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At least 145 records · Page 8

Integrative genomics reveals paths to sex dimorphism in Salix purpurea L

Sex dimorphism and gene expression were studied in developing catkins in 159 F 2 individuals from the bioenergy crop Salix purpurea , and potential mechanisms and pathways for regulating sex development were explored. Differential expression, eQTL, bisulfite sequencing, and network analysis were used to characterize sex dimorphism, detect candidate master regulator genes, and identify pathways through which the sex determination region (SDR) may mediate sex dimorphism. Eleven genes are presented as candidates for master regulators of sex, supported by gene expression and network analyses. These include genes putatively involved in hormone signaling, epigenetic modification, and regulation of transcription. eQTL analysis revealed a suite of transcription factors and genes involved in secondary metabolism and floral development that were predicted to be under direct control of the sex determination region. Furthermore, data from bisulfite sequencing and small RNA sequencing revealed strong differences in expression between males and females that would implicate both of these processes in sex dimorphism pathways. These data indicate that the mechanism of sex determination in Salix purpurea is likely different from that observed in the related genus Populus . This further demonstrates the dynamic nature of SDRs in plants, which involves a multitude of mechanisms of sex determination and a high rate of turnover.

59 BASIC BIOLOGICAL SCIENCES↗

Creb5 controls its own expression and directly induces the joint interzone regulatory program

Prior studies have indicated that the transcription factor Creb5 is expressed in the joint interzone, which contains the progenitors for all synovial joint tissues in both mouse and human embryos. In the absence of Creb5 function, most synovial joint interzones fail to form and the cartilage templates in the long bones remain fused. This earlier work did not clarify whether Creb5 initiates a cascade of signaling molecules, such as growth and differentiation factor 5 (Gdf5) and Wnt-family members, that in turn induce the formation of the joint interzone, or instead directly activates the expression of joint interzone markers. In the present study, an integrative analysis of the transcriptome, chromatin accessibility, and Creb5-occupancy in joint progenitors revealed that Creb5 directly binds to both its own two promoters and to the regulatory regions of Gdf5 and Sfrp2, each of whose expression in the joint interzone is Creb5-dependent. Functional enhancer analysis indicated that Creb5 binding sites in either the two Creb5 promoters, or in Gdf5 and Sfrp2 regulatory elements are necessary for these sequences to drive transgene expression in the developing synovial joints. While Creb5 directly drives Gdf5 and Sfrp2 expression in the inner joint interzone, Creb5 activates Barx1 expression specifically in the outer joint interzone. Our findings indicate that Creb5 initiates a regulatory network that both promotes the formation of synovial joints, and subsequently activates distinct transcriptional targets in the inner versus the outer regions of the joint interzone, thus regionalizing gene expression in the developing joint.

Zhang, Cheng-Hai↗

Self-assembly and condensation of intermolecular poly(UG) RNA quadruplexes

Abstract Poly(UG) or ‘pUG’ dinucleotide repeats are highly abundant sequences in eukaryotic RNAs. In Caenorhabditis elegans, pUGs are added to RNA 3′ ends to direct gene silencing within Mutator foci, a germ granule condensate. Here, we show that pUG RNAs efficiently self-assemble into gel condensates through quadruplex (G4) interactions. Short pUG sequences form right-handed intermolecular G4s (pUG G4s), while longer pUGs form left-handed intramolecular G4s (pUG folds). We determined a 1.05 Å crystal structure of an intermolecular pUG G4, which reveals an eight stranded G4 dimer involving 48 nucleotides, 7 different G and U quartet conformations, 7 coordinated potassium ions, 8 sodium ions and a buried water molecule. A comparison of the intermolecular pUG G4 and intramolecular pUG fold structures provides insights into the molecular basis for G4 handedness and illustrates how a simple dinucleotide repeat sequence can form complex structures with diverse topologies.

