scholarly journals Experimental Evolution Reveals a Genetic Basis for Membrane-Associated Virus Release

2020 ◽  
Author(s):  
Juan-Vicente Bou ◽  
Rafael Sanjuán
Keyword(s):  
Experimental Evolution ◽  
Genetic Basis ◽  
Close Association ◽  
Site Directed Mutagenesis ◽  
Full Genome ◽  
Virus Release ◽  
Viral Shedding ◽  
Free Virion ◽  
Viral Particles ◽  
Evolution Experiment

Abstract Many animal viruses replicate and are released from cells in close association to membranes. However, whether this is a passive process or is controlled by the virus remains poorly understood. Importantly, the genetic basis and evolvability of membrane-associated viral shedding have not been investigated. To address this, we performed a directed evolution experiment using coxsackievirus B3, a model enterovirus, in which we repeatedly selected the free-virion or the fast-sedimenting membrane-associated viral subpopulations. The virus responded to this selection regime by reproducibly fixing a series of mutations that altered the extent of membrane-associated viral shedding, as revealed by full-genome ultra-deep sequencing. Specifically, using site-directed mutagenesis, we showed that substitution N63H in the viral capsid protein VP3 reduced the ratio of membrane-associated to free viral particles by 2 orders of magnitude. These findings open new avenues for understanding the mechanisms and implications of membrane-associated viral transmission.

scholarly journals Genetics of a de novo origin of undifferentiated multicellularity

2018 ◽  
Vol 5 (8) ◽  
pp. 180912 ◽  
Author(s):  
Matthew D. Herron ◽  
William C. Ratcliff ◽  
Jacob Boswell ◽  
Frank Rosenzweig
Keyword(s):  
Experimental Evolution ◽  
Large Scale ◽  
Genetic Basis ◽  
De Novo ◽  
Microbial Evolution ◽  
Land Plants ◽  
Volvocine Algae ◽  
Major Transition ◽  
Evolution Experiment ◽  
Reproductive Processes

The evolution of multicellularity was a major transition in evolution and set the stage for unprecedented increases in complexity, especially in land plants and animals. Here, we explore the genetics underlying a de novo origin of multicellularity in a microbial evolution experiment carried out on the green alga Chlamydomonas reinhardtii . We show that large-scale changes in gene expression underlie the transition to a multicellular life cycle. Among these, changes to genes involved in cell cycle and reproductive processes were overrepresented, as were changes to C. reinhardtii -specific and volvocine-specific genes. These results suggest that the genetic basis for the experimental evolution of multicellularity in C. reinhardtii has both lineage-specific and shared features, and that the shared features have more in common with C. reinhardtii 's relatives among the volvocine algae than with other multicellular green algae or land plants.

scholarly journals Genetic and Antigenic Characterization of Avian Avulavirus Type 6 (AAvV-6) Circulating in Canadian Wild Birds (2005–2017)

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 543
Author(s):  
Tamiko Hisanaga ◽  
Catherine Soos ◽  
Nicola Lewis ◽  
Oliver Lung ◽  
Matthew Suderman ◽  
...  
Keyword(s):  
Clinical Symptoms ◽  
Fusion Gene ◽  
Full Genome ◽  
Genome Sequences ◽  
Viral Shedding ◽  
Genetic Groups ◽  
Antigenic Characterization ◽  
Specific Pathogen ◽  
First Time

