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Proteome-wide characterization of PTMs reveals host cell responses to viral infection and identifies putative antiviral drug targets
Post-translational modifications (PTMs) are biochemical modifications that can significantly alter protein structure, function, stability, localization, and interactions with other molecules, thereby activating or inactivating intracellular processes. A growing body of research has begun to highlight the role of PTMs, including phosphorylation, ubiquitination, acetylation, and redox modifications, during virus-host interactions. Collectively, these PTMs regulate key steps in mounting the host immune response and control critical host pathways required for productive viral replication. This has led to the conception of antiviral therapeutics that focus on controlling host protein PTMs, potentially offering pathogen-agnostic treatment options and revolutionizing our capacity to prevent virus transmission. On the other hand, viruses can hijack the host cellular PTM machinery to modify viral proteins in promoting viral replication and evading immune surveillance. PTM regulation during virus-host interactions is complex and poorly mapped, and the development of effective PTM-targeted antiviral drugs will require a more comprehensive understanding of the cellular pathways essential for virus replication. In this review, we discuss the roles of PTMs in virus infection and how technological advances in mass spectrometry-based proteomics can capture systems-level PTM changes during viral infection. Additionally, we explore how such knowledge is leveraged to identify PTM-targeted candidates for developing antiviral drugs. Looking ahead, studies focusing on the discovery and functional elucidation of PTMs, either on the host or viral proteins, will not only deepen our understanding of molecular pathology but also pave the way for developing better drugs to fight emerging viruses.
Improving photovoltaic hosting capacity of distribution networks with coordinated inverter control: A case study of the EPRI J1 feeder
Abstract Adding photovoltaic (PV) systems in distribution networks, while desirable for reducing the carbon footprint, can lead to voltage violations under high solar‐low load conditions. The inability of traditional volt‐VAr control in eliminating all the violations is also well‐known. This article presents a novel coordinated inverter control methodology that leverages system‐wide situational awareness to significantly improve hosting capacity (HC). The methodology employs a real‐time voltage‐reactive power (VQ) sensitivity matrix in an iterative linear optimizer to calculate the minimum reactive power intervention from PV inverters needed for mitigating over‐voltage without resorting to active power curtailing or requiring step voltage regulator setting changes. The algorithm is validated using the EPRI J1 feeder under an extensive set of realistic use cases and is shown to provide 3x improvement in HC under all scenarios.
Plant-Enhanced Degradation Of Munitions by Engineered TERrestrial microbes (PEDOMETER) (Final Report)
LLNL led two major Technical Areas (TAs) within the PEDOMETER program: TA3 focused on biocontainment and TA4 focused on developing electrochemical TNT degradation sensors and testbeds. A key takeaway from our work is the importance of chassis host strain choice for kill switch design and actuator choice. Genetic instability of the kill switch circuit is a major barrier toward establishing a kill switch, which is host dependent. Addition of a host down-selection step to regulator and actuator screening stages would be beneficial to hasten kill switch development.
From photosynthetic electron flow to gene regulation: redox signal transduction in cyanobacteria
In cyanobacteria, the free-living ancestors of chloroplasts, photosynthesis simultaneously sustains growth and generates reactive oxygen species (ROS) that damage proteins, lipids, and DNA when light capture outpaces carbon fixation. Maintaining redox balance, therefore, requires cells to read photosynthetic electron flow as a signal that continuously tunes gene expression and protein activity. This review traces how these redox signals are transduced to transcription machinery through three routes: membrane-localized sensors, cytoplasmic redox sensors downstream of photosystem I, and ROS generated when electron sinks are saturated. Membrane-bound histidine kinases (two-component systems) relay the redox state of the plastoquinone pool to control photosystem remodeling, pigment biosynthesis, and circadian timing. Cytoplasmic one-component regulators, by contrast, sense redox directly through thiol-disulfide switches, glutathionylation, iron-sulfur clusters, and metal-catalyzed oxidation to control photosystem-cofactor, electron-carrier, and transition-metal homeostasis. Because many of these regulators persist in algal and plant chloroplasts, cyanobacteria illuminate principles of redox control across photosynthetic eukaryotes. Post-transcriptional and translational control further shapes redox-dependent gene expression programs through transcript stability, ribosome assembly, and translation initiation, extending redox regulation beyond transcription to every step of protein synthesis and even activity modulation. Finally, we connect redox regulation to photosynthetic physiology, stress resilience, and the rational engineering of cyanobacteria for sustainable bioproduction.
