Effect of liquid cultivations on N2 and AB1 strains of C. elegans

Abrupt environment changes can elicit an array of genetic effects. However, many of these effects can be overlooked by functional genomic studies conducted in static laboratory conditions. We studied the transcriptomic responses of Caenorhabditis elegans under single generation exposures to drastically different culturing conditions. In our experimental scheme, P0 worms were maintained on terrestrial environments (agar plates), F1 in aquatic cultures, and F2 back to terrestrial environments. The laboratory N2 strain and the wild isolate AB1 strain were utilized to examine how the genotype contributes to the transcriptome dynamics. Significant variations were found in the gene expressions between the “domesticated” laboratory strain and the wild isolate in the different environments. The results showed that 20% - 27% of the transcriptional responses to the environment changes were transmitted to the subsequent generation. In aquatic conditions, the domesticated strain showed differential gene expression particularly for the genes functioning in the reproductive system and the cuticle development. In accordance with the transcriptomic responses, phenotypic abnormalities were detected in the germline and cuticle of the domesticated strain. Further studies showed that distinct groups of genes are exclusively expressed under specific environmental conditions, and many of these genes previously lacked supporting biochemical evidence. Overall design: To induce an adaptive response and observe its sustained effects on the following generation, the P0 generation C. elegans was grown on bacteria-seeded agar plates, the F1 generation in liquid, and the F2 generation back on agar. We carried out three sets of experiments with different food sources and animal strains. For the first experiment, the F1 generation N2 strain was grown in axenic CeHR Medium. To examine the effect of dietary changes in the liquid cultures, we cultured F1 generation N2 strain in bacterial S-Medium for the second experiment. Finally, the adaptive response differences were investigated by growing F1 generation AB1 strain in CeHR Medium. For each generation, RNA-seq was performed on young adult animals to determine the transcriptional responses剧烈的环境变化可引发一系列遗传效应，然而在静态实验室条件下开展的功能基因组研究往往会忽略其中诸多效应。 我们针对秀丽隐杆线虫（Caenorhabditis elegans）在单代暴露于极端迥异的培养条件下的转录组响应展开了研究。 本实验方案中，亲本代（P0）线虫培养于陆生环境（即琼脂平板），子一代（F1）培养于水生培养液中，子二代（F2）则回置陆生环境培养。 我们利用实验室驯化的N2菌株与野生分离株AB1，探究基因型如何影响转录组动态变化。 在不同环境下，驯化实验室菌株与野生分离株之间的基因表达存在显著差异。 研究结果显示，约20%至27%的环境变化转录响应可传递至后代。 在水生培养条件下，驯化菌株的差异表达基因显著富集于生殖系统与表皮发育相关功能通路。 与转录组响应结果一致，我们在驯化菌株的生殖系与表皮中检测到了表型异常。 进一步研究发现，不同基因簇仅在特定环境条件下表达，其中多数基因此前尚未获得生化实验证据支持。 实验整体设计：为诱导适应性响应并观察其对后代的持续影响，本研究将秀丽隐杆线虫P0代培养于涂布细菌的琼脂平板，F1代培养于液体培养基，F2代则回置琼脂平板培养。 我们设置了三组不同食物来源与线虫菌株的对照实验。 第一组实验中，F1代N2菌株培养于无菌CeHR培养基。 第二组实验中，我们将F1代N2菌株培养于含细菌的S培养基中，以探究液体培养环境中食物来源变化的影响。 最后一组实验中，我们将F1代AB1菌株培养于CeHR培养基，以探究不同菌株间的适应性响应差异。 针对每一代线虫，我们均对年轻成虫进行RNA测序（RNA-seq），以解析其转录组响应。