Search NASA⌕ Search

SEARCH · Search NASA

Results for “sequencing test”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Origin of replication discovery for environmentally isolated Pantoea strain enables expression of heterologous proteins, pathways and products

Leveraging predicted origin sequences from a previously characterized groundwater plasmidome, we constructed a barcoded plasmid library to screen for previously unknown origins. Testing this library against a panel of representative bacterial strains led to the identification of 3 previously unknown origins that replicate in gram-negative bacteria not previously associated with these origin sequences. Experimental validation confirmed that a plasmid bearing origin 6911 as the sole origin could replicate with a copy number of 9 (±2) in Pantoea sp. MT58, a fast growing and metal tolerant, environmentally important bacterium. Plasmids based on this new origin were used to express the reporter protein GFP, and non-native metabolite pathways for the natural product indigoidine and the terpenoid compound isoprenol. Functional previously unknown origins of replication in such non-model organisms can expand the toolkit for genetic manipulations of both model and less-studied bacteria.

molecular biology↗
DOE OSTI2024

Extending evolutionary forecasts across bacterial species

Improving evolutionary forecasting requires progressing from studying repeated evolution of a single genotype under identical conditions to formulating broad principles. These principles should enable predictions of how similar species will adapt to similar selective pressures. Evolve-and-resequence experiments with multiple species allow testing forecasts on different biological levels and elucidating the causes for failed predictions. Here, we show that forecasts for adaptation to static culture conditions can be extended to multiple species by testing previous predictions for Pseudomonas syringae and Pseudomonas savastanoi. In addition to sequence divergence, these species differ in their repertoire of biofilm regulatory genes and structural components. Consistent with predictions, both species repeatedly produced biofilm mutants with a wrinkly spreader phenotype. Predominantly, mutations occurred in the wsp operon, with less frequent promoter mutations near uncharacterized diguanylate cyclases. However, mutational patterns differed on the gene level, which was explained by a lack of conservation in relative fitness of mutants between more divergent species. The same mutation was the most frequent for both species suggesting that conserved mutation hotspots can increase parallel evolution. This study shows that evolutionary forecasts can be extended across species, but that differences in the genotype–phenotype–fitness map and mutational biases limit predictability on a detailed molecular level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Inserting a Low-Refractive-Index Dielectric Rear Reflector into PERC Cells: Challenges and Opportunities

One of the simplest and most effective ways to reduce the operating temperature of photovoltaic systems in the field is to reflect unusable, 'sub-bandgap' light with energies below the cell absorber's bandgap energy. In this work, low-refractive index SiO2 nanoparticle films inserted between c-Si wafers and metal electrodes significantly increase the reflectance of sub-bandgap light in fabricated test structures. These films are then integrated into the standard PERC fabrication sequence, revealing that the reflection benefits remains after some processing steps but are lost in certain conditions. The SiO2 nanoparticle films are easily ablated during laser contact opening, but are undesirably etched during post-laser cleaning. After Al metallization, the fully fabricated devices show enhanced sub-bandgap reflection when annealed at moderate temperatures, but energy-dispersive X-ray spectroscopy shows that high-temperature firing causes unwanted Al penetration into the SiO2 nanoparticle film, compromising reflection.

14 SOLAR ENERGY↗
DOE OSTI2022

Long-Term and Low-Level Envelope C2V3 Stimulation by Highly Diverse Virus Isolates Leads to Frequent Development of Broad and Elite Antibody Neutralization in HIV-1-Infected Individuals

