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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Sarcocystis cruzi (Hasselmann, 1923) Wenyon, 1926: redescription, molecular characterization and deposition of life cycle stages specimens in the Smithsonian Museum

Currently, 7 named Sarcocystis species infect cattle: Sarcocystis hirsuta, S. cruzi, S. hominis, S. bovifelis, S. heydorni, S. bovini and S. rommeli; other, unnamed species also infect cattle. Of these parasites of cattle, a complete life cycle description is known only for S. cruzi, the most pathogenic species in cattle. The life cycle of S. cruzi was completed experimentally in 1982, before related parasite species were structurally characterized, and before the advent of molecular diagnostics; to our knowledge, no archived frozen tissues from the cattle employed in the original descriptions remain for DNA characterization. Here, we isolated DNA from a paraffin-embedded kidney of a calf experimentally infected with S. cruzi in 1980; we then sequenced portions of 18S rRNA, 28S rRNA, COX1 and Acetyl CoA genes and verified that each shares 99–100% similarity to other available isolates attributed to S. cruzi from naturally infected cattle. We also reevaluated histological sections of tissues of calves experimentally infected with S. cruzi in the original description, exploiting improvements in photographic technology to render clearer morphological detail. Finally, we reviewed all available studies of the life cycle of S. cruzi, noting that S. cruzi was transmitted between bison (Bison bison) and cattle (Bos taurus) and that the strain of parasite derived from bison appeared more pathogenic than the cattle strain. Based on these newfound molecular, morphological and physiological data, we thereby redescribed S. cruzi and deposited reference material in the Smithsonian Museum for posterity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Emerging wild virus of native grass bioenergy feedstock is well–established in the Midwestern USA and associated with premature stand senescence

The North American native prairie grass Panicum virgatum (switchgrass) is a primary bioenergy feedstock candidate. Its widespread distribution and genetic diversity enable the possibility of developing this perennial grass for high production in a variety of conditions, including on marginal lands. A critical concern in feedstock development and deployment is the risk of novel pathogen emergence. Here we investigate the landscape-scale prevalence and epidemiology of a little-studied North American virus first detected in switchgrass and other grasses in bioenergy trials in the US Midwest. Switchgrass mosaic virus (SwMV, Genus Marafivirus, Family Tymoviridae) is transmitted by leafhoppers and phylogenetically sister to Maize rayado fino virus, a significant pathogen of maize in parts of the Americas. Our goal was to determine whether SwMV is uniquely limited to specific bioenergy trials or well-established and circulating more broadly. We used molecular diagnostics to quantify naturally occurring SwMV infection in leafhoppers and switchgrass in naturalistic stands throughout a large Midwestern landscape, and quantified leafhopper abundances and stand performance. Our analysis revealed that this apparently wild virus is well-established and widespread. Infection was present at nearly all sites, across diverse landscape contexts, with prevalences ranging as high as 33%–60%. Infection appeared to accumulate and persist in stands over time. It was associated with increases in premature stand senescence but not with reductions in stand height. Although wild viruses are believed to evolve benign relationships with their natural hosts, these data suggest that SwMV has potential to impact yield components. Viruses are frequently overlooked in crop development efforts, but represent the majority of emerging plant pathogens. For SwMV, it is imperative to quantify its impact on host performance, to identify the extent of any host resistance, and to assess any risks of virus spillover to agricultural plantings of other Poaceae species, including maize and sorghum.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Reveal-CoV Diaagnostic Platform (Final Report)

LLNL designed and built a rapid, RT-LAMP-based molecular diagnostics platform as a potential tool to quickly diagnose COVID-19 in under one hour. This point-of-care testing approach involves an initial high temperature swab sample inactivation step followed by amplification of viral RNA using up to 5 control and pathogen-specific assays. Results are determined based on a discreet reaction color change from red to yellow but can also be determined using fluorescence detection. Testing of this prototype platform was conducted with synthetic viral RNA and dried, stabilized reagents. Buffer systems, swab selection, and assay stabilization formulations were evaluated for performance. Limits of detection were determined using RNA; however, testing was not performed with viable SARS-CoV-2 virus or clinical samples.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Emerging Trends and Technologies Used for the Identification, Detection, and Characterisation of Plant-Parasitic Nematode Infestation in Crops

