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DOE OSTI2024

40th Eastern Regional Photosynthesis Conference

Photosynthesis has shaped global biochemistry and geochemistry in its production of almost all atmospheric oxygen, and almost every electron that supports the processes of life on Earth was extracted from water by the light-dependent reactions, many of which were then used to fix carbon in the dark reactions. To humans, that fixed carbon is the originator of all fossil fuels and a critical step in conversion of solar photons to human-usable energy. The Eastern Regional Photosynthesis Conference (ERPC) serves as a forum for advancement of science in this field. As a regional-level conference, it specializes in providing developmental opportunities for early-career researchers from undergraduates to pre-tenure professors, as well as broadening the field in terms of participating scholars and research approaches to produce new interdisciplinary collaborations. Funding from the Department of Energy is used to mitigate registration and attendance costs for junior (non-PI) researchers. The ERPC is one of the three regional conferences in the field of photosynthesis research in the United States, alongside the Western Photosynthesis Conference (currently in California) and the Midwestern Photosynthesis Conference (Turkey Run, Indiana). A longstanding incubator for scientific discourse, discovery, and collaborations, this conference has spawned many collaborations which led to Department of Energy-funded projects and brought two full generations of scientists into the field. In 2023 the landmark 40th such conference was held at the Woods Hole Marine Biological Laboratory in Massachusetts. The conference was held April 14th-16th, 2023. The majority of the total attendees are traditionally undergraduates, graduate students, and postdoctoral researchers, whose scientific development greatly benefits from conferences like these. Almost all talks besides the ones given by invited speakers were given by young scientists who benefited from this award. Many posters presented at this conference were also the work of junior scientists. This conference is many young scientists' first exposure to the photosynthesis research community and its primary goal is to provide a positive atmosphere for those attendees, as exemplified by the three poster sessions and dedicated interactions between senior and junior scientists. Additionally, this was the first year of a successful equitable outreach and speaker recruitment plan to provide fair representation at the conference in line with Department of Energy policies and mission. The central focus of the ERPC is the understanding of energy flow from photons to usable chemical products in both natural and artificial photosynthesis. We support the DOE-BES aim of understanding of the biochemical/biophysical processes of photosynthesis to inform new technology development and field applications. This year’s theme, “Photosynthesis Across Scales,” reflected the scope of work being done from the individual exciton to the crop scale. This research encompasses applied biology, chemistry, physics, and materials engineering. The aim of this conference is to present new discoveries, techniques, and questions which can be sourced from any of these disciplines and provide an audience which is broadly qualified to use or respond to these developments.

08 HYDROGEN↗
DOE OSTI2025

Evaluation of Howard A. Hanson Dam Juvenile Fish Passage and Survival Study: Downstream Passage and Survival (Acoustic Telemetry) (Task Final Report)

The Downstream Passage and Survival (Acoustic Telemetry) task was one of several tasks for the Evaluation of Howard A. Hanson Dam (HAHD) Juvenile Fish Passage and Survival study. For this task, a juvenile fish passage and survival study was conducted at HAHD from March 10, 2024 through June 27, 2024 for arrays in the HAHD Reservoir and Green River, and through July 9, 2024 for the arrays in the Duwamish River. Fish releases occurred over four times from March through May. Active tag (acoustic telemetry) technology was used to provide biological baseline information for the passage and survival of juvenile Puget Sound (PS) Chinook salmon (Oncorhynchus tshawytscha). Results will be used by biologists, engineers, resource managers, and regional decision-makers to inform the engineering design of the new fish passage facility (FPF) at HAHD. However, hatchery sub-yearling PS Chinook salmon of the appropriate size for tag implantation during the study period (> 95 mm in fork length, Geist et al. 2018) were unavailable. Therefore, yearling Coho salmon (O. kisutch) were used as a surrogate species for this acoustic telemetry study.

