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  1. Weather sensing and forecasting has become increasingly accurate in the last decade thanks to high-resolution radars, efficient computational algorithms, and high-performance computing facilities. Through a distributed and federated network of radars, scientists can make high-resolution observations of the weather conditions on a scale that benefits public safety, commerce, transportation, and other fields. While weather radars are critical infrastructure, they are often located in remote areas with poor network connectivity. Data retrieved from these radars are often delayed or lost, or even lack proper synchronization, resulting in sub-optimal weather prediction. This work applies Named Data Networking (NDN) to a federation of weather sensing radars for efficient content addressing and retrieval. We identify weather data based on a hierarchical naming scheme that allows us to explicitly access desired files. We demonstrate that compared to the window-based mechanism in TCP/IP, an NDN based mechanism improves data quality, reduces uncertainty, and enhances weather prediction.
    Free, publicly-accessible full text available September 12, 2023
  2. Long non-coding RNAs (lncRNAs) are an increasingly studied group of non-protein coding transcripts with a wide variety of molecular functions gaining attention for their roles in numerous biological processes. Nearly 6,000 lncRNAs have been identified in Arabidopsis thaliana but many have yet to be studied. Here, we examine a class of previously uncharacterized lncRNAs termed CONSERVED IN BRASSICA RAPA ( lncCOBRA ) transcripts that were previously identified for their high level of sequence conservation in the related crop species Brassica rapa , their nuclear-localization and protein-bound nature. In particular, we focus on lncCOBRA1 and demonstrate that its abundance is highly tissue and developmental specific, with particularly high levels early in germination. lncCOBRA1 contains two snoRNAs domains within it, making it the first sno-lincRNA example in a non-mammalian system. However, we find that it is processed differently than its mammalian counterparts. We further show that plants lacking lncCOBRA1 display patterns of delayed germination and are overall smaller than wild-type plants. Lastly, we identify the proteins that interact with lncCOBRA1 and propose a novel mechanism of lincRNA action in which it may act as a scaffold with the RACK1A protein to regulate germination and development, possibly through a role in ribosome biogenesis.
    Free, publicly-accessible full text available May 25, 2023
  3. Morrell, P (Ed.)
    Abstract By modeling the homoeologous gene losses that occurred in 50 genomes deriving from ten distinct polyploidy events, we show that the evolutionary forces acting on polyploids are remarkably similar, regardless of whether they occur in flowering plants, ciliates, fishes, or yeasts. We show that many of the events show a relative rate of duplicate gene loss before the first postpolyploidy speciation that is significantly higher than in later phases of their evolution. The relatively weak selective constraint experienced by the single-copy genes these losses produced leads us to suggest that most of the purely selectively neutral duplicate gene losses occur in the immediate postpolyploid period. Nearly all of the events show strong evidence of biases in the duplicate losses, consistent with them being allopolyploidies, with 2 distinct progenitors contributing to the modern species. We also find ongoing and extensive reciprocal gene losses (alternative losses of duplicated ancestral genes) between these genomes. With the exception of a handful of closely related taxa, all of these polyploid organisms are separated from each other by tens to thousands of reciprocal gene losses. As a result, it is very unlikely that viable diploid hybrid species could form between these taxa, since matings betweenmore »such hybrids would tend to produce offspring lacking essential genes. It is, therefore, possible that the relatively high frequency of recurrent polyploidies in some lineages may be due to the ability of new polyploidies to bypass reciprocal gene loss barriers.« less
    Free, publicly-accessible full text available April 22, 2023
