To see the other types of publications on this topic, follow the link: Substitution rate variability.
Journal articles on the topic 'Substitution rate variability'
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the top 50 journal articles for your research on the topic 'Substitution rate variability.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Browse journal articles on a wide variety of disciplines and organise your bibliography correctly.
1
Hicks, A. L., and S. Duffy. "Genus-Specific Substitution Rate Variability among Picornaviruses." Journal of Virology 85, no. 15 (May 25, 2011): 7942–47. http://dx.doi.org/10.1128/jvi.02535-10.
Full text
2
Grigoras, Ioana, Tatiana Timchenko, Ana Grande-Pérez, Lina Katul, Heinrich-Josef Vetten, and Bruno Gronenborn. "High Variability and Rapid Evolution of a Nanovirus." Journal of Virology 84, no. 18 (June 30, 2010): 9105–17. http://dx.doi.org/10.1128/jvi.00607-10.
Full textAbstract:
ABSTRACT Nanoviruses are multipartite single-stranded DNA (ssDNA) plant viruses that cause important diseases of leguminous crops and banana. Little has been known about the variability and molecular evolution of these viruses. Here we report on the variability of faba bean necrotic stunt virus (FBNSV), a nanovirus from Ethiopia. We found mutation frequencies of 7.52 × 10−4 substitutions per nucleotide in a field population of the virus and 5.07 × 10−4 substitutions per nucleotide in a laboratory-maintained population derived thereof. Based on virus propagation for a period of more than 2 years, we determined a nucleotide substitution rate of 1.78 × 10−3 substitutions per nucleotide per year. This high molecular evolution rate places FBNSV, as a representative of the family Nanoviridae, among the fastest-evolving ssDNA viruses infecting plants or vertebrates.
3
Alvarez-Valin, Fernando, José Francisco Tort, and Giorgio Bernardi. "Nonrandom Spatial Distribution of Synonymous Substitutions in the GP63 Gene From Leishmania." Genetics 155, no. 4 (August 1, 2000): 1683–92. http://dx.doi.org/10.1093/genetics/155.4.1683.
Full textAbstract:
AbstractIn this work we analyze the variability in substitution rates in the GP63 gene from Leishmania. By using a sliding window to estimate substitution rates along the gene, we found that the rate of synonymous substitutions along the GP63 gene is highly correlated with both the rate of amino acid substitution and codon bias. Furthermore, we show that comparisons involving genes that represent independent phylogenetic lines yield very similar divergence/conservation patterns, thus suggesting that deterministic forces (i.e., nonstochastic forces such as selection) generated these patterns. We present evidence indicating that the variability in substitution rates is unambiguously related to functionally relevant features. In particular, there is a clear relationship between rates and the tertiary structure of the encoded protein since all divergent segments are located on the surface of the molecule and facing one side (almost parallel to the cell membrane) on the exposed surface of the organism. Remarkably, the protein segments encoded by these variable regions encircle the active site in a funnel-like distribution. These results strongly suggest that the pattern of nucleotide divergence and, notably, of synonymous divergence is affected by functional constraints.
4
Imran, Mohd. "Substitution Trends in the Mitochondrial Cytochrome B Protein Coding Gene and the Corresponding Changes in its Amino Acid Sequence in Catfish Species." International Journal of Research in Science and Technology 12, no. 03 (2022): 11–18. http://dx.doi.org/10.37648/ijrst.v12i03.003.
Full textAbstract:
The study describes the divergence trends in the partial segment cytochrome b gene (cyt. b) in six catfish species on the basis of the nucleotide substitutions and their location in the triplet codons of the resulting amino acid sequence. The nucleotide sequences of all six species were found A+T rich with average nucleotide frequencies as A: 28.6%; T: 29.3%; G: 13.6%; C: 28.5%, showing an antiguanine bias which was found strongest in R. rita. The transition substitution rate was found highest at 3rd codon position in all the species. The evolutionary divergence follows the trend as highest at 3rd codon position followed by 1st codon position and the least on 2 nd codon position among all species. When amino acid sequences of cytochrome b were aligned, only 12 sites were found with a total 29 amino acid substitutions. which is a resultant of the substitution trend of three codon positions. Majority of the amino acid substitutions were found synonymous and conservative. Three different variability trends are observed in the cyt. b gene which run simultaneously on three different codon positions of triplet codons. Nucleotide substitutions at three codon positions follows the order 3 rd (87) >1st (32) >2nd (03) the frequency of amino acid substitution follows the order 1 st (11) >3rd (04) >2 nd (02); and the frequency of non-conservative amino acid changes found as 2 nd (1:2) >1st (5:11) >3rd (1:4). The study has provided an in-depth understanding of the relative variability and substitution trends in the mitochondrial cytochrome b gene in catfish species at both DNA and protein level.
5
Martínez-Arias, Rosa, Francesc Calafell, Eva Mateu, David Comas, Aida Andrés, and Jaume Bertranpetit. "Sequence Variability of a Human Pseudogene." Genome Research 11, no. 6 (May 8, 2001): 1071–85. http://dx.doi.org/10.1101/gr.167701.
Full textAbstract:
We have obtained haplotypes from the autosomal glucocerebrosidase pseudogene (psGBA) for 100 human chromosomes from worldwide populations, as well as for four chimpanzee and four gorilla chromosomes. In humans, in a 5420-nucleotide stretch analyzed, variation comprises 17 substitutions, a 3-bp deletion, and a length polymorphism at a polyadenine tract. The substitution rate on the pseudogene (1.23 ± 0.22 × 10−9 per nucleotide and year) is within the range of previous estimates considering phylogenetic estimations. Recombination within the pseudogene was recognized, although the low variability of this locus prevented an accurate measure of recombination rates. At least 13% of the psGBAsequence could be attributed to gene conversion from the contiguousGBA gene, whereas the reciprocal event has been shown to lead to Gaucher disease. Human psGBA sequences showed a recent coalescence time (∼200,000 yr ago), and the most ancestral haplotype was found only in Africans; both observations are compatible with the replacement hypothesis of human origins. In a deeper timeframe, phylogenetic analysis showed that the duplication event that created psGBA could be dated at ∼27 million years ago, in agreement with previous estimates.
6
Grishin, N. V. "From Complete Genomes to Measures of Substitution Rate Variability Within and Between Proteins." Genome Research 10, no. 7 (July 1, 2000): 991–1000. http://dx.doi.org/10.1101/gr.10.7.991.
Full text
7
Yeh, So-Wei, Tsun-Tsao Huang, Jen-Wei Liu, Sung-Huan Yu, Chien-Hua Shih, Jenn-Kang Hwang, and Julian Echave. "Local Packing Density Is the Main Structural Determinant of the Rate of Protein Sequence Evolution at Site Level." BioMed Research International 2014 (2014): 1–10. http://dx.doi.org/10.1155/2014/572409.
Full textAbstract:
Functional and biophysical constraints result in site-dependent patterns of protein sequence variability. It is commonly assumed that the key structural determinant of site-specific rates of evolution is the Relative Solvent Accessibility (RSA). However, a recent study found that amino acid substitution rates correlate better with two Local Packing Density (LPD) measures, the Weighted Contact Number (WCN) and the Contact Number (CN), than with RSA. This work aims at a more thorough assessment. To this end, in addition to substitution rates, we considered four other sequence variability scores, four measures of solvent accessibility (SA), and other CN measures. We compared all properties for each protein of a structurally and functionally diverse representative dataset of monomeric enzymes. We show that the best sequence variability measures take into account phylogenetic tree topology. More importantly, we show that both LPD measures (WCN and CN) correlate better than all of the SA measures, regardless of the sequence variability score used. Moreover, the independent contribution of the best LPD measure is approximately four times larger than that of the best SA measure. This study strongly supports the conclusion that a site’s packing density rather than its solvent accessibility is the main structural determinant of its rate of evolution.
8
Mannino, Frank, Sadie Wisotsky, Sergei L. Kosakovsky Pond, and Spencer V. Muse. "Equiprobable discrete models of site-specific substitution rates underestimate the extent of rate variability." PLOS ONE 15, no. 3 (March 2, 2020): e0229493. http://dx.doi.org/10.1371/journal.pone.0229493.
Full text
9
Pesole, Graziano, and Cecilia Saccone. "A Novel Method for Estimating Substitution Rate Variation Among Sites in a Large Dataset of Homologous DNA Sequences." Genetics 157, no. 2 (February 1, 2001): 859–65. http://dx.doi.org/10.1093/genetics/157.2.859.
Full textAbstract:
Abstract We present here a novel method to estimate the site-specific relative variability in large sets of homologous sequences. It is based on the simple idea that the more closely related are the compared sequences, the higher the probability of observing nucleotide changes at rapidly evolving sites. A simulation study has been carried out to support the reliability of the method, which has been applied also to analyzing the site variability of all available human sequences corresponding to the two hypervariable regions of the mitochondrial D-loop.
10
Ryynänen, Heikki J., and Craig R. Primmer. "Varying signals of the effects of natural selection during teleost growth hormone gene evolution." Genome 49, no. 1 (January 1, 2006): 42–53. http://dx.doi.org/10.1139/g05-079.
Full textAbstract:
The growth hormone (GH) gene of teleost fish exhibits a higher degree of variability compared with other vertebrate groups. However, the different selective constraints at the sequence level are not well understood. In this study, maximum-likelihood (ML) models of codon substitutions were used to investigate Darwinian adaptive evolution of the GH gene in teleost fishes. Complete GH gene sequences of 54 fish species were classified into 4 orders, and the variable nature of GH was examined by determining the dN and dS rate variation and the rates of molecular evolution for each teleost order. The results indicate that although the overall evolution rate for teleost GH is high ((1.15 ± 0.01) × 10–9 substitutions/(aa site·y)) compared with the "slow phases" in mammals ((0.21 to 0.28 ± 0.05) × 10–9), the vital structure of this gene has been retained. While the majority of the amino acid changes appear to be due to relaxation of purifying selection, some positively selected sites were detected in regions with no specifically identified role in protein function. The positively selected regions observed in salmoniformes lineage suggests a possible role for positive selection driving functional divergence in paralogous forms of the GH gene after whole-genome duplication in this lineage.Key words: teleost fish, growth hormone, positive selection, synonymous substitution, non-synonymous substitution, molecular evolution.
