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At least 1,333 records · Page 74
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Using root and soil traits to forecast woody encroachment dynamics in mesic grassland

Grasslands are a widespread and globally important biome providing key ecosystem services including C storage and regulation of the water cycle. Grasslands face multiple threats, including changes in drought intensity and woody encroachment - a process that results in increased woody plant abundance corresponding with decreased herbaceous plant abundance. The combination of reduced soil moisture and shifts in plant dominance from herbaceous to woody are likely to alter C pools in the soil profile. We currently do not have the capacity to predict either the magnitude or rates of change in these C pools. In order to predict changes in grassland vegetation structure and the associated impacts on C cycling requires greater understanding of changes in soil C pools at multiple soil depths, and the responses of these pools to changes in precipitation. To support and perform this parameterization of Land Surface Models, we performed detailed investigations of root (anatomical and physiological) and soil traits (microbial function) at varying soil depths, to capture the belowground impacts of changing dominant plant growth forms (grasses to shrubs) and the impacts of frequent drought.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Science Plan for the Deployment of the Third ARM Mobile Facility to the Southeastern United States at the Bankhead National Forest, Alabama (AMF3 BNF)

In 2018, the U.S. Department of Energy (DOE) held a workshop for the Atmospheric Radiation Measurement (ARM) (Mather and Voyles 2013) user facility to discuss critical climate challenges and locations where key ARM Mobile Facility (AMF) observational assets could impact Earth system modeling (ESM). As an outcome, the southeast United States (SE U.S.) was identified as a high-priority region to target climate-process studies that promote a deeper understanding of the climate system and bolster ARM interactions with the community to drive ESM advancement. The DOE ARM user facility is a globally recognized leader in deploying and operating strategically located observation sites around the world for studying the properties of aerosols and clouds and their interaction with radiation, precipitation, and the Earth’s surface. In partnering with the DOE Atmospheric System Research (ASR) program, ARM solicited a multi-agency Site Science Team approach to provide input and close interaction with ARM management towards a successful SE U.S. deployment of the ARM third Mobile Facility (AMF3) (Miller et al. 2016). These efforts included identifying key locations, science drivers and instruments, and measurement strategies to address the wider climate-process needs and ESM improvement. Community input served a vital role in establishing, refining, and informing the relevant drivers and decisions regarding this AMF3 deployment. The team has identified Northern Alabama (N. AL) as regionally representative to unlock the key opportunities that will improve our understanding and model representation of aerosol, cloud, and land-surface processes and their couplings in the SE U.S. A defining aspect of the AMF3 deployment is its commitment to long-term (anticipated five-year) observations to mitigate potential seasonal-to-annual variability that often limits appropriate attribution of phenomena to local or larger-scale processes. The proposed location may leverage nearby surface networks and multi-agency and partner assets to enrich this multi-year deployment. One motivation is to understand the role of spatiotemporal variability (thermodynamic, land-surface) across aspects of the climate system, with our AMF3 team anticipating future demands on characterizing the relationships between local-to-regional cloud development and surface processes across a diverse patchwork of natural, managed, and urban landscapes as found throughout the N. AL regions. The main site targets an intact, representative, forested region – the Bankhead National Forest (BNF) – underscoring further team commitment to regionally important land-atmosphere two-way interactive studies “from the canopy to the clouds”, with enhanced tower instrumentation augmenting traditional ARM capabilities adjacent to this site. Multiple supplemental sites will also be distributed across this region, prioritizing added needs for biodiversity. Anticipated high-priority cloud science themes will target N. AL as a regional SE U.S. hotbed for high-impact weather, convective cloud onset, and shallow-to-deep cloud transitioning. Anticipated aerosol drivers will focus on chemical processes that control the evolution of organic aerosol, the seasonality and spatial distribution of water vapor and particle-phase water, and its role on aerosol optical properties. Anticipated land-atmosphere drivers consider the two-way feedbacks between surface influence on aerosols, clouds, and precipitation properties and the associated radiative impacts on plant physiology and canopy-scale fluxes. Emphasis will include the study of the impact of surface processes on aerosols via precursor emission, and on clouds via moisture flux and thermal development.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Engineered human vascular models to study endothelial dysfunction in infectious disease