Accurate identification and estimation of the population densities of microscopic, soil-dwelling plant-parasitic nematodes (PPNs) are essential, as PPNs cause significant economic losses in agricultural production systems worldwide. This study presents a comprehensive review of emerging techniques used for the identification of PPNs, including morphological identification, molecular diagnostics such as polymerase chain reaction (PCR), high-throughput sequencing, meta barcoding, remote sensing, hyperspectral analysis, and image processing. Classical morphological methods require a microscope and nematode taxonomist to identify species, which is laborious and time-consuming. Alternatively, quantitative polymerase chain reaction (qPCR) has emerged as a reliable and efficient approach for PPN identification and quantification; however, the cost associated with the reagents, instrumentation, and careful optimisation of reaction conditions can be prohibitive. High-throughput sequencing and meta-barcoding are used to study the biodiversity of all tropical groups of nematodes, not just PPNs, and are useful for describing changes in soil ecology. Convolutional neural network (CNN) methods are necessary to automate the detection and counting of PPNs from microscopic images, including complex cases like tangled nematodes. Remote sensing and hyperspectral methods offer non-invasive approaches to estimate nematode infestations and facilitate early diagnosis of plant stress caused by nematodes and rapid management of PPNs. This review provides a valuable resource for researchers, practitioners, and policymakers involved in nematology and plant protection. It highlights the importance of fast, efficient, and robust identification protocols and decision-support tools in mitigating the impact of PPNs on global agriculture and food security.

Plant Sciences↗
DOE OSTI2022

Data from: Emerging wild virus of native grass bioenergy feedstock is well established in the Midwestern USA and associated with premature stand senescence

This dataset includes values for the prevalence of switchgrass mosaic virus (Genus Marafivirus, Family Tymoviridae) detected with molecular diagnostics (RT-PCR) in individual Panicum virgatum (switchgrass) plants and in Graminella leafhoppers that feed on them. Surveys were conducted in 15 sites in August 2012. Stands surveyed had been established for some time and represent a range of landscape contexts. Measures of stand height and percent senescence were also collected. Land cover composition surrounding each site was calculated from the USDA-NASS Cropland Data Layer and estimates of drought impact were derived from the US Drought Monitor.

09 BIOMASS FUELS↗
NASA NTRS1988

The global Cretaceous-Tertiary fire: Biomass or fossil carbon

The global soot layer at the K-T boundary indicates a major fire triggered by meteorite impact. However, it is not clear whether the principal fuel was biomass or fossil carbon. Forests are favored by delta value of C-13, which is close to the average for trees, but the total amount of elemental C is approximately 10 percent of the present living carbon, and thus requires very efficient conversion to soot. The PAH was analyzed at Woodside Creek, in the hope of finding a diagnostic molecular marker. A promising candidate is 1-methyl-7-isopropyl phenanthrene (retene,), which is probably derived by low temperature degradation of abietic acid. Unlike other PAH that form by pyrosynthesis at higher temperatures, retene has retained the characteristic side chains of its parent molecule. A total of 11 PAH compounds were identified in the boundary clay. Retene is present in substantial abundance. The identification was confirmed by analysis of a retene standard. Retene is characteristic of the combustion of resinous higher plants. Its formation depends on both temperature and oxygen access, and is apparently highest in oxygen-poor fires. Such fires would also produce soot more efficiently which may explain the high soot abundance. The relatively high level of coronene is not typical of a wood combustion source, however, though it can be produced during high temperature pyrolysis of methane, and presumably other H, C-containing materials. This would require large, hot, low O2 zones, which may occur only in very large fires. The presence of retene indicates that biomass was a significant fuel source for the soot at the Cretaceous-Tertiary boundary. The total amount of elemental C produced requires a greater than 3 percent soot yield, which is higher than typically observed for wildfires. However, retene and presumably coronene imply limited access of O2 and hence high soot yield.

Gilmour, Iain↗
NASA NTRS1990

The nature of interstellar/pre-cometary dust

During the past 15 years considerable progress in observational techniques has been achieved in the middle-infrared region (5000-500/cm, 2-20 microns), the region where most diagnostic molecular vibrations occur. Spectra of many different astronomical infrared sources, some deeply embedded in dark molecular clouds and others obscured only by dust in the diffuse interstellar medium are now available. These spectra provide a powerful probe, not only for the identification of interstellar molecules in both the gas and solid phases, but also of the physical and chemical conditions which prevail in these two very different domains. By comparing these spectra with laboratory spectra one can determine the composition and abundance of the icy material frozen on the cold (- 10K) dust in the dark interior of molecular clouds and of the hydrocarbon component of dust in the diffuse interstellar medium. As these are the building blocks of comets, the work described here also gives insight into the nature of comets.