11
Lepore, Luciana, Claudia Fabrizio, Davide Fiore Bavaro, Eugenio Milano, Anna Volpe, Antonella Lagioia, Gioacchino Angarano, Annalisa Saracino, and Laura Monno. "Gp120 substitutions at positions associated with resistance to fostemsavir in treatment-naive HIV-1-positive individuals." Journal of Antimicrobial Chemotherapy 75, no. 6 (March 19, 2020): 1580–87. http://dx.doi.org/10.1093/jac/dkaa034.
Full textAbstract:
Abstract Objectives Fostemsavir, a novel attachment inhibitor targeting the HIV-1 gp120, has demonstrated wide in vitro activity. However, the high rate of HIV gp120 substitutions could jeopardize its efficacy. We investigated envelope (env) substitutions at positions associated with resistance to fostemsavir in patients with a new HIV-1 diagnosis according to HIV subtype and tropism. Methods Gp120 sequences from 409 subjects were retrospectively analysed and the presence of the L116P, A204D, S375H/M/T, M426L, M434I and M475I mutations was evaluated. Other amino acid changes at the same positions were also recorded. The variability at each amino acid position was evaluated using Shannon entropy. Results The frequency of mutations was: S375T (13.2%); M426L (6.8%); M434I (2.9%); M475I (2.7%); S375H (1.0%)/M (0.8%) and L116P (0.31%). Statistically significant differences were found at positions 375 (R5/non-R5 strains and B/non-B subtypes) and 426 (B/non-B subtypes); post hoc analysis revealed that significance for position 375 was steered by S375T while for position 426 significance was governed by unusual substitutions, in particular M426R (B/non-B, P < 0.00001). The variability of env constant domains appeared to be more relevant in the non-B virus population. Conclusions In conclusion, gp120 substitutions were detected in different subtypes and in both R5 and non-R5 variants. Despite the great variability of gp120, the frequency of mutations was low overall and the predominant substitution was S375T, the role of which in reducing fostemsavir efficacy is less substantial.
12
Pereira, Sergio L., Erwin T. Grau, and Anita Wajntal. "Molecular architecture and rates of DNA substitutions of the mitochondrial control region of cracid birds." Genome 47, no. 3 (June 1, 2004): 535–45. http://dx.doi.org/10.1139/g04-009.
Full textAbstract:
The control region (CR) plays an important role in replication and transcription in the mitochondrial genome. Its supposedly high rate of DNA substitution makes it a suitable marker for studies of population and closely related species. Three domains can be identified in CR, each having its own characteristics regarding base composition, pattern of variability and rate of DNA substitution. We sequenced the complete CR for 27 cracids, including all 11 genera to characterize its molecular organization, describe patterns of DNA substitution along the gene, and estimate absolute rates of DNA substitution. Our results show that cracid CR organization and patterns of DNA substitution are typical of other birds. Conserved blocks C and B, fused CSB2/3, and a putative segment for bidirectional replication not usually present in birds were identified in cracids. We also suggest a new delimitation for domains to allow better comparisons among CRs at different taxonomic ranking. Our estimates of absolute rates of DNA substitution show that, in general, CR evolves at a rate slower than that of two protein-coding genes (CR, 0.14%–0.3%; ND2, 0.37%–0.47%; and cytochrome b, 0.29%–0.35% per site per million years within genera). Within CR domains, rates within genera ranged from 0.05% to 0.8% per site per million years.Key words: mitochondrial control region, molecular evolution, Cracidae, Aves.
13
Burgaard, Johan, and Mogens Steffensen. "Eliciting Risk Preferences and Elasticity of Substitution." Decision Analysis 17, no. 4 (December 2020): 314–29. http://dx.doi.org/10.1287/deca.2020.0415.
Full textAbstract:
Risk aversion and elasticity of intertemporal substitution (EIS) are separated via the celebrated recursive utility building on certainty equivalents of indirect utility. Based on an alternative separation method, we formulate a questionnaire for simultaneous and consistent estimation of risk aversion, subjective discount rate, and EIS. From a representative group of 1,153 respondents, we estimate parameters for these preferences and their variability within the population. Risk aversion and the subjective discount rate are found to be in the orders of 2 and 0, respectively, not diverging far away from results from other studies. Our estimate of EIS in the order of 10 is larger than often reported. Background variables like age and income have little predictive power for the three estimates. Only gender has a significant influence on risk aversion in the usually perceived direction that females are more risk-averse than males. Using individual estimates of preference parameters, we find covariance between preferences toward risk and EIS. We present the background reasoning on objectives, the questionnaire, a statistical analysis of the results, and economic interpretations of these, including relations to the literature.
14
Fournier, B., and P. H. Roy. "Variability of chromosomally encoded beta-lactamases from Klebsiella oxytoca." Antimicrobial Agents and Chemotherapy 41, no. 8 (August 1997): 1641–48. http://dx.doi.org/10.1128/aac.41.8.1641.
Full textAbstract:
The beta-lactamase genes of Klebsiella oxytoca were previously divided into two main groups: bla(OXY-1) and bla(OXY-2). The two beta-lactamase groups were each represented by beta-lactamases with four different pIs. In each group, one form of beta-lactamase is more frequent than the others combined. The beta-lactamase gene of each representative beta-lactamase with a different pI that was not yet sequenced (pIs 5.7, 6.8 [OXY-2], 7.1, 8.2, and 8.8 [OXY-1]) was cloned and sequenced. The susceptibility patterns as well as relative rates and kinetic parameters for beta-lactam hydrolysis revealed that OXY-2 enzymes hydrolyzed several of the beta-lactams that were examined (carbenicillin, cephalothin, cefamandole, ceftriaxone, and aztreonam) at a greater rate than the OXY-1 enzymes did. Comparison of K. oxytoca beta-lactamases with plasmid-mediated extended-spectrum beta-lactamases MEN-1 and TOHO-1 implied that the threonine at position 168 present in OXY-2 beta-lactamase instead of the alanine in OXY-1 could be responsible for its modified substrate hydrolysis. In each group, the beta-lactamase with a variant pI differs from the main form of beta-lactamase by one to five amino acid substitutions. The substrate profile and the 50% inhibitory concentrations revealed that all substitutions differing from the main form of beta-lactamase were neutral except one difference in the OXY-1 group. This substitution of an Ala to a Gly at position 237 increases the hydrolysis of some beta-lactams, particularly aztreonam; decreases the hydrolysis of benzylpenicillin, cephaloridine, and cefamandole, and decreases the susceptibility to clavulanic acid (fivefold increase in the 50% inhibitory concentration).
15
Yakubu, Abdulmojeed, Adebowale Salako, Donato de, Michael Takeet, Sunday Peters, Moses Okpeku, Mathew Wheto, and Ikhide Imumorin. "Nucleotide sequence variability analysis of Major Histocompatibility Complex Class II DQA1 gene in Nigerian goats." Genetika 49, no. 3 (2017): 865–74. http://dx.doi.org/10.2298/gensr1703865y.
Full textAbstract:
Major Histocompatibility Complex (MHC) molecules loaded with peptides derived from invading pathogens are recognised by the immune system to produce a highly effective and specific response against foreign pathogens. A 310-bp fragment of exon 2 of the MHC Class II DQA1 gene was amplified in 27 animals made up of three major Nigerian goat breeds [West African Dwarf (WAD), Red Sokoto (RS) and Sahel (SH)]. Twenty amino acid polymorphic sites were found in Nigerian goats. Comparison of predicted amino acid residues of DQA1 exon 2 alleles of Nigerian goats with similar alleles from other caprine species revealed considerable congruence in amino acid substitution pattern. A significant positive selection signature was detected at the DQA1 locus of Nigerian goats in that non-synonymous substitutions occurred at a faster rate compared to synonymous substitutions (dN:dS ratio = 1.28 ; Z-Statistics= 1.634; P<0.05). The evolutionary tree constructed using UPGMA, revealed that the southern WAD goat appeared to be more related to the northern RS than SH goat at the DQA1 locus. It will be interesting therefore, for future studies to investigate the association of the genetic variants in DQA1 gene of Nigerian goats with resistance/susceptiblity to diseases in order to conserve these precious animal genetic resources.
16
Gillespie, J. H. "Substitution processes in molecular evolution. III. Deleterious alleles." Genetics 138, no. 3 (November 1, 1994): 943–52. http://dx.doi.org/10.1093/genetics/138.3.943.
Full textAbstract:
Abstract The substitution processes for various models of deleterious alleles are examined using computer simulations and mathematical analyses. Most of the work focuses on the house-of-cards model, which is a popular model of deleterious allele evolution. The rate of substitution is shown to be a concave function of the strength of selection as measured by alpha = 2N sigma, where N is the population size and sigma is the standard deviation of fitness. For alpha < 1, the house-of-cards model is essentially a neutral model; for alpha > 4, the model ceases to evolve. The stagnation for large alpha may be understood by appealing to the theory of records. The house-of-cards model evolves to a state where the vast majority of all mutations are deleterious, but precisely one-half of those mutations that fix are deleterious (the other half are advantageous). Thus, the model is not a model of exclusively deleterious evolution as is frequently claimed. It is argued that there are no biologically reasonable models of molecular evolution where the vast majority of all substitutions are deleterious. Other models examined include the exponential and gamma shift models, the Hartl-Dykhuizen-Dean (HDD) model, and the optimum model. Of all those examined, only the optimum and HDD models appear to be reasonable candidates for silent evolution. None of the models are viewed as good candidates for protein evolution, as none are both biologically reasonable and exhibit the variability in substitutions commonly observed in protein sequence data.
