Results for “Replicate Data” — Page 40

NASA NTRS1992

A case of type I polar stratospheric cloud formation by heterogeneous nucleation

The NASA ER-2 aircraft flew on January 24, 1989, from Stavanger to Spitsbergen, Norway, at the 430-440 K potential temperature surface (19.2-19.8 km pressure altitude). Aerosols were sampled continuously by an optical particle counter (PMS-FSSP300) for concentration and size analyses, and during five 10-min intervals by four wire and one replicator impactor for concentration, size, composition, and phase analysis. During sampling, the air saturation of H2O with respect to ice changed from 20 to 100 percent, and of HNO3 with respect to nitric acid trihydrate (NAT) from subsaturation to supersaturation. Data from both instruments indicate a condensation of hydrochloric acid and, later, nitric acid on the background aerosol particles as the ambient temperature decreases along the flight track. This heterogeneous nucleation mechanism generates type I polar stratospheric cloud particles of 10-fold enhanced optical depth, which could play a role in stratospheric ozone depletion.

Pueschel, R. F.↗

NASA NTRS2007

Primary Objective Grating Astronomical Telescope

It has been 370 years since a seventeenth century French mathematician, Mersenne, presciently sketched out an astronomical telescope based on dual parabolic reflectors. Since that time the concept of the primary objective has been virtually unchanged. Now a new class of astronomical telescope with a primary objective grating (POG) has been studied as an alternative. The POG competes with mirrors, in part, because diffraction gratings provide the very chromatic dispersion that mirrors defeat. The resulting telescope deals effectively with long-standing restrictions on multiple object spectroscopy (MOS). Other potential benefits include unprecedented apertures and collection areas. The new design also favors space deployment as a gossamer membrane. The inventor, Tom Ditto, first discovered that higher-order diffraction images contain hidden depth cues, for which he was granted a seminal range finding patent in 1987. Subsequently, he invented and patented 3D localizers, profilometers and microscopes using POGs. The POG telescope was placed in the public domain to expedite research. The function of a telescopes primary objective is to collect flux and to deliver images. Both functions dictate that size matters, and bigger is better. For that reason, there has been a steady push over the past century to ramp up the size of the primary mirror. However, for every doubling of mirror diameter, the elapsed time between initial effort and first light has also doubled. Meanwhile, costs escalated beyond the mirror alone, because larger instruments required larger enclosures and better pointing mechanisms. One key catalog of observation, spectrographic data, is far more difficult to amass than two-dimensional imagery. While the number of observable objects has increased with mirror size, the capacity to take spectra has not increased proportionately. In the best of circumstances, spectrograms are available for one per cent of the all objects surveyed. Spectroscopy was a historical afterthought introduced in the nineteenth century shortly after the invention of the diffraction grating and over a century after Newtons 1670 telescope. Spectroscopy is generally accomplished using a diffraction grating as the disperser in the secondary. The light being delivered to the spectrograph is first captured by a primary mirror which provides no chromatic magnification by itself. Sizeable spectrographs could not be deployed while diffraction gratings were rare commodities scribed using mechanical ruling engines that produced one grating line at a time. Today diffraction gratings are commonplace. Their recent availability is a product of both the invention of holography and the mass replication of surface microstructures. Holography permits all lines in a grating to be made simultaneously in a single photographic exposure. Holograms can then be reproduced by embossing processes. The improvement in replication is analogous to how Gutenberg changed the availability of books. The masters may be expensive, but the copies are not. Computer science is another technology that emerged in the second half of the twentieth century without which our proposed spectrographic instrument could not function due to the complexity of image processing required in data reduction. The employment of very large diffraction gratings as primary objectives for astronomical telescopes requires a novel

spectroscopy↗

DOE OSTI2022

Identification of Novel, Replicable Genetic Risk Loci for Suicidal Thoughts and Behaviors Among US Military Veterans

