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[
International Worm Meeting,
2021]
The genome size variation is an "old" question in evolutionary biology. However, its causes and consequences are still a debate. There are various intraspecies models to study genome size variations, which usually hold very limited size change between pairs. As a result, sophisticated and pricy detection methods are required to monitor the change of genome size. And the impact of large size variation can not be tested. The inter-species models, however, could have significant genome size variation. One close sister pair among Caenorhabditis clade, the C. briggsae and C. nigoni, has around 30% genome size difference. They can cross with each other and produce fertile females, and can be used to study genome size variation and hybrid incompatibility. One major disadvantage of inter-species model is that, the F1 male is either dead for sterile, which hinder the monitoring of further offspring by F1 crossing. We generated a lot of introgression strains with C. nigoni genome background with a small fragment from C. briggsae genome. By incorporating different C. briggsae X chromosome fragments into C. nigoni background, we are able to produce a homozygotic introgression strain (ZZY10253), which could mate with C. briggsae male and produce both fertile F1 females and males. By breeding the F1 worms with 10 x 10 crossing, we can monitor the competition of the two haplotypes, which has 30% size difference, by checking the ratio of two haplotypes using NGS sequencing. We have sequenced some F7 and F20 lines. And the long haplotype, the C. nigoni haplotype, has become dominant (78%) in F7 populations, especially in the X chromosome (92%). With this speed, we expected to see a 100% recovery of ZZY10253 genotype after F15. But to our surprise, the F20 lines still maintained at least 8% of C. briggsae haplotype, and all these lines (n=8) have two autosomes remained. These remained autosomes may reflect an interaction between the X introgression fragment and autosomes, which grant these individuals some advantage in growing.
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Zhao, Zhongying, Li, Runsheng, Young, Amanda, Zhang, Zhihong, Ren, Xiaoliang, Hsieh, Chia-Ling
[
International Worm Meeting,
2015]
Next-Generation Sequencing permits rapid acquisition of high-throughput DNA sequences, but its reads are relatively short in length, limiting their use in genome-based studies. Illumina has recently released a technology called Synthetic Long-Read Sequencing that can produce reads of unusual length, i.e., predominately around 10 Kb. However, a systematic assessment of their use in genome finishing and assembly is still lacking, especially in resolving the repetitive sequences. We evaluate the promise and deficiency of the long reads in these aspects using C. elegans genome. First, the reads are highly accurate and capable of recovering most types of repetitive sequences. However, the presence of tandem repetitive sequences that extend over certain length prevents pre-assembly of the long reads inside this genomic region. Second, the reads can reliably recover the missing but not the extra sequences in C. elegans genome. 24X of the long reads allow the recovery of at least 40 Kb of missing genomic DNAs that are located inside or outside coding region. Finally, an N50 size of at least 86 Kb can be achieved for the contigs that are de novo assembled with the 24X reads. However, substantial mis-assembly errors are observed which are caused by either mis-assembled long read or flanking repetitive sequences, highlighting a need for novel assembly algorithm to accommodate the long reads in de novo genome assembly. The long reads are expected to be useful in generating a "finished-grade" genome of other nematode species if coupled with independent data such as those from PacBio or mate-pair sequencing or repairing the existing nematode draft genomes on its own.
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[
International Worm Meeting,
2017]
Differential expression of orthologous genes could be a product of divergence in cis-regulatory elements and/or trans-factors. Analysis of transcriptomes in F1 hybrids between closely related species provides an opportunity for systematically dissecting the roles of cis-elements and the trans-factors in controlling allele-specific expression. This analysis could also provide insight into the mechanism controlling genome stability, for example, through transposon silencing. The F1 hybrid transcriptomes have been analyzed in most model organisms, but never been examined in nematode species. Here we perform transcriptome analyses in the F1 female hybrids from reciprocal crosses between C. briggsae and C. nigoni with their parental hermaphrodites/females as a control. The reciprocal transcriptomes demonstrate a nearly perfect correlation between each other, indicating few genomic imprinting events in the parents. Approximately 8,000 orthologous pairs have at least 10 sequencing reads which are used in the subsequent analysis. Over 5,000 of them demonstrate differential allelic expressions in the hybrids, which mirror their expression divergences in their respective parents, indicating that cis-regulation plays a major role in controlling expression of these pairs in the hybrids. Roughly another 800 pairs show a significant averaging effect of their parental expression divergences in the hybrids, supporting the allelic expression in the hybrids is predominately regulated by trans-factors. The remaining 2,000 pairs demonstrate conserved expression in both parents and their hybrids. Unlike the F1 hybrids in Drosophila species in which a sharp increase in transposon expression is frequently observed, we barely see any significant increase in the expression of the mobile elements, suggesting compatible endogenous RNAi pathways between the two species in transposon silencing. Taken together, we demonstrate a lack of parent-of-origin differential allelic expression in female reciprocal F1 hybrids between C. briggsae and C. nigoni, in which allele-specific expressions of orthologous pairs are mostly controlled by cis-regulatory elements. Transposon-silencing mechanisms appear to be conserved between the two species.
