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At least 235 records · Page 13

Conjugation-based genome engineering enables rapid prototyping and bioproduction in non-model bacteria

Abstract Non-model bacteria offer unique metabolic capabilities for sustainable bioproduction, yet their limited genetic accessibility hinders systematic strain development. Here we present conjugation-based serine recombinase-assisted genome engineering (cSAGE), a broad-host-range platform that enables predictable, iterative genomic integration in transformation-resistant bacteria. cSAGE combines conjugative DNA delivery, standardized low-copy vectors, orthogonal recombinases, and modular genetic parts to support rapid pathway assembly and cross-host benchmarking. Using purple nonsulfur bacteria as a testbed, we integrate promoter engineering, multi-payload genome modification, and genome-scale metabolic modeling to empirically evaluate host-dependent pathway performance. Applying this workflow, we identify strain-specific differences in photosynthetic conversion of lignin-derived p -coumarate to the thermoplastic precursor p -vinylphenol. By enabling genome engineering and functional comparison across diverse bacteria using a single plasmid system, cSAGE provides a general framework for non-model strain prototyping and biotransformation discovery.

Guzman, Michael S. [Department of Chemical Enginee↗

Multigene engineering in plants: Technologies, applications, and future prospects

The emerging bioeconomy presents a promising solution to both economic and environmental challenges. Within the bioeconomy, plants serve as a renewable, sustainable, and cost-effective source of foods, fuels, chemicals, and materials. However, traditional breeding and single-gene engineering approaches fall short in addressing complex traits (e.g., drought tolerance, disease resistance, yield, nutrient use efficiency) which are controlled by multiple genes. The complexity of plant biology often necessitates the use of multigene engineering (MGE), which involves simultaneous ectopic expression, up/down-regulation, or editing of multiple genes, to enhance plant traits relevant to the bioeconomy. These genes may be associated with distinct traits or function as components of specific metabolic and regulatory pathways. This review summarizes current technologies for MGE within the synthetic biology-driven Design-Build-Test-Learn (DBTL) framework, detailing its four key stages: Design – gene construct development; Build – DNA assembly and plant transformation; Test – the molecular, biochemical, and physiological characterization of engineered plants; and Learn – computational modeling to refine, multiplex and iterate the process. Despite good progress in the applications of MGE in biofortification, metabolic engineering, and stress resilience, challenges remain in construct stability, coordinated gene expression, and regulatory predictability. We identified optimization paths and future directions to accelerate MGE deployment in sustainable agriculture, with possible societal benefits including reduced production costs, increased yield, and improved food and nutritional security.

AI-aided plant engineering↗

Combining chemistry and protein engineering for new-to-nature biocatalysis

Biocatalysis, the application of enzymes to solve synthetic problems of human import, has blossomed into a powerful technology for chemical innovation. In the past decade, a threefold partnership, where nature provides blueprints for enzymatic catalysis, chemists introduce innovative activity modes with abiological substrates, and protein engineers develop new tools and algorithms to tune and improve enzymatic function, has unveiled the frontier of new-to-nature enzyme catalysis. In this Perspective, we highlight examples of interdisciplinary studies, which have helped to expand the scope of biocatalysis, including concepts of enzymatic versatility explored through the lens of biomimicry, to achieve activities and selectivities beyond those currently possible with chemocatalysis. We indicate how modern tools, such as directed evolution, computational protein design and machine learning-based protein engineering methods, have already impacted and will continue to influence enzyme engineering for new abiological transformations. As a result, a sustained collaborative effort across disciplines is anticipated to spur further advances in biocatalysis in the coming years.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Surface Chemistry and Reactions for Bimetallic Au Catalysis (Final Report)

Gold-based catalysts offer tremendous opportunities for developing new technologies for selective oxidation reactions that directly use gas-phase oxygen as a benign reagent and produce either no byproducts or water as the only byproduct. These processes are urgently needed and critical for achieving the sustainable production of chemicals. While recent studies demonstrate that the catalytic properties of gold can be significantly enhanced by addition of other metals, the development of these catalysts with sufficient performance for commercialization is hindered by a lack of fundamental understanding of how the catalytic properties of gold can be controlled and tailored. This project addressed this need by synergistically combining experimental and computational studies to establish fundamental composition-structure-activity relationships for gold-based catalysts for several industrially important reactions. Results from surface spectroscopy, atomic imaging and thermal desorption experiments were combined with molecular models and reaction mechanisms from quantum chemical calculations to link observable reaction rates to the structure and composition of surfaces at the molecular level. The results were used to develop improved catalyst formulations and identify optimized reaction conditions for gold-based catalysts. For broader impacts, the developed methodology was extended to other metallic catalysts, such as silver, platinum-molybdenum and nickel-tin, for improved catalytic efficiency and sustainable production of specialty and commodity chemicals.