Importance: Suicide is a leading cause of death; however, the molecular genetic basis of suicidal thoughts and behaviors (SITB) remains unknown. Objective: To identify novel, replicable genomic risk loci for SITB. Design, Setting, and Participants: This genome-wide association study included 633 778 US military veterans with and without SITB, as identified through electronic health records. GWAS was performed separately by ancestry, controlling for sex, age, and genetic substructure. Cross-ancestry risk loci were identified through meta-analysis. Study enrollment began in 2011 and is ongoing. Data were analyzed from November 2021 to August 2022. Main Outcome and Measures: SITB. Results: A total of 633 778 US military veterans were included in the analysis (57 152 [9%] female; 121 118 [19.1%] African ancestry, 8285 [1.3%] Asian ancestry, 452 767 [71.4%] European ancestry, and 51 608 [8.1%] Hispanic ancestry), including 121 211 individuals with SITB (19.1%). Meta-analysis identified more than 200 GWS (P < 5 × 10 -8 ) cross-ancestry risk single-nucleotide variants for SITB concentrated in 7 regions on chromosomes 2, 6, 9, 11, 14, 16, and 18. Top single-nucleotide variants were largely intronic in nature; 5 were independently replicated in ISGC, including rs6557168 in ESR1, rs12808482 in DRD2, rs77641763 in EXD3, rs10671545 in DCC, and rs36006172 in TRAF3. Associations for FBXL19 and AC018880.2 were not replicated. Gene-based analyses implicated 24 additional GWS cross-ancestry risk genes, including FURIN, TSNARE1, and the NCAM1-TTC12-ANKK1-DRD2 gene cluster. Cross-ancestry enrichment analyses revealed significant enrichment for expression in brain and pituitary tissue, synapse and ubiquitination processes, amphetamine addiction, parathyroid hormone synthesis, axon guidance, and dopaminergic pathways. Seven other unique European ancestry–specific GWS loci were identified, 2 of which (POM121L2 and METTL15/LINC02758) were replicated. Two additional GWS ancestry-specific loci were identified within the African ancestry (PET112/GATB) and Hispanic ancestry (intergenic locus on chromosome 4) subsets, both of which were replicated. Further, no GWS loci were identified within the Asian ancestry subset; however, significant enrichment was observed for axon guidance, cyclic adenosine monophosphate signaling, focal adhesion, glutamatergic synapse, and oxytocin signaling pathways across all ancestries. Within the European ancestry subset, genetic correlations (r > 0.75) were observed between the SITB phenotype and a suicide attempt-only phenotype, depression, and posttraumatic stress disorder. Additionally, polygenic risk score analyses revealed that the Million Veteran Program polygenic risk score had nominally significant main effects in 2 independent samples of veterans of European and African ancestry.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Standards, dissemination, and best practices in systems biology

In this study, the reproducibility of scientific research is crucial to the success of the scientific method. Here, we review the current best practices when publishing mechanistic models in systems biology. We recommend, where possible, to use software engineering strategies such as testing, verification, validation, documentation, versioning, iterative development, and continuous integration. In addition, adhering to the Findable, Accessible, Interoperable, and Reusable modeling principles allows other scientists to collaborate and build off of each other’s work. Existing standards such as Systems Biology Markup Language, CellML, or Simulation Experiment Description Markup Language can greatly improve the likelihood that a published model is reproducible, especially if such models are deposited in well-established model repositories. Where models are published in executable programming languages, the source code and their data should be published as open-source in public code repositories together with any documentation and testing code. For complex models, we recommend container-based solutions where any software dependencies and the run-time context can be easily replicated.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Dual Context: Leveraging Structured Application Context for Code Generation and Runtime Feature Activation via Chat Interfaces