13 HYDRO ENERGY↗
DOE OSTI2025

Exploring Water System Vulnerabilities in California's Central Valley Under the Late Renaissance Megadrought and Climate Change

Abstract California faces cycles of drought and flooding that are projected to intensify, but these extremes may impact water users across the state differently due to the region's natural hydroclimate variability and complex institutional framework governing water deliveries. To assess these risks, this study introduces a novel exploratory modeling framework informed by paleo and climate‐change based scenarios to better understand how impacts propagate through the Central Valley's complex water system. A stochastic weather generator, conditioned on tree‐ring data, produces a large ensemble of daily weather sequences conditioned on drought and flood conditions under the Late Renaissance Megadrought period (1550–1580 CE). Regional climate changes are applied to this weather data and drive hydrologic projections for the Sacramento, San Joaquin, and Tulare Basins. The resulting streamflow ensembles are used in an exploratory stress test using the California Food‐Energy‐Water System model, a highly resolved, daily model of water storage and conveyance throughout California's Central Valley. Results show that megadrought conditions lead to unprecedented reductions in inflows and storage at major California reservoirs. Both junior and senior water rights holders experience multi‐year periods of curtailed water deliveries and complete drawdowns of groundwater assets. When megadrought dynamics are combined with climate change, risks for unprecedented depletion of reservoir storage and sustained curtailment of water deliveries across multiple years increase. Asymmetries in risk emerge depending on water source, rights, and access to groundwater banks.

Gupta, Rohini S. [School of Civil and Environmenta↗
DOE OSTI2025

Phenylpropanoid methyl esterase unlocks catabolism of aromatic biological nitrification inhibitors

Microbial nitrification of fertilizers represents is a significant global source of greenhouse gas emissions. This process increases emissions, fosters toxic algal blooms, and raises crop production costs. Some plants naturally release biological nitrification inhibitors to suppress ammonium-oxidizing microbes and reduce nitrification. Engineering nitrification inhibitor production into food and bioenergy crops via synthetic biology offers a promising mitigation strategy, but its success depends on addressing gaps in our understanding of inhibitor degradation in soil. This study begins to fill this gap by identifying a previously unknown microbial pathway for degrading phenylpropanoid methyl esters, a key class of aromatic nitrification inhibitors. Using transcriptomics and high-throughput functional genomics, we discovered genes essential for phenylpropanoid methyl ester degradation. Genetic and biochemical analyses revealed two novel enzymes, including a newly identified phenylpropanoid methyl esterase, that direct phenylpropanoid methyl esters into known metabolic pathways. Importantly, transferring these genes into bacteria capable of metabolizing other phenylpropanoids enabled them to use the methyl esters as a carbon source. This work provides critical insights into microbial nitrification inhibitor degradation, a poorly understood element of the nitrification cycle.

Genetic Engineering↗
DOE OSTI2020

A bacterial toolkit for plants

Here, we highlight efforts to engineer microorganisms and their plant hosts to address the challenges of sustainable agriculture.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Engineering Crassulacean Acid Metabolism in C3 and C4 Plants

Carbon dioxide (CO2) is a major greenhouse gas contributing to changing climatic conditions, which is a grand challenge affecting the security of food, energy, and environment. Photosynthesis plays the central role in plant-based CO2 reduction. Plants performing CAM (crassulacean acid metabolism) photosynthesis have a much higher water use efficiency than those performing C3 or C4 photosynthesis. Therefore, there is a great potential for engineering CAM in C3 or C4 crops to enhance food/biomass production and carbon sequestration on arid, semiarid, abandoned, or marginal lands. Recent progresses in CAM plant genomics and evolution research, along with new advances in plant biotechnology, have provided a solid foundation for bioengineering to convert C3/C4 plants into CAM plants. Here, we first discuss the potential strategies for CAM engineering based on our current understanding of CAM evolution. Then we describe the technical approaches for engineering CAM in C3 and C4 plants, with a focus on an iterative four-step pipeline: (1) designing gene modules, (2) building the gene modules and transforming them into target plants, (3) testing the engineered plants through an integration of molecular biology, biochemistry, metabolism, and physiological approaches, and (4) learning to inform the next round of CAM engineering. Finally, we discuss the challenges and future opportunities for fully realizing the potential of CAM engineering.

