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At least 829 records · Page 46
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly

The programmable synthesis of rationally engineered crystal architectures for the precise arrangement of molecular species is a foundational goal in nanotechnology, and DNA has become one of the most prominent molecules for the construction of these materials. In particular, branched DNA junctions have been used as the central building block for the assembly of 3D lattices. Here, crystallography is used to probe the effect of all 36 immobile Holliday junction sequences on self-assembling DNA crystals. Contrary to the established paradigm in the field, most junctions yield crystals, with some enhancing the resolution or resulting in unique crystal symmetries. Unexpectedly, even the sequence adjacent to the junction has a significant effect on the crystal assemblies. Six of the immobile junction sequences are completely resistant to crystallization and thus deemed “fatal,” and molecular dynamics simulations reveal that these junctions invariably lack two discrete ion binding sites that are pivotal for crystal formation. The structures and dynamics detailed here could be used to inform future designs of both crystals and DNA nanostructures more broadly, and have potential implications for the molecular engineering of applied nanoelectronics, nanophotonics, and catalysis within the crystalline context.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Conceptual Design of a Water Tank Critical Facility for SPARC

Critical experiments, sometimes referred to zero-power reactors, are crucial tools in developing and validating nuclear physics predictions and thus an indispensable capability to ensure criticality safety during all parts of the nuclear fuel cycle and in reducing uncertainties in reactor physics predictions toward optimizing nuclear energy production. The System Physics Advanced Reactor Facility (SPARC) project was recently initiated to enable large-scale criticality experiments using a horizontal split table machine well suited toward solid core materials systems (fuel, moderator, reflector). The facility selected for this mission was a former pool-type research reactor building and thus also well suited toward a second critical experiment capability able to house full-size light-water reactor (LWR) fuel bundles. A conceptual design study was undertaken to review past water tank critical experiments used for LWR physics experiments and to develop an early engineering design for a new critical assembly tank (CAT). The work described here shows that a relatively simple CAT concept can be constructed and deployed in the SPARC facility to meet the urgent demands for new critical experiments on advanced LWR fuel bundles designs. The SPARC facility layout is conducive to the receipt and upending of LWR fuel bundles using existing containers and equipment from the LWR industry. The facility’s overhead crane can then be used to handle fuel bundles and place them in a vertical storage rack or in the CAT for critical experiments, both of which fit within the building’s “open basement” alongside other equipment planned for SPARC and the horizontal split table. A slightly lower area in the basement can serve as a large drain tank so that fail-safe valves drain the CAT reactor tank for safe shutdown. Neutronic configurations were determined where a 3 × 3 array of fuel bundles can be surrounded by full-length “loose rods” to adjust reactivity so that critical is achieved when the bundles are fully submerged. Viable configurations were determined for both pressurized- and boiling-water-reactor-type fuel bundles. This design concept was used to develop an early planning basis for establishing the CAT capability alongside the otherwise planned SPARC project in order to help streamline the process. Recent presidential executive orders have highlighted the need to achieve power uprates in LWR plants and the CAT capability will be a crucial element of these initiatives. Based on the work described herein, it is recommended that an earnest and timely project begin in order to establish this urgently needed capability.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2026

Cyanobacterial Biofertilizer Production by Guanidine-Producing Enzymes

Cyanobacterial production of a biofertilizer shows promise as an environmentally benign alternative to conventional nitrogen fertilizers, reducing environmental and energy burdens through light-driven nitrogen and carbon fixation. One route to realizing the potential for a nitrogen-rich, slow-releasing biofertilizer involves the genetic engineering of cyanobacteria to produce guanidine. Recent advances have demonstrated enzymatic guanidine production in cyanobacteria, but an understanding of cyanobacterial guanidine metabolism is still limited. This Perspective highlights strategies and opportunities for cyanobacterial guanidine production in a Design−Build−Test−Learn cycle. Exploring new guanidine-producing enzymes via phylogenetics could expand candidate enzymes, while understanding the metabolism of substrates can identify constraints and opportunities in substrate utilization. Additionally, guanidine sensing and export are crucial areas of study to enable continuous fertilizer production and stable nitrogen flux. These strategies will guide the development of advanced nitrogen biofertilizer strategies for the agricultural sector.