Integrating artificial intelligence (AI) capabilities into software applications typically involves two common paths. For developers, AI assists in generating and documenting source code and other related software engineering efforts. For users, AI assists them through question-and-answer exchanges via chatbots. Both approaches have their value, but neither effectively leverages the modularity of component-based architectures that modern web application frameworks offer. We implement a proof of concept within a centralized suite of applications used for the Atmospheric Radiation Measurement (ARM) Data Center Operational Tools, where we introduce a third integration path through the ARM Context Engine (ACE). ACE is a context driven system that uses structured contextual specifications to enable Large Language Models (LLMs) to render interactive and feature-rich user interface (UI) components directly within chat responses, alongside or in place of conventional text outputs. These specifications serve two important purposes across what we call code context and UI context. Code context provides AI-assisted development tools with structured application knowledge beyond raw code, including component relationships, architectural patterns and schematic information, enabling the generation of consistent, well-structured code. UI context defines the rules for enabling and rendering component features at runtime based on the user's natural language input, allowing end users to activate capabilities such as data export, filtering, and pagination within chat responses, without requiring code changes or redeployment. We demonstrate, through a comparative evaluation against general-purpose AI chatbots, that context-driven component rendering provides interactive capabilities that text-based responses cannot replicate, including deterministic component behavior, application-consistent design language, and on-demand feature activation. A development effort comparison further shows that features that traditionally require multi-step development cycles can be activated with a single naturallanguage request. In this ongoing work, we present ACE as an emerging approach to AI integration that positions modular, well-documented software architecture as the foundation for AI-ready applications. ACE treats context as a shared resource across both development and user-facing AI, bringing cohesion to conventionally disconnected efforts, bridging developer tooling and end-user capabilities within a single framework.

Tadimeti, Vijay [ORNL]↗

DOE OSTI2023

Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes

Abstract Background Stable isotope probing (SIP) approaches are a critical tool in microbiome research to determine associations between species and substrates, as well as the activity of species. The application of these approaches ranges from studying microbial communities important for global biogeochemical cycling to host-microbiota interactions in the intestinal tract. Current SIP approaches, such as DNA-SIP or nanoSIMS allow to analyze incorporation of stable isotopes with high coverage of taxa in a community and at the single cell level, respectively, however they are limited in terms of sensitivity, resolution or throughput. Results Here, we present an ultra-sensitive, high-throughput protein-based stable isotope probing approach (Protein-SIP), which cuts cost for labeled substrates by 50–99% as compared to other SIP and Protein-SIP approaches and thus enables isotope labeling experiments on much larger scales and with higher replication. The approach allows for the determination of isotope incorporation into microbiome members with species level resolution using standard metaproteomics liquid chromatography-tandem mass spectrometry (LC–MS/MS) measurements. At the core of the approach are new algorithms to analyze the data, which have been implemented in an open-source software ( https://sourceforge.net/projects/calis-p/ ). We demonstrate sensitivity, precision and accuracy using bacterial cultures and mock communities with different labeling schemes. Furthermore, we benchmark our approach against two existing Protein-SIP approaches and show that in the low labeling range used our approach is the most sensitive and accurate. Finally, we measure translational activity using 18 O heavy water labeling in a 63-species community derived from human fecal samples grown on media simulating two different diets. Activity could be quantified on average for 27 species per sample, with 9 species showing significantly higher activity on a high protein diet, as compared to a high fiber diet. Surprisingly, among the species with increased activity on high protein were several Bacteroides species known as fiber consumers. Apparently, protein supply is a critical consideration when assessing growth of intestinal microbes on fiber, including fiber-based prebiotics. Conclusions We demonstrate that our Protein-SIP approach allows for the ultra-sensitive (0.01 to 10% label) detection of stable isotopes of elements found in proteins, using standard metaproteomics data.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Putting Data to Work (Final Technical Report)

The Putting Data to Work project was designed to pilot and summarize the use of building energy performance data to improve energy efficiency program design and delivery in DC and NYC. By doing this, the project aimed to expand the market for energy efficiency in multifamily and commercial buildings by producing a toolkit of resources for other jurisdictions to replicate the successes found in the project cities.