Allamandola, Louis↗
NASA NTRS1994

The Origins of Polycyclic Aromatic Hydrocarbons: Are They Everywhere?

During the past 15 years considerable progress in observational techniques has been achieved in the middle-infrared region (5000-500 per centimeter, 2-20 micron), the region where most diagnostic molecular vibrations occur. Spectra of many different astronomical infrared sources, some deeply embedded in dark molecular clouds and others at their edges, are now available. These spectra provide a powerful probe, not only for the identification of interstellar molecules in both the gas and solid phases, but also of the physical and chemical conditions which prevail in these two very different domains. The two lectures will focus on the evidence that polycyclic aromatic hydrocarbons (PAHs) are an important, ubiquitous and abundant interstellar species. PAHs are. extremely stable species which can range in size from a few angstroms across to several hundred angstroms (PAHs are also the building blocks of amorphous carbon particles). This identification rests on the suggestive agreement between the laboratory spectra of PAHs with a set of IR emission bands which emanate from many different sources where ultraviolet starlight impinges on a "dusty" region. The picture is that individual PAHs are first pumped into highly vibrationally excited states and relax by fluorescence at their fundamental vibrational frequencies. That PAHs are a ubiquitous interstellar component has serious ramifications in other spectral regions as well, including the strong extinction in the ultraviolet, and the classic visible diffuse interstellar bands discovered more than 50 years ago (but unexplained to this day) The first part of the course will focus on the interpretation of astronomical spectra. The second lecture will start by showing how recent laboratory data on PAHs taken under realistic interstellar conditions has con borated the PAH hypothesis and led to great insight into the conditions in the PAH containing regions. This lecture will end by reviewing the ever-increasing evidence for interstellar PAHs in meteorites and interplanetary dust particles. This in conjunction with the recent suggestion that PAHs are abundant in Jupiter's atmosphere will make the point that "PAHs are Everywhere".

Allamandola, L. J.↗
NASA NTRS2003

Carbon Nanotube Electrode Arrays For Enhanced Chemical and Biological Sensing

Applications of carbon nanotubes for ultra-sensitive electrical sensing of chemical and biological species have been a major focus in NASA Ames Center for Nanotechnology. Great progress has been made toward controlled growth and chemical functionalization of vertically aligned carbon nanotube arrays and integration into micro-fabricated chip devices. Carbon nanotube electrode arrays devices have been used for sub-attomole detection of DNA molecules. Interdigitated carbon nanotubes arrays devices have been applied to sub ppb (part per billion) level chemical sensing for many molecules at room temperature. Stability and reliability have also been addressed in our device development. These results show order of magnitude improvement in device performance, size and power consumption as compared to micro devices, promising applications of carbon nanotube electrode arrays for clinical molecular diagnostics, personal medical testing and monitoring, and environmental monitoring.

Han, Jie↗
NASA NTRS2003

Carbon Nanotube Nanoelectrode Array for Ultrasensitive DNA Detection

A reliable nanoelectrode array based on vertically aligned multi-walled carbon nanotubes (MWNTs) embedded in SiO2 is used for ultrasensitive DNA detection. Characteristic nanoelectrode behavior is observed using low-density MWNT arrays for measuring both bulk and surface immobilized redox species such as K4Fe(CN)6. The open-end of MWNTs present similar properties as graphite edge-plane electrodes with wide potential window, flexible chemical functionalities, and good biocompatibility. Oligonucleotide probes are selectively functionalized at the open ends cf the nanotube array and specifically hybridized with oligonucleotide targets. The guanine groups are employed as the signal moieties in the electrochemical measurements. Ru(bpy)3(2+) mediator is used to further amplify the guanine oxidation signal. The hybridization of subattomoles of PCR amplified DNA targets is detected electrochemically by combining the MWNT nanoelectrode array with the Ru(bpy)32' amplification mechanism. This system provides a general platform of molecular diagnostics for applications requiring ultrahigh sensitivity, high-degree of miniaturization, and simple sample preparations.

