Reliable and accurate diagnostics from highly multiplexed sequencing assays

Scalable, inexpensive, and secure testing for SARS-CoV-2 infection is crucial for control of the novel coronavirus pandemic. Recently developed highly multiplexed sequencing assays (HMSAs) that rely on high-throughput sequencing can, in principle, meet these demands, and present promising alternatives to currently used RT-qPCR-based tests. However, reliable analysis, interpretation, and clinical use of HMSAs requires overcoming several computational, statistical and engineering challenges. Using recently acquired experimental data, we present and validate a computational workflow based on kallisto and bustools, that utilizes robust statistical methods and fast, memory efficient algorithms, to quickly, accurately and reliably process high-throughput sequencing data. We show that our workflow is effective at processing data from all recently proposed SARS-CoV-2 sequencing based diagnostic tests, and is generally applicable to any diagnostic HMSA

Lunar radiation environment and space weathering from the Cosmic Ray Telescope for the Effects of Radiation (CRaTER)

[1] The Cosmic Ray Telescope for the Effects of Radiation (CRaTER) measures linear energy transfer by Galactic Cosmic Rays (GCRs) and Solar Energetic Particles (SEPs) on the Lunar Reconnaissance Orbiter (LRO) Mission in a circular, polar lunar orbit. GCR fluxes remain at the highest levels ever observed during the space age. One of the largest SEP events observed by CRaTER during the LRO mission occurred on June 7, 2011. We compare model predictions by the Earth-Moon-Mars Radiation Environment Module (EMMREM) for both dose rates from GCRs and SEPs during this event with results from CRaTER. We find agreement between these models and the CRaTER dose rates, which together demonstrate the accuracy of EMMREM, and its suitability for a real-time space weather system. We utilize CRaTER to test forecasts made by the Relativistic Electron Alert System for Exploration (REleASE), which successfully predicts the June 7th event. At the maximum CRaTER-observed GCR dose rate (∼11.7 cGy/yr where Gy is a unit indicating energy deposition per unit mass, 1 Gy = 1 J/kg), GCRs deposit ∼88 eV/molecule in water over 4 billion years, causing significant change in molecular composition and physical structure (e.g., density, color, crystallinity) of water ice, loss of molecular hydrogen, and production of more complex molecules linking carbon and other elements in the irradiated ice. This shows that space weathering by GCRs may be extremely important for chemical evolution of ice on the Moon. Thus, we show comprehensive observations from the CRaTER instrument on the Lunar Reconnaissance Orbiter that characterizes the radiation environment and space weathering on the Moon

Spatially structured brown-headed cowbird control measures and their effects on Kirtland’s warbler long-term population sustainability

Context: Brown-headed cowbirds (Molothrus ater), through brood parasitism, can exert extrinsic population growth pressures on North American songbirds. Cowbird removal programs may reduce parasitism rates on host species but can be expensive and difficult to implement throughout a host species’ breeding range. Aim: We estimated cowbird abundance and nest parasitism rates within Kirtland’s warbler (Setophaga kirtlandii) primary breeding range in Michigan, USA, and determined the maximum sustainable parasitism rate for Kirtland’s warblers under several spatially structured cowbird removal designs. Methods: We conducted point counts to estimate cowbird abundance and monitored nests to quantify nest parasitism rates during 2019–2021. We used the modelling software STELLA to determine the maximum sustainable parasitism rate for Kirtland’s warblers under different spatially structured cowbird removal scenarios (complete, core-only, and no removal). Key results: Cowbird abundance and parasitism rates remained low following cowbird trap closures in 2018. In the simulation study, complete removal was the most robust scenario with no replications having \u3c1000 Kirtland’s warbler males. The core-only removal scenario had a substantially higher sustainable parasitism rate in the peripheral breeding area than the no removal scenario. Assumed hatch-year dispersal distance had the greatest impact on the maximum sustainable parasitism rate in the core-only scenario. Conclusions: Low cowbird abundance and nest parasitism following suspension of cowbird removal efforts showed resuming the removal program may not be required in the short-term. If cowbird abundance increases, however, adaptive cowbird removal programs can be used to sustain Kirtland’s warbler populations long-term. Implications: Our results indicate that incorporating spatial structure of host species’ habitat into designing cowbird removal programs may minimise costs of cowbird management while sustaining populations of Kirtland’s warbler and possibly other host species that are affected by brood parasitism