17
Maddulapalli, A. K., and S. Azarm. "Product Design Selection With Preference and Attribute Variability for an Implicit Value Function." Journal of Mechanical Design 128, no. 5 (November 4, 2005): 1027–37. http://dx.doi.org/10.1115/1.2216728.
Full textAbstract:
An important aspect of engineering product design selection is the inevitable presence of variability in the selection process. There are mainly two types of variability: variability in the preferences of the decision maker (DM) and variability in attribute levels of the design alternatives. We address both kinds of variability in this paper. We first present a method for selection with preference variability alone. Our method is interactive and iterative and assumes only that the preferences of the DM reflect an implicit value function that is differentiable, quasi-concave and non-decreasing with respect to attributes. The DM states his/her preferences with a range (due to the variability) for marginal rate of substitution (MRS) between attributes at a series of trial designs. The method uses the range of MRS preferences to eliminate “dominated designs” and then to find a set of “potentially optimal designs.” We present a payload design selection example to demonstrate and verify our method. Finally, we extend our method for selection with preference variability to the case where the attribute levels of design alternatives also have variability. We assume that the variability in attribute levels can be quantified with a range of attribute levels.
18
Chen, Yiping, Paul M. Sharp, Mary Fowkes, Olivier Kocher, Jeffrey T. Joseph, and Igor J. Koralnik. "Analysis of 15 novel full-length BK virus sequences from three individuals: evidence of a high intra-strain genetic diversity." Journal of General Virology 85, no. 9 (September 1, 2004): 2651–63. http://dx.doi.org/10.1099/vir.0.79920-0.
Full textAbstract:
To determine the variability of BK virus (BKV) in vivo, the sequences of nine full-length molecular clones from the striated muscle and heart DNA of a patient with BKV-associated capillary leak syndrome (BKVCAP), as well as three clones each from the urine of one human immunodeficiency virus type 2-positive (BKVHI) and one healthy control subject (BKVHC), were analysed. The regulatory region of all clones corresponded to the archetypal regulatory region usually found in urine isolates. Analysis of the predicted conformation of BKVCAP proteins did not suggest any structural differences on the surface of the viral particles compared with BKVHI and BKVHC clones. No amino acid changes common to most BKVCAP clones could be identified that have not already been reported in non-vasculotropic strains. However, the coding region of each clone had unique nucleotide substitutions, and intra-host variability was greater among BKVCAP clones, with a mean difference of 0·29 % per site compared with 0·16 % for BKVHI and 0·14 % for BKVHC. The clones from each strain formed monophyletic clades, suggesting a single source of infection for each subject. The most divergent BKVCAP clones differed at 0·55 % of sites, implying a rate of nucleotide substitution of approximately 5×10−5 substitutions per site per year, which is two orders of magnitude faster than estimated for the other human polyomavirus, JC virus.
19
Qaswar, Jing, Ahmed, Shujun, Dongchu, Lu, lisheng, et al. "Substitution of Inorganic Nitrogen Fertilizer with Green Manure (GM) Increased Yield Stability by Improving C Input and Nitrogen Recovery Efficiency in Rice Based Cropping System." Agronomy 9, no. 10 (October 3, 2019): 609. http://dx.doi.org/10.3390/agronomy9100609.
Full textAbstract:
A long-term field experiment was carried out (since 2008) for evaluating the effects of different substitution rates of inorganic nitrogen (N) fertilizer by green manure (GM) on yield stability and N balance under double rice cropping system. Treatments included, (1) N0 (no N fertilizer and no green manure); (2) N100 (recommended rate of N fertilizer and no green manure); (3) N100-M (recommended rate of N fertilizer and green manure); (4) N80-M (80% of recommended N fertilizer and green manure); (5) N60-M (60% of recommended N fertilizer and green manure); and (6) M (green manure without N fertilization). Results showed that, among all treatments, annual crop yield under N80-M treatment was highest. Crop yield did not show significant differences between N100-M and N80-M treatments. Substitution of different N fertilizer rates by GM reduced the yield variability index. Compared to the N0 treatment, yield variability index of early rice under N100-M, N80-M, and N60-M treatments was decreased by 11%, 26%, and 36%, respectively. Compared to the N0 treatment, yield variability index of late rice was decreased by 12%, 38%, 49%, 47%, and 24% under the N100, N100-M, N80-M, N60-M, and M treatments, respectively. During period of 2009–2013 and 2014–2018, nitrogen recovery efficiency (NRE) was highest under N80-M treatment and N balance was highest under N100 treatment. NRE of all treatments with GM was increased over the time from 2009–2013 to 2014–2018. All treatments with GM showed increasing trend of SOC over the years. Substitution of N fertilizer by GM also increased C inputs and soil C:N ratio compared to the N100 and N0 treatments. Boosted regression model indicated that C input, N uptake and AN were most influencing factors of crop yield. Thus, we concluded that N fertilization rates should be reduced by 20% under GM rotation to attain high yield stability of double rice cropping system through increasing NRE and C inputs.
20
Jiménez-Santos, María José, Miguel Arenas, and Ugo Bastolla. "Influence of mutation bias and hydrophobicity on the substitution rates and sequence entropies of protein evolution." PeerJ 6 (October 5, 2018): e5549. http://dx.doi.org/10.7717/peerj.5549.
Full textAbstract:
The number of amino acids that occupy a given protein site during evolution reflects the selective constraints operating on the site. This evolutionary variability is strongly influenced by the structural properties of the site in the native structure, and it is quantified either through sequence entropy or through substitution rates. However, while the sequence entropy only depends on the equilibrium frequencies of the amino acids, the substitution rate also depends on the exchangeability matrix that describes mutations in the mathematical model of the substitution process. Here we apply two variants of a mathematical model of protein evolution with selection for protein stability, both against unfolding and against misfolding. Exploiting the approximation of independent sites, these models allow computing site-specific substitution processes that satisfy global constraints on folding stability. We find that site-specific substitution rates do not depend only on the selective constraints acting on the site, quantified through its sequence entropy. In fact, polar sites evolve faster than hydrophobic sites even for equal sequence entropy, as a consequence of the fact that polar amino acids are characterized by higher mutational exchangeability than hydrophobic ones. Accordingly, the model predicts that more polar proteins tend to evolve faster. Nevertheless, these results change if we compare proteins that evolve under different mutation biases, such as orthologous proteins in different bacterial genomes. In this case, the substitution rates are faster in genomes that evolve under mutational bias that favor hydrophobic amino acids by preferentially incorporating the nucleotide Thymine that is more frequent in hydrophobic codons. This appearingly contradictory result arises because buried sites occupied by hydrophobic amino acids are characterized by larger selective factors that largely amplify the substitution rate between hydrophobic amino acids, while the selective factors of exposed sites have a weaker effect. Thus, changes in the mutational bias produce deep effects on the biophysical properties of the protein (hydrophobicity) and on its evolutionary properties (sequence entropy and substitution rate) at the same time. The program Prot_evol that implements the two site-specific substitution processes is freely available at https://ub.cbm.uam.es/prot_fold_evol/prot_fold_evol_soft_main.php#Prot_Evol.
21
Holder, Mark T., Derrick J. Zwickl, and Christophe Dessimoz. "Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes." Philosophical Transactions of the Royal Society B: Biological Sciences 363, no. 1512 (October 7, 2008): 4013–21. http://dx.doi.org/10.1098/rstb.2008.0162.
Full textAbstract:
Computer simulations provide a flexible method for assessing the power and robustness of phylogenetic inference methods. Unfortunately, simulated data are often obviously atypical of data encountered in studies of molecular evolution. Unrealistic simulations can lead to conclusions that are irrelevant to real-data analyses or can provide a biased view of which methods perform well. Here, we present a software tool designed to generate data under a complex codon model that allows each residue in the protein sequence to have a different set of equilibrium amino acid frequencies. The software can obtain maximum-likelihood estimates of the parameters of the Halpern and Bruno model from empirical data and a fixed tree; given an arbitrary tree and a fixed set of parameters, the software can then simulate artificial datasets. We present the results of a simulation experiment using randomly generated tree shapes and substitution parameters estimated from 1610 mammalian cytochrome b sequences. We tested tree inference at the amino acid, nucleotide and codon levels and under parsimony, maximum-likelihood, Bayesian and distance criteria (for a total of more than 650 analyses on each dataset). Based on these simulations, nucleotide-level analyses seem to be more accurate than amino acid and codon analyses. The performance of distance-based phylogenetic methods appears to be quite sensitive to the choice of model and the form of rate heterogeneity used. Further studies are needed to assess the generality of these conclusions. For example, fitting parameters of the Halpern Bruno model to sequences from other genes will reveal the extent to which our conclusions were influenced by the choice of cytochrome b . Incorporating codon bias and more sources heterogeneity into the simulator will be crucial to determining whether the current results are caused by a bias in the current simulation study in favour of nucleotide analyses.
22
Baele, Guy, Mandev S. Gill, Paul Bastide, Philippe Lemey, and Marc A. Suchard. "Markov-Modulated Continuous-Time Markov Chains to Identify Site- and Branch-Specific Evolutionary Variation in BEAST." Systematic Biology 70, no. 1 (May 16, 2020): 181–89. http://dx.doi.org/10.1093/sysbio/syaa037.