Deliberate Design: Creating Electricity Rates with Purpose
Today’s electricity rates often are legacy designs that do not reflect the dynamics of an evolving power grid or align with current policy objectives. Four steps will assist utilities, regulators, and industry stakeholders in modernizing outdated electricity rate designs. 1. Understand the context for rate design change: The power system is changing at a pace that the industry has not experienced for decades. It is essential to understand the implications of these changes so rates can evolve to remain consistent with changes to the underlying cost profile, customer preferences, and power system requirements. 2. Establish ratemaking objectives: Rates can do more than recover utility costs. They can be a tool for promoting desired outcomes such as improved energy affordability, flexible and efficient electricity consumption, or promoting technology adoption. First, these objectives must be clearly defined and prioritized. 3. Account for tradeoffs when designing new rates: Rate design is the art of balancing tradeoffs. It is essential to understand these tradeoffs when designing new rates, particularly if the rates are being used as a tool for accomplishing policy objectives that extend beyond the basic goal of cost reflectivity. 4. Transition to the new rates with a plan: The move to well-designed rates requires a transition plan. This will ensure that rate design changes do not happen in isolation and are consistent with a long-term, holistic vision. The report, published as an interactive web tool for which the content can be separately downloaded as a standalone document, is intended to allow state energy regulators, utility rates staff, and other industry stakeholders with an interest in rate design to selectively “drill down” on content that is relevant to their interests and situation.
Monthly hydropower generation data for Western Canada to support Western-US interconnect power system studies
Hydroelectric power generation in Western Canada significantly contributes to power grid operations of the North American Western Interconnection through substantial generation, some of which is exported to the United States (U.S.). However, the lack of publicly available hydropower generation datasets poses challenges for future market projections and resource adequacy evaluations. We present a simulation-based monthly power system model-ready hydropower generation dataset for 110 facilities in British Columbia and Alberta from 1981 to 2019. These monthly hydropower generation estimates are developed from integrated hydrologic model simulations of runoff and reservoir-operated streamflow, followed by scaling that considers diversion inflow constraints based on hydropower water license information. To address the lack of comparable hydropower generation records, we conduct step-by-step evaluations for simulated runoff, regulated streamflow, and hydropower generation using available observations or estimates. The presented hydropower dataset aims to enhance the representation of hydropower resources in Western Canada, supporting power grid system studies for the Western Interconnection of the U.S. and Canada.
Metabolic flux, metabolite, and transcript analysis uncover reprogramming of metabolism toward higher seed oil
Overexpression of WRINKLED1 (WRI1), a master regulator of glycolysis and fatty acid biosynthesis, together with DIACYLGLYCEROL ACYLTRANSFERASE1 (DGAT1), which catalyzes the final step of triacylglycerol assembly, is a promising strategy for enhancing seed oil content. However, how these regulators coordinate system-wide metabolic reprogramming at the levels of gene expression, metabolite pools, and fluxes remains poorly understood. To address this, we performed 13 C-metabolic flux analysis, metabolomics, and transcriptomics on in vitro cultured pennycress (Thlaspi arvense L.) embryos overexpressing the native WRI1 and DGAT1 homologs. Here, in cultured embryos, WRI1/DGAT1 overexpression increased triacylglycerol accumulation by 28% while reducing protein content by 34%, relative to the wild type. Embryos showed ∼20-fold and 50-fold upregulation of WRI1 and DGAT1 along with induction of WRI1 target genes in glycolysis and fatty acid biosynthesis. Genes associated with photosynthesis and Calvin cycle functions were also upregulated, whereas genes encoding ribosomal proteins and seed storage proteins were strongly repressed, consistent with the observed lipid–protein tradeoff. Flux analysis revealed that enhanced triacylglycerol biosynthesis is supported by increased flux through the Rubisco shunt and cytosolic pyruvate kinase, while the oxidative pentose phosphate pathway and malic enzyme contributed little to NADPH or pyruvate supply. Metabolomic profiling revealed extensive perturbations in glycolytic intermediates, tricarboxylic acid cycle metabolites, and amino acids. In plant grown seeds, WRI1/DGAT1 lines also showed a modest but significant increase in total lipid content. Collectively, these findings reveal how WRI1 and DGAT1 reprogram central metabolism to enhance oil accumulation, with relevance to mature seeds.
