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Summary Nuclear speckles are membraneless organelles implicated in multiple RNA processing steps. In this work, we systematically characterize the sequence logic determining RNA localization to nuclear speckles. We find extensive similarities between the speckle localization code and the RNA splicing code, even for transcripts that do not undergo splicing. Specifically, speckle localization is enhanced by the presence of unspliced exon-like or intron-like sequence features. We demonstrate that interactions required for early splicesomal complex assembly contribute to speckle localization. We also show that speckle localization of isolated endogenous exons is reduced by disease-associated single nucleotide variants. Finally, we find that speckle localization strongly correlates with splicing kinetics of splicing-competent constructs and is tightly linked to the decision between exon inclusion and skipping. Together, these results suggest a model in which RNA speckle localization is associated with the formation of the early spliceosomal complex and enhances the efficiency of splicing reactions. HighlightsSequences containing hallmarks of pre-mRNA dictate speckle localizationRNA speckle localization is coupled to early spliceosome assemblyDisease-associated single nucleotide variants reduce localization of isolated exonsRNA speckle localization strongly correlates with splicing kineticsGraphical Abstract 

RNA molecules often play critical roles in assisting the formation of membraneless organelles in eukaryotic cells. Yet, little is known about the organization of RNAs within membraneless organelles. Here, using super-resolution imaging and nuclear speckles as a model system, we demonstrate that different sequence domains of RNA transcripts exhibit differential spatial distributions within speckles. Specifically, we image transcripts containing a region enriched in binding motifs of serine/arginine-rich (SR) proteins and another region enriched in binding motifs of heterogeneous nuclear ribonucleoproteins (hnRNPs). We show that these transcripts localize to the outer shell of speckles, with the SR motif-rich region localizing closer to the speckle center relative to the hnRNP motif-rich region. Further, we identify that this intra-speckle RNA organization is driven by the strength of RNA-protein interactions inside and outside speckles. Our results hint at novel functional roles of nuclear speckles and likely other membraneless organelles in organizing RNA substrates for biochemical reactions. 

Coastal environments around the globe are subject to anthropogenic stresses due to dense coastal populations. The response of development activities on dynamic estuarine ecosystems, influenced by tidal forces, freshwater flows, salinity variations, and intricate coastal land morphology, is often uncertain. This case study evaluates how connectivity and coastal geomorphology influence flow patterns by modeling the effects of a proposed hydraulic reconnection project on water movement between the Manchester Waterway, a coastal residential community, and Charlotte Harbor, a large open water estuary in the Gulf of Mexico. An unstructured grid, 2D model was developed utilizing Delft3D Flexible Mesh to simulate estuary hydrodynamics under proposed conditions for four different weather conditions, including recorded 2021–2022 weather, future sea level rise, an extreme weather event, and a combination of extreme weather and sea level rise. Simulated flow results for proposed conditions were compared to present day flow patterns for analysis of the predicted changes in water levels and velocity magnitudes in the waterway. The results show that increased connectivity between the Manchester Waterway and Charlotte Harbor is expected to increase tidal amplitudes largely due to a lowering of minimum water levels in the waterway. During storm events, water elevations are predicted to drop to lower elevations following peak storm surge due to proposed conditions, which may provide flooding relief. Model simulation results will aid hydraulic reconnection and guide a more comprehensive ecological restoration plan. This case study will also improve understanding of the major influencing forces in intricate estuarine environments and how ecosystems may respond to land development, sea level rise, and increasing magnitude and frequency of tropical storms. 

Large river systems, particularly those shared by developing nations in the tropics, exemplify the interconnected and thorny challenges of achieving sustainability with respect to food, energy, and water ( 1 ). Numerous countries in South America, Africa, and Asia have committed to hydropower as a means to supply affordable energy with net-zero emissions by 2050 ( 2 ). The placement, size, and number of dams within each river basin network have enormous consequences for not only the ability to produce electricity ( 3 ) but also how they affect people whose livelihoods depend on the local river systems ( 4 ). On page 753 of this issue, Flecker et al. ( 5 ) present a way to assess a rich set of environmental parameters for an optimization analysis to efficiently sort through an enormous number of possible combinations for dam placements and help find the combination(s) that can achieve energy production targets while minimizing environmental costs in the Amazon basin. 

Carbon dioxide (CO 2 ) supersaturation in lakes and rivers worldwide is commonly attributed to terrestrial–aquatic transfers of organic and inorganic carbon (C) and subsequent, in situ aerobic respiration. Methane (CH 4 ) production and oxidation also contribute CO 2 to freshwaters, yet this remains largely unquantified. Flood pulse lakes and rivers in the tropics are hypothesized to receive large inputs of dissolved CO 2 and CH 4 from floodplains characterized by hypoxia and reducing conditions. We measured stable C isotopes of CO 2 and CH 4 , aerobic respiration, and CH 4 production and oxidation during two flood stages in Tonle Sap Lake (Cambodia) to determine whether dissolved CO 2 in this tropical flood pulse ecosystem has a methanogenic origin. Mean CO 2 supersaturation of 11,000 ± 9,000 μ atm could not be explained by aerobic respiration alone. 13 C depletion of dissolved CO 2 relative to other sources of organic and inorganic C, together with corresponding 13 C enrichment of CH 4 , suggested extensive CH 4 oxidation. A stable isotope-mixing model shows that the oxidation of 13 C depleted CH 4 to CO 2 contributes between 47 and 67% of dissolved CO 2 in Tonle Sap Lake. 13 C depletion of dissolved CO 2 was correlated to independently measured rates of CH 4 production and oxidation within the water column and underlying lake sediments. However, mass balance indicates that most of this CH 4 production and oxidation occurs elsewhere, within inundated soils and other floodplain habitats. Seasonal inundation of floodplains is a common feature of tropical freshwaters, where high reported CO 2 supersaturation and atmospheric emissions may be explained in part by coupled CH 4 production and oxidation.