scholarly journals Lack of signal for the impact of venom gene diversity on speciation rates in cone snails

2018 ◽  
Author(s):  
Mark A Phuong ◽  
Michael E Alfaro ◽  
Gusti N Mahardika ◽  
Ristiyanti M Marwoto ◽  
Romanus Edy Prabowo ◽  
...  
Keyword(s):  
Gene Diversity ◽  
Rapid Evolution ◽  
Limiting Factor ◽  
Exon Capture ◽  
Speciation Rates ◽  
Intrinsic Capacity ◽  
Cone Snails ◽  
Species Specific ◽  
Capture Techniques ◽  
The Impact

AbstractUnderstanding why some groups of organisms are more diverse than others is a central goal in macroevolution. Evolvability, or lineages’ intrinsic capacity for evolutionary change, is thought to influence disparities in species diversity across taxa. Over macroevolutionary time scales, clades that exhibit high evolvability are expected to have higher speciation rates. Cone snails (family: Conidae, >900 spp.) provide a unique opportunity to test this prediction because their venom genes can be used to characterize differences in evolvability between clades. Cone snails are carnivorous, use prey-specific venom (conotoxins) to capture prey, and the genes that encode venom are known and diversify through gene duplication. Theory predicts that higher gene diversity confers a greater potential to generate novel phenotypes for specialization and adaptation. Therefore, if conotoxin gene diversity gives rise to varying levels of evolvability, conotoxin gene diversity should be coupled with macroevolutionary speciation rates. We applied exon capture techniques to recover phylogenetic markers and conotoxin loci across 314 species, the largest venom discovery effort in a single study. We paired a reconstructed timetree using 12 fossil calibrations with species-specific estimates of conotoxin gene diversity and used trait-dependent diversification methods to test the impact of evolvability on diversification patterns. Surprisingly, did not detect any signal for the relationship between conotoxin gene diversity and speciation rates, suggesting that venom evolution may not be the rate-limiting factor controlling diversification dynamics in Conidae. Comparative analyses showed some signal for the impact of diet and larval dispersal strategy on diversification patterns, though whether or not we detected a signal depended on the dataset and the method. If our results remain true with increased sampling in future studies, they suggest that the rapid evolution of Conidae venom may cause other factors to become more critical to diversification, such as ecological opportunity or traits that promote isolation among lineages.

scholarly journals Lack of Signal for the Impact of Conotoxin Gene Diversity on Speciation Rates in Cone Snails

2019 ◽  
Vol 68 (5) ◽  
pp. 781-796 ◽  
Author(s):  
Mark A Phuong ◽  
Michael E Alfaro ◽  
Gusti N Mahardika ◽  
Ristiyanti M Marwoto ◽  
Romanus Edy Prabowo ◽  
...  
Keyword(s):  
Gene Diversity ◽  
Rapid Evolution ◽  
Limiting Factor ◽  
Exon Capture ◽  
Speciation Rates ◽  
Intrinsic Capacity ◽  
Cone Snails ◽  
Species Specific ◽  
Capture Techniques ◽  
The Impact

Abstract Understanding why some groups of organisms are more diverse than others is a central goal in macroevolution. Evolvability, or the intrinsic capacity of lineages for evolutionary change, is thought to influence disparities in species diversity across taxa. Over macroevolutionary time scales, clades that exhibit high evolvability are expected to have higher speciation rates. Cone snails (family: Conidae, $>$900 spp.) provide a unique opportunity to test this prediction because their toxin genes can be used to characterize differences in evolvability between clades. Cone snails are carnivorous, use prey-specific venom (conotoxins) to capture prey, and the genes that encode venom are known and diversify through gene duplication. Theory predicts that higher gene diversity confers a greater potential to generate novel phenotypes for specialization and adaptation. Therefore, if conotoxin gene diversity gives rise to varying levels of evolvability, conotoxin gene diversity should be coupled with macroevolutionary speciation rates. We applied exon capture techniques to recover phylogenetic markers and conotoxin loci across 314 species, the largest venom discovery effort in a single study. We paired a reconstructed timetree using 12 fossil calibrations with species-specific estimates of conotoxin gene diversity and used trait-dependent diversification methods to test the impact of evolvability on diversification patterns. Surprisingly, we did not detect any signal for the relationship between conotoxin gene diversity and speciation rates, suggesting that venom evolution may not be the rate-limiting factor controlling diversification dynamics in Conidae. Comparative analyses showed some signal for the impact of diet and larval dispersal strategy on diversification patterns, though detection of a signal depended on the dataset and the method. If our results remain true with increased taxonomic sampling in future studies, they suggest that the rapid evolution of conid venom may cause other factors to become more critical to diversification, such as ecological opportunity or traits that promote isolation among lineages.