Vascular involvement plays a pivotal role in the pathogenesis of numerous emerging viral threats, with climate changes amplifying the likelihood of these diseases evolving into pandemics. Establishing an infectable and physiologically relevant human in vitro model holds immense importance in comprehending the pathogenesis of these threats and devising effective countermeasures. Although in vivo models provide valuable insight into disease, their application is restricted by interspecies variations, particularly concerning pathogens exclusive to humans. Moreover, animal models often fail to replicate comorbidities prevalent in patient populations, thus limiting our understanding of disease behavior in humans. In this study, we have devised a testing platform aimed at exploring pathogen interactions with innate immunity within the vasculature, encompassing both healthy and dysfunctional endothelial conditions.

42 ENGINEERING↗
DOE OSTI2024

Effects of salinity and nutrients on metabolism and growth of Ulva lactuca: implications for bioremediation in San Diego Bay and Coastal Watershed

Our project sought to explore the ability of seaweed (Ulva lactuca) farms to clean polluted waterways of excess nitrogen and phosphorus through bioremediation. We addressed this goal in three primary ways. First, we worked with an undergraduate student from the Environmental Sciences Department at SDSU (Emily Bews) to examine how Ulva would perform under elevated nutrients and decreased salinity conditions, such as would be expected on the seaweed farms during periods of high rainwater runoff. This would show whether Ulva could indeed be grown on farms during these periods. We conducted laboratory experiments at SDSU’s CMIL (marine laboratory) using orthogonal combinations of two salinities and three nutrient loadings, and measured several aspects of Ulva physiology, namely growth, photosynthetic rates, chlorophyll fluorescence, and stable isotope analyses of Ulva’s tissues, and tissue uptake of phosphorus and nitrogen. Our results clearly show Ulva is an ideal candidate for using on farms during periods of heavy rains and takes up excess nutrients. The results of this were published in Marine Pollution Bulletin, with undergraduate Bews as lead author (Bews, E., L. Booher, T. Polizzi, C. Long, J-H Kim, MS Edwards. 2021. Effects of salinity and nutrients on metabolism and growth of Ulva lactuca: implications for bioremediation of coastal watersheds. Marine Pollution Bulletin 166: 121299.).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Optimizing DOE Opportunities to Research Land–Atmosphere Interactions in the U.S. Southeast (Workshop Report)

The southeastern United States (Southeast), with its complex and varied environments, is an area of tremendous economic, ecological, and societal importance to the country. The region is characterized by heterogeneous landscapes (i.e., geology and soil type) and a long history of human land use coupled with a warm temperature regime and high precipitation. As a result, soil erosion and deposition are pronounced, vegetation recovery is rapid, and human modification is extensive across the region. To better understand land–atmosphere interactions in this important and complex region, research communities supported by the U.S. Department of Energy’s Biological and Environmental Research (BER) program identified the Southeast as a priority region of interest. In fall 2024, the third Atmospheric Radiation Measurement Mobile Facility (AMF3), one of three mobile monitoring facilities designed to collect atmospheric and climate data from undersampled regions around the world, will begin operations in northwestern Alabama’s Bankhead National Forest (BNF). The AMF3-BNF 5-year deployment, from 2024–2029, will monitor the effects of feedbacks among aerosols, clouds, and precipitation on plant physiology and canopy-scale fluxes. It will also focus on scale aggregation to resolve the role of local forcing on larger-scale processes. To enable broader AMF3 involvement by the science community, the BER Environmental System Science (ESS) program organized the Southeast Land– Atmosphere Research Opportunities (SELARO) workshop in August 2023. The purpose was to identify gaps in scientific understanding of terrestrial processes in the Southeast (defined as states bounded by the Gulf of Mexico to the south, the Atlantic Ocean to east, the Mississippi River to the west, and extending through Tennessee and North Carolina to the north) and explore opportunities to use the AMF3-BNF deployment to coordinate and leverage research efforts across the region. Many parts of the Southeast have experienced repeated anthropogenic forcings. Farming, hunting, burning, and settlement of the region by Indigenous Peoples first shaped the distribution of plant communities, which in turn influenced European colonization patterns. Timber harvesting was common during the expansion of European settlements, and production forestry continues today. Agricultural production was extensive and then waned through the 20th century, creating a period of afforestation following agricultural abandonment. Today, many formerly agricultural landscapes are undergoing rapid urbanization and suburbanization. Overlying these patterns of anthropogenic land use are frequent disturbances from hurricanes, tornadoes, wildfires, drought, flooding, ice storms, and the occasional blizzard. An additional characteristic of the Southeast is its overall landscape complexity. Unlike the western United States, where broad expanses may share similar characteristics, Southeast topography, drainage patterns, vegetation, and development patterns vary widely across relatively small spatial scales (<1 km). This is due to the region’s underlying geology and soil development, species biodiversity patterns, and land ownership and use coupled with strong forces of erosion, weathering, and rapid plant growth in the warm, wet climate.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Developing a pipeline to expand the genetic code of diverse bacteria for microbial engineering

