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Origination and evolution of orphan genes and de novo genes in the genome of caenorhabditis elegans

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Science China(Life Sciences) 2019年第4期62卷 579-593页

作者： Wenyu Zhang Yuanxiao Gao Manyuan Long Bairong Shen Institutes for Systems Genetics West China Hospital Sichuan University Department of Ecology and Evolution the University of Chicago Department of Evolutionary Genetics Max-Planck Institute for Evolutionary Biology Department of Evolutionary Theory Max-Planck Institute for Evolutionary Biology Committee on Genetics the University of Chicago

Orphan genes that lack detectable homologues in other lineages could contribute to a variety of biological functions. However,their origination and function mechanisms remain largely unknown. Herein, through a comprehensive and systematic computational pipeline, we identified 893 orphan genes in the lineage of C. elegans, of which only a low fraction(0.9%) were derived from transposon elements. Six new protein-coding genes that de novo originated from non-coding DNA sequences in the genome of C. elegans were also identified. The authenticity and functionality of these orphan genes and de novo genes are supported by three lines of evidences, consisting of transcriptional data, and in silico proteomic data, and the fixation status data in wild populations. Orphan genes and de novo genes exhibited simple gene structures, such as, short in protein length, of fewer exons,and are frequently X-linked. RNA-seq data analysis showed these orphan genes are enriched with expression in embryo development and gonad, and their potential function in early development was further supported by gene ontology enrichment analysis results. Meanwhile, de novo genes were found to be with significant expression in gonad, and functional enrichment analysis of the co-expression genes of these de novo genes suggested they may be functionally involved in signaling transduction pathway and metabolism process. Our results presented the first systematic evidence on the evolution of orphan genes and de novo origin of genes in nematodes and their impacts on the functional and phenotypic evolution, and thus could shed new light on our appreciation of the importance of these new genes.

关键词： caenorhabditis elegans,orphan genes de novo genes

Anti-parasitic effects of water-soluble alkaloid fractions from ethanolic extracts of Sophora moorcroftiana seeds in caenorhabditis elegans

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Chinese Journal of Natural Medicines 2018年第9期16卷 665-673页

作者： LUO Yan-Ping ZHANG Yuan ZHANG Hui-Min ZHANG Hong ZHANG Lin YU Hong-Juan CAO Ming-Qiang SHI Yan-Bin ZHI De-Juan MA Xing-Ming DONG Kai-Zhong Department of Immunology School of Basic Medical Sciences Lanzhou University Lanzhou 730000 China Key Lab of Preelinical Study for New Drugs of Gansu Province Lanzhou 730000 China School of Pharmacy Lanzhou University Lanzhou 730000 China Department of Microbiology Medical College Northwest Minzu University Lanzhou 730000 China

Parasite infections of humans and animals remain a major global health problem, with limited choice of drugs being available to the treatment of parasitosis in the clinic. Sophora moorcroftiana(S. moorcroftiana) is a shrub that grows in Tibet Plateau of China. Decoction of the seeds has been used as a traditional Tibetan medicine to treat parasitosis for years. But the anti-parasitic effects of water-soluble fractions in the seeds need further investigation. In the present study, the water-soluble alkaloid fractions(E2) were obtained from S. moorcroftiana seeds by refluxing extraction with 60% ethanol and low polarity fraction(E2-a) and high polarity fraction(E2-b) were subsequently isolated from E2 using column chromatography. As a parasite model, caenorhabditis elegans(C. elegans) were treated with different fractions and their survivals were recorded. The results showed that that E2-a induced a lower survival rate in C. elegans than E2-b and E2. The protoscoleces of Echinococcus granulosus(E. granulosus) were cultured in the presence of E2-a. Compared with E2-b and E2, protoscoleces exhibited decreased survival rate following E2-a treatment. Furtherly, the effects of E2-a on the behavior, brood size, and lifespan of the worms were investigated. Body bend frequencies of the worms treated with the high concentration of E2-a were reduced by two-thirds compared with the control group(P < 0.01). Compared with non-E2-a-treated group, exposure of nematodes to E2-a led to a decrease in head thrashes and pharyngeal pumps frequency(P < 0.01). E2-a treatment resulted in a significantly lower brood size(P < 0.01). Additional E2-a treatment induced a significantly shortened lifespan, compared with the control(P < 0.05). These findings indicated that water-soluble fraction E2-a from S. moorcroftiana seeds was a potential helminthic agent.

