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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 937 records · Page 52
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Arrayed Guide RNA Libraries for CRISPR-based Gene Knockout Screening

collaboration to develop arrayed formatted genomic screening libraries based on recently developed genome-editing technology termed CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats). CRISPR-based screening allows for potent knockout of cellular genes with a genome-wide level scalability. With the development of CRISPR knockout libraries, comprehensive analysis of pathogen-host interaction and therapeutic target discovery can be performed against pathogens of biothreat concern and national security interest. Under this work, a CRISPR knockout screen was executed against the mosquito-borne pathogens Zika virus and Rift Valley fever virus. We identified existing as well as novel host genes involved in infection by these viruses. By discovering host genes essential for infection, we can design anti-viral treatments using those identified gene or gene products as targets. The scope of this partnership was within Sandia’s mission area and national security of reducing biological dangers from emerging infections or biodefense threats.

Negrete, Oscar↗
DOE OSTI2019

Engineering a therapeutic microbe for site-of-infection delivery of encapsulated antimicrobial peptides (AMPs)

Antimicrobial peptides (AMPs) are promising therapeutics against antibiotic resistant pathogens, but they are difficult to administer at the site of infection due to poor stability. To enhance the stability of AMPs for effective and specific delivery at a site of infection, this project aimed to develop components of a novel, cell-based, drug delivery platform for AMPs in which a therapeutic microbe is engineered to specifically detect a pathogen of interest and effectively release AMPs at high, local concentrations in response. We focused the majority of our project on developing a system to produce normally host-toxic AMPs in our model therapeutic microbe (Escherichia coli) in high quantities using a protein cage system called an encapsulin (Enc) nanocompartment system. We were able to successfully produce an AMP called HBCM2 (HB), which is effective in killing our model pathogen, Pseudomonas aeruginosa, in E. coli by fusing it to an engineered, non-cage forming Enc protein, which prevented its toxicity to the E. coli. This engineered Enc protein could then be digested by a specific protease (TEV protease) for release of HB when desired. In addition to the HB production system, we also constructed a preliminary engineered E. coli capable of sensing P. aeruginosa via its specific quorum-sensing molecule, producing HB peptide, and releasing it via self-lysis in response. Preliminary characterization of this system was conducted, but we hope to fully characterize the system in future studies. The overall results produced from this study demonstrate the power of synthetic biology to confer novel functions on cells for biomanufacturing and therapeutic applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Technology Summary DNATRAX

DNATrax (DNA Tagged Reagents for Aerosol eXperiments) was developed to provide a safe simulant for understanding the transport and dispersion of pathogens. Specifically, it was developed as a safe surrogate for the Bacillus anthrasis spore bioagent, since most naturally occurring spores are not safe for public release. As DNA-tagged sugar particles, DNATrax aerosols are safe for public release. Scientists can add unique DNA barcode sequences to the sugar particles to produce a wide variety of test particles that can be easily differentiated, making it possible to release and test them simultaneously. The unique barcodes also eliminate the need to conduct decontamination between tests, dramatically reducing the cost and time to run experiments. Additionally, the surrogate offers a high-sensitivity detection method to understand key public health issues. We conducted both lab-based and largescale field studies using DNATrax to validate its capabilities for use as a pathogen surrogate. We have demonstrated the ability to produce DNATrax in a range of sizes, adjusting the microparticles to simulate different sized pathogens with ability to create unique sequences of DNA bases, enabling them to create a nearly unlimited variety of test particles.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Using Deep Mutational Data and Machine Learning to Guide Outbreak and Pandemic Response

A significant fraction of pathogens known to infect humans originate in non-human (zoonotic) hosts (Taylor, Latham, and Woolhouse 2001), and new and emerging pathogens continue to spill over into the human population more frequently at an alarming rate (e.g., SARS, MERS, Cholera, etc.). The recent outbreaks of Ebola virus in West Africa and the ongoing SARS-CoV-2 pandemic demonstrate the need for rapid and reliable assessments of viral phenotype information to help inform scientists and policy makers how best to control the spread of disease. Further understanding of the virus pathogenic evolutionary space and potential trajectory could guide appropriate control measures to limit the spread of a new virus throughout the local and global human population.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Characterizing the Defense Hierarchy of Populus trichocarpa