30 DIRECT ENERGY CONVERSION↗

DOE OSTI2024

Process–Property–Performance Mapping of Additively Manufactured 316H Stainless Steel Components

The Advanced Materials and Manufacturing Technologies Program is focused on accelerating the development of advanced materials and components fabricated via additive manufacturing, and is using laser powder bed fusion (LPBF) of 316H stainless steel as an initial case study. In the previous fiscal year, miniature high-throughput specimens were printed on multiple LPBF systems to provide initial processing windows to minimize porosity and limit epitaxial grain growth during prints. This fiscal year, scaled builds were completed on three different LPBF systems at ORNL: a GE Concept Laser M2, a Renishaw AM400, and an EOS M290. Builds on the Concept Laser were conducted on multiple powder lots and processing parameter ranges to provide microstructure effects on time-independent and time-dependent mechanical properties. Builds on the Renishaw were produced using Oak Ridge National Laboratory (ORNL)-optimized printing parameters and Argonne National Laboratory (ANL)-optimized printing parameters to compare outcomes of parallel process optimization efforts at different national laboratories on the same LPBF system. Similarly, the build completed on the EOS M290 replicated the processing parameters of builds completed at Los Alamos National Laboratory (LANL). Optical microscopy and electron backscatter diffraction characterization was completed on all builds. In addition to the general round robin characterization, this work-package generated time-independent data, including tensile and fracture toughness test data on scaled Concept Laser builds as a function of processing parameters and post-build heat treatment. This analysis is complimentary to work in parallel work packages aiming to establish heat treatment and processing effects on time-dependent properties. It was found that although the stress-relief heat treatment provides the highest strength at lower-temperatures, tensile strength begins to converge at higher temperatures regardless of heat treatment condition. In addition, the more rigorous solution annealing and hot-isostatic pressing post-build heat treatments result in higher fracture toughness than the stress-relieved condition. The root-causes of the lower fracture toughness of the stress-relieved LPBF 316H material was informed via a stress-relief optimization study on a scaled concept laser print, where it was found that although dislocation recovery was largely complete after only a couple hours at 650°C, the extended hold of the current 24h heat treatment employed on scaled builds likely caused increased carbide volume fractions along the LPBF 316H grain boundaries, thereby deteriorating crack propagation resistance. This trend was seen to become more deleterious with additional increases of stress-relief temperature to 750°C or 850°C. These results have helped inform a new optimal stress-relief annealing condition for LPBF 316H for future campaign testing (650°C for 2h).

36 MATERIALS SCIENCE↗

DOE OSTI2024

Process–Property–Performance Mapping of Additively Manufactured 316H Stainless Steel Components

The Advanced Materials and Manufacturing Technologies Program is focused on accelerating the development of advanced materials and components fabricated via additive manufacturing, and is using laser powder bed fusion (LPBF) of 316H stainless steel as an initial case study. In the previous fiscal year, miniature high-throughput specimens were printed on multiple LPBF systems to provide initial processing windows to minimize porosity and limit epitaxial grain growth during prints. This fiscal year, scaled builds were completed on three different LPBF systems at ORNL: a GE Concept Laser M2, a Renishaw AM400, and an EOS M290. Builds on the Concept Laser were conducted on multiple powder lots and processing parameter ranges to provide microstructure effects on time-independent and time-dependent mechanical properties. Builds on the Renishaw were produced using Oak Ridge National Laboratory (ORNL)-optimized printing parameters and Argonne National Laboratory (ANL)-optimized printing parameters to compare outcomes of parallel process optimization efforts at different national laboratories on the same LPBF system. Similarly, the build completed on the EOS M290 replicated the processing parameters of builds completed at Los Alamos National Laboratory (LANL). Optical microscopy and electron backscatter diffraction characterization was completed on all builds. In addition to the general round robin characterization, this work-package generated time-independent data, including tensile and fracture toughness test data on scaled Concept Laser builds as a function of processing parameters and post-build heat treatment. This analysis is complimentary to work in parallel work packages aiming to establish heat treatment and processing effects on time-dependent properties. It was found that although the stress-relief heat treatment provides the highest strength at lower-temperatures, tensile strength begins to converge at higher temperatures regardless of heat treatment condition. In addition, the more rigorous solution annealing and hot-isostatic pressing post-build heat treatments result in higher fracture toughness than the stress-relieved condition. The root-causes of the lower fracture toughness of the stress-relieved LPBF 316H material was informed via a stress-relief optimization study on a scaled concept laser print, where it was found that although dislocation recovery was largely complete after only a couple hours at 650°C, the extended hold of the current 24h heat treatment employed on scaled builds likely caused increased carbide volume fractions along the LPBF 316H grain boundaries, thereby deteriorating crack propagation resistance. This trend was seen to become more deleterious with additional increases of stress-relief temperature to 750°C or 850°C. These results have helped inform a new optimal stress-relief annealing condition for LPBF 316H for future campaign testing (650°C for 2h).