Biochemistry & Molecular Biology↗

CROCUS Sodar Measurements of Lower Atmospheric Wind Profiles at Argonne Testbed for Multiscale Observational Science (ATMOS) Site

The Scintec MFAS Sodar (Multiple-Frequency Acoustic Sounder) is an autonomous, ground-based acoustic remote sensing system designed to measure vertical profiles of horizontal wind speed, wind direction, and vertical velocity in the lower atmosphere. The instrument transmits sequences of acoustic pulses and detects the Doppler-shifted sound waves backscattered by small-scale temperature and velocity fluctuations caused by atmospheric turbulence. From these Doppler shifts, the system derives three-dimensional wind vectors by combining radial velocities from multiple beam orientations.The MFAS Sodar operates with a first usable range gate beginning at approximately 30 m above ground level and a configurable vertical resolution of 10 m. Under favorable acoustic conditions, the system provides wind profiles extending up to 600 m above ground level. Measurements are processed into 15-minute averaged profiles containing wind speed, direction, vertical velocity, and diagnostic quantities such as signal-to-noise ratio and echo strength.This dataset was collected at the Argonne Testbed for Multiscale Observational Science (ATMOS) facility in Lemont, Illinois, as part of DOE's CROCUS Urban Integrated Field Laboratory (UIFL) initiative. The purpose of these observations is to characterize the vertical wind structure and boundary-layer evolution across the urban–suburban gradient of the greater Chicago region. In particular, these data are intended to improve understanding of how local meteorology, such as lake-breeze penetration, nocturnal jets, and daytime mixing, varies between the densely built urban core and the suburban periphery. The MFAS observations provide critical context for evaluating high-resolution model simulations and for integrating with complementary lidar, radar, and in-situ meteorological measurements within the broader CROCUS UIFL network.All data are archived in NetCDF (Network Common Data Form) format and include wind and diagnostic parameters. The files can be accessed and analyzed using standard software that supports NetCDF, such as Python (e.g., xarray, netCDF4), MATLAB, R (e.g., ncdf4, raster), or Panoply (NASA’s NetCDF visualization application).

54 ENVIRONMENTAL SCIENCES↗

Machine learning predicts new anti-CRISPR proteins

The increasing use of CRISPR–Cas9 in medicine, agriculture, and synthetic biology has accelerated the drive to discover new CRISPR–Cas inhibitors as potential mechanisms of control for gene editing applications. Many anti-CRISPRs have been found that inhibit the CRISPR–Cas adaptive immune system. However, comparing all currently known anti-CRISPRs does not reveal a shared set of properties for facile bioinformatic identification of new anti-CRISPR families. Here, we describe AcRanker, a machine learning based method to aid direct identification of new potential anti-CRISPRs using only protein sequence information. Using a training set of known anti-CRISPRs, we built a model based on XGBoost ranking. We then applied AcRanker to predict candidate anti-CRISPRs from predicted prophage regions within self-targeting bacterial genomes and discovered two previously unknown anti-CRISPRs: AcrllA20 (ML1) and AcrIIA21 (ML8). We show that AcrIIA20 strongly inhibits Streptococcus iniae Cas9 (SinCas9) and weakly inhibits Streptococcus pyogenes Cas9 (SpyCas9). We also show that AcrIIA21 inhibits SpyCas9, Streptococcus aureus Cas9 (SauCas9) and SinCas9 with low potency. The addition of AcRanker to the anti-CRISPR discovery toolkit allows researchers to directly rank potential anti-CRISPR candidate genes for increased speed in testing and validation of new anti-CRISPRs. A web server implementation for AcRanker is available online at http://acranker.pythonanywhere.com/.

59 BASIC BIOLOGICAL SCIENCES↗

DNA affinity purification sequencing and transcriptional profiling reveal new aspects of nitrogen regulation in a filamentous fungus

Significance Microorganisms have evolved transcriptional networks to prioritize utilization of available nutrient sources. For filamentous fungi, such as Neurospora crassa , this entails distinguishing between a variety of organic and inorganic nitrogen sources. Here, we transcriptionally profiled the response of N. crassa to a variety of nitrogen sources and used DNA affinity purification sequencing to characterize the role of regulatory genes and their direct downstream targets. We identified a transcription factor responsible for regulating genes involved in amino acid and mannose metabolism. By comparing the genes regulated by transcription factors that regulate specific nitrogen utilization pathways and transcription factors that regulate utilization of all nitrogen sources that require metabolic processing before utilization, we revealed aspects of the nitrogen regulatory network.