The U.S. Departments of Energy and Agriculture are developing bioenergy crops as a sustainable alternative to traditional fossil fuels. Plant disease threatens this effort by inhibiting the efficient production of plant feedstocks for bioenergy. In particular, biotrophic Melampsora leaf rust pathogens can increase morbidity in Populus trichocarpa and its hybrids (aka poplars), the primary woody feedstocks for bioenergy. Controlling rust disease in plantations is thus critical to the success of the poplar bioenergy program. Current efforts to control rust disease focus on plant genetic resistance. However, with novel pathogenic variation generated by the global movement of pathogens and their hybridization, it is increasingly clear that controlling rust disease in a long-lived plant like Populus depends on our ability to understand and manage not only genes for rust resistance, but also short-lived plant microorganisms that contribute to defense against rust (aka “defense mutualists”). Our proposed research thus seeks to develop an integrative, hierarchical model of P. trichocarpa defense that integrates genetic resistance and defense mutualists. Our overarching hypothesis is that defense against Melampsora rust is biologically degenerate, with major and minor plant resistance genes, plant defense compounds, and defense mutualists within the microbiome each contributing to rust resistance under different circumstances. The specific aims of our study will test the placement of each of these factors in the defense hierarchy. Ultimately, it is our hope that disease management strategies harnessing both resistance genes and naturally occurring defense mutualists of P. trichocarpa, and an appreciation of the ecological circumstances in which each is effective, will maximize plant resistance and productivity while minimizing impacts on the surrounding ecological landscape.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Combined Imaging and RNA-Seq on a Microfluidic Platform for Viral Infection Studies

The goal of this work was to pioneer a novel, low-overhead protocol for simultaneously assaying cell-surface markers and intracellular gene expression in a single mammalian cell. The purpose of developing such a method is to be able to understand the mechanisms by which pathogens engage with individual mammalian cells, depending on their cell surface proteins, and how both host and pathogen gene expression changes are reflective of these mechanisms. The knowledge gained from such analyses of single cells will ultimately lead to more robust pathogen detection and countermeasures. Our method was aimed at streamlining both the upstream cell sample preparation using microfluidic methods, as well as the actual library making protocol. Specifically, we wanted to implement a random hexamer-based reverse transcription of all RNA within a single cell (as opposed to oligo dT-based which would only capture polyadenylated transcripts), and then use a CRISPR-based method called scDash to deplete ribosomal DNAs (since ribosomal RNAs make up the majority of the RNA in a mammalian cell). After significant troubleshooting, we demonstrate that we are able to prepare cDNA from RNA using the random hexamer primer, and perform the rDNA depletion. We also show that we can visualize individually stained cells, setting up the pipeline for connecting surface markers to RNA-sequencing profiles. Finally, we test a number of devices for various parts of the pipeline, including bead generation, optical barcoding and cell dispensing, and demonstrate that while some of these have potential, more work is needed to optimize this part of the pipeline.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Conserved genetic mechanisms for biotic stress in sorghum (Final report)

Developing durable disease resistance for biofuel crops is crucial, particularly as the range of biofuel crop production expands and pathogens of other plant species evolve to cause diseases of bioenergy feedstocks. Setosphaeria species are significant pathogens of the Andropogonae, and S. turcica can infect both maize and sorghum. Sorghum leaf blight (SLB), caused by S. turcica, is widespread and can decrease grain yields up to 50%, reduce forage quantity and quality, and predispose plants to other diseases, such as anthracnose. Our overall objective was to gain a systems-level understanding of the pathosystem by leveraging natural genetic variation, host specificity of the pathogen, and transcriptome analysis to improve biotic stress resistance in sorghum. We proposed three specific goals: 1) Identify sorghum alleles conferring resistance to S. turcica using natural genetic variation. 2) Characterize genes associated with biotic stress response in sorghum. 3) Identify fungal genes responsible for host specificity.

