scholarly journals Evolutionary coupling range varies widely among enzymes depending on selection pressure

2021 ◽  
Author(s):  
Julian Echave
Keyword(s):  
Selection Pressure ◽  
Evolutionary Coupling

scholarly journals Evolutionary coupling range varies widely among enzymes

2020 ◽  
Author(s):  
Julian Echave
Keyword(s):  
Long Range ◽  
Selection Pressure ◽  
Active Sites ◽  
Short Range ◽  
Evolutionary Constraints ◽  
Evolutionary Coupling

AbstractRecent studies proposed that active sites induce long-range evolutionary constraints in enzymes. However, the prevalence of such long-range evolutionary coupling is unknown and its relationship to the underlying physical coupling is unclear. Here I show that evolutionary coupling is not universally long range, but that range varies widely among enzymes, from 2Å to 20Å, influencing from 10% to 87% of protein sites. Moreover, evolutionary coupling range is not determined by physical coupling, which is short-range for all enzymes, but by selection pressure. The reason for this is that increasing selection pressure turns small physical couplings into large evolutionary couplings.

scholarly journals Amino-Acid Co-Variation in HIV-1 Gag Subtype C: HLA-Mediated Selection Pressure and Compensatory Dynamics

PLoS ONE ◽  
2010 ◽  
Vol 5 (9) ◽  
pp. e12463 ◽  
Author(s):  
Morgane Rolland ◽  
Jonathan M. Carlson ◽  
Siriphan Manocheewa ◽  
J. Victor Swain ◽  
Erinn Lanxon-Cookson ◽  
...  
Keyword(s):  
Amino Acid ◽  
Selection Pressure ◽  
Subtype C ◽  
Hiv 1

scholarly journals Whole-Genome Sequence Analysis of Pseudorabies Virus Clinical Isolates from Pigs in China between 2012 and 2017 in China

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1322
Author(s):  
Ruiming Hu ◽  
Leyi Wang ◽  
Qingyun Liu ◽  
Lin Hua ◽  
Xi Huang ◽  
...  
Keyword(s):  
Selection Pressure ◽  
Pseudorabies Virus ◽  
Viral Evolution ◽  
Infectious Agent ◽  
Genomic Diversity ◽  
Whole Genome Sequence ◽  
Evolutionary Constraint ◽  
The Novel ◽  
Novel Variants ◽  
Pressure Analysis

Pseudorabies virus (PRV) is an economically significant swine infectious agent. A PRV outbreak took place in China in 2011 with novel virulent variants. Although the association of viral genomic variability with pathogenicity is not fully confirmed, the knowledge concerning PRV genomic diversity and evolution is still limited. Here, we sequenced 54 genomes of novel PRV variants isolated in China from 2012 to 2017. Phylogenetic analysis revealed that China strains and US/Europe strains were classified into two separate genotypes. PRV strains isolated from 2012 to 2017 in China are highly related to each other and genetically close to classic China strains such as Ea, Fa, and SC. RDP analysis revealed 23 recombination events within novel PRV variants, indicating that recombination contributes significantly to the viral evolution. The selection pressure analysis indicated that most ORFs were under evolutionary constraint, and 19 amino acid residue sites in 15 ORFs were identified under positive selection. Additionally, 37 unique mutations were identified in 19 ORFs, which distinguish the novel variants from classic strains. Overall, our study suggested that novel PRV variants might evolve from classical PRV strains through point mutation and recombination mechanisms.

scholarly journals Metagenomic analyses and genetic diversity of Tomato leaf curl Arusha virus affecting tomato plants in Kenya

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Edith Khamonya Avedi ◽  
Adedapo Olutola Adediji ◽  
Dora Chao Kilalo ◽  
Florence Mmogi Olubayo ◽  
Isaac Macharia ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Selection Pressure ◽  
Management Strategies ◽  
Purifying Selection ◽  
Tomato Leaf ◽  
Amino Acid Sequences ◽  
Virus Population ◽  
Tomato Production ◽  
Tomato Leaf Curl ◽  
Leaf Curl

Abstract Background Tomato production is threatened worldwide by the occurrence of begomoviruses which are associated with tomato leaf curl diseases. There is little information on the molecular properties of tomato begomoviruses in Kenya, hence we investigated the population and genetic diversity of begomoviruses associated with tomato leaf curl in Kenya. Methods Tomato leaf samples with virus-like symptoms were obtained from farmers’ field across the country in 2018 and Illumina sequencing undertaken to determine the genetic diversity of associated begomoviruses. Additionally, the occurrence of selection pressure and recombinant isolates within the population were also evaluated. Results Twelve complete begomovirus genomes were obtained from our samples with an average coverage of 99.9%. The sequences showed 95.7–99.7% identity among each other and 95.9–98.9% similarities with a Tomato leaf curl virus Arusha virus (ToLCArV) isolate from Tanzania. Analysis of amino acid sequences showed the highest identities in the regions coding for the coat protein gene (98.5–100%) within the isolates, and 97.1–100% identity with the C4 gene of ToLCArV. Phylogenetic algorithms clustered all Kenyan isolates in the same clades with ToLCArV, thus confirming the isolates to be a variant of the virus. There was no evidence of recombination within our isolates. Estimation of selection pressure within the virus population revealed the occurrence of negative or purifying selection in five out of the six coding regions of the sequences. Conclusions The begomovirus associated with tomato leaf curl diseases of tomato in Kenya is a variant of ToLCArV, possibly originating from Tanzania. There is low genetic diversity within the virus population and this information is useful in the development of appropriate management strategies for the disease in the country.