关键词： Sophora moorcroftiana Alkaloids Anthelmintics caenorhabditis elegans Protoscoleces

Effects of Treatment with Different Combinations of Bisphenol Compounds on the Mortality of caenorhabditis Elegans

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Biomedical and Environmental Sciences 2020年第2期33卷 145-149页

作者： Naomi HAMAMBA LI Jie ZHANG Xiao Wei ZHANG Cai Qin Frederick SARPONG ZHOU Xing Hua School of Food and Biological Engineering Jiangsu UniversityZhenjiang 212013Jiangsu China

Bisphenol A(BPA)is believed to affect a variety of physiological functions associated with human diseases[1].Bisphenol F(BPF)is an alternative to bisphenol *** percent of BPF is used as a monomer in the synthesis of polyvinyl chloride(PVC)and other compounds[2].Bisphenol S(BPS)is a structural analog of bisphenol A,which is widely used as a substitute in a variety of daily-use consumer goods and *** compound is often detected in indoor dust,urine,and human blood.

关键词： Effects Treatment caenorhabditis

α-Mangostin Promotes DAF-16-Mediated Thermotolerance in caenorhabditis elegans

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Food and Nutrition Sciences 2018年第6期9卷 693-702页

作者： Nattapong Thammawong Haruka Takahashi Takaya Sugawara Kazuichi Sakamoto Graduate School of Life and Environmental Sciences University of Tsukuba Tsukuba Japan

Garcinia mangostana, commonly known as mangosteen, is a tropical fruit with a reddish-purple pericarp. In Southeast Asia, the pericarp has traditionally been used as a medicine to treat various diseases, including inflammation, wounds, and bacterial infections, as well as aging. α-mangostin is an abundant xanthone in the pericarp, and is thought to play a critical role in the medicinal effects of mangosteens. Previous studies have demonstrated numerous beneficial effects of α-mangostin, such as cytotoxicity in cancer cells. However, the effects of this xanthone in in vivo have not yet been studied. In the current study, C. elegans was used to test the in vivo effects of α-mangostin using several bioassays, including fat accumulation, pharyngeal movement (pumping) and heat-stress assays. Quantitative real time PCR (qRT-PCR) was also used to examine the expression of heat shock proteins. The results revealed that α-mangostin appeared to cause an increase in fat accumulation, which correlated with an increase in pharyngeal movement. The thrashing movement of the worms after heat stress also showed a correlation with an increase in heat shock protein mRNA expression.

关键词： Mangosteen α-Mangostin Thermotolerance caenorhabditis elegans DAF-16

Age Does Not Affect the Induction of Mortality by the Foodborne Pathogen Salmonella entericain caenorhabditis elegans

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Advances in Microbiology 2017年第10期7卷 689-695页

作者： Dawn M. F. Burns James M. Harper Aaron M. Lynne Department of Biological Sciences Sam Houston State University Huntsville TX USA

Salmonella is a common cause of foodborne illness within the United States with the severity of the infection being a factor of both the age and overall health of the infected individual. The nematode worm caenorhabditis elegans has proven to be a useful model to study infection dynamics of pathogenic bacteria, including Salmonella enterica, and its short lifespan makes it a powerful model system to assess the effect of organismal age on infection severity. In this study, we infected C. elegans with each of 6 serovars of S. enterica at 1, 3 or 5 days of worm age and monitored their survival. Worms infected with E. coli OP50 were used as a control. Infection with S. enterica resulted in a significant reduction in mean longevity relative to OP50 (p < 0.05);however, there was no significant effect of age on mean survival time regardless of the strain of bacteria used.

关键词： Salmonella enterica caenorhabditis elegans Aging Infection

Expression of hepatitis B virus surface antigens induces defective gonad phenotypes in caenorhabditis elegans

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World Journal of Virology 2017年第1期6卷 17-25页

作者： Yi-Yin Chen Li-Wei Lee Wei-Ning Hong Szecheng J Lo Department of Biomedical Science College of Medicine Chang Gung University Graduate Institute of Biomedical Science College of Medicine Chang Gung University

