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1. From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

   https://doi.org/10.1126/science.abk3112  

   Hoyt, Savannah J. ; Storer, Jessica M. ; Hartley, Gabrielle A. ; Grady, Patrick G. ; Gershman, Ariel ; de Lima, Leonardo G. ; Limouse, Charles ; Halabian, Reza ; Wojenski, Luke ; Rodriguez, Matias ; et al ( April 2022 , Science)

   INTRODUCTION Transposable elements (TEs), repeat expansions, and repeat-mediated structural rearrangements play key roles in chromosome structure and species evolution, contribute to human genetic variation, and substantially influence human health through copy number variants, structural variants, insertions, deletions, and alterations to gene transcription and splicing. Despite their formative role in genome stability, repetitive regions have been relegated to gaps and collapsed regions in human genome reference GRCh38 owing to the technological limitations during its development. The lack of linear sequence in these regions, particularly in centromeres, resulted in the inability to fully explore the repeat content of the human genome in the context of both local and regional chromosomal environments. RATIONALE Long-read sequencing supported the complete, telomere-to-telomere (T2T) assembly of the pseudo-haploid human cell line CHM13. This resource affords a genome-scale assessment of all human repetitive sequences, including TEs and previously unknown repeats and satellites, both within and outside of gaps and collapsed regions. Additionally, a complete genome enables the opportunity to explore the epigenetic and transcriptional profiles of these elements that are fundamental to our understanding of chromosome structure, function, and evolution. Comparative analyses reveal modes of repeat divergence, evolution, and expansion or contraction with locus-level resolution. RESULTS We implementedmore »a comprehensive repeat annotation workflow using previously known human repeats and de novo repeat modeling followed by manual curation, including assessing overlaps with gene annotations, segmental duplications, tandem repeats, and annotated repeats. Using this method, we developed an updated catalog of human repetitive sequences and refined previous repeat annotations. We discovered 43 previously unknown repeats and repeat variants and characterized 19 complex, composite repetitive structures, which often carry genes, across T2T-CHM13. Using precision nuclear run-on sequencing (PRO-seq) and CpG methylated sites generated from Oxford Nanopore Technologies long-read sequencing data, we assessed RNA polymerase engagement across retroelements genome-wide, revealing correlations between nascent transcription, sequence divergence, CpG density, and methylation. These analyses were extended to evaluate RNA polymerase occupancy for all repeats, including high-density satellite repeats that reside in previously inaccessible centromeric regions of all human chromosomes. Moreover, using both mapping-dependent and mapping-independent approaches across early developmental stages and a complete cell cycle time series, we found that engaged RNA polymerase across satellites is low; in contrast, TE transcription is abundant and serves as a boundary for changes in CpG methylation and centromere substructure. Together, these data reveal the dynamic relationship between transcriptionally active retroelement subclasses and DNA methylation, as well as potential mechanisms for the derivation and evolution of new repeat families and composite elements. Focusing on the emerging T2T-level assembly of the HG002 X chromosome, we reveal that a high level of repeat variation likely exists across the human population, including composite element copy numbers that affect gene copy number. Additionally, we highlight the impact of repeats on the structural diversity of the genome, revealing repeat expansions with extreme copy number differences between humans and primates while also providing high-confidence annotations of retroelement transduction events. CONCLUSION The comprehensive repeat annotations and updated repeat models described herein serve as a resource for expanding the compendium of human genome sequences and reveal the impact of specific repeats on the human genome. In developing this resource, we provide a methodological framework for assessing repeat variation within and between human genomes. The exhaustive assessment of the transcriptional landscape of repeats, at both the genome scale and locally, such as within centromeres, sets the stage for functional studies to disentangle the role transcription plays in the mechanisms essential for genome stability and chromosome segregation. Finally, our work demonstrates the need to increase efforts toward achieving T2T-level assemblies for nonhuman primates and other species to fully understand the complexity and impact of repeat-derived genomic innovations that define primate lineages, including humans. Telomere-to-telomere assembly of CHM13 supports repeat annotations and discoveries. The human reference T2T-CHM13 filled gaps and corrected collapsed regions (triangles) in GRCh38. Combining long read–based methylation calls, PRO-seq, and multilevel computational methods, we provide a compendium of human repeats, define retroelement expression and methylation profiles, and delineate locus-specific sites of nascent transcription genome-wide, including previously inaccessible centromeres. SINE, short interspersed element; SVA, SINE–variable number tandem repeat– Alu ; LINE, long interspersed element; LTR, long terminal repeat; TSS, transcription start site; pA, xxxxxxxxxxxxxxxx.« less
2. Active Safety Envelopes using Light Curtains with Probabilistic Guarantees

   https://doi.org/10.15607/RSS.2021.XVII.045  

   Ancha, Siddharth ; Pathak, Gaurav ; Narasimhan, Srinivasa ; Held, David ( July 2021 , Robotics: Science and Systems)