We describe for the first time the genetic and antigenic characterization of 18 avian avulavirus type-6 viruses (AAvV-6) that were isolated from wild waterfowl in the Americas over the span of 12 years. Only one of the AAvV-6 viruses isolated failed to hemagglutinate chicken red blood cells. We were able to obtain full genome sequences of 16 and 2 fusion gene sequences from the remaining 2 isolates. This is more than double the number of full genome sequences available at the NCBI database. These AAvV-6 viruses phylogenetically grouped into the 2 existing AAvV-6 genotype subgroups indicating the existence of an intercontinental epidemiological link with other AAvV-6 viruses isolated from migratory waterfowl from different Eurasian countries. Antigenic maps made using HI assay data for these isolates showed that the two genetic groups were also antigenically distinct. An isolate representing each genotype was inoculated in specific pathogen free (SPF) chickens, however, no clinical symptoms were observed. A duplex fusion gene based real-time assay for the detection and genotyping of AAvV-6 to genotype 1 and 2 was developed. Using the developed assay, the viral shedding pattern in the infected chickens was examined. The chickens infected with both genotypes were able to shed the virus orally for about a week, however, no significant cloacal shedding was detected in chickens of both groups. Chickens in both groups developed detectable levels of anti-hemagglutinin antibodies 7 days after infection.

scholarly journals Characterization of the Nurr1 ligand-binding domain co-activator interaction surface

2006 ◽  
Vol 37 (2) ◽  
pp. 317-326 ◽  
Author(s):  
Nikolaos Volakakis ◽  
Michal Malewicz ◽  
Banafsheh Kadkhodai ◽  
Thomas Perlmann ◽  
Gerard Benoit
Keyword(s):  
Ligand Binding ◽  
Binding Site ◽  
Close Association ◽  
Binding Domain ◽  
Ligand Binding Domain ◽  
Site Directed Mutagenesis ◽  
Orphan Nuclear Receptor ◽  
Hydrophobic Region ◽  
Binding Surface

The recently solved crystal structure of the orphan nuclear receptor (NR) Nurr1 ligand-binding domain (LBD) showed that Nurr1 lacks a cavity for ligand binding and a canonical NR co-activator-binding site. Computer modeling of the Nurr1 LBD structure identified a hydrophobic region on the surface of the Nurr1 LBD that was positioned on the opposite side from the classical co-activator-binding site. Site-directed mutagenesis demonstrated that this region is critical for the activity of the Nurr1 LBD. Most mutations introduced in this region reduced or abolished transcriptional activity of the Nurr1 LBD, but mutation at lysine (K577) resulted in a drastically increased activity. Moreover, the activity of the Nurr1 LBD was shown to correlate with a propensity for proteasome-dependent degradation revealing a close association between activity and Nurr1 protein turnover. These data provide novel insights into the mechanisms of transcription via the Nurr1 LBD and identify an alternative co-activator-binding surface that is unique to the NR4A family of NRs.

scholarly journals Gene-level quantitative trait mapping in an expandedC. elegansmultiparent experimental evolution panel

2019 ◽  
Author(s):  
Luke M. Noble ◽  
Matthew V. Rockman ◽  
Henrique Teotónio
Keyword(s):  
Experimental Evolution ◽  
Recombinant Inbred Lines ◽  
Single Gene ◽  
Ancestral Population ◽  
C Elegans ◽  
Quantitative Trait Mapping ◽  
Trait Variance ◽  
Gene Level ◽  
Evolution Experiment

ABSTRACTTheCaenorhabditis elegansmultiparental experimental evolution (CeMEE) panel is a collection of genome-sequenced, cryopreserved recombinant inbred lines useful for mapping the genetic basis and evolution of quantitative traits. We have expanded the resource with new lines and new populations, and here report updated additive and epistatic mapping simulations and the genetic and haplotypic composition of CeMEE version 2. Additive QTL explaining 3% of trait variance are detected with >80% power, and the median detection interval is around the length of a single gene on the highly recombinant chromosome arms. Although CeMEE populations are derived from a long-term evolution experiment, genetic structure is dominated by variation present in the ancestral population and is not obviously associated with phenotypic differentiation.C. elegansprovides exceptional experimental advantages for the study of phenotypic evolution.

