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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Multiplexed Knockouts in the Model Diatom Phaeodactylum by Episomal Delivery of a Selectable Cas9

Marine diatoms are eukaryotic microalgae that play significant ecological and biogeochemical roles in oceans. They also have significant potential as organismal platforms for exploitation to address biotechnological and industrial goals. In order to address both modes of research, sophisticated molecular and genetic tools are required. We presented here new and improved methodologies for introducing CRISPRCas9 to the model diatom Phaeodactylum tricornutum cells and a streamlined protocol for genotyping mutant cell lines with previously unknown phenotypes. First, bacterialconjugation was optimized for the delivery of Cas9 by transcriptionally fusing Cas9 to a selectable marker by the 2A peptide. An episome cloning strategy using both negative and positive selection was developed to streamline CRISPR-episome assembly. Next, cell line picking and genotyping strategies, that utilize manual sequencing curation, TIDE sequencing analysis, and a T7 endonuclease assay, were developed to shorten the time required to generate mutants. Following this new experimental pipeline, both singlegene and two-gene knockout cell lines were generated at mutagenesis efficiencies of 48% and 25%, respectively. Lastly, a protocol for precise gene insertions via CRISPRCas9 targeting was developed using particle-bombardment transformation methods. Overall, the novel Cas9 episome design and improved genotyping methods presented here allow for quick and easy genotyping and isolation of Phaeodactylum mutant cell lines (less than 3 weeks) without relying on a known phenotype to screen for mutants.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1972

Tornado occurrences related to overshooting cloud-top heights as determined from ATS pictures

A sequence of ATS 3 pictures including the development history of large anvil clouds near Salina, Kansas was enlarged by NASA into 8X negatives which were used to obtain the best quality prints by mixing scan lines in 8 steps to minimize checker-board patterns. These images resulted in the best possible resolution, permitting use to compute the heights of overshooting tops above environmental anvil levels based on cloud shadow relationships along with the techniques of lunar topographic mapping. Of 39 heights computed, 6 were within 15 miles of reported positions of 3 tornadoes. It was found that the tornado proximity tops were mostly less than 5000 ft, with one exception of 7000 ft, suggesting that tornadoes are most likely to occur when overshooting height decreases. In order to simulate surface vortices induced by cloud-scale rotation and updraft fields, a laboratory model was constructed. The model experiment has shown that the rotation or updraft field induces a surface vortex but their combination does prevent the formation of the surface vortex. This research leads to a conclusion that the determination of the cloud-top topography and its time variation is of extreme importance in predicting severe local storms for a period of 0 to 6 hours.

Fujita, T. T.↗
NASA NTRS2014

Postlaunch Performance of the Suomi National Polar-Orbiting Partnership Ozone Mapping and Profiler Suite (OMPS) Nadir Sensors

The prelaunch specifications for nadir sensors of the Ozone Mapping and Profiler Suite (OMPS) were designed to ensure that measurements from them could be used to retrieve total column ozone and nadir ozone profile information both for operational use and for use in long-term ozone data records. In this paper, we will show results from our extensive analysis of the performance of the nadir mapper (NM) and nadir profiler (NP) sensors during the first year and a half of OMPS nadir operations. In most cases, we determined that both sensors meet or exceed their prelaunch specifications. Normalized radiance (radiance divided by irradiance) measurements have been determined to be well within their 2% specification for both sensors. In the case of stray light, the NM sensor is within its 2% specification for all but the shortest wavelengths, while the NP sensor is within its 2% specification for all but the longest wavelengths. Artifacts that negatively impacted the sensor calibration due to diffuser features were reduced to less than 1% through changes made in the solar calibration sequence. Preliminary analysis of the disagreement between measurements made by the NM and NP sensors in the region where their wavelengths overlap indicates that it is due to shifts in the shared dichroic filter after launch and that it can be corrected. In general, our analysis indicates that both the NM and NP sensors are performing well, that they are stable, and that any deviations from nominal performance can be well characterized and corrected.

