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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

LAMP detection assays for boxwood blight pathogens: A comparative genomics approach

Rapid and accurate molecular diagnostic tools are critical to efforts to minimize the impact and spread of emergent pathogens. The identification of diagnostic markers for novel pathogens presents several challenges, especially in the absence of information about population diversity and where genetic resources are limited. The objective of this study was to use comparative genomics datasets to find unique target regions suitable for the diagnosis of two fungal species causing a newly emergent blight disease of boxwood. Candidate marker regions for loop-mediated isothermal amplification (LAMP) assays were identified from draft genomes of Calonectria henricotiae and C. pseudonaviculata , as well as three related species not associated with this disease. To increase the probability of identifying unique targets, we used three approaches to mine genome datasets, based on (i) unique regions, (ii) polymorphisms, and (iii) presence/absence of regions across datasets. From a pool of candidate markers, we demonstrate LAMP assay specificity by testing related fungal species, common boxwood pathogens, and environmental samples containing 445 diverse fungal taxa. In conclusion, this comparative-genomics-based approach to the development of LAMP diagnostic assays is the first of its kind for fungi and could be easily applied to diagnostic marker development for other newly emergent plant pathogens.

1st report↗
NASA NTRS2007

Design and Simulation of a MEMS Structure for Electrophoretic and Dielectrophoretic Separation of Particles by Contactless Electrodes

Rapid identification of pathogenic bacterial species is an important factor in combating public health problems such as E. coli contamination. Food and waterborne pathogens account for sickness in 76 million people annually (CDC). Diarrheagenic E. coli is a major source of gastrointestinal illness. Severe sepsis and Septicemia within the hospital environment are also major problems. 75 1,000 cases annually with a 30-50% mortality rate (Crit Care Med, July '01, Vol. 29, 1303-10). Patient risks run the continuum from fever to organ failure and death. Misdiagnosis or inappropriate treatment increases mortality. There exists a need for rapid screening of samples for identification of pathogenic species (Certain E. coli strains are essential for health). Critical to the identification process is the ability to isolate analytes of interest rapidly. This poster discusses novel devices for the separation of particles on the basis of the dielectric properties, mass and surface charge characteristics is presented. Existing designs involve contact between electrode surfaces and analyte medium resulting in contamination of the electrode bearing elements Two different device designs using different bulk micromachining MEMS processes (PolyMUMPS and a PyrexBIGold electrode design) are presented. These designs cover a range of particle sizes from small molecules through eucaryotic cells. The application of separation of bacteria is discussed in detail. Simulation data for electrostatic and microfluidic characteristics are provided. Detailed design characteristics and physical features of the as fabricated PolyMUMPS design are provided. Analysis of the simulation data relative to the expected performance of the devices will be provided and subsequent conclusions discussed.

Shaw, Harry C.↗
DOE OSTI2022

Identification and distribution of pathogens coinfecting with Brucella spp., Coxiella burnetii and Rift Valley fever virus in humans, livestock and wildlife

Zoonotic diseases, such as brucellosis, Q fever and Rift Valley fever (RVF) caused by Brucella spp., Coxiella burnetii and RVF virus, respectively, can have devastating effects on human, livestock, and wildlife health and cause economic hardship due to morbidity and mortality in livestock. Coinfection with multiple pathogens can lead to more severe disease outcomes and altered transmission dynamics. These three pathogens can alter host immune responses likely leading to increased morbidity, mortality and pathogen transmission during coinfection. Developing countries, such as those commonly afflicted by outbreaks of brucellosis, Q fever and RVF, have high disease burden and thus common coinfections. A literature survey provided information on case reports and studies investigating coinfections involving the three focal diseases. Fifty five studies were collected demonstrating coinfections of Brucella spp., C. burnetii or RVFV with 50 different pathogens, of which 64% were zoonotic. While the literature search criteria involved ‘coinfection’, only 24/55 studies showed coinfections with direct pathogen detection methods (microbiology, PCR and antigen test), while the rest only reported detection of antibodies against multiple pathogens, which only indicate a history of co-exposure, not concurrent infection. These studies lack the ability to test whether coinfection leads to changes in morbidity, mortality or transmission dynamics. We describe considerations and methods for identifying ongoing coinfections to address this critical blind spot in disease risk management.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Identification of Adaptive Fungal Pathogen Resistance Loci in Switchgrass (Final Report)

