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At least 1,351 records · Page 75

Influence of Uranium Concentration and pH on U-Phosphate Biomineralization by Caulobacter OR37

Uranium contamination of soils and groundwater in the United States represents a significant health risk and will require multiple remediation approaches. Microbial phosphatase activity coupled to the addition of an organic P source has recently been studied as a remediation strategy that provides an extended release of inorganic P (Pi) into U-contaminated sites, resulting in the precipitation of meta-autunite minerals. Previous laboratory- and field-based biomineralization studies have investigated environments with relatively high U concentrations (>20 μM). However, most contaminated sites have much lower U concentrations (<2 μM). The Environmental Protection Agency (EPA) limit for U in drinking water is 0.126 μM. Reaching this regulatory limit becomes challenging as U concentrations approach autunite solubility. Furthermore, we studied the precipitation of U(VI)-phosphate minerals by an environmental isolate of Caulobacter sp. (strain OR37) from an Oak Ridge, Tennessee, U-contaminated site. Abiotic U(VI) solubility experiments reveal that U(VI)-phosphate minerals do not form in the presence of excess Pi (500 μM) when U(VI) concentrations are <1 μM and pH is <5. When OR37 cells are reacted under the same conditions with Pi or glycerol-2-phosphate, U(VI)-phosphate mineral formation was observed, along with the formation of intracellular polyphosphate granules. These results show that bacteria provide supersaturated microenvironments needed for U(VI)-phosphate mineralization while hydrolyzing organic P sources. This provides a pathway to lower U concentrations to below EPA limits for drinking water.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Can Common Pool Resource Theory Catalyze Stakeholder-Driven Solutions to the Freshwater Salinization Syndrome?

Freshwater salinity is rising across many regions of the United States as well as globally, a phenomenon called the freshwater salinization syndrome (FSS). The FSS mobilizes organic carbon, nutrients, heavy metals, and other contaminants sequestered in soils and freshwater sediments, alters the structures and functions of soils, streams, and riparian ecosystems, threatens drinking water supplies, and undermines progress toward many of the United Nations Sustainable Development Goals. There is an urgent need to leverage the current understanding of salinization’s causes and consequences–in partnership with engineers, social scientists, policymakers, and other stakeholders–into locally tailored approaches for balancing our nation’s salt budget. In this feature, we propose that the FSS can be understood as a common pool resource problem and explore Nobel Laureate Elinor Ostrom’s social-ecological systems framework as an approach for identifying the conditions under which local actors may work collectively to manage the FSS in the absence of top-down regulatory controls. We adopt as a case study rising sodium concentrations in the Occoquan Reservoir, a critical water supply for up to one million residents in Northern Virginia (USA), to illustrate emerging impacts, underlying causes, possible solutions, and critical research needs.

54 ENVIRONMENTAL SCIENCES↗

A Deep Learning Based Framework to Identify Undocumented Orphaned Oil and Gas Wells from Historical Maps: A Case Study for California and Oklahoma

Undocumented Orphaned Wells (UOWs) are wells without an operator that have limited or no documentation with regulatory authorities. An estimated 310,000 to 800,000 UOWs exist in the United States (US), whose locations are largely unknown. These wells can potentially leak methane and other volatile organic compounds to the atmosphere, and contaminate groundwater. In this study, we developed a novel framework utilizing a state-of-the-art computer vision neural network model to identify the precise locations of potential UOWs. The U-Net model is trained to detect oil and gas well symbols in georeferenced historical topographic maps, and potential UOWs are identified as symbols that are further than 100 m from any documented well. A custom tool was developed to rapidly validate the potential UOW locations. We applied this framework to four counties in California and Oklahoma, leading to the discovery of 1301 potential UOWs across >40,000 km 2 . We confirmed the presence of 29 UOWs from satellite images and 15 UOWs from magnetic surveys in the field with a spatial accuracy on the order of 10 m. This framework can be scaled to identify potential UOWs across the US since the historical maps are available for the entire nation.

