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1. Coupling of microRNA-directed phased small interfering RNA generation from long noncoding genes with alternative splicing and alternative polyadenylation in small RNA-mediated gene silencing

   https://doi.org/10.1111/nph.14934  

   Ma, Wuqiang ; Chen, Chengjie ; Liu, Yuanlong ; Zeng, Ming ; Meyers, Blake C. ; Li, Jianguo ; Xia, Rui ( March 2018 , New Phytologist)
2. Coordination of alternative splicing and alternative polyadenylation revealed by targeted long read sequencing

   https://doi.org/10.1038/s41467-023-41207-8  

   Zhang, Zhiping ; Bae, Bongmin ; Cuddleston, Winston H. ; Miura, Pedro ( September 2023 , Nature Communications)

   Nervous system development is associated with extensive regulation of alternative splicing (AS) and alternative polyadenylation (APA). AS and APA have been extensively studied in isolation, but little is known about how these processes are coordinated. Here, the coordination of cassette exon (CE) splicing and APA inDrosophilawas investigated using a targeted long-read sequencing approach we call Pull-a-Long-Seq (PL-Seq). This cost-effective method uses cDNA pulldown and Nanopore sequencing combined with an analysis pipeline to quantify inclusion of alternative exons in connection with alternative 3’ ends. Using PL-Seq, we identified genes that exhibit significant differences in CE splicing depending on connectivity to short versus long 3’UTRs. Genomic long 3’UTR deletion was found to alter upstream CE splicing in short 3’UTR isoforms and ELAV loss differentially affected CE splicing depending on connectivity to alternative 3’UTRs. This work highlights the importance of considering connectivity to alternative 3’UTRs when monitoring AS events.

    

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3. Invasive plant feedbacks promote alternative states in California vernal pools: Feedbacks promote vernal pool alternative states

   https://doi.org/10.1111/rec.12571  

   Faist, Akasha M. ; Beals, Stower C. ( March 2018 , Restoration Ecology)
4. Historical land use as a driver of alternative states for stream form and function in forested mountain watersheds of the Southern Rocky Mountains: Alternative states of forested Southern Rocky Mountain streams

   https://doi.org/10.1002/esp.4275  

   Livers, Bridget ; Wohl, Ellen ; Jackson, Karen J. ; Sutfin, Nicholas A. ( March 2018 , Earth Surface Processes and Landforms)
5. Continental Scale Hydrostratigraphy: Basin‐Scale Testing of Alternative Data‐Driven Approaches

   https://doi.org/10.1111/gwat.13357  

   Tijerina‐Kreuzer, Danielle ; Swilley, Jackson S. ; Tran, Hoang V. ; Zhang, Jun ; West, Benjamin ; Yang, Chen ; Condon, Laura E. ; Maxwell, Reed M. ( October 2023 , Groundwater)

   Integrated hydrological modeling is an effective method for understanding interactions between parts of the hydrologic cycle, quantifying water resources, and furthering knowledge of hydrologic processes. However, these models are dependent on robust and accurate datasets that physically represent spatial characteristics as model inputs. This study evaluates multiple data‐driven approaches for estimating hydraulic conductivity and subsurface properties at the continental‐scale, constructed from existing subsurface dataset components. Each subsurface configuration represents upper (unconfined) hydrogeology, lower (confined) hydrogeology, and the presence of a vertical flow barrier. Configurations are tested in two large‐scale U.S. watersheds using an integrated model. Model results are compared to observed streamflow and steady state water table depth (WTD). We provide model results for a range of configurations and show that both WTD and surface water partitioning are important indicators of performance. We also show that geology data source, total subsurface depth, anisotropy, and inclusion of a vertical flow barrier are the most important considerations for subsurface configurations. While a range of configurations proved viable, we provide a recommended Selected National Configuration 1 km resolution subsurface dataset for use in distributed large‐and continental‐scale hydrologic modeling.

    

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