36 MATERIALS SCIENCE↗

NASA NTRS1975

On the comparison of numerical theories of orbital motion

The requirements for the independent numerical replication of an ephemeris generated by numerical integration are examined and an investigation concerned with the duplication of the ephemeris of the numerical theory reported by Oesterwinter and Cohen (1972) is discussed. Discrepancies between the results of the investigation and the data reported by Oesterwinter and Cohen are considered. It was found very difficult to determine the cause for the discrepancies. Proposals are, therefore, made to provide together with the results of a numerical calculation sufficient information concerning the theoretical and computational basis on which the data were obtained.

Mulholland, J. D.↗

NASA NTRS1999

Superpolishing and Precision Metrology on a Metal Mandrel and Replicated Segments for Constellation-X

We have superpolished a diamond-turned aluminum mandrel (coated with electroless Ni) to an axial roughness of 6.34 nm rms. The mandrel is made to the Astro-E secondary mirror design for the 81st shell. Precision metrology at 100 mm to submicron scales has established the power spectral density of the mandrel and ultralightweight gold coated replicated segments. Predicted image quality of a set of optimally aligned replicated segments of this and a matching primary is substantially improved as compared to the flight mirrors for Astro-E. This approach using metal mandrels, superpolishing, and replicated ultralightweight foil mirrors, may represent a cost-effective approach to meeting the 15 arcsec half-energy width and weight requirements for the Constellation-X mission. Descriptions of the polishing apparatus, the precision metrology instruments, and the surface data analysis are presented. The general methods described are applicable to precision optics for both normal incidence and grazing incidence optics.

Content, D.↗

NASA NTRS1999

Superpolishing and Precision Metrology on a Metal Mandrel and Replicated Segments for Constellation-X

We have superpolished a diamond-turned aluminum mandrel (coated with electroless Ni) to an axial roughness of 0.34 nm rms. The mandrel is made to the Astro-E secondary mirror design for the 81st shell. Precision metrology at 100 mm to submicron scales has established the power spectral density of the mandrel and ultralightweight gold coated replicated segments. Predicted image quality of a set of optimally aligned replicated segments of this and a matching primary is substantially improved as compared to the flight mirrors for Astro-E. This approach using metal mandrels, superpolishing, and replicated ultralightweight foil mirrors, may represent a cost-effective approach to meeting the 15 arcsec half-energy width and weight requirements for the Constellation-X mission. Descriptions of the polishing apparatus, the precision metrology instruments, and the surface data analysis are presented. The general methods described are applicable to precision optics for both normal incidence and grazing incidence optics.

