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At least 217 records · Page 12

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DOE OSTI2026

Genetic and epigenetic signatures of Populus trichocarpa in response to abiotic stresses

Plants respond to abiotic stresses such as drought, heat, and salinity through both shared and stress-specific regulatory pathways. However, the role of epigenetic mechanisms, particularly DNA methylation, in modulating these responses is still underexplored. Here, we integrated transcriptome profiling with whole-genome bisulfite sequencing (WGBS) to investigate the dynamic relationship between gene expression and DNA methylation in Populus trichocarpa during brief early-stage exposure to abiotic stress. Each stress elicited distinct transcriptional and methylation signatures; however, a subset of conserved stress-responsive genes was commonly regulated across treatments. We found that ∼5-6% of differentially expressed genes also displayed differential methylation patterns, suggesting a coordinated role for DNA methylation in regulating gene expression. Motif enrichment analysis of differentially methylated regions revealed binding sites of key transcription factor families, including ERF, bHLH, and ABF, highlighting potential role for methylation in modulating transcription factor targeting. Furthermore, we identified stress-inducible molecular markers with potential applications in early stress detection and functional dissection of gene regulatory pathways. Together, these findings provide new insights into the coordinated genetic and epigenetic responses to abiotic stress and provide a foundation for developing biosensors and breeding strategies to enhance stress resilience woody plants.

DNA methylation↗

DOE OSTI2025

Genetic_and_epigenetic_signatures_of_Populus_Trichocarpa_in_response_to_abiotic_stress

Plants respond to abiotic stresses such as drought, heat, and salinity through both shared and stress-specific regulatory pathways. However, the role of epigenetic mechanisms, particularly DNA methylation, in modulating these responses is still underexplored. Here, we integrated transcriptome profiling with whole-genome bisulfite sequencing (WGBS) to investigate the dynamic relationship between gene expression and DNA methylation in Populus trichocarpa during brief early-stage exposure to abiotic stress. Each stress elicited distinct transcriptional and methylation signatures; however, a subset of conserved stress-responsive genes was commonly regulated across treatments. Approximately 5% of differentially expressed genes also displayed differential methylation patterns, suggesting a coordinated role for DNA methylation in regulating gene expression. Motif enrichment analysis of differentially methylated regions revealed binding sites of key transcription factor families, including ERF, bHLH, and ABF, highlighting potential role for methylation in modulating transcription factor targeting. Furthermore, we identified stress-inducible molecular markers with potential applications in early stress detection and functional dissection of gene regulatory pathways. Together, these findings provide new insights into the coordinated genetic and epigenetic responses to abiotic stress and provide a foundation for developing biosensors and breeding strategies to enhance stress resilience woody plants.

CBI↗

DOE OSTI2023

Impact of Transportation Electrification on the System's Dynamic Frequency Response

Transportation electrification is an integral component of the energy decarbonization transition. This paper investigates the impact of distributed energy resources (DERs), including distributed photovoltaics (DPV) and electric vehicles (EVs), in the primary frequency response of the power grid. Increasing DER adoption poses challenges to maintaining grid frequency stability. However, DERs' ability to provide fast frequency regulation services-primary frequency response (PFR) and secondary frequency response (SFR)-can be exploited to recover the frequency after an N-1 contingency event in the system. This paper also investigates the importance of a droop control strategy through dynamic models of DPV and EV to provide the primary frequency regulation services following the contingency event. A dynamic EV model, based on the PVD1 model Western Electricity Coordinating Council (WECC) introduced, has been used for the simulation. Further, DERs' primary frequency response is studied for five different cases of DER penetration levels after the system is exposed to the generator trip. Additionally, different frequency regulation capacities of EVs are analyzed. The studies show that an increment in DERs capacity providing effective PFR can improve the system frequency nadir and stabilize the frequency faster after the generation trip contingency.

distributed energy resources↗

DOE OSTI2023

Impact of Transportation Electrification on the System's Dynamic Frequency Response: Preprint

