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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 1,333 records · Page 74
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Genome, transcriptome and secretome analyses of the antagonistic, yeast-like fungus Aureobasidium pullulans to identify potential biocontrol genes

Aureobasidium pullulans is an extremotolerant, cosmopolitan yeast-like fungus that successfully colonises vastly different ecological niches. The species is widely used in biotechnology and successfully applied as a commercial biocontrol agent against postharvest diseases and fireblight. However, the exact mechanisms that are responsible for its antagonistic activity against diverse plant pathogens are not known at the molecular level. Thus, it is difficult to optimise and improve the biocontrol applications of this species. As a foundation for elucidating biocontrol mechanisms, we have de novo assembled a high-quality reference genome of a strongly antagonistic A. pullulans strain, performed dual RNA-seq experiments, and analysed proteins secreted during the interaction with the plant pathogen Fusarium oxysporum. Based on the genome annotation, potential biocontrol genes were predicted to encode secreted hydrolases or to be part of secondary metabolite clusters (e.g., NRPS-like, NRPS, T1PKS, terpene, and β-lactone clusters). Transcriptome and secretome analyses defined a subset of 79 A. pullulans genes (among the 10,925 annotated genes) that were transcriptionally upregulated or exclusively detected at the protein level during the competition with F. oxysporum. These potential biocontrol genes comprised predicted secreted hydrolases such as glycosylases, esterases, and proteases, as well as genes encoding enzymes, which are predicted to be involved in the synthesis of secondary metabolites. This study highlights the value of a sequential approach starting with genome mining and consecutive transcriptome and secretome analyses in order to identify a limited number of potential target genes for detailed, functional analyses.

transcriptome↗
DOE OSTI2012

Study of the structure and function of a novel bacterial virulence factor isolated from Francisella tularensis

During my internship at Lawrence Livermore National Laboratory (LLNL), I studied a novel virulence factor of the potential bioterrorism agent, Francisella tularensis. This bacterium is a facultative intracellular pathogen with a broad host range, and is known to be the causative agent of the zoonotic disease tularemia (1). F. tularensis is highly infectious, requiring only 1 to 10 bacteria to cause severe disease (2). Due to its high rate of infectivity, F. tularensis has potential use as a bioterrorism agent. As a result, it has been categorized as a class A biothreat pathogen by the Centers for Disease Control and Prevention (3).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Infectious Disease Proteome Biomarkers: Final Technical Report

Research for the DOE Infectious Disease Proteome Biomarkers focused on Rift Valley fever virus (RVFV) and Venezuelan Equine Encephalitis Virus (VEEV). RVFV and VEEV are Category A and B pathogens respectively. Among the priority threats, RVFV and VEEV rank high in their potential for being weaponized and introduced to the United States, spreading quickly, and having a large health and economic impact. In addition, they both have live attenuated vaccine, which allows work to be performed at BSL-2. While the molecular biology of RVFV and VEEV are increasingly well-characterized, little is known about its host-pathogen interactions. Our research is aimed at determining critical alterations in host signaling pathways to identify therapeutics targeted against the host.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Towards understanding of Nipah virus attachment protein assembly and the role of protein affinity and crowding for membrane curvature events.

Pathogenic viruses are a primary threat to our national security and to the health and economy of our world. Effective defense strategies to combat viral infection and spread require the development of understanding of the mechanisms that these pathogens use to invade the host cell. We present in this report results of our research into viral particle recognition and fusion to cell membranes and the role that protein affinity and confinement in lipid domains plays in membrane curvature in cellular fusion and fission events. Herein, we describe 1) the assembly of the G attachment protein of Nipah virus using point mutation studies to define its role in viral particle fusion to the cell membrane, 2) how lateral pressure of membrane bound proteins induce curvature in model membrane systems, and 3) the role of membrane curvature in the selective partitioning of molecular receptors and specific affinity of associated proteins.

