Managing for Heterogeneity and Complexity on Dynamic Landscapes

AbstracttRNAs and tRNA-derived RNA fragments (tRFs) play various roles in many cellular processes outside of protein synthesis. However, comprehensive investigations of tRNA/tRF regulation are rare. In this study, we used new algorithms to extensively analyze the publicly available data from 1332 ChIP-Seq and 42 small-RNA-Seq experiments in human cell lines and tissues to investigate the transcriptional and posttranscriptional regulatory mechanisms of tRNAs. We found that histone acetylation, cAMP, and pluripotency pathways play important roles in the regulation of the tRNA gene transcription in a cell-specific manner. Analysis of RNA-Seq data identified 950 high-confidence tRFs, and the results suggested that tRNA pools are dramatically distinct across the samples in terms of expression profiles and tRF composition. The mismatch analysis identified new potential modification sites and specific modification patterns in tRNA families. The results also show that RNA library preparation technologies have a considerable impact on tRNA profiling and need to be optimized in the future.

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Assessing the Impact of Urban Expansion on Surrounding Forested Landscape Connectivity across Space and Time

Land ◽

10.3390/land10040359 ◽

2021 ◽

Vol 10 (4) ◽

pp. 359

Author(s):

Zhouqiao Ren ◽

Jianhua He ◽

Qiaobing Yue

Keyword(s):

Landscape Connectivity ◽

Urban Expansion ◽

Landscape Fragmentation ◽

Sustainable Urban Development ◽

Delayed Response ◽

Conservation Practices ◽

Rapid Urbanization ◽

Dynamic Landscapes ◽

The Impact ◽

Over Time

Landscape connectivity is important for all organisms as it directly affects population dynamics. Yet, rapid urbanization has caused serious landscape fragmentation, which is the primary contributor of species extinctions worldwide. Previous studies have mostly used spatial snap-shots to evaluate the impact of urban expansion on landscape connectivity. However, the interactions among habitats over time in dynamic landscapes have been largely ignored. Here, we demonstrated that overlooking temporal connectivity can lead to the overestimation of the impact of urban expansion. How much greater the overestimation is depends on the amount of net habitat loss. Moreover, we showed that landscape connectivity may have a delayed response to urban expansion. Our analysis shifts the way to understand the ecological consequences of urban expansion. Our framework can guide sustainable urban development and can be inspiring to conservation practices under other contexts (e.g., climate change).

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