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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Unveiling the Arsenal of Apple Bitter Rot Fungi: Comparative Genomics Identifies Candidate Effectors, CAZymes, and Biosynthetic Gene Clusters in Colletotrichum Species

The bitter rot of apple is caused by Colletotrichum spp. and is a serious pre-harvest disease that can manifest in postharvest losses on harvested fruit. In this study, we obtained genome sequences from four different species, C. chrysophilum, C. noveboracense, C. nupharicola, and C. fioriniae, that infect apple and cause diseases on other fruits, vegetables, and flowers. Our genomic data were obtained from isolates/species that have not yet been sequenced and represent geographic-specific regions. Genome sequencing allowed for the construction of phylogenetic trees, which corroborated the overall concordance observed in prior MLST studies. Bioinformatic pipelines were used to discover CAZyme, effector, and secondary metabolic (SM) gene clusters in all nine Colletotrichum isolates. We found redundancy and a high level of similarity across species regarding CAZyme classes and predicted cytoplastic and apoplastic effectors. SM gene clusters displayed the most diversity in type and the most common cluster was one that encodes genes involved in the production of alternapyrone. Our study provides a solid platform to identify targets for functional studies that underpin pathogenicity, virulence, and/or quiescence that can be targeted for the development of new control strategies. With these new genomics resources, exploration via omics-based technologies using these isolates will help ascertain the biological underpinnings of their widespread success and observed geographic dominance in specific areas throughout the country.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Genome-Wide Informative Microsatellite Markers and Population Structure of Fusarium virguliforme from Argentina and the USA

Soybean sudden death syndrome (SDS) is a destructive disease that causes substantial yield losses in South and North America. Whereas four Fusarium species were identified as the causal agents, F. virguliforme is the primary SDS-causing pathogen in North America and it also contributes substantially to SDS in Argentina. In this study, we comparatively analyzed genome assemblies of four F. virguliforme strains and identified 29 informative microsatellite markers. Sixteen of the 29 markers were used to investigate the genetic diversity and population structure of this pathogen in a collection of 90 strains from Argentina and the USA. A total of 37 multilocus genotypes (MLGs) were identified, including 10 MLGs in Argentina and 26 in the USA. Only MLG2, the most dominant MLG, was found in both countries. Analyses with three different approaches showed that these MLGs could be grouped into three clusters. Cluster IA consisting of four MLGs exclusively from the USA has much higher genetic diversity than the other two clusters, suggesting that it may be the ancestral cluster although additional data are necessary to support this hypothesis. Clusters IB and II consisted of 13 and 21 MLGs, respectively. MLGs belonging to these two clusters were present in all four sampled states in Argentina and all five sampled states in the USA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Phylogeny and Expression Atlas of the NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY in Agave

Agave species are widely cultivated crassulacean acid metabolism (CAM) plants for alcoholic beverages, food and fiber production. Among these, the Agave hybrid H11648 ((A. amaniensis × A. angustifolia) × A. amaniensis) is the main cultivar for sisal fiber in the tropical areas of Brazil, China, and African countries. The plants of Agave hybrid H11648 have a long life cycle and large leaves, which require a huge amount of nitrogen nutrient. However, the molecular basis of nitrogen transport and allocation has not been well understood in agave. In this study, we identified 19 NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY(NPF) genes (called AhNPFs) with full-length coding sequences in Agave hybrid H11648. Our analysis of gene expression in various types of tissues revealed the tissue-specific expression pattern of AhNPFs. We further examined their expression patterns at different leaf developmental stages, under abiotic/biotic stresses and nutrient deficiency. The results reveal several candidate regulators in the agave NPF family, including AhNPF4.3/5.2/7.1. We first characterized the NPF genes in agave based on published leaf transcriptome datasets and emphasized their potential functions. The study will benefit future studies related to nitrogen nutrient in agave.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Protoplast-Based Transient Expression and Gene Editing in Shrub Willow ( Salix purpurea L .)