Stachowiak, Jeanne C.↗
DOE OSTI2014

A Novel Application of Synthetic Biology and Directed Evolution to Engineer Phage-based Antibiotics

The emergence of multiple drug resistant bacteria poses threats to human health, agriculture and food safety. Annually over 100,000 deaths and up to $20 billion loss to the U.S. economy are attributed to multiple drug resistant bacteria. With only four new chemical antibiotics in the drug development pipeline, we are in dire need of new solutions to address the emerging threat of multiple drug resistance. We propose a paradigm-changing approach to address the multi-drug resistant bacteria problem by utilizing Synthetic Biology (SynBio) methodologies to create and evolve “designer” bacteriophages or phages – viruses that specifically infect bacteria – to infect and kill newly emerging pathogenic bacterial strains WITHOUT the need for chemical antibiotics. A major advantage of using phage to combat pathogenic bacteria is that phages can co-evolve with their bacterial host, and Sandia can be the first in the world to establish an industrial scale Synthetic Biology pipeline for phage directed evolution for safe, targeted, customizable solution to bacterial drug resistance. Since there is no existing phage directed evolution effort within or outside of Sandia, this proposal is suitable as a high-risk LDRD effort to create the first pipeline for such an endeavor. The high potential reward nature of this proposal will be the immediate impact in decontamination and restoration of surfaces and infrastructure, with longer term impact in human or animal therapeutics. The synthetic biology and screening approaches will lead to fundamental knowledge of phage/bacteria co-evolution, making Sandia a world leader in directed evolution of bacteriophages.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

DHS Internship Final Report

I spent the last ten weeks working in the Systems Biology department at Sandia National Laboratories in Livermore, CA. Under the direction of Zachary Bent, I helped do preliminary testing/optimization of a vacuum-driven, capture-based system for pathogen RNA transcript enrichment. I also worked on a project to create mutant Yersinia enterocolitica strains in order to test which genes are involved in intracellular pathogen virulence, as well as sequencing several Klebsiella pneumoniae samples for use by a bioinformaticist.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

DHS Internship Final Report

This summer I worked on projects that involved RNA sequencing of pathogens after an infection of host cells. The goal of these projects was to continue developing pathogen enrichment strategies for transcriptomic analysis, and also to perform hostpathogen interaction studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Portable Microfluidic Raman System for Rapid, Label-free Early Disease Signature Detection

In the early stages of infection, patients develop non-specific or no symptoms at all. While waiting for identification of the infectious agent, precious window of opportunity for early intervention is lost. The standard diagnostics require affinity reagents and sufficient pathogen titers to reach the limit of detection. In the event of a disease outbreak, triaging the at-risk population rapidly and reliably for quarantine and countermeasure is more important than the identification of the pathogen by name. To expand Sandia's portfolio of Biological threat management capabilities, we will utilize Raman spectrometry to analyze immune subsets in whole blood to rapidly distinguish infected from non-infected, and bacterial from viral infection, for the purpose of triage during an emergency outbreak. The goal of this one year LDRD is to determine whether Raman spectroscopy can provide label-free detection of early disease signatures, and define a miniaturized Raman detection system meeting requirements for low- resource settings.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Development of a Novel Vaccine to Prevent Urinary Tract Infections, CRADA TC02219.0

This project was a collaborative effort between Lawrence Livermore National Security, LLC as manager and operator of Lawrence Livermore National Laboratory (LLNL) and Syntiron LLC to develop novel vaccine formulations against bacterial urinary tract infections (UTIs). The project leveraged expertise at Syntiron to develop vaccine antigens for bacterial pathogens and nanoparticle technology at LLNL to enchance the efficacy of vaccine formulations. In particular, Syntiron has developed vaccine antigens by identifying and isolating specific proteins from the membranes of extraintestinal pathogenic E. coli , the bacteria responsible for the majority of UTIs. These membrane protein antigens consist of iron regulating proteins (IRPs), a class of highly conserved putative antigens. Membrane protein antigens are difficult to formulate for vaccine applications. The formulations typically required to solubilize membrane protein antigens often result in non-native protein folding, thereby masking the antigenic epitopes required for efficacy. LLNL's nanolipoprotein particle (NLP) platform provides a mimic of a membrane protein's native environment, greatly increasing the proteins' native attributes. In addition, the NLP can accommodate myriad other biomolecules in addition to the protein antigen, facilitating the co-localized delivery of both antigen and immune stimulating compounds necessary for eliciting a protective immune response in vivo. The goal of this project was to incorporate membrane protein antigens into NLPs and evaluate the efficacy of these formulations to protect against urinary tract infections in an animal model.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Advanced Diagnostic and Sample Preparation Platform for Early Threat Surveillance