ozone↗
DOE OSTI2022

Non-target RNA depletion strategy to improve sensitivity of next-generation sequencing for the detection of RNA viruses in poultry

PCR-based assays have become the benchmark for detecting pathogens of poultry and other livestock; however, these techniques are limited in their ability to detect multiple infecting agents, provide limited genetic information on the pathogen, and, for RNA viruses, must be reviewed frequently to assure high sensitivity and specificity. In contrast, untargeted, high-throughput sequencing can rapidly detect all infecting agents in a sample while providing genomic sequence information to allow more in-depth characterization of viruses. Although next-generation sequencing (NGS) offers many advantages, one of its primary limitations is low sensitivity to pathogens given the abundance of host and other non-target sequences in sequencing libraries. We explored methods for improving the sensitivity of NGS to detect respiratory and enteric viruses in poultry from RNA extracts of swab samples. We employed commercial and custom-designed negative enrichment strategies to selectively deplete the most abundant rRNA reads from the host and non-target bacteria; host RNA was diminished from up to 40% of total reads to as low as 3%, and the total number of reads assigned to abundant bacterial classes were reduced greatly. Our treatment resulted in up to a 700-fold increase in the number of viral reads, detection of a greater number of viral agents, and higher average genome coverage for pathogens. Depletion assays added only 2 h to the NGS library preparation workflow. Custom depletion probe design offered significant cost savings (US$7–12 per sample) compared to commercial kits (US$30–50 per sample).

Parris, D. Joshua↗
DOE OSTI2024

EHR-BERT: A BERT-based model for effective anomaly detection in electronic health records

Objective: Physicians and clinicians rely on data contained in electronic health records (EHRs), as recorded by health information technology (HIT), to make informed decisions about their patients. The reliability of HIT systems in this regard is critical to patient safety. Consequently, better tools are needed to monitor the performance of HIT systems for potential hazards that could compromise the collected EHRs, which in turn could affect patient safety. In this paper, we propose a new framework for detecting anomalies in EHRs using sequence of clinical events. This new framework, EHR-Bidirectional Encoder Representations from Transformers (BERT), is motivated by the gaps in the existing deep-learning related methods, including high false negatives, sub-optimal accuracy, higher computational cost, and the risk of information loss. EHR-BERT is an innovative framework rooted in the BERT architecture, meticulously tailored to navigate the hurdles in the contemporary BERT method; thus, enhancing anomaly detection in EHRs for healthcare applications.Methods: The EHR-BERT framework was designed using the Sequential Masked Token Prediction (SMTP) method. This approach treats EHRs as natural language sentences and iteratively masks input tokens during both training and prediction stages. This method facilitates the learning of EHR sequence patterns in both directions for each event and identifies anomalies based on deviations from the normal execution models trained on EHR sequences.Results: Extensive experiments on large EHR datasets across various medical domains demonstrate that EHR-BERT markedly improves upon existing models. It significantly reduces the number of false positives and enhances the detection rate, thus bolstering the reliability of anomaly detection in electronic health records. This improvement is attributed to the model’s ability to minimize information loss and maximize data utilization effectively.Conclusion: EHR-BERT showcases immense potential in decreasing medical errors related to anomalous clinical events, positioning itself as an indispensable asset for enhancing patient safety and the overall standard of healthcare services. The framework effectively overcomes the drawbacks of earlier models, making it a promising solution for healthcare professionals to ensure the reliability and quality of health data.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2023

Distribution of rare earth and other critical elements in lignites from the Eocene Jackson Group, Texas