09 BIOMASS FUELS↗
DOE OSTI2024

Conserved genetic mechanisms for biotic stress in sorghum (Final Report)

Developing durable disease resistance for biofuel crops is crucial, particularly as the range of biofuel crop production expands and pathogens of other plant species evolve to cause diseases of bioenergy feedstocks. Setosphaeria species are significant pathogens of the Andropogonae, and S. turcica can infect both maize and sorghum. Sorghum leaf blight (SLB), caused by S. turcica, is widespread and can decrease grain yields up to 50%, reduce forage quantity and quality, and predispose plants to other diseases, such as anthracnose. Our overall objective was to gain a systems-level understanding of the pathosystem by leveraging natural genetic variation, host specificity of the pathogen, and transcriptome analysis to improve biotic stress resistance in sorghum. We proposed three specific goals: 1) Identify sorghum alleles conferring resistance to S. turcica using natural genetic variation. 2) Characterize genes associated with biotic stress response in sorghum. 3) Identify fungal genes responsible for host specificity.

09 BIOMASS FUELS↗
DOE OSTI2025

Controlling Host Responses to Infection

Pathogen invasion of host cells causes a myriad of functional changes including alterations of chromatin accessibility often limiting defense responses, shunting of cellular resources to centers of viral replication, and rearrangement of intracellular membranes to facilitate genome reproduction and progeny release. Systems biology approaches provide global snapshots of pathogen induced changes following infection and provide a variety of tools to begin to define how cellular homeostasis is disrupted, but improvements on these tools are required to determine how cellular functions are altered post infection. Chromatin accessibility techniques, biochemical assays to assess the activity of epigenetic enzymes, scalable sample collection platforms, and activity-based probes were used to characterize how human respiratory viruses modify host responses in infected human lungs over time. These studies enhanced our knowledge of how pathogens usurp the host environment during infection and identify additional targets for future evaluations of medical countermeasures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

PNNL DataHub NIAID Program Project: Modeling Host Responses to Understand Severe Human Virus Infections, Multi-Omic Viral Dataset Catalog Collection

The National Institute of Allergy and Infectious Diseases (NIAID) "Modeling Host Responses to Understand Severe Human Virus Infections" program project was a highly integrated and comprehensive systems biology research core, funded by the National Institute of Health (U19AI106772) from 2013-06-01 to 2018-05-31, investigating the complex host response to category A, B, and C priority pathogen infections. Resulting project deliverables include an extensive comprehensive collections of linked primary and secondary transformation viral experimental infection data. Here we provide a never before released comprehensive infectious disease collection of primary and secondary transformation multi-Omics data profiling a series of priority pathogen primary experimental studies for enhanced open access to viral Omics lifecycle datasets and project metadata. Using a highly integrated and multidisciplinary approach, linked primary data and metadata supporting secondary normalization datasets, provide critical information necessary for research reproducibility and long-term preservation. Enabling on-demand data access for research community consumption and developer reuse, serves to support new mechanistic insights and discoveries into host-pathogen interactions for aiding future biohazard data preparedness efforts in emergency response to global health crises involving viral infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Application of multi-criteria decision analysis techniques and decision support framework for informing plant select agent designation and decision making

The United States Department of Agriculture (USDA) Division of Agricultural Select Agents and Toxins (DASAT) established a list of biological agents (Select Agents List) that threaten crops of economic importance to the United States and regulates the procedures governing containment, incident response, and the security of entities working with them. Every 2 years the USDA DASAT reviews their select agent list, utilizing assessments by subject matter experts (SMEs) to rank the agents. We explored the applicability of multi-criteria decision analysis (MCDA) techniques and a decision support framework (DSF) to support the USDA DASAT biennial review process. The evaluation includes both current and non-select agents to provide a robust assessment. We initially conducted a literature review of 16 pathogens against 9 criteria for assessing plant health and bioterrorism risk and documented the findings to support this analysis. Technical review of published data and associated scoring recommendations by pathogen-specific SMEs was found to be critical for ensuring accuracy. Scoring criteria were adopted to ensure consistency. The MCDA supported the expectation that select agents would rank high on the relative risk scale when considering the agricultural consequences of a bioterrorism attack; however, application of analytical thresholds as a basis for designating select agents led to some exceptions to current designations. A second analytical approach used agent-specific data to designate key criteria in a DSF logic tree format to identify pathogens of low concern that can be ruled out for further consideration as select agents. Both the MCDA and DSF approaches arrived at similar conclusions, suggesting the value of employing the two analytical approaches to add robustness for decision making.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