A minority of HIV-1-infected patients produce broadly neutralizing antibodies (bNAbs). Identification of viral and host correlates of bNAb production may help develop vaccines. We aimed to characterize the neutralizing response and viral and host-associated factors in Angola, which has one of the oldest, most dynamic, and most diverse HIV-1 epidemics in the world. Three hundred twenty-two HIV-1-infected adults from Angola were included in this retrospective study. Phylogenetic analysis of C2V3C3 env gene sequences was used for virus subtyping. Env-binding antibody reactivity was tested against polypeptides comprising the C2, V3, and C3 regions. Neutralizing-antibody responses were determined against a reference panel of tier 2 Env pseudoviruses in TZM-bl cells; neutralizing epitope specificities were predicted using ClustVis. All subtypes were found, along with untypeable strains and recombinant forms. Notably, 56% of the patients developed cross neutralizing, broadly neutralizing, or elite neutralizing responses. Broad and elite neutralization was associated with longer infection time, subtype C, lower CD4 + T cell counts, higher age, and higher titer of C2V3C3-specific antibodies relative to failure to develop bNAbs. Neutralizing antibodies targeted the V3-glycan supersite in most patients. V3 and C3 regions were significantly less variable in elite neutralizers than in weak neutralizers and nonneutralizers, suggesting an active role of V3C3-directed bNAbs in controlling HIV-1 replication and diversification. In conclusion, prolonged and low-level envelope V3C3 stimulation by highly diverse and ancestral HIV-1 isolates promotes the frequent elicitation of bNAbs. These results provide important clues for the development of an effective HIV-1 vaccine. Studies on neutralization by antibodies and their determinants in HIV-1-infected individuals have mostly been conducted in relatively recent epidemics caused by subtype B and C viruses. Results have suggested that elicitation of broadly neutralizing antibodies (bNAbs) is uncommon. The mechanisms underlying the elicitation of bNAbs are still largely unknown. We performed the first characterization of the plasma neutralizing response in a cohort of HIV-1-infected patients from Angola. Angola is characterized by an old and dynamic epidemic caused by highly diverse HIV-1 variants. Remarkably, more than half of the patients produced bNAbs, mostly targeting the V3-glycan supersite in HIV-1. This was associated with higher age, longer infection time, lower CD4 + T cell counts, subtype C infection, or higher titer of C2V3C3-specific antibodies relative to patients that did not develop bNAbs. These results may help develop the next generation of vaccine candidates for HIV-1.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Modeling Exhaust-Generated Aerodynamic Pressure Loads on Airfield Matting Repair Systems

Airfield matting systems are commonly used for rapid repair of damaged runways to facilitate continuity of critical operations. Under normal service conditions, matting repair systems are subject not only to wheel loads exerted by airfield traffic but also to aerodynamic pressure loads resulting from high-speed, turbulent exhaust plumes produced by jets during taxi and take-off. Matting systems employed by the U.S. Air Force have been tested with respect to wheel loads, but probabilities of failure because of pressure loads produced by jet exhaust have not yet been established. This study presents a numerical approach for preliminary estimation of worst-case matting anchor forces resulting from exhaust-generated pressure loads. Using a two-dimensional computational fluid dynamics model, system behavior is evaluated by means of a parametric study of six system variables, of which the most significant are: (1) distance between engine and matting, (2) depth of cavity openings at matting edges, and (3) engine exhaust velocity. The results demonstrate that matting systems are likely to experience net uplift in typical service scenarios, driven by the combined effects of flow separation and cavity pressurization. Worst-case anchor pull-out forces, computed according to a tributary-area approach, are estimated to fall in the range of 130 lb (581 N) to 979 lb (4,350 N), depending on assumed load-sharing behavior among anchors and the size of the repair site. Field testing of instrumented matting systems during jet taxi and take-off sequences is recommended as the best next step toward understanding system behavior.

Engineering↗
DOE OSTI2022

Tracking and Rejection of Biased Sinusoidal Signals Using Generalized Predictive Controller

Some novel applications require the tracking/rejection of biased sinusoidal reference/distur-bances. According to the internal model principle (IMP), a controller must embed the model of a biased sinusoidal signal to track references and also reject perturbations modeled through the aforementioned signal. However, the design of that kind of controller is not straightforward, especially when they are implemented in digital processors. This paper presents a controller, based on generalized predictive control (GPC), designed for tracking/rejection of biased sinusoidal signals. In general, GPC is based on the prediction of the plant responses through an augmented prediction model. The proposed approach develops an augmented model that predicts the future errors. The prediction model and the control law used in the proposed approach embed the discrete-time model of a biased sinusoidal signal. Thus, the proposed controller can track/reject biased sinusoidal references/disturbances. The predicted errors and the future inputs of the proposed augmented model are used to define the cost function that measures the control performance. An optimization technique was applied to obtain the solution of the cost function, which is the optimal sequence of future model inputs that allows defining the control law. Experimental tests prove that the proposed controller can asymptotically track and reject biased sinusoidal signals.