Yang, Xiaohan↗
DOE OSTI2025

Turbo‐charging crop improvement: harnessing multiplex editing for polygenic trait engineering and beyond

Multiplex CRISPR editing has emerged as a transformative platform for plant genome engineering, enabling the simultaneous targeting of multiple genes, regulatory elements, or chromosomal regions. This approach is effective for dissecting gene family functions, addressing genetic redundancy, engineering polygenic traits, and accelerating trait stacking and de novo domestication. Its applications now extend beyond standard gene knockouts to include epigenetic and transcriptional regulation, chromosomal engineering, and transgene‐free editing. These capabilities are advancing crop improvement not only in annual species but also in more complex systems such as polyploids, undomesticated wild relatives, and species with long generation times. At the same time, multiplex editing presents technical challenges, including complex construct design and the need for robust, scalable mutation detection. We discuss current toolkits and recent innovations in vector architecture, such as promoter and scaffold engineering, that streamline workflows and enhance editing efficiency. High‐throughput sequencing technologies, including long‐read platforms, are improving the resolution of complex editing outcomes such as structural rearrangements—often missed by standard genotyping—when targeting repetitive or tandemly spaced loci. To fully realize the potential of multiplex genome engineering, there is growing demand for user‐friendly, synthetic biology‐compatible, and scalable computational workflows for gRNA design, construct assembly, and mutation analysis. Experimentally validated inducible or tissue‐specific promoters are also highly desirable for achieving spatiotemporal control. As these tools continue to evolve, multiplex CRISPR editing is poised to become a foundational technology of next‐generation crop improvement to address challenges in agriculture, sustainability, and climate resilience.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Secure biosystems design in Saccharomyces cerevisiae establishes effective biocontainment strategies and mechanisms of escape

The widespread application of recombinant DNA and synthetic biology approaches for microbial metabolic engineering pursuits has motivated the development of biocontainment strategies, targeting safe and secure deployment of genetically modified microorganisms (GMMs). However, the design rules and mechanistic drivers governing biocontainment efficacy, as well as impacts of biocontainment upon microbial fitness, remain to be comprehensively evaluated, hindering predictive design and application of these strategies. We have developed a platform for high-resolution analysis of a transactivated kill switch in laboratory and industrial strains of Saccharomyces cerevisiae to assess modes of biocontainment escape and establish design rules for development of kill switch systems in diverse microbes. A camphor-regulated, RelE toxin system was systematically deployed to assess the impacts of differential kill switch copy number and ploidy in laboratory vs industrial strains. CRISPR-mediated integration of the biocontainment system at various loci revealed rapid escape events driven, in part, by mutations to both the Cam-transactivator (cam-TA) and RelE toxin. Genetic engineering enabled recapitulation of escape phenotypes, confirming mechanisms of escape and establishing structure-function relationships in the cam-TA system. Interestingly, genomic resequencing of escape mutants also revealed a series of off-target mutations, implicating additional modes of kill switch escape. Multi-copy integration of the kill switch system mitigated these effects by orders of magnitude, without compromising the biosynthetic capacity of the microbes, but proved insufficient to establish sustained biocontainment. The resultant data define a series of key design rules for next-generation biocontainment strategies and add to a growing foundational knowledge base targeting establishment of secure biosystems designs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Engineering of increased L-Threonine production in bacteria by combinatorial cloning and machine learning

The goal of this study is to develop a general strategy for bacterial engineering using an integrated synthetic biology and machine learning (ML) approach. This strategy was developed in the context of increasing L-threonine production in Escherichia coli ATCC 21277. A set of 16 genes was initially selected based on metabolic pathway relevance to threonine biosynthesis and used for combinatorial cloning to construct a set of 385 strains to generate training data (i.e., a range of L-threonine titers linked to each of the specific gene combinations). Hybrid (regression/classification) deep learning (DL) models were developed and used to predict additional gene combinations in subsequent rounds of combinatorial cloning for increased L-threonine production based on the training data. As a result, E. coli strains built after just three rounds of iterative combinatorial cloning and model prediction generated higher L-threonine titers (from 2.7 g/L to 8.4 g/L) than those of patented L-threonine strains being used as controls (4-5 g/L). Interesting combinations of genes in L-threonine production included deletions of the tdh, metL, dapA, and dhaM genes as well as overexpression of the pntAB, ppc, and aspC genes. Mechanistic analysis of the metabolic system constraints for the best performing constructs offers ways to improve the models by adjusting weights for specific gene combinations. Graph theory analysis of pairwise gene modifications and corresponding levels of L-threonine production also suggests additional rules that can be incorporated into future ML models.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Toughening Brittle Bio‐P3HB with Synthetic P3HB of Engineered Stereomicrostructures