Transportation electrification is an integral component of the energy decarbonization transition. This paper investigates the impact of distributed energy resources (DERs), including distributed photovoltaics (DPV) and electric vehicles (EVs), in the primary frequency response of the power grid. Increasing DER adoption poses challenges to maintaining grid frequency stability. However, DERs' ability to provide fast frequency regulation services-primary frequency response (PFR) and secondary frequency response (SFR)-can be exploited to recover the frequency after an N-1 contingency event in the system. This paper also investigates the importance of a droop control strategy through dynamic models of DPV and EV to provide the primary frequency regulation services following the contingency event. A dynamic EV model, based on the PVDl model Western Electricity Coordinating Council (WECC) introduced, has been used for the simulation. Further, DERs' primary frequency response is studied for five different cases of DER penetration levels after the system is exposed to the generator trip. Additionally, different frequency regulation capacities of EVs are analyzed. The studies show that an increment in DERs capacity providing effective PFR can improve the system frequency nadir and stabilize the frequency faster after the generation trip contingency.

ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2024

Programmed cell death regulator BAP2 is required for IRE1-mediated unfolded protein response in Arabidopsis

Environmental and physiological situations can challenge the balance between protein synthesis and folding capacity of the endoplasmic reticulum (ER) and cause ER stress, a potentially lethal condition. The unfolded protein response (UPR) restores ER homeostasis or actuates programmed cell death (PCD) when ER stress is unresolved. The cell fate determination mechanisms of the UPR are not well understood, especially in plants. Here, we integrate genetics and ER stress profiling with natural variation and quantitative trait locus analysis of 350 natural accessions of the model species Arabidopsis thaliana . Our analyses implicate a single nucleotide polymorphism to the loss of function of the general PCD regulator BON-ASSOCIATED PROTEIN2 (BAP2) in UPR outcomes. We establish that ER stress-induced BAP2 expression is antagonistically regulated by the UPR master regulator, inositol-requiring enzyme 1 (IRE1), and that BAP2 controls adaptive UPR amplitude in ER stress and ignites pro-death mechanisms in conditions of UPR insufficiency.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Dynamic regulation of water potential in Juniperus osteosperma mediates ecosystem carbon fluxes

Summary Some plants exhibit dynamic hydraulic regulation, in which the strictness of hydraulic regulation (i.e. iso/anisohydry) changes in response to environmental conditions. However, the environmental controls over iso/anisohydry and the implications of flexible hydraulic regulation for plant productivity remain unknown. InJuniperus osteosperma, a drought‐resistant dryland conifer, we collected a 5‐month growing season time series ofin situ, high temporal‐resolution plant water potential () and stand gross primary productivity (GPP). We quantified the stringency of hydraulic regulation associated with environmental covariates and evaluated how predawn water potential contributes to empirically predicting carbon uptake. Juniperus osteospermashowed less stringent hydraulic regulation (more anisohydric) after monsoon precipitation pulses, when soil moisture and atmospheric demand were high, and corresponded with GPP pulses. Predawn water potential matched the timing of GPP fluxes and improved estimates of GPP more strongly than soil and/or atmospheric moisture, notably resolving GPP underestimation before vegetation green‐up. Flexible hydraulic regulation appears to allowJ. osteospermato prolong soil water extraction and, therefore, the period of high carbon uptake following monsoon precipitation pulses. Water potential and its dynamic regulation may account for why process‐based and empirical models commonly underestimate the magnitude and temporal variability of dryland GPP.

Plant Sciences↗

DOE OSTI2021

Linking species traits and demography to explain complex temperature responses across levels of organization

Significance Microbes regulate nutrient flux and carbon storage within ecosystems, making them essential to the global carbon cycle and ecosystem responses to climate change. Understanding how climate change will alter microbial communities and how this will feed back to influence the pace of climate change requires linking processes across levels of organization, from individual organisms to whole ecosystems. We show that the physical characteristics (traits) of protist species influence how their populations will respond to changes in temperature. These species-level temperature responses also alter the composition, dynamics, and functioning of whole microbial communities. Using traits to understand how complex, multilevel microbial processes change with temperature can help us anticipate possible consequences of rapid global climate change.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Differential DNA methylation and metabolite profiling of Atlantic killifish (Fundulus heteroclitus) from the New Bedford Harbor Superfund site