42 ENGINEERING↗
DOE OSTI2023

Insights from a workplace SARS-CoV-2 specimen collection program, with genomes placed into global sequence phylogeny

In 2020, the Department of Energy established the National Virtual Biotechnology Laboratory (NVBL) to address key challenges associated with COVID-19. As part of that effort, Pacific Northwest National Laboratory (PNNL) established a capability to collect and analyze specimens from employees who self-reported symptoms consistent with the disease. During the spring and fall of 2021, 688 specimens were screened for SARS-CoV-2, with 64 (9.3%) testing positive using reverse-transcriptase quantitative PCR (RT-qPCR). Of these, 36 samples were released for research. All 36 positive samples released for research were sequenced and genotyped. Here, the relationship between patient age and viral load as measured by Ct values was measured and determined to be only weakly significant. Consensus sequences for each sample were placed into a global phylogeny and transmission dynamics were investigated, revealing that the closest relative for many samples was from outside of Washington state, indicating mixing of viral pools within geographic regions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Whole genome resequencing reveals genomic regions associated with thermal adaptation in redband trout

Abstract Adaptation to local environments involves evolution of ecologically important traits and underlying physiological processes. Here, we used low coverage whole‐genome resequencing (lcWGR) on individuals to identify genome regions involved in thermal adaptation in wild redband trout Oncorhynchus mykiss gairdneri , a subspecies of rainbow trout that inhabits ecosystems ranging from cold montane forests to high elevation deserts. This study includes allele frequency‐based analyses for selective sweeps among populations, followed by multiple association tests for specific sets of phenotypes measured under thermal stress (acute and chronic survival/mortality; high or low cardiac performance groups). Depending on the groups in each set of analyses, sequencing reads covered 43%–75% of the genome at ≥15× and each analysis included millions of SNPs across the genome. In tests for selective sweeps among populations, a total of six chromosomal regions were significant. The further association tests for specific phenotypes revealed that the region on chromosome 4 was consistently the most significant and contains the cerk gene (ceramide kinase). This study provides insight into a potential genetic mechanism of local thermal adaptation and suggests c erk may be an important candidate gene. However, further validation of this cerk gene is necessary to determine if the association with cardiac performance results in a functional role to influence thermal performance when exposed to high water temperatures and hypoxic conditions.

Chen, Zhongqi↗
DOE OSTI2023

Impact of sanitizer application on Salmonella mitigation and microbiome shift on diced tomato during washing and storage

Here, this study examined the shift in Salmonella and indigenous microbiota on diced tomato after washing with three different sanitizers and during post-wash cold storage. Roma tomatoes were inoculated with a Salmonella cocktail (initial level ~ 5.6 CFU g –1 ), diced and washed along with uninoculated diced tomato in simulated flume wash water with sanitizers, including 10 mg L –1 free chlorine (FC10), 90 mg L –1 peracetic acid (PA90), PA90 in combination with a proprietary acidified surfactant blend (PS90), and unsanitized control (CK). Salmonella, total mesophilic aerobic bacteria (MAB), and yeast and mold (YM) populations on both inoculated and uninoculated samples were measured before and after washing, and during storage at 4 °C. 16S rRNA amplicon sequencing was also performed to determine the shift in bacterial microbiome. Washing with all tested sanitizers, especially PS90 (> 4 log Salmonella reduction), reduced Salmonella and MAB populations on inoculated diced tomatoes. Additionally, application of sanitizers mitigated Salmonella cross-contamination onto uninoculated samples. PS90 treatment inhibited the proliferation of most dominant bacteria on diced tomatoes during storage, including Erwiniaceae, Curtobacterium, Pantoea, Erwinia and Enterobacterales, which may benefit product quality and safety.