Content, D.↗

NASA NTRS1999

Superpolishing and Precision Metrology on a Metal Mandrel and Replicated Segments for Constellation-X

We have superpolished a diamond-turned aluminum mandrel (coated with electroless Ni) to an axial roughness of 0.34 nm rms. The mandrel is made to the Astro-E secondary mirror design for the 81st shell. Precision metrology at 100 mm to submicron scales has established the power spectral density of the mandrel and ultralightweight gold coated replicated segments. Predicted image quality of a set of optimally aligned replicated segments of this and a matching primary is substantially improved as compared to the flight mirrors for Astro-E. This approach using metal mandrels, superpolishing, and replicated ultralightweight foil mirrors, may represent a cost-effective approach to meeting the 15 arcsec half-energy width and weight requirements for the Constellation-X mission. Descriptions of the polishing apparatus, the precision metrology instruments, and the surface data analysis are presented. The general methods described are applicable to precision optics for both normal incidence and grazing incidence optics.

Content, D.↗

NASA NTRS2004

Habitat Utilization Assessment - Building in Behaviors

Habitability, and the associated architectural and design attributes of an environment, is a powerful performance shaping factor. By identifying how inhabitants use an area, we can draw conclusions about what design or architectural attributes cause what behaviors and systematically design in desired human performance. We are analyzing how a crew uses a long duration habitat and work environment during a four-day underwater mission and identifying certain architectural and design attributes that are related to, and potential enablers of, certain crew behaviors. By identifying how inhabitants use the habitat, we can draw conclusions about what habitability attributes cause what behaviors and systematically design in desired human performance (applicable to NASA's Bioastronautics Human Behavior and Performance Critical Path Roadmap question 6.12). This assessment replicates a methodology reported in a chapter titled "Sociokinetic Analysis as a Tool for Optimization of Environmental Design" by C. Adams.' That study collected video imagery of certain areas of a closed habitat during a 91 day test and from that data calculated time spent in different volumes during the mission, and characterized the behaviors occurring in certain habitat volumes thus concluding various rules for design of such habitats. This study assesses the utilization of the Aquarius Habitat, an underwater station, which will support six Aquanauts for a fourteen-day mission during which the crew will perform specific scientific and engineering studies. Video is recorded for long uninterrupted periods of time during the mission and from that data the time spent in each area is calculated. In addition, qualitative and descriptive analysis of the types of behaviors in each area is performed with the purpose of identifying any behaviors that are not typical of a certain area. If a participant uses an area in a way different from expected, a subsequent analysis of the features of that area may result in conclusions of performance shaping factors. With the addition of this study, we can make comparisons between the two different habitats and begin drawing correlation judgments about design features and behavior. Ideally, this methodology should be repeated in additional Aquarius missions and other analog environments because the real information will come from comparisons between habitats.

Whitmore, Mihriban↗

NASA NTRS2005

Gesture Based Control and EMG Decomposition

This paper presents two probabilistic developments for use with Electromyograms (EMG). First described is a new-electric interface for virtual device control based on gesture recognition. The second development is a Bayesian method for decomposing EMG into individual motor unit action potentials. This more complex technique will then allow for higher resolution in separating muscle groups for gesture recognition. All examples presented rely upon sampling EMG data from a subject's forearm. The gesture based recognition uses pattern recognition software that has been trained to identify gestures from among a given set of gestures. The pattern recognition software consists of hidden Markov models which are used to recognize the gestures as they are being performed in real-time from moving averages of EMG. Two experiments were conducted to examine the feasibility of this interface technology. The first replicated a virtual joystick interface, and the second replicated a keyboard. Moving averages of EMG do not provide easy distinction between fine muscle groups. To better distinguish between different fine motor skill muscle groups we present a Bayesian algorithm to separate surface EMG into representative motor unit action potentials. The algorithm is based upon differential Variable Component Analysis (dVCA) [l], [2] which was originally developed for Electroencephalograms. The algorithm uses a simple forward model representing a mixture of motor unit action potentials as seen across multiple channels. The parameters of this model are iteratively optimized for each component. Results are presented on both synthetic and experimental EMG data. The synthetic case has additive white noise and is compared with known components. The experimental EMG data was obtained using a custom linear electrode array designed for this study.