Shrub willows (Salix section Vetrix) are grown as a bioenergy crop in multiple countries and as ornamentals across the northern hemisphere. To facilitate the breeding and genetic advancement of shrub willow, there is a strong interest in the characterization and functional validation of genes involved in plant growth and biomass production. While protocols for shoot regeneration in tissue culture and production of stably transformed lines have greatly advanced this research in the closely related genus Populus, a lack of efficient methods for regeneration and transformation has stymied similar advancements in willow functional genomics. Moreover, transient expression assays in willow have been limited to callus tissue and hairy root systems. Here we report an efficient method for protoplast isolation from S. purpurea leaf tissue, along with transient overexpression and CRISPR-Cas9 mediated mutations. This is the first such report of transient gene expression in Salix protoplasts as well as the first application of CRISPR technology in this genus. These new capabilities pave the way for future functional genomics studies in this important bioenergy and ornamental crop.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Portuguese Wood Pellets Market: Organization, Production and Consumption Analysis

Wood pellets are a form of energy that can be seen as an alternative to fossil fuels, thus contributing to the reduction of greenhouse gas emissions. In other words, wood pellets can be considered a solution contributing to the mitigation of climate change. The use of wood pellets has grown significantly in recent years, with different markets emerging, such as Portugal, both from production and consumption perspectives. The wood pellet industry in Portugal began its development about 15 years ago, with the companies installed in the country initially almost exclusively dedicated to the production of wood pellets for export to central and northern European markets. However, over the years, the domestic market, initially considered insignificant, began to develop; it recently reached a considerable consuming share of the national production. This study presents an analysis of the Portuguese wood pellet market using data collected on the sector, and specifically on producers and consumers. The information was gathered using surveys presented directly to consumers and producers and through interviews with other stakeholders in the sector. From the analysis of the information, it was possible to understand the market’s dynamics, its current evolution and its prospects for the upcoming years, since it can already be considered mature and consolidated.

Nunes, Leonel J. R. (ORCID:0000000154048163)↗
DOE OSTI2023

Using Atmospheric Inverse Modelling of Methane Budgets with Copernicus Land Water and Wetness Data to Detect Land Use-Related Emissions

Climate change mitigation requires countries to report their annual greenhouse gas (GHG) emissions and sinks, including those from land use, land use change, and forestry (LULUCF). In Finland, the LULUCF sector plays a crucial role in achieving net-zero GHG emissions, as the sector is expected to be a net sink. However, accurate estimates of LULUCF-related GHG emissions, such as methane (CH 4 ), remain challenging. We estimated LULUCF-related CH 4 emissions in Finland in 2013–2020 by combining national land cover and remote-sensed surface wetness data with CH 4 emissions estimated by an inversion model. According to our inversion model, most of Finland’s CH 4 emissions were attributed to natural sources such as open pristine peatlands. However, our research indicated that forests with thin tree cover surrounding open peatlands may also be a significant source of CH 4 . Unlike open pristine peatlands and pristine peatlands with thin tree cover, surrounding transient forests are included in the Finnish GHG inventory if they meet the criteria used for forest land. The current Finnish national GHG inventory may therefore underestimate CH 4 emissions from forested organic soils surrounding open peatlands, although more precise methods and data are needed to verify this. Given the potential impact on net GHG emissions, CH 4 emissions from transitional forests on organic soils should be further investigated. Furthermore, the results demonstrate the potential of combining atmospheric inversion modelling of GHGs with diverse data sources and highlight the need for methods to more easily combine atmospheric inversions with national GHG inventories.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Design, Build, and Initial Testing of a Portable Methane Measurement Platform