scholarly journals Sex ratio and the evolution of aggression in fruit flies

2021 ◽  
Vol 288 (1947) ◽  
Author(s):  
Eleanor Bath ◽  
Danielle Edmunds ◽  
Jessica Norman ◽  
Charlotte Atkins ◽  
Lucy Harper ◽  
...  
Keyword(s):  
Social Environment ◽  
Experimental Evolution ◽  
Genetic Basis ◽  
Female Aggression ◽  
Female Competition ◽  
Sexual Competition ◽  
The Social ◽  
Males And Females ◽  
Competition For Resources ◽  
Shared Genetic

Aggressive behaviours are among the most striking displayed by animals, and aggression strongly impacts fitness in many species. Aggression varies plastically in response to the social environment, but we lack direct tests of how aggression evolves in response to intra-sexual competition. We investigated how aggression in both sexes evolves in response to the competitive environment, using populations of Drosophila melanogaster that we experimentally evolved under female-biased, equal, and male-biased sex ratios. We found that after evolution in a female-biased environment—with less male competition for mates—males fought less often on food patches, although the total frequency and duration of aggressive behaviour did not change. In females, evolution in a female-biased environment—where female competition for resources is higher—resulted in more frequent aggressive interactions among mated females, along with a greater increase in post-mating aggression. These changes in female aggression could not be attributed solely to evolution either in females or in male stimulation of female aggression, suggesting that coevolved interactions between the sexes determine female post-mating aggression. We found evidence consistent with a positive genetic correlation for aggression between males and females, suggesting a shared genetic basis. This study demonstrates the experimental evolution of a behaviour strongly linked to fitness, and the potential for the social environment to shape the evolution of contest behaviours.

scholarly journals ANTIVIRAL TREATMENT OPTIONS FOR COVID-19 BY REDUCTION OF VIRAL LOAD AND VIRAL SHEDDING

2020 ◽  
Vol 4 (6) ◽  
Author(s):  
Chandrika Murugaiah
Keyword(s):  
Viral Load ◽  
Antiviral Treatment ◽  
Treatment Options ◽  
Cardiac Injury ◽  
Respiratory Illness ◽  
Viral Shedding ◽  
Viral Particles ◽  
Wide Range ◽  
Highly Correlated ◽  
Viral Development

The coronavirus disease 2019 (COVID-19) virus is a public health emergency of international concern, without known effective pharmaceutical treatment so far. It is difficult to treat infected patients who are experiencing acute respiratory failure, liver or cardiac injury, gastroenteritis and many other complications without any drug recommendation. Reducing the viral load is the most important key for Covid-19 treatment, where complication due to infection is highly correlated with the number of viral particles present in the lung and other organs of the patient. Most antivirals are effective against a wide range of viruses, where they inhibit viral development. Some of the possible antiviral treatment options for COVID-19 could be discovered from flu viral treatment that had led to quick respiratory illness recovery through reduction of viral load and viral shedding.

scholarly journals Selection maintains protein interactome resilience in the long-term evolution experiment with Escherichia coli

2021 ◽  
Author(s):  
Rohan Maddamsetti
Keyword(s):  
Experimental Evolution ◽  
Long Term Evolution ◽  
Rate Of Change ◽  
Network Resilience ◽  
Protein Protein Interaction ◽  
Ppi Networks ◽  
Term Evolution ◽  
Protein Interactome ◽  
Evolution Experiment

