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[
BMC Evol Biol,
2011]
BACKGROUND: Genome wide analysis of variation within a species can reveal the evolution of fundamental biological processes such as mutation, recombination, and natural selection. We compare genome wide sequence differences between two independent isolates of the nematode Caenorhabditis elegans (CB4856 and CB4858) and the reference genome (N2). RESULTS: The base substitution pattern when comparing N2 against CB4858 reveals a transition over transversion bias (1.32:1) that is not present in CB4856. In CB4856, there is a significant bias in the direction of base substitution. The frequency of A or T bases in N2 that are G or C bases in CB4856 outnumber the opposite frequencies for transitions as well as transversions. These differences were not observed in the N2/CB4858 comparison. Similarly, we observed a strong bias for deletions over insertions in CB4856 (1.44: 1) that is not present in CB4858. In both CB4856 and CB4858, there is a significant correlation between SNP rate and recombination rate on the autosomes but not on the X chromosome. Furthermore, we identified numerous significant hotspots of variation in the CB4856-N2 comparison.In both CB4856 and CB4858, based on a measure of the strength of selection (ka/ks), all the chromosomes are under negative selection and in CB4856, there is no difference in the strength of natural selection in either the autosomes versus X or between any of the chromosomes. By contrast, in CB4858, ka/ks values are smaller in the autosomes than in the X chromosome. In addition, in CB4858, ka/ks values differ between chromosomes. CONCLUSIONS: The clear bias of deletions over insertions in CB4856 suggests that either the CB4856 genome is becoming smaller or the N2 genome is getting larger. We hypothesize the hotspots found represent alleles that are shared between CB4856 and CB4858 but not N2. Because the ka/ks ratio in the X chromosome is higher than the autosomes on average in CB4858, purifying selection is reduced on the X chromosome.
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[
Inorg Chem,
2015]
A new class of fluorescein/rhodamine hybrids with two spirolactone rings was reported to exhibit dual-output fluorescent behaviors independently. Isolation and characterization for two diastereomers, trans-RhOH and cis-RhOH, have been made and their X-ray crystal structures determined. In a basic environment, the spirolactone ring on the hydroxyl side will be opened to give a fluorescein-like optical output with the lowest absorptions at 485 and 530 nm emission. On the other hand, a rhodamine-like optical output, i.e., 528 nm absorption and 575 nm emission, will be switched on by a H(+) or a Hg(2+) ion, attributed to the spirolactone ring opening on the amino side. In a methanol-buffer system with different pH values, the corresponding pKa values for the hydroxyl and amino groups were determined as 5.7 and 2.3, respectively. Selective Hg(2+)-sensing properties have also been discussed, and log Ks values of about 3.60 and 3.73 were determined. Confocal microscopic images of Caenorhabditis elegans incubated with RhOH were found to show enhanced fluorescent intensity with a Hg(2+) ion, demonstrating the potential application of RhOH for in vivo biological imaging.
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[
Oecologia,
1982]
The food dependence of larval duration, fecundity and the intrinsic rate of natural increase follow a hyperbolic form, which can for the former be described by the Michaelis-Menten function. Maximal larval duration at 20C is 62 h, maximal fecundity is 153 eggs per female and rmax is 1.136 per day. The lower food threshold is 10*8 E. coli cells ml-1 (=0.06 mg dry weight ml-1) for larval growth and 2x10*8 cells ml-1 for reproduction and "r". 50% of maximal performances (Ks) are attained at 5x10*8 and 7.5x10*8 cells ml-1 respectively. Reproductive effort at dense food is highest immediately after maturation (e.g. 50% of the total eggs produced by a female are laid within 2 days after onset of egg production). At lower food densities the reproductive effort is delayed. Larval mortality increases strongly below 10*9 cells ml-1. The results reported sofar were obtained with E. coli cells which were harvested at the phase of decreasing population growth in batch cultures. With cells from the exponential and the stationary phase, performances are increased and decreased respectively. This is partly due to differences in bacterial biomass per unit cell, partly an expression of the change of nutritive value of bacterial cells with
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O'Rourke J, Barstead R, Pugh CW, Schofield CJ, Tian Y-M, Dhanda A, Mukherji M, McNeill LA, Ratcliffe PJ, Gleadle JM, Epstein ACR, Wilson MI, Hodgkin J, Maxwell PH, Jaakkola P, Masson N, Hamilton DL, Metzen E, Hewitson KS, Mole DR
[
Cell,
2001]
HIF is a transcriptional complex that plays a central role in mammalian oxygen homeostasis. Recent studies have defined posttranslational modification by prolyl hydroxylation as a key regulatory event that targets HIF-alpha. subunits for proteasomal destruction via the von Hippel-Lindau ubiquitylation complex. Here, we define a conserved HIF-VHL-prolyl hydroxylase pathway in C. elegans, and use a genetic approach to identify EGL-9 as a dioxygenase that regulates HIF by prolyl hydroxylation. In mammalian cells, we show that the HIF-prolyl hydroxylases are represented by a series of isoforms bearing a conserved 2-histidine-1-carboxylate iron coordination motif at the catalytic site. Direct modulation of recombinant enzyme activity by graded hypoxia, iron chelation, and cobaltous ions mirrors the characteristics of HIF induction in vivo, fulfilling requirements for these enzymes being oxygen sensors that regulate HIF.