The quantification of methane concentrations in air is essential for the quantification of methane emissions, which in turn is necessary to determine absolute emissions and the efficacy of emission mitigation strategies. These are essential if countries are to meet climate goals. Large-scale deployment of methane analyzers across millions of emission sites is prohibitively expensive, and lower-cost instrumentation has been recently developed as an alternative. Currently, it is unclear how cheaper instrumentation will affect measurement resolution or accuracy. To test this, the Wireless Autonomous Transportable Methane Emission Reporting System (WATCH 4 ERS) has been developed, comprising four commercially available sensing technologies: metal oxide (MOx,), Non-dispersion Infrared (NDIR), integrated infrared (INIR), and tunable diode laser absorption spectrometer (TDLAS). WATCHERS is the accumulated knowledge of several long-term methane measurement projects at Colorado State University’s Methane Emission Technology Evaluation Center (METEC), and this study describes the integration of these sensors into a single unit and reports initial instrument response to calibration procedures and controlled release experiments. Specifically, this paper aims to describe the development of the WATCH 4 ERS unit, report initial sensor responses, and describe future research goals. Meanwhile, future work will use data gathered by multiple WATCH 4 ERS units to 1. better understand the cost–benefit balance of methane sensors, and 2. identify how decreasing instrumentation costs could increase deployment coverage and therefore inform large-scale methane monitoring strategies. Both calibration and response experiments indicate the INIR has little practical use for measuring methane concentrations less than 500 ppm. The MOx sensor is shown to have a logarithmic response to methane concentration change between background and 600 ppm but it is strongly suggested that passively sampling MOx sensors cannot respond fast enough to report concentrations that change in a sub-minute time frame. The NDIR sensor reported a linear change to methane concentration between background and 600 ppm, although there was a noticeable lag in reporting changing concentration, especially at higher values, and individual peaks could be observed throughout the experiment even when the plumes were released 5 s apart. The TDLAS sensor reported all changes in concentration but remains prohibitively expensive. Our findings suggest that each sensor technology could be optimized by either operational design or deployment location to quantify methane emissions. The WATCH4ERS units will be deployed in real-world environments to investigate the utility of each in the future.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Quality Control Methods for Advanced Metering Infrastructure Data

While urban-scale building energy modeling is becoming increasingly common, it currently lacks standards, guidelines, or empirical validation against measured data. Empirical validation necessary to enable best practices is becoming increasingly tractable. The growing prevalence of advanced metering infrastructure has led to significant data regarding the energy consumption within individual buildings, but is something utilities and countries are still struggling to analyze and use wisely. In partnership with the Electric Power Board of Chattanooga, Tennessee, a crude OpenStudio/EnergyPlus model of over 178,000 buildings has been created and used to compare simulated energy against actual, 15-min, whole-building electrical consumption of each building. In this study, classifying building type is treated as a use case for quantifying performance associated with smart meter data. This article attempts to provide guidance for working with advanced metering infrastructure for buildings related to: quality control, pathological data classifications, statistical metrics on performance, a methodology for classifying building types, and assess accuracy. Advanced metering infrastructure was used to collect whole-building electricity consumption for 178,333 buildings, define equations for common data issues (missing values, zeros, and spiking), propose a new method for assigning building type, and empirically validate gaps between real buildings and existing prototypes using industry-standard accuracy metrics.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2023

Sustainable Water Management: Understanding the Socioeconomic and Cultural Dimensions

With the pressing challenges of water scarcity and pollution, achieving sustainable water management is imperative for promoting long-term development. Therefore, this paper aims to examine the socio-economic and cultural factors that shape the sustainability of water management strategies in Brazil and Portugal. This study highlights various factors that influence water management, including robust legal frameworks, socio-economic disparities, cultural practices, agricultural water usage, knowledge sharing, public participation, climate change resilience, water scarcity risks, industrial water consumption, and urbanization. By conducting a SWOT analysis of water management strategies, this research synthesizes information through an extensive literature review, encompassing the legal frameworks, policies, and implemented strategies in both countries. Additionally, it investigates comparative studies among Brazil, Portugal, and other European nations to facilitate the exchange of knowledge and experiences in water management practices. The findings of this study offer valuable insights into the strengths, weaknesses, opportunities, and threats associated with water management strategies in Brazil and Portugal, thereby guiding the development of tailored policies and strategies that foster sustainability in water resource management. Additionally, the research highlights the role of digital transformation in optimizing water management practices. By integrating socio-economic, cultural, and digital factors, this study contributes to effective and sustainable water management in Brazil and Portugal, ensuring responsible utilization and preservation of water resources.