Microbial biotechnologies are key to addressing grand challenges to promote human health, reverse carbon emissions, recycle mixed plastic waste, remediate contaminated soils, and achieve sustainable economies. Synthetic biology has enabled design of diverse microbes and their proteins for useful purposes, but the narrowness of the natural genetic code limits functional diversity (e.g., biosynthesis) of engineered microbes. The natural genetic code defines the fundamental rules of translating genetic information into proteins comprised of 22 ‘canonical’ amino acids. However, using a technique called genetic code expansion (GCE), the chemical properties and therefore functions of proteins can be transformed by incorporation of one or more of ~200 chemically diverse ‘non-canonical’ amino acids. The effective application of genetic code expansion in diverse microbes has the potential to revolutionize biotechnology. However, despite over 50 years of research and its transformative potential, the application of genetic code expansion has been limited to a handful of bacterial species. In this project, we will perform three tasks to both overcome the barriers that prevent wide spread adoption of GCE as molecular tool and demonstrate its potential for biotechnological applications. Specifically, we will (1) develop a genetic engineering methodology that will enable use of GCE in a broad range of bacterial hosts, (2) use high-throughput functional genomics methods to identify physiological responses to both genetic code expansion and exposure to non-canonical amino acids in three different bacteria, and (3) demonstrate an application of GCE by selectively incorporate non-canonical amino acids into surface displayed peptides such as those used for biomining.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Evaluating the Influence of Plants on Hydrologic Cycling: Quantifying and Validating the Role of Plant Processes and Stomatal Conductance (Final Report)

Plants can exert strong controls on water cycling, both locally and across the globe. The impacts are driven by how plants control the exchange of water and energy between the land and the atmosphere, which in turn are influenced by how plants photosynthesize and grow (e.g. biogeochemical cycling). Our team has shown previously that plant responses to increasing CO 2 in the atmosphere can influence the water cycle through changes in rainfall and the amount of water on land with implications for drought. Plant responses can also alter both average and extreme flow of water in rivers, with implications for freshwater availability and flood frequency. Although the impact of plant responses on water cycling has been demonstrated to exist, significant uncertainty remains in our understanding of the magnitude and form of the plant responses themselves, as well as their ultimate impact on water availability for people and ecosystems. In this project we worked to quantify the role of plant processes in regulating water cycling (e.g., precipitation, evapotranspiration, runoff, droughts, etc.). We addressed the following objectives: quantify the control of physiological vs. radiative effects on water cycling across many coupled models in idealized and realistic scenarios, as well as to quantify how our assumptions about leaf-level processes (e.g. coupling between stomatal conductance and photosynthesis), and organism-level processes (e.g. leaf area response to high CO 2 ) contributed to uncertainties and biases in water cycling. We focused on the impact of these processes on water cycling to assess the sensitivities of precipitation, evapotranspiration, and runoff to model assumptions about plant processes at the leaf, organism, and community level. As part of this project we used measurements of stable carbon isotopes to generate observationally based estimates of plant functioning during the historical period. This work is directly relevant to DOE’s primary scientific research questions in the RGMA topic area (b) on Biogeochemical processes, feedbacks, and interactions in the Earth system.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

