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Results for “Modular cell engineering”

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.

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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Bypassing the Pentose Phosphate Pathway: Towards Modular Utilization of Xylose

The efficient use of hemicellulose in the plant cell wall is critical for the economic conversion of plant biomass to renewable fuels and chemicals. Previously, the yeast Saccharomyces cerevisiae has been engineered to convert the hemicellulose-derived pentose sugars xylose and arabinose to D-xylulose-5-phosphate for conversion via the pentose phosphate pathway (PPP). However, efficient pentose utilization requires PPP optimization and may interfere with its roles in NADPH and pentose production. Here, we developed an alternative xylose utilization pathway that largely bypasses the PPP. In the new pathway, D-xylulose is converted to D-xylulose-1-phosphate, a novel metabolite to S. cerevisiae, which is then cleaved to glycolaldehyde and dihydroxyacetone phosphate. This synthetic pathway served as a platform for the biosynthesis of ethanol and ethylene glycol. The use of D-xylulose-1-phosphate as an entry point for xylose metabolism opens the way for optimizing chemical conversion of pentose sugars in S. cerevisiae in a modular fashion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Modular cell-free expression plasmids to accelerate biological design in cells

Industrial biotechnology aims to produce high-value products from renewable resources. This can be challenging because model microorganisms—organisms that are easy to use like Escherichia coli—often lack the machinery required to utilize desired feedstocks like lignocellulosic biomass or syngas. Non-model organisms, such as Clostridium, are industrially proven and have desirable metabolic features but have several hurdles to mainstream use. Namely, these species grow more slowly than conventional laboratory microbes, and genetic tools for engineering them are far less prevalent. To address these hurdles for accelerating cellular design, cell-free synthetic biology has matured as an approach for characterizing non-model organisms and rapidly testing metabolic pathways in vitro. Unfortunately, cell-free systems can require specialized DNA architectures with minimal regulation that are not compatible with cellular expression. In this work, we develop a modular vector system that allows for T7 expression of desired enzymes for cell-free expression and direct Golden Gate assembly into Clostridium expression vectors. Utilizing the Joint Genome Institute’s DNA Synthesis Community Science Program, we designed and synthesized these plasmids and genes required for our projects allowing us to shuttle DNA easily between our in vitro and in vivo experiments. We next validated that these vectors were sufficient for cell-free expression of functional enzymes, performing on par with the previous state-of-the-art. Lastly, we demonstrated automated six-part DNA assemblies for Clostridium autoethanogenum expression with efficiencies ranging from 68% to 90%. We anticipate this system of plasmids will enable a framework for facile testing of biosynthetic pathways in vitro and in vivo by shortening development cycles.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

An extensible vector toolkit and parts library for advanced engineering of plant genomes

Abstract Plant biotechnology is rife with new advances in transformation and genome engineering techniques. A common requirement for delivery and coordinated expression in plant cells, however, places the design and assembly of transformation constructs at a crucial juncture as desired reagent suites grow more complex. Modular cloning principles have simplified some aspects of vector design, yet many important components remain unavailable or poorly adapted for rapid implementation in biotechnology research. Here, we describe a universal Golden Gate cloning toolkit for vector construction. The toolkit chassis is compatible with the widely accepted Phytobrick standard for genetic parts, and supports assembly of arbitrarily complex T‐DNAs through improved capacity, positional flexibility, and extensibility in comparison to extant kits. We also provision a substantial library of newly adapted Phytobricks, including regulatory elements for monocot and dicot gene expression, and coding sequences for genes of interest such as reporters, developmental regulators, and site‐specific recombinases. Finally, we use a series of dual‐luciferase assays to measure contributions to expression from promoters, terminators, and from cross‐cassette interactions attributable to enhancer elements in certain promoters. Taken together, these publicly available cloning resources can greatly accelerate the testing and deployment of new tools for plant engineering.