36 MATERIALS SCIENCE↗

Impact of Biofuel Blending on Hydrocarbon Speciation and Particulate Matter from a Medium-Duty Multimode Combustion Strategy

The U.S. Department of Energy’s Co-Optima initiative simultaneous focused on diversifying fuel sources, improving efficiency, and reducing emissions through using novel combustion strategies and sustainable fuel blends. For medium-duty/heavy-duty diesel engines, research in this area has led to the development of a multimode strategy that uses premixed charge compression ignition (PCCI) at low loads and conventional diesel combustion (CDC) at mid–high loads. The aim of this study was to understand how emissions were impacted when using PCCI instead of CDC at low loads and switching to an oxygenated biofuel blend. It provides a detailed speciation of the hydrocarbon (HC) and particulate matter (PM) emissions from a multimode medium-duty engine operating at low loads in PCCI and CDC modes and high loads in CDC. The effect of the oxygenated biofuel blend on emissions was studied at all three mode–load conditions using #2 ULSD and a bio-derived fuel (25% hexyl hexanoate (HHN)) blended in #2 ULSD. The PCCI mode effectively decreased NOx, total HC, and PM/PN emissions, with a substantial decrease in larger particles (≥50 nm). A PM/PN reduction was observed at high loads with the 25% HHN fuel. While the total HC emissions were not impacted by fuel type, the detailed HC analysis exposed changes in the HC’s composition.

09 BIOMASS FUELS↗

Downregulation of Squalene Synthase Broadly Impacts Isoprenoid Biosynthesis in Guayule

Production of natural rubber by Parthenium argentaum (guayule) requires increased yield for economic sustainability. An RNAi gene silencing strategy was used to engineer isoprenoid biosynthesis by downregulation of squalene synthase (SQS), such that the pool of farnesyl diphosphate (FPP) substrate might instead be available to initiate natural rubber synthesis. Downregulation of SQS resulted in significantly reduced squalene and slightly increased rubber, but not in the same tissues nor to the same extent, partially due to an apparent negative feedback regulatory mechanism that downregulated mevalonate pathway isoprenoid production, presumably associated with excess geranyl pyrophosphate levels. A detailed metabolomics analysis of isoprenoid production in guayule revealed significant differences in metabolism in different tissues, including in active mevalonate and methylerythritol phosphate pathways in stem tissue, where rubber and squalene accumulate. New insights and strategies for engineering isoprenoid production in guayule were identified.

59 BASIC BIOLOGICAL SCIENCES↗

Opportunities for Process Intensification with Membranes to Promote Circular Economy Development for Critical Minerals

Critical minerals are essential to the future of clean energy, especially energy storage, electric vehicles, and advanced electronics. In this paper, we argue that process systems engineering (PSE) paradigms provide essential frameworks for enhancing the sustainability and efficiency of critical mineral processing pathways. As a concrete example, we review challenges and opportu-nities across material-to-infrastructure scales for process intensification (PI) with membranes. Within critical mineral processing, there is a need to reduce environmental impact, especially con-cerning chemical reagent usage. Feed concentrations and product demand variability require flex-ible, intensified processes. Further, unique feedstocks require unique processes (i.e., no one-size-fits-all recycling or refining system exists). Membrane materials span a vast design space that allows significant optimization. Therefore, there is a need to rapidly identify the best opportunities for membrane implementation, thus informing materials optimization with process and infrastructure scale performance targets. Finally, scale-up must be accelerated and de-risked across the materials-to-process levels to fully realize the opportunity presented by membranes, thereby fostering the development of a circular economy for critical minerals. Tackling these challenges requires integrating efforts across diverse disciplines. We advocate for a holistic molecular-to-systems perspective for fully realizing PI with membranes to address sustainability challenges in critical mineral processing. The opportunities for PI with membranes are excellent applications for emerging research in machine learning, data science, automation, and optimization.