Proactive Regulatory Approaches to Electrification and Load Growth: Workshop Report
On July 10 and 11, 2024, Pacific Northwest National Laboratory and RMI led a workshop in Aurora, Colorado, to explore novel and proactive approaches to electrification and load growth while minimizing risks and costs to customers. Over the next decade, a unique opportunity exists to invest strategically in the electricity system to enable electrification across the transportation, industrial, and building sectors and respond to data and technology-based load growth. However, current utility and regulatory planning practices are insufficient to identify and enable the right investments, and work must be done to reduce the risk and decisional uncertainty faced by utility regulatory commissions and utilities. Ensuring timely electrification investments may require new approaches to address risk, uncertainty, prudence, and cost recovery. Understanding the decision-making process and information needs of utilities and regulators is critical. New policies (or application of policies), financial tools, systems analysis, regulatory mechanisms, and enhanced process transparency may be required. The workshop's goal was to identify proactive regulatory approaches for electrification and load growth that minimize costs and risks to customers. Our intention was that the conversations and the resulting solutions and takeaways would be specific and tactical rather than general and theoretical and that together we would create actionable next steps for key actors in the system, including utilities, regulators, thought leaders, researchers, and the U.S. Department of Energy (DOE). This report is intended to provide workshop attendees with a record and summary of the discussion and proposals raised at the workshop and to provide interested entities who did not attend, such as other regulators, policymakers, utilities, and U.S. DOE offices, with an understanding of what was discussed and with ideas to explore in their organizations.
PHIL Interface Design for Use With a Voltage-Regulated Amplifier
Power hardware-in-the-loop (PHIL) has emerged as a leading strategy to thoroughly assess the impact of proprietary inverter controls on a specific power system. The development of a PHIL test bed typically involves an inverter under test, a power amplifier, controllable DC supply, and a digital real-time simulator (DRTS) to simulate the power system under study. As a result of PHIL nonidealities, a form of digital compensation within the DRTS is used, which is commonly referred to as a PHIL interface. Many existing methods use legacy power amplifiers that do not contain internal voltage regulation. These existing interface methods are based around a voltage regulator within the DRTS and do not consider the interaction with the controls in newer amplifiers. In this study, a three-step approach of PHIL interface development for modern power amplifiers with built-in voltage regulation is introduced and is validated in hardware with a 30-kW grid-following inverter.
Towards the Flexibility of HVDC-Interconnected Systems: A Novel Emergency Freqeuncy Response Model
In this paper, we propose a novel multi-time scale emergency frequency response model by unlocking the flexibility of High Voltage Direct Current (HVDC) systems. Unlike assigning power ramping rates for FACTS to regulate frequency in traditional methods, this paper designs a step-change electromagnetic power frequency response (EPFR) scheme, by leveraging the temporal over/under DC voltage capability of HVDC. Wherein the Kullback-Leibler Divergence is adopted to convexify the modified swing equation after integrating the step-change power. Further, to avoid the complicated differential equations, we equivalently reformulate the duration limits of DC voltage deviation into the HVDC decreasing power ramping rates, which participate in the system primary frequency response. Finally, the new steady-state operation level of HVDC is involved with the secondary frequency response. As a result, an improved three-level algorithm is developed to solve the model, wherein the instant step-change, primary, and secondary frequency response are coordinated together. After applying the proposed frequency response scheme on the test system, the EPFR is validated to effectively provide the most instantaneous supports when faced with bulk power loss due to extreme contingencies, and the resilience is ensured within acceptable expenditures.
Real-time estimators for scattering observables: A full account of finite-volume errors for quantum simulation
The real-time correlators of quantum field theories can be directly probed through new approaches to simulation, such as quantum computing and tensor networks. This provides a new framework for computing scattering observables in lattice formulations of strongly interacting theories, such as lattice quantum chromodynamics. In this paper, we prove that the proposal of real-time estimators of scattering observables is universally applicable to all scattering observables of gapped quantum field theories. All finite-volume errors are exponentially suppressed, and the rate of this suppression is controlled by the regulator considered, namely, a displacement of the spectrum of the theory into the complex plane. A partial restoration of Lorentz symmetry by averaging over different boosts gives an additional suppression of finite volume errors. Our results also apply to the simulation of wave packet scattering, where a similar averaging is performed to construct the wave packets that regulate the finite volume effects. This result represents a necessary key step toward determining a broad class of scattering observables via quantum computing that are currently inaccessible via classical computing. Such observables are relevant for various applications, including hadron spectroscopy, hadron structure, and precision tests of the Standard Model. We also comment on potential applications of our results to traditional computational schemes.