54 ENVIRONMENTAL SCIENCES↗

Predictive Assessment of the Chemical Composition of Coal Ash in Reserve at U.S. Disposal Sites

In the United States, more than 2 Gt of coal combustion residuals (i.e., coal ash) are stored in hundreds of disposal units. Recent federal regulations mandate the closure or retrofitting of most coal ash impoundments, presenting significant challenges for waste management. These regulatory pressures also present opportunities to reuse coal ash. However, the quality and quantity of discarded coal ash across the U.S. are not well known, even though this information is crucial for spurring its reuse for conventional and new material applications. This study describes a predictive model for the major element composition of coal ash in reserve at disposal sites of major U.S. coal-fired power plants. This model was constructed from coal purchase records of 705 power stations from 1973 to 2022 and was trained on coal ash composition data, showing that coal ash elemental composition is strongly associated with the source of feedstock coal. The model showed regional shifts in the major element contents of ash produced by power plants in the last 50 years, particularly for calcium and iron (expressed as %CaO and %Fe2O3), as power stations changed their source of coal over this time frame. Our approach enables an estimation of chemical composition for ash stored in waste impoundments at individual power stations. Such information can help to delineate the regional market resource potential of supplementary cements for concrete and other material innovations that would utilize coal ash harvested from disposal sites across the U.S.

01 COAL, LIGNITE, AND PEAT↗

Enzymatic Biocontrol of Fire Blight ( Erwinia amylovora ) Using an Engineered Glycosyl Hydrolase

Current management of fire blight, caused by Erwinia amylovora , relies heavily on streptomycin a practice that has contributed to the emergence of antibiotic-resistant strains and raised environmental and regulatory concerns. Enzyme-based biocontrol agents offer a promising antibiotic-free approach that combines target specificity with environmental compatibility. This study evaluates CAase, a bacteriophage-derived glycosyl hydrolase, for its ability to disrupt E. amylovora biofilms and reduce disease severity. Biochemical assays and scanning electron microscopy confirmed that CAase efficiently degraded the extracellular polysaccharide (EPS) matrix, releasing cells from biofilms. Gas chromatography–mass spectrometry (GC–MS) linkage analysis of EPS isolated from two Erwinia amylovora strains demonstrated that CAase preferentially cleaves galactan-rich amylovoran produced by strain EA273, while exhibiting only limited activity toward the levan-rich EPS from strain EA1430. Functional assays revealed that CAase reduced bacterial viability by nearly 2 orders of magnitude at higher enzyme concentrations, strongly suppressed surface motility, and induced ultrastructural damage visible by transmission electron microscopy. Importantly, field trials showed that CAase significantly lowered blossom and shoot blight incidence under orchard conditions. These results highlight CAase as a potent enzyme-based strategy for reducing the virulence of E. amylovora and demonstrate its potential as a sustainable alternative to antibiotics in fire blight management.

antibiotic resistance↗

The Chemical Management System (CMS): A Useful Tool for Inventory Management

Comprehensive inventory management is central to the efficient operation of any facility that uses and stores chemicals. There are numerous software packages available that perform this function satisfactorily. Most commercially available inventory management software is regulatory or procurement focused and usually comes with upfront or monthly fees. Finally, this report describes freely downloadable software developed at Sandia National Laboratories that delivers an effective inventory management system with an additional focus on chemical security.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Tools and Incentives for Implementing Codes of Ethics to Help Prevent the Reemergence of Chemical Weapons