Atlantic killifish (Fundulus heteroclitus) is a valuable model in evolutionary toxicology to study how the interactions between genetic and environmental factors serve the adaptive ability of organisms to resist chemical pollution. Killifish populations inhabiting environmental toxicant-contaminated New Bedford Harbor (NBH) show phenotypes tolerant to polychlorinated biphenyls (PCBs) and differences at the transcriptional and genomic levels. However, limited research has explored epigenetic alterations and metabolic effects in NBH killifish. To identify the involvement of epigenetic and metabolic regulation in the adaptive response of killifish, we investigated tissue- and sex-specific differences in global DNA methylation and metabolomic profiles of NBH killifish populations, compared to sensitive populations from a non-polluted site, Scorton Creek (SC). The results revealed that liver-specific global DNA hypomethylation and differential metabolites were evident in fish from NBH compared with those from SC. The sex-specific differences were not greater than the tissue-specific differences. We demonstrated liver-specific enriched metabolic pathways (e.g., amino acid metabolic pathways converged into the urea cycle and glutathione metabolism), suggesting possible crosstalk between differential metabolites and DNA hypomethylation in the livers of NBH killifish. Additional investigation of methylated gene regions is necessary to understand the functional role of DNA hypomethylation in the regulation of enzyme-encoding genes associated with metabolic processes and physiological changes in NBH populations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Structured interactions drive abrupt transitions in the spatial organization of microbial communities

Bacteria possess diverse mechanisms to regulate their motility in response to environmental and physiological signals, enabling them to navigate complex habitats and adapt their behavior. Some of these mechanisms are species specific and enable cells to modulate their movement based on the ecological identity of neighboring species. Here, we introduce a model in which bacteria interact via local signals that either enhance or suppress the motility of neighboring cells depending on species type. Through large-scale simulations and a coarse-grained stochastic model, we demonstrate the emergence of a sharp transition driven by nucleation processes: increasing the density of motility-suppressing interactions drives the system from a fully mixed, motile phase to a state characterized by large, stationary bacterial clusters. Remarkably, in systems with a large number of interacting species, this transition can be triggered solely by altering the structure of the motility-regulation interaction matrix while maintaining species and interaction densities constant. In particular, we find that heterogeneous and modular interactions promote the transition more readily than homogeneous random ones. These findings add a dimension to the theory of motility-induced phase separation and contribute to the ongoing effort to understand microbial interactions, suggesting that structured, nonrandom ones may be key to reproducing commonly observed spatial patterns in microbial communities.

bacterial communities↗

DOE OSTI2020

Autonomous Strategies for Improved Performance and Reliability of Li‐Ion Batteries

Abstract The battery community has devoted significant effort to improve the performance and reliability of Li‐ion batteries through the development of new materials. The integration of autonomous function provides an alternative strategy to further extend performance. Autonomous material systems mimic the ability of biological systems to self‐protect, sense, regulate, and heal in response to damage and other environmental changes. When incorporated in batteries, these materials enable autonomic restoration of battery performance upon degradation, as well as autonomic shutdown or extinguishment in response to thermal runaway. Successful strategies for improving Li‐ion battery performance include controlled release of microencapsulated functional additives and the integration of self‐healing or adaptive interlayers and binders. These methods have been effective for stabilizing the solid electrolyte interface, preventing battery fires, restoring electrode conductivity, and suppressing Li dendrite growth. Challenges and opportunities exist in the further application of autonomous strategies in the battery environment. A greater variety of encapsulated additives with precise triggered‐release are needed to address specific battery degradation mechanisms. Incorporation of self‐healing polymers in solid‐state batteries facilitates improvement in interfacial and mechanical stability. The integration of autonomous strategies with battery management systems potentially enables enhanced control over multiple battery cycling parameters.

Zhao, Lihong↗

DOE OSTI2020

Molecular dynamics analysis of the binding of human interleukin-6 with interleukin-6 α-receptor