59 BASIC BIOLOGICAL SCIENCES↗

High-throughput functional variant screens via in vivo production of single-stranded DNA

Significance We report a methodology for the pooled construction of mutants bearing precise genomic sequence variations and multiplex phenotypic characterization of these mutants using next-generation sequencing (NGS). Unlike existing techniques depending on CRISPR-Cas–directed genomic breaks for genome editing, this strategy instead uses single-stranded DNA produced by a retron element for recombineering. This enables libraries of millions of elements to be constructed and offers relaxed design constraints which permit natural DNA or random variation to be used as inputs.

59 BASIC BIOLOGICAL SCIENCES↗

Sensitive and error-tolerant annotation of protein-coding DNA with BATH

We present BATH, a tool for highly sensitive annotation of protein-coding DNA based on direct alignment of that DNA to a database of protein sequences or profile hidden Markov models (pHMMs). BATH is built on top of the HMMER3 code base, and simplifies the annotation workflow for pHMM-based translated sequence annotation by providing a straightforward input interface and easy-to-interpret output. BATH also introduces novel frameshift-aware algorithms to detect frameshift-inducing nucleotide insertions and deletions (indels). BATH matches the accuracy of HMMER3 for annotation of sequences containing no errors, and produces superior accuracy to all tested tools for annotation of sequences containing nucleotide indels. These results suggest that BATH should be used when high annotation sensitivity is required, particularly when frameshift errors are expected to interrupt protein-coding regions, as is true with long-read sequencing data and in the context of pseudogenes.

59 BASIC BIOLOGICAL SCIENCES↗

Study of the Protection Improvements for a Weak Grid Area With High Inverter-Based Resources (IBRs)

This project designs enhanced protection scheme for the real-world weak grid area with a high penetration of IBRs. As the existing protection schemes are originally designed for traditional synchronous machines, we first evaluate if the protection scheme will continue to operate reliably in systems with high levels of IBRs. Hardware relays are tested using a controller-hardware-in-the-loop setup. PSCAD electromagnetic transient simulation with IBR original equipment manufacturer black-box models is used to perform fault studies and generate COMTRADE data, which are replayed by a real-time digital simulator (RTDS) to feed input to the hardware relays. Three scenarios are analyzed: normal operation, an N-1 contingency, and an IBR-only scenario. The evaluation results reveal the following: 1) the protection scheme remains reliable under normal conditions and N-1 contingencies and 2) in IBR-only scenarios, differential protection (87L) continues to operate reliably, whereas local protection elements, such as distance and directional elements, fail because of the lack of regulated negative sequence current contributed by IBRs. Enhanced protection is designed to address the challenge of lack of negative sequence current from IBRs, including increased restraining factors a2 and k2 to block 32Q or using V instead QV ORDER for ground faults, enhanced mho distance element with voltage and phase angle supervision for L-L faults. The efficacy of enhanced protection logic is validated and proven to work reliably. Additionally, IEEE Std. 2800-2022 negative sequence current compliant GFL and GFM IBRs from another vendor are tested and proven to work reliably without need for enhanced logic. Therefore, this work provides valuable decision-making for utilities facing protection system challenges due to IBRs, either designing enhanced protection scheme or requesting their IBRs being IEEE Std. 2800-2022 compliant to produce regulated negative sequence current for protection relay to make correct decision.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Potential Role of Malassezia restricta in Pterygium Development

Pterygium is a condition affecting the ocular surface, marked by a triangular-shaped growth of fibrotic tissue extending from the nasal conjunctiva toward the corneal center, potentially causing visual impairment. While ultraviolet (UV )light exposure is the primary risk factor for pterygium, its underlying cause remains unclear. In order to better understand the true genesis of pterygium development, we investigated pterygium tissue and compared it with healthy conjunctiva controls. Given the eye’s direct environmental exposure, we analyzed the microbiota composition using metagenomic sequencing of pterygium tissue to identify microbes potentially associated with this condition. Metagenomic sequencing revealed a higher prevalence of the fungus Malassezia restricta in five pterygium samples, confirmed by in situ hybridization. The CHIT1 gene, which plays a role in antifungal defenses, displayed the highest expression in five pterygium tissue samples compared to healthy conjunctiva controls, suggesting the potential involvement of Malassezia restricta in pterygium development. Gene expression profiling of pterygium highlighted an IL-33 and IL-4 gene expression signature, along with an increased presence of M2 macrophages, emphasizing their role in promoting fibrosis—a hallmark feature of pterygium. The detection of Malassezia restricta in the pterygium samples and associated molecular changes provides novel insights into the ocular microbiome and raises the possibility of Malassezia’s involvement in pterygium pathology.