Since the entry into force of the Chemical Weapons Convention (CWC) and the establishment of the Organisation for Prohibition of Chemical Weapons (OPCW) in 1997, 96% of the world’s declared stockpile, comprising 72,305 metric tons of chemical warfare agents have been destroyed. Despite this notable progress, the convergence of chemistry and biology brings new challenges to preventing chemical weapons production, as the technical capability to manipulate the chemistry of microorganisms has diffused beyond the chemical industry and academic research communities. The development and voluntary adoption by chemical practitioners around the world of ethical codes or guidelines, such as The Hague Ethical Guidelines and the Global Chemists’ Code of Ethics (GCCE) , are important steps in strengthening international nonproliferation efforts through their potential to impact the intent of the individual by normalizing ethical behavior. However, the simple act of adopting a code does not guarantee ethical behavior. Care must be taken to ensure those adopting the code understand specifically the behavior being asked of them, and they must be given ample opportunities to practice exercising those behaviors in low-risk situations and encouragement to keep trying when they fail. Furthermore, in small-to-medium chemical companies, concerns that adopting such measures could negatively impact profit margins may dissuade some business owners from voluntarily adopting ethical codes, while a country’s decision makers may not prioritize establishment of new regulatory mechanisms that could address some of these concerns. In this paper, factors that may positively influence a chemical company’s decision to adopt ethical guidelines, such as integration of social sustainability elements into frameworks and approaches to maintain social legitimacy in the eyes of the broader community, are explored. Voluntary adoption of ethical codes gives teeth to arms control regimes. By encouraging chemical companies to become engaged in the community around them and providing easy-to-use tools like scenario-based E-learning to enable remote engagement and facilitate understanding of the principles undergirding the GCCE, they actively participate in making the world a better place and minimizing the potential for reemergence of chemical weapons.

Small Chemical Companies, Codes of Ethics, E-learn↗

Free Energy and Flexibility Analysis of Autoinhibited Human BRAF

The RAF serine/threonine protein kinases function as direct effectors of RAS in the intracellular transmission of extracellular growth signals, and they are key targets for drug discovery, given the high incidence of oncogenic mutations in RAF and other components of this signaling pathway. In its inactive state, RAF is held in an autoinhibited conformation in the cytosol through a combination of intramolecular interactions and binding to a regulatory 14−3−3 protein dimer. Activation of RAF is initiated by its interaction with membrane-localized GTP-bound RAS, which induces conformational changes that release RAF from its autoinhibited state. However, the molecular mechanisms governing RAF activation remain incomplete, largely due to the challenges in experimentally capturing the intermediate conformational states in this process. To address this gap, we developed a comprehensive all-atom model of BRAF based on existing cryo-EM structures. Using this model, we performed extensive molecular dynamics simulations to evaluate the stability and free energy landscape of autoinhibited BRAF in solution. Our analysis reveals conformational flexibility within the autoinhibited complex, suggesting that this dynamic behavior may play a role in facilitating BRAF activation upon engagement with the membrane-bound RAS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

phosaa14SB and phosaa19SB: Updated Amber Force Field Parameters for Phosphorylated Amino Acids

Phosphorylated amino acids are involved in many cell regulatory networks; proteins containing these post-translational modifications are widely studied both experimentally and computationally. Simulations are used to investigate a wide range of structural and dynamic properties of biomolecules, such as ligand binding, enzyme-reaction mechanisms, and protein folding. However, the development of force field parameters for the simulation of proteins containing phosphorylated amino acids using the Amber program has not kept pace with the development of parameters for standard amino acids, and it is challenging to model these modified amino acids with accuracy comparable to proteins containing only standard amino acids. In particular, the popular ff14SB and ff19SB models do not contain parameters for phosphorylated amino acids. Here, the dihedral parameters for the side chains of the most common phosphorylated amino acids are trained against reference data from QM calculations adopting the ff14SB approach, followed by validation against experimental data. Finally, library files and corresponding parameter files are provided, with versions that are compatible with both ff14SB and ff19SB.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Investigating Carboxysome Morphology Dynamics with a Rotationally Invariant Variational Autoencoder

Carboxysomes are a class of bacterial microcompartments that form proteinaceous organelles within the cytoplasm of cyanobacteria and play a central role in photosynthetic metabolism by defining a cellular microenvironment permissive to CO2 fixation. Critical aspects of the assembly of the carboxysomes remain relatively unknown, especially with regard to the dynamics of this microcompartment. Progress in understanding carboxysome dynamics is impeded in part because analysis of the subtle changes in carboxysome morphology with microscopy remains a low-throughput and subjective process. Here we use deep learning techniques, specifically a Rotationally Invariant Variational Autoencoder (rVAE), to analyze fluorescence microscopy images of cyanobacteria bearing a carboxysome reporter and quantitatively evaluate how carboxysome shell remodelling impacts subtle trends in the morphology of the microcompartment over time. Toward this goal, we use a recently developed tool to control endogenous protein levels, including carboxysomal components, in the model cyanobacterium Synechococcous elongatus PCC 7942. By utilization of this system, proteins that compose the carboxysome can be tuned in real time as a method to examine carboxysome dynamics. We find that rVAEs are able to assist in the quantitative evaluation of changes in carboxysome numbers, shape, and size over time. Further, we propose that rVAEs may be a useful tool to accelerate the analysis of carboxysome assembly and dynamics in response to genetic or environmental perturbation and may be more generally useful to probe regulatory processes involving a broader array of bacterial microcompartments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Human Coronavirus 229E Infection Alters Histone Proteoforms