Switchgrass (Panicum virgatum) has great potential as a sustainable bioenergy and bioproducts feedstock. However, there are a number of challenges that must be overcome to achieve this goal. One of the most significant challenges to switchgrass productivity are fungal pathogens, especially rusts and smuts. The primary goals of our project were to characterize the distribution of fungal pathogens on switchgrass across central North America and to identify genetic loci that control resistance to those pathogens. The research was primarily conducted with large common garden plantings of a switchgrass, distributed along a latitudinal gradient from South Texas to South Dakota. By conducting this research simultaneously at 10 field locations, we were able establish the relative contributions of genes and the environment to pathogen resistance. Through this research, we identified multiple genomic regions (loci) that contribute to rust resistance and found that the effects of these loci on resistance were highly influenced by field site location. Our research revealed that most of the rust damage to switchgrass from Texas to the northern United States is caused by a single fungal species, Puccinia novopanici. Therefore, genetic variation within this species and/or local environmental conditions are responsible for the inconsistent efficacy of pathogen resistance loci. We are currently investigating these two non-mutually exclusive hypotheses. In addition to our studies of rust pathogens, we were able to identify resistance loci for the head smut fungal pathogen Tilletia maclaganii. The funding from this grant facilitated a collaboration with the DOE Joint Genome Institute to develop a reference genome for T. maclaganii. A reference genome will make population genetic studies of this smut fungus possible, which in turn will facilitate the development of strategies to mitigate its impact. Overall, the funded research has greatly advanced our understanding of the genetic basis of fungal pathogen resistance switchgrass. This knowledge will help facilitate the breeding of more resistant cultivars and thus, increase the productivity of swichgrass generally.

09 BIOMASS FUELS↗
DOE OSTI2026

Zeteotech, LLC TRGR Project Final Report

Reliable detection of aerosolized pathogens is difficult due to need to distinguish between the benign bioaerosols such as dander and pollen and the thousands of pathogens capable of infecting people. Accurate identification of airborne pathogens of concern in the past has required the collection of aerosol samples in a filter, periodic collection of the samples, and processing and identification in the laboratory. This process is labor intensive and expensive. Additionally, this method necessarily has a time to detection window of hours to days depending on the collection frequency. Biological pathogens have an incubation period before the onset of symptoms and severe health effects and/or mortality, people will typically be exposed to them without realizing it. This has resulted in a detect to treat strategy for protection against bio releases. While prophylactic measures can still be effective over these time scales, reducing the time to detection will significantly improve the effectiveness of these measures and subsequently reduce the consequences of a release. Various attempts to reduce the time to detection and identification have been plagued by highly undesirable false-positives which degrade confidence in the system. Zeteotech, LLC has developed a mass spectrometer based bioaerosol sensing system which is capable of autonomously identifying airborne pathogens of concern and alert authorities within minutes instead of hours to days. They have deployed these instruments to protect high-risk facilities by alerting authorities of public health events and intentional bioterrorism events in near real time. This makes it possible to more accurately identify the time and location of the release and minimize the number of people that are exposed through prompt quarantining of affected areas.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Multiplex detection and identification of viral, bacterial, and protozoan pathogens in human blood and plasma using an expanded high-density resequencing microarray platform

Introduction: Nucleic acid tests for blood donor screening have improved the safety of the blood supply; however, increasing numbers of emerging pathogen tests are burdensome. Multiplex testing platforms are a potential solution. Methods: The Blood Borne Pathogen Resequencing Microarray Expanded (BBP-RMAv.2) can perform multiplex detection and identification of 80 viruses, bacteria and parasites. This study evaluated pathogen detection in human blood or plasma. Samples spiked with selected pathogens, each with one of 6 viruses, 2 bacteria and 5 protozoans were tested on this platform. The nucleic acids were extracted, amplified using multiplexed sets of primers, and hybridized to a microarray. The reported sequences were aligned to a database to identify the pathogen. To directly compare the microarray to an emerging molecular approach, the amplified nucleic acids were also submitted to nanopore next generation sequencing (NGS). Results: The BBP-RMAv.2 detected viral pathogens at a concentration as low as 100 copies/ml and a range of concentrations from 1,000 to 100,000 copies/ml for all the spiked pathogens. Coded specimens were identified correctly demonstrating the effectiveness of the platform. The nanopore sequencing correctly identified most samples and the results of the two platforms were compared. Discussion: These results indicated that the BBP-RMAv.2 could be employed for multiplex detection with potential for use in blood safety or disease diagnosis. The NGS was nearly as effective at identifying pathogens in blood and performed better than BBP-RMAv.2 at identifying pathogen-negative samples.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