42 ENGINEERING↗
DOE OSTI2019

Innovative Hot Lab Concept for Advanced D and D Application - 19175

Hot Labs are used in the nuclear industry for various purposes: maintenance of nuclear reactor, sampling and testing of fuel, inspection activities and decommissioning. Despite their vast use, their current designs and operations do not meet entirely today's needs and requirements of the operations nor tomorrow's. This paper will give an overview of the research and investigations performed around Hot Cells design and concept in order to integrate new operability modes and functions. The overall idea is to bring modularity, flexibility and adaptability to the Hot Lab nuclear industry. Taking the key principles of Model Based System Engineering, an interoperable data model, the most advanced digital technologies (Building Information Modelling - BIM, Virtual Reality / Augmented Reality, Artificial Intelligence), and looking at all the life-cycle of such a facility, a concept design of a new type of Hot Lab has been developed. Four mains aspects are implemented during this study: Implement the principles of the Industry 4.0; use modular and flexible solutions; explore the concept of in service maintenance and predictive maintenance; optimise the decommissioning and dismantling process by taking into account the entire life-cycle of the facility. The design was developed as a case study taking several assumptions to adapt to any project. The design developed demonstrates that modularity and flexibility can be brought in without compromising the core safety functions of such a facility. This Hot Lab concept brings the current Hot Lab to the next level as the design has been adapted to meet the current operational needs, implement novel ideas and consider its entire life-cycle. This paper will demonstrate how decommissioning and dismantling operations can become more efficient and safer with such a concept. In addition, the Model Based System Engineering approach used from the beginning of the design phase allows to have an optimum architecture during its entire lifetime. It also allowed to flag new topics to be further developed for the benefit of the nuclear industry as a whole. A first example would be the development of the Control System using digital tools and artificial intelligence to run remotely controlled equipment inside the Hot Lab. Assystem is an international engineering group. As a key participant in the nuclear industry for over 50 years, the Group supports its clients in managing their capital expenditure throughout their asset life-cycles. Assystem can offer support in project management, design, digital engineering, industrial control systems, security and safety and industrial digitalisation. Assystem's Imagine program is an internal program intending to serve as an incubator for the development of innovations. The Innovative Hot Lab project integrates one of the four innovation projects Assystem choose to develop and invest in. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Light-inducible protein degradation in E. coli with the LOVdeg tag

Molecular tools for optogenetic control allow for spatial and temporal regulation of cell behavior. In particular, light-controlled protein degradation is a valuable mechanism of regulation because it can be highly modular, used in tandem with other control mechanisms, and maintain functionality throughout growth phases. Here, we engineered LOVdeg, a tag that can be appended to a protein of interest for inducible degradation in Escherichia coli using blue light. We demonstrate the modularity of LOVdeg by using it to tag a range of proteins, including the LacI repressor, CRISPRa activator, and the AcrB efflux pump. Additionally, we demonstrate the utility of pairing the LOVdeg tag with existing optogenetic tools to enhance performance by developing a combined EL222 and LOVdeg system. Finally, we use the LOVdeg tag in a metabolic engineering application to demonstrate post-translational control of metabolism. Together, our results highlight the modularity and functionality of the LOVdeg tag system and introduce a powerful new tool for bacterial optogenetics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Light-inducible protein degradation in E. coli with the LOVdeg tag

Molecular tools for optogenetic control allow for spatial and temporal regulation of cell behavior. In particular, light-controlled protein degradation is a valuable mechanism of regulation because it can be highly modular, used in tandem with other control mechanisms, and maintain functionality throughout growth phases. Here, we engineered LOVdeg, a tag that can be appended to a protein of interest for inducible degradation in Escherichia coli using blue light. We demonstrate the modularity of LOVdeg by using it to tag a range of proteins, including the LacI repressor, CRISPRa activator, and the AcrB efflux pump. Additionally, we demonstrate the utility of pairing the LOVdeg tag with existing optogenetic tools to enhance performance by developing a combined EL222 and LOVdeg system. Finally, we use the LOVdeg tag in a metabolic engineering application to demonstrate post-translational control of metabolism. Together, our results highlight the modularity and functionality of the LOVdeg tag system and introduce a powerful new tool for bacterial optogenetics.