Coal is increasingly evaluated as a source of rare earth elements (REEs) in the United States to address the overreliance on imported REEs. The objective of this study was to assess the distribution of REEs in lignites from selected mining areas in the Texas Gulf Coastal Plain region. Thirty-one archived lignite and rock samples previously collected by the U.S. Geological Survey were analyzed for their rare earth element and critical mineral content. These include samples from one core (5400 and 5500 lignite horizons) and two opencast lignite mines (Gibbons Creek 3500 and 4500 horizons, and San Miguel horizons A to D) in the Eocene Jackson Group of the Texas Gulf of Mexico Coastal Plain. Some lithologies in the Gibbons Creek 3500 and 4500 lignite-bearing sections have high total rare earth, yttrium (Y), and scandium (Sc) (REYSc) values, up to 7800 ppm (ash basis) REYSc. The lignite lithologies show an enrichment in rare earths, [samarium (Sm) through gadolinium (Gd)]. The basal Gibbons Creek 3500 lignite bench shows a heavy rare earth element enrichment pattern resembling that often seen in peats through high volatile A bituminous coals. The 5500 lignite sequence, overlying the latter lignite sections, shows a light rare earth enrichment. The San Miguel lignite benches have heavy rare earth enrichments with a negative europium (Eu) anomaly.

58 GEOSCIENCES↗
NASA NTRS1980

The influence of isothermal annealing on the molybdenum fibers of a directed solid gamma/gamma prime - alpha alloy

The mechanical characteristics of the directed solid eutectic Ni-Al-Mo (gamma/gamma prime)-alpha alloy at high temperatures make it useful in the blades of gas turbines. Structural changes are observed for the alloy under isothermal annealing, particularly the formation of molybdenum plates at the grain boundary and an increase of the gamma phase in relation to the gamma prime phase. Molybdenum lamellas appear at the grain boundary above 1100 C which can have a negative influence on the mechanical properties. The change in the structure near the grain boundary with the increase in temperature is illustrated through a sequence of pictures.

Whittenberger, J. D.↗
NASA NTRS2002

Association between simian virus 40 and non-Hodgkin lymphoma

BACKGROUND: Non-Hodgkin lymphoma has increased in frequency over the past 30 years, and is a common cancer in HIV-1-infected patients. Although no definite risk factors have emerged, a viral cause has been postulated. Polyomaviruses are known to infect human beings and to induce tumours in laboratory animals. We aimed to identify which one of the three polyomaviruses able to infect human beings (simian virus 40 [SV40], JC virus, and BK virus) was associated with non-Hodgkin lymphoma. METHODS: We analysed systemic non-Hodgkin lymphoma from 76 HIV-1-infected and 78 HIV-1-uninfected patients, and non-malignant lymphoid samples from 79 HIV-1-positive and 107 HIV-1-negative patients without tumours; 54 colon and breast carcinoma samples served as cancer controls. We used PCR followed by Southern blot hybridisation and DNA sequence analysis to detect DNAs of polyomaviruses and herpesviruses. FINDINGS: Polyomavirus T antigen sequences, all of which were SV40-specific, were detected in 64 (42%) of 154 non-Hodgkin lymphomas, none of 186 non-malignant lymphoid samples, and none of 54 control cancers. This difference was similar for HIV-1-infected patients and HIV-1-uninfected patients alike. Few tumours were positive for both SV40 and Epstein-Barr virus. Human herpesvirus type 8 was not detected. SV40 sequences were found most frequently in diffuse large B-cell and follicular-type lymphomas. INTERPRETATION: SV40 is significantly associated with some types of non-Hodgkin lymphoma. These results add lymphomas to the types of human cancers associated with SV40.

Non-NASA Center↗
NASA NTRS1994

Cusp/cleft auroral activity in relation to solar wind dynamic pressure, interplanetary magnetic field B(sub z) and B(sub y)

