De novo creation of protein coding genes involves the formation of short ORFs from noncoding regions; some of these ORFs might then become fixed in the population. These orphan proteins need to, at ...the bare minimum, not cause serious harm to the organism, meaning that they should for instance not aggregate. Therefore, although the creation of short ORFs could be truly random, the fixation should be subjected to some selective pressure. The selective forces acting on orphan proteins have been elusive, and contradictory results have been reported. In Drosophila young proteins are more disordered than ancient ones, while the opposite trend is present in yeast. To the best of our knowledge no valid explanation for this difference has been proposed. To solve this riddle we studied structural properties and age of proteins in 187 eukaryotic organisms. We find that, with the exception of length, there are only small differences in the properties between proteins of different ages. However, when we take the GC content into account we noted that it could explain the opposite trends observed for orphans in yeast (low GC) and Drosophila (high GC). GC content is correlated with codons coding for disorder promoting amino acids. This leads us to propose that intrinsic disorder is not a strong determining factor for fixation of orphan proteins. Instead these proteins largely resemble random proteins given a particular GC level. During evolution the properties of a protein change faster than the GC level causing the relationship between disorder and GC to gradually weaken.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The genomes of many vertebrates show a characteristic heterogeneous distribution of GC content, the so-called GC isochore structure. The origin of isochores has been explained via the mechanism of ...GC-biased gene conversion (gBGC). However, although the isochore structure is declining in many mammalian genomes, the heterogeneity in GC content is being reinforced in the avian genome. Despite this discrepancy, which remains unexplained, examinations of individual substitution frequencies in mammals and birds are both consistent with the gBGC model of isochore evolution. On the other hand, a negative correlation between substitution and recombination rate found in the chicken genome is inconsistent with the gBGC model. It should therefore be important to consider along with gBGC other consequences of recombination on the origin and fate of mutations, as well as to account for relationships between recombination rate and other genomic features. We therefore developed an analytical model to describe the substitution patterns found in the chicken genome, and further investigated the relationships between substitution patterns and several genomic features in a rigorous statistical framework. Our analysis indicates that GC content itself, either directly or indirectly via interrelations to other genomic features, has an impact on the substitution pattern. Further, we suggest that this phenomenon is particularly visible in avian genomes due to their unusually low rate of chromosomal evolution. Because of this, interrelations between GC content and other genomic features are being reinforced, and are as such more pronounced in avian genomes as compared with other vertebrate genomes with a less stable karyotype.
The major codon preference model suggests that codons read by tRNAs in high concentrations are preferentially utilized in highly expressed genes. However, the identity of the optimal codons differs ...between species although the forces driving such changes are poorly understood. We suggest that these questions can be tackled by placing codon usage studies in a phylogenetic framework and that bacterial genomes with extreme nucleotide composition biases provide informative model systems. Switches in the background substitution biases from GC to AT have occurred in Gardnerella vaginalis (GC = 32%), and from AT to GC in Lactobacillus delbrueckii (GC = 62%) and Lactobacillus fermentum (GC = 63%). We show that despite the large effects on codon usage patterns by these switches, all three species evolve under selection on synonymous sites. In G. vaginalis, the dramatic codon frequency changes coincide with shifts of optimal codons. In contrast, the optimal codons have not shifted in the two Lactobacillus genomes despite an increased fraction of GC-ending codons. We suggest that all three species are in different phases of an on-going shift of optimal codons, and attribute the difference to a stronger background substitution bias and/or longer time since the switch in G. vaginalis. We show that comparative and correlative methods for optimal codon identification yield conflicting results for genomes in flux and discuss possible reasons for the mispredictions. We conclude that switches in the direction of the background substitution biases can drive major shifts in codon preference patterns even under sustained selection on synonymous codon sites.
Abstract
Coding sequence evolution is influenced by both natural selection and neutral evolutionary forces. In many species, the effects of mutation bias, codon usage, and GC-biased gene conversion ...(gBGC) on gene sequence evolution have not been detailed. Quantification of how these forces shape substitution patterns is therefore necessary to understand the strength and direction of natural selection. Here, we used comparative genomics to investigate the association between base composition and codon usage bias on gene sequence evolution in butterflies and moths (Lepidoptera), including an in-depth analysis of underlying patterns and processes in one species, Leptidea sinapis. The data revealed significant G/C to A/T substitution bias at third codon position with some variation in the strength among different butterfly lineages. However, the substitution bias was lower than expected from previously estimated mutation rate ratios, partly due to the influence of gBGC. We found that A/T-ending codons were overrepresented in most species, but there was a positive association between the magnitude of codon usage bias and GC-content in third codon positions. In addition, the tRNA-gene population in L. sinapis showed higher GC-content at third codon positions compared to coding sequences in general and less overrepresentation of A/T-ending codons. There was an inverse relationship between synonymous substitutions and codon usage bias indicating selection on synonymous sites. We conclude that the evolutionary rate in Lepidoptera is affected by a complex interaction between underlying G/C -> A/T mutation bias and partly counteracting fixation biases, predominantly conferred by overall purifying selection, gBGC, and selection on codon usage.