scholarly journals Pest Status and Management of Corn Earworm (Lepidoptera: Noctuidae) in Field Corn in the United States

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Francis P F Reay-Jones
Keyword(s):  
United States ◽  
Selection Pressure ◽  
The United States ◽  
Corn Earworm ◽  
Bt Corn ◽  
Pest Status ◽  
Field Corn ◽  
Type Of Injury ◽  
The Impact ◽  
Economic Pest

Abstract The corn earworm, Helicoverpa zea (Boddie), is a common lepidopteran pest of corn (Zea mays L.) in the United States. This article provides an overview of the life history, ecology, plant injury, and management of H. zea in corn. Leaf injury by H. zea feeding can occur in vegetative stage corn, though this type of injury is rare. The most common type of injury is caused by larval feeding in ears. Because kernel injury is typically limited to the tip of the ear, H. zea is generally not considered an economic pest. The use of transgenic corn hybrids expressing insecticidal Cry proteins from Bacillus thuringiensis (Bt) Berliner can reduce injury from H. zea, though complete control is not achieved with most Bt traits. Resistance has been reported to several Bt toxins. Because H. zea is a major economic pest in cotton (Gossypium hirsutum L.) and because H. zea moths that developed on corn can migrate to cotton, selection pressure on H. zea in Bt corn has major implications for the pest status and injury to Bt cotton. Although the impact of H. zea on yield of field corn is generally negligible, the selection pressure exerted by Bt corn has led to management issues in cotton.

Emergence of ceftazidime/avibactam resistance in KPC-3-producing Klebsiella pneumoniae in vivo

2019 ◽  
Vol 74 (11) ◽  
pp. 3211-3216 ◽  
Author(s):  
Stephan Göttig ◽  
Denia Frank ◽  
Eleonora Mungo ◽  
Anika Nolte ◽  
Michael Hogardt ◽  
...  
Keyword(s):  
Combination Therapy ◽  
Klebsiella Pneumoniae ◽  
Selection Pressure ◽  
Galleria Mellonella ◽  
Phenotypic Characterization ◽  
Infection Model ◽  
Development Of Resistance ◽  
Time Kill

Abstract Objectives The β-lactam/β-lactamase inhibitor combination ceftazidime/avibactam is active against KPC-producing Enterobacterales. Herein, we present molecular and phenotypic characterization of ceftazidime/avibactam resistance in KPC-3-producing Klebsiella pneumoniae that emerged in vivo and in vitro. Methods Sequence analysis of blaKPC-3 was performed from clinical and in vitro-generated ceftazidime/avibactam-resistant K. pneumoniae isolates. Time–kill kinetics and the Galleria mellonella infection model were applied to evaluate the activity of ceftazidime/avibactam and imipenem alone and in combination. Results The ceftazidime/avibactam-resistant clinical K. pneumoniae isolate revealed the amino acid change D179Y in KPC-3. Sixteen novel mutational changes in KPC-3 among in vitro-selected ceftazidime/avibactam-resistant isolates were described. Time–kill kinetics showed the emergence of a resistant subpopulation under selection pressure with either imipenem or ceftazidime/avibactam. However, combined selection pressure with imipenem plus ceftazidime/avibactam prevented the development of resistance and resulted in bactericidal activity. Concordantly, the G. mellonella infection model revealed that monotherapy with ceftazidime/avibactam is prone to select for resistance in vivo and that combination therapy with imipenem results in significantly better survival. Conclusions Ceftazidime/avibactam is a valuable antibiotic against MDR and carbapenem-resistant Enterobacterales. Based on time–kill kinetics as well as an in vivo infection model we postulate a combination therapy of ceftazidime/avibactam and imipenem as a strategy to prevent the development of ceftazidime/avibactam resistance in KPC-producing Enterobacterales in vivo.

Stability of spinosad resistance inFrankliniella occidentalis(Pergande) under laboratory conditions

2008 ◽  
Vol 98 (4) ◽  
pp. 355-359 ◽  
Author(s):  
P. Bielza ◽  
V. Quinto ◽  
C. Grávalos ◽  
E. Fernández ◽  
J. Abellán ◽  
...  
Keyword(s):  
Resistant Strain ◽  
Selection Pressure ◽  
Frankliniella Occidentalis ◽  
Western Flower Thrips ◽  
Laboratory Conditions ◽  
Flower Thrips ◽  
Factors Influencing ◽  
Stability Of Resistance ◽  
The Stability ◽  
Successive Generations

AbstractThe stability of spinosad resistance in western flower thrips (WFT),Frankliniella occidentalis(Pergande), populations with differing initial frequencies of resistance was studied in laboratory conditions. The stability of resistance was assessed in bimonthly residual bioassays in five populations with initial frequencies of 100, 75, 50, 25 and 0% of resistant individuals. There were no consistent changes in susceptibility of the susceptible strain after eight months without insecticide pressure. In the resistant strain, very highly resistant to spinosad (RF50>23,000-fold), resistance was maintained up to eight months without further exposure to spinosad. In the absence of any immigration of susceptible genes into the population, resistance was stable. In the case of the population with different initial frequency of resistant thrips, spinosad resistance declined significantly two months later in the absence of selection pressure. With successive generations, these strains did not change significantly in sensitivity. Spinosad resistance inF. occidentalisdeclined significantly in the absence of selection pressure and the presence of susceptible WFT. These results suggest that spinosad resistance probably is unstable under field conditions, primarily due to the immigration of susceptible WFT. Factors influencing stability or reversion of spinosad resistance are discussed.

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