Knocking out the carboxyltransferase interactor 1 (CTI1) in Chlamydomonas boosted oil content by fivefold without affecting cell growth
Summary The first step in chloroplast de novo fatty acid synthesis is catalysed by acetyl‐CoA carboxylase (ACCase). As the rate‐limiting step for this pathway, ACCase is subject to both positive and negative regulation. In this study, we identify a Chlamydomonas homologue of the plant carboxyltransferase interactor 1 (CrCTI1) and show that this protein interacts with the Chlamydomonas α‐carboxyltransferase (Crα‐CT) subunit of the ACCase by yeast two‐hybrid protein–protein interaction assay. Three independent CRISPR‐Cas9 mediated knockout mutants for CrCTI1 each produced an ‘enhanced oil’ phenotype, accumulating 25% more total fatty acids and storing up to fivefold more triacylglycerols (TAGs) in lipid droplets. The TAG phenotype of the crcti1 mutants was not influenced by light but was affected by trophic growth conditions. By growing cells under heterotrophic conditions, we observed a crucial function of CrCTI1 in balancing lipid accumulation and cell growth. Mutating a previously mapped in vivo phosphorylation site (CrCTI1 Ser108 to either Ala or to Asp), did not affect the interaction with Crα‐CT. However, mutating all six predicted phosphorylation sites within Crα‐CT to create a phosphomimetic mutant reduced this pairwise interaction significantly. Comparative proteomic analyses of the crcti1 mutants and WT suggested a role for CrCTI1 in regulating carbon flux by coordinating carbon metabolism, antioxidant and fatty acid β‐oxidation pathways, to enable cells to adapt to carbon availability. Taken together, this study identifies CrCTI1 as a negative regulator of fatty acid synthesis in algae and provides a new molecular brick for the genetic engineering of microalgae for biotechnology purposes.
PDPTW-DB: MILP-Based Offline Route Planning for PDPTW with Driver Breaks
The Pickup and Delivery Problem with Time Windows (PDPTW) involves optimizing routes for vehicles to meet pickup and delivery requests within specific time constraints, a challenge commonly faced in logistics and transportation. Microtransit, a flexible and demand-responsive service using smaller vehicles within defined zones, can be effectively modeled as a PDPTW. Yet, the need for driver breaks—a key human constraint—is frequently overlooked in PDPTW solutions, despite being necessary for regulatory compliance. This study presents a novel mixed-integer linear programming formulation for the Pickup and Delivery Problem with Time Windows and Driver Breaks (PDPTW-DB). To the best of our knowledge this formulation is the first to consider mandatory periodic driver breaks within optimized Microtransit routes. The proposed model incorporates regulatory compliant break scheduling directly within the vehicle routing optimization framework. By considering driver break requirements as an integral component of the optimization process, rather than as a post-processing step, the model enables the generation of routes that respect hours of service regulations while minimizing operational costs. This integrated approach facilitates the generation of schedules that are operationally efficient and prioritize driver welfare through driver breaks. We work with a public transit agency from the southern USA, and highlight the specific nuances of driver break optimization, and present a Pickup and Delivery Problem with Time Windows formulation for optimizing Microtransit operations and scheduling driver breaks. We validate our approach using real-world data from the transit agency. Our results validate our formulation in producing cost-effective, and regulation-compliant solutions.
Role of Histidine‐Containing Peptoids in Accelerating the Kinetics of Calcite Growth
Carbonate mineralization, the conversion of CO 2 into stable, thermodynamically favorable carbonate minerals, offers a promising strategy for permanent and environmentally friendly carbon storage, with minimal risk of long-term leakage and minimal monitoring requirements. Drawing inspiration from carbonic anhydrase (CA), a family of zinc-containing metalloenzymes that catalyze the hydration of CO 2 to bicarbonate and promote carbonate precipitation, a class of histidine-containing peptoids was designed that is capable of coordinating with Zn 2+ ions to act as CA mimetics for accelerating calcite step growth. In situ atomic force microscopy (AFM) measurements reveal that these peptoids significantly enhance step advancement, with a more pronounced effect observed when combined with Zn 2+ ions and under higher calcium-to-carbonate activity ratios, indicating that peptoids facilitate the incorporation of CO 3 2− ions at step edges. Solution NMR and 3D atomic force microscopy (3D AFM) analyses show that the coordination of peptoids with Zn 2+ promotes both the deprotonation of HCO 3 − to CO 3 2− and restructures the interfacial hydration layers of calcite, collectively lowering the activation barrier for step growth. These findings establish a design framework for sequence-defined polymers to regulate carbonate mineralization, offering promising applications in CO 2 capture and long-term storage.
Viral‐mediated delivery of morphogenic regulators enables leaf transformation in Sorghum bicolor (L.)