scholarly journals Targeted sequencing of venom genes from cone snail genomes reveals coupling between dietary breadth and conotoxin diversity

2017 ◽  
Author(s):  
Mark A Phuong ◽  
Gusti N Mahardika
Keyword(s):  
Gene Diversity ◽  
Gene Families ◽  
Targeted Sequencing ◽  
Toxin Gene ◽  
Cone Snail ◽  
Genetic Changes ◽  
Marine Gastropods ◽  
Dietary Breadth ◽  
Cone Snails ◽  
The Impact

AbstractAlthough venomous taxa provide an attractive system to study the genetic basis of adaptation and speciation, the slow pace of toxin gene discovery through traditional laboratory techniques (e.g., cDNA cloning) have limited their utility in the study of ecology and evolution. Here, we applied targeted sequencing techniques to selectively recover venom gene superfamilies and non-toxin loci from the genomes of 32 species of cone snails (family, Conidae), a hyper diverse group of carnivorous marine gastropods that capture their prey using a cocktail of neurotoxic proteins (conotoxins). We were able to successfully recover conotoxin gene superfamilies across all species sequenced in this study with high confidence (> 100X coverage). We found that conotoxin gene superfamilies are composed of 1-6 exons and adjacent noncoding regions are not enriched for simple repetitive elements. Additionally, we provided further evidence for several genetic factors shaping venom composition in cone snails, including positive selection, extensive gene turnover, expression regulation, and potentially, presence-absence variation. Using comparative phylogenetic methods, we found that while diet specificity did not predict patterns of conotoxin gene superfamily size evolution, dietary breadth was positively correlated with total conotoxin gene diversity. These results continue to emphasize the importance of dietary breadth in shaping venom evolution, an underappreciated ecological correlate in venom biology. Finally, the targeted sequencing technique demonstrated here has the potential to radically increase the pace at which venom gene families are sequenced and studied, reshaping our ability to understand the impact of genetic changes on ecologically relevant phenotypes and subsequent diversification.

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 16S rRNA gene and 18S rRNA gene diversity in microbial mat communities in meltwater ponds on the McMurdo Ice Shelf, Antarctica

Polar Biology ◽  
2021 ◽  
Author(s):  
Eleanor E. Jackson ◽  
Ian Hawes ◽  
Anne D. Jungblut
Keyword(s):  
16S Rrna ◽  
18S Rrna ◽  
High Throughput Sequencing ◽  
Microbial Mats ◽  
Gene Diversity ◽  
Salinity Gradient ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Ice Shelf ◽  
The Impact

AbstractThe undulating ice of the McMurdo Ice Shelf, Southern Victoria Land, supports one of the largest networks of ice-based, multiyear meltwater pond habitats in Antarctica, where microbial mats are abundant and contribute most of the biomass and biodiversity. We used 16S rRNA and 18S rRNA gene high-throughput sequencing to compare variance of the community structure in microbial mats within and between ponds with different salinities and pH. Proteobacteria and Cyanobacteria were the most abundant phyla, and composition at OTU level was highly specific for the meltwater ponds with strong community sorting along the salinity gradient. Our study provides the first detailed evaluation of eukaryote communities for the McMurdo Ice Shelf using the 18S rRNA gene. They were dominated by Ochrophyta, Chlorophyta and Ciliophora, consistent with previous microscopic analyses, but many OTUs belonging to less well-described heterotrophic protists from Antarctic ice shelves were also identified including Amoebozoa, Rhizaria and Labyrinthulea. Comparison of 16S and 18S rRNA gene communities showed that the Eukaryotes had lower richness and greater similarity between ponds in comparison with Bacteria and Archaea communities on the McMurdo Ice shelf. While there was a weak correlation between community dissimilarity and geographic distance, the congruity of microbial assemblages within ponds, especially for Bacteria and Archaea, implies strong habitat filtering in ice shelf meltwater pond ecosystems, especially due to salinity. These findings help to understand processes that are important in sustaining biodiversity and the impact of climate change on ice-based aquatic habitats in Antarctica.

scholarly journals Salivary Digestion Extends the Range of Sugar-Aversions in the German Cockroach

Insects ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 263
Author(s):  
Ayako Wada-Katsumata ◽  
Coby Schal
Keyword(s):  
Rapid Evolution ◽  
German Cockroach ◽  
Gustatory System ◽  
Resistance Trait ◽  
Cockroach Blattella Germanica ◽  
Behavioral Resistance ◽  
Gustatory Information ◽  
The Impact ◽  
Hydrolysis Of ◽  
Glucose Aversion