Tague, Nathan (ORCID:0000000281146700)↗
DOE OSTI2012

Accelerating Development of EV Batteries Through Computer-Aided Engineering (Presentation)

The Department of Energy's Vehicle Technology Program has launched the Computer-Aided Engineering for Automotive Batteries (CAEBAT) project to work with national labs, industry and software venders to develop sophisticated software. As coordinator, NREL has teamed with a number of companies to help improve and accelerate battery design and production. This presentation provides an overview of CAEBAT, including its predictive computer simulation of Li-ion batteries known as the Multi-Scale Multi-Dimensional (MSMD) model framework. MSMD's modular, flexible architecture connects the physics of battery charge/discharge processes, thermal control, safety and reliability in a computationally efficient manner. This allows independent development of submodels at the cell and pack levels.

25 ENERGY STORAGE↗
DOE OSTI2012

Engineering naturally occurring trans -acting non-coding RNAs to sense molecular signals

Non-coding RNAs (ncRNAs) are versatile regulators in cellular networks. While most trans-acting ncRNAs possess well-defined mechanisms that can regulate transcription or translation, they generally lack the ability to directly sense cellular signals. In this work, we describe a set of design principles for fusing ncRNAs to RNA aptamers to engineer allosteric RNA fusion molecules that modulate the activity of ncRNAs in a ligand inducible way in Escherichia coli. We apply these principles to ncRNA regulators that can regulate translation (IS10 ncRNA) and transcription (pT181 ncRNA), and demonstrate that our design strategy exhibits high modularity between the aptamer ligand-sensing motif and the ncRNA target recognition motif, which allows us to reconfigure these two motifs to engineer orthogonally acting fusion molecules that respond to different ligands and regulate different targets in the same cell. Finally, we show that the same ncRNA fused with different sensing domains results in a sensory-level NOR gate that integrates multiple input signals to perform genetic logic. These ligand-sensing ncRNA regulators provide useful tools to modulate the activity of structurally related families of ncRNAs, and building upon the growing body of RNA synthetic biology, our ability to design aptamer–ncRNA fusion molecules offers new ways to engineer ligand-sensing regulatory circuits.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Advanced Bottom‐Up Engineering of Living Architectures

Abstract Bottom‐up tissue engineering is a promising approach for designing modular biomimetic structures that aim to recapitulate the intricate hierarchy and biofunctionality of native human tissues. In recent years, this field has seen exciting progress driven by an increasing knowledge of biological systems and their rational deconstruction into key core components. Relevant advances in the bottom‐up assembly of unitary living blocks toward the creation of higher order bioarchitectures based on multicellular‐rich structures or multicomponent cell–biomaterial synergies are described. An up‐to‐date critical overview of long‐term existing and rapidly emerging technologies for integrative bottom‐up tissue engineering is provided, including discussion of their practical challenges and required advances. It is envisioned that a combination of cell–biomaterial constructs with bioadaptable features and biospecific 3D designs will contribute to the development of more robust and functional humanized tissues for therapies and disease models, as well as tools for fundamental biological studies.