EvoNet: A phylogenomic and systems biology approach to identify genes underlying plant survival in marginal, low‐N soils

The DOE‐BER “EvoNet” project investigates the genetic and molecular basis of plant resilience in extreme environments. We do this by identifying key genes that enable “extreme survivor” species to thrive in the nitrogen-poor soils of Chile’s hyper-arid Atacama Desert. Our collections focus on 32 Atacama extremophile species, including seven grass species with potential biofuel applications. To identify genes-of-importance to survival we compared genomic and transcriptomic profiles of extremophile species that thrive in the Atacama to those of closely related “sister” species from nitrogen-rich arid and mesic regions of California. Deep RNA sequencing and de novo transcriptome assembly across these triplet species sets supported a phylogenomic framework for identifying positively selected genes associated with adaptive divergence. Our integrative analysis combined ecological and environmental data, metagenomics, evolutionary and systems biology, and metabolomics. This enabled us to create an unprecedented framework for systematically understanding how non-model plants have adapted to survive in extreme conditions. Our resulting database of positively selected ortholog groups in the extremophile plants offers promising targets for engineering crop and biofuel species with enhanced resilience to drought and extreme weather. Additionally, our newest dataset explores and exploits a complementary metabolomic approach. This new aspect provides innovative strategies to manipulate plant cell metabolism, further supporting efforts to improve agricultural productivity in the face of extreme climates. Importantly, our combined evolutionary- and metabolomic-based strategies focused on convergent patterns of adaptation, providing a genetic and metabolomic toolkit for improving crop and biofuel resilience across diverse plant species. Finally, our novel exploration of ecological and evolutionary dynamics delivered to the community a phylogenomic computational pipeline called “PhyloGeneious.” Our continued adaptations of this pipeline are publicly available to expedite evolutionary genomic research for future scientific discoveries. In total, our DOE-BER has provided genomic, metabolomic, and computational strategies to understand how extremophile plants provide evolutionary and physiological targets for improving agricultural and biofuel production.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Neutrons in Structural Biology: Challenges and Opportunities (Workshop Report)

Gaining a thorough understanding of biological systems requires building our knowledge about biological processes from the level of atoms and electrons, and up to whole organisms. Such comprehensive knowledge will allow for a predictive understanding of complex biological systems behavior. It will guide us in the design and development of novel therapeutics and vaccines to tackle existing health threats and to prepare for future pandemics, and it will provide information necessary to create new biomaterials and bio-inspired technologies through manipulation of biological macromolecules, their assemblies, single cells and even microorganisms. Reaching these goals will require a synergistic combination of multiple experimental techniques with molecular calculations and predictive simulations, and the design and development of new techniques and capabilities that bridge current knowledge and technology gaps. Neutron scattering provides unique information about the biomacromolecular structure and function and can play a major role in achieving these goals. A workshop was held to engage the scientific community in identifying pressing challenges in biochemistry, structural biology, enzymology and structure-guided drug design not solved with the current neutron scattering technologies or utilizing other structural biology techniques such as X-ray crystallography, NMR, and cryo-EM. The workshop brought together structural biology, biochemistry and computational experts, as well as early career researchers and students, creating a forum for discussing scientific advancement and collaboration. The workshop included a one-day satellite training workshop where graduate students and postdoctoral researchers were educated in the application of neutron crystallography and small-angle scattering in structural biology. Furthermore, the Instrument Scientific Advisory Board (ISAB) for the development of a macromolecular neutron diffractometer at ORNL’s Second Target Station was introduced at the workshop. The major outcome was that neutrons can provide atomic-level understanding of biomacromolecular structure, function and dynamics which is of paramount importance for addressing the identified challenges. Neutron crystallography, in particular, can resolve long-standing biochemical issues regarding enzyme function by delineating the underlying chemistry and can have a major impact on the design of small-molecule therapeutics, especially in combination with molecular computation (quantum chemistry and molecular dynamics simulations) and the emerging artificial intelligence (AI)-assisted drug design technologies. The unique properties of neutrons, including their high sensitivity to hydrogen and their non-destructive nature, make them ideal probes of biological matter. There is a palpable need in the scientific community to expand and enhance the impact of neutron sciences on biology. Neutron crystallography is the only structural biology method capable of determining positions of all hydrogen atoms in proteins, nucleic acids and their complexes at near-physiological temperatures and of unstable species at cryogenic temperatures. Moreover, neutron analysis is non-ionizing, non-destructive and does not perturb the structure or redox chemistry of active site metal centers and clusters in proteins, which can be invaluable for studying radiation-sensitive metalloprotein complexes. Further, neutron energies used in scattering applications are similar to atomic motions, permitting neutron spectroscopies to characterize the dynamics of biomacromolecules on the picosecond to microsecond timescales. The different sensitivities of neutrons to protium (H) and deuterium (D) isotopes of hydrogen allow enhanced visibility of specific parts of biological complexes through isotopic labeling. The impact of neutrons will be most powerful when neutron scattering is combined with complementary experimental techniques that use photons and electrons, and with high-performance computing. The interconnection and mutuality of the experimental and theoretical capabilities will drive discoveries in biological and health sciences to generate more complete picture of complex biological systems. The major limitation in the field of biological neutron crystallography has been signal-to-noise, demanding large samples that are difficult to produce for the majority of biomacromolecules and limiting the applicability of this technique in biological sciences. A neutron crystallography instrument at the Second Target Station will revolutionize biological science with neutrons by engaging a large scientific community of structural biologists, enabling successful neutron diffraction experiments from radically smaller biomacromolecular crystals, resolving unanswered biochemical questions, and meaningfully contributing to rational drug design. The meeting highlighted 10 grand challenges that will be addressed with this advanced capability over the next decade and beyond, and the recommendations required to help address them are given below.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Engineering Yeast for the Production of Acids and Esters (CRADA Final Report)