Recent advancements in monocot transformation, using leaf tissue as explant material, have expanded the number of grass species capable of transgenesis. However, the complexity of vectors and reliance on inducible excision of essential morphogenic regulators have so far limited widespread application. Plant RNA viruses, such as Foxtail Mosaic Virus (FoMV), present a unique opportunity to express morphogenic regulator genes, such as Babyboom (Bbm), Wuschel2 (Wus2), Wuschel-like homeobox protein 2a (Wox2a) and the GROWTH-REGULATING FACTOR 4 (GRF4) GRF-INTERACTING FACTOR 1 (GIF1) fusion protein transiently in leaf explant tissues. Furthermore, altruistic delivery of conventional and viral vectors could provide opportunities to simplify vectors used for leaf transformation—facilitating vector optimization and reducing reliance on morphogenic regulator gene integration. In this study, both viral and conventional T-DNA vectors were tested for their ability to promote the formation of embryonic calli, a critical step in leaf transformation protocols, using Sorghum bicolor leaf explants. Although conventional leaf transformation vectors yielded viable embryonic calli (43.2 ± 2.9%: GRF4-GIF1, 50.2 ± 3%: Bbm/Wus2), altruistic conventional vectors employing the GRF4-GIF1 morphogenic regulator resulted in improved efficiencies (61.3 ± 4.7%). Altruistic delivery was further enhanced with the use of viral vectors employing both GRF4-GIF1 and Bbm/Wus2 regulators, resulting in 75.1 ± 2.3% and 79.2 ± 2.5% embryonic calli formation, respectively. Embryonic calli generated from both conventional and viral vectors produced shoots expressing fluorescent reporters, which were confirmed using molecular analysis. This work provides an important proof-of-concept for the use of both altruistic vectors and viral-expressed morphogenic regulators for improving plant transformation.
Data for "Viral-mediated Delivery of Morphogenic Regulators Enables Leaf Transformation in Sorghum bicolor (L.)"
Recent advancements in monocot transformation, using leaf tissue as explant material, have expanded the number of grass species capable of transgenesis. However, the complexity of vectors and reliance on inducible excision of essential morphogenic regulators have so far limited widespread application. Plant RNA viruses, such as Foxtail Mosaic Virus (FoMV), present a unique opportunity to express morphogenic regulator genes, such as Babyboom ( Bbm ), Wuschel2 ( Wus2 ), Wuschel-like homeobox protein 2a ( Wox2a ) and the GROWTH-REGULATING FACTOR 4 (GRF4) GRF-INTERACTING FACTOR 1 (GIF1) fusion protein transiently in leaf explant tissues. Furthermore, altruistic delivery of conventional and viral vectors could provide opportunities to simplify vectors used for leaf transformation—facilitating vector optimization and reducing reliance on morphogenic regulator gene integration. In this study, both viral and conventional T-DNA vectors were tested for their ability to promote the formation of embryonic calli, a critical step in leaf transformation protocols, using Sorghum bicolor leaf explants. Although conventional leaf transformation vectors yielded viable embryonic calli (43.2 ± 2.9%: GRF4-GIF1, 50.2 ± 3%: Bbm/Wus2), altruistic conventional vectors employing the GRF4-GIF1 morphogenic regulator resulted in improved efficiencies (61.3 ± 4.7%). Altruistic delivery was further enhanced with the use of viral vectors employing both GRF4-GIF1 and Bbm/Wus2 regulators, resulting in 75.1 ± 2.3% and 79.2 ± 2.5% embryonic calli formation, respectively. Embryonic calli generated from both conventional and viral vectors produced shoots expressing fluorescent reporters, which were confirmed using molecular analysis. This work provides an important proof-of-concept for the use of both altruistic vectors and viral-expressed morphogenic regulators for improving plant transformation.
Method of tuning physical properties of thermosets
Polymerization-induced phase separation enables fine control over thermoset network morphologies, yielding heterogeneous structures with domain sizes tunable over 1-100 nm. However, the controlled chain-growth polymerization techniques exclusively employed to regulate morphology at these length scales are unsuitable for most thermoset materials typically formed through step-growth mechanisms. By employing binary mixtures in place of the classic constituents of phase-separating thermosets—resin, curing agent, and secondary polymer—facile tunability over morphology can be achieved through a single compositional parameter. Indeed, this method yields morphologies spanning nano-scale to macro-scale, controlled by the relative reactivities and thermodynamic compatibility of the network components. Due to the connection between chain dynamics and microstructure in these materials, the tunable morphology enables exquisite control over glass transition and other physical and mechanical properties.