Li, Jun↗
NASA NTRS2003

Carbon Nanotube Nanoelectrode Array as an Electronic Chip for Ultrasensitive Label-free DNA Detection

A reliable nanoelectrode array based on vertically aligned multi-walled carbon nanotubes (MWNTs) embedded in SiO2 is used for ultrasensitive DNA detection. Characteristic nanoelectrode behavior is observed using low-density MWNT arrays for measuring both bulk and surface immobilized redox species such as K4Fe(CN)6 and ferrocene derivatives. The open-end of MWNTs are found to present similar properties as graphite edge-plane electrodes with wide potential window, flexible chemical functionalities, and good biocompatibility. BRCA1 related oligonucleotide probes with 18 bp are selectively functionalized at the open ends of the nanotube array and specifically hybridized with oligonucleotide targets incorporated with a polyG tag. The guanine groups are employed as the signal moieties in the electrochemical measurements. R(bpy)(sup 2+, sub 3) mediator is used to further amplify the guanine oxidation signal. The hybridization of sub-attomoles of DNA targets is detected electrochemically by combining the MWNT nanoelectrode array with the R(bpy)(sup 2+, sub 3) amplification mechanism. This technique was employed for direct electrochemical detection of label-free PCR amplicon from a healthy donor through specific hybridization with the BRCA1 probe. The detection limit is estimated to be less than 1000 DNA molecules since abundant guanine bases in the PCR amplicon provides a large signal. This system provides a general platform for rapid molecular diagnostics in applications requiring ultrahigh sensitivity, high-degree of miniaturization, and simple sample preparation, and low-cost operation.

Li, Jun↗
NASA NTRS2004

Ultrasensitive Label-free Electronic Chip for DNA Analysis Using Carbon Nanotube Nanoelectrode Arrays

There is a strong need for faster, cheaper, and simpler methods for nucleic acid analysis in today s clinical tests. Nanotechnologies can potentially provide solutions to these requirements by integrating nanomaterials with biofunctionalities. Dramatic improvement in the sensitivity and multiplexing can be achieved through the high-degree miniaturization. Here, we present our study in the development of an ultrasensitive label-free electronic chip for DNA/RNA analysis based on carbon nanotube nanoelectrode arrays. A reliable nanoelectrode array based on vertically aligned multi-walled carbon nanotubes (MWNTs) embedded in a SiO2 matrix is fabricated using a bottom-up approach. Characteristic nanoelectrode behavior is observed with a low-density MWNT nanoelectrode array in measuring both the bulk and surface immobilized redox species. The open-end of MWNTs are found to present similar properties as graphite edge-plane electrodes, with a wide potential window, flexible chemical functionalities, and good biocompatibility. A BRCA1 related oligonucleotide probe with 18 bases is covalently functionalized at the open ends of the MWNTs and specifically hybridized with an oligonucleotide target as well as a PCR amplicon. The guanine bases in the target molecules are employed as the signal moieties for the electrochemical measurements. Ru(bpy)3(2+) mediator is used to further amplify the guanine oxidation signal. This technique has been employed for direct electrochemical detection of label-free PCR amplicon through specific hybridization with the BRCAl probe. The detection limit is estimated to be less than approximately 1000 DNA molecules, approaching the limit of the sensitivity by laser-based fluorescence techniques in DNA microarray. This system provides a general electronic platform for rapid molecular diagnostics in applications requiring ultrahigh sensitivity, high-degree of miniaturization, simple sample preparation, and low- cost operation.

Li, Jun↗
NASA NTRS2007

Super-long Anabiosis of Ancient Microorganisms in Ice and Terrestrial Models for Development of Methods to Search for Life on Mars, Europa and other Planetary Bodies

Successful missions to Mars, Europe and other bodies of the Solar system have created a prerequisite to search for extraterrestrial life. The first attempts of microbial life detection on the Martian surface by the Viking landed missions gave no biological results. Microbiological investigations of the Martian subsurface ground ice layers seem to be more promising. It is well substantiated to consider the Antarctic ice sheet and the Antarctic and Arctic permafrost as terrestrial analogues of Martian habitats. The results of our long-standing microbiological studies of the Antarctic ice would provide the basis for detection of viable microbial cells on Mars. Our microbiological investigations of the deepest and thus most ancient strata of the Antarctic ice sheet for the first time gave evidence for the natural phenomenon of long-term anabiosis (preservation of viability and vitality for millennia years). A combination of classical microbiological methods, epifluorescence microscopy, SEM, TEM, molecular diagnostics, radioisotope labeling and other techniques made it possible for us to obtain convincing proof of the presence of pro- and eukaryotes in the Antarctic ice sheet. In this communication, we will review and discuss some critical issues related to the detection of viable microorganisms in cold terrestrial environments with regard to future searches for microbial life and/or its biological signatures on extraterrestrial objects.