Abstract Poly(3‐hydroxybutyrate) (P3HB), a biologically produced, biodegradable natural polyester, exhibits excellent thermal and barrier properties but suffers from mechanical brittleness, largely limiting its applications. Here we report a mono‐material product design strategy to toughen stereoperfect, brittle bio or synthetic P3HB by blending it with stereomicrostructurally engineered P3HB. Through tacticity ([ mm ] from 0 to 100 %) and molecular weight ( M n to 788 kDa) tuning, high‐performance synthetic P3HB materials with tensile strength to ≈30 MPa, fracture strain to ≈800 %, and toughness to 126 MJ m −3 (>110× tougher than bio‐P3HB) have been produced. Physical blending of the brittle P3HB with such P3HB in 10 to 90 wt % dramatically enhances its ductility from ≈5 % to 95–450 % and optical clarity from 19 % to 85 % visible light transmittance while maintaining desirably high elastic modulus (>1 GPa), tensile strength (>35 MPa), and melting temperature (160–170 °C). This P3HB‐toughening‐P3HB methodology departs from the traditional approach of incorporating chemically distinct components to toughen P3HB, which hinders chemical or mechanical recycling, highlighting the potential of the mono‐material product design solely based on biodegradable P3HB to deliver P3HB materials with diverse performance properties.

Zhang, Zhen↗
DOE OSTI2023

Toughening Brittle Bio‐P3HB with Synthetic P3HB of Engineered Stereomicrostructures

Abstract Poly(3‐hydroxybutyrate) (P3HB), a biologically produced, biodegradable natural polyester, exhibits excellent thermal and barrier properties but suffers from mechanical brittleness, largely limiting its applications. Here we report a mono‐material product design strategy to toughen stereoperfect, brittle bio or synthetic P3HB by blending it with stereomicrostructurally engineered P3HB. Through tacticity ([ mm ] from 0 to 100 %) and molecular weight ( M n to 788 kDa) tuning, high‐performance synthetic P3HB materials with tensile strength to ≈30 MPa, fracture strain to ≈800 %, and toughness to 126 MJ m −3 (>110× tougher than bio‐P3HB) have been produced. Physical blending of the brittle P3HB with such P3HB in 10 to 90 wt % dramatically enhances its ductility from ≈5 % to 95–450 % and optical clarity from 19 % to 85 % visible light transmittance while maintaining desirably high elastic modulus (>1 GPa), tensile strength (>35 MPa), and melting temperature (160–170 °C). This P3HB‐toughening‐P3HB methodology departs from the traditional approach of incorporating chemically distinct components to toughen P3HB, which hinders chemical or mechanical recycling, highlighting the potential of the mono‐material product design solely based on biodegradable P3HB to deliver P3HB materials with diverse performance properties.

Chemistry↗
DOE OSTI2023

Prospects for engineering Ralstonia eutropha and Zymomonas mobilis for the autotrophic production of 2,3-butanediol from CO 2 and H 2

The decarbonization of the chemical industry and a shift toward circular economies because of high global CO 2 emissions make CO 2 an attractive feedstock for manufacturing chemicals. Moreover, H 2 is a low-cost and carbon-free reductant because technologies such as solar-driven electrolysis and supercritical water (scH 2 O) gasification enable sustainable production of molecular hydrogen (H 2 ). We review the recent advances in engineering Ralstonia eutropha, the representative species of "Knallgas" bacteria, for utilizing CO 2 and H 2 to autotrophically produce 2,3-butanediol (2,3-BDO). This assessment is focused on state-of-the-art approaches for splitting H 2 to supply energy in the form of ATP and NADH to power cellular reactions and employing the Calvin-Benson-Bassham cycle for CO 2 fixation. Major challenges and opportunities for application and future perspectives are discussed in the context of developing other promising CO 2 and H 2 -utilizing microorganisms, exemplified by Zymomonas mobilis.