Emerging infectious diseases present a profound threat to global health, economic development, and political stability, and therefore represent a significant national security concern for the United States. The increased prevalence of international travel and globalized trade further amplify the threat of infectious disease outbreaks of catastrophic effect. The key to containing and eradicating an outbreak before it goes global is rapid identification of index cases and initial clusters of affected individuals. This depends upon establishment of a biosurveillance network that effectively reaches infectious disease hotspots in even the most remote regions of the world and provides a network-integrated, location-appropriate diagnostic capability. At present, there are two critical needs which must be addressed in order to extend biosurveillance activities beyond centralized laboratory facilities: 1) A simple, reliable, and safe method for immediate stabilization of clinical specimens in the field; and 2) A flexible sample processing platform that enables in-field preparation of clinical specimens for rapid, on-site analysis using a variety of diagnostic assay platforms. These needs are not necessarily mutually exclusive; in fact, we propose that they are most efficiently addressed by a deployable sample processing platform that immediately stabilizes the information content of clinical specimens through transformation of the inherently unstable analytes of interest into stable equivalents that are appropriately formatted for downstream analysis. In order to address this problem, we have developed a sample processing pipeline and microfluidics-based platform modules enabling: 1) Extraction of total RNA from finger-stick quantities of human whole blood; and 2) Microscale synthesis of appropriately-formatted cDNA products that capture the information content of blood RNA in a stable form that supports pathogen detection and/or characterization via PCR and/or Second Generation Sequencing (SGS). Through this research we have discovered new, effective solutions for problems that thus far have hindered use of digital microfluidics (DMF) in biomedical applications. Our work reveals a clear path forward to fieldable, automated sample processing systems that will enable rapid, on-site identification of usual-suspect and novel pathogens in clinical specimens for improved biosurveillance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Short papers on current state of sequencing, metagenomics, and RNAseq for diagnostics

This report contains three papers on the current state of sequencing, metagenomics, and RNAseq for diagnostics. 1) There are many factors that must be evaluated before ascertaining what type of technology is most cost effective, and/or most technically effective. In general, long read technologies are primarily used for in field/in situ sequencing and for closing isolate genomes, while short read sequencing lends itself to rapid high quality determination of strain identity and to applications that require high depth, such as metagenomes and counting applications, like in RNAseq. 2) RNAseq can provide some important insights into the biology of active infections and provide advances in diagnostics approaches. Depth of sequencing coverage is critical to determine gene expression profiles. Full use of RNAseq data from both host and pathogen(s) for diagnostics and informed treatment options will require further investigation. 3) RNAseq can provide some important insights into the biology of active infections and provide advances in diagnostics approaches. Depth of sequencing coverage is critical to determine gene expression profiles. Full use of RNAseq data from both host and pathogen(s) for diagnostics and informed treatment options will require further investigation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Developing an engineered therapeutic microbe to release antimicrobial peptides (AMPs)

Antibiotic resistance is a public health threat that will need alternatives in the future to combat it. Antimicrobial peptides (AMPs) have been identified as potential therapeutic candidates compared to traditional antibiotics. A therapeutic microbe has been developed that protects and releases AMPs in an encapsulin cage coupled with a pathogen-sensing detection system. The proposed system uses Escherichia coli as the therapeutic microbe and Pseudomonas aeruginosa as the pathogen.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Concurrent evaluation of autophagy induction and Burkholderia infection at the single cell level