Wheeler, Kevin R.↗

DOE OSTI2020

Insights into the dynamics between viruses and their hosts in a hot spring microbial mat

Abstract Our current knowledge of host–virus interactions in biofilms is limited to computational predictions based on laboratory experiments with a small number of cultured bacteria. However, natural biofilms are diverse and chiefly composed of uncultured bacteria and archaea with no viral infection patterns and lifestyle predictions described to date. Herein, we predict the first DNA sequence-based host–virus interactions in a natural biofilm. Using single-cell genomics and metagenomics applied to a hot spring mat of the Cone Pool in Mono County, California, we provide insights into virus–host range, lifestyle and distribution across different mat layers. Thirty-four out of 130 single cells contained at least one viral contig (26%), which, together with the metagenome-assembled genomes, resulted in detection of 59 viruses linked to 34 host species. Analysis of single-cell amplification kinetics revealed a lack of active viral replication on the single-cell level. These findings were further supported by mapping metagenomic reads from different mat layers to the obtained host–virus pairs, which indicated a low copy number of viral genomes compared to their hosts. Lastly, the metagenomic data revealed high layer specificity of viruses, suggesting limited diffusion to other mat layers. Taken together, these observations indicate that in low mobility environments with high microbial abundance, lysogeny is the predominant viral lifestyle, in line with the previously proposed “Piggyback-the-Winner” theory.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Proteome-wide association study and functional validation identify novel protein markers for pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) remains a lethal malignancy, largely due to the paucity of reliable biomarkers for early detection and therapeutic targeting. Existing blood protein biomarkers for PDAC often suffer from replicability issues, arising from inherent limitations such as unmeasured confounding factors in conventional epidemiologic study designs. To circumvent these limitations, we use genetic instruments to identify proteins with genetically predicted levels to be associated with PDAC risk. Leveraging genome and plasma proteome data from the INTERVAL study, we established and validated models to predict protein levels using genetic variants. By examining 8,275 PDAC cases and 6,723 controls, we identified 40 associated proteins, of which 16 are novel. Functionally validating these candidates by focusing on 2 selected novel protein-encoding genes, GOLM1 and B4GALT1, we demonstrated their pivotal roles in driving PDAC cell proliferation, migration, and invasion. Furthermore, we also identified potential drug repurposing opportunities for treating PDAC.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Data for "RT-EZ: A Golden Gate Assembly Toolkit for Streamlined Genetic Engineering of Rhodotorula toruloides"

For economic and sustainable biomanufacturing, the oleaginous yeast Rhodotorula toruloides has emerged as a promising platform for producing biofuels, pharmaceuticals, and other valuable chemicals. However, genetic manipulation of R. toruloides has been limited by its high GC content and the lack of a replicating plasmid, necessitating gene integration into the genome of the yeast. To address these challenges, we developed the RT-EZ ( R. toruloides Efficient Zipper) toolkit, a versatile tool based on Golden Gate assembly, designed to streamline R. toruloides engineering with improved efficiency and flexibility. The RT-EZ toolkit simplifies vector construction by incorporating new features such as bidirectional promoters and 2A peptides, color-based screening using RFP, and sequences optimized for both Agrobacterium tumefaciens-mediated transformation (ATMT) and easy linearization, enabling straightforward selection and transformation. Notably, the RT-EZ kit can be used to construct an expression cassette with four different genes in one assembly reaction, significantly improving vector construction speed and efficiency. The utility of the RT-EZ toolkit was demonstrated through the successful synthesis of arachidonic acid in R. toruloides by coexpressing fatty acid elongases and desaturases. This result underscores the potential of the RT-EZ toolkit to advance synthetic biology in R. toruloides , providing a streamlined method for addressing genetic engineering challenges in the yeast.

gene editing↗