Gaspar, Vítor M.↗
DOE OSTI2017

Reliable SOFC Systems

The goal of this U.S. Department of Energy (DOE) sponsored project was to advance the reliability, robustness and endurance of low-cost SOFC technology suitable for ultimate deployment in ≥100 MWe Integrated Gasification Fuel Cell (IGFC) or Natural Gas Fuel Cell (NGFC) systems capable of ≥97% CO2 capture. The ultimate SOFC program goals are ≤ 0.2% per 1000 hours power degradation over a 5-plus year stack life, high-volume (≥ 250 MW/year) stack production cost of ≤$225/kWsystem net AC, and “power block” (exclusive of fuel supply, contaminant removal, and CO2 capture subsystems) capital cost of ≤ 900/kWsystem net AC (in year 2011). To progress towards the ultimate program goals, the specific objectives of this project were to achieve an SOFC stack power degradation rate of ≤1.5% per 1000 hours in a 100 kW (125 kW Peak) Modular Power Block (MPB) stand-alone power system under thermally self-sustained normal operating conditions and to verify the prospects for high volume SOFC stack production cost below the DOE target of ≤ 225/kW. This final technical report summarizes the progress made during the project period of 36 months. Significant progress was made in the areas of cell and stack technology development, Modular Power Block (MPB) development, sub-MW MPB system development, and MW-class SOFC System Development and Costing. The work focused on areas necessary for comprehensive development of an SOFC fuel cell system, including, active cell improvement, contaminant resistance, process engineering, and development of non-repeat module components. Additionally, several custom built balance-of-plant components were designed and fabricated to support the fuel cell system. SOFC cell and stack development focused on improving cell performance and durability. Enhancements were achieved in areas of electrode stability and impurity tolerance. Additionally, several quality control techniques and tools were developed to ensure predictable and repeatable fabrication of SOFC stacks. Module development continued previous development efforts to achieve footprint reduction and higher efficiency by incorporating balance-of-plant functional equipment into the fuel cell containment module. Several improvements were made to prior design. Control and instrumentation hardware was integrated within the module for serviceability and size reduction. The design efforts culminated in a complete SOFC power plant system. The designed plant was constructed and tested at FCE. Stack and system costs were updated, reflecting advances made in this program.

20 FOSSIL-FUELED POWER PLANTS↗
DOE OSTI2018

BioBits™ Explorer: A modular synthetic biology education kit

Hands-on demonstrations greatly enhance the teaching of science, technology, engineering, and mathematics (STEM) concepts and foster engagement and exploration in the sciences. While numerous chemistry and physics classroom demonstrations exist, few biology demonstrations are practical and accessible due to the challenges and concerns of growing living cells in classrooms. We introduce BioBits™ Explorer, a synthetic biology educational kit based on shelf-stable, freeze-dried, cell-free (FD-CF) reactions, which are activated by simply adding water. The FD-CF reactions engage the senses of sight, smell, and touch with outputs that produce fluorescence, fragrances, and hydrogels, respectively. We introduce components that can teach tunable protein expression, enzymatic reactions, biomaterial formation, and biosensors using RNA switches, some of which represent original FD-CF outputs that expand the toolbox of cell-free synthetic biology. The BioBits™ Explorer kit enables hands-on demonstrations of cutting-edge science that are inexpensive and easy to use, circumventing many current barriers for implementing exploratory biology experiments in classrooms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Engineered binding to erythrocytes induces immunological tolerance to E. coli asparaginase

Antigen-specific immune responses to protein drugs can hinder efficacy and compromise safety because of drug neutralization and secondary clinical complications. We report a tolerance induction strategy to prevent antigen-specific humoral immune responses to therapeutic proteins. Our modular, biomolecular approach involves engineering tolerizing variants of proteins such that they bind erythrocytes in vivo upon injection, on the basis of the premise that aged erythrocytes and the payloads they carry are cleared tolerogenically, driving the deletion of antigen-specific T cells. We demonstrate that binding the clinical therapeutic enzyme Escherichia coli L-asparaginase to erythrocytes in situ antigen-specifically abrogates development of antibody titers by >1000-fold and extends the pharmacodynamic effect of the drug 10-fold in mice. Additionally, a single pretreatment dose of erythrocyte-binding asparaginase tolerized mice to multiple subsequent doses of the wild-type enzyme. This strategy for reducing antigen-specific humoral responses may enable more effective and safer treatment with therapeutic proteins and drug candidates that are hampered by immunogenicity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A modular vaccine platform enabled by decoration of bacterial outer membrane vesicles with biotinylated antigens