16S rRNA amplicon sequencing↗
DOE OSTI2025

Sequential Stress Identifies Processing Defects in Bifacial Photovoltaic Modules That Limit Durability

Here, we use sequential stress to investigate hurdles to bifacial photovoltaic (PV) module durability from lamination defects. We test mini-modules with glass/glass (G/G) and glass/transparent-backsheet (G/TB) constructions using either ethylene vinyl acetate or polyolefin elastomer (POE) based encapsulants under a modified IEC 63209-2 sequential stress. This sequence includes multiple iterations of damp heat (DH200), full spectrum light exposure (A3), thermal cycling (TC50), and humidity/freeze (HF10). We compare indoor stress with outdoor exposure. Results show similar relative trends in degradation after a year outdoors compared to our first stress cycle. Subsequent stress cycles impart more severe damage than outdoor exposure for the short outdoor duration used here. Edge-pinch lamination defects in G/G mini-modules limit durability causing delamination and cell cracks. Conversely, we observe greater degradation in G/TB mini-modules compared to G/G in the later stages of the stress sequence when the backsheets are directly exposed to UV-containing light. Our results highlight: 1) the utility of sequential stress testing to uncover degradation modes in bifacial PV, 2) implications of using mini-modules for testing PV quality, and 3) the importance of lamination defects that must be avoided to ensure durability as the industry adopts G/G or G/TB packaging.

14 SOLAR ENERGY↗
DOE OSTI2025

Design of Experiments for Dynamic Test Runs in Solvent-Based CO 2 Capture Pilot Plants

Test runs in the pilot plants consume significant resources, and therefore, the learning from test runs should be maximized. Test runs conducted in the pilot plants are often steady state. It takes several hours for reaching steady-state in the pilot plants, and thus, the duration of the test runs needs to be long even for collecting few steady-state data points. On the other hand, a large number of measurements can be collected through dynamic test runs in a short span of time. This paper presents a systematic design of dynamic experiments (DoDEs) for identifiability of model parameters, which is achieved by persistently exciting the inputs signals. A pseudorandom binary sequence (PRBS) is designed as the input signal for DoDE due to its efficiency in obtaining sufficient spectral content. However, due to the long sequence size of the PRBS signal, a Schroeder-phase input signal, which is a multisine signal, is also designed. Tests for both types of signals are run in the Pilot Solvent Test Unit (PSTU) at the National Carbon Capture Center in Wilsonville, Alabama. The transient data are used to solve dynamic data reconciliation and parameter estimation problem. The estimated parameters are found to be not only superior to those estimated from using data collected from hundreds of steady-state test runs in a nonreactive (air–water) system, but the parameters could be estimated by using the dynamic data collected for about 24 h from the pilot plant for the MEA-H 2 O–CO 2 system.

CO2 capture↗
DOE OSTI2021

Generic Multi-Frequency Modelling of Converter-Connected Renewable Energy Generators Considering Frequency and Sequence Couplings

Frequency and sequence couplings can compromise the trustworthiness of multi-frequency models for converter-based systems. There have been effective attempts to address the couplings mainly by linearized averaged models. Only a few studies have been conducted on practical optimization of such models with enormous matrices and experimental results. This paper provides a generic theory for coupling patterns and proposes a multi-frequency modelling method to detect and address only the main couplings in the sequence domain for converter-connected renewable energy generators. The proposed generic model is based on empirical tests using small-signal perturbations and adopting Fourier transform on the switching converter response. The proposed theory and modelling methodology are verified using a 7MVA grid emulator for voltage perturbation tests on a 2MVA photo-voltaic converter. Accordingly, the couplings can exist in more generic forms, including multiples of perturbation and fundamental frequencies. To the best of our knowledge, the patterns with the multiples of the perturbation frequency have been overlooked in the literature. Furthermore, the mirror frequency concept is valid for all coupling patterns and is included in the proposed model. Besides, the proposed patterns and the environment noise levels have been practical criteria for selecting the main couplings.

frequency and sequence couplings↗
DOE OSTI2021

A SSTDR Methodology, Implementations, and Challenges

Sequence time-domain reflectometry (STDR) and spread spectrum time-domain reflectometry (SSTDR) detect, locate, and diagnose faults in live (energized) electrical systems. In this paper, we survey the present SSTDR literature for discussions on theory, algorithms used in its analysis, and its more prominent implementations and applications. Our review includes both scientific litera-ture and selected patents. We also discuss future applications of SSTDR.