Continuous optical observations of cusp/cleft auroral activities within approximately equal to 09-15 MLT and 70-76 deg magnetic latitude are studied in relation to changes in solar wind dynamic pressure and interplanetary magnetic field (IMF) variability. The observed latitudinal movements of the cusp/cleft aurora in response to IMF B(sub z) changes may be explained as an effect of a variable magnetic field intensity in the outer dayside magnetosphere associated with the changing intensity of region 1 field-aligned currents and associated closure currents. Ground magnetic signatures related to such currents were observed in the present case (January 10, 1993). Strong, isolated enhancements in solar wind dynamic pressure (Delta p/p is greater than or equal to 0.5) gave rise to equatorward shifts of the cusp/cleft aurora, characteristic auroral transients, and distinct ground magnetic signatures of enhanced convection at cleft latitudes. A sequence of auroral events of approximately equal to 5-10 min recurrence time, moving eastward along the poleward boundary of the persistent cusp/cleft aurora in the approximately equal to 10-14 MLT sector, during negative IMF B(sub z) and B(sub y) conditions, were found to be correlated with brief pulses in solar wind dynamic pressure (0.1 is less than Delta p/p is less than 0.5). Simultaneous photometer observations from Ny Alesund, Svalbard, and Danmarkshavn, Greenland, show that the events often appeared on the prenoon side (approximately equal to 10-12 MLT), before moving into the postnoon sector in the case we study here, when IMF B(sub y) is less than 0. In other cases, similar auroral event sequences have been observed to move westward in the prenoon sector, during intervals of positive B(sub y). Thus a strong prenoon/postnoon asymmetry of event occurence and motion pattern related to the IMF B(sub y) polarity is observed. We find that this category of auroral event sequence is stimulated bursts of electron precipitation that originate from magnetosheath plasma that has accessed that dayside magnetosphere in the noon or near-noon sector, possibly at high latitudes, partly governed by the IMF orientation as well as by solar wind dynamic pressure pulses.

Sandholt, P. E.↗
DOE OSTI2020

Deconvolute individual genomes from metagenome sequences through short read clustering

Metagenome assembly from short next-generation sequencing data is a challenging process due to its large scale and computational complexity. Clustering short reads by species before assembly offers a unique opportunity for parallel downstream assembly of genomes with individualized optimization. However, current read clustering methods suffer either false negative (under-clustering) or false positive (over-clustering) problems. Here we extended our previous read clustering software, SpaRC, by exploiting statistics derived from multiple samples in a dataset to reduce the under-clustering problem. Using synthetic and real-world datasets we demonstrated that this method has the potential to cluster almost all of the short reads from genomes with sufficient sequencing coverage. The improved read clustering in turn leads to improved downstream genome assembly quality.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Teredinibacter haidensis sp. nov., Teredinibacter purpureus sp. nov. and Teredinibacter franksiae sp. nov., marine, cellulolytic endosymbiotic bacteria isolated from the gills of the wood-boring mollusc Bankia setacea (Bivalvia: Teredinidae) and emended description of the genus Teredinibacter

Here, we describe three endosymbiotic bacterial strains isolated from the gills of the shipworm, Bankia setacea (Teredinidae: Bivalvia). These strains, designated as Bs08 T , Bs12 T and Bsc2 T , are Gram-stain-negative, microaerobic, gammaproteobacteria that grow on cellulose and a variety of substrates derived from lignocellulose. Phenotypic characterization, phylogeny based on 16S rRNA gene and whole genome sequence data, amino acid identity and percentage of conserved proteins analyses, show that these strains are novel and may be assigned to the genus Teredinibacter. The three strains may be differentiated and distinguished from other previously described Teredinibacter species based on a combination of four characteristics: colony colour (Bs12 T , purple; others beige to brown), marine salt requirement (Bs12 T , Bsc2 T and Teredinibacter turnerae strains), the capacity for nitrogen fixation (Bs08 T and T. turnerae strains) and the ability to respire nitrate (Bs08 T ). Based on these findings, we propose the names Teredinibacter haidensis sp. nov. (type strain Bs08 T =ATCC TSD-121 T =KCTC 62964 T ), Teredinibacter purpureus sp. nov. (type strain Bs12 T =ATCC TSD-122 T =KCTC 62965 T ) and Teredinibacter franksiae sp. nov. (type strain Bsc2 T =ATCC TSD-123 T =KCTC 62966 T ).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Clostridium autoethanogenum isopropanol production via native plasmid pCA replicon