60 APPLIED LIFE SCIENCES↗

Lost and Found Opportunities Around the Chlorine Worth Study

Los Alamos National Laboratory performed a series of critical experiments in 2021 to examine the worth of chlorine in plutonium-fueled systems. This series of experiments has been dubbed the “Chlorine Worth Study,” and the evaluation of the experiments was presented to the International Criticality Safety Benchmark Evaluation Project (ICSBEP) Technical Review Group in April, 2023. The primary purpose of these experiments was to enable validation of aqueous solutions crediting neutron absorption in 35 Cl. An external, independent view of the events leading up to the design and execution of these experiments indicates a missed opportunity to leverage sensitivity/uncertainty (S/U) analysis to assert validation without the experiments by taking an additional margin for the lack of direct validation of chlorine. On the other hand, the execution of these experiments also presents a rare opportunity to examine the efficacy of the S/U approach and extract useful information about the evaluated chlorine covariance data. TSUNAMI-1D models of representative application solutions were created and used to generate sensitivity data. Varying plutonium and chlorine concentrations were considered to examine the impact of these differences on the chlorine sensitivities and uncertainties. The data-induced uncertainty in k eff resulting from chlorine was calculated directly from uncertainty information calculated in the TSUNAMI-1D sequence. In all cases, this uncertainty was less than 0.1 %Δk. This result could potentially be used to justify a reactivity margin to account for the validation gap related to chlorine in the validation set. On the other hand, given that the experiments were performed, the community should endeavor to extract as much value from them and their results as possible. The results can be used to examine the actual bias associated with chlorine in these systems once the evaluations have been released. These data can be compared with the data-induced uncertainty margin discussed above to test the sufficiency of the validation gap penalty. This result will provide an indication of the performance of the chlorine covariance data specifically and the S/U validation approach generally. More advanced S/U techniques may also be employed to determine reactivity sensitivities associated with the chlorine in the experiments, potentially generating a more robust test of the chlorine covariance data.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Evaluating Protection System Performance for a Real-World Weak Grid Area With High Inverter-Based Resources: Preprint

This paper evaluates an existing protection scheme implemented in a real-world weak grid area with a high penetration of inverter-based resources (IBRs). The study aims to assess the reliability and adequacy of protection schemes originally designed for traditional synchronous machine systems and determine whether they can continue to operate reliably in systems with high levels of IBRs. Hardware relays are tested using a controller-hardware-in-the-loop setup. PSCAD electromagnetic transient simulation with an IBR original equipment manufacturer black-box model is used to perform fault studies and generate COMTRADE data, which are replayed by a real-time digital simulator (RTDS) to feed input to the hardware relays. Three scenarios are analyzed: normal operation, an N-1 contingency, and an IBR-only scenario. The evaluation results reveal the following: 1) the protection scheme remains reliable under normal conditions and N-1 contingencies and 2) in IBR-only scenarios, differential protection (87L) continues to operate reliably, whereas local protection elements, such as distance and directional elements, fail because of the lack of regulated negative sequence current contributed by IBRs. These findings provide utilities with valuable insights for improving their protection systems in high-IBRs.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Host Star Metallicity of Directly Imaged Wide-orbit Planets: Implications for Planet Formation