Weather and Climate Change Drive Annual Variation of Reproduction by an Aerial Insectivore

For many bird species, but especially aerial insectivores, reproduction depends on weather. Climate change is likely to intensify effects, but with uncertain consequences. We report 22 years of data on Eastern Kingbird (Tyrannus tyrannus) reproduction for two populations located in different hygric environments undergoing climate change; mesic central New York, USA, (NY; 12 years) and xeric southeastern Oregon, USA, (OR: 10 years). Laying date became earlier with increasing temperature in the 30-day period preceding laying in identical fashion at both sites, and in years of early laying, clutch size was larger, length of laying season increased, and failed initial nesting attempts were more often replaced. High temperature in the 10-days preceding mean laying date was associated with shorter laying seasons, while a site by 10-day temperature interaction reflected an increase and decrease of clutch size with increasing 10-day temperature in NY and OR, respectively. Seasonal rate of clutch size decline was higher when the laying season was short but also slowed in xeric OR when rain was abundant in the 10-days prior to mean laying date. Nest predation drove annual variation in young fledged/nest, but the latter also increased and decreased with increasing maximum temperature during the nestling phase in mesic NY and xeric OR, respectively. Potential effects of climate change on kingbird populations are thus high given the dependence of reproduction on weather, and climate change likely contributed to declines of kingbirds in OR. Declines of kingbirds in NY appear unrelated to warming climates because higher temperatures advanced laying dates and yielded greater nest productivity. However, length of laying season declined across years at both sites, and thus early season gains may be negated by poor conditions late in the season that may be causing shorter laying seasons. Further work is needed to identify causes for the latter changes

Reliable and accurate diagnostics from highly multiplexed sequencing assays

Scalable, inexpensive, and secure testing for SARS-CoV-2 infection is crucial for control of the novel coronavirus pandemic. Recently developed highly multiplexed sequencing assays (HMSAs) that rely on high-throughput sequencing can, in principle, meet these demands, and present promising alternatives to currently used RT-qPCR-based tests. However, reliable analysis, interpretation, and clinical use of HMSAs requires overcoming several computational, statistical and engineering challenges. Using recently acquired experimental data, we present and validate a computational workflow based on kallisto and bustools, that utilizes robust statistical methods and fast, memory efficient algorithms, to quickly, accurately and reliably process high-throughput sequencing data. We show that our workflow is effective at processing data from all recently proposed SARS-CoV-2 sequencing based diagnostic tests, and is generally applicable to any diagnostic HMSA

The Planteome database:an integrated resource for reference ontologies, plant genomics and phenomics

The Planteome project (http://www.planteome.org) provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. The Planteome project is developing a plant gene annotation platform; Planteome Noctua, to facilitate community engagement. All the Planteome ontologies are publicly available and are maintained at the Planteome GitHub site (https://github.com/Planteome) for sharing, tracking revisions and new requests. The annotated data are freely accessible from the ontology browser (http://browser.planteome.org/amigo) and our data repository

Leading Disability Research and Workforce Development: A Western Sydney Collaboration

In this White Paper we draw attention to the potential of excellence in research and workforce development as a means, in part, to foster greater inclusion and participation for people with disability. We present a critique of the current limitations in research and workforce development and highlight the urgency to address such shortcomings to realise inclusion within our communities. We demonstrate that Western Sydney University is well positioned as a leading institution to address many of these concerns. This White paper showcases the innovative work of our team, and calls for seven key actions, to advance inclusion and participation for people and communities in Greater Western Sydney, Australia, and beyond