NREL and Lygos have a mutual interest in engineering yeast for the production of acids and esters as intermediates towards fuels or bioproducts. In particular, the yeast Pichia kudriavzevii is a fantastic candidate for the production of acid and ester based products including butyric acid and ethyl butyrate. However, the strain is relatively uncommon in the biotechnological space and as such there are not an abundant amount of genetic tools that are publically available. However, Lygos has been working with this species in particular for several years and has developed genetic tools and physiological characteristics and are well versed in engineering this strain for acid based products. While currently focusing on malonic acid-derived products, Lygos is not currently targeting butyric acid and ethyl butyrate but have a long term interest in these molecules and derivatives therein. This CRADA proposal seeks to leverage NREL’s immediate focus on butyric acid and ethyl butyrate, and general bioprocess expertise with Lygos’ specific knowledge on engineering P. kudriavzevii for the production of acid-based products.

09 BIOMASS FUELS↗
DOE OSTI2025

Uncertainty Analysis of Inhalation Dose Coefficients for Nuclear Incident Response

This study addressed the need to characterize variability in inhalation dose coefficients due to uncertainties in respiratory tract deposition, systemic biokinetics, and physiological parameters. A Python-based implementation of the International Commission on Radiological Protection Publication 66 Human Respiratory Tract Model was developed called the Radiological Exposure Dose Calculator (REDCAL) to propagate parameter uncertainty.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2025

Hot, Cold, or Just Right? Using a Wide-View Infrared Biometric Sensor to Improve Occupant Comfort and Reduce Overcooling in Buildings via Closed-loop Control (CRADA Final Report)

This research adds to the understanding of building energy management by fundamentally challenging the long-standing paradigm of controlling an environmental parameter—air temperature—and assuming occupant comfort will follow. The project developed and demonstrated a novel approach that directly senses physiological indicators of human comfort to enable closedloop, human-centric control of heating, ventilation, and air conditioning (HVAC) systems. This work shifts the focus from open-loop environmental control to a closed-loop system that prioritizes the occupants' actual thermal state. The primary benefit to the public is the potential for a simultaneous improvement in the quality of indoor environments, where people spend most of their time, and a significant reduction in national energy consumption. Overcooling, or the overuse of cooling energy in a way that discomforts occupants, wastes approximately 0.5 Quads of primary energy annually in U.S. commercial buildings and creates unproductive indoor environments.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2025

Enhancing chemical bioproduction with rational control of bacterial post-translational modifications