Clostridium autoethanogenum is a model gas-fermenting acetogen for commercial ethanol production. It is also a platform organism being developed for the carbon-negative production of acetone and isopropanol by gas fermentation. We have assembled a 5.5 kb pCA plasmid for type strain DSM10061 (JA1-1) using three genome sequence datasets. pCA is predicted to encode seven open-reading frames and estimated to be a low-copy number plasmid present at approximately 12 copies per chromosome. RNA-seq analyses indicate that pCA genes are transcribed at low levels and two proteins, CAETHG_05090 (putative replication protein) and CAETHG_05115 (hypothetical, a possible Mob protein), were detected at low levels during batch gas fermentations. Thiolase (thlA), CoA-transferase (ctfAB), and acetoacetate decarboxylase (adc) genes were introduced into a vector for isopropanol production in C. autoethanogenum using the native plasmid origin of replication. The availability of the pCA sequence will facilitate studies into its physiological role and could form the basis for genetic tool optimization.

09 BIOMASS FUELS↗
NASA NTRS1980

Solar energy facility at North Hampton Recreation Center, Dallas, Texas

The solar energy facility located at the North Hampton Park Recreation and Health Center, Dallas, Texas is presented. The solar energy system is installed in a single story (two heights), 16,000 sq ft building enclosing a gymnasium, locker area, and health care clinic surrounded by a recreational area and athletic field. The solar energy system is designed to provide 80 percent of the annual space heating, 48 percent of the annual space cooling, and 90 percent of the domestic hot water requirements. The system's operation modes and performance data acquisition system are described. The system's performance during the months of June, July, August, September, and October of 1979 are presented and show a negative savings of energy. Experience to date indicates however that the system concept has promise of acceptable performance. It is concluded that if proper control and sequencing components was maintained, then the system performance would improve to an acceptable level.

Source record↗
DOE OSTI2021

FG nucleoporins feature unique patterns that distinguish them from other IDPs

FG nucleoporins (FG Nups) are intrinsically disordered proteins and are the putative regulators of nucleocytoplasmic transport. They allow fast, yet selective, transport of molecules through the nuclear pore complex, but the underlying mechanism of nucleocytoplasmic transport is not yet fully discovered. As a result, FG Nups have been the subject of extensive research in the past two decades. Although most studies have been focused on analyzing the conformation and function of FG Nups from a biophysical standpoint, some recent studies have investigated the sequence-function relationship of FG Nups, with a few investigating amino acid sequences of a large number of FG Nups to understand common characteristics that might enable their function. Previously, we identified an evolutionarily conserved feature in FG Nup sequences, which are extended subsequences with low charge density, containing only positive charges, and located toward the N-terminus of FG Nups. We named these patterns longest positive like charge regions (lpLCRs). These patterns are specific to positively charged residues, and negatively charged residues do not demonstrate such a pattern. In this study, we compare FG Nups with other disordered proteins obtained from the DisProt and UniProt database in terms of presence of lpLCRs. Our results show that the lpLCRs are virtually exclusive to FG Nups and are not observed in other disordered proteins. Also, lpLCRs are what differentiate FG Nups from DisProt proteins in terms of charge distribution, meaning that excluding lpLCRs from the sequences of FG Nups make them similar to DisProt proteins in terms of charge distribution. We also previously showed the biophysical effect of lpLCRs in conformation of FG Nups. The results of this study are in line with our previous findings and imply that lpLCRs are virtually exclusive and functionally significant characteristics of FG Nups and nucleocytoplasmic transport.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

