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All sources NASA NTRS DOE OSTI

DOE OSTI2021

Counting mRNA copies in intact bacterial cells by fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH)

A method for measuring mRNA copies in intact bacterial cells by fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH) is presented. Unlike conventional single molecule FISH, where the presence of a transcript is determined by fluorescence intensity, fliFISH relies on On-Off duty cycles of photo-switching dyes to set a predetermined threshold for distinguishing true signals from background noise. The method provides a quantitative approach for detecting and counting true mRNA copies and rejecting false signals with high accuracy.

Hu, Dehong↗

NASA NTRS2010

Evaluation of an ATP Assay to Quantify Bacterial Attachment to Surfaces in Reduced Gravity

Aim: To develop an assay to quantify the biomass of attached cells and biofilm formed on wetted surfaces in variable-gravity environments. Methods and Results: Liquid cultures of Pseudomonas aeruginosa were exposed to 30-35 brief cycles of hypergravity (< 2-g) followed by free fall (i.e., reduced gravity) equivalent to either lunar-g (i.e., 0.17 normal Earth gravity) or micro-g (i.e., < 0.001 normal Earth gravity) in an aircraft flying a series of parabolas. Over the course of two days of parabolic flight testing, 504 polymer or metal coupons were exposed to a stationary-phase population of P. aeruginosa strain ERC1 at a concentration of 1.0 x 10(exp 5) cells per milliliter. After the final parabola on each flight test day, half of the material coupon samples were treated with either 400 micro-g/L ionic silver fluoride (microgravity-exposed cultures) or 1% formalin (lunar-gravity-exposed cultures). The remaining sample coupons from each flight test day were not treated with a fixative. All samples were returned to the laboratory for analysis within 2 hours of landing, and all biochemical assays were completed within 8 hours of exposure to variable gravity. The intracellular ATP luminescent assay accurately reflected cell physiology compared to both cultivation-based and direct-count microscopy analyses. Cells exposed to variable gravity had more than twice as much intracellular ATP as control cells exposed only to normal Earth gravity.

Birmele, Michele N.↗

NASA NTRS2003

Ribbon Synaptic Plasticity in Gravity Sensors of Rats Flown on Neurolab

Previous spaceflight experiments (Space Life Sciences-1 and -2 (SLS-1 and SLS-2)) first demonstrated the extraordinary ability of gravity sensor hair cells to change the number, kind, and distribution of connections (synapses) they make to other cells while in weightlessness. The number of synapses in hair cells in one part of the inner ear (the utricle) was markedly elevated on flight day 13 (FD13) of SLS-2. Unanswered questions, however, were whether these increases in synapses occur rapidly and whether they remain stable in weightlessness. The answers have implications for long-duration human space travel. If gravity sensors can adapt quickly, crews may be able to move easily between different gravity levels, since the sensors will adapt rapidly to weightlessness on the spacecraft and then back to Earth's gravity when the mission ends. This ability to adapt is also important for recovery from balance disorders. To further our understanding of this adaptive potential (a property called neuronal synaptic plasticity), the present Neurolab research was undertaken. Our experiment examined whether: (a) increases in synapses would remain stable throughout the flight, (b) changes in the number of synapses were uniform across different portions of the gravity sensors (the utricle and saccule), and (c) synaptic changes were similar for the different types of hair cells (Type I and Type II). Utricular and saccular maculae (the gravity-sensing portions of the inner ear) were collected in flight from rats on FD2 and FD14. Samples were also collected from control rats on the ground. Tissues were prepared for ultrastructural study. Hair cells and their ribbon synapses were examined in a transmission electron microscope. Synapses were counted in all hair cells in 50 consecutive sections that crossed the striolar zone. Results indicate that utricular hair cell synapses initially increased significantly in number in both types of hair cells by FD2. Counts declined by FD14, but the mean number of synapses in utricular Type II cells remained significantly higher than in the ground control rats. For saccular samples, synaptic number in Type I and Type II cells declined on FD2, but returned to near-baseline values by FD14. These findings indicate that: (a) synaptic plasticity occurs rapidly in weightlessness, and (b) synaptic changes are not identical for the two types of hair cells or for the two maculae.