09 BIOMASS FUELS↗
DOE OSTI2025

Direct Observations of Solute Dispersion in Rocks With Distinct Degree of Sub‐Micron Porosity

Abstract The transport of chemical species in rocks is affected by their structural heterogeneity to yield a wide spectrum of local solute concentrations. To quantify such imperfect mixing, advanced methodologies are needed that augment the traditional breakthrough curve analysis by probing solute concentration within the fluids locally. Here, we demonstrate the application of asynchronous, multimodality imaging by X‐ray computed tomography (XCT) and positron emission tomography (PET) to the study of passive tracer experiments in laboratory rock cores. The four‐dimensional concentration maps measured by PET reveal specific signatures of the transport process, which we have quantified using fundamental measures of mixing and spreading. We observe that the extent of solute spreading correlate strongly with the strength of subcore‐scale porosity heterogeneity measured by XCT, while dilution is enhanced in rocks containing substantial sub‐micron porosity. We observe that the analysis of different metrics is necessary, as they can differ in their sensitivity to the strength and forms of heterogeneity. The multimodality imaging approach is uniquely suited to probe the fundamental difference between spreading and mixing in heterogeneous media. We propose that when multi‐dimensional data is available, mixing and spreading can be independently quantified using the same metric. We also demonstrate that one‐dimensional transport models have limited predictive ability toward the internal evolution of the solute concentration, when the model is solely calibrated against the effluent breakthrough curves. The data set generated in this study can be used to build realistic digital rock models and to benchmark transport simulations that account deterministically for rock property heterogeneity.

Kurotori, Takeshi [Department of Chemical Engineer↗
DOE OSTI2024

A Perspective on Scalable AI on High-Performance Computing and Leadership Class Supercomputing Facilities [Industrial and Governmental Activities]

Many scientific applications that support the mission of the US Department of Energy (US-DoE) require modeling complex engineering and/or physical systems. Here, examples of such complex systems arise from: (a) materials science to develop new compounds with exceptional mechanical and thermodynamical properties (e.g., resistance to mechanical stresses and high temperatures), (b) structural and nuclear engineering to model the temporal evolution of the structural damage of concrete shields exposed to continuous neutron and gamma radiations emitted by the nuclear reactor core, (c) urban sciences (e.g., transportation and smart buildings), and (d) power grid systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Computational Estimation by Scientific Data Mining with Classical Methods to Automate Learning Strategies of Scientists

Experimental results are often plotted as 2-dimensional graphical plots (aka graphs) in scientific domains depicting dependent versus independent variables to aid visual analysis of processes. Repeatedly performing laboratory experiments consumes significant time and resources, motivating the need for computational estimation. The goals are to estimate the graph obtained in an experiment given its input conditions, and to estimate the conditions that would lead to a desired graph. Existing estimation approaches often do not meet accuracy and efficiency needs of targeted applications. We develop a computational estimation approach called AutoDomainMine that integrates clustering and classification over complex scientific data in a framework so as to automate classical learning methods of scientists. Knowledge discovered thereby from a database of existing experiments serves as the basis for estimation. Challenges include preserving domain semantics in clustering, finding matching strategies in classification, striking a good balance between elaboration and conciseness while displaying estimation results based on needs of targeted users, and deriving objective measures to capture subjective user interests. These and other challenges are addressed in this work. The AutoDomainMine approach is used to build a computational estimation system, rigorously evaluated with real data in Materials Science. Our evaluation confirms that AutoDomainMine provides desired accuracy and efficiency in computational estimation. It is extendable to other science and engineering domains as proved by adaptation of its sub-processes within fields such as Bioinformatics and Nanotechnology.

Computer Science↗
DOE OSTI2021

Steady-State Ultrasonic Non-Destructive Evaluation for Aerospace & Additive Manufacturing Applications [Slides]

How does ultrasonic inspection work? Rich phenomenology of interactions between ultrasonic waves and features in plate-like structures. Hidden defects/discontinuities create measurable changes in the surface wavefield. Based on these measurements, we can build tools that detect the presence of different kinds of defects and estimate structural/material properties (e.g. local thickness).