Dougher, Molly↗

Building Blocks for Secure and Prosperous Defense Critical Supply Chains: A Case Study from Microelectronics

Securing defense-critical supply chains, built on resilient and sustainable microelectronics fabrication and deployment, is a national imperative and one that requires an investment in basic and applied research, development, and deployment into industries in (and out of) the Defense Industrial Base (DIB). Critical next steps include the development of pilots for revolutionary concepts in a new formal verification model and the Cyber-Physical Passport (CPP) concept for chain of custody. Critical infrastructure leadership should take action with a sense of urgency. Working in conjunction with the Under Secretary for Acquisition and Sustainment, the Assistant Secretary of Defense for Research and Engineering should establish pilot programs with the Defense Advanced Research Projects Agency and the service labs to build and test both concepts in legacy and new system development.. Additionally, the Pentagon may be aware that an existing Manufacturing Innovation Institute is piloting, with the semiconductor industry, cyber innovations to provide verifiable security properties and guarantees of physical functions to build a more cyber secure, resilient and efficient micro-electronics supply chain.

99 GENERAL AND MISCELLANEOUS↗

Investigation of powertrain system decarbonization using electrically assisted turbocharging and hybridization in off-road vehicles

In recent years, the causes, effects, and existential threat of a global anthropogenic climate shift have drawn significant attention and stimulated mitigation efforts from all genres of scientific, political, and industrial bodies. The greenhouse effect and the detrimental environmental impact of excess greenhouse gas (GHG) emissions, like carbon dioxide, is well studied and targeted as the primary culprit for aversive action. However, some fields exist where reducing GHG emissions is met by considerable challenges. One such field is the production and operations of off-road vehicles. Applications of these vehicles are highly diverse and are often characterized by rugged, especially transient, and power intensive duty cycles that make one-fits-all vehicle configuration solutions impractical. This research surveys existing literature to identify the modern technologies packages and challenges that face development and configuration of powertrain systems which currently navigate the regulated emissions and unique duty cycle requirements of this market space. A novel powertrain concept is proposed and evaluated with respect to the pinnacle objectives of load performance improvement, criteria pollutant reduction, and reducing the life cycle GHG intensity of its operation. A sure-fire path to vehicular GHG reduction is through improving the fuel efficiency of internal combustion engines (ICEs), an entrenched component of the off-road vehicle sector. Unfortunately, this is more easily said than done. An approach that has proven successful in this endeavor is engine downsizing and turbocharging, where a larger engine is replaced with a smaller one with added air system boosting via turbocharger to reduce frictional and pumping losses while also enabling access to additional fuel energy. However, practical realization of these potential benefits is often impeded by the transient response capability of the smaller engine across the operating space. For this reason, downsized ICE powertrains have turned to electrified forced induction systems (EFISs) for a decoupling of exhaust energy and engine speed from boost capability. Platformed on 48V hybrid technology, these systems introduce the need for more sophisticated controls around the engine gas-exchange process for the management of boost performance and exhaust gas emissions. On this account, simulation studies utilizing a GT-POWER model of a turbocharged 4.5 L engine outfit with an EFIS using an electrically driven compressor (eBooster®) are conducted to provide insight into the performance of this air handling architecture on an off-road engine. The results show that improvement in transient torque response time in sync with reduction in engine-out soot and NOx emissions are possible with an engine recalibration that leverages the transient air-fuel ratio authority of the eBooster®. Benefits are further demonstrated when duty cycle simulations of the 48V mild-hybrid engine concept are exercised, showing an acute decrease in cumulative fuel usage and soot production. Powertrain hybridization is another technological pathway achieving pronounced GHG reduction successes in modern on-road vehicle applications through integration of Li-ion battery technology. In the off-road vehicle segment, a review of available literature concludes that hybridized architectures are present but generally lack the depth of technologies that have both high specific energy and power capabilities, and thus are limited in their inclusion of Li-ion batteries for ICE assistance and enhanced energy storage capability. Therefore, building on the mild-hybrid engine results, the downsized and eBoosted engine concept was integrated into a larger high-voltage battery-hybrid series-electric powertrain system. Hybrid powertrain parameter sensitivity studies were carried out in a numerical charge-sustaining framework, providing novel insights into power flows between the battery and the engine and how their respective capabilities and operation contribute to GHG and criteria pollutant emissions of diverse duty cycles. Application of supervisory power management introduced robustness into the power sourcing and battery SOC control process and showed that optimum specification of battery properties can yield synergies between GHG emissions and battery energy capacity. Furthermore, examination of recent literature on Li-ion batteries has shown that pack manufacturing is a highly energy intensive process, thereby producing considerable quantities of GHGs that scale with energy storage capacity. Also scaling with a battery’s energy storage capacity is its investment cost. In consideration of these factors, an inclusive technoeconomic and GHG life cycle analysis is conducted. This analysis systematically compares the carbon footprint and total cost of ownership associated with the proposed hybrid powertrain concept to reference and alternative powertrain configurations, facilitating a thorough evaluation of the decarbonization effectiveness and economic viability.