Efficient conversion of inexpensive feedstocks to valuable chemicals by microbes is critical for a robust bioeconomy, but the ability to rationally design bacteria is hampered by insufficient knowledge of how post translational modifications (PTMs) control bacterial protein function and thus bioproduction phenotypes. Our study will focus on the lysine acetylation, a ubiquitous bacterial PTM that can affect the function of enzymes in central metabolism that are often critical for bioproduction processes, disrupt transcriptional regulation, and reduce translation. However, most lysine acetylation data is observational, which means that we do not know when, how, and what specific acetylated residues affect protein function and bacterial physiology. For our model host, we will use a Pseudomonas putida strain that we previously engineered to convert lignocellulosic feedstocks into chemicals such as itaconic acid (ITA). With this strain, we use a dynamic two-stage bioproduction process in which ITA is produced during a non-growth associated production phase. Production is highest during growth stages when lysine acetylation is low in other organisms (early stationary phase) and stalls in conditions where acetylation is highest (late stationary phase). The switch from high to stalled ITA production is also correlated with an unexpected increase in acetate levels – the precursor to non-enzymatic lysine acetylation. As such, we predict that lysine acetylation plays a substantial role in regulating the metabolic pathways required for ITA production. We will develop a generalizable approach that combines high-throughput genetic screens and cutting-edge genome engineering with state-of-the-art proteomics, metabolomics, and genetic code expansion methods to identify and modulate lysine acetylation patterns in bacteria. Ultimately, these strategies aim to manipulate protein expression and acetylation patterns to enhance bioproduction phenotypes (e.g., sustained ITA production in late stationary phase).

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

LDRD 2024 Annual Report: Laboratory Directed Research and Development Program Activities

One fundamental question underlying all living organisms is the need to understand their hierarchical organizations and physical changes with the necessary spatial and temporal resolutions under physiological or pathological conditions. This is a multi-scale challenge requiring imaging from sub-nanometers to micrometers in a cellular context. While individual imaging techniques are available, there is a critical need to integrate them into a workflow capability. Our objective is to develop an integrated multi-disciplinary and multi-scale bioimaging capability at Brookhaven National Laboratory (BNL). The capability expands BNL’s existing facility operation program in bioimaging and positions BNL in a leadership position in bioimaging research. The capability also addresses the grand challenges of the Department of Energy (DOE) science programs for national bioenergy sustainability and security.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2025

Versatile & Intelligent Biodetection via Environmental Sensing (VIBES)

Reactive health monitoring strategies during events like the COVID-19 pandemic highlighted the need for predictive, threat-agnostic diagnostics that can detect both known diseases and novel chemical or biological threats. To address this, we investigated an optical biosensor as a breath volatile organic compound (VOC) analyzer, aiming to emulate biological olfaction. We assembled and validated the device with thin film metal coated substrate-based sensors. We immobilized small biological recognition elements on the substrates and delivered controlled concentrations of target VOCs. The sensor was irradiated with a visible laser and the sensor signal was recorded. We characterized the laser performance and tested 3 recognition elements for 2 VOCs with varying concentrations (1-100 ppm). We also evaluated enhancement of the signal using nanostructures on the metal film in comparison with planar film substrate. We demonstrated detecting ethanol reliably at concentrations as low as ~2 ppm along with preliminary detection of acetone (<100 ppm). We also found several unexpected factors that influence the sensor behavior that should be addressed to further refine the device’s performance. The nanostructures were, as expected, found to amplify the sensor signals. These findings demonstrate the feasibility of the optical bio-sensing modality for breath VOC monitoring at physiologically relevant levels. This positions LLNL to develop a low-cost, scalable, broad-spectrum health monitoring capability aligned with the Early Detection thrust of the Bioresilience Mission Focus Area and attract external funding.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Development of emerging model microorganisms: Megasphaera elsdenii for biomass and organic acid upgrading to fuels and chemicals