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[
BMC Microbiol,
2020]
BACKGROUND: Stenotrophomonas maltophilia is an emerging nosocomial pathogen that causes infection in immunocompromised patients. S. maltophilia isolates are genetically diverse, contain diverse virulence factors, and are variably pathogenic within several host species. Members of the Stenotrophomonas genus are part of the native microbiome of C. elegans, being found in greater relative abundance within the worm than its environment, suggesting that these bacteria accumulate within C. elegans. Thus, study of the C. elegans-Stenotrophomonas interaction is of both medical and ecological significance. To identify host defense mechanisms, we analyzed the C. elegans transcriptomic response to S. maltophilia strains of varying pathogenicity: K279a, an avirulent clinical isolate, JCMS, a virulent strain isolated in association with soil nematodes near Manhattan, KS, and JV3, an even more virulent environmental isolate. RESULTS: Overall, we found 145 genes that are commonly differentially expressed in response to pathogenic S. maltophilia strains, 89% of which are upregulated, with many even further upregulated in response to JV3 as compared to JCMS. There are many more JV3-specific differentially expressed genes (225, 11% upregulated) than JCMS-specific differentially expressed genes (14, 86% upregulated), suggesting JV3 has unique pathogenic mechanisms that could explain its increased virulence. We used connectivity within a gene network model to choose pathogen-specific and strain-specific differentially expressed candidate genes for functional analysis. Mutations in 13 of 22 candidate genes caused significant differences in C. elegans survival in response to at least one S. maltophilia strain, although not always the strain that induced differential expression, suggesting a dynamic response to varying levels of pathogenicity. CONCLUSIONS: Variation in observed pathogenicity and differences in host transcriptional responses to S. maltophilia strains reveal that strain-specific mechanisms play important roles in S. maltophilia pathogenesis. Furthermore, utilizing bacteria closely related to strains found in C. elegans natural environment provides a more realistic interaction for understanding host-pathogen response.
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[
BMC Genomics,
2007]
ABSTRACT: BACKGROUND: Insects constitute the vast majority of known species with their importance including biodiversity, agricultural, and human health concerns. It is likely that the successful adaptation of the Insecta clade depends on specific components in its proteome that give rise to specialized features. However, proteome determination is an intensive undertaking. Here we present results from a computational method that uses genome analysis to characterize insect and eukaryote proteomes as an approximation complementary to experimental approaches. RESULTS: Homologs in common to Drosophila melanogaster, Anopheles gambiae, Bombyx mori, Tribolium castaneum, and Apis melifera were compared to the complete genomes of three non-insect eukaryotes (opisthokonts) Homo sapiens, Caenorhabditis elegans and Saccharomyces cerevisiae. This operation yielded 154 groups of orthologous proteins in Drosophila to be insect-specific homologs; 466 groups were determined to be common to eukaryotes (represented by three opisthokonts). ESTs from the hemimetabolous insect Locust migratoria were also considered in order to approximate their corresponding genes in the insect-specific homologs. Stress and stimulus response proteins were found to constitute a higher fraction in the insect-specific homologs than in the homologs common to eukaryotes. CONCLUSIONS: The significant representation of stress response and stimulus response proteins in proteins determined to be insect-specific, along with specific cuticle and pheromone/odorant binding proteins, suggest that communication and adaptation to environments may distinguish insect evolution relative to other eukaryotes. The tendency for low Ka/Ks ratios in the insect-specific protein set suggests purifying selection pressure. The generally larger number of paralogs in the insect-specific proteins may indicate adaptation to environment changes. Instances in our insect-specific protein set have been arrived at through experiments reported in the literature, supporting the accuracy of our approach.
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[
BMC Evol Biol,
2013]
BACKGROUND: Gene duplicates often exhibit asymmetric rates of molecular evolution in their early evolutionary existence. This asymmetry in rates is thought to signify the maintenance of the ancestral function by one copy and the removal of functional constraint on the other copy, enabling it to embark on a novel evolutionary trajectory. Here I focused on a large population of evolutionarily young gene duplicates (KS 0.14) in the Caenorhabditis elegans genome in order to conduct the first combined analysis of four predictors (evolutionary age, chromosomal location, structural resemblance between duplicates, and duplication span) which may be implicated in the asymmetric sequence divergence of paralogs at the nucleotide and amino acid level. In addition, I investigate if either paralog is equally likely to embark on a trajectory of accelerated sequence evolution or whether the derived paralog is more likely to exhibit faster sequence evolution. RESULTS: Three predictors (evolutionary age of duplicates, chromosomal location and duplication span) serve as major determinants of sequence asymmetry between C. elegans paralogs. Paralogs diverge asymmetrically in sequence with increasing evolutionary age, the relocation of one copy to a different chromosome and attenuated duplication spans that likely fail to capture the entire ancestral repertoire of coding sequence and regulatory elements. Furthermore, for paralogs residing on the same chromosome, opposite transcriptional orientation and increased genomic distance do not increase sequence asymmetry between paralogs. For a subset of duplicate pairs wherein the ancestral versus derived paralog could be distinguished, the derived paralogs are more likely to evolve at accelerated rates. CONCLUSIONS: This genome-wide study of evolutionarily young duplicates stemming primarily from DNA-mediated small-scale duplication events demonstrates that genomic relocation to a new chromosome has important consequences for asymmetric divergence of paralogs, akin to paralogs arising from RNA-mediated duplication events. Additionally, the duplication span is negatively correlated with sequence rate asymmetry among paralogs, suggesting that attenuated duplication spans stemming from incomplete duplication of the ORF and/or ancestral regulatory elements further accelerate sequence divergence between paralogs. Cumulatively, derived copies exhibit accelerated rates of sequence evolution suggesting that they are primed for a divergent evolutionary trajectory by changes in structure and genomic context at inception.