42 ENGINEERING↗
DOE OSTI2021

Cost-Effectiveness of ANSI/ASHRAE/IES Standard 90.1-2019 for Michigan

This report describes the methodology and results of a state cost-effectiveness analysis of ASHRAE Standard 90.1-2019. Moving to the Standard 90.1-2019 edition from Standard 90.1-2016 is found to be cost-effective for the state. Annual energy cost savings, added construction costs, and life-cycle costs are all described and presented here for various building types and climate zones.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2023

A Planetary Defense System For Responsive Space Missions

As King et al succinctly write, “Collision between the Earth and small objects in the solar system are known to occur regularly, and can result in extinction-level events at their most energetic or more commonly widespread loss of life or economic destruction even for relatively low-energy impacts.” Currently, the JPL Sentry System and the NASA NEO Surveyor mission track, identify, and monitor potential asteroid threats. The JPL Sentry System4 is an automated collision monitoring system which scans the current asteroid catalog for potential impact trajectories with Earth. A 2017 study led by P. Tricarico titled “The near-Earth asteroid population from two decades of observations” analyzes the combined observations of nine leading asteroid surveys. The NASA NEO Surveyor mission seeks to identify 90% of near-Earth objects (NEO) with diameters greater than 140 meters (460 feet) within 10 years. The NEO Surveyor combines data from two infrared imaging detectors to measure NEO size, composition, shape, rotational state, and orbits. Recently, the NASA Double Asteroid Redirection Test (DART) mission successfully altered the orbit of asteroid moon Dimorphos in 2022. This demonstrated that orbit alteration is possible. Thus, collisions between the Earth and asteroids are both likely and demonstrate potential for great harm. There is ongoing work to identify, catalog, and track potential threats. However, when a threat is identified there is not yet a system in place to target the threatening asteroid and defend the planet from potentially existential threats. Building on the DART Mission, we explore a planetary defense system to mitigate asteroid threats.

42 ENGINEERING↗
DOE OSTI2024

CAD-based Energy & Cost Models Prove Affordable Net Zero Energy Performance for WonderWindows + 24" On-center Framing

Windows are thermally the “weakest link” in the building envelope. Increasing the thermal resistance of windows can make buildings more energy efficient and reduce the cost of electricity needed for conditioning the building. The proper design and placement of framing can also help to reduce the thermal bridging that occurs near the window frame area. This study investigates the energy performance of multi-pane acrylic windows fitting 24" on-center framing. Initial parametric analysis is done for a single zone accessory dwelling unit (ADU). Then, an energy model was developed for three types of wood-framed buildings: townhomes, stacked flats and hotels. A whole building energy simulation is performed for each of these building types in hot-humid Houston, mixed-humid New York, and cold-humid Minneapolis climates. The results show up to a 39% reduction in heating, ventilation, and air-conditioning (HVAC) related electricity consumption for the cold climate compared to the Base case which has window and wall properties based on ASHRAE standard 90.1 2019. In the hot climate, a modest increase in electricity consumption was seen due to an increase in cooling electricity demand. The ADU achieved Net Zero Energy performance in all 3 Climate Zones despite having the highest exterior surface area-to-floor area ratio: the ADU also had the highest PV kW to floor area ratio compared to the other multi-story building types. The townhomes, hotel and stacked flats respectively met 73, 52 and 57 % of electrical use in Houston, 71, 48 and 56 % in New York, and 63, 40 and 53 % in Minneapolis from energy produced by rooftop solar. If 400 W solar panels are used instead of 320 W panel used for energy simulation, it is estimated that in the townhomes, hotel and stacked flats rooftop solar can meet 91, 65 and 71 % of electrical use in Houston; 89, 60 and 70% in New York, and 79, 50 and 66 % in Minneapolis. A preliminary evaluation of cost shows that such superior performance can potentially be achieved at less first cost with this 24"on-center solution than conventional construction. All the building types at the three locations used for simulation had net energy use intensity under 20 kBtu/sf/year with 320 W solar panel and under 17 kBtu/sf/year with 400 W solar panel. Further tailoring of building envelope R-values and window solar heat gain to particular Climate Zone locations for each building type shows promise in reducing the HVAC electricity use that comprises almost half of building energy use.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2024

Description of the Gas Sampling and Circulation System for the LYNM PE1-A Experiment

A series of multiphysics experiments, referred to as Physics Experiment 1 (PE1) is underway at the U.S. Nevada National Security Site. The PE1 series includes detonations of three underground chemical explosions. As the name implies, there are a number of experiments investigating the signals generated by the explosion. The experiment series objectives are outlined in a report from Lawrence Livermore National Laboratory.1 One of the experiments is a gas migration experiment. Gas tracers were imbedded in the explosives and gas sampling boreholes were installed in the formation in the test bed. Connected to the monitoring points is a circulation system that moves gas to a central measurement location. This report does not describe the gas analysis or collection systems, but rather the circulation system that provides the gas for measurement. Here, we have combined four project documents into a single report that describes the design, build, installation, testing, and operation of the gas sampling network.