AIM To test whether a simple animal, caenorhabditis elegans(C. elegans), can be used as an alternative model to study the interaction between hepatitis B virus antigens(HBs Ag) and host factors. METHODS Three plasmids that were able to express the large, middle and small forms of HBs Ags(LHBs Ag, MHBs Ag, and SHBs Ag, respectively) driven by a ubiquitous promoter(fib-1) and three that were able to express SHBs Ag driven by different tissue-specific promoters were constructed and microinjected into worms. The brood size, egglaying rate, and gonad development of transgenic worms were analyzed using microscopy. Levels of m RNA related to endoplasmic reticulum stress, enpl-1, hsp-4, pdi-3 and xbp-1, were determined using reverse transcription polymerase reaction(RT-PCRs) in three lines of transgenic worms and dithiothreitol(DTT)-treated wild-type worms. RESULTS Severe defects in egg-laying, decreases in brood size, and gonad retardation were observed in transgenic worms expressing SHBs Ag whereas moderate defects were observed in transgenic worms expressing LHBs Ag and MHBs Ag. RT-PCR analysis revealed that enpl-1, hsp-4 and pdi-3 transcripts were significantly elevated in worms expressing LHBs Ag and MHBs Ag and in wild-type worms pretreated with DTT. By contrast, only pdi-3 was increased in worms expressing SHBs Ag. To further determine which tissue expressing SHBs Ag could induce gonad retardation, we substituted the fib-1 promoter with three tissue-specific promoters(myo-2 for the pharynx, est-1 for the intestines and mec-7 for the neurons) and generated corresponding transgenic animals. Moderate defective phenotypes were observed in worms expressing SHBs Ag in the pharynx and intestines but not in worms expressing SHBs Ag in the neurons, suggesting that the secreted SHBs Ag may trigger a cross-talk signal between the digestive track and the gonad resulting in defective phenotypes. CONCLUSION Ectopic expression of three forms of HBs Ag that causes recognizable pheno

关键词： Hepatitis B virus caenorhabditis elegans Green fluorescence proteins Endoplasmic reticulum stress Gonad retardation Surface antigens

食细菌线虫caenorhabditis elegans的取食偏好性

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生态学报 2010年第24期30卷 7101-7105页

作者：肖海峰焦加国胡锋李辉信南京农业大学资源与环境科学学院江苏南京210095

通过设置平板培养试验,以模式种线虫caenorhabditis elegans为材料,观察了食细菌线虫的取食行为。结果表明:***在取食细菌时对原位土壤中分离的一种Pseudomonas sp细菌存在最大的取食偏好性。这种取食偏好性表现在大部分***在24 h内都... 详细信息

通过设置平板培养试验,以模式种线虫caenorhabditis elegans为材料,观察了食细菌线虫的取食行为。结果表明:***在取食细菌时对原位土壤中分离的一种Pseudomonas sp细菌存在最大的取食偏好性。这种取食偏好性表现在大部分***在24 h内都直接朝Pseudomonas sp迁移,说明***能通过某种机制识别Pseudomonas sp。距离迁移试验及***迁移率表明它可能是通过辨别细菌所发出的气味识别它喜欢的食物。***的繁殖率跟其取食的偏好性是相关的,在迁移率较高的细菌培养基中线虫表现出更高的繁殖率。结果还表明:相对于G+细菌而言,***偏好取食G-细菌。为进一步了解土壤生态系统中食细菌线虫与细菌群落结构间相互关系提供了帮助。

关键词： caenorhabditis elegans Pseudomonas sp 取食偏好性

Reproductive isolation in the Elegans-Group of caenorhabditis

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Natural Science 2013年第4期5卷 18-25页

作者： Scott Everet Baird Sara R. Seibert Department of Biological Sciences Wright State University Dayton USA

Reproductive isolation is the basis of the Biological Species Definition and can be a driving force of speciation. Theoretical studies have provided models of how reproductive isolation can arise within individual species. Genetic tests of these models are limited to populations in which reproductive isolation is present but not complete. Here, reproductive isolation in the Elgans-Group of the nematode genus caenorhabditis is reviewed. Pre-mating barriers, assortative fertilization and post-zygotic barriers all have been observed in this clade. In some combinations of species, fertile F1 hybrids can be obtained. Therefore, the Elegans-Group of caenorhabditis is poised to become an important experimental system for the study of reproductive isolation.

关键词： caenorhabditis Pre-Mating Isolation Assortative Fertilization Post-Zygotic Isolation

原位杂交检测lin-28 mRNA在caenorhabditis elegans中的分布

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厦门大学学报（自然科学版） 2008年第A02期47卷 54-58页

作者：杨玉荣郑卫玲厦门大学生命科学学院福建厦门361005

利用原位杂交检测了异时性基因lin-28 mRNA在野生型和lin-4,lin-14突变体以及lin-4,lin-14双突变体中的分布,发现lin-28 mRNA在胚胎和成虫生殖腺中存在.还发现lin-4突变不改变lin-28 mRNA分布,证明了lin-28表达独立于lin-4抑制通路的存在.

关键词： caenorhabditis elegans lin-28 lin-4 lin-14 原位杂交