Ross, Muriel D.↗

DOE OSTI2023

flifish

Identifying single molecules from fluorescence images obtained by a camera and obtain their location and intensity has many applications. We have developed an efficient mathematical algorithm for this task and translate it into computer software. Our algorithm are fast, stable and accurate comparing other programs to do the similar task. We have used our software in several scientific research areas, such as tracking receptors in live cells, super resolution fluorescence microscopy, and counting mRNA copies in cells.

Hu, Dehong↗

DOE OSTI2022

Influence of Vane Trailing Edge Flow on the Formation of Cavity Cells and Rim Sealing

Abstract Hot gas ingestion into the turbine rim seal cavity is an important concern for engine designers. To prevent ingestion, rim seals use high-pressure purge flow; however, the penalty is that excessive use of the purge flow decreases engine thermal efficiency. In this paper, a one-stage turbine operating at engine-representative conditions was used to study the effect of steady and time-resolved under-platform cavity temperatures and pressures across a range of coolant flowrates in the presence of vane trailing edge (VTE) flow. This study correlates time-resolved pressure with time-resolved temperature to identify primary frequencies driving ingestion. At certain flowrates, the time-resolved pressures are out of phase with the temperatures, indicating ingestion. Measurements from high-frequency response pressure sensors in the rim seal and vane platform were also used to determine rotational speed and quantity of large-scale structures (cells). In a parallel effort, a computational model using Unsteady Reynolds-averaged Navier–Stokes (URANS) was applied to determine swirl ratio in the rim seal cavity and time-resolved rim sealing effectiveness. The experimental results confirm that at low purge flowrates, the VTE flow influences the unsteady flow field by decreasing pressure unsteadiness in the rim seal cavity. Results show an increase in purge flow increases the number of unsteady large-scale structures in the rim seal and decreases their rotational speed. However, VTE flow was shown to not significantly change the cell speed and count in the rim seal. Simulations point to the importance of the large-scale cell structures in influencing rim sealing unsteadiness, which is not captured in current rim sealing predictive models.

Engineering↗

DOE OSTI2019

HeadCount (Automated & Anonymous In-Vehicle Occupancy Detection and Counting) [SWR 19-14]

The HeadCount software is filling a transportation information gap by counting how many people take each rideshare ride. The transportation industry is undergoing rapid transformation. Personally-driven trips via privately owned vehicles are being replaced by commercial services such as ride-hailing and car-sharing. In the same time, municipalities have increasingly expressed interest in the movement of people, rather than just vehicles. However, there is a lack of technology to collect vehicle occupancy data to quantify the movement of people at a large scale. Existing means of counting vehicle occupants have proven insufficient for a variety of reasons. Most notably, these include complicated installations (outfitted seatbelt sensors with dedicated wiring), reliance on technology adoption (cell phone signal counting), driver participation (manual survey entry), etc. These limitations have hindered all interested stakeholders: vehicle fleet owners continue to be unaware of the number of serviced customers, researchers still rely on hand written survey information, and municipalities have no reliable technology to enforce occupancy-based measures (HOV lanes, passenger-based tolls, etc.). Therefore, an automated in-vehicle occupancy detection and counting system was designed to collect vehicle occupancy data with minimal human effort involved. This technology is the first of its kind with low cost, simple installation, and high accuracy. In fact, the device correctly identified the number of occupants in 99.7% of cases. Occupancy detection relates to many applications, ranging from energy intensity quantification and incentivizing high occupancy vehicle to fleet management and optimization.

Moniot, Matthew↗

NASA NTRS1977

Blood volume changes

Red cell mass measurements on Skylab crewmembers revealed a statistically significant decrease in circulating red cells. Low reticulocyte counts at crewmember recovery indicated increased splenic removal of reticulum or decreased bone marrow production rates. After the initial loss there is at least a 30-day delay before red cell mass begins to reconstitute itself.