42 ENGINEERING↗
DOE OSTI2023

The Circular Home: Development and Demonstration of a Net Negative Carbon, Reusable Residence

This project started the development of an innovative modular building system intended for residential construction. The project was centered around single-family homes that were carbon-negative cradle-to-grave over a 100 year time frame, which is approximately double the current standard for operational life. The project sought to accomplish this objective by designing the modular home in a manner that ensures circularity, where the main house components can be used over several consecutive 50-year lifespans. To accomplish these objectives, this project utilized integrated design with the inclusion of life-cycle assessment to design the single-family house for architectural, structural, energy, mechanical, thermal, and moisture demands, while ensuring carbon negativity and annual net-zero energy use. The core technology of this project was the use of cross-laminated timber and biogenic materials, such as wood-fiber insulation, in the construction of the modular building units. The robustness and factory manufacturing ability of cross-laminated timber allow for factory construction of most of the home, which minimizes on-site time, saving money and reducing construction waste. During this project, initial milestones were met that delivered the architectural plans for the circular home and an initial structural testing matrix. Compared to current code-built homes, which average 13 kg CO2eq. / ft2 and are demolished at their end of life, the circular home has an estimated -30 kg CO2eq. / ft2 of embodied carbon emissions during its first build iteration. It is estimated that approximately 60%-70% of the total building mass could be reused and/or recycled during subsequent rebuilds. This project was concluded at approximately the 1/3 point and a separate project was established to conclude the remaining milestones. This project promises to benefit the public by delivering another option for single-family, and eventually multi-family, housing using a novel building construction system. The system of reusable modular construction facilitates not only lower emissions during the first building iteration, but also lower emissions during subsequent iterations that drastically reduce waste and help society meet its climate goals. Many other industries, such as clothing and technology sectors, are starting to focus on circularity and this project adds the residential building construction industry to that list.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2020

Metabolic Pathway Engineering

Modern microbial and enzyme engineering and their advancement are increasingly dependent on the marriage of a wide range of sophisticated technologies. For students entering the field of biotechnology, the outlook is indeed daunting. Expertise at levels beyond that of simple familiarity will be needed to conduct competitive research. It goes without saying that to be competitive, all new researchers in this field will need basic preparation in molecular biology, biochemistry, and genetics. Further, experience working with concepts and experimental tools in enzyme biochemistry and kinetics, gene editing, computational metabolic pathway modeling, experimental pathway flux analysis, and computational clustering tools to process complex data sets will be vital for success. We speculate that most biotechnology researchers in early career at this time will build teams of collaborators to address these disparate science fields rather than attempt to become experts in one lab.

BASIC BIOLOGICAL SCIENCES,BIOMASS FUELS↗
DOE OSTI2021

Further engineering of R. toruloides for the production of terpenes from lignocellulosic biomass

Abstract Background Mitigation of climate change requires that new routes for the production of fuels and chemicals be as oil-independent as possible. The microbial conversion of lignocellulosic feedstocks into terpene-based biofuels and bioproducts represents one such route. This work builds upon previous demonstrations that the single-celled carotenogenic basidiomycete, Rhodosporidium toruloides , is a promising host for the production of terpenes from lignocellulosic hydrolysates. Results This study focuses on the optimization of production of the monoterpene 1,8-cineole and the sesquiterpene α-bisabolene in R. toruloides . The α-bisabolene titer attained in R. toruloides was found to be proportional to the copy number of the bisabolene synthase (BIS) expression cassette, which in turn influenced the expression level of several native mevalonate pathway genes. The addition of more copies of BIS under a stronger promoter resulted in production of α-bisabolene at 2.2 g/L from lignocellulosic hydrolysate in a 2-L fermenter. Production of 1,8-cineole was found to be limited by availability of the precursor geranylgeranyl pyrophosphate (GPP) and expression of an appropriate GPP synthase increased the monoterpene titer fourfold to 143 mg/L at bench scale. Targeted mevalonate pathway metabolite analysis suggested that 3-hydroxy-3-methyl-glutaryl-coenzyme A reductase (HMGR), mevalonate kinase (MK) and phosphomevalonate kinase (PMK) may be pathway bottlenecks are were therefore selected as targets for overexpression. Expression of HMGR, MK, and PMK orthologs and growth in an optimized lignocellulosic hydrolysate medium increased the 1,8-cineole titer an additional tenfold to 1.4 g/L. Expression of the same mevalonate pathway genes did not have as large an impact on α-bisabolene production, although the final titer was higher at 2.6 g/L. Furthermore, mevalonate pathway intermediates accumulated in the mevalonate-engineered strains, suggesting room for further improvement. Conclusions This work brings R. toruloides closer to being able to make industrially relevant quantities of terpene from lignocellulosic biomass.