Santos, Eleonora↗
DOE OSTI2022

Predictive Risk Mapping of Schistosomiasis in Madagascar Using Ecological Niche Modeling and Precision Mapping

Schistosomiasis is a neglected tropical disease (NTD) found throughout tropical and subtropical Africa. In Madagascar, the condition is widespread and endemic in 74% of all administrative districts in the country. Despite the significant burden of the disease, high-resolution risk maps have yet to be produced to guide national control programs. This study used an ecological niche modeling (ENM) and precision mapping approach to estimate environmental suitability and disease transmission risk. The results show that suitability for schistosomiasis is widespread and covers 264,781 km 2 (102,232 sq miles). Covariates of significance to the model were the accessibility to cities, distance to water, enhanced vegetation index (EVI), annual mean temperature, land surface temperature (LST), clay content, and annual precipitation. Disease transmission risk is greatest in the central highlands, tropical east coast, arid-southwest, and northwest. An estimated 14.9 million people could be at risk of schistosomiasis; 11.4 million reside in rural areas, while 3.5 million are in urban areas. This study provides valuable insight into the geography of schistosomiasis in Madagascar and its potential risk to human populations. Because of the focal nature of the disease, these maps can inform national surveillance programs while improving understanding of areas in need of medical interventions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

What Should Health Departments Do with HIV Sequence Data?

Many countries and US states have mandatory statues that require reporting of HIV clinical data including genetic sequencing results to the public health departments. Because genetic sequencing is a part of routine care for HIV infected persons, health departments have extensive sequence collections spanning years and even decades of the HIV epidemic. How should these data be used (or not) in public health practice? This is a complex, multi-faceted question that weighs personal risks against public health benefit. The answer is neither straightforward nor universal. However, to make that judgement—of how genetic sequence data should be used in describing and combating the HIV epidemic—we need a clear image of what a phylogenetically enhanced HIV surveillance system can do and what benefit it might provide. In this paper, we present a positive case for how up-to-date analysis of HIV sequence databases managed by health departments can provide unique and actionable information of how HIV is spreading in local communities. We discuss this question broadly, with examples from the US, as it is globally relevant for all health authorities that collect HIV genetic data.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Large Evolutionary Rate Heterogeneity among and within HIV-1 Subtypes and CRFs

HIV-1 is a fast-evolving, genetically diverse virus presently classified into several groups and subtypes. The virus evolves rapidly because of an error-prone polymerase, high rates of recombination, and selection in response to the host immune system and clinical management of the infection. The rate of evolution is also influenced by the rate of virus spread in a population and nature of the outbreak, among other factors. HIV-1 evolution is thus driven by a range of complex genetic, social, and epidemiological factors that complicates disease management and prevention. Here, we quantify the evolutionary (substitution) rate heterogeneity among major HIV-1 subtypes and recombinants by analyzing the largest collection of HIV-1 genetic data spanning the widest possible geographical (100 countries) and temporal (1981–2019) spread. We show that HIV-1 substitution rates vary substantially, sometimes by several folds, both across the virus genome and between major subtypes and recombinants, but also within a subtype. Across subtypes, rates ranged 3.5-fold from 1.34 × 10−3 to 4.72 × 10−3 in env and 2.3-fold from 0.95 × 10−3 to 2.18 × 10−3 substitutions site−1 year−1 in pol. Within the subtype, 3-fold rate variation was observed in env in different human populations. It is possible that HIV-1 lineages in different parts of the world are operating under different selection pressures leading to substantial rate heterogeneity within and between subtypes. We further highlight how such rate heterogeneity can complicate HIV-1 phylodynamic studies, specifically, inferences on epidemiological linkage of transmission clusters based on genetic distance or phylogenetic data, and can mislead estimates about the timing of HIV-1 lineages.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The 2022 Outbreaks of African Swine Fever Virus Demonstrate the First Report of Genotype II in Ghana