Directly imaged planets (DIPs) are self-luminous companions of pre-main-sequence and young main-sequence stars. They reside in wider orbits (∼tens to thousands of astronomical units) and generally are more massive compared to the close-in (≲10 au) planets. Determining the host star properties of these outstretched planetary systems is important to understand and discern various planet formation and evolution scenarios. We present the stellar parameters and metallicity ([Fe/H]) for a subsample of 18 stars known to host planets discovered by the direct imaging technique. We retrieved the high-resolution spectra for these stars from public archives and used the synthetic spectral fitting technique and Bayesian analysis to determine the stellar properties in a uniform and consistent way. For eight sources, the metallicities are reported for the first time, while the results are consistent with the previous estimates for the other sources. Our analysis shows that metallicities of stars hosting DIPs are close to solar with a mean [Fe/H] = −0.04 ± 0.27 dex. The large scatter in metallicity suggests that a metal-rich environment may not be necessary to form massive planets at large orbital distances. We also find that the planet mass–host star metallicity relation for the directly imaged massive planets in wide orbits is very similar to that found for the well-studied population of short-period (≲1 yr) super-Jupiters and brown dwarfs around main-sequence stars.

36 MATERIALS SCIENCE↗

Depth-resolved sagebrush root metabolomics, rhizosphere microbial communities, and geochemistry at the East River Watershed

This data set consists of results from soil nutrient profile, untargeted metabolomics, mass spec imaging, and amplicon sequencing. Data for soil nutrient profile includes common cations (Ca, Mg, Na, and K etc.) extracted from 3 digesting steps – ammonia acetate (for exchangeable cations), nitric acid (for acid dissolved fraction), and hydrofluoric acid/perchloric acid (HF/HClO4) for whole soil digestion. It also includes concentration of organic carbon, inorganic nitrogen (ammonia and nitrate) and phosphorus (Bray-1 P and nitric acid extract), and total nitrogen and phosphorus. Data for untargeted metabolomics includes metabolomic profile for root exudate/tissues and soil extracts from depths at surface soil to saprolite, that were measured using gas chromatography – mass spectrometry (GC-MS), and liquid chromatography – tandem mass spectrometry (LC-MS/MS). Data for mass spec imaging includes spatial distribution of metabolites that were detected and annotated with Fourier transformation ion cyclotron resonance mass spectrometer (FTICR-MS). Data for amplicon sequencing includes the base paired 16S and ITS ribosomal RNA sequences from Miseq Illumina sequencing. All samples were collected from 2 sampling campaign October 2022 and June 2023. Collectively, these datasets enable a mechanistic evaluation of how nutrient acquisition, especially nitrogen and phosphorus, differs between shallow roots operating in soil and deep roots functioning within the fractured bedrock zone. All files are provided as comma-separated values (CSV) fies (.csv) and (GZIP) file (.gz). The compressed .gz FASTQ files can be read directly in R using the dada2 package as part of the amplicon sequence analysis workflow. This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231. This research was performed on a project award 60563 (https://dx.doi.org/10.46936/expl.proj.2022.60563/60008727) from the Environmental Molecular Sciences Laboratory, a DOE Office of Science User Facility sponsored by the Biological and Environmental Research program under Contract No. DE-AC05-76RL01830.

EARTH SCIENCE > AGRICULTURE > SOILS > CARBON↗

Adaptive Pore Opening to Form Tailored Adsorption Sites in a Cooperatively Flexible Framework Enables Record Inverse Propane/Propylene Separation

A proposed low-energy alternative to the separation of alkanes from alkenes by energy-intensive cryogenic distillation is separation by porous adsorbents. Unfortunately, most adsorbents preferentially take up the desired, high-value major component alkene, requiring frequent regeneration. Adsorbents with inverse selectivity for the minor component alkane would enable the direct production of purified, reagent-grade alkene, greatly reducing global energy consumption. However, such materials are exceedingly rare, especially for propane/propylene separation. Here, we report that through adaptive and spontaneous pore size and shape adaptation to optimize an ensemble of weak noncovalent interactions, the structurally responsive metal-organic framework CdIF-13 (sod-Cd(benzimidazolate) 2 ) exhibits inverse selectivity for propane over propylene with record-setting separation performance under industrially relevant temperature, pressure, and mixture conditions. Powder synchrotron X-ray diffraction measurements combined with first-principles calculations yield atomic-scale insight and reveal the induced fit mechanism of adsorbate-specific pore adaptation and ensemble interactions between ligands and adsorbates. Dynamic column breakthrough measurements confirm that CdIF-13 displays selectivity under mixed-component conditions of varying ratios, with a record measured selectivity factor of α ≈ 3 at 95:5 propylene:propane at 298 K and 1 bar. When sequenced with a low-cost rigid adsorbent, we demonstrated the direct purification of propylene under ambient conditions. In conclusion, this combined atomic-level structural characterization and performance testing firmly establishes how cooperatively flexible materials can be capable of unprecedented separation factors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Highly efficient and simple SSPER and rrPCR approaches for the accurate site-directed mutagenesis of large and small plasmids