14 SOLAR ENERGY↗
DOE OSTI2023

Identification and Characterization of ten Escherichia coli Strains Encoding Novel Shiga Toxin 2 Subtypes, Stx2n as Well as Stx2j, Stx2m, and Stx2o, in the United States

The sharing of genome sequences in online data repositories allows for large scale analyses of specific genes or gene families. This can result in the detection of novel gene subtypes as well as the development of improved detection methods. Here, we used publicly available WGS data to detect a novel Stx subtype, Stx2n in two clinical E. coli strains isolated in the USA. During this process, additional Stx2 subtypes were detected; six Stx2j, one Stx2m strain, and one Stx2o, were all analyzed for variability from the originally described subtypes. Complete genome sequences were assembled from short- or long-read sequencing and analyzed for serotype, and ST types. The WGS data from Stx2n- and Stx2o-producing STEC strains were further analyzed for virulence genes pro-phage analysis and phage insertion sites. Nucleotide and amino acid maximum parsimony trees showed expected clustering of the previously described subtypes and a clear separation of the novel Stx2n subtype. WGS data were used to design OMNI PCR primers for the detection of all known stx1 (283 bp amplicon), stx2 (400 bp amplicon), intimin encoded by eae (221 bp amplicon), and stx2f (438 bp amplicon) subtypes. These primers were tested in three different laboratories, using standard reference strains. An analysis of the complete genome sequence showed variability in serogroup, virulence genes, and ST type, and Stx2 pro-phages showed variability in size, gene composition, and phage insertion sites. The strains with Stx2j, Stx2m, Stx2n, and Stx2o showed toxicity to Vero cells. Stx2j carrying strain, 2012C-4221, was induced when grown with sub-inhibitory concentrations of ciprofloxacin, and toxicity was detected. Taken together, these data highlight the need to reinforce genomic surveillance to identify the emergence of potential new Stx2 or Stx1 variants. The importance of this surveillance has a paramount impact on public health. Per our description in this study, we suggest that 2017C-4317 be designated as the Stx2n type-strain.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Native Top-Down Mass Spectrometry Characterization of Model Integral Membrane Protein Bacteriorhodopsin

Bacteriorhodopsin (bR) from Halobacterium salinarum has been a model system for structural biology and is a structural template for the characterization of membrane G-protein couple receptors (GPCRs) in particular. Here, in this study, wild-type bacteriorhodopsin and two single-residue mutants were characterized by native top-down mass spectrometry (nTD-MS) with Orbitrap-based high-energy collision dissociation (HCD) and electron capture dissociation (ECD). After in-source dissociation ejected the membrane protein from detergent micelles, high-resolution native MS measurement allowed for identification of multiple proteoforms as well as lipid-bound forms. Further top-down MS measurements by HCD produced a large number of product ions for in-depth sequencing and unambiguous localization of post-translational modifications. For the first time, native TD-MS with ECD was used to characterize an integral membrane protein. ECD yielded fragments originating from all helices and loop regions, even accessing a sequence stretch that HCD could not. Combining HCD and ECD fragmentation patterns significantly enhanced the sequence coverage of bR. We propose bR to be a model analyte for testing nTD-MS performance for membrane proteins.

crystal cleavage↗
DOE OSTI2024

Machine learning approaches for influenza A virus risk assessment identifies predictive correlates using ferret model in vivo data