99 GENERAL AND MISCELLANEOUS↗

3P Program: Phenotyping X Prediction = Productivity (Final Scientific/Technical Report)

The goal of the 3P Program was to establish integrated, real-time phenotyping and to analyze above- and below-ground plant architecture and total carbon partitioning and allocation to predict heterosis and develop superior crop hybrids by fully leveraging the Sorghum gene pool. There were two overarching themes: 1) the development of a new crop improvement approach utilizing advances in high-throughput phenotyping (HTP), computing, and genomics for public dissemination and 2) leveraging this platform for sorghum crop improvement and commercialization. The Clemson team worked on creating genomic resources and using both statistical learning and high-throughput phenotyping in genomics-assisted breeding. Research was broadly interested in the genetics of carbon partitioning, with the aim of improving crop performance and achieving sustainability. The technology and resources created can be readily found in the public domain and serve to advance scientific understanding of crop genomics and breeding. Genomic prediction was able to identify top crosses to be made, and a hybrid prediction pipeline is in place to drive year-over-year genetic gain. Roots have long been ignored by plant breeders and agronomists, not because they are unimportant but because they are hard to measure. This is an untapped white space of potential insight and innovation. To address this, Hi Fidelity Genetics developed the RootTracker to measure roots in the field on a continuous basis. A database system called RootTracker Tracker was developed to handle data coming from the RootTrackers. In using this device, valuable data was observed for plant breeding, hydrochemical development, and other agricultural biology applications. Carnegie Mellon’s goal was developing new techniques to generate high-resolution 3D models of plants from data collected in the field. The idea was that more useful and more informative phenotypes could be extracted by resolving small features, such as seeds and flowers, and that by modeling in 3D, the spatial structure of plants could be examined. To achieve this, multiple images collected by a new small format structured light stereo imager were fused together. A sorghum panicle modeling pipeline was developed to allow the collection and processing of data. Carolina Seed Systems is an agricultural technology company focused on decarbonizing the agricultural system. Their technology pipeline serves to drive fundamental progress towards creation and distribution of carbon negative crops. The genomic and the engineering technology developed through the 3P Program was leveraged to deliver both value and sustainability from the grower to the consumer. Promising sorghum hybrids were scaled up and commercialized. The overall goal of our research was to integrate, create, and deploy genetic and engineering concepts and technologies to enhance crop productivity in a sustainable fashion. The combination of public and private partners allowed the basic research and hypothesis testing to be quickly accelerated for commercial application by the companies yet maintained that the core framework and academic insights remain in the public domain for continued market disruption, competition, and innovation.

59 BASIC BIOLOGICAL SCIENCES↗

Recent developments of oleaginous yeasts toward sustainable biomanufacturing

Oleaginous yeast are remarkably versatile organisms, distinguished by their natural capacities to accumulate high levels of neutral lipids and broad substrate range. With recent growing interests in engineering non-model organisms as superior biomanufacturing platforms, oleaginous yeasts have emerged as promising chassis for oleochemicals, terpenoids, organic acids, and other valuable products. Advancement in systems biology along with genetic tool development have significantly expanded our understanding of the metabolism in these species and enabled engineering efforts to produce biofuels and bioproducts from diverse feedstocks. This review examines the latest technical advances in oleaginous yeast research toward sustainable biomanufacturing. We cover recent developments in systems biology-enabled metabolism understanding, genetic tools, feedstock utilization, and strain engineering approaches for the production of various valuable chemicals.

59 BASIC BIOLOGICAL SCIENCES↗

Semi‐Continuous Ex Situ Carbon Dioxide Mineralization in Produced Water for Calcite Production

ABSTRACT The mineralization of carbon dioxide (CO 2 ) to stable carbonate products is a desirable process for carbon capture utilization and storage (CCUS). However, improving the process economics through creative use of available reactants is necessary to develop a scalable mineralization process. This study details the development of a semi‐continuous CO 2 mineralization process that uses flue gas as a point CO 2 source, produced water (PW) as an alkaline source of Ca 2+ , and NaOH effluent (potentially sourced from integration with the chlor‐alkali process. Operating at a controlled pH allowed for both complete reaction of available Ca 2+ (100% carbonation potential or 9.9 g CO 2 .L –1 PW brine) and for reproducible control of the produced calcium carbonate (CaCO 3 ) product. A full factorial design of experiments was implemented to study the effects of reaction temperature, pH, and gaseous CO 2 concentration on the mineralization and CO 2 capture rates as well as product crystalline structure and morphology. A maximum CO 2 capture rate of 0.315 ± 0.007 kg.L –1 .d –1 was achieved at 25°C and 25% CO 2 . CO 2 gas to liquid phase mass transport is believed to be the rate limiting step. With improved reactor design and optimization, the proposed semi‐continuous mineralization process shows promise for scaling to a pilot scale CO 2 capture technology.

