Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “sequence”

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 1,783 records · Page 99
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Eukaryotic initiation factor 3 (eIF3) and 5’ mRNA leader sequences as agents of translational regulation in Arabidopsis. Final report

Protein synthesis, or translation, consumes a sizable fraction of the cell’s energy budget, estimated at 5% and up to 50% in differentiated and growing cells, respectively. Plants also invest significant energy and biomass to construct and maintain the translation apparatus. Translation is regulated by a variety of external stimuli. Compared to transcriptional control, attributes of translational control include reduced sensitivity to stochastic fluctuation, a finer gauge of control, and more rapid responsiveness to environmental stimuli. Yet, our murky understanding of translational control allows few generalizations. Consequently, translational regulation is underutilized in the context of transgene regulation, although synthetic biologists are now beginning to appropriate RNA-level gene regulation into their regulatory circuits. We also know little about how translational control contributes to the diversity of plant form and function. This project explored how an emerging regulatory mRNA sequence element, upstream open reading frames (uORFs), is integrated with the general translation initiation machinery to permit translational regulation on specific mRNAs.

09 BIOMASS FUELS↗
DOE OSTI2015

LLNL's Big Science Capabilities Help Spur Over $796 Billion in U.S. Economic Activity Sequencing the Human Genome

LLNL’s successful history of taking on big science projects spans beyond national security and has helped create billions of dollars per year in new economic activity. One example is LLNL’s role in helping sequence the human genome. Over $796 billion in new economic activity in over half a dozen fields has been documented since LLNL successfully completed this Grand Challenge.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Next-Gen 3 : Sequencing, Modeling, and Advanced Biofuels - Final Technical Report

Successful, scalable implementation of biofuels is dependent on the efficient and near complete utilization of diverse biomass sources. One approach is to utilize the large recalcitrant biomass fraction (or any organic waste stream) through the thermochemical conversion of organic compounds to syngas, a mixture of carbon monoxide (CO), carbon dioxide (CO 2 ), and hydrogen (H 2 ), which can subsequently be metabolized by acetogenic microorganisms to produce next-gen biofuels. The goal of this proposal was to advance the development of the acetogen Clostridium ljungdahlii as a chassis organism for next-gen biofuel production from cheap, renewable sources and to detail the interconnectivity of metabolism, energy conservation, and regulation of acetogens using next-gen sequencing and next-gen modeling. To achieve this goal we determined optimization of carbon and energy utilization through differential translational efficiency in C. ljungdahlii. Furthermore, we reconstructed a next-generation model of all major cellular processes, such as macromolecular synthesis and transcriptional regulation and deployed this model to predicting proteome allocation, overflow metabolism, and metal requirements in this model acetogen. In addition we explored the evolutionary significance of tRNA operon structure using the next-gen model and determined the optimal operon structure for bioproduction. Our study substantially enhanced the knowledgebaase for chemolithoautotrophs and their potential for advanced biofuel production. It provides next-generation modeling capability, offer innovative tools for genome-scale engineering, and provide novel methods to utilize next-generation models for the design of tunable systems that produce commodity chemicals from inexpensive sources.

09 BIOMASS FUELS↗
DOE OSTI2018

HIV Sequence Compendium 2018

This compendium is an annual summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Sequence Capture to Monitor Functional Potential of Microbial Communities

Microorganisms play key roles in environmental functioning and understanding their responses to environmental perturbation is critical to developing accurate climate change models, a need highlighted by the DOE. However, their phylogenetic and functional diversity, abundance in the environment, and lack of cultured status make microorganisms challenging to study. While there are several molecular methods available that have been extremely important in advancing our knowledge of microbial ecology, there are serious drawbacks to each of the available methods. In Phase I of this project, we tested the use of a sequence capture method on microbial communities using mock microbial communities and capture probes for 3 different genes (nifH, nirK, and dsrA). We optimized library preparation steps and then tested mock communities with different proportions of members and different hybridization conditions. Our Phase I work demonstrated the feasibility of using this technology for capturing and enriching specific functional genes from microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Workbench Analysis Sequence Processor

The Workbench Analysis Sequence Processor (WASP) was developed to streamline lexing, parsing, access, validation, and analysis of ascii text files. The foundation of WASP resides on the parse tree data structure, where each node in the tree represents the syntax of the input document. Nodes can parent nodes with children. Nodes that have no children are known as terminal or leaf nodes , and they represent tokens (string, number, delimiter, etc.) in the text file. The fast lexical analyzer generator (flex - https://www.gnu.org/software/flex/) and GNU Bison parser generator (https://www.gnu.org/software/bison/) are extensively used for lexing and parsing.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

HIV Databases video tutorial on use of the HIV sequence quality control tool

The HIV Databases at LANL (https://www.hiv.lanl.gov) provide many tools for HIV data retrieval and analysis. The quality control tool (https://www.hiv.lanl.gov/content/sequence/QC/index.html) is used to check the quality of new HIV sequence data, help the user determine which subtype of virus belongs to, and prepare the data for submission to the database. This video gives a 10 minute overview of the use of the tool and illustrates results form a sample data set.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Illumina Sequencing for SARS-CoV-2 Training [Slides]

This report compiles Wetlab training slides for DTRA sponsored training and has presentations titled: 1) Library Validation Step 2: Bioanalyzer DNA HS Assay, 2) Library Validation Step 3: qPCR, 3) Setting up a MiSeq Run, 4) Sample Prep & Initial QC, 5) Detailed Illumina MiSeq Sequencing, 6) AmpliSeq for Illumina: Best Practices, and 7) Sample/Data Management for SARS-CoV-2 Samples.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Data Analysis of the 2020 Central Idaho Mainshock-Aftershock Sequence