09 BIOMASS FUELS↗
DOE OSTI2022

Development and Demonstration of a Fuel-Efficient, Class 8 Tractor & Trailer Engine System (SuperTruck II)

Navistar presents the SuperTruck II (ST II) Final Report to the Unites States Department of Energy (US DOE), which covers the five Budget Periods (BPs) from 10-1-2016 through 6-30-2022. For ST II, Navistar built on the achievements of the SuperTruck I (ST I) Program as a catalyst to continue critical research, design and development, testing, and operations to reach the ambitious goals of the ST II project. This approach allowed Navistar to continue contributing to the essential needs of our nation for safe, efficient, and cost-effective delivery of goods and services, as we reduced negative environmental effects and improved operational productivity. This document contains information specified in DOE F 4600.2, Final Scientific/Technical Report DOE F 241.3, B. SCIENTIFIC/TECHNICAL REPORTS, explaining how we met and exceeded program requirements. Throughout this Final Report, Navistar extracted information from documents prepared during the project that represent our management, design and development, building, and testing efforts to meet and exceed SuperTruck II project goals. Navistar followed Plan requirements to achieve / exceed Project Objectives: a) >100% improvement in vehicle freight efficiency (FE) (on ton-MPG basis) relative to 2009 baseline with stretch goal of 140% improvement [actual: 170%); b) >55% engine brake thermal efficiency (BTE) demonstrated in operational engine at a 65-mph cruise point on a dynamometer – ≥31% increase from 2009 baseline [actual: 55.20% of combined BTE) ; and c) development and implementation of commercially cost effective technologies (in terms of a simple payback). Technology selection / development path focused on developing technologies applicable for production within 3-year approach, while ensuring technology readiness and cost of ownership for end users. The Program was organized into five budget periods: Requirements / Technology Assessment and Initial Hardware Testing; Technology Development and Concept Readiness Demonstration; Technology Finalization and Validation Tractor / Trailer Fabrication, Integration and Commissioning Demonstration; and Fuel Economy (FE) and Brake Thermal Efficiency (BTE) and Program Completion. Leadership was provided by DOE, with tasks performed by laboratories (Argonne National Laboratory, Lawrence Livermore National Laboratory); partners at Bosch, TPI, Dana, and J.B. Hunt; , and support from University of Michigan and Clemson University. Navistar lead this team with Principal Investigator / Contracting Officer; Project Manager (PM); Vehicle, Engine, and Aftertreatment Engineers; Finance Manager, Technical Program Leads, and Legal/IP; and other key personnel. Work also included personnel in risk management; funding / budget / finance. Work involved analysis, development, testing, and down selection of individual/system engine, aftertreatment, and vehicle technologies, with integration of selected technologies into a prototype vehicle for demonstration of fuel-efficiency gain. Work also included component/integrated system level development of truck and trailer aerodynamics, base engine efficiency, advanced aftertreatment, combustion efficiency, waste heat recovery, hybrid powertrain, reduced rolling resistance, weight reduction, idle reduction, and driver feedback. As ST II progressed, Navistar performed computer-based modeling / simulations of technologies focused on the primary operational areas: Engine, Aftertreatment, and Vehicle. During the ST II Program, the COVID Virus outbreak unexpectedly challenged by the effects of, which affected staffing, scheduling, design, supplies, availability of materials, production procedures, and testing. The DOE responded by extending the program by three quarters to ensure that project tasks were completed for this vital project. Focus continued on analyzing, developing, testing, and down selecting individual-/system-level engine and vehicle technologies for integration of the final selected technologies into a prototype vehicle that would demonstrate fuel-efficiency gains made possible through these technologies. This included component/integrated system-level development of truck and trailer aerodynamics, base engine efficiency, advanced aftertreatment, combustion efficiency, waste heat recovery, solar power, distributed and intelligent vehicle power, hybrid powertrain, reduced rolling resistance, weight reduction, idle reduction, and driver feedback. Throughout the program, function, reliability, and performance at all levels were ensured through testing. Proof of this approach was demonstrated in multiple, on-road demonstrations: Scenario A (Flatland) Fuel Economy, Scenario B (Hilly) Fuel Economy, and City Cycle Tests. Other benefits derived from ST II included new/improved products, publications, patents, and next-step capabilities related to electric/hydrogen vehicles and autonomous driving.