Engineered outer membrane vesicles (OMVs) derived from Gram-negative bacteria are a promising technology for the creation of non-infectious, nanoparticle vaccines against diverse pathogens. However, antigen display on OMVs can be difficult to control and highly variable due to bottlenecks in protein expression and localization to the outer membrane of the host cell, especially for bulky and/or complex antigens. Here, we describe a universal approach for avidin-based vaccine antigen crosslinking (AvidVax) whereby biotinylated antigens are linked to the exterior of OMVs whose surfaces are remodeled with multiple copies of a synthetic antigen-binding protein (SNAP) comprised of an outer membrane scaffold protein fused to a biotin-binding protein. We show that SNAP-OMVs can be readily decorated with a molecularly diverse array of biotinylated subunit antigens, including globular and membrane proteins, glycans and glycoconjugates, haptens, lipids, and short peptides. When the resulting OMV formulations are injected in mice, strong antigen-specific antibody responses are observed that depend on the physical coupling between the antigen and SNAP-OMV delivery vehicle. Overall, these results demonstrate AvidVax as a modular platform that enables rapid and simplified assembly of antigen-studded OMVs for application as vaccines against pathogenic threats.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Modular adjuvant-free pan-HLA-DR-immunotargeting subunit vaccine against SARS-CoV-2 elicits broad sarbecovirus-neutralizing antibody responses

Subunit vaccines typically require co-administration with an adjuvant to elicit protective immunity, adding development hurdles that can impede rapid pandemic responses. To circumvent the need for adjuvant in a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) subunit vaccine, we engineer a thermostable immunotargeting vaccine (ITV) that leverages the pan-HLA-DR monoclonal antibody 44H10 to deliver the viral spike protein receptor-binding domain (RBD) to antigen-presenting cells. X-ray crystallography shows that 44H10 binds to a conserved epitope on HLA-DR, providing the basis for its broad HLA-DR reactivity. Adjuvant-free ITV immunization in rabbits and ferrets induces robust anti-RBD antibody responses that neutralize SARS-CoV-2 variants of concern and protect recipients from SARS-CoV-2 challenge. We demonstrate that the modular nature of the ITV scaffold with respect to helper T cell epitopes and diverse RBD antigens facilitates broad sarbecovirus neutralization. Our findings support anti-HLA-DR immunotargeting as an effective means to induce strong antibody responses to subunit antigens without requiring an adjuvant.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

iSeq 2.0: A Modular and Interchangeable Toolkit for Interaction Screening in Yeast

Here, we developed a flexible toolkit for combinatorial screening in Saccharomyces cerevisiae , which generates large libraries of cells, each uniquely barcoded to mark a combination of DNA elements. This interaction sequencing platform (iSeq 2.0) includes genomic landing pads that assemble combinations through sequential integration of plasmids or yeast mating, 15 barcoded plasmid libraries containing split selectable markers (URA3 AI , KanMX AI , HphMX AI , and NatMX AI ), and an array of ~24,000 “double-barcoder” strains that can make existing yeast libraries iSeq compatible. Various DNA elements are compatible with iSeq: DNA introduced on integrating plasmids, engineered genomic modifications, or entire genetic backgrounds. DNA element libraries are modular and interchangeable, and any two libraries can be combined, making iSeq capable of performing many new combinatorial screens by short-read sequencing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Computer Aided Battery Engineering Consortium

A multi-national lab collaborative team was assembled that includes experts from academia and industry to enhance recently developed Computer-Aided Battery Engineering for Electric Drive Vehicles (CAEBAT)-II battery crush modeling tools and to develop microstructure models for electrode design - both computationally efficient. Task 1. The new Multi-Scale Multi-Domain model framework (GH-MSMD) provides 100x to 1,000x computation speed-up in battery electrochemical/thermal simulation while retaining modularity of particles and electrode-, cell-, and pack-level domains. The increased speed enables direct use of the full model in parameter identification. Task 2. Mechanical-electrochemical-thermal (MECT) models for mechanical abuse simulation were simultaneously coupled, enabling simultaneous modeling of electrochemical reactions during the short circuit, when necessary. The interactions between mechanical failure and battery cell performance were studied, and the flexibility of the model for various batteries structures and loading conditions was improved. Model validation is ongoing to compare with test data from Sandia National Laboratories. The ABDT tool was established in ANSYS. Task 3. Microstructural modeling was conducted to enhance next-generation electrode designs. This 3- year project will validate models for a variety of electrodes, complementing Advanced Battery Research programs. Prototype tools have been developed for electrochemical simulation and geometric reconstruction.

25 ENERGY STORAGE↗