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[
J Pharmacol Exp Ther,
2015]
NaCT (SLC13A5) is a Na(+)-coupled transporter for Krebs cycle intermediates and is expressed predominantly in the liver. Human NaCT is relatively specific for citrate compared with other Krebs cycle intermediates. The transport activity of human NaCT is stimulated by Li(+), whereas that of rat NaCT is inhibited by Li(+). We studied the influence of Li(+) on NaCTs cloned from eight different species. Li(+) stimulated the activity of only NaCTs from primates (human, chimpanzee, and monkey); by contrast, NaCTs from nonprimate species (mouse, rat, dog, and zebrafish) were inhibited by Li(+). Caenorhabditis elegans NaCT was not affected by Li(+). With human NaCT, the Li(+)-induced increase in transport activity was associated with the conversion of the transporter from a low-affinity/high-capacity type to a high-affinity/low-capacity type. H(+) was able to substitute for Li(+) in eliciting the stimulatory effect. The amino acid Phe500 in human NaCT was critical for Li(+)/H(+)-induced stimulation. Mutation of this amino acid to tryptophan (F500W) markedly increased the basal transport activity of human NaCT in the absence of Li(+), but the ability of Li(+) to stimulate the transporter was almost completely lost with this mutant. Substitution of Phe500 with tryptophan in human NaCT converted the transporter from a low-affinity/high-capacity type to a high-affinity/low-capacity type, an effect similar to that of Li(+) on the wild-type NaCT. These studies show that Li(+)-induced activation of NaCT is specific for the transporter in primates and that the region surrounding Phe500 in primate NaCTs is important for the Li(+) effect.
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[
International C. elegans Meeting,
1997]
Lithium (Li) has long been known to have teratogenic effects on the development of many organisms, including sea urchin, Xenopus and Dictyostelium. In Li-treated Xenopus embryos, ventral blastmeres are respecified to develop into dorsal structures, leading to dorsalized embryos lacking ventral mesodermal tissues. In Dictyostelium, Li alters the fate of prespore cells to become prestalk cells instead. Besides teratogenic effects, Li is also known to be a most effective treatment of manic-depressive illness.!@Although several models have been proposed to explain Li action, the molecular mechanism has remained unclear. Recently, GSK (glycogen synthase kinase)-3b was proposed to be a target of Li, suggesting that Li affects the wnt signaling pathway. To understand the mechanism of Li action, I first examined the effect of Li on C. elegans embryogenesis. I inoculated N2 animals at the late L4 stage onto NG plates containing 20 mM LiCl, incubated them at 20 oC. The number of eggs produced by treated animals was reduced to about half of the untreated control. Although cell division seemed to proceed, no embryos hatched on Li plates. Treated-embryos developed to produce gut granules, but did not execute normal morphogenesis at later embryonic stages. To identify genes involved in the action of Li, I have begun to screen for Li-resistant mutants that propagated on Li-containing medium. Several mutants were isolated, and one of them was mapped on the left side of
unc-42 on chromosome V. On Li plates, the hatching rate of mutant eggs cross-fertilized by wild-type males was essentially the same as that for self-fertilized mutant eggs. On the contrary, no wild-type eggs cross-fertilized by mutant males hatched on Li-containing plates. So, this mutation appeared to be maternal. Further genetic analyses of the mutants and the observation on the cellular phenotype of Li-treated embryos are underway.
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[
Worm Breeder's Gazette,
1996]
Lithium (Li) has long been known to have teratogenic effects on the development of many organisms, including sea urchin, Xenopus and Dictyostelium. In Li-treated Xenopus embryos, ventral blastmeres are respecified to develop into dorsal structures, leading to dorsalized embryos lacking ventral mesodermal tissues. In Dictyostelium, Li alters the fate of prespore cells to become prestalk cells instead. Besides teratogenic effects, Li is also known to bea most effective treatment of manic-depressive illness. Although several models have been proposed to explain Li action, the molecular mechansm remains unclear. The most widely accepted model is the inositol depletion hypothesis, in which Li is thought to affect inositol phosphate turnover by inhibiting inositol monophosphatase, thus resulting in the depletion of endogenous inositol. To understand the mechanism of Li action, I first examined the effect of Li on C. elegans embryogenesis. I inoculated N2 animals at the late L4 stage onto NG plates containing 20 mM LiCl, incubated them at 20 C and observed the laid embryos. The number of eggs produced by treated animals was reduced to about half of the untreated control. Although cell division seemed to proceed, no embryos hatched on Li plates. Treated-embryos developed to produce gut granules, but did not execute normal morphogenesis at later embryonic stages. To identify genes involved in the action of Li, I have begun to screen for Li-resistant mutants, which propagated on Li-containing medium. So far, I obtained one mutant. The mutation was tentatively assigned to chromosome V. Preliminary genetic analysis showed that the mutation showed maternal effect. On Li plates, the hatching rate of mutant eggs cross-fertilized by wild-type males was essentially the same as that for self-fertilized mutant eggs. On the contrary, no wild-type eggs cross-fertilized by mutant males hatched on Li-containing plates. I am now trying to isolate other mutants and also to identify early defects of embryogenesis caused by lithium treatment. I would like to thank J. Miwa for encouragement and discussions.