AbstractMost cellular functions are carried out by a dynamic network of interacting proteins. An open question is whether the network properties of protein interactomes represent phenotypes under natural selection. One proposal is that protein interactomes have evolved to be resilient, such that they tend to maintain connectivity when proteins are removed from the network. This hypothesis predicts that interactome resilience should be maintained during long-term experimental evolution. I tested this prediction by modeling the evolution of protein-protein interaction (PPI) networks in Lenski’s long-term evolution experiment with Escherichia coli (LTEE). In this test, I removed proteins affected by nonsense, insertion, deletion, and transposon mutations in evolved LTEE strains, and measured the resilience of the resulting networks. I compared the rate of change of network resilience in each LTEE population to the rate of change of network resilience for corresponding randomized networks. The evolved PPI networks are significantly more resilient than networks in which random proteins have been deleted. Moreover, the evolved networks are generally more resilient than networks in which the random deletion of proteins was restricted to those disrupted in LTEE. These results suggest that evolution in the LTEE has favored PPI networks that are, on average, more resilient than expected from the genetic variation across the evolved populations. My findings therefore support the hypothesis that selection maintains protein interactome resilience over evolutionary time.Significance StatementUnderstanding how protein-protein interaction (PPI) networks evolve is a central goal of evolutionary systems biology. One property that has been hypothesized to be important for PPI network evolution is resilience, which means that networks tend to maintain connectivity even after many nodes (proteins in this case) have been removed. This hypothesis predicts that PPI network resilience should be maintained during long-term experimental evolution. Consistent with this prediction, I found that the PPI networks that evolved over 50,000 generations of Lenski’s long-term evolution experiment with E. coli are more resilient than expected by chance.

scholarly journals Tell Me Where You’ve Been and I’ll Tell You How You’ll Evolve

mBio ◽  
2020 ◽  
Vol 11 (5) ◽  
Author(s):  
Marco Fumasoni
Keyword(s):  
High Temperatures ◽  
Adaptive Evolution ◽  
Experimental Evolution ◽  
Evolutionary Biology ◽  
Genetic Basis ◽  
Microbial Populations ◽  
Evolutionary Processes ◽  
Link Type ◽  
Selection Experiments ◽  
Evolutionary Trajectories

ABSTRACT The reproducibility of adaptive evolution is a long-standing debate in evolutionary biology. Kempher et al. (M. L. Kempher, X. Tao, R. Song, B. Wu, et al., mBio 11:e00569-20, 2020, https://doi.org/10.1128/mBio.00569-20) used experimental evolution to investigate the effect of previous evolutionary trajectories on the ability of microbial populations to adapt to high temperatures. Despite the divergence caused by adaptation to previous environments, all populations reproducibly converged on similar final levels of fitness. Nevertheless, the genetic basis of adaptation depended on past selection experiments, reinforcing the idea that previous adaptation can dictate the trajectories of later evolutionary processes.

scholarly journals Experimental evolution of the megaplasmid pMPPla107 in Pseudomonas stutzeri enables identification of genes contributing to sensitivity to an inhibitory agent

2021 ◽  
Vol 377 (1842) ◽  
Author(s):  
Brian A. Smith ◽  
Kevin Dougherty ◽  
Meara Clark ◽  
David A. Baltrus
Keyword(s):  
Pseudomonas Syringae ◽  
Experimental Evolution ◽  
Genetic Basis ◽  
Pseudomonas Stutzeri ◽  
Large Deletion ◽  
Host Cells ◽  
Single Amino Acid ◽  
Fitness Costs ◽  
Nonsynonymous Change ◽  
Single Amino Acid Change

Horizontally transferred elements, such as plasmids, can burden host cells with various metabolic and fitness costs and may lead to other potentially detrimental phenotypic effects. Acquisition of the Pseudomonas syringae megaplasmid pMPPla107 by various Pseudomonads causes sensitivity to a growth-inhibiting substance that is produced in cultures by Pseudomonads during growth under standard laboratory conditions. After approximately 500 generations of laboratory passage of Pseudomonas stutzeri populations containing pMPPla107, strains from two out of six independent passage lines displayed resistance to this inhibitory agent. Resistance was transferable and is, therefore, associated with mutations occurring on pMPPla107. Resequencing experiments demonstrated that resistance is likely due to a large deletion on the megaplasmid in one line, and to a nonsynonymous change in an uncharacterized megaplasmid locus in the other strain. We further used allele exchange experiments to confirm that resistance is due to this single amino acid change in a previously uncharacterized megaplasmid protein, which we name SkaA. These results provide further evidence that costs and phenotypic changes associated with horizontal gene transfer can be compensated through single mutational events and emphasize the power of experimental evolution and resequencing to better understand the genetic basis of evolved phenotypes. This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.

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