42 ENGINEERING↗
DOE OSTI2020

Metamaterials for Mechanically Directing Cell Phenotype

Recently, abundant research has begun to reveal how microscale surface topography can influence a wide range of cell phenotypes in vitro, such as cell mobility, cell size and cell viability (Flemming et al. 1999, Nikkhah et al. 2012, Wang et al. 2016). However, while these studies shed some light on cell interactions with 2D surfaces of different length scales, cells in vivo experience their surroundings in 3D. Therefore, investigations into cell interactions with varying 3D microstructures are needed to gain biologically relevant insight into how microarchitecture and feature size influences cell behavior. Understanding this relationship between 3D microstructure and cell behavior will have a huge impact on tissue engineering and mechanobiology. Until now, the ability to fabricate complex 3D microstructures for cell behavior studies has been limited. This study harnessed LLNL’s Projection Micro-Stereolithography (PμSL) capability to probe the effects of micron-scale changes in 3D architecture on cell phenotype. Furthermore, our studies explored the application of external forces—such as cyclic loading and flow-induced shear stress—to cell-seeded 3D microstructures to further examine cell behavior.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Biological Lignin Valorization

Given lignin's heterogeneity, catalytic depolymerization results in aromatic compound mixtures, and conversion of this complex substrate to a single product is challenging. To that end, the Biological Lignin Valorization (BLV) project is pursuing biological funneling, wherein aromatic catabolic microbes are engineered to convert a mixture of lignin-derived compounds to a single product. Namely, we employ Pseudomonas putida and pursue atom-efficient products, such as muconic acid, which can be further converted to direct replacements or used in performance-advantaged bioproducts. Overall, biological lignin conversion can make major contributions to reduce the minimum fuel selling price of the integrated biorefinery. Early industrial efforts in this area are also leading to value-added products, including in collaboration with the BLV project. Primary challenges associated with BLV efforts include accessing bio-available monomers from lignin (with the Lignin Utilization project), enabling commercial titers, rates, and yields of bioproducts from lignin-derived compounds, and overcoming substrate and product toxicity. To date, we have 1) demonstrated 49 g/L of muconate from aromatic compounds and 4 g/L of muconate from lignin, 2) improved the toxicity tolerance of P. putida to key aromatic substrates, 3) debottlenecked biological funneling for higher rates, and 4) engineered P. putida to convert S, G, and H-type lignin-derived compounds to a single product.

BIOMASS FUELS,INORGANIC, ORGANIC, PHYSICAL, AND AN↗
DOE OSTI2021

Multifunctional Fibroblasts Enhanced via Thermal and Freeze-Drying Post-treatments of Aligned Electrospun Nanofiber Membranes

Parallel fibrous scaffolds play a critical role in controlling the morphology of cells to be more natural and biologically inspired. Among popular tissue engineering materials, poly(2-hydroxyethyl methacrylate) (pHEMA) has been widely investigated in conventional forms due to its biocompatibility, low toxicity, and hydrophilicity. However, the swelling of pHEMA in water remains a major concern. To address this issue, randomly oriented and aligned as-spun pHEMA nanofibrous scaffolds were first fabricated at speeds of 300 and 2000 rpm in this study, which were then post-treated using either a thermal or a freeze-drying method. In cell assays, human dermal fibroblasts (HDFs) adhered to the freeze-drying treated substrates at a significantly faster rate, whereas they had a higher cell growth rate on thermally-treated substrates. Results indicated that the structural properties of pHEMA nanofibrous scaffolds and subsequent cellular behaviors were largely dependent on post-treatment methods. Moreover, this study suggests that aligned pHEMA nanofibrous substrates tended to induce regular fibroblast orientation and unidirectionally oriented actin cytoskeletons over random pHEMA nanofibrous substrates. Such information has predictive power and provides insights into promising post-treatment methods for improving the properties of aligned pHEMA scaffolds for numerous tissue engineering applications.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Cell-free styrene biosynthesis at high titers