Johnson, P. C.↗

DOE OSTI2018

Quantifying Platelet Margination in Diabetic Blood Flow

According to this article, patients with type 2 diabetes mellitus (T2DM) develop thrombotic abnormalities strongly associated with cardiovascular diseases. In addition to the changes of numerous coagulation factors such as elevated levels of thrombin and fibrinogen, the abnormal rheological effects of red blood cells (RBCs) and platelets flowing in blood are crucial in platelet adhesion and thrombus formation in T2DM. An important process contributing to the latter is the platelet margination. We employ the dissipative particle dynamics method to seamlessly model cells, plasma, and vessel walls. We perform a systematic study on RBC and platelet transport in cylindrical vessels by considering different cell shapes, sizes, and RBC deformabilities in healthy and T2DM blood, as well as variable flowrates and hematocrit. In particular, we use cellular-level RBC and platelet models with parameters derived from patient-specific data and present a sensitivity study. We find T2DM RBCs, which are less deformable compared to normal RBCs, lower the transport of platelets toward the vessel walls, whereas platelets with higher mean volume (often observed in T2DM) lead to enhanced margination. Furthermore, increasing the flowrate or hematocrit enhances platelet margination. We also investigated the effect of platelet shape and observed a nonmonotonic variation with the highest near-wall concentration corresponding to platelets with a moderate aspect ratio of 0.38. We examine the role of white blood cells (WBCs), whose count is increased notably in T2DM patients. We find that WBC rolling or WBC adhesion tends to decrease platelet margination due to hydrodynamic effects. To the best of our knowledge, such simulations of blood including all blood cells have not been performed before, and our quantitative findings can help separate the effects of hydrodynamic interactions from adhesive interactions and potentially shed light on the associated pathological processes in T2DM such as increased inflammatory response, platelet activation and adhesion, and ultimately thrombus formation.

Biophysics↗

NASA NTRS2000

Changes in ribbon synapses and rough endoplasmic reticulum of rat utricular macular hair cells in weightlessness

This study combined ultrastructural and statistical methods to learn the effects of weightlessness on rat utricular maculae. A principle aim was to determine whether weightlessness chiefly affects ribbon synapses of type II cells, since the cells communicate predominantly with branches of primary vestibular afferent endings. Maculae were microdissected from flight and ground control rat inner ears collected on day 13 of a 14-day spaceflight (F13), landing day (R0) and day 14 postflight (R14) and were prepared for ultrastructural study. Ribbon synapses were counted in hair cells examined in a Zeiss 902 transmission electron microscope. Significance of synaptic mean differences was determined for all hair cells contained within 100 section series, and for a subset of complete hair cells, using SuperANOVA software. The synaptic mean for all type II hair cells of F13 flight rats increased by 100%, and that for complete cells by 200%. Type I cells were less affected, with synaptic mean differences statistically insignificant in complete cells. Synapse deletion began within 8 h upon return to Earth. Additionally, hair cell laminated rough endoplasmic reticulum of flight rats was reversibly disorganized on R0. Results support the thesis that synapses in type II hair cells are uniquely affected by altered gravity. Type II hair cells may be chiefly sensors of gravitational and type I cells of translational linear accelerations.

short duration↗

NASA NTRS2012

Plasticity of Neurovestibular Systems Following Micro- and Hyper-Gravity Exposure and Readaptation to Earth's 1G

The gravity-sensing organs sense the sum of inertial force due to head translation and head orientation relative to gravity. Normally gravity is constant, and yet the neural sensors show remarkable plasticity. When the force of gravity changes, such as in spaceflight or during centrifugation, the neurovestibular system responds by regulating its neural output, and this response is similar for the vertebrate utricular nerve afferents and for the statocyst hair cell in invertebrates. First, we examine the response of utricular afferents in toadfish following exposure to G on two orbital missions (STS-90 and 95). Within the first day after landing, magnitude of neural response to an applied acceleration was significantly elevated, and re-adaptation back to control values occurred within approximately 30 hours. Time course of return to normal approximately parallels the decrease in vestibular disorientation in astronauts following return. Next, we use well-controlled hyper-G experiments in the vertebrate model to address: If G leads to adaptation and subsequent re-adaptation neural processes, does the transfer from 1G to hyper-G impart the opposite effects and do the effects accompanying transfer from the hyper-G back to the 1G conditions resemble as an analog the transfer from 1G to the microG Results show a biphasic pattern in reaction to 3G exposures: an initial sensitivity up-regulation (3- and 4-day) followed by a significant decrease after longer exposure. Return to control values is on the order of 4-8 days. Utricular sensitivity is strongly regulated up or down by gravity load and the duration of exposure. Interestingly, we found no correlation of response and hair cell synaptic body counts despite the large gain difference between 4- and 16-Day subjects. Lastly, we examine responses of statocyst receptors in land snail following exposure to G on two unmanned Russian Orbital missions (Foton M-2 and -3). Here, we have the ability to measure the output directly from the hair cells. Similar to afferents in vertebrates the hair cells increased their response sensitivity to vestibular stimulation. Two major pieces of information are needed: the precise vertebrate hair cell response to altered gravity and the impact of longer duration exposures on sensory plasticity.

