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Estimating quality of archive urban stream macroinvertebrate samples for genomic, transcriptomic and proteomic assessment
Ecological Indicators ( IF 7.0 ) Pub Date : 2021-02-19 , DOI: 10.1016/j.ecolind.2021.107509
Valerija Begić , Mirela Sertić Perić , Suzana Hančić , Mihaela Štargl , Matea Svoboda , Petra Korać , Ines Radanović

The existence of archival collections of macroinvertebrates opens the possibility of using these organisms as biological indicators and model organisms for developing indices of aquatic ecosystem health and stress, which provide a powerful basis for sustainable environmental monitoring and management of water resources. The environmental assessment of urbanization influence on urban stream biota over time can include molecular (proteomic, transcriptomic and genomic) analyses of aquatic insects isolated from archive samples. These analyses could include confirmation of detected species by barcoding, determination of the changes in the expression of specific genes and detection of changes in signaling pathways in cells of the studied organisms. Since the preservation of the organisms’ macromolecules (DNA, RNA and proteins) is a prerequisite for the implementation of molecular methods, the aim of this study was to assess the quality of macromolecule preservation within archival samples of aquatic macroinvertebrates collected in urban streams during last 28 years. Results indicated that the optimal way for archive storage is 3.6% formaldehyde solution if they have a purpose of morphological assessment or protein analyses, and in absolute ethanol for nucleic acids evaluation. Furthermore, it is of great importance that samples are treated with fixative in situ and processed in a laboratory as soon as possible.



中文翻译:

评估用于基因组,转录组和蛋白质组学评估的城市河流大型无脊椎动物档案的质量

大型无脊椎动物档案馆藏的存在开辟了将这些生物用作生物指标和模型生物以发展水生生态系统健康和压力指标的可能性,这为可持续的环境监测和水资源管理提供了有力的基础。随着时间的推移,城市化对城市河流生物区系影响的环境评估可以包括从档案样本中分离出的水生昆虫的分子(蛋白质组学,转录组学和基因组学)分析。这些分析可能包括通过条形码确认检测到的物种,确定特定基因表达的变化以及检测被研究生物细胞中信号通路的变化。由于生物体的大分子(DNA,RNA和蛋白质)是实施分子方法的先决条件,这项研究的目的是评估过去28年在城市河流中收集的水生无脊椎动物档案中大分子保存的质量。结果表明,如果要进行形态学评估或蛋白质分析,并且在无水乙醇中进行核酸评估,则归档存储的最佳方法是使用3.6%甲醛溶液。此外,用固定剂处理样品也很重要 6%甲醛溶液(如果要进行形态评估或蛋白质分析),并在无水乙醇中进行核酸评估。此外,用固定剂处理样品也很重要 6%甲醛溶液(如果要进行形态评估或蛋白质分析),并在无水乙醇中进行核酸评估。此外,用固定剂处理样品也很重要原位并尽快在实验室中处理。

更新日期:2021-02-19
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