Full textAbstract:
Abstract Markov models of character substitution on phylogenies form the foundation of phylogenetic inference frameworks. Early models made the simplifying assumption that the substitution process is homogeneous over time and across sites in the molecular sequence alignment. While standard practice adopts extensions that accommodate heterogeneity of substitution rates across sites, heterogeneity in the process over time in a site-specific manner remains frequently overlooked. This is problematic, as evolutionary processes that act at the molecular level are highly variable, subjecting different sites to different selective constraints over time, impacting their substitution behavior. We propose incorporating time variability through Markov-modulated models (MMMs), which extend covarion-like models and allow the substitution process (including relative character exchange rates as well as the overall substitution rate) at individual sites to vary across lineages. We implement a general MMM framework in BEAST, a popular Bayesian phylogenetic inference software package, allowing researchers to compose a wide range of MMMs through flexible XML specification. Using examples from bacterial, viral, and plastid genome evolution, we show that MMMs impact phylogenetic tree estimation and can substantially improve model fit compared to standard substitution models. Through simulations, we show that marginal likelihood estimation accurately identifies the generative model and does not systematically prefer the more parameter-rich MMMs. To mitigate the increased computational demands associated with MMMs, our implementation exploits recent developments in BEAGLE, a high-performance computational library for phylogenetic inference. [Bayesian inference; BEAGLE; BEAST; covarion, heterotachy; Markov-modulated models; phylogenetics.]
23
Wahl, Lindi M., and David C. Krakauer. "Models of Experimental Evolution: The Role of Genetic Chance and Selective Necessity." Genetics 156, no. 3 (November 1, 2000): 1437–48. http://dx.doi.org/10.1093/genetics/156.3.1437.
Full textAbstract:
Abstract We present a theoretical framework within which to analyze the results of experimental evolution. Rapidly evolving organisms such as viruses, bacteria, and protozoa can be induced to adapt to laboratory conditions on very short human time scales. Artificial adaptive radiation is characterized by a list of common observations; we offer a framework in which many of these repeated questions and patterns can be characterized analytically. We allow for stochasticity by including rare mutations and bottleneck effects, demonstrating how these increase variability in the evolutionary trajectory. When the product Np, the population size times the per locus error rate, is small, the rate of evolution is limited by the chance occurrence of beneficial mutations; when Np is large and selective pressure is strong, the rate-limiting step is the waiting time while existing beneficial mutations sweep through the population. We derive the rate of divergence (substitution rate) and rate of fitness increase for the case when Np is large and illustrate our approach with an application to an experimental data set. A minimal assumption of independent additive fitness contributions provides a good fit to the experimental evolution of the bacteriophage φX174.
24
Yermalovich, M. A., V. V. Khrustalev, T. A. Khrustaleva, V. V. Poboinev, and E. O. Samoilovich. "Biochemical features of parvovirus B19 genovariant 1a2 dominating during the incidence rise in Belarus." Proceedings of the National Academy of Sciences of Belarus, Medical series 17, no. 2 (June 6, 2020): 211–20. http://dx.doi.org/10.29235/1814-6023-2020-17-2-211-220.
Full textAbstract:
Two genovariants (1a1 and 1a2) are distinguished among Human parvovirus B19 (B19P) of subgenotype 1a, of which 1a2 was predominantly distributed during the incidence rise in Belarus. The aim of this study was a comparative analysis of the amino acid variability and of the mutational pressure directions in different parts of the genome between genovariants 1a1 and 1a2.The analysis of the consensus amino acid sequences of two genovariants and the three-dimensional structure models of protein fragments was carried out. In total, two unique amino acid substitutions in the main non-structural protein NS1 of 1a2 were found (I181M and E114G), one of which E114G is close to the DNA-binding domain (OBD) responsible for attachment to the replication origin site and can affect the rate of virus replication and transcription. Three unique amino acid substitutions were found in the structural polypeptide VP of 1a2: V30L, S98N, and N533S. Two of them are located in the most immunogenic region VP1u and can contribute to the escape from immune response. The investigation of the mutational pressure direction revealed a decrease in the frequency of G to T transversions in the second reading frame of 1a2, which reflects a higher transcription rate as a result of amino acid substitution in the OBD protein.The differences revealed between the genetic variants of subgenotype 1a B19P both in the antigenic sites and in the replication and transcription system can provide an increased “fitness” for the genetic variant 1a2 and explain its predominant distribution during the incidence rise.
25
Laurie-Ahlberg, C. C., P. T. Barnes, J. W. Curtsinger, T. H. Emigh, B. Karlin, R. Morris, R. A. Norman, and A. N. Wilton. "GENETIC VARIABILITY OF FLIGHT METABOLISM IN DROSOPHILA MELANOGASTER. II. RELATIONSHIP BETWEEN POWER OUTPUT AND ENZYME ACTIVITY LEVELS." Genetics 111, no. 4 (December 1, 1985): 845–68. http://dx.doi.org/10.1093/genetics/111.4.845.
Full textAbstract:
ABSTRACT The major goal of the studies reported here was to determine the extent to which genetic variation in the activities of the enzymes participating in flight metabolism contributes to variation in the mechanical power output of the flight muscles in Drosophila melanogaster. Isogenic chromosome substitution lines were used to partition the variance of both types of quantitative trait into genetic and environmental components. The mechanical power output was estimated from the wingbeat frequency, wing amplitude and wing morphology of tethered flies by applying the aerodynamic models of Weis-Fogh and Ellington. There were three major results. (1) Chromosomes sampled from natural populations provide a large and repeatable genetic component to the variation in the activities of most of the 15 flight metabolism enzymes investigated and to the variation in the mechanical power output of the flight muscles. (2) The mechanical power output is a sensitive indicator of the rate of flight metabolism (i.e., rate of oxygen consumption during tethered flight). (3) In spite of (1) and (2), no convincing cases of individual enzyme effects on power output were detected, although the number and sign of the significant enzyme-power correlations suggests that such effects are not totally lacking.
26
Cento, Valeria, Carmen Mirabelli, Salvatore Dimonte, Romina Salpini, Yue Han, Pascale Trimoulet, Ada Bertoli, et al. "Overlapping structure of hepatitis B virus (HBV) genome and immune selection pressure are critical forces modulating HBV evolution." Journal of General Virology 94, no. 1 (January 1, 2013): 143–49. http://dx.doi.org/10.1099/vir.0.046524-0.
Full textAbstract:
How the overlap between the hepatitis B virus (HBV) reverse transcriptase (RT) and HBV S antigen (HBsAg) genes modulates the extent of HBV genetic variability is still an open question, and was investigated here. The rate of nucleotide conservation (≤1 % variability) followed an atypical pattern in the RT gene, due to an overlap between RT and HBsAg (69.9 % nucleotide conservation in the overlapping region vs 41.2 % in the non-overlapping region; P<0.001), with a consequently lower rate of synonymous substitution within the overlapping region [median(interquartile range)dS = 3.1(1.5–7.4) vs 20.1(10.6–30.0); P = 3.249×10−22]. The most conserved RT regions were located within the YMDD motif and the N-terminal parts of the palm and finger domains, critical for RT functionality. These regions also corresponded to highly conserved HBsAg domains that are critical for HBsAg secretion. Conversely, the genomic region encoding the HBsAg antigenic loop (where immune-escape mutations are localized) showed a sharp decrease in the extent of conservation (40.6 %), which was less pronounced in the setting of human immunodeficiency virus (HIV)-driven immune suppression (48.8 % in HIV–HBV co-infection vs 21.5 % in mono-infected patients; P = 0.020). In conclusion, the overlapping reading frame and the immune system appear to have shaped the patterns of RT and HBsAg genetic variability. Highly conserved regions in RT and HBsAg may deserve further attention as novel therapeutic targets.
27
Eustatia-Rutten, Carmen F. A., Eleonora P. M. Corssmit, Karen A. Heemstra, Johannes W. A. Smit, Rik C. Schoemaker, Johannes A. Romijn, and Jacobus Burggraaf. "Autonomic Nervous System Function in Chronic Exogenous Subclinical Thyrotoxicosis and the Effect of Restoring Euthyroidism." Journal of Clinical Endocrinology & Metabolism 93, no. 7 (July 1, 2008): 2835–41. http://dx.doi.org/10.1210/jc.2008-0080.
Full textAbstract:
Abstract Context: Knowledge on the relationship between the autonomic nervous system and subclinical hyperthyroidism is mainly based upon cross-sectional studies in heterogeneous patient populations, and the effect of restoration to euthyroidism in subclinical hyperthyroidism has not been studied. Objective: We investigated the long-term effects of exogenous subclinical hyperthyroidism on the autonomic nervous system and the potential effects of restoration of euthyroidism. Design: This was a prospective single-blinded, placebo-controlled, randomized trial. Setting: The study was performed at a university hospital. Patients: A total of 25 patients who were on more than 10-yr TSH suppressive therapy after thyroidectomy was examined. Intervention: Patients were studied at baseline and subsequently randomized to a 6-month thyroid hormone substitution regimen to obtain either euthyroidism or maintenance of the subclinical hyperthyroid state. Main Outcome Measures: Urinary excretion of catecholamines and heart rate variability were measured. Baseline data of the subclinical hyperthyroidism patients were compared with data obtained in patients with hyperthyroidism and controls. Results: Urinary excretion of norepinephrine and vanillylmandelic acid was higher in the subclinical hyperthyroidism patients compared with controls and lower compared with patients with overt hyperthyroidism. Heart rate variability was lower in patients with hyperthyroidism, intermediate in subclinical hyperthyroidism patients, and highest in the healthy controls. No differences were observed after restoration of euthyroidism. Conclusions: Long-term exogenous subclinical hyperthyroidism has effects on the autonomic nervous system measured by heart rate variability and urinary catecholamine excretion. No differences were observed after restoration to euthyroidism. This may indicate the occurrence of irreversible changes or adaptation during long-term exposure to excess thyroid hormone that is not remedied by 6-month euthyroidism.