   To safely navigate unknown environments; robots must accurately perceive dynamic obstacles. Instead of directly measuring the scene depth with a LiDAR sensor; we explore the use of a much cheaper and higher resolution sensor: programmable light curtains. Light curtains are controllable depth sensors that sense only along a surface that a user selects. We use light curtains to estimate the safety envelope of a scene: a hypothetical surface that separates the robot from all obstacles. We show that generating light curtains that sense random locations (from a particular distribution) can quickly discover the safety envelope for scenes with unknown objects. Importantly; we produce theoretical safety guarantees on the probability of detecting an obstacle using random curtains. We combine random curtains with a machine learning based model that forecasts and tracks the motion of the safety envelope efficiently. Our method accurately estimates safety envelopes while providing probabilistic safety guarantees that can be used to certify the efficacy of a robot perception system to detect and avoid dynamic obstacles. We evaluate our approach in a simulated urban driving environment and a real-world environment with moving pedestrians using a light curtain device and show that we can estimate safety envelopes efficiently and effectively.
3. Retrieval of Salt Marsh Above-Ground Biomass from High-Spatial Resolution Hyperspectral Imagery Using PROSAIL

   https://doi.org/10.3390/rs11111385  

   Eon, Rehman S. ; Goldsmith, Sarah ; Bachmann, Charles M. ; Tyler, Anna Christina ; Lapszynski, Christopher S. ; Badura, Gregory P. ; Osgood, David T. ; Brett, Ryan ( June 2019 , Remote Sensing)

   Salt marsh vegetation density varies considerably on short spatial scales, complicating attempts to evaluate plant characteristics using airborne remote sensing approaches. In this study, we used a mast-mounted hyperspectral imaging system to obtain cm-scale imagery of a salt marsh chronosequence on Hog Island, VA, where the morphology and biomass of the dominant plant species, Spartina alterniflora, varies widely. The high-resolution hyperspectral imagery allowed the detailed delineation of variations in above-ground biomass, which we retrieved from the imagery using the PROSAIL radiative transfer model. The retrieved biomass estimates correlated well with contemporaneously collected in situ biomass ground truth data ( R 2 = 0.73 ). In this study, we also rescaled our hyperspectral imagery and retrieved PROSAIL salt marsh biomass to determine the applicability of the method across spatial scales. Histograms of retrieved biomass changed considerably in characteristic marsh regions as the spatial scale of the imagery was progressively degraded. This rescaling revealed a loss of spatial detail and a shift in the mean retrieved biomass. This shift is indicative of the loss of accuracy that may occur when scaling up through a simple averaging approach that does not account for the detail found in the landscape at the natural scalemore »of variation of the salt marsh system. This illustrated the importance of developing methodologies to appropriately scale results from very fine scale resolution up to the more coarse-scale resolutions commonly obtained in airborne and satellite remote sensing.« less
4. Estimations of Fine-Scale Species Distributions of Aedes aegypti and Aedes albopictus (Diptera: Culicidae) in Eastern Florida

   https://doi.org/10.1093/jme/tjaa216  

   Hopperstad, Kristen A ; Sallam, Mohamed F ; Reiskind, Michael H ( October 2020 , Journal of Medical Entomology)

   Hamer, Gabriel (Ed.)

   Abstract Many species distribution maps indicate the ranges of Aedes aegypti (Linnaeus) and Aedes albopictus (Skuse) overlap in Florida despite the well-documented range reduction of Ae. aegypti. Within the last 30 yr, competitive displacement of Ae. aegypti by Ae. albopictus has resulted in partial spatial segregation of the two species, with Ae. aegypti persisting primarily in urban refugia. We modeled fine-scale distributions of both species, with the goal of capturing the outcome of interspecific competition across space by building habitat suitability maps. We empirically parameterized models by sampling 59 sites in south and central Florida over time and incorporated climatic, landscape, and human population data to identify predictors of habitat suitability for both species. Our results show human density, precipitation, and urban land cover drive Ae. aegypti habitat suitability, compared with exclusively climatic variables driving Ae. albopictus habitat suitability. Remotely sensed variables (macrohabitat) were more predictive than locally collected metrics (microhabitat), although recorded minimum daily temperature showed significant, inverse relationships with both species. We detected minor Aedes habitat segregation; some periurban areas that were highly suitable for Ae. albopictus were unsuitable for Ae. aegypti. Fine-scale empirical models like those presented here have the potential for precise risk assessment and themore »improvement of operational applications to control container-breeding Aedes mosquitoes.« less
5. Measuring change at Earth’s surface: On-demand vertical and three-dimensional topographic differencing implemented in OpenTopography

   https://doi.org/10.1130/GES02259.1  

   Scott, Chelsea ; Phan, Minh ; Nandigam, Viswanath ; Crosby, Christopher ; Arrowsmith, J Ramon ( May 2021 , Geosphere)

   Abstract Topographic differencing measures landscape change by comparing multitemporal high-resolution topography data sets. Here, we focused on two types of topographic differencing: (1) Vertical differencing is the subtraction of digital elevation models (DEMs) that span an event of interest. (2) Three-dimensional (3-D) differencing measures surface change by registering point clouds with a rigid deformation. We recently released topographic differencing in OpenTopography where users perform on-demand vertical and 3-D differencing via an online interface. OpenTopography is a U.S. National Science Foundation–funded facility that provides access to topographic data and processing tools. While topographic differencing has been applied in numerous research studies, the lack of standardization, particularly of 3-D differencing, requires the customization of processing for individual data sets and hinders the community’s ability to efficiently perform differencing on the growing archive of topography data. Our paper focuses on streamlined techniques with which to efficiently difference data sets with varying spatial resolution and sensor type (i.e., optical vs. light detection and ranging [lidar]) and over variable landscapes. To optimize on-demand differencing, we considered algorithm choice and displacement resolution. The optimal resolution is controlled by point density, landscape characteristics (e.g., leaf-on vs. leaf-off), and data set quality. We provide processing options derived frommore »metadata that allow users to produce optimal high-quality results, while experienced users can fine tune the parameters to suit their needs. We anticipate that the differencing tool will expand access to this state-of-the-art technology, will be a valuable educational tool, and will serve as a template for differencing the growing number of multitemporal topography data sets.« less