The Influence of Contrasting Microbial Lifestyles on the Pre-symbiotic Metabolite Responses of Eucalyptus grandis Roots

Plant roots co-inhabit the soil with a diverse consortium of microbes of which a number attempt to enter symbiosis with the plant. These microbes may be pathogenic, mutualistic, or commensal. Hence, the health and survival of plants is heavily reliant on their ability to perceive different microbial lifestyles and respond appropriately. Emerging research suggests that there is a pivotal role for plant root secondary metabolites in responding to microbial colonization. However, it is largely unknown if plants are able to differentiate between microbes of different lifestyles and respond differently during the earliest stages of pre-symbiosis (i.e., prior to physical contact). In studying plant responses to a range of microbial isolates, we questioned: (1) if individual microbes of different lifestyles and species caused alterations to the plant root metabolome during pre-symbiosis, and (2) if these early metabolite responses correlate with the outcome of the symbiotic interaction in later phases of colonization. We compared the changes of the root tip metabolite profile of the model tree Eucalyptus grandis during pre-symbiosis with two isolates of a pathogenic fungus (Armillaria luteobubalina), one isolate of a pathogenic oomycete (Phytophthora cinnamomi), two isolates of an incompatible mutualistic fungus (Suillus granulatus), and six isolates of a compatible mutualistic fungus (Pisolithus microcarpus). Untargeted metabolite profiling revealed predominantly positive root metabolite responses at the pre-symbiosis stage, prior to any observable phenotypical changes of the root tips. Metabolite responses in the host tissue that were specific to each microbial species were identified. A deeper analysis of the root metabolomic profiles during pre-symbiotic contact with six strains of P. microcarpus showed a connection between these early metabolite responses in the root with later colonization success. Further investigation using isotopic tracing revealed a portion of metabolites found in root tips originated from the fungus. RNA-sequencing also showed that the plant roots undergo complementary transcriptomic reprogramming in response to the fungal stimuli. Taken together, our results demonstrate that the early metabolite responses of plant roots are partially selective toward the lifestyle of the interacting microbe, and that these responses can be crucial in determining the outcome of the interaction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Feed status and skin injury modulate immunopathology, global gene expression, and survival in channel catfish during virulent Aeromonas hydrophila infection

Introduction VirulentAeromonas hydrophilais a major pathogen in channel catfish (Ictalurus punctatus), that causes motileAeromonassepticemia and significant economic losses. We investigated the effect of feeding status and skin integrity on the host immune response, disease survival, and gastrointestinal pathology following a vAh challenge. Methods Using a bath immersion model, channel catfish were divided into four treatment groups: fin clipped and fed (FCF), fin clipped but not fed (FCN), not fin clipped but fed (NCF), and not fin clipped nor fed (NCN) alongside non-challenged control groups The FCF and NCF groups were fed 2 h prior to the challenge, but the FCN and NCN groups were not. Survival analysis, histopathological assessment, and RNA sequencing were conducted across groups at different time intervals throughout the vAh challenge. Results Survival rates were lowest in the FCF and FCN groups (30% and 23% survival, respectively), suggesting that both feeding and skin damage contributed to disease severity. Histopathological analyses revealed more severe intestinal and gastric lesions in fed groups, characterized by epithelial necrosis, hemorrhage, and edema. Transcriptomic analysis among the groups identified significant differentially expressed genes associated with inflammation, apoptosis, and metabolic stress, with notable upregulation of interleukin 1-beta (il-1β), and complement C3 (c3). Gene ontology enrichment highlighted distinct immune activation patterns between fed and unfed groups, with enhanced pathogen recognition and pro-inflammatory responses in unfed fish. Discussion These findings suggest feeding prior to infection may exacerbate disease pathology, potentially by creating a physiological state conducive to facilitate pathogen proliferation and dampened early immune responses, whereas short-term fasting appears to promote early immune activation. This study provides novel insights into the complex interplay between feed status, physical injury, and immune response to vAh infection.