28
Wang, Juan, Li Zhang, Qi-Lin Zhang, Min-Qiang Zhou, Xiao-Tong Wang, Xing-Zhuo Yang, and Ming-Long Yuan. "Comparative mitogenomic analysis of mirid bugs (Hemiptera: Miridae) and evaluation of potential DNA barcoding markers." PeerJ 5 (August 3, 2017): e3661. http://dx.doi.org/10.7717/peerj.3661.
Full textAbstract:
The family Miridae is one of the most species-rich families of insects. To better understand the diversity and evolution of mirids, we determined the mitogenome ofLygus pratenszsand re-sequenced the mitogenomes of four mirids (i.e.,Apolygus lucorum,Adelphocoris suturalis,Ade. fasciaticollisandAde. lineolatus). We performed a comparative analysis for 15 mitogenomic sequences representing 11 species of five genera within Miridae and evaluated the potential of these mitochondrial genes as molecular markers. Our results showed that the general mitogenomic features (gene content, gene arrangement, base composition and codon usage) were well conserved among these mirids. Four protein-coding genes (PCGs) (cox1,cox3,nad1andnad3) had no length variability, wherenad5showed the largest size variation; no intraspecific length variation was found in PCGs. Two PCGs (nad4andnad5) showed relatively high substitution rates at the nucleotide and amino acid levels, wherecox1had the lowest substitution rate. The Ka/Ks values for all PCGs were far lower than 1 (<0.59), but the Ka/Ks values ofcox1-barcode sequences were always larger than 1 (1.34 –15.20), indicating that the 658 bp sequences ofcox1may be not the appropriate marker due to positive selection or selection relaxation. Phylogenetic analyses based on two concatenated mitogenomic datasets consistently supported the relationship ofNesidiocoris+ (Trigonotylus+ (Adelphocoris+ (Apolygus+Lygus))), as revealed bynad4,nad5,rrnLand the combined 22 transfer RNA genes (tRNAs), respectively. Taken sequence length, substitution rate and phylogenetic signal together, the individual genes (nad4,nad5andrrnL) and the combined 22 tRNAs could been used as potential molecular markers for Miridae at various taxonomic levels. Our results suggest that it is essential to evaluate and select suitable markers for different taxa groups when performing phylogenetic, population genetic and species identification studies.
29
Junior, Cezário Ferreira dos Santos, Claudio Córdoba Correoso, Marcos Copacheski, Pedro Boff, and Mari Inês Carissimi Boff. "High dynamic dilutions and genetic variability to phytosanitary management and yield of beans (Phaseolus vulgaris L)." June 2021, no. 15(06):2021 (June 10, 2021): 821–26. http://dx.doi.org/10.21475/ajcs.21.15.06.p2857.
Full textAbstract:
The substitution of landrace populations of beans (Phaseolus vulgaris L.) by commercial cultivars provided genetic uniformity and loss of rusticity. It makes the bean plants more vulnerable to pests, increasing the use of pesticides. The objective of this work was to evaluate the productivity and health of beans landraces compared to commercial cultivars, reducing the effect of high dynamic dilutions. The evaluated traits were grain yield (kg ha-1), thousand grain weight (g), and occurrence of anthracnose (Colletotrichum lindemuthianum) and bacteriosis (Xanthomonas sp.). Evaluation of high dynamic dilutions was also done in addition to the previous variables, was evaluated number of pods per plant and pods with the presence of anthracnose. The analysis of the data did not show any differences in the productivity and disease rate between the landraces and the commercial cultivars of beans. The high dynamic dilutions do not show any conclusive results in terms of productivity. However, all treatments were superior in phytosanitary management compared to control
30
SHRESTHA, S., M. ABDALLA, T. HENNESSY, D. FORRISTAL, and M. B. JONES. "Irish farms under climate change – is there a regional variation on farm responses?" Journal of Agricultural Science 153, no. 3 (May 1, 2014): 385–98. http://dx.doi.org/10.1017/s0021859614000331.
Full textAbstract:
SUMMARYThe current paper aims to determine regional impacts of climate change on Irish farms examining the variation in farm responses. A set of crop growth models were used to determine crop and grass yields under a baseline scenario and a future climate scenario. These crop and grass yields were used along with farm-level data taken from the Irish National Farm Survey in an optimizing farm-level (farm-level linear programming) model, which maximizes farm profits under limiting resources. A change in farm net margins under the climate change scenario compared to the baseline scenario was taken as a measure to determine the effect of climate change on farms. The growth models suggested a decrease in cereal crop yields (up to 9%) but substantial increase in yields of forage maize (up to 97%) and grass (up to 56%) in all regions. Farms in the border, midlands and south-east regions suffered, whereas farms in all other regions generally fared better under the climate change scenario used in the current study. The results suggest that there is a regional variability between farms in their responses to the climate change scenario. Although substituting concentrate feed with grass feeds is the main adaptation on all livestock farms, the extent of such substitution differs between farms in different regions. For example, large dairy farms in the south-east region adopted total substitution of concentrate feed while similar dairy farms in the south-west region opted to replace only 0·30 of concentrate feed. Farms in most of the regions benefitted from increasing stocking rate, except for sheep farms in the border and dairy farms in the south-east regions. The tillage farms in the mid-east region responded to the climate change scenario by shifting arable production to beef production on farms.
31
Jara-Vera, Vicente, and Carmen Sánchez-Ávila. "Cryptobiometrics for the Generation of Cancellable Symmetric and Asymmetric Ciphers with Perfect Secrecy." Mathematics 8, no. 9 (September 8, 2020): 1536. http://dx.doi.org/10.3390/math8091536.
Full textAbstract:
Security objectives are the triad of confidentiality, integrity, and authentication, which may be extended with availability, utility, and control. In order to achieve these goals, cryptobiometrics is essential. It is desirable that a number of characteristics are further met, such as cancellation, irrevocability, unlinkability, irreversibility, variability, reliability, and biometric bit-length. To this end, we designed a cryptobiometrics system featuring the above-mentioned characteristics, in order to generate cryptographic keys and the rest of the elements of cryptographic schemes—both symmetric and asymmetric—from a biometric pattern or template, no matter the origin (i.e., face, fingerprint, voice, gait, behaviour, and so on). This system uses perfect substitution and transposition encryption, showing that there exist two systems with these features, not just one (i.e., the Vernam substitution cipher). We offer a practical application using voice biometrics by means of the Welch periodogram, in which we achieved the remarkable result of an equal error rate of (0.0631, 0.9361). Furthermore, by means of a constructed template, we were able to generate the prime value which specifies the elliptic curve describing all other data of the cryptographic scheme, including the private and public key, as well as the symmetric AES key shared between the templates of two users.
32
Yamamoto, Chikako, Shintaro Nagashima, Channarena Chuon, Ko Ko, Son Huy Do, Oline Lim, Sirany Hok, et al. "Substitution of the CD81 Binding Site and β-Sandwich Area in E2 of HCV in Cambodia." Viruses 12, no. 5 (May 16, 2020): 551. http://dx.doi.org/10.3390/v12050551.
Full textAbstract:
The high genetic variability of hepatitis C virus (HCV) is the main obstacle to developing a vaccine. E2 has attracted attention for vaccine development because targeting this protein could potentially overcome issues related to the genetic diversity of HCV. In this study, we analyzed HCV genes in the general population of Cambodia and investigated the E2 locus as a candidate for vaccine development. HCV sero-epidemiological surveys were conducted between the period 2010 and 2014, with an HCV RNA–positive rate of 1.3% (11/868). Follow-up blood samples were collected from four anti-HCV– and HCV RNA– positive patients (genotype 1b: 2 cases, 6e: 1 case, 6r: 1 case) after 4.12 years. Analysis of HCV full-length nucleotide sequences in paired specimens revealed that the mutation rates of HCV genotypes 1b and 6e/6r were 1.61–2.03 × 10−3 and 2.52–2.74 × 10−3 substitutions/site/year, respectively. Non-synonymous substitutions were detected in HVR1, the front layer of the CD81 binding site, and the β-sandwich, but not in the N-terminal region or adjacent to the CD81 binding site. Therefore, we conclude that the CD81 binding site is a promising locus for HCV vaccine development.
33
Ballantyne, J. S., and M. E. Chamberlin. "Adaptation and evolution of mitochondria: osmotic and ionic considerations." Canadian Journal of Zoology 66, no. 5 (May 1, 1988): 1028–35. http://dx.doi.org/10.1139/z88-152.
Full textAbstract:
Mitochondrial evolution has been examined on the basis of properties of mitochondria from representatives of key adaptive stages. The major step in the evolution of mitochondria was the transfer of mitochondrial genes to the nucleus to take advantage of recombination during meiosis. The ensuing increase in variability facilitated adaptation to environmental stress. The role of environmental factors such as atmospheric oxygen levels in the evolution of mitochondria is discussed on the basis of evidence obtained from mitochondria of living representatives of important groups and the fossil record. Rate enhancement has been a central theme in the evolution of animal mitochondria. Optimization of mitochondrial oxidation rates occurred through adjustments in intracellular solute systems. This took place in several stages, including (i) a reduction of intracellular inorganic ion levels by substitution of a variety of compatible solutes, (ii) a counteracting solute system (urea and methylamines), and (iii) osmoregulation.
34
Seegmuller, Thomas. "TASTE FOR VARIETY AND ENDOGENOUS FLUCTUATIONS IN A MONOPOLISTIC COMPETITION MODEL." Macroeconomic Dynamics 12, no. 4 (September 2008): 561–77. http://dx.doi.org/10.1017/s1365100508070314.