Viruses rely on host machinery to replicate, and growing evidence demonstrates that they utilize host epigenetic regulation, including histone modification, to modulate host gene expression for their benefit. Herein, we employed top-down proteomics to quantify histone proteoforms in a model human lung cell line following human coronavirus 229E (HCoV-229E) infection and compared them to mock-infected controls. A total of 572 proteoforms from mock-infected and HCoV-229E infected human lung fibroblast (MRC5) cells (N = 5 per condition) were identified; this included 461 histone proteoforms that were assigned to H2A, H2B, H3, or H4. 200 histone proteoforms were quantifiable, and differential abundance analysis revealed several statistically significant changes in both reversible post-translational modifications (e.g. phosphorylation, acetylation) and the truncation states of core histones. Notably, we found decreased abundance of C-terminally truncated histone H2A and N-terminally truncated histone H3 in HCoV-229E-infected samples. These findings underscore the power of top-down proteomics to resolve unique truncation states of proteoforms and support the hypothesis that viruses alter histone length (removing regulatory sites) to influence host gene expression.

60 APPLIED LIFE SCIENCES↗

Chlorophyllase from Arabidopsis thaliana Reveals an Emerging Model for Controlling Chlorophyll Hydrolysis

Chlorophyll (Chl) is one of Nature’s most complex pigments to biosynthesize and derivatize. This pigment is vital for survival and also paradoxically toxic if overproduced or released from a protective protein scaffold. Therefore, along with the mass production of Chl, organisms also invest in mechanisms to control its degradation and recycling. One important enzyme that is involved in these latter processes is chlorophyllase. This enzyme is employed by numerous photosynthetic organisms to hydrolyze the phytol tail of Chl. Although traditionally thought to catalyze the first step of Chl degradation, recent work suggests that chlorophyllase is instead employed during times of abiotic stress or conditions that produce reactive oxygen species. However, the molecular details regarding how chlorophyllases are regulated to function under such conditions remain enigmatic. Here, we investigate the Arabidopsis thaliana chlorophyllase isoform AtCLH2 using site-directed mutagenesis, mass spectrometry, dynamic light scattering, size-exclusion multiangle light scattering, and both steady-state enzyme kinetic and thermal stability measurements. Through these experiments, we show that AtCLH2 exists as a monomer in solution and contains two disulfide bonds. One disulfide bond putatively maps to the active site, whereas the other links two N-terminal Cys residues together. These disulfide bonds are cleaved by chemical or chemical and protein-based reductants, respectively, and are integral to maintaining the activity, stability, and substrate scope of the enzyme. This work suggests that Cys residue oxidation in chlorophyllases is an emerging regulatory strategy for controlling the hydrolysis of Chl pigments.

59 BASIC BIOLOGICAL SCIENCES↗

Tunable Heteroassembly of a Plant Pseudoenzyme–Enzyme Complex

Pseudoenzymes have emerged as key regulatory elements in all kingdoms of life despite being catalytically nonactive. Yet many factors defining why one protein is active while its homologue is inactive remain uncertain. For pseudoenzyme–enzyme pairs, the similarity of both subunits can often hinder conventional characterization approaches. In plants, a pseudoenzyme, PDX1.2, positively regulates vitamin B 6 production by association with its active catalytic homologues such as PDX1.3 through an unknown assembly mechanism. Here we used an integrative experimental approach to learn that such pseudoenzyme–enzyme pair associations result in heterocomplexes of variable stoichiometry, which are unexpectedly tunable. We also present the atomic structure of the PDX1.2 pseudoenzyme as well as the population averaged PDX1.2–PDX1.3 pseudoenzyme–enzyme pair. Finally, we dissected hetero-dodecamers of each stoichiometry to understand the arrangement of monomers in the heterocomplexes and identified symmetry-imposed preferences in PDX1.2–PDX1.3 interactions. In this work, our results provide a new model of pseudoenzyme–enzyme interactions and their native heterogeneity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Subventricular Accumulation of Cu in the Aging Mouse Brain Does Not Associate with Anticipated Increases in Markers of Oxidative Stress