In vivo assessments of influenza A virus (IAV) pathogenicity and transmissibility in ferrets represent a crucial component of many pandemic risk assessment rubrics, but few systematic efforts to identify which data from in vivo experimentation are most useful for predicting pathogenesis and transmission outcomes have been conducted. To this aim, we aggregated viral and molecular data from 125 contemporary IAV (H1, H2, H3, H5, H7, and H9 subtypes) evaluated in ferrets under a consistent protocol. Three overarching predictive classification outcomes (lethality, morbidity, transmissibility) were constructed using machine learning (ML) techniques, employing datasets emphasizing virological and clinical parameters from inoculated ferrets, limited to viral sequence-based information, or combining both data types. Among 11 different ML algorithms tested and assessed, gradient boosting machines and random forest algorithms yielded the highest performance, with models for lethality and transmission consistently better performing than models predicting morbidity. Comparisons of feature selection among models was performed, and highest performing models were validated with results from external risk assessment studies. Our findings show that ML algorithms can be used to summarize complex in vivo experimental work into succinct summaries that inform and enhance risk assessment criteria for pandemic preparedness that take in vivo data into account.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts

Abstract Summary Genomics has become an essential technology for surveilling emerging infectious disease outbreaks. A range of technologies and strategies for pathogen genome enrichment and sequencing are being used by laboratories worldwide, together with different and sometimes ad hoc, analytical procedures for generating genome sequences. A fully integrated analytical process for raw sequence to consensus genome determination, suited to outbreaks such as the ongoing COVID-19 pandemic, is critical to provide a solid genomic basis for epidemiological analyses and well-informed decision making. We have developed a web-based platform and integrated bioinformatic workflows that help to provide consistent high-quality analysis of SARS-CoV-2 sequencing data generated with either the Illumina or Oxford Nanopore Technologies (ONT). Using an intuitive web-based interface, this workflow automates data quality control, SARS-CoV-2 reference-based genome variant and consensus calling, lineage determination and provides the ability to submit the consensus sequence and necessary metadata to GenBank, GISAID and INSDC raw data repositories. We tested workflow usability using real world data and validated the accuracy of variant and lineage analysis using several test datasets, and further performed detailed comparisons with results from the COVID-19 Galaxy Project workflow. Our analyses indicate that EC-19 workflows generate high-quality SARS-CoV-2 genomes. Finally, we share a perspective on patterns and impact observed with Illumina versus ONT technologies on workflow congruence and differences. Availability and implementation https://edge-covid19.edgebioinformatics.org, and https://github.com/LANL-Bioinformatics/EDGE/tree/SARS-CoV2. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

RNA‐Seq analysis revealed the molecular mechanisms of photobiomodulation effect on human fibroblasts

Abstract Background The photobiomodulation (PBM) effect has been applied to various clinical therapy for a long time. However, the mechanism related to the PBM effect in terms of wavelengths has been lack of in‐depth study, except that ultraviolet radiation has attracted much attention due to its strong cell‐killing effect. Purpose To clarify the principle behind PBM and the main mechanism of improvement. Methods To carry on this study, we created light equipment using three LED chips, which emit 390 nm ultraviolet radiation, 415 nm blue light and 660 nm red light, respectively. We choose human fibroblasts (HF) to be irradiated by three different wavelengths for PBM test. In this study, we used cell counting kit (CCK‐8) test to show the cell proliferation roughly and reported on a systematic RNA sequencing (RNA‐seq) analysis at transcriptional expression levels from HF, which accepted PBM of different wavelengths of light. Results We found that 415 nm blue light inhibited cell proliferation and 660 nm red light stimulated cell proliferation while 390 nm ultraviolet radiation has little influence on cell proliferation. Furthermore, RNA‐seq results showed that CSF1R, PPP3CC, ITGAL, ITGAM, IL2RB, and several other differentially expressed genes (DEGs) are involved in the cell proliferation. Relative DEGs values for matrix metalloproteinases (MMPs) gene family have shown a great difference in blue and red light radiation especially on MMP25, MMP9, MMP21, and MMP13. Conclusion Taken together, the results provide a valuable resource to describe the variation of HFs under PBM of different light at gene level.

Li, Wenqi↗