The metabolic diversity of microorganisms in nature represents a largely untapped source of valuable compounds that are difficult or impossible to produce in the limited number of available model systems. Efforts to produce longer-chain alcohols, such as hexanol, in organisms like Escherichia coli have met with limited success; production of C6 and larger products remains low, highlighting the challenges of extending chain elongation pathways beyond a single cycle. Megasphaera elsdenii naturally condenses acetyl-CoA to efficiently generate C4–C8 organic acids, making it a promising candidate for producing fuels and chemicals from lactate and plant-derived carbohydrates. This high native flux through the chain elongation pathway offers the potential for higher yields and titers of medium-chain products, such as hexanol, compared to conventional hosts. Recent advances—most notably the development of a transformation method for M. elsdenii—have further opened the organism to detailed physiological studies and bioengineering. While full development of M. elsdenii as a hexanol-producing platform was not achieved, significant progress was made in understanding its metabolism and building foundational genetic tools for future engineering.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Porin-Inspired Ionomers with sub-nm Gated Ion Channels for High Ion Conductivity and Selectivity (Final Project Report (2026))

The physiological functions of living systems heavily rely on biological ion channels, whose malfunction can lead to disease. These channels enable selective and regulated transport of water, ions, or small molecules across membranes. Analogously, ionomers used in energy conversion and storage technologies govern ion transport within membrane separators and catalyst binder layers. This DOE Office of Science Early CAREER project aimed to achieve molecular-level control over ionic conductivity and ion permselectivity by translating the functionalities of biological, gated ion channels into a novel class of ion-conducting polymers (ionomers) incorporating macrocyclic calix[4]arene-based repeat units. The overarching goal was to establish fundamental design principles and elucidate proton conduction mechanisms through strategic design of macrocyclic calix[4]arene-containing ionomers, with close relevance to energy conversion and storage devices, including proton exchange membrane fuel cells (PEMFCs). The project leveraged sub-nm-sized macrocyclic pores to facilitate exceptionally fast ion transport (beneficial to addressing sluggish ORR kinetics of PEMFC electrodes) and achieve functionalities of ionic diodes under applied electrochemical fields, beneficial for selective transport/separation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Harnessing Heterologous Bacterial Two-Component Systems as Biosensors to Address Challenges in Fermentation Scale-Up

Scaling up bacterial fermentation from bench to industrial scale often results in unpredictable performance losses, possibly in part due to changes in microenvironmental conditions such as pH. To investigate this, we developed a suite of pH-sensitive biosensors from bacterial two-component systems (TCSs) that provide a dynamic, fluorescent readout in response to extracellular pH changes. TCSs consist of a periplasmic sensor histidine kinase (HK) that, in response to an extracellular stimulus, autophosphorylates intracellularly and subsequently transfers the phosphate to a cognate response regulator (RR) that modulates transcription of target genes. We utilized three pH-responsive TCSs (referred to here as CVJ1, CVJ30, and CVJ79) and linked their output to GFP. This was achieved by placing the RR promoter upstream of GFP or by constructing a chimeric RR composed of the native receiver domain and the DNA-binding domain of another well-characterized RR with a defined promoter. All components - HK, RR (native or chimeric), and GFP under its corresponding promoter - were cloned into a broad-host-range plasmid. Sensors were validated in Escherichia coli and Pseudomonas putida, including the muconic acid-producing strain P. putida TL207. All three biosensors successfully reported pH, with fluorescence (normalized to optical density) correlating strongly with media pH. Among the native sensors, CVJ79 showed the most robust performance while CVJ1 also performed best in its native form; CVJ30 exhibited improved functionality as a chimera, suggesting that modular RR design can enhance compatibility in some heterologous hosts. Further, CVJ79 was activated by alkaline conditions, while CVJ30 responded to acidic environments. Notably, CVJ1 was induced by high pH in wild-type E. coli and P. putida, but low pH in TL207. The observed differences in sensor activation between strains - particularly the divergent response of CVJ1 - suggest that host-specific regulatory pathways may influence how cells perceive and adapt to pH stress. Moving forward, these biosensors can be used to guide the rational design of more robust strains, optimize process conditions in real time, and inform strategies to minimize physiological heterogeneity during scale-up. Integrating these tools into high-throughput screening and bioreactors will be a key step toward improving predictability and performance in industrial bioprocesses.

09 BIOMASS FUELS↗