Advances are needed in the site-directed mutagenesis of large plasmids for protein structure-function studies, as current methods are often inefficient, complicated and time-consuming. Here two new methods are reported that overcome these difficulties, namely the single primer extension reaction (SSPER) strategy that reaches 100% efficiency and the reduce recycle PCR (rrPCR) method that is advantageous in generating single and pairwise combinations of mutations. Both methods are distinguished from current technologies by the addition of a step that easily removes the oligonucleotide primer(s) after the first reaction, thus allowing for the addition of a second reaction in chronological sequence to generate and isolate the appropriate DNA product with the site-directed mutation(s). High efficiency of the methods is demonstrated by generating single and paired combinations of the 11 site-directed mutations targeted on 5 different plasmid DNA templates ranging from 10 to 12 kb and 57–60% GC-content at a rate of 50–100%. Overall, the methods are demonstrated to be (i) highly accurate, allowing for screening of plasmids by DNA sequencing, (ii) streamlined to generate the mutations within a single day, (iii) cost-effective in requiring only two primers and two enzymes (DpnI and a proofreading DNA polymerase), (iv) straightforward in primer design, (v) applicable for both large and small plasmids, and (vi) easily implemented by entry level researchers.

59 BASIC BIOLOGICAL SCIENCES↗

Method for quantification of porcine type I interferon activity using luminescence, by direct and indirect means

Abstract Background Type I interferons are widely used in research applications and as biotherapeutics. Current assays used to measure interferon concentrations, such as plaque reduction assays and ELISA, are expensive, technically challenging, and may take days to provide results. We sought to develop a robust and rapid assay to determine interferon concentrations produced from transiently transfected cell cultures. Method Indirect quantification of recombinant interferon was evaluated using a novel bi-cistronic construct encoding the Foot-and-mouth disease virus 2A translational interrupter sequence to yield equimolar expression of Gaussia princeps luciferase and porcine interferon α. Direct quantification was evaluated by expression of a novel fusion protein comprised of Gaussia princeps luciferase and porcine type I interferon. Plasmids encoding constructs are transiently transfected into cell cultures and supernatant harvested for testing of luminescence, ELISA determined concentration, and anti-viral activity against vesicular stomatitis virus. Results Bi-cistronic constructs, utilized for indirect quantification, demonstrate both luciferase activity and anti-viral activity. Fusion proteins, utilized for direct quantification, retained secretion and luminescence however only the interferon α fusion protein had antiviral activity comparable to wildtype porcine interferon α. A strong linear correlation was observed between dilution and luminescence for all compounds over a dynamic range of concentrations. Conclusion The correlation of antiviral and luciferase activities demonstrated the utility of this approach, both direct and indirect, to rapidly determine recombinant interferon concentrations. Concentration can be determined over a more dynamic concentration range than available ELISA based assays using this methodology.

59 BASIC BIOLOGICAL SCIENCES↗

Up up down down left right left right B A Start for the catalytic hackers of programmable materials

Catalysts have advanced over the last century to accelerate and control reactions based on static active sites. More effective catalysis can be achieved using catalysts that change with time over the course of a reaction, providing a dynamic free energy landscape that is tailored to each step in the reaction sequence. Here, the catalyst is modulated via an input program that directs the surface to change physically or electronically with time, providing information regarding the extent and duration of change optimized for specific combinations of chemistry and programmable catalyst surfaces. While in its infancy, programmable catalysis is advancing with parallel efforts to establish fundamental principles of dynamic catalysts, design of programmable materials, and strategies to design input programs that will control catalysis for faster and more selective reactions.

catalyst↗