Autophagy is a natural, regulated cellular process that "cleans up" cellular debris by degrading and recycling dysfunctional proteins. There is a high potential impact of exploiting the benefits of autophagy to complement existing treatments, but little has been done to date on bacterial pathogens of defense concern such as Burkholderia pseudomallei, a highly virulent Select Agent pathogen that is intrinsically resistant to most classes of antibiotics. Assessment of autophagy in the context of infection typically requires use of multiple technologies in combination (e.g., Western analysis paired with microscopy or flow cytometry) as applied to heterogeneous populations of cells. To address this, we have developed a dual target reporter cell line (RAW264.7 LC3-BFP:mPlum, GFP-RelA) that enables concurrent visualization of infection and autophagy induction. We assessed the effect of clinically approved small molecule inducers of autophagy on infection by Burkholderia thailendensis, a closely related but less virulent surrogate for B. pseudomallei. The reporter cells were first infected with a B. thailendensis strain that constitutively expresses GFP, then treated with one of four known autophagy inducers (rapamycin, niclosamide, bromhexine HC1, or flubendazole) for 4 hours. Confocal fluorescence imaging was used to quantify autophagy stimulation at the single cell level. Autophagy maturation was observed as a decrease in BFP LC3 puncta with a concurrent increase in mPlum LC3 puncta. B. thailendensis infection was assessed by monitoring translocation of GFP-RelA (an NFkB subunit) into the nucleus and through quantitating the intracellular bacterial presence in single cells. Preliminary results indicate that bromhexine HC1 and niclosamide may hinder B. thailendensis' ability to replicate intracellularly and reduce overall bacterial survival.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Bioscience COVID Rapid Response Report

The COVID-19 disease outbreak and its impact on global health and economies have highlighted the national security threat posed by pathogens with pandemic potential and the need for rapid development of effective diagnostics and medical countermeasures. The Bioscience IA selected for funding rapid COVID LDRD project proposals that addressed critical R&D gaps in pandemic response that could be accomplished in 1-3 months with the requested funding. In total, the Bioscience IA funded nine rapid projects that addressed 1) rapid and accurate methods for SARS-CoV-2 RNA detection, 2) modeling tools to help prioritize populations for diagnostic testing, 3) bioinformatic tools to track SARS-CoV-2 genomic sequence changes over time, 4) molecular inhibitors of SARS-CoV-2 cellular infection, and 5) method for rapid staging of COVID19 disease to enable administration of more effective treatments. In addition, LDRD funded one larger project to be completed in FY21 that leverages Sandia capabilities to address the need for platform diagnostics and therapeutics that can be rapidly tailored against emerging pathogen targets.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A targeted opsonization platform for programming innate immunity against rapidly evolving novel viruses.

Recent work has shown that artificial opsonins stimulate the targeted destruction of bacteria by phagocyte immune cells. Artificial opsonization has the potential to direct the innate immune system to target novel antigens, potentially even viral pathogens. Furthermore, the engagement of innate immunity presents a potential solution for the spread of pandemics in a scenario when a vaccine is unavailable or ineffective. Funded by the LDRD late start bioscience pandemic response program, we tested whether artificial opsonins can be developed to target viral pathogens using phage MS2 and a SARS-CoV-2 surrogate. To direct opsonization against these viruses we purified antibody derived viral targeting motifs and attempted the same chemical conjugation strategies that produced bacterial targeting artificial opsonins. However, the viral targeting motifs proved challenging to conjugate using these methods, frequently resulting in precipitation and loss of product. Future studies may be successful with this approach if a smaller and more soluble viral-targeting peptide could be used.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Studies of Alternative Ventilation Configurations to Mitigate Airborne Exposure Risks in Office Spaces