Styrene is an important petroleum-derived molecule that is polymerized to make versatile plastics, including disposable silverware and foamed packaging materials. Finding more sustainable methods, such as biosynthesis, for producing styrene is essential due to the increasing severity of climate change as well as the limited supply of fossil fuels. Recent metabolic engineering efforts have enabled the biological production of styrene in Escherichia coli, but styrene toxicity and volatility limit biosynthesis in cells. To address these limitations, we have developed a cell-free styrene biosynthesis platform. The cell-free system provides an open reaction environment without cell viability constraints, which allows exquisite control over reaction conditions and greater carbon flux toward product formation rather than cell growth. The two biosynthetic enzymes required for styrene production were generated via cell-free protein synthesis and mixed in defined ratios with supplemented L-phenylalanine and buffer. By altering the time, temperature, pH, and enzyme concentrations in the reaction, this approach increased the cell-free titer of styrene from 5.36 ± 0.63 mM to 40.33 ± 1.03 mM, the highest amount achieved using biosynthesis without process modifications and product removal strategies. Finally, cell-free systems offer a complimentary approach to cellular synthesis of small molecules, which can provide particular benefits for producing toxic molecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Chemical Functional Groups Regulate Ion Concentrations and pHs in Nanopores

Understanding ion behaviors in functionalized nanopores is essential to deciphering reactions in both natural and engineered systems, such as sediments, biological ion channels, and membranes. While many efforts have shown the modified ion behaviors in the functionalized nanopores, a direct measurement and analysis to show how chemical functional groups affect ion concentrations in nanopores are critically needed. In this work, we present a plasmonic nanosensor that can measure the local concentrations of protons, anions (phosphate, nitrate, sulfate, and arsenate), and cations (mercury, lead, and copper) in functionalized nanopores, and we compare their concentrations in nanopores with the corresponding bulk concentrations. Notably, chemical functional groups induced ion concentrations differently in nanopores. In pristine nanopores and methyl- and phenyl-functionalized nanopores, we discovered an unexpected concurrence of an enhanced anion concentration and a suppressed cation concentration. In addition, the nanopore pH is dependent on bulk solution compositions and can be lower by 2.5 units, even when the bulk solution is well-buffered. In contrast, for hydrophilic (amine, thiol, and carboxyl) nanopores, pH depended on the p K a of the functional groups, and the heavy metal concentrations depended on chemical interactions with the functional groups. Our findings provide a better understanding of water chemistry in nanopores and can help precisely control ions in nanopores to benefit the design of membrane-based desalination techniques, CO 2 storage, and porous catalysts.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Development of a Freeze-Dried CRISPR-Cas12 Sensor for Detecting Wolbachia in the Secondary Science Classroom

Training the future synthetic biology workforce requires the opportunity for students to be exposed to biotechnology concepts and activities in secondary education. Detecting Wolbachia bacteria in arthropods using polymerase chain reaction (PCR) has become a common way for secondary students to investigate and apply recombinant DNA technology in the science classroom. Despite this important activity, cutting-edge biotechnologies such as clustered regularly interspaced short palindromic repeat (CRISPR)-based diagnostics have yet to be widely implemented in the classroom. To address this gap, we present a freeze-dried CRISPR-Cas12 sensing reaction to complement traditional recombinant DNA technology education and teach synthetic biology concepts. The reactions accurately detect Wolbachia from arthropod-derived PCR samples in under 2 h and can be stored at room temperature for over a month without appreciable degradation. Here, the reactions are easy-to-use and cost less than $40 to implement for a classroom of 22 students including the cost of reusable equipment. We see these freeze-dried CRISPR-Cas12 reactions as an accessible way to incorporate synthetic biology education into the existing biology curriculum, which will expand biology educational opportunities in science, technology, engineering, and mathematics.

59 BASIC BIOLOGICAL SCIENCES↗