Immunology↗
DOE OSTI2018

The Bacterial Symbiont Phaeobacter inhibens Shapes the Life History of Its Algal Host Emiliania huxleyi

Marine microbes form host-associated biofilm communities that are shaped by complex interactions between bacteria and their host. The roseobacter Phaeobacter inhibens exploits both symbiotic and pathogenic niches while interacting with its microalgal host Emiliania huxleyi. During co-cultivation over extended periods with E. huxleyi, we show that P. inhibens selectively kills two host cell types, the diploid calcifying strain and the haploid flagellated strain. Meanwhile, various non-calcifying diploid strains are resistant to this pathogen or the pathogen is avirulent to this cell type. This differential pathogenesis has the potential of dramatically altering the composition of E. huxleyi blooms, which are typically dominated by the roseobacter-susceptible calcifying strain. This cell type makes calcite plates, which are an important sink in the marine carbon cycle and forms part of the marine paleobotanic record. P. inhibens kills the haploid cells, which have been proposed as critical to the survival of the algae, as they readily escape both eukaryotic predation and viral infection. Consequently, bacteria such as P. inhibens could influence E. huxleyi's life history by selective pathogenesis, thereby altering the composition of cell types within E. huxleyi populations and its bloom-bust lifestyle.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Comparative analysis of secretomes from Ectomycorrhizal fungi with an emphasis on small-secreted proteins

Fungi are major players in the carbon cycle in forest ecosystems due to the wide range of interactions they have with plants either through soil degradation processes by litter decayers or biotrophic interactions with pathogenic and ectomycorrhizal symbionts. Secretion of fungal proteins mediates these interactions by allowing the fungus to interact with its environment and/or host. Ectomycorrhizal (ECM) symbiosis independently appeared several times throughout evolution and involves approximately 80% of trees. Despite extensive physiological studies on ECM symbionts, little is known about the composition and specificities of their secretomes. In this study, we used a bioinformatics pipeline to predict and analyze the secretomes of 49 fungal species, including 11 ECM fungi, wood and soil decayers and pathogenic fungi to tackle the following questions: (1) Are there differences between the secretomes of saprophytic and ECM fungi? (2) Are small-secreted proteins (SSPs) more abundant in biotrophic fungi than in saprophytic fungi? and (3) Are there SSPs shared between ECM, saprotrophic and pathogenic fungi? We showed that the number of predicted secreted proteins is similar in the surveyed species, independently of their lifestyle. The secretome from ECM fungi is characterized by a restricted number of secreted CAZymes, but their repertoires of secreted proteases and lipases are similar to those of saprotrophic fungi. Focusing on SSPs, we showed that the secretome of ECM fungi is enriched in SSPs compared with other species. Most of the SSPs are coded by orphan genes with no known PFAM domain or similarities to known sequences in databases. Finally, based on the clustering analysis, we identified shared- and lifestyle-specific SSPs between saprotrophic and ECM fungi. The presence of SSPs is not limited to fungi interacting with living plants as the genome of saprotrophic fungi also code for numerous SSPs. As a result, ECM fungi shared lifestyle-specific SSPs likely involved in symbiosis that are good candidates for further functional analyses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Phylogenetic Analyses of Shigella and Enteroinvasive Escherichia coli for the Identification of Molecular Epidemiological Markers: Whole-Genome Comparative Analysis Does Not Support Distinct Genera Designation