The objective of this study was to evaluate the impact of alternative ventilation configurations on airflow patterns and potential exposure risks in office spaces. Two existing conference rooms at Sandia NM were modeled using Computational Fluid Dynamics (CFD) simulations to characterize airflow patterns and potential airborne exposure risks in well-mixed and once-through (through-flow) ventilation conditions. Multiple scenarios were studied to evaluate the impact of occupancy, Plexiglass barriers, and a modified-return airflow configuration. Experimental and visualization tests were also conducted to validate the well-mixed and through-flow models and findings. The simulations demonstrated that the modified-return airflow configuration that promoted through-flow conditions reduced pathogen concentrations within the space compared to the well-mixed airflow configuration; occupancy reduction only reduced the number of exposed individuals, and Plexiglass barriers had almost no effect. The experimentally measured air speeds at nine anemometer locations generally matched the simulated airflow velocities, and a fog-purge visualization test was also consistent with simulated results of plume movement and dissipation. The visualization tests demonstrated improvements in air change rate with the modified return, which promoted through-flow conditions, versus the original well-mixed ventilation configuration. The results of this study demonstrate that minor modifications to a space that promote through-flow conditions can improve air quality and reduce pathogen concentrations. Additional airflow modeling and testing of alternative occupied space configurations are recommended to further inform room designs that mitigate airborne exposure risks for occupants.

42 ENGINEERING↗
DOE OSTI2022

Integrated Pest Management (IPM) for Early Detection Algal Crop Protection. Final Report

During large-scale, outdoor algal biomass growth, production strain(s) are subject to attack by pathogens, predators, and non-productive competitors, compromising the biomass yield. The project team at UCSD developed and demonstrated the effectiveness of Volatile Organic Compound, VOC, analysis via mass spectrometry (MS) as an early detection system for the presence of production algal ponds infection. The MS detection can then trigger high-resolution melt analysis (HRMA) and enhanced quantitative PCR (qPCR) to identify predatory or pathogenic species precisely. This study gathered the foundational data informing how wholly automated systems monitor the health of production ponds. By detecting the presence of low molecular weight VOCs in the air space above ponds, the instrument was able to mimic “sniffing” the health of the algae pond. This early warning system will be free growers from time-consuming and costly regular surveillance of ponds with the current techniques, such as qPCR and flow-cam assays, which are slower, less sensitive, and not easily fully automated, resulting in increased production efficiency through the reduction of crop loss. This project demonstrated that Chemical Ionization Mass Spectrometry, CIMS, could serve as a real-time monitor of ponds health tracking up to 100 different VOCs simultaneously for continuous periods up to 60 days without interruption, signaling infection within an algal crop 24 to 36 hours prior to techniques such as qPCR and microscopy. While mass spectrometry is an expensive tool, this simple VOC sampling system proved not only to be sensitive and robust but could to multiplexed to monitor several ponds, lowering the overall cost serially. This technology demonstrated a reduction in biomass production cost by approximately 50% compared to growers not employing any detection methodology.

09 BIOMASS FUELS↗
DOE OSTI2022

Reconfiguration of the Respiratory Tract Microbiome to Prevent and Treat Burkholderia Infection

New approaches to preventing and treating infections, particularly of the respiratory tract, are needed. One promising strategy is to reconfigure microbial communities (microbiomes) within the host to improve defense against pathogens. Probiotics and prebiotics for gastrointestinal (GI) infections offer a template for success. We sought to develop comparable countermeasures for respiratory infections. First, we characterized interactions between the airway microbiome and a biodefense-related respiratory pathogen ( Burkholderia thailandensis ; Bt), using a mouse model of infection. Then, we recovered microbiome constituents from the airway and assessed their ability to re-colonize the airway and protect against respiratory Bt infection. We found that microbiome constituents belonging to Bacillus and related genuses frequently displayed colonization and anti-Bt activity. Comparative growth requirement profiling of these Bacillus strains vs Bt enabled identification of candidate prebiotics. This work serves as proof of concept for airway probiotics, as well as a strong foundation for development of airway prebiotics.

59 BASIC BIOLOGICAL SCIENCES↗