Bennett, Quinn [Institute for Sustainable Energy &↗

Plant-based engineering for production of high-valued natural products

Plants are a unique source of complex specialized metabolites, many of which play significant roles in human society. In many cases, however, the availability of these metabolites from naturally occurring sources fails to meet current demands. Thus, there is much interest in expanding the production capacity of target plant molecules. Traditionally, plant breeding, chemical synthesis, and microbial fermentation are considered the primary routes towards large scale production of natural products. Here, in this paper, we explore the advances, challenges, and future of plant engineering as a complementary path. Although plants are an integral part of our food and agricultural systems and sustain an extensive array of chemical constituents, their complex genetics and physiology have prevented the optimal exploitation of plants as a production chassis. We highlight emerging engineering tools and scientific advances developed in recent years that have improved the prospects of using plants as a sustainable and scalable production platform. We also discuss technological limitations and overall economic outlook of plant-based production of natural products.

59 BASIC BIOLOGICAL SCIENCES↗

Co-catabolism of arginine and succinate drives symbiotic nitrogen fixation

Biological nitrogen fixation emerging from the symbiosis between bacteria and crop plants holds promise to increase the sustainability of agriculture. One of the biggest hurdles for the engineering of nitrogen-fixing organisms is an incomplete knowledge of metabolic interactions between microbe and plant. In contrast to the previously assumed supply of only succinate, we describe here the CATCH-N cycle as a novel metabolic pathway that co-catabolizes plant provided arginine and succinate to drive the energy-demanding process of symbiotic nitrogen fixation in endosymbiotic rhizobia. Using systems biology, isotope labeling studies and transposon sequencing in conjunction with biochemical characterization, we uncovered highly redundant network components of the CATCH-N cycle including transaminases that interlink the co-catabolism of arginine and succinate. The CATCH-N cycle uses N2 as an additional sink for reductant and therefore delivers up to 25% higher yields of nitrogen than classical arginine catabolism—two alanines and three ammonium ions are secreted for each input of arginine and succinate. We argue that the CATCH-N cycle has evolved as part of a synergistic interaction to sustain bacterial metabolism in the microoxic and highly acid environment of symbiosomes. Thus, the CATCHN cycle entangles the metabolism of both partners to promote symbiosis. Our results provide a theoretical framework and metabolic blueprint for the rational design of plants and plant-associated organisms with new properties to improve nitrogen fixation.

59 BASIC BIOLOGICAL SCIENCES↗

Enhancing the Multifunctional Photocatalytic Activity of Sustainable Magnetic Nanoparticles

The development of efficient photocatalytic materials has intensified in response to increasing emphasis on sustainable energy conversion and environmental restoration. However, the excessive use and indiscriminate release of heavy metals from photocatalytic nanoparticles pose potential environmental risks. This study provides insights into optimizing visible-light-active photocatalysts to enhance their photocatalytic properties and stability. Specifically, cobalt doping and controlled pH modulation are employed on the modified Fe 3 O 4 , forming two distinct samples: Co@Fe 3 O 4 -B (base-treated) and Co@Fe 3 O 4 -A (acid-treated) nanoparticles. Microscopic characterization reveals that Co@Fe 3 O 4 -A undergoes a phase transition to hematite, whereas Co@Fe 3 O 4 -B retains its mixed-phase configuration. Spectroscopic analyses confirm that the cobalt dopants decorate the outskirts of each nanoparticle, forming a core–shell structure. However, Co@Fe 3 O 4 -B exhibit Co 2+ states with a high oxygen vacancy content, whereas Co@Fe 3 O 4 -A contain mixed Co 2+/3+ states. The high density of defect states in the Co@Fe 3 O 4 -B results in superior photocatalytic efficiency, achieving near-complete oxidation of furfuraldehyde (97% conversion) and 5-hydroxymethylfurfural (94% conversion), as well as effective degradation of toluene (78% conversion). This study demonstrates that the combined approach of doping and pH treatment is promising for the surface-defect engineering of photocatalysts, enhancing their multifunctional performance and reusability for sustainable energy conversion.

Fe3 O4 nanoparticles↗