In an effort to inform the Senior Seismic Hazard Analysis Committee for the Idaho National Laboratory, we provide an improved aftershock catalog related to the March 31, 2020, Mw6.5 Stanley, Idaho earthquake from picks related to a temporary network of two real-time and 15 non-telemetered seismometers within the epicentral area. From the permanent and temporary (XP) real-time network, the USGS cataloged 1,946 aftershocks between April 1, 2020 and October 31, 2020. To improve aftershock location and magnitudes, we manually picked arrival times of P and S waves from off-line stations in the XP temporary network, generated a new crustal velocity model, and independently relocated each event using the HypoDD double-difference earthquake algorithm. We created our new velocity model from existing broadband and active source seismic campaign data that were acquired near the epicentral region prior to the 2020 earthquake. We compare arrival time differences, epicentral locations and depths between aftershocks recorded with the two catalogs. We find the addition of local stations provides tighter aftershock clustering that suggests an improved aftershock locations. To detect lower magnitude events, we employed deep learning. Our method solves common problems associated with detecting many events that have a low signal-to-noise ratio. From the machine learning database, we detected more than 74,000 aftershocks. Based on the number of identified earthquakes and Gutenberg-Richter relationships derived from the USGS catalog, we estimate that we have reduced the completion magnitude for the Stanley earthquake sequence to below M1 using this machine learning approach. We located each aftershock with our new velocity model. Our new velocity model and picks suggests aftershocks occurred mostly at shallower depths than assessed in the USGS catalog. These aftershocks align along two linear trends that suggest the activation of two unnamed primary faults.

58 GEOSCIENCES↗
DOE OSTI2024

Merefa Community Microgrid: Conceptual Design and Sequence of Operations [Slides]

A conceptual design is described for a community microgrid in Ukraine. Microgrid resources include solar photovoltaics, battery energy storage, and conventional natural gas fueled reciprocating engine generators. The conceptual architecture was informed by the microgrid developer, NREL subject matter experts, and the application of REopt, an NREL-developed software tool created for identification of least-cost combination of resources for achieving cost savings, resilience, and renewable energy goals. The report includes conceptual architecture, estimates of key summary financial metrics, and sequence of operations.

14 SOLAR ENERGY↗
DOE OSTI2025

Develop High-Throughput Workflows for Whole-Genome Sequencing and Insertion Site Screening (CRADA Final Report)

The engineering of microbes for biomanufacturing (e.g. of fuels, chemicals, materials) applications has advanced to a stage where researchers screen genetic libraries with millions of variations each for those with enhanced productivity. This screening, however, can be slow and expensive, as screening individual variants in a high-throughput yet cost-effective manner is challenging. In this project, we aimed to reduce by 3-fold costs associated with the sequencing aspects of the screening process (to determine which genetic variant is responsible for an observed change in productivity), while being able to process over 1,000 samples per batch.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Develop High-Throughput Workflows for Whole-Genome Sequencing and Insertion Site Screening

The engineering of microbes for biomanufacturing (e.g. of fuels, chemicals, materials) applications has advanced to a stage where researchers screen genetic libraries with millions of variations each for those with enhanced productivity. This screening, however, can be slow and expensive, as screening individual variants in a high-throughput yet cost-effective manner is challenging. In this project, we aimed to reduce by 3-fold costs associated with the sequencing aspects of the screening process (to determine which genetic variant is responsible for an observed change in productivity), while being able to process over 1,000 samples per batch.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Mesh-Sequenced Realizations for Evaluation of Subgrid-Scale Models for Turbulent Combustion

This paper develops a new approach for analysis of subgrid closures for turbulent combustion as modeled using direct quadrature (finite-rate chemistry) techniques. The approach, termed multiresolution analysis through mesh-sequenced realizations (MRA-MSR), conducts simultaneous, constrained large-eddy simulations on a set of hierarchically coarsened meshes. Furthermore, the availability of underlying fine-mesh (subgrid) data corresponding to coarse-mesh locations allows a clearer assessment of the effects of unresolved fluctuations on apparent reactivity. A key to MRA-MSR is the correlation of eddy structures at coarser mesh levels, which is facilitated by the transfer of filtered fine-mesh velocity information. A seven-mesh MRA-MSR hierarchy using three resolution levels is applied to one of the Sydney bluff-body stabilized methane–hydrogen flames. Analysis of the simultaneously evolved data at different resolution levels reveals several interesting trends. First, at high Damköhler numbers, there is clear evidence of attenuation of apparent reactivity due to the effects of unresolved fluctuations. Secondly, single-point, single-time filtered density functions of a normalized subgrid Damköhler number show a characteristic beta probability density function (PDF) form and display evidence of scale similarity. Interrogation of the MRA-MSR database also shows that the recently-proposed least-squares minimization (LSM) turbulence–chemistry interaction model can account for the observed diminishment in reactivity at high Damköhler numbers but cannot reduce scatter significantly. A new form of the LSM model, which makes use of the normalized subgrid Damköhler number beta PDF distribution, performs slightly better than the original model, illustrating the potential of MRA-MSR both in assessing existing closure concepts and in developing new ones.

42 ENGINEERING↗
DOE OSTI2019

16S rRNA Amplicon sequence data and community assembly process file

Soils along a salinity gradient from a coastal forested floodplain (Beaver Creek in Western Washington) were analyzed for their microbial community composition and community assembly processes. These files contain processed 16S rRNA amplicon sequences into OTU table, the corresponding tree file, metadata, community assembly process analysis and results, microbial phyla abundances, and codes evaluating BNTI indices and community assembly process estimates.

54 ENVIRONMENTAL SCIENCES↗