Natural aging is associated with mild memory loss and cognitive decline, and age is the greatest risk factor for neurodegenerative diseases, such as Alzheimer’s disease. There is substantial evidence that oxidative stress is a major contributor to both natural aging and neurodegenerative disease, and coincidently, levels of redox active metals such as Fe and Cu are known to be elevated later in life. Recently, a pronounced age-related increase in Cu content has been reported to occur in mice and rats around a vital regulatory brain region, the subventricular zone of lateral ventricles. In our study herein, we have characterized lateral ventricle Cu content in a unique murine model of accelerated aging, senescence accelerated mouse-prone 8 (SAMP8) mice. Our results confirm an age-related increase in ventricle Cu content, consistent with the studies by others in wild-type mice and rats. Specifically, we observed Cu content to increase over the time frame 1 to 5 months and 5 to 9 months, but interestingly, no significant increase occurred between 9 and 12 months (although brain Cu content at 12 months was significantly elevated relative to 1 and 5 month-old animals). Despite the magnitude of Cu increase observed within the cells that comprise the subventricular zone of lateral ventricles (average 3 mM Cu, with isolated subcellular concentrations of 17 mM), we did not detect spectroscopic markers of thiol oxidation, protein aggregation, or lipid oxidation. The lack of evidence for oxidative stress in ex vivo animal tissue is in contrast to in vitro studies demonstrating that thiol, protein, and lipid oxidation is pronounced at these Cu concentrations. We suggest that our findings most likely indicate that the Cu ions in this brain region are sequestered in an unreactive form, possibly extended chains of Cu-thiolate complexes, which do not readily redox cycle in the aqueous cytosol. In conclusion, these results also appear to partially challenge the long-held view that age-related increases in brain metal content drive oxidative stress as we did not observe a concomitant association between age-related Cu increase and markers of oxidative stress, nor did we observe a net increase in Cu content between mice aged 9 and 12 months.

X-ray fluorescence↗

Cost and Energy Metrics for Municipal Water Reuse

Municipal water reuse can contribute to a circular water economy in different contexts and with various treatment trains. This study synthesized information regarding the current technological and regulatory statuses of municipal reuse. It provides process-level information on cost and energy metrics for three potable reuse and one nonpotable reuse case studies using the new Water Techno-economic Assessment Pipe-Parity Platform (WaterTAP3). WaterTAP3 enabled comparisons of cost and energy metrics for different treatment trains and for different alternative water sources consistently with a common platform. A carbon-based treatment train has both a lower calculated levelized cost of water (LCOW) ($0.40/m3) and electricity intensity (0.30 kWh/m3) than a reverse osmosis (RO)-based treatment train ($0.54/m3 and 0.84 kWh/m3). In comparing LCOW and energy intensity for water production from municipal reuse, brackish water, and seawater based on the largest facilities of each type in the United States, municipal reuse had a lower LCOW and electricity than seawater but higher values than for production from brackish water. For a small (2.0 million gallon per day) inland RO-based municipal reuse facility, WaterTAP3 evaluated different deep well injection and zero liquid discharge (ZLD) scenarios for management of RO concentrate. Adding ZLD to a facility that currently allows surface discharge of concentrate would approximately double the LCOW. For all four case studies, LCOW is most sensitive to changes in weighted average cost of capital, on-stream capacity, and plant life. Baseline assessments, pipe parity metrics, and scenario analyses can inform greater observability and understanding of reuse adoption and the potential for cost-effective and energy-efficient reuse.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Renewable Activated Carbon Sorbent for the Desulfurization of Liquid Fuels