A GC–MS method for the simultaneous determination of hexanal, heptanal, octanal, nonanal and decanal in exhaled breath was established and validated. The aldehydes were derivatized on PDMS/DVB fibres ...using
O-2,2,4,5,6-(pentafluorobenzyl) hydroxylamine hydrochloride (PFBHA) as the headspace derivatization reagent. The resultant oximes were quantified by GC–MS in selected ion monitoring (SIM) mode. The method provides detection limits of 0.01–0.03
nM for the aldehydes, with a linear response in the concentration range 0.002–20
nM. Within-day precision values for the five aldehydes at 0.02–0.04
nM and 0.2–0.4
nM were in the ranges: 3–9% and 3–8%, respectively; the corresponding between-day precision values were 11–22% and 10–24%. Exhaled breath samples could be stored at −20
°C for 48
h.
The cultivated peanut (
L.) is an important oilseed crop worldwide, and fatty acid composition is a major determinant of peanut oil quality. In the present study, we conducted a genome-wide ...association study (GWAS) for nine fatty acid traits using the whole genome sequences of 160 representative Chinese peanut landraces and identified 6-1195 significant SNPs for different fatty acid contents. Particularly for oleic acid and linoleic acid, two peak SNP clusters on Arahy.09 and Arahy.19 were found to contain the majority of the significant SNPs associated with these two fatty acids. Additionally, a significant proportion of the candidate genes identified on Arahy.09 overlap with those identified in early studies, among which three candidate genes are of special interest. One possesses a significant missense SNP and encodes a known candidate gene
. The second gene is the gene closest to the most significant SNP for linoleic acid. It codes for an MYB protein that has been demonstrated to impact fatty acid biosynthesis in
. The third gene harbors a missense SNP and encodes a JmjC domain-containing protein. The significant phenotypic difference in the oleic acid/linoleic acid between the genotypes at the first and third candidate genes was further confirmed with PARMS analysis. In addition, we have also identified different candidate genes (i.e.,
,
,
and
) for the remaining fatty acids. Our findings can help us gain a better understanding of the genetic foundation of peanut fatty acid contents and may hold great potential for enhancing peanut quality in the future.
The essential companion to Stieg Larsson's bestselling trilogy and director David Fincher's 2011 film adaptationStieg Larsson's bestselling Millennium Trilogy—The Girl with the Dragon Tattoo, The ...Girl Who Played with Fire,and The Girl Who Kicked the Hornet's Nest—is an international phenomenon. These books express Larsson's lifelong war against injustice, his ethical beliefs, and his deep concern for women's rights. The Girl with the Dragon Tattoo and Philosophyprobes the compelling philosophical issues behind the entire trilogy. What philosophies do Lisbeth Salander and Kant have in common? To catch a criminal, can Lisbeth and Mikael be criminals themselves? Can revenge be ethical? Drawing on some of history's greatest philosophical minds, this book gives fresh insights into Larsson's ingeniously plotted tale of crime and corruption.Looks at compelling philosophical issues such as a feminist reading of Lisbeth Salander, Aristotelian arguments for why we love revenge, how Kant can explain why so many women sleep with Mikael Blomkvist, and many moreIncludes a chapter from a colleague of Larsson's—who worked with him in anti-Nazi activities—that explores Larsson's philosophical views on skepticism and quotes from never-before-seen correspondence with LarssonOffers new insights into the novels' key characters, including Lisbeth Salander and Mikael Blomkvist, and investigates the author, Stieg LarssonAs engrossing as the quest to free Lisbeth Salander from her past, The Girl with the Dragon Tattoo and Philosophyis ideal reading for anyone interested in unraveling the subtext and exploring the greater issues at work in the story.
The sweet potato whitefly,
, is one of the most invasive insect pests worldwide. The two most destructive whitefly cryptic species are MEAM1/B and MED/Q. Given that MED/Q has replaced MEAM1/B in ...China and the invasion of MED/Q has coincided with the outbreak of tomato yellow leaf curl virus (TYLCV), we hypothesize that pre-infestation with viruliferous
will affect the subsequent host preferences. To test this hypothesis, we (1) conducted bioassays to compare the host preference of viruliferous and non-viruliferous MEAM1/B and MED/Q, respectively, on plants pre-infested with viruliferous and non-viruliferous MEAM1/B and MED/Q; (2) profiled plant volatiles using GC-MS; and (3) functionally characterized chemical cues could potentially modulate
-TYLCV-tomato interactions, including ρ-cymene, thujene and neophytadiene, using a Y-tube olfactometer. As a result, plants pre-infested with MEAM1/B whiteflies carrying TYLCV or not, did not attract more or less B or Q whiteflies. Plants pre-infested with non-viruliferous MED/Q resisted MEAM1/B but did not affect MED/Q. However, plants pre-infested with viruliferous MED/Q attracted more whiteflies. Feeding of viruliferous MED/Q reduced the production of ρ-cymene, and induced thujene and neophytadiene. Functionally analyses of these plant volatiles show that ρ-cymene deters while neophytadiene recruits whiteflies. These combined results suggest that pre-infestation with viruliferous MED/Q promotes the subsequent whitefly infestation and induces plant volatile neophytadiene which recruits whiteflies.
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