Boyle, Richard D.↗

NASA NTRS2006

An Improved Flow Cytometry Method For Precise Quantitation Of Natural-Killer Cell Activity

The ability to assess NK cell cytotoxicity using flow cytometry has been previously described and can serve as a powerful tool to evaluate effector immune function in the clinical setting. Previous methods used membrane permeable dyes to identify target cells. The use of these dyes requires great care to achieve optimal staining and results in a broad spectral emission that can make multicolor cytometry difficult. Previous methods have also used negative staining (the elimination of target cells) to identify effector cells. This makes a precise quantitation of effector NK cells impossible due to the interfering presence of T and B lymphocytes, and the data highly subjective to the variable levels of NK cells normally found in human peripheral blood. In this study an improved version of the standard flow cytometry assay for NK activity is described that has several advantages of previous methods. Fluorescent antibody staining (CD45FITC) is used to positively identify target cells in place of membranepermeable dyes. Fluorescent antibody staining of target cells is less labor intensive and more easily reproducible than membrane dyes. NK cells (true effector lymphocytes) are also positively identified by fluorescent antibody staining (CD56PE) allowing a simultaneous absolute count assessment of both NK cells and target cells. Dead cells are identified by membrane disruption using the DNA intercalating dye PI. Using this method, an exact NK:target ratio may be determined for each assessment, including quantitation of NK target complexes. Backimmunoscatter gating may be used to track live vs. dead Target cells via scatter properties. If desired, NK activity may then be normalized to standardized ratios for clinical comparisons between patients, making the determination of PBMC counts or NK cell percentages prior to testing unnecessary. This method provides an exact cytometric determination of NK activity that highly reproducible and may be suitable for routine use in the clinical setting.

Crucian, Brian↗

DOE OSTI2018

Alleviation of A disintegrin and metalloprotease 10 (ADAM10) on thromboangiitis obliterans involves the HMGB1/RAGE/ NF-κB pathway

Highlights: • TAO rats displayed higher whole blood viscosity and blood platelet count. • TAO rats had structural damages of vascular smooth muscle and endothelial cells. • ADAM treatment alleviated the symptoms of TAO rats in a dose-dependent pattern. • HMGB1, RAGE and NF-κB increased in TAO rats in both mRNA and protein level. • HMGB1, RAGE and NF-κB decreased by ADAM10 treatment in both mRNA and protein level. Thromboangiitis obliterans (TAO), also known as Buerger's disease, is a nonatherosclerotic inflammatory disease that influences medium- and small-sized blood vessels of extremities. However, mechanisms underlying TAO are still unclear. As a mediator associated with inflammation, A disintegrin and metalloprotease 10 (ADAM10) was hypothesized to play inhibitory roles in the development of TAO. Thus, the objective of this study is to investigate the effects of ADAM10 in a sodium laurate-induced TAO rat model and elucidate underlying mechanisms. Male Wistar rats were randomly divided into four groups (n = 6) for treatment: sham-operated (SHAM), TAO model (TAO), ADAM10 low dose injection (3 mg/kg; ADAM10-LD) and ADAM10 high dose injection (6 mg/kg; ADAM10-HD). After 14-day treatment, color Doppler ultrasound and hematology analysis indicated TAO rats displayed higher whole blood viscosity and blood platelet count compared with those in the SHAM group. Histologic evaluation and transmission electron microscopy revealed that the ultrastructural damages of vascular smooth muscle and endothelial cells were observed in TAO rats, such as fractured endoplasmic reticulum, decreased cell counts, and fibrillation. On the other hand, the typical signs and symptoms of TAO rats were significantly alleviated via ADAM10 treatment with a dose-dependent pattern. Real-time PCR and western blot results revealed that the expression of high-mobility-group box 1 (HMGB1), receptor for advanced glycation end-products (RAGE) and nuclear factor-kappa B (NF-κB) increased in TAO rats whereas decreased by ADAM10 treatment in both mRNA and protein levels. In conclusion, the results suggest ADAM10 alleviates symptoms of sodium laurate-induced TAO in rats via the RAGE/NF-κB signaling pathway and provides insight into the molecular basis and a potential therapeutic strategy for TAO.

