Phylogenetic Comparative Analysis: A Modeling Approach for Adaptive Evolution

A high-leakage core has been known to be a challenging problem not only for a two-step homogenization approach but also for a direct heterogeneous approach. In this paper the DIMPLE S06 core, which is a small high-leakage core, has been analyzed by a direct heterogeneous modeling approach and by a two-step homogenization modeling approach, using contemporary code systems developed for reactor core analysis. The focus of this work is a comprehensive comparative analysis of the conventional approaches and codes with a small core design, DIMPLE S06 critical experiment. The calculation procedure for the two approaches is explicitly presented in this paper. Comprehensive comparative analysis is performed by neutronics parameters: multiplication factor and assembly power distribution. Comparison of two-group homogenized cross sections from each lattice physics codes shows that the generated transport cross section has significant difference according to the transport approximation to treat anisotropic scattering effect. The necessity of the ADF to correct the discontinuity at the assembly interfaces is clearly presented by the flux distributions and the result of two-step approach. Finally, the two approaches show consistent results for all codes, while the comparison with the reference generated by MCNP shows significant error except for another Monte Carlo code, SERPENT2.

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Phylogenetic comparative analysis and the secondary structure of ribonuclease P RNA — a review

Gene ◽

10.1016/0378-1119(89)90031-0 ◽

1989 ◽

Vol 82 (1) ◽

pp. 65-75 ◽

Cited By ~ 57

Author(s):

Norman R. Pace ◽

David K. Smith ◽

Gary J. Olsen ◽

Bryan D. James

Keyword(s):

Comparative Analysis ◽

Secondary Structure ◽

Ribonuclease P ◽

Phylogenetic Comparative Analysis ◽

Ribonuclease P Rna

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Phylogenetic comparative analysis of RNA structure on Macintosh computers

Bioinformatics ◽

10.1093/bioinformatics/7.3.391 ◽

1991 ◽

Vol 7 (3) ◽

pp. 391-393 ◽

Cited By ~ 2

Author(s):

James W. Brown

Keyword(s):

Comparative Analysis ◽

Rna Structure ◽

Phylogenetic Comparative Analysis

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Comparative analysis reveals adaptive evolution of bat IFITMs and a novel antiviral determinant

10.1101/737841 ◽

2019 ◽

Author(s):

Camilla T O Benfield ◽

Farrell MacKenzie ◽

Markus Ritzefeld ◽

Michela Mazzon ◽

Stuart Weston ◽

...

Keyword(s):

Comparative Analysis ◽

Adaptive Evolution ◽

Transmembrane Proteins ◽

Cysteine Residue ◽

Cysteine Residues ◽

Restriction Factors ◽

Emerging Viruses ◽

Molecular Determinant ◽

Natural Hosts ◽

Important Site

ABSTRACTHost interferon-induced transmembrane proteins (IFITMs) are broad-spectrum antiviral restriction factors. Of these, IFITM3 potently inhibits viruses that enter cells through acidic endosomes, many of which are zoonotic and emerging viruses with bats (order Chiroptera) as natural hosts. We previously demonstrated that microbat IFITM3 is antiviral. Here we show that bat IFITMs are characterized by strong adaptive evolution and identify a highly variable and functionally important site - codon 70 - within the conserved CD225 domain of IFITMs. Mutation of this residue in microbat IFITM3 impairs restriction of four different virus families that enter cells via endosomes. This mutant shows altered subcellular localization and reduced S-palmitoylation, a phenotype copied by mutation of conserved cysteine residues in microbat IFITM3. Furthermore, we show that microbat IFITM3 is S-palmitoylated on cysteine residues C71, C72 and C105, mutation of each cysteine residue individually impairs virus restriction, and a triple C71-C72-C105 mutant loses all restriction, concomitant with subcellular re-localization of microbat IFITM3 to Golgi-associated sites. Thus, we propose that S-palmitoylation is critical for Chiropteran IFITM3 function and identify a key molecular determinant of IFITM3 S-palmitoylation.

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Pteridine pigments compensate for environmental availability of carotenoids

10.22541/au.161132817.77514172/v1 ◽

2021 ◽

Author(s):

Devi Stuart-Fox ◽

Katrina Rankin ◽

Adrian Lutz ◽

Adam Elliott ◽

Andrew Hugall ◽

...

Keyword(s):

Sexual Selection ◽

Comparative Analysis ◽

Skin Tissue ◽

Honest Signalling ◽

Colour Variation ◽

Phylogenetic Comparative Analysis ◽

Environmental Availability ◽

Pigment Concentrations ◽

Production Mechanisms

Carotenoid-based colours are a textbook example of honest signalling because carotenoids must be acquired from the environment. However, many species produce similar colours using self-synthesised pteridine pigments. A compelling but untested hypothesis is that pteridines compensate for low environmental availability of carotenoids because it is metabolically cheaper to synthesise pteridines than to acquire and sequester carotenoids. Based on a phylogenetic comparative analysis of 11 pigment concentrations in skin tissue of agamid lizards, we show that pteridine concentrations are higher and carotenoid concentrations lower in less productive environments. Both carotenoid and pteridine pigments were present in all species, but only pteridine concentrations explained colour variation among species. Furthermore, pigment concentrations were uncorrelated with indices of sexual selection. These results suggest that variation among species in pteridine synthesis compensates for environmental availability of carotenoids and challenge the paradigm of honest carotenoid signalling in vertebrates with complex colour production mechanisms.

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