Saliva has diverse functions in feeding behavior of animals. However, the impact of salivary digestion of food on insect gustatory information processing is poorly documented. Glucose-aversion (GA) in the German cockroach, Blattella germanica, is a highly adaptive heritable behavioral resistance trait that protects the cockroach from ingesting glucose-containing-insecticide-baits. In this study, we confirmed that GA cockroaches rejected glucose, but they accepted oligosaccharides. However, whereas wild-type cockroaches that accepted glucose also satiated on oligosaccharides, GA cockroaches ceased ingesting the oligosaccharides within seconds, resulting in significantly lower consumption. We hypothesized that saliva might hydrolyze oligosaccharides, releasing glucose and terminating feeding. By mixing artificially collected cockroach saliva with various oligosaccharides, we demonstrated oligosaccharide-aversion in GA cockroaches. Acarbose, an alpha-glucosidase inhibitor, prevented the accumulation of glucose and rescued the phagostimulatory response and ingestion of oligosaccharides. Our results indicate that pre-oral and oral hydrolysis of oligosaccharides by salivary alpha-glucosidases released glucose, which was then processed by the gustatory system of GA cockroaches as a deterrent and caused the rejection of food. We suggest that the genetic mechanism of glucose-aversion support an extended aversion phenotype that includes glucose-containing oligosaccharides. Salivary digestion protects the cockroach from ingesting toxic chemicals and thus could support the rapid evolution of behavioral and physiological resistance in cockroach populations.

Genetic Diversity of Wild Oat (Avena fatua)Populations from China and the United States

Weed Science ◽  
2007 ◽  
Vol 55 (2) ◽  
pp. 95-101 ◽  
Author(s):  
Runzhi Li ◽  
Shiwen Wang ◽  
Liusheng Duan ◽  
Zhaohu Li ◽  
Michael J. Christoffers ◽  
...  
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
The United States ◽  
Mantel Test ◽  
Wild Oat ◽  
Chinese Populations ◽  
Nei's Distance ◽  
The Impact

Weed genetic diversity is important for understanding the ability of weeds to adapt to different environments and the impact of herbicide selection on weed populations. Genetic diversity within and among six wild oat populations in China varying in herbicide selection pressure and one population in North Dakota were surveyed using 64 polymorphic alleles resulting from 25 microsatellite loci. Mean Nei's gene diversity (h) for six wild oat populations from China was between 0.17 and 0.21, and total diversity (HT) was 0.23. A greater proportion of this diversity, however, was within (Hs= 0.19) rather than among (Gst= 0.15) populations. For the wild oat population from the United States,h= 0.24 andHT= 0.24 were comparable to the values for the six populations from China. Cluster analysis divided the seven populations into two groups, where one group was the United States population and the other group included the six Chinese populations. The genetic relationships among six populations from China were weakly correlated with their geographic distribution (r= 0.22) using the Mantel test. Minimal difference in gene diversity and small genetic distance (Nei's distance 0.07 or less) among six populations from China are consistent with wide dispersal of wild oat in the 1980s. Our results indicate that the wild oat populations in China are genetically diverse at a level similar to North America, and the genetic diversity of wild oat in the broad spatial scale is not substantially changed by environment, agronomic practices, or herbicide usage.

Evolutionary origin of the cell nucleus and its functional architecture

2010 ◽  
Vol 48 ◽  
pp. 1-24 ◽  
Author(s):  
Jan Postberg ◽  
Hans J. Lipps ◽  
Thomas Cremer
Keyword(s):  
Cell Nucleus ◽  
Interdisciplinary Research ◽  
Nuclear Organization ◽  
Nuclear Architecture ◽  
Evolutionary Origin ◽  
Cell Type ◽  
Research Strategies ◽  
Evolutionarily Conserved ◽  
Species Specific ◽  
The Impact

Understanding the evolutionary origin of the nucleus and its compartmentalized architecture provides a huge but, as expected, greatly rewarding challenge in the post-genomic era. We start this chapter with a survey of current hypotheses on the evolutionary origin of the cell nucleus. Thereafter, we provide an overview of evolutionarily conserved features of chromatin organization and arrangements, as well as topographical aspects of DNA replication and transcription, followed by a brief introduction of current models of nuclear architecture. In addition to features which may possibly apply to all eukaryotes, the evolutionary plasticity of higher-order nuclear organization is reflected by cell-type- and species-specific features, by the ability of nuclear architecture to adapt to specific environmental demands, as well as by the impact of aberrant nuclear organization on senescence and human disease. We conclude this chapter with a reflection on the necessity of interdisciplinary research strategies to map epigenomes in space and time.

scholarly journals The impact of using digital textbooks in the formation of scientific thinking in the discipline of Natural Sciences