Full textAbstract:
In past years, imperfect competition has been introduced in several dynamic models to show how markup variability, increasing returns (decreasing marginal cost), and monopoly profits affect the occurrence of endogenous fluctuations. In this paper, we focus on another possible feature of imperfectly competitive economies: consumers' taste for variety as a result of endogenous product diversity. Introducing monopolistic competition [Dixit and Stiglitz (1977), Benassy (1996)] in an overlapping generations model in which consumers have taste for variety, we show that local indeterminacy can occur under the three following conditions: a high substitution between capital and labor, increasing returns arbitrarily small, and a not too elastic labor supply. The key mechanism for this result is based on the fact that, because of taste for variety, the aggregate price decreases with the procyclical product diversity, which has a direct influence on the real wage and the real interest rate.
35
Kimball, Rebecca T., and Edward L. Braun. "Dynamic Patterns of Sex Chromosome Evolution in Neognath Birds: Many Independent Barriers to Recombination at the ATP5F1A Locus." Birds 3, no. 1 (January 30, 2022): 51–70. http://dx.doi.org/10.3390/birds3010004.
Full textAbstract:
Avian sex chromosomes evolved after the divergence of birds and crocodilians from their common ancestor, so they are younger than the better-studied chromosomes of mammals. It has long been recognized that there may have been several stages to the evolution of avian sex chromosomes. For example, the CHD1 undergoes recombination in paleognaths but not neognaths. Genome assemblies have suggested that there may be variation in the timing of barriers to recombination among Neognathae, but there remains little understanding of the extent of this variability. Here, we look at partial sequences of ATP5F1A, which is on the avian Z and W chromosomes. It is known that recombination of this gene has independently ceased in Galliformes, Anseriformes, and at least five neoavian orders, but whether there are other independent cessations of recombination among Neoaves is not understood. We analyzed a combination of data extracted from published chromosomal-level genomes with data collected using PCR and cloning to identify Z and W copies in 22 orders. Our results suggest that there may be at least 19 independent cessations of recombination within Neognathae, and 3 clades that may still be undergoing recombination (or have only recently ceased recombination). Analyses of ATP5F1A protein sequences revealed an increased amino acid substitution rate for W chromosome gametologs, suggesting relaxed purifying selection on the W chromosome. Supporting this hypothesis, we found that the increased substitution rate was particularly pronounced for buried residues, which are expected to be more strongly constrained by purifying selection. This highlights the dynamic nature of avian sex chromosomes, and that this level of variation among clades means they should be a good system to understand sex chromosome evolution.
36
Freer, M., H. Dove, A. Axelsen, and J. R. Donnelly. "Responses to supplements by weaned lambs when grazing mature pasture or eating hay cut from the same pasture." Journal of Agricultural Science 110, no. 3 (June 1988): 661–67. http://dx.doi.org/10.1017/s0021859600082277.
Full textAbstract:
SummaryWeaned cross-bred lambs either grazed mature pasture or were confined to yards where they were offered material cut from ungrazed areas of the same pasture. A 1:2 mixture (on an air-dry basis) of sunflower meal and oat grain was offered for 81 days at 0, 200, 400 or 600 g/head or ad libitum. Individual estimates of intake of pasture and supplement by grazing sheep at four levels of supplementation were made on four adjacent plots.Weight gain increased from –30 to 178 g/day in the grazing animals as supplement intake increased up to 1030 g D.M./day and from –25 to 142 g/day in the yarded animals as supplement intake increased to 1076 g D.M./day. Growth of greasy wool increased from 4·5 to 11·7 g/day for grazing animals and from 4·5 to 10·2 g/day for those kept in yards.At levels of supplement intake below 400 g D.M./day, the intake of grazed pasture increased by up to 58% compared with unsupplemented animals. However, when the intake of supplement was increased to about 650 g D.M./day, pasture intake fell, with an estimated substitution rate of 1·1 g D.M. pasture per g D.M. supplement. At all levels of supplementation, the intake of hay by the yarded lambs was less than half the intake of herbage in the field. However, at levels of supplement intake between 300 and 500 g D.M./day, the substitution rate was similar to that measured in the grazing animals, suggesting that this is an attribute of roughage quality, rather than differential eating behaviour between grazing and yarded animals.The wastage, w (g D.M./day), of supplement was linearly related to the amount offered, s (g D.M./day), by the equationw = 0·263s − 38·8; R2 = 0·89Variability in supplement intake between individual grazing lambs was not affected by the level of supplementation but the coefficient of variation of supplement intake was considerably greater than that of the intake of unsupplemented pasture. Variability in the intake of pasture increased with the level of supplementation but variability in the total intake of food was similar at each level of supplement, indicating some degree of individual compensation in the intake of the two components.
37
Kucharski, Mirosław, Urszula Kaczor, and Katarzyna Piórkowska. "Genetic Variability in the Loci of FABP4, PPARγ and SCD Genes of Sheep Breeds Raised for Different Purposes." Annals of Animal Science 19, no. 4 (October 1, 2019): 937–54. http://dx.doi.org/10.2478/aoas-2019-0033.
Full textAbstract:
AbstractThe present study was undertaken to analyse the genetic variation in coding sequences, splicing sites and regulatory sequences of FABP4, PPARγ and SCD genes in five breeds of sheep raised in Poland with different purposes: meat (Suffolk, Ile de France), dairy/prolific (Olkuska sheep, Kołuda) and primitive breeds (Polish Mountain Sheep). To identify genetic variability HRM-PCR, sequencing and PCR-RFLP method were used. Determining the genetic structure of the mentioned genes revealed six SNPs: FABP4 – c.73 + 13A>T and c.348 + 85G>A, PPARγ – c.391 – 66C>T (c.481 – 66C>T) and c.529 + 27G>C (c.619 + 27G>C), SCD – c.*945G>A and c.*1116A>G. For the c.*1116A>G SNP, a potential association with specific sheep body type and breeding purpose was found. In turn, the substitution c.*945G>A located in the regulatory region of the 3'-UTR of the Ovis aries SCD gene was identified for the first time. Based on the relationship demonstrated between sheep body constitution and productive type (dairy, meat) and the polymorphism of the SCD gene, further research is needed. The correlation between c.*1116A>G polymorphism and growth rate, slaughter and carcass value as well as meat quality of lambs needs to be studied in more detail. Such studies may lead to more effective selection processes in sheep breeding in the future.
38
Feng, Jie, Fang Liao, Deying Kong, Ruihua Ren, Tao Sun, Wei Liu, Yanyan Yin, Haoyu Ma, Jiahao Tang, and Guanrong Li. "Genetic diversity of the cultivated Salvia miltiorrhiza populations revealed by four intergenic spacers." PLOS ONE 17, no. 4 (April 6, 2022): e0266536. http://dx.doi.org/10.1371/journal.pone.0266536.
Full textAbstract:
For better understanding the genetic diversity and phylogeny of the cultivated Salvia miltiorrhiza populations, four intergenic spacer sequences, ETS, psbA-trnH, trnL-trnF, and ycf1-rps15 of the 40 populations collected from China were Polymerase Chain Reaction (PCR) amplified, analyzed both individually and in combination. Haplotype diversity analysis showed that the cultivated S. miltiorrhiza populations had a very rich genetic diversity and an excellent capacity to resist environmental pressure. The best-fit nucleotide substitution models for ETS, psbA-trnH, trnL-trnF, ycf1-rps15, and their combined sequences were HKY+I, T92, T92, T92+G, and T92+G, respectively; the nucleotide conversion frequency in the combined sequences was lower than the transversion, and the relatively high nucleotide substitution frequencies suggests its high genetic variability. Neutral tests showed that the spacer sequences of the populations conform with the neutral evolution model, and there has been no current expansion events occurred. Phylogeny analyses based on both the individual and the combined sequences showed that the 40 populations were clustered in two clades with a very similar topological structure. The discrimination rate of the combined sequence marker is significantly increased to 52.5% (21 populations) over the highest 35% (13 populations) by the single marker of ETS, though still inadequate but a big step forward. Further exploration of more DNA markers is needed. This study for the first time revealed the rich genetic diversity and phylogeny of the currently cultivated S. miltiorrhiza populations in China and provides novel alternative molecular markers for the genetic identification and resources evaluation of the cultivated S. miltiorrhiza populations.
39
Dikariyanto, Vita, Leanne Smith, Lucy Francis, May Robertson, Eslem Kusaslan, Molly O'Callaghan-Latham, Camille Palanche, et al. "Snacking on whole almonds for 6 weeks improves endothelial function and lowers LDL cholesterol but does not affect liver fat and other cardiometabolic risk factors in healthy adults: the ATTIS study, a randomized controlled trial." American Journal of Clinical Nutrition 111, no. 6 (May 15, 2020): 1178–89. http://dx.doi.org/10.1093/ajcn/nqaa100.
Full textAbstract:
Abstract Background There is convincing evidence that daily whole almond consumption lowers blood LDL cholesterol concentrations, but effects on other cardiometabolic risk factors such as endothelial function and liver fat are still to be determined. Objectives We aimed to investigate whether isoenergetic substitution of whole almonds for control snacks with the macronutrient profile of average snack intakes, had any impact on markers of cardiometabolic health in adults aged 30–70 y at above-average risk of cardiovascular disease (CVD). Methods The study was a 6-wk randomized controlled, parallel-arm trial. Following a 2-wk run-in period consuming control snacks (mini-muffins), participants consumed either whole roasted almonds (n = 51) or control snacks (n = 56), providing 20% of daily estimated energy requirements. Endothelial function (flow-mediated dilation), liver fat (MRI/magnetic resonance spectroscopy), and secondary outcomes as markers of cardiometabolic disease risk were assessed at baseline and end point. Results Almonds, compared with control, increased endothelium-dependent vasodilation (mean difference 4.1%-units of measurement; 95% CI: 2.2, 5.9), but there were no differences in liver fat between groups. Plasma LDL cholesterol concentrations decreased in the almond group relative to control (mean difference −0.25 mmol/L; 95% CI: −0.45, −0.04), but there were no group differences in triglycerides, HDL cholesterol, glucose, insulin, insulin resistance, leptin, adiponectin, resistin, liver function enzymes, fetuin-A, body composition, pancreatic fat, intramyocellular lipids, fecal SCFAs, blood pressure, or 24-h heart rate variability. However, the long-phase heart rate variability parameter, very-low-frequency power, was increased during nighttime following the almond treatment compared with control (mean difference 337 ms2; 95% CI: 12, 661), indicating greater parasympathetic regulation. Conclusions Whole almonds consumed as snacks markedly improve endothelial function, in addition to lowering LDL cholesterol, in adults with above-average risk of CVD. This trial was registered at clinicaltrials.gov as NCT02907684.