  4. In this paper, we describe how we extended the Pegasus Workflow Management System to support edge-to-cloud workflows in an automated fashion. We discuss how Pegasus and HTCondor (its job scheduler) work together to enable this automation. We use HTCondor to form heterogeneous pools of compute resources and Pegasus to plan the workflow onto these resources and manage containers and data movement for executing workflows in hybrid edge-cloud environments. We then show how Pegasus can be used to evaluate the execution of workflows running on edge only, cloud only, and edge-cloud hybrid environments. Using the Chameleon Cloud testbed to set up and configure an edge-cloud environment, we use Pegasus to benchmark the executions of one synthetic workflow and two production workflows: CASA-Wind and the Ocean Observatories Initiative Orcasound workflow, all of which derive their data from edge devices. We present the performance impact on workflow runs of job and data placement strategies employed by Pegasus when configured to run in the above three execution environments. Results show that the synthetic workflow performs best in an edge only environment, while the CASA - Wind and Orcasound workflows see significant improvements in overall makespan when run in a cloud only environment. The resultsmore »demonstrate that Pegasus can be used to automate edge-to-cloud science workflows and the workflow provenance data collection capabilities of the Pegasus monitoring daemon enable computer scientists to conduct edge-to-cloud research.« less
    Free, publicly-accessible full text available May 1, 2023
  5. Desiccation tolerance is an ancient and complex trait that spans all major lineages of life on earth. Although important in the evolution of land plants, the mechanisms that underlay this complex trait are poorly understood, especially for vegetative desiccation tolerance (VDT). The lack of suitable closely related plant models that offer a direct contrast between desiccation tolerance and sensitivity has hampered progress. We have assembled high-quality genomes for two closely related grasses, the desiccation-tolerant Sporobolus stapfianus and the desiccation-sensitive Sporobolus pyramidalis . Both species are complex polyploids; S. stapfianus is primarily tetraploid, and S. pyramidalis is primarily hexaploid. S. pyramidalis undergoes a major transcriptome remodeling event during initial exposure to dehydration, while S. stapfianus has a muted early response, with peak remodeling during the transition between 1.5 and 1.0 grams of water (gH 2 O) g −1 dry weight (dw). Functionally, the dehydration transcriptome of S. stapfianus is unrelated to that for S. pyramidalis . A comparative analysis of the transcriptomes of the hydrated controls for each species indicated that S. stapfianus is transcriptionally primed for desiccation. Cross-species comparative analyses indicated that VDT likely evolved from reprogramming of desiccation tolerance mechanisms that evolved in seeds and that the tolerance mechanismmore »of S. stapfianus represents a recent evolution for VDT within the Chloridoideae. Orthogroup analyses of the significantly differentially abundant transcripts reconfirmed our present understanding of the response to dehydration, including the lack of an induction of senescence in resurrection angiosperms. The data also suggest that failure to maintain protein structure during dehydration is likely critical in rendering a plant desiccation sensitive.« less
    Free, publicly-accessible full text available February 1, 2023
  6. RNA silencing pathways control eukaryotic gene expression transcriptionally or posttranscriptionally in a sequence-specific manner. In RNA silencing, the production of double-stranded RNA (dsRNA) gives rise to various classes of 20–24 nucleotide (nt) small RNAs (smRNAs). In Arabidopsis thaliana, smRNAs are often derived from long dsRNA molecules synthesized by one of the six genomically encoded RNA-dependent RNA Polymerase (RDR) proteins. However, the full complement of the RDR-dependent smRNAs and functions that these proteins and their RNA-binding cofactors play in plant RNA silencing has not been fully uncovered. To address this gap, we performed a global genomic analysis of all six RDRs and two of their cofactors to find new substrates for RDRs and targets of the resulting RDR-derived siRNAs to uncover new functions for these proteins in plants. Based on these analyses, we identified substrates for the three RDRγ clade proteins (RDR3–5), which had not been well-characterized previously. We also identified new substrates for the other three RDRs (RDR1, RDR2, and RDR6) as well as the RDR2 cofactor RNA-directed DNA methylation 12 (RDM12) and the RDR6 cofactor suppressor of gene silencing 3 (SGS3). These findings revealed that the target substrates of SGS3 are not limited to those solely utilized by RDR6,more »but that this protein seems to be a more general cofactor for the RDR family of proteins. Additionally, we found that RDR6 and SGS3 are involved in the production of smRNAs that target transcripts related to abiotic stresses, including water deprivation, salt stress, and ABA response, and as expected the levels of these mRNAs are increased in rdr6 and sgs3 mutant plants. Correspondingly, plants that lack these proteins (rdr6 and sgs3 mutants) are hypersensitive to ABA treatment, tolerant to high levels of PEG8000, and have a higher survival rate under salt treatment in comparison to wild-type plants. In total, our analyses have provided an extremely data-rich resource for uncovering new functions of RDR-dependent RNA silencing in plants, while also revealing a previously unexplored link between the RDR6/SGS3-dependent pathway and plant abiotic stress responses.« less