Zukouski, Russ↗
DOE OSTI2023

Rapid and robust squashed spore/colony PCR of industrially important fungi

Fungi have been utilized for centuries in medical, agricultural, and industrial applications. Development of systems biology techniques has enabled the design and metabolic engineering of these fungi to produce novel fuels, chemicals, and enzymes from renewable feedstocks. Many genetic tools have been developed for manipulating the genome and creating mutants rapidly. However, screening and confirmation of transformants remain an inefficient step within the design, build, test, and learn cycle in many industrial fungi because extracting fungal genomic DNA is laborious, time-consuming, and involves toxic chemicals. In this study we developed a rapid and robust technique called “Squash-PCR” to break open the spores and release fungal genomic DNA as a template for PCR. The efficacy of Squash-PCR was investigated in eleven different filamentous fungal strains. Clean PCR products with high yields were achieved in all tested fungi. Spore age and type of DNA polymerase did not affect the efficiency of Squash-PCR. However, spore concentration was found to be the crucial factor for Squash-PCR in Aspergillus niger, with the dilution of starting material often resulting in higher PCR product yield. We then further evaluated the applicability of the squashing procedure for nine different yeast strains. We found that Squash-PCR can be used to improve the quality and yield of colony PCR in comparison to direct colony PCR in the tested yeast strains. The developed technique will enhance the efficiency of screening transformants and accelerate genetic engineering in filamentous fungi and yeast.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

An Enhanced Vertical Ground Heat Exchanger Model for Whole-Building Energy Simulation

This paper presents an enhanced vertical ground heat exchanger (GHE) model for whole-building energy simulation (WBES). WBES programs generally have computational constraints that affect the development and implementation of component simulation sub-models. WBES programs require models that execute quickly and efficiently due to how the programs are utilized by design engineers. WBES programs also require models to be formulated so their performance can be determined from boundary conditions set by upstream components and environmental conditions. The GHE model developed during this work utilizes an existing response factor model and extends its capabilities to accurately and robustly simulate at timesteps that are shorter than the GHE transit time. This was accomplished by developing a simplified dynamic borehole model and then exercising that model to generate exiting fluid temperature response factors. This approach blends numerical and analytical modeling methods. The existing response factor models are then extended to incorporate the exiting fluid temperature response factor to provide a better estimate of the GHE exiting fluid temperature at short simulation timesteps.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2020

Genetic circuit design automation for yeast

Cells can be programmed to monitor and react to their environment using genetic circuits. Design automation software maps a desired circuit function to a DNA sequence, a process that requires units of gene regulation (gates) that are simple to connect and behave predictably. This poses a challenge for eukaryotes due to their complex mechanisms of transcription and translation. To this end, we have developed gates for yeast (Saccharomyces cerevisiae) that are connected using RNA polymerase flux as the signal carrier and are insulated from each other and host regulation. They are based on minimal constitutive promoters (~120 base pairs), for which rules are developed to insert operators for DNA-binding proteins. Using this approach, in this work we constructed nine NOT/NOR gates with nearly identical response functions and 400-fold dynamic range. In circuits, they are transcriptionally insulated from each other by placing ribozymes downstream of terminators to block nuclear export of messenger RNAs resulting from RNA polymerase readthrough. Based on these gates, Cello 2.0 was used to build circuits with up to 11 regulatory proteins. A simple dynamic model predicts the circuit response over days. Genetic circuit design automation for eukaryotes simplifies the construction of regulatory networks as part of cellular engineering projects, whether it be to stage processes during bioproduction, serve as environmental sentinels or guide living therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