40
Dikariyanto, Vita, Leanne Smith, May Robertson, Eslem Kusaslan, Molly O'Callaghan-Latham, Philip Chowienczyk, Sarah Berry, and Wendy Hall. "Effects of Daily Intake of Almonds on Cardiac Autonomic Functions Measured by Heart Rate Variability in Response to Acute Stress: A Randomized Controlled Trial." Current Developments in Nutrition 4, Supplement_2 (May 29, 2020): 20. http://dx.doi.org/10.1093/cdn/nzaa040_020.
Full textAbstract:
Abstract Objectives Stress is inversely associated with heart rate variability (HRV), an indicator of cardiac autonomic function and a predictor of risk of sudden cardiac death. At times of stress, people tend to favor high sugar and fatty foods, often as snacks, with potential adverse effects on cardiometabolic health. Dietary recommendations for cardiovascular disease (CVD) prevention emphasize fruits, vegetables, wholegrains and nuts. There is evidence that consumption of nuts can reduce LDL cholesterol and blood pressure and help with weight management, however the impact of nuts on HRV in response to stress is unknown. The ATTIS dietary intervention study investigated the HRV response to acute stress following 6-week substitution of almonds for typical snacks high in refined starch, free sugars and saturated fats, and low in fibre. The study population comprised adults aged 30–70 y, who were habitual snack consumers, and at moderate risk of developing CVD. It was hypothesized that snacking on almonds would increase HRV during stress tasks, when HRV is expected to be reduced due to increased sympathetic activity. Methods A 6-week randomized controlled parallel trial was conducted. Participants were randomized to 1) control snacks (mini-muffins formulated to follow the average UK snack nutrient profile), or 2) dry-roasted whole almonds, both providing 20% estimated energy requirement. Supine HRV was measured (Mega Electronics Emotion Faros 180°, 2-leads wearable ECG-HRV monitor) during resting (5 min), physical stress (blood pressure monitor cuff inflation 200 mmHg, 5 min) and mental stress (Stroop colour-word test, 5 min) tasks pre- and post-intervention. A total of 105 participants (73 females and 32 males; mean age 56.2 y, SD 10.4) completed the trial. Results Almonds significantly increased the beat-to-beat HRV parameter, high-frequency power, during the mental stress test (mean difference 124 ms2; 95% CI 11, 237; P = 0.031) relative to control, indicating increased parasympathetic regulation. There were no treatment effects during resting and the physical stress task. Conclusions Snacking on whole almonds as a replacement for typical snacks increases HRV during mental stress, indicating an increased resilience in cardiac autonomic function and a novel mechanism whereby nuts may be cardioprotective. Funding Sources Almond Board of California.
41
Almeida, Alex-Alan F. de, Raúl R. Valle, Marcelo S. Mielke, and Fábio P. Gomes. "Tolerance and prospection of phytoremediator woody species of Cd, Pb, Cu and Cr." Brazilian Journal of Plant Physiology 19, no. 2 (June 2007): 83–98. http://dx.doi.org/10.1590/s1677-04202007000200001.
Full textAbstract:
High concentrations of Cd, Pb, Cu and Cr can cause harmful effects to the environment. These highly toxic pollutants constitute a risk for aquatic and terrestrial life. They are associated with diverse bioavailable geochemical fractions, like the water-soluble fraction and the exchangeable fraction, and non-available fractions like those associated with the crystalline net of clays and silica minerals. Depending upon their chemical and physical properties we can distinguish different mechanisms of metal toxicity in plants, such as production of reactive oxygen species from auto-oxidation, blocking and/or displacement of essential functional groups or metallic ions of biomolecules, changes in the permeability of cellular membranes, reactions of sulphydryl groups with cations, affinity for reactions with phosphate groups and active groups of ADP or ATP, substitution of essential ions, induction of chromosomal anomalies and decrease of the cellular division rate. However, some plant species have developed tolerance or resistance to these metals naturally. Such evolution of ecotypes is a classic example of local adaptation and microevolution, restricted to species with appropriate genetic variability. Phytoremediator woody species, with (i) high biomass production, (ii) a deep root system, (iii) high growth rate, (iv) high capacity to grow in impoverished soils, and (v) high capacity to allocate metals in the trunk, can be an alternative for the recovery of degraded soils due to excess of metallic elements. Phytoremediation using woody species presents advantageous characteristics as an economic and ecologically viable system, making it an appropriate, practical and successful technology.
42
Mubin, Muhammad, Arzoo Shabbir, Nazia Nahid, Iram Liaqat, Muhammad Hassan, Nada H. Aljarba, Ahmed Al Qahtani, Claude M. Fauquet, Jian Ye, and Muhammad Shah Nawaz-ul-Rehman. "Patterns of Genetic Diversity among Alphasatellites Infecting Gossypium Species." Pathogens 11, no. 7 (July 4, 2022): 763. http://dx.doi.org/10.3390/pathogens11070763.
Full textAbstract:
Alphasatellites are small single-stranded circular DNA molecules associated with geminiviruses and nanoviruses. In this study, a meta-analysis of known alphasatellites isolated from the genus Gossypium (cotton) over the last two decades was performed. The phylogenetic and pairwise sequence identity analysis suggested that cotton-infecting begomoviruses were associated with at least 12 different alphasatellites globally. Three out of twelve alphasatellite were associated with cotton leaf curl geminiviruses but were not isolated from cotton plants. The cotton leaf curl Multan alphasatellite, which was initially isolated from cotton, has now been reported in several plant species, including monocot plants such as sugarcane. Our recombination analysis suggested that four alphasatellites, namely cotton leaf curl Lucknow alphasatellites, cotton leaf curl Multan alphasatellites, Ageratum yellow vein Indian alphasatellites and Ageratum enation alphasatellites, evolved through recombination. Additionally, high genetic variability was detected among the cotton-infecting alphasatellites at the genome level. The nucleotide substitution rate for the replication protein of alphasatellites (alpha-Rep) was estimated to be relatively high (~1.56 × 10−3). However, unlike other begomoviruses and satellites, the first codon position of alpha-Rep rapidly changed compared to the second and third codon positions. This study highlights the biodiversity and recombination of alphasatellites associated with the leaf curl diseases of cotton crops.
43
Paul, Paola, Essia Belhaj, Cécile Diliberto, Komla Lolonyo Apedo, and Françoise Feugeas. "Comprehensive Characterization of Spent Chemical Foundry Sand for Use in Concrete." Sustainability 13, no. 22 (November 21, 2021): 12881. http://dx.doi.org/10.3390/su132212881.
Full textAbstract:
The foundry industry generates large amounts of spent foundry sands, which are stored, available for recovery in other industrial sectors but unfortunately poorly exploited. Different authors have studied the possibility of recovering them in concretes, which would also allow production of more sustainable cementitious materials. The variability of their results highlights the importance of a better understanding of the potential influential parameters of the by-products. Unfortunately, exhaustive characterizations of the materials are rarely performed, especially for chemically bound foundry sands. This article presents a case study for the recovery of a spent chemical foundry sand with an exhaustive physicochemical characterization of the by-product and an analysis of its influence on the workability and mechanical strengths of cementitious materials. The tests recommended by the European standard for aggregates for concrete confirmed the suitability of the by-product. Associated with additional chemical tests (scanning electron microscopy, X-ray fluorescence, X-ray diffraction, etc.) as well as metallic particles characterization, they highlighted possible influential parameters. The workability and mechanical resistance tests carried out on mortars and concretes confirmed the influence of the fineness of the by-product associated with other parameters. Its use at a substitution rate of 30% results in a strength class C 30/37 concrete.
44
Ray, Stuart C., Qing Mao, Robert E. Lanford, Suzanne Bassett, Oliver Laeyendecker, Yu-Ming Wang, and David L. Thomas. "Hypervariable Region 1 Sequence Stability during Hepatitis C Virus Replication in Chimpanzees." Journal of Virology 74, no. 7 (April 1, 2000): 3058–66. http://dx.doi.org/10.1128/jvi.74.7.3058-3066.2000.
Full textAbstract:
ABSTRACT The putative envelope 2 (E2) gene of hepatitis C virus (HCV) contains a highly variable region referred to as hypervariable region 1 (HVR1). We hypothesized that this genetic variability is driven by immune selection pressure, rather than representing the accumulation of random mutations in a region with relatively little functional constraint. To test this hypothesis, we examined the E2 sequence of a human inoculum that was passaged through eight chimpanzees, which appear to have a replicative rate (opportunity for chance mutation) similar to that of humans. Acute-phase plasma samples from a human (the inoculum) and six of eight serially infected chimpanzees were studied. For each, 33 cloned cDNAs were examined by a combined heteroduplex–single-stranded conformational polymorphism assay to assess quasispecies complexity and optimize selection of clones with unique gel shift patterns (clonotypes) for sequencing. The sequence diversity of HCV was significantly lower in the chimpanzees than in the humans, and during eight serial passages there was no change in the sequence of the majority clonotype from each animal examined. Similarly, the rates of protein sequence altering (nonsynonymous) substitution were lower in the chimpanzees than in the humans. These findings demonstrate that nonsynonymous mutations indicate selection pressure rather than being an incidental result of HCV replication.