SUMOylation regulates nuclear localization and stability of TRAIP/RNF206

TRAIP/RNF206 plays diverse roles in cell cycle progression, DNA damage response, and DNA repair pathways. Physiological importance of TRAIP is highlighted by the identification of pathogenic mutations of TRAIP gene in patients diagnosed with primordial dwarfism. Although the diverse functions of TRAIP in the nucleus have been well characterized, molecular mechanism of TRAIP retention in the nucleus has not been determined. Here, we discovered that TRAIP is post-translationally modified by the small ubiquitin-like protein (SUMO). In addition, we identified five SUMOylation sites in TRAIP, and successfully generated SUMOylation deficient mutant of TRAIP. In an attempt to define the functional roles of TRAIP SUMOylation, we discovered that SUMOylation deficient TRAIP is not retained in the nucleus. In addition, protein stability of SUMOylation deficient TRAIP is lower than wild type TRAIP, demonstrating that SUMOylation is critical for both proper subcellular localization and protein stability of TRAIP. Taken together, these findings improve the understanding clinical implication of TRAIP in various diseases including primordial dwarfism and cancers. - Highlights: • TRAIP is post-translationally modified by SUMO. • SUMOylation affects subcellular localization of TRAIP. • SUMOylation regulates protein stability of TRAIP.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Dielectrophoresis assisted rapid, selective and single cell detection of antibiotic resistant bacteria with G-FETs

Time-consuming, expensive and low sensitivity diagnostic methods used for monitoring bacterial infections lead to unnecessary or delays in prescription of the right antibiotic treatment. Determining an optimal clinical treatment requires rapid detection and identification of pathogenic bacteria and their sensitivity to specific antimicrobials. However, diagnostic devices that meet all of these criteria have proven elusive thus far. Graphene field effect transistors (G-FET) are a promising solution, since they are highly sensitive to chemical/biological modification, can have fast detection times and can be placed on different substrates. Here, by integrating specific peptide probes over G-FETs, we present a proof-of-concept study for species and strain specific label-free detection of clinical strains of pathogenic bacteria with high specificity and sensitivity. We found that pyrene-conjugated peptides immobilized on G-FETs were capable of detecting pathogenic Staphylococcus aureus at the single-cell level and discriminate against other gram-positive and gram-negative bacterial pathogens. A similar device was able to discriminate between antibiotic resistant and sensitive strains of Acinetobacter baumannii , suggesting that these devices can also be used for detecting antibiotic resistive pathogens. Furthermore, a new means of enhancing attachment, electric-field assisted binding, reduced the detection limit to 104 cells/ml and the detection time to below 5 minutes. Here, the combination of single step attachment, inexpensive production, rapid, selective and sensitive detection suggest G-FETs plus pyrene-conjugated peptides are a new platform for solving major challenges faced in point of care diagnostics to fight infectious diseases and antimicrobial resistance.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2019

Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information

Pulmonary exacerbations are the leading cause of death in cystic fibrosis (CF) patients. To track microbial dynamics during acute exacerbations, a CF rapid response (CFRR) strategy was developed. The CFRR relies on viromics, metagenomics, metatranscriptomics, and metabolomics data to rapidly monitor active members of the viral and microbial community during acute CF exacerbations. To highlight CFRR, a case study of a CF patient is presented, in which an abrupt decline in lung function characterized a fatal exacerbation. The microbial community in the patient’s lungs was closely monitored through the multi-omics strategy, which led to the identification of pathogenic shigatoxigenic Escherichia coli (STEC) expressing Shiga toxin. This case study illustrates the potential for the CFRR to deconstruct complicated disease dynamics and provide clinicians with alternative treatments to improve the outcomes of pulmonary exacerbations and expand the life spans of individuals with CF. Proper management of polymicrobial infections in patients with cystic fibrosis (CF) has extended their life span. Information about the composition and dynamics of each patient’s microbial community aids in the selection of appropriate treatment of pulmonary exacerbations. We propose the cystic fibrosis rapid response (CFRR) as a fast approach to determine viral and microbial community composition and activity during CF pulmonary exacerbations. The CFRR potential is illustrated with a case study in which a cystic fibrosis fatal exacerbation was characterized by the presence of shigatoxigenic Escherichia coli . The incorporation of the CFRR within the CF clinic could increase the life span and quality of life of CF patients.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform

The detection of pathogens in complex sample backgrounds has been revolutionized by wide access to next-generation sequencing (NGS) platforms. However, analytical methods to support NGS platforms are not as uniformly available. Pathosphere (found at Pathosphere.org) is a cloud - based open - sourced community tool that allows for communication, collaboration and sharing of NGS analytical tools and data amongst scientists working in academia, industry and government. The architecture allows for users to upload data and run available bioinformatics pipelines without the need for onsite processing hardware or technical support. The pathogen detection capabilities hosted on Pathosphere were tested by analyzing pathogen-containing samples sequenced by NGS with both spiked human samples as well as human and zoonotic host backgrounds. Pathosphere analytical pipelines developed by Edgewood Chemical Biological Center (ECBC) identified spiked pathogens within a common sample analyzed by 454, Ion Torrent, and Illumina sequencing platforms. ECBC pipelines also correctly identified pathogens in human samples containing arenavirus in addition to animal samples containing flavivirus and coronavirus. These analytical methods were limited in the detection of sequences with limited homology to previous annotations within NCBI databases, such as parvovirus. Utilizing the pipeline-hosting adaptability of Pathosphere, the analytical suite was supplemented by analytical pipelines designed by the United States Army Medical Research Institute of Infectious Diseases and Walter Reed Army Institute of Research (USAMRIID-WRAIR). These pipelines were implemented and detected parvovirus sequence in the sample that the ECBC iterative analysis previously failed to identify. By accurately detecting pathogens in a variety of samples, this work demonstrates the utility of Pathosphere and provides a platform for utilizing, modifying and creating pipelines for a variety of NGS technologies developed to detect pathogens in complex sample backgrounds. These results serve as an exhibition for the existing pipelines and web-based interface of Pathosphere as well as the plug-in adaptability that allows for integration of newer NGS analytical software as it becomes available.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1995

Portable Immune-Assessment System

Portable immune-assessment system developed for use in rapidly identifying infections or contaminated environment. System combines few specific fluorescent reagents for identifying immune-cell dysfunction, toxic substances, buildup of microbial antigens or microbial growth, and potential identification of pathogenic microorganisms using fluorescent microplate reader linked to laptop computer. By using few specific dyes for cell metabolism, DNA/RNA conjugation, specific enzyme activity, or cell constituents, one makes immediate, onsite determination of person's health or of contamination of environment.

Pierson, Duane L.↗
NASA NTRS2014

Comparison of Sample and Detection Quantification Methods for Salmonella Enterica from Produce

The purpose of this study was to identify and optimize fast and reliable sampling and detection methods for the identification of pathogens that may be present on produce grown in small vegetable production units on the International Space Station (ISS), thus a field setting. Microbiological testing is necessary before astronauts are allowed to consume produce grown on ISS where currently there are two vegetable production units deployed, Lada and Veggie.

methods of salmonella from produce↗
NASA NTRS2019

Leafy Greens Grown on the International Space Station May Provide a Nutritious Supplement to Astronauts' Diet

Supplemental safe food production has been an essential goal of NASA to meet the nutritional needs of astronauts on the International Space Station (ISS) as well as for future long duration missions to the moon and beyond. Food crops grown in space experience different environmental conditions than plants grown on Earth (i.e. microgravity and spaceflight physical sciences impacts). To test the growth methods and effects of the space environment, red romaine lettuce Lactuca sativa cv. 'Outredgeous', was grown in Veggie plant growth chambers on the ISS. Microbiological food safety of the plants grown on the ISS was determined by heterotrophic plate counts to assess total microbial load for bacteria and fungi as well as screening for specific pathogens and isolate identification. Molecular characterization was completed using Next Generation Sequencing (NGS) to provide valuable information on the taxonomic composition and community structure of the plant microbiome. Chemical analyses of plant tissue were conducted to understand spaceflight-induced changes in key elements in the space diet, phenolics, anthocyanin levels, and Oxygen radical absorbance capacity (ORAC), a measure of antioxidant capacity. Three growth tests of red romaine lettuce were completed on ISS, VEG-01A, VEG-01B, and VEG-03A. Plants were harvested using two harvest methods, either a single terminal harvest (after 33 days) or cut-and-come-again repetitive harvesting (64 days total growth). Ground controls were grown simultaneously with a delay to accommodate condition monitoring and replication. A comparison of the plant tissue returned to Earth showed leaves from the second grow-out had significantly higher bacterial counts than the preceding or subsequent growth test or any of the ground controls. Fungal counts were significantly higher on the final cut-and-come-again harvest of the third grow out. None of the potential foodborne pathogens that were screened for were detected. Bacterial and fungal isolate identification and community characterization indicated similar diversity between VEG-01A and VEG-01B growth tests, however, there appeared to be subtle differences in diversity and distribution among the three growth tests. Chemical analysis of plant tissue revealed significant variation in a few elemental data, but variation in levels of phenolics, anthocyanins, and ORAC was not significantly different. This study indicated that leafy vegetable crops could safely provide an edible supplement to astronauts' diet, and our analysis provided baseline data for continual operation of the Veggie plant growth units on ISS. This research was funded by NASA's space biology program.