2021 ◽  
Author(s):  
Marieta IORDACHE (NEAGU) ◽  
◽  
◽  
Keyword(s):  
Direct Contact ◽  
Rapid Evolution ◽  
Natural Sciences ◽  
Quality Education ◽  
Learning Context ◽  
Digital Textbook ◽  
Digital World ◽  
Evolution Of Technology ◽  
Quality Learning ◽  
The Impact

Quality education should ensure a cultural and value balance. The rapid evolution of technology is a reality today in all areas of activity, including the education system. Creating a favorable quality learning context becomes an imperative of the time. The education acquired today in school is not enough to cope with the avalanche of changes facing humanity The use of the digital textbook in primary school contributes to the awareness of students of the possibility of using technology for their own training, being a bridge between its digital world and school. In particular, in the natural sciences classes, it makes possible a better understanding of phenomena and knowledge, making up for the impossibility of direct contact with a virtual reality. Thus, the rational thinking based on science is stimulated, explaining the phenomena that happened in nature on the students' understanding.

scholarly journals Fertilization the Omission One Test as Determination Limiting Factors for Maize Biomass (Zea mays L.)

2021 ◽  
Vol 4 (2) ◽  
pp. 94-105
Author(s):  
Koko Tampubolon ◽  
Bagus Fitra Azmi ◽  
Perdana Andriano Tamba ◽  
Ayu Widya Lestari ◽  
Kamaruddin Kamaruddin ◽  
...  
Keyword(s):  
Plant Height ◽  
Leaf Growth ◽  
Block Design ◽  
Relative Yield ◽  
Animal Husbandry ◽  
Dry Weight ◽  
Limiting Factors ◽  
Limiting Factor ◽  
Test Technique ◽  
The Impact

Introduction: The research was aimed to obtain information on the impact of omission one test fertilization as a determination limiting factors for the growth and biomass of maize in variety Bonanza F1. Materials and Methods: The research was located in the experimental field, Faculty of Agriculture and Animal Husbandry, Universitas Tjut Nyak Dhien, Medan from December 2020 until February 2021. The research was applied by Randomized Block Design in non-factorial through fertilization of omission one test that has been converted (urea : SP-36 : KCl = 0.75 : 0.50 : 0.125 g polybag-1). The treatment of this research include P0 = non-fertilization; P1= N+P+K; P2= P+K; P3= N+K; P4= N+P using three replications. The parameters include plant height, leaf growth, total fresh weight, total dry weight, and the percentage of relative yield then processed using ANOVA and continued with DMRT at 5% ± standard error with SPSS v.20 software. Results: Informed that the omission one test technique significantly improved all the characteristics of maize in the variety Bonanza F1. The highest increase in plant height was found in the N+P of 83.65%, meanwhile, the highest leaf and biomass growth characters were found in N+P+K, ranged of 50.00 to 177.81% and 487.60 to 507.37%, respectively. It was obtained that the limiting factor for the maize growth in variety Bonanza F1 was found in the un-fertilization of nitrogen.

scholarly journals Effects of reindeer grazing and recovery after cessation of grazing on the ground-dwelling spider assemblage in Finnish Lapland

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7330
Author(s):  
Teemu Saikkonen ◽  
Varpu Vahtera ◽  
Seppo Koponen ◽  
Otso Suominen
Keyword(s):  
Species Richness ◽  
Rangifer Tarandus ◽  
Forest Ecosystems ◽  
Grazing Pressure ◽  
Ground Vegetation ◽  
Total Abundance ◽  
Finnish Lapland ◽  
Species Specific ◽  
The Impact

The effect of reindeer Rangifer tarandus L. grazing on the ground-dwelling spider assemblage in Northern Finland was studied. Changes in species richness, abundance and evenness of spider assemblages were analyzed in relation to changes in vegetation and environmental factors in long term grazed and ungrazed sites as well as sites that had recently switched from grazed to ungrazed and vice versa. Grazing was found to have a significant impact on height and biomass of lichens and other ground vegetation. However, it seemed not to have an impact on the total abundance of spiders. This is likely caused by opposing family and species level responses of spiders to the grazing regime. Lycosid numbers were highest in grazed and linyphiid numbers in ungrazed areas. Lycosidae species richness was highest in ungrazed areas whereas Linyphiidae richness showed no response to grazing. Four Linyphiidae, one Thomisidae and one Lycosidae species showed strong preference for specific treatments. Sites that had recovered from grazing for nine years and the sites that were grazed for the last nine years but were previously ungrazed resembled the long term grazed sites. The results emphasize the importance of reindeer as a modifier of boreal forest ecosystems but the impact of reindeer grazing on spiders seems to be family and species specific. The sites with reversed grazing treatment demonstrate that recovery from strong grazing pressure at these high latitudes is a slow process whereas reindeer can rapidly change the conditions in previously ungrazed sites similar to long term heavily grazed conditions.

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