YPK9 and WHI2 Negatively Interact during Oxidative Stress

Yeast PARK9 (YPK9) shares homology with human ATP13A2, which encodes a polyamine transporter implicated in juvenile forms of Parkinson’s disease. We used YPK9 to gain insight into how ATP13A2 affects cell growth and sensitivity to oxidative stress. Surprisingly, the YPK9 deletion strain from the Saccharomyces cerevisiae deletion collection (YKO) in wildtype BY4741 (mating type a) grew faster and was more resistant to hydrogen peroxide than a commercial, putative parental BY4741 wildtype strain (BY4741 COM ). In contrast, deleting YPK9 from BY4741 COM rendered it very sensitive to hydrogen peroxide, suggesting its background is different from that of the deletion collection. Whole-genome sequencing revealed that BY4741 COM and BY4741 COM ypk9Δ contain a novel premature stop codon near the 3' end of WHI2 (WHI2 G1324T ), whereas the collection’s YPK9 deletion strain contains WHI2, which encodes a 486 amino acid protein, Whi2p. Replacing full-length WHI2 with the sequence coding for the predicted truncation (Whi2p E442* ) rendered strains more sensitive to hydrogen peroxide, whereas the converse replacement rendered them more resistant. The sequences of WHI2 in 20 randomly chosen strains from the collection encode the full-length protein, indicating that the putative parental BY4741 WHI2 G1324T strain’s genetic background differs from that of the deletion collection. Examination of WHI2 sequences in several commonly used wildtype S. cerevisiae strains and isolates revealed other Whi2p truncations that might yield altered phenotypes. Together, these results demonstrate a novel premature stop codon in WHI2 that renders yeast sensitive to hydrogen peroxide; they also reveal a negative genetic interaction between WHI2 and YPK9 in the presence of hydrogen peroxide in the BY4741 background.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1982

Coordinate generation with precise controls over mesh properties

Powerful local controls have been developed for mesh generation with the class of multisurface coordinate transformations. The controls come from local piecewise linear interpolants, and the resulting coordinates have continuous first derivatives. At the boundaries, the mesh controls provide the capability of joining distinct coordinate systems together with continuous derivatives. Away from boundaries, a local region can be given a particular mesh form to model internal objects or to simplify a problem. Applications of the controls are illustrated with a sequence of two-dimensional examples. For simplicity, each is generated about a NACA0012 airfoil which is of unit length and with leading edge pointed in a negative x-direction.

Eiseman, P. R.↗
NASA NTRS1992

Learning class descriptions from a data base of spectral reflectance with multiple view angles

A learning program has been developed which combines 'learning by example' with the generate-and-test paradigm to furnish a robust learning environment capable of handling error-prone data. The problem is shown to be capable of learning class descriptions from positive and negative training examples of spectral and directional reflectance data taken from soil and vegetation. The program, which used AI techniques to automate very tedious processes, found the sequence of relationships that contained the most important information which could distinguish the classes.

Kimes, Daniel S.↗
NASA NTRS1995

Two cis elements collaborate to spatially repress transcription from a sea urchin promoter

The expression pattern of many territory-specific genes in metazoan embryos is maintained by an active process of negative spatial regulation. However, the mechanism of this strategy of gene regulation is not well understood in any system. Here we show that reporter constructs containing regulatory sequence for the SM30-alpha gene of Stronglyocentrotus purpuratus are expressed in a pattern congruent with that of the endogenous SM30 gene(s), largely as a result of active transcriptional repression in cell lineages in which the gene is not normally expressed. Chloramphenicol acetyl transferase assays of deletion constructs from the 2600-bp upstream region showed that repressive elements were present in the region from -1628 to -300. In situ hybridization analysis showed that the spatial fidelity of expression was severely compromised when the region from -1628 to -300 was deleted. Two highly repetitive sequence motifs, (G/A/C)CCCCT and (T/C)(T/A/C)CTTTT(T/A/C), are present in the -1628 to -300 region. Representatives of these elements were analyzed by gel mobility shift experiments and were found to interact specifically with protein in crude nuclear extracts. When oligonucleotides containing either sequence element were co-injected with a correctly regulated reporter as potential competitors, the reporter was expressed in inappropriate cells. When composite oligonucleotides, containing both sequence elements, were fused to a misregulated reporter, the expression of the reporter in inappropriate cells was suppressed. Comparison of composite oligonucleotides with oligonucleotides containing single constituent elements show that both sequence elements are required for effective spatial regulation. Thus, both individual elements are required, but only a composite element containing both elements is sufficient to function as a tissue-specific repressive element.

Non-NASA Center↗