African swine fever (ASF) is a lethal disease of domestic pigs that has been causing outbreaks for over a century in Africa ever since its first discovery in 1921. Since 1957, there have been sporadic outbreaks outside of Africa; however, no outbreak has been as devastating and as far-reaching as the current pandemic that originated from a 2007 outbreak in the Republic of Georgia. Derivatives with a high degree of similarity to the progenitor strain, ASFV-Georgia/2007, have been sequenced from various countries in Europe and Asia. However, the current strains circulating in Africa are largely unknown, and 24 different genotypes have been implicated in different outbreaks. In this study, ASF isolates were collected from samples from swine suspected of dying from ASF on farms in Ghana in early 2022. While previous studies determined that the circulating strains in Ghana were p72 Genotype I, we demonstrate here that the strains circulating in 2022 were derivatives of the p72 Genotype II pandemic strain. Therefore, this study demonstrates for the first time the emergence of Genotype II ASFV in Ghana.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Rapid Detection and Quick Characterization of African Swine Fever Virus Using the VolTRAX Automated Library Preparation Platform

African swine fever virus (ASFV) is the causative agent of a severe and highly contagious viral disease affecting domestic and wild swine. The current ASFV pandemic strain has a high mortality rate, severely impacting pig production and, for countries suffering outbreaks, preventing the export of their pig products for international trade. Early detection and diagnosis of ASFV is necessary to control new outbreaks before the disease spreads rapidly. One of the rate-limiting steps to identify ASFV by next-generation sequencing platforms is library preparation. Here, we investigated the capability of the Oxford Nanopore Technologies’ VolTRAX platform for automated DNA library preparation with downstream sequencing on Nanopore sequencing platforms as a proof-of-concept study to rapidly identify the strain of ASFV. Within minutes, DNA libraries prepared using VolTRAX generated near-full genome sequences of ASFV. Thus, our data highlight the use of the VolTRAX as a platform for automated library preparation, coupled with sequencing on the MinION Mk1C for field sequencing or GridION within a laboratory setting. These results suggest a proof-of-concept study that VolTRAX is an effective tool for library preparation that can be used for the rapid and real-time detection of ASFV.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Assessment of the Reversion to Virulence and Protective Efficacy in Pigs Receiving the Live Attenuated Classical Swine Fever Recombinant Vaccine Candidate FlagT4G

Background/Objectives: Control of classical swine fever virus (CSFV) in endemic countries relies on vaccination using live attenuated vaccines (LAVs). Most of these LAVs do not allow for the differentiation of vaccinated animals from infected animals (DIVA) based on their serological response. FlagT4G vaccine is a novel candidate that confers robust protective immunity early after vaccination and shows DIVA capabilities. Methods: This report presents the characterization of FlagT4G virus in terms of the stability of its genomic and attenuated phenotypes assessed by a reversion to virulence protocol, as well as its protective efficacy by determining the minimal protective dose. Results: Results presented here demonstrate that after five consecutive passages in groups of 5-week-old susceptible domestic pigs, FlagT4G virus remains genetically stable, and its attenuated phenotype remains unaltered. In terms of efficacy, FlagT4G virus induced solid protection against the intranasal challenge with 105 tissue culture infectious dose (TCID50) of virulent field isolate Brescia virus, even with a vaccine dose as low as 102 TCID50. Conclusions: Results presented here indicate that the FlagT4G vaccine may be a useful tool for CSFV control.