60 APPLIED LIFE SCIENCES↗

NASA NTRS2001

Neocytolysis on descent from altitude: a newly recognized mechanism for the control of red cell mass

BACKGROUND: Studies of space-flight anemia have uncovered a physiologic process, neocytolysis, by which young red blood cells are selectively hemolyzed, allowing rapid adaptation when red cell mass is excessive for a new environment. OBJECTIVES: 1) To confirm that neocytolysis occurs in another situation of acute plethora-when high-altitude dwellers with polycythemia descend to sea level; and 2) to clarify the role of erythropoietin suppression. DESIGN: Prospective observational and interventional study. SETTING: Cerro de Pasco (4380 m) and Lima (sea level), Peru. PARTICIPANTS: Nine volunteers with polycythemia. INTERVENTIONS: Volunteers were transported to sea level; three received low-dose erythropoietin. MEASUREMENTS: Changes in red cell mass, hematocrit, hemoglobin concentration, reticulocyte count, ferritin level, serum erythropoietin, and enrichment of administered(13)C in heme. RESULTS: In six participants, red cell mass decreased by 7% to 10% within a few days of descent; this decrease was mirrored by a rapid increase in serum ferritin level. Reticulocyte production did not decrease, a finding that establishes a hemolytic mechanism.(13)C changes in circulating heme were consistent with hemolysis of young cells. Erythropoietin was suppressed, and administration of exogenous erythropoietin prevented the changes in red cell mass, serum ferritin level, and(13)C-heme. CONCLUSIONS: Neocytolysis and the role of erythropoietin are confirmed in persons with polycythemia who descend from high altitude. This may have implications that extend beyond space and altitude medicine to renal disease and other situations of erythropoietin suppression, hemolysis, and polycythemia.

Non-NASA Center↗

DOE OSTI2024

Single-nuclei transcriptome analysis of channel catfish spleen provides insight into the immunome of an aquaculture-relevant species

The catfish industry is the largest sector of U.S. aquaculture production. Given its role in food production, the catfish immune response to industry-relevant pathogens has been extensively studied and has provided crucial information on innate and adaptive immune function during disease progression. To further examine the channel catfish immune system, we performed single-cell RNA sequencing on nuclei isolated from whole spleens, a major lymphoid organ in teleost fish. Libraries were prepared using the 10X Genomics Chromium X with the Next GEM Single Cell 3’ reagents and sequenced on an Illumina sequencer. Each demultiplexed sample was aligned to the Coco_2.0 channel catfish reference assembly, filtered, and counted to generate feature-barcode matrices. From whole spleen samples, outputs were analyzed both individually and as an integrated dataset. The three splenic transcriptome libraries generated an average of 278,717,872 reads from a mean 8,157 cells. The integrated data included 19,613 cells, counts for 20,121 genes, with a median 665 genes/cell. Cluster analysis of all cells identified 17 clusters which were classified as erythroid, hematopoietic stem cells, B cells, T cells, myeloid cells, and endothelial cells. Subcluster analysis was carried out on the immune cell populations. Here, distinct subclusters such as immature B cells, mature B cells, plasma cells, γδ T cells, dendritic cells, and macrophages were further identified. Differential gene expression analyses allowed for the identification of the most highly expressed genes for each cluster and subcluster. This dataset is a rich cellular gene expression resource for investigation of the channel catfish and teleost splenic immunome.