In recent years, significant efforts have been devoted to the reduction of sulfur levels in transportation fuels in order to reach regulatory limits and reduce the emission of harmful SO x into the atmosphere. In particular, adsorptive desulfurization (ADS) has the potential to produce zero-sulfur fuels without the need for a high energy intensity process, high H 2 pressure, and long process times as in the case of other technologies such as hydrodesulfurization. In this work, we have demonstrated the effectiveness of renewable activated carbons derived from food waste (FWAC) for the ADS of model jet and diesel fuels. The optimal FWAC materials were those fabricated to maximize the micropore volume, providing available sites for the adsorption of dibenzothiophene (DBT) and dimethyldibenzothiophene (DMDBT). The FWAC had a greater sulfur adsorption capacity than commercial AC, Y zeolite sorbents, and AC derived from other biomass sources including miscanthus, coconut shell, and walnut shell. Elemental analysis suggests that the inorganic impurities inherent in food waste, notably K, Ca, P, and Na, may contribute to its improved sulfur adsorption compared to other AC materials. Microscopy and X-ray diffraction studies further demonstrated the presence of inorganic species on FWAC that may provide active sites for the chemisorption of sulfur molecules.

Adsorption↗

Coupling Waste Feedstocks to Microbial Protein Production in a Circular Food System

Global food production is a major contributor to greenhouse gas emissions, water consumption, and land use. As an alternative to conventional agriculture, the production of waste-derived microbial protein (MP) holds promise for reducing environmental impacts. MP can be mass-produced in volumetrically scalable fermentation processes on short time scales, enabling facile scale-up with lower greenhouse gas emissions, land use, and water impacts than animal and, in some cases, plant protein. MP can also be produced from waste feedstocks, diverting waste from landfills or the natural environment. This Perspective explores the availability and suitability of waste feedstocks for MP production, suggesting that MP generated from waste feedstocks in the United States could fulfill twice the current national protein demand. Here, we also discuss the biotechnological and separations processes required to produce food-grade MP for human consumption from waste. Key challenges include MP consistency, consumer and regulatory acceptance, and the process utilities (electricity, heat, and nutrients) that account for up to 85% of MP costs and most environmental impacts, all of which present opportunities for innovation in the microbiology and process design spaces. Overall, this work highlights the potential of MP to contribute to a more circular, resilient, and sustainable food system.

09 BIOMASS FUELS↗

Coupling High-Throughput and Targeted Screening for Identification of Nonobvious Metabolic Engineering Targets

Identification of metabolic engineering targets is a fundamental challenge in strain development programs. While high-throughput (HTP) genetic engineering methodologies capable of generating vast diversity are being developed at a rapid rate, a majority of industrially interesting molecules cannot be screened at sufficient throughput to leverage these techniques. We propose a workflow that couples HTP screening of common precursors (e.g., amino acids) that can be screened either directly or by artificial biosensors, with low-throughput targeted validation of the molecule of interest to uncover nonintuitive beneficial metabolic engineering targets and combinations hereof. Using this workflow, we identified several nonobvious novel targets for improving p-coumaric acid (p-CA) and L -DOPA production from two large 4k gRNA libraries each deregulating 1000 metabolic genes in the yeast Saccharomyces cerevisiae. We initially screened yeast cells transformed with gRNA library plasmids for individual regulatory targets improving the production of l-tyrosine-derived betaxanthins, identifying 30 targets that increased intracellular betaxanthin content 3.5–5.7 fold. Hereafter, we screened the targets individually in a high-producing p-CA strain, narrowing down the targets to six that increased the secreted titer by up to 15%. To investigate whether any of the six targets could be additively combined to improve p-CA production further, we created a gRNA multiplexing library and subjected it to our proposed coupled workflow. The combination of regulating PYC1 and NTH2 simultaneously resulted in the highest (threefold) improvement of the betaxanthin content, and an additive trend was also observed in the p-CA strain. Lastly, we tested the initial 30 targets in a L -DOPA producing strain, identifying 10 targets that increased the secreted titer by up to 89%, further validating our screening by proxy workflow. This coupled approach is useful for strain development in the absence of direct HTP screening assays for products of interest.

59 BASIC BIOLOGICAL SCIENCES↗