Immunology↗
DOE OSTI2023

Envisioning urban environments resilient to vector-borne diseases: a protocol to study dengue in Vietnam

Transmitted primarily by Aedes aegypti (Ae. aegypti) and Aedes albopictus (Ae. albopictus), arboviral diseases pose a major global public health threat. Dengue, chikungunya, and zika are increasingly prevalent in Southeast Asia. Among other arboviruses, dengue and zika are becoming more common in Central and South America. Given human encroachment into previously uninhabited, often deforested areas, to provide new housing in regions of population expansion, conceptualizing built urban environments in a novel way is urgently needed to safeguard against the growing climate change-driven threat of vector-borne diseases. By understanding the spread from a One Health perspective, enhanced control and prevention can be achieved. This is particularly important considering that climate change is likely to significantly impact the persistence of ponded water where mosquitoes breed due to increasing temperature and shifting rainfall patterns with regard to magnitude, duration, frequency, and season. Models can incorporate aquatic mosquito stages and adult spatial dynamics when habitats are heterogeneously available, thereby including dispersal and susceptible-exposed-infected-recovered (SEIR) epidemiology. Coupled with human population distribution (density, locations), atmospheric conditions (air temperature, precipitation), and hydrological conditions (soil moisture distribution, ponding persistence in topographic depressions), modeling has improved predictive ability for infection rates. However, it has not informed interventional approaches from an urban environment perspective which considers the role of ponds/lakes that support green spaces, the density of population that enables rapid spread of disease, and varying micro-habitats for various mosquito stages under climate change. Here, for an example of dengue in Vietnam, a preventive and predictive approach to design resilient urban environments is proposed, which uses data from rapidly expanding metropolitan communities to learn continually. This protocol deploys computational approaches including simulation and machine learning/artificial intelligence, underpinned by surveillance and medical data for validation and adaptive learning. Its application may best inform urban planning in low-middle income countries in tropical zones where arboviral pathogens are prevalent.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Advancing Offshore Wind Resource Characterization Using Buoy-based Observations

As countries continue to implement sustainable and renewable energy goals, the need for affordable low-carbon technologies, including those related to offshore wind energy, is accelerating. The U.S. federal government recognizes the environmental and economic benefits of offshore wind development and is taking the necessary steps to overcome critical challenges facing the industry to realize these benefits. The U.S. Department of Energy (DOE) is investing in buoy-mounted lidar systems to facilitate offshore measurement campaigns that will advance our understanding of the offshore environment and provide the observational data needed for model validation, particularly at hub height where offshore observations are particularly lacking. On behalf of the DOE, Pacific Northwest National Laboratory manages a Lidar Buoy Program that facilitates meteorological and oceanographic data collection using validated methods to support the U.S. offshore wind industry. Since being acquired in 2014, two DOE lidar buoys have been deployed on the U.S. east and west coasts; and their data represent the first publicly available multi-seasonal hub height data to be collected in U.S. waters. In addition, the buoys have undergone performance testing, significant upgrades, and a lidar validation campaign to ensure the accuracy and reliability of the lidar data needed to support wind resource characterization and model validation. The Lidar Buoy Program is providing valuable offshore data to the wind energy community, while focusing data collection on areas of acknowledged high priority.

offshore wind energy, lidar buoy, wind resource ch↗
DOE OSTI2020

Foreward: Advancing the U.S. Offshore Renewable Energy Industry through Marine Renewable and Offshore Wind Energy Development

Foreward to special issue of MTSJ Journal: Energy security … it’s what everyone is talking about, and for good reason. Against the backdrop of a changing climate in which nearly two-thirds of electricity generation is credited to fossil fuels (IEA, 2019a), countries around the world are diversifying their energy portfolios, suppliers, and energy routes to reduce vulnerabilities to energy security risks (U.S. Chamber of Commerce, 2020). Energy security concerns are related to fuel supply chains, electricity generation, transmission, distribution, energy market functionality, and energy system resiliency (DOE, 2017). These concerns demonstrate the need for well-functioning and competitive energy markets and diverse sources and routes of energy supply (DOE, 2017). In addition, environmental protection, efficiency and infrastructure improvements, energy innovation, emergency response, and resilience are also needed (DOE, 2017). Renewable energy generation is, and will continue to be, a major contributor in energy portfolio diversification, which will reduce reliance on foreign energy sources (IEA, 2019b; Aslantürk & Kiprizli, 2020) and support global decarbonization (Sims, 2004; Rockström et al., 2017; Arabzadeh et al., 2020).

marine renewable energy (MRE), offshore wind energ↗