Abyzov, S. S.↗
NASA NTRS2006

Molecular Rayleigh Scattering Diagnostic for Dynamic Temperature, Velocity, and Density Measurements

A molecular Rayleigh scattering technique is developed to measure dynamic gas temperature, velocity, and density in unseeded turbulent flows at sampling rates up to 16 kHz. A high power CW laser beam is focused at a point in an air jet plume and Rayleigh scattered light is collected and spectrally resolved. The spectrum of the light, which contains information about the temperature and velocity of the flow, is analyzed using a Fabry-Perot interferometer. The circular interference fringe pattern is divided into four concentric regions and sampled at 1 and 16 kHz using photon counting electronics. Monitoring the relative change in intensity within each region allows for measurement of gas temperature and velocity. Independently monitoring the total scattered light intensity provides a measure of gas density. A low speed heated jet is used to validate the measurement of temperature fluctuations and an acoustically excited nozzle flow is studied to validate velocity fluctuation measurements. Power spectral density calculations of the property fluctuations, as well as mean and fluctuating quantities are presented. Temperature fluctuation results are compared with constant current anemometry measurements and velocity fluctuation results are compared with constant temperature anemometry measurements at the same locations.

Mielke, Amy R.↗
NASA NTRS1986

C3H2 observations as a diagnostic probe for molecular clouds

Recently the three-membered ring molecule, cyclopropenylidene, C3H2, has been identified in the laboratory and detected in molecular clouds by Thaddeus, Vrtilek and Gottlieb (1985). This molecule is wide-spread throughout the Galaxy and has been detected in 25 separate sources including cold dust clouds, circumstellar envelopes, HII regions, and the spiral arms observed against the Cas supernova remnant. In order to evaluate the potential of C3H2 as a diagnostic probe for molecular clouds, and to attempt to identify the most useful transitions, statistical equilibrium calculations were carried out for the lowest 24 levels of the ortho species and the lowest 10 levels of the para species. Many of the sources observed by Matthews and Irvine (1985) show evidence of being optically thick in the 1(10)-1(01) line. Consequently, the effects of radiative trapping should be incorporated into the equilibrium calculations. This was done using the Large Velocity Gradient approximation for a spherical cloud of uniform density. Some results of the calculations for T(K)=10K are given. Figures are presented which show contours of the logarithm of the ratio of peak line brightness temperatures for ortho-para pairs of lines at similar frequencies. It appears that the widespread nature of C3H2, the relatively large strength of its spectral lines, and their sensitivity to density and molecular abundance combine to make this a useful molecule for probing physical conditions in molecular clouds. The 1(10)-1(01) and 2(20)-2(11) K-band lines may be especially useful in this regard because of the ease with which they are observed and their unusual density-dependent emission/absorption properties.

Avery, L. W.↗
NASA NTRS2005

Molecular Rayleigh Scattering Diagnostic for Measurement of High Frequency Temperature Fluctuations

A novel technique for measurement of high frequency temperature fluctuations in unseeded gas flows using molecular Rayleigh scattering is investigated. The spectrum of laser light scattered from molecules in a gas flow is resolved using a Fabry-Perot interferometer. The width of the spectral peak is broadened by thermal motion of the molecules and hence is related to gas temperature. The interference fringe pattern containing spectral information is divided into four concentric regions using a series of mirrors angled with respect to one another. Light from each of these regions is directed towards photomultiplier tubes and sampled at 10 kHz using photon counting electronics. Monitoring the relative change in intensity within each region allows measurement of gas temperature. Independently monitoring the total scattered intensity provides a measure of gas density. This technique also has the potential to simultaneously measure a single component of flow velocity by monitoring the spectral peak location. Measurements of gas temperature and density are demonstrated using a low speed heated air jet surrounded by an unheated air co-flow. Mean values of temperature and density are shown for radial scans across the jet flow at a fixed axial distance from the jet exit plane. Power spectra of temperature and density fluctuations at several locations in the jet are also shown. The instantaneous measurements have fairly high uncertainty; however, long data records provide highly accurate statistically quantities, which include power spectra. Mean temperatures are compared with thermocouple measurements as well as the temperatures derived from independent density measurements. The accuracy for mean temperature measurements was +/- 7 K.

Mielke, Amy F.↗
NASA NTRS2015

Molecular-Based Optical Diagnostics for Hypersonic Nonequilibrium Flows

This presentation package consists of seven different talks rolled up into one. These talks are all invited orals presentations in a special session at the Aviation 2015 conference and represent contributions that were made to a recent AIAA book that will be published entitled 'Hypersonic Nonequilibrium Flows: Fundamentals and Recent Advances'. Slide 5 lists the individual presentations that will be given during the special session.

Paul Danehy↗