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[
J Appl Toxicol,
2015]
Lithium (Li) has been widely used to treat bipolar disorder, and industrial use of Li has been increasing; thus, environmental pollution and ecological impacts of Li have become a concern. This study was conducted to clarify the potential biological effects of LiCl and Li(2)CO(3) on a nematode, Caenorhabditis elegans as a model system for evaluating soil contaminated with Li. Exposure of C. elegans to LiCl and Li(2)CO(3) decreased growth/maturation and reproduction. The lowest observed effect concentrations for growth, maturation and reproduction were 1250, 313 and 10 000m, respectively, for LiCl and 750, 750 and 3000m, respectively, for Li(2)CO(3). We also investigated the physiological function of LiCl and LiCO(3) in C. elegans using DNA microarray analysis as an eco-toxicogenomic approach. Among approximately 300 unique genes, including metabolic genes, the exposure to 78m LiCl downregulated the expression of 36 cytochrome P450, 16 ABC transporter, 10 glutathione S-transferase, 16 lipid metabolism and two vitellogenin genes. On the other hand, exposure to 375m Li(2)CO(3) downregulated the expression of 11 cytochrome P450, 13 ABC transporter, 13 lipid metabolism and one vitellogenin genes. No gene was upregulated by LiCl or Li(2)CO(3). These results suggest that LiCl and Li(2)CO(3) potentially affect the biological and physiological function in C. elegans associated with alteration of the gene expression such as metabolic genes. Our data also provide experimental support for the utility of toxicogenomics by integrating gene expression profiling into a toxicological study of an environmentally important organism such as C. elegans.
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[
J Biol Chem,
2008]
Lithium (Li+) has been used to treat mood affect disorders, including bipolar, for decades (1;2). This drug is neuroprotective and has several identified molecular targets. However, it has a narrow therapeutic range and the underlying mechanism(s) of its therapeutic action is not understood. Here we describe a pharmacogenetic study of Li+ in the nematode Caenorhabditis elegans. Exposure to Li+ at clinically relevant concentrations throughout adulthood increases survival during normal aging (up to 46% median increase). Longevity is extended via a novel mechanism with altered expression of genes encoding nucleosome-associated functions. Li+ treatment results in reduced expression of the worm ortholog of LSD-1 (T08D10.2), a histone demethylase; knockdown by RNA interference (RNAi) of T08D10.2 is sufficient to extend longevity (~25% median increase), suggesting Li+ regulates survival by modulating histone methylation and chromatin structure.
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[
International C. elegans Meeting,
2001]
Little is known about how ions permeate the C. elegans gut and cuticle. How various ions influence development and behavior is also not understood. One ion with considerable impact in human biology is Li + , which modulates bipolar disorder by an unknown mechanism. In particular, the targets of lithium that cause side effects remain to be identified. We are using C. elegans to genetically identify targets of lithium and to elaborate on mechanisms of transport, which may have an impact on human health. Li + has dosage-dependent effects on C. elegans embryos. When L4 animals mature on NGM plates with Li + added to the final concentrations of 10mM-20mM, they produce embryos that are unable to hatch. We demonstrated that this failure to hatch is due to defects in cytokinesis that result in multi-nucleated embryos and symmetrically partitioned cells. Li + also has a dosage-dependent effect on larval development. When adult hermaphrodites are permitted to lay embryos on 10mM-20mM Li + NGM plates, the resulting offspring experience a developmental delay proportional to the concentration of Li + . The offspring become progressively paralyzed as they reach adulthood. We demonstrated earlier that there is a delay in the entry into the S phase of the cell cycle larval stages. To learn more about the biology of Li + sensitivity, we screened for Li + resistant mutants. We developed three screens that took advantage of the embryonic arrest and the larval delay caused by Li + . We isolated one mutant
bz71 , in a screen of 44,000 haploid genomes, that is resistant to both the larval and embryonic blocks of 16mM Li + .
bz71 is dominant. Using classical mapping techniques, we positioned it on LGIII between
unc-32 and
dpy-18 . We are currently using SNP strategy to obtain a higher resolution map and we hope to report on the identification and cloning of this locus.
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[
Worm Breeder's Gazette,
1992]
Characterization of the axonal guidance and outgrowth gene
unc-33 W. Li, R. K. Herman and J. E. Shaw Department of Genetics and Cell biology, University of Minnesota, St Paul, MN 55108