Science & Technology - Other Topics↗

DOE OSTI2017

Analysis of the Temporal Response of Coupled Asymmetrical Zero-Power Subcritical Bare Metal Reactor Systems

The behavior of symmetrical coupled-core systems has been extensively studied, yet there is a dearth of research on asymmetrical systems due to the increased complexity of the analysis of such systems. In this research, the multipoint kinetics method is applied to asymmetrical zeropower, subcritical, bare metal reactor systems. Existing research on asymmetrical reactor systems assumes symmetry in the neutronic coupling; however, it will be shown that this cannot always be assumed. Deep subcriticality adds another layer of complexity and requires modification of the multipoint kinetics equations to account for the effect of the external neutron source. A modified set of multipoint kinetics equations is derived with this in mind. Subsequently, the Rossi-alpha equations are derived for a two-region asymmetrical reactor system. The predictive capabilities of the radiation transport code MCNP6 for neutron noise experiments are shown in a comparison to the results of a series of Rossi-alpha measurements performed by J. Mihalczo utilizing a coupled set of symmetrical bare highly-enriched uranium (HEU) cylinders. The ptrac option within MCNP6 can generate time-tagged counts in a cell (list-mode data). The list-mode data can then be processed similarly to measured data to obtain values for system parameters such as the dual prompt neutron decay constants observable in a coupled system. The results from the ptrac simulations agree well with the historical measured values. A series of case studies are conducted to study the effects of geometrical asymmetry in the coupling between two bare metal HEU cylinders. While the coupling behavior of symmetrical systems has been reported on extensively, that of asymmetrical systems remains sparse. In particular, it appears that there has been no previous research in obtaining the coupling time constants for asymmetrically-coupled systems. The difficulty in observing such systems is due in part to the inability to determine the individual coupling coefficients from measurement: unlike the symmetrical cases, only the product of the values can be obtained. A method is proposed utilizing MCNP6 tally ratios to separate the coupling coefficients for such systems. This work provides insight into the behavior of asymmetrically-coupled systems as the separation distance between the two cores is changed and also as the asymmetry is increased. As the asymmetry increases, both the slower and the faster observable prompt neutron decay constants increase in magnitude. The coupling time constants are determined from the measured decay constants. As the separation distance increases, both coupling coefficients decrease as expected. Based on these findings, an effective computational method utilizing MCNP6 and the Rossialpha technique can be applied to the prediction of asymmetrical coupled system measurements.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2021

HyLiPoD: Parallel Particle Advection via a Hybrid of Lifeline Scheduling and Parallelization-Over-Data

Performance characteristics of parallel particle advection algorithms can vary greatly based on workload.With this short paper, we build a new algorithm based on results from a previous bake-off study which evaluated the performance of four algorithms on a variety of workloads. Our algorithm, called HyLiPoD, is a ''meta-algorithm,'' i.e., it considers the desired workload to choose from existing algorithms to maximize performance. To demonstrate HyliPoD's benefit, we analyze results from 162 tests including concurrencies of up to 8192 cores, meshes as large as 34 billion cells, and particle counts as large as 300 million. Our findings demonstrate that HyLiPoD's adaptive approach allows it to match the best performance of existing algorithms across diverse workloads.

high performance computing↗

NASA NTRS1990

Experiment K-6-16. Morphological examination of rat testes. The effect of Cosmos 1887 flight on spermatogonial population and testosterone level in rat testes

Testes from rats flown on Cosmos 1887 for twelve and a half days were compared to basal control, synchronous control and vivarium maintained rats. When the mean weights of flight testes, normalized for weight/100 gms, were compared to the vivarium controls they were 6.7 percent lighter. Although the flight testes were lighter than the synchronous, the difference is not significant. Counts of spermatogonial cells from 5 animals in each group revealed a 4 percent decrease in flight compared to vivarium controls. In both cases the t-Test significance was less than 0.02. The serum testosterone levels of all animals (flight, synchronous and vivarium) were significantly below the basal controls.

Philpott, D. E.↗

NASA NTRS1989

A quasi-passive CMOS pipeline D/A converter

A novel pipeline digital-to-analog converter configuration, based on switched-capacitor techniques, is described. An n-bit D/A conversion can be implemented by cascading n + 1 unit cells. The device count of the circuit increases linearly, not exponentially, with the conversion accuracy. The new configuration can be pipelined. Hence, the conversion rate can be increased without requiring a higher clock rate. An experimental 10-bit DAC prototype has been fabricated using a 3-micron CMOS process. The results show that high-speed, high-accuracy, and low-power operation can be achieved without special process or postprocess trimming.

Wang, Fong-Jim↗