Food Production↗
DOE OSTI2018

A new comprehensive method for detection of livestock-related pathogenic viruses using a target enrichment system

Highlights: • Development of a comprehensive method to detect viruses using SureSelect system. • A method by which almost the full length of the viral genome can be determined without virus isolation. • Widely available methods for comprehensive analysis of virus genomic information. We tested usefulness of a target enrichment system SureSelect, a comprehensive viral nucleic acid detection method, for rapid identification of viral pathogens in feces samples of cattle, pigs and goats. This system enriches nucleic acids of target viruses in clinical/field samples by using a library of biotinylated RNAs with sequences complementary to the target viruses. The enriched nucleic acids are amplified by PCR and subjected to next generation sequencing to identify the target viruses. In many samples, SureSelect target enrichment method increased efficiencies for detection of the viruses listed in the biotinylated RNA library. Furthermore, this method enabled us to determine nearly full-length genome sequence of porcine parainfluenza virus 1 and greatly increased Breadth, a value indicating the ratio of the mapping consensus length in the reference genome, in pig samples. Our data showed usefulness of SureSelect target enrichment system for comprehensive analysis of genomic information of various viruses in field samples.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Method for genetic identification of unknown organisms

A method of rapid, genome and proteome based identification of unknown pathogenic or non-pathogenic organisms in a complex sample. The entire sample is analyzed by creating millions of emulsion encapsulated microdroplets, each containing a single pathogenic or non-pathogenic organism sized particle and appropriate reagents for amplification. Following amplification, the amplified product is analyzed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Identification of equine mares as reservoir hosts for pathogenic species of Leptospira

Equine leptospirosis can result in abortion, stillbirth, neonatal death, placentitis, and uveitis. Horses can also act as subclinical reservoir hosts of infection, which are characterized as asymptomatic carriers that persistently excrete leptospires and transmit disease. In this study, PCR and culture were used to assess urinary shedding of pathogenic Leptospira from 37 asymptomatic mares. Three asymptomatic mares, designated as H2, H8, and H9, were PCR-positive for lipL32, a gene specific for pathogenic species of Leptospira. One asymptomatic mare, H9, was culture-positive, and the recovered isolate was classified as L. kirschneri serogroup Australis serovar Rushan. DNA capture and enrichment of Leptospira genomic DNA from PCR-positive, culture-negative samples determined that asymptomatic mare H8 was also shedding L. kirschneri serogroup Australis, whereas asymptomatic mare H2 was shedding L. interrogans serogroup Icterohaemorrhagiae. Sera from all asymptomatic mares were tested by the microscopic agglutination test (MAT) and 35 of 37 (94.6%) were seropositive with titers ranging from 1:100 to 1:3200. In contrast to asymptomatic mares, mare H44 presented with acute spontaneous abortion and a serum MAT titer of 1:102,400 to L. interrogans serogroup Pomona serovar Pomona. Comparison of L. kirschneri serogroup Australis strain H9 with that of L. interrogans serogroup Pomona strain H44 in the hamster model of leptospirosis corroborated differences in virulence of strains. Since lipopolysaccharide (LPS) is a protective antigen in bacterin vaccines, the LPS of strain H9 (associated with subclinical carriage) was compared with strain H44 (associated with spontaneous abortion). This revealed different LPS profiles and immunoreactivity with reference antisera. It is essential to know what species and serovars of Leptospira are circulating in equine populations to design efficacious vaccines and diagnostic tests. Our results demonstrate that horses in the US can act as reservoir hosts of leptospirosis and shed diverse pathogenic Leptospira species via urine. This report also details the detection of L. kirschneri serogroup Australis serovar Rushan, a species and serotype of Leptospira, not previously reported in the US.

60 APPLIED LIFE SCIENCES↗