45
Carulli, J. P., D. E. Krane, D. L. Hartl, and H. Ochman. "Compositional heterogeneity and patterns of molecular evolution in the Drosophila genome." Genetics 134, no. 3 (July 1, 1993): 837–45. http://dx.doi.org/10.1093/genetics/134.3.837.
Full textAbstract:
Abstract The rates and patterns of molecular evolution in many eukaryotic organisms have been shown to be influenced by the compartmentalization of their genomes into fractions of distinct base composition and mutational properties. We have examined the Drosophila genome to explore relationships between the nucleotide content of large chromosomal segments and the base composition and rate of evolution of genes within those segments. Direct determination of the G + C contents of yeast artificial chromosome clones containing inserts of Drosophila melanogaster DNA ranging from 140-340 kb revealed significant heterogeneity in base composition. The G + C content of the large segments studied ranged from 36.9% G + C for a clone containing the hunchback locus in polytene region 85, to 50.9% G + C for a clone that includes the rosy region in polytene region 87. Unlike other organisms, however, there was no significant correlation between the base composition of large chromosomal regions and the base composition at fourfold degenerate nucleotide sites of genes encompassed within those regions. Despite the situation seen in mammals, there was also no significant association between base composition and rate of nucleotide substitution. These results suggest that nucleotide sequence evolution in Drosophila differs from that of many vertebrates and does not reflect distinct mutational biases, as a function of base composition, in different genomic regions. Significant negative correlations between codon-usage bias and rates of synonymous site divergence, however, provide strong support for an argument that selection among alternative codons may be a major contributor to variability in evolutionary rates within Drosophila genomes.
46
Jeffery, A. J., R. Gertisser, R. A. Jackson, B. O'Driscoll, and A. Kronz. "On the compositional variability of dalyite, K2ZrSi6O15: a new occurrence from Terceira, Azores." Mineralogical Magazine 80, no. 4 (June 2016): 547–65. http://dx.doi.org/10.1180/minmag.2016.080.018.
Full textAbstract:
AbstractThe rare potassium zirconium silicate dalyite has been identified for the first time on Terceira, Azores, within syenitic ejecta of the Caldeira-Castelinho Ignimbrite Formation. New quantitative analyses of this dalyite were combined with the small number of published analyses from various locations worldwide to evaluate the mineral's compositional variability. Additionally, solid-state modelling has been applied to assess the site allocations of substituting elements. The new analyses yield the average formula (K1.84Na0.15)∑=1.99(Zr0.94Ti0.012Hf0.011Fe0.004)∑=0.967Si6.03O15. Model results predict the placement of substituting Hf and Ti in the octahedral site, and highlight the overall complexity in the incorporation of Fe, Mg and Ba. The combined dataset reveals that dalyite found within peralkaline granites and syenites is generally defined by higher Na↔K substitution and lower Ti↔Zr substitution relative to dalyite from highly potassic rocks. The Terceira dalyite exhibits a bimodal variation in the degree of Na↔K substitution which is attributed to a K-enrichment trend induced by late-stage pore wall crystallization and albitization, coupled with the control of pore size upon the degree of supersaturation required to initiate nucleation of dalyite in pores of varying size.
47
Buehler, Deborah M., and Allan J. Baker. "Characterization of the red knot (Calidris canutus) mitochondrial control region." Genome 46, no. 4 (August 1, 2003): 565–72. http://dx.doi.org/10.1139/g03-034.
Full textAbstract:
We sequenced the complete mitochondrial control regions of 11 red knots (Calidris canutus). The control region is 1168 bp in length and is flanked by tRNA glutamate (glu) and the gene ND6 at its 5' end and tRNA phenylalanine (phe) and the gene 12S on its 3' end. The sequence possesses conserved sequence blocks F, E, D, C, CSB-1, and the bird similarity box (BSB), as expected for a mitochondrial copy. Flanking tRNA regions show correct secondary structure, and a relative rate test indicated no significant difference between substitution rates in the sequence we obtained versus the known mitochondrial sequence of turnstones (Charadriiformes: Scolopacidae). These characteristics indicate that the sequence is mitochondrial in origin. To confirm this, we sequenced the control region of a single individual using both purified mitochondrial DNA and genomic DNA. The sequences were identical using both methods. The sequence and methods presented in this paper may now serve as a reference for future studies using knot and other avian control regions. Furthermore, the discovery of five variable sites in 11 knots towards the 3' end of the control region, and the variability of this region in contrast to the more conserved central domain in the alignment between knots and other Charadriiformes, highlights the importance of this area as a source of variation for future studies in knots and other birds.Key words: D-loop, Calidris canutus, Charadriiformes, Aves, evolution.
48
Otieno, James R., Charles N. Agoti, Caroline W. Gitahi, Ann Bett, Mwanajuma Ngama, Graham F. Medley, Patricia A. Cane, and D. James Nokes. "Molecular Evolutionary Dynamics of Respiratory Syncytial Virus Group A in Recurrent Epidemics in Coastal Kenya." Journal of Virology 90, no. 10 (March 2, 2016): 4990–5002. http://dx.doi.org/10.1128/jvi.03105-15.
Full textAbstract:
ABSTRACTThe characteristic recurrent epidemics of human respiratory syncytial virus (RSV) within communities may result from the genetic variability of the virus and associated evolutionary adaptation, reducing the efficiency of preexisting immune responses. We analyzed the molecular evolutionary changes in the attachment (G) glycoprotein of RSV-A viruses collected over 13 epidemic seasons (2000 to 2012) in Kilifi (n= 649), Kenya, and contemporaneous sequences (n= 1,131) collected elsewhere within Kenya and 28 other countries. Genetic diversity in the G gene in Kilifi was dynamic both within and between epidemics, characterized by frequent new variant introductions and limited variant persistence between consecutive epidemics. Four RSV-A genotypes were detected in Kilifi: ON1 (11.9%), GA2 (75.5%), GA5 (12.3%), and GA3 (0.3%), with predominant genotype replacement of GA5 by GA2 and then GA2 by ON1. Within these genotypes, there was considerable variation in potentialN-glycosylation sites, with GA2 and ON1 viruses showing up to 15 different patterns involving eight possible sites. Further, we identified 15 positively selected and 34 genotype-distinguishing codon sites, with six of these sites exhibiting both characteristics. The mean substitution rate of the G ectodomain for the Kilifi data set was estimated at 3.58 × 10−3(95% highest posterior density interval = 3.04 to 4.16) nucleotide substitutions/site/year. Kilifi viruses were interspersed in the global phylogenetic tree, clustering mostly with Kenyan and European sequences. Our findings highlight ongoing genetic evolution and high diversity of circulating RSV-A strains, locally and globally, with potential antigenic differences. Taken together, these provide a possible explanation on the nature of recurrent local RSV epidemics.IMPORTANCEThe mechanisms underlying recurrent epidemics of RSV are poorly understood. We observe high genetic diversity in circulating strains within and between epidemics in both local and global settings. On longer time scales (∼7 years) there is sequential replacement of genotypes, whereas on shorter time scales (one epidemic to the next or within epidemics) there is a high turnover of variants within genotypes. Further, this genetic diversity is predicted to be associated with variation in antigenic profiles. These observations provide an explanation for recurrent RSV epidemics and have potential implications on the long-term effectiveness of vaccines.
49
Pettersson, Bertil, Göran Bölske, François Thiaucourt, Mathias Uhlén, and Karl-Erik Johansson. "Molecular Evolution of Mycoplasma capricolum subsp. capripneumoniae Strains, Based on Polymorphisms in the 16S rRNA Genes." Journal of Bacteriology 180, no. 9 (May 1, 1998): 2350–58. http://dx.doi.org/10.1128/jb.180.9.2350-2358.1998.
Full textAbstract:
ABSTRACT Mycoplasma capricolum subsp.capripneumoniae belongs to the so-called Mycoplasma mycoides cluster and is the causal agent of contagious caprine pleuropneumonia (CCPP). All members of the M. mycoidescluster have two rRNA operons. The sequences of the 16S rRNA genes of both rRNA operons from 20 strains of M. capricolum subsp.capripneumoniae of different geographical origins in Africa and Asia were determined. Nucleotide differences which were present in only one of the two operons (polymorphisms) were detected in 24 positions. The polymorphisms were not randomly distributed in the 16S rRNA genes, and some of them were found in regions of low evolutionary variability. Interestingly, 11 polymorphisms were found in all theM. capricolum subsp. capripneumoniae strains, thus defining a putative ancestor. A sequence length difference between the 16S rRNA genes in a poly(A) region and 12 additional polymorphisms were found in only one or some of the strains. A phylogenetic tree was constructed by comparative analysis of the polymorphisms, and this tree revealed two distinct lines of descent. The nucleotide substitution rate of strains within line II was up to 50% higher than within line I. A tree was also constructed from individual operonal 16S rRNA sequences, and the sequences of the two operons were found to form two distinct clades. The topologies of both clades were strikingly similar, which supports the use of 16S rRNA sequence data from homologous operons for phylogenetic studies. The strain-specific polymorphism patterns of the 16S rRNA genes of M. capricolum subsp.capripneumoniae may be used as epidemiological markers for CCPP.
50
Chapman, Eric G., Helen Piontkivska, Jennifer M. Walker, Donald T. Stewart, Jason P. Curole, and Walter R. Hoeh. "Extreme primary and secondary protein structure variability in the chimeric male-transmitted cytochrome c oxidase subunit II protein in freshwater mussels: Evidence for an elevated amino acid substitution rate in the face of domain-specific purifying selection." BMC Evolutionary Biology 8, no. 1 (2008): 165. http://dx.doi.org/10.1186/1471-2148-8-165.
Full text