1-minute PG exhibited rapid fluctuations between high positive and high negative values, its frequency distribution extending from −10 to 18 kV/m, with peaks at −10 and 3 kV/m.

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