As a leading cause of bacterial dysentery, Shigella represents a significant threat to public health and food safety. Related, but often overlooked, enteroinvasive Escherichia coli (EIEC) can also cause dysentery. Current typing methods have limited ability to identify and differentiate between these pathogens despite the need for rapid and accurate identification of pathogens for clinical treatment and outbreak response. We present a comprehensive phylogeny of Shigella and EIEC using whole genome sequencing of 169 samples, constituting unparalleled strain diversity, and observe a lack of monophyly between Shigella and EIEC and among Shigella taxonomic groups. The evolutionary relationships in the phylogeny are supported by analyses of population structure and hierarchical clustering patterns of translated gene homolog abundance. Lastly, we identified a panel of 404 single nucleotide polymorphism (SNP) markers specific to each phylogenetic cluster for more accurate identification of Shigella and EIEC. Our findings show that Shigella and EIEC are not distinct evolutionary groups within the E. coli genus and, thus, EIEC as a group is not the ancestor to Shigella. The multiple analyses presented provide evidence for reconsidering the taxonomic placement of Shigella. The SNP markers offer more discriminatory power to molecular epidemiological typing methods involving these bacterial pathogens.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Early Recovery of Salmonella from Food Using a 6-Hour Non-selective Pre-enrichment and Reformulation of Tetrathionate Broth

Culture based methods are commonly employed to detect pathogens in food and environmental samples. These methods are time consuming and complex, requiring multiple non-selective and selective enrichment broths, and usually take at least 1 week to recover and identify pathogens. Improving pathogen detection in foods is a primary goal for regulatory agencies and industry. Salmonella detection in food relies on a series of culture steps in broth formulations optimized to resuscitate Salmonella and reduce the abundance of competitive bacteria. Examples of non-selective pre-enrichment broths used to isolate Salmonella from food include Lactose, Universal Pre-enrichment, BPW, and Trypticase Soy broths. Tetrathionate (TT) and Rappaport–Vassiliadis (RV) broths are employed after a 24-h non-selective enrichment to select for Salmonella and hamper the growth of competitive bacteria. In this study, we tested a new formulation of TT broth that lacks brilliant green dye and has lower levels of TT . We employed this TT broth formulation in conjunction with a 6-h non-selective pre-enrichment period and determined that Salmonella recovery was possible one day earlier than standard food culture methods. We tested the shortened culture method in different non-selective enrichment broths, enumerated Salmonella in the non-selective enrichments, and used 16S rRNA gene sequencing to determine the proportional abundances of Salmonella in the TT and RV selective enrichments. Together these data revealed that a 6-h nonselective pre-enrichment reduces the levels of competitive bacteria inoculated into the selective TT and RV broths, enabling the recovery of Salmonella 1 day earlier than standard culture enrichment methods.

16S rRNA↗
DOE OSTI2020

Microbiome Variation Across Two Hemlock Species With Hemlock Woolly Adelgid Infestation

The hemlock woolly adelgid ( Adelges tsugae , HWA), an invasive insect, is devastating native hemlock populations in eastern North America, and management outcomes have so far had limited success. While many plant microbiomes influence and even support plant immune responses to insect herbivory, relatively little is known about the hemlock microbiome and its interactions with pathogens or herbivores such as HWA. Using 16S rRNA and ITS gene amplicon sequencing, we characterized the needle, branch, root, and rhizosphere microbiome of two hemlock species, Tsuga canadensis and T. sieboldii , that displayed low and high levels of HWA populations. We found that both archaeal/bacterial and fungal needle communities, as well as the archaeal/bacterial branch and root communities, varied in composition in both hemlock species relative to HWA population levels. While host species and plant-associated habitats explained a greater proportion of the variance in the microbiome than did HWA population level, high HWA populations were associated with enrichment of 100 likely fungal pathogen sequence variants across the four plant-associated habitats (e.g., needle, branch, root, rhizosphere) compared to trees with lower HWA populations. This work contributes to a growing body of literature linking plant pathogens and pests with the changes in the associated plant microbiome and host health. Furthermore, this work demonstrates the need to further investigate plant microbiome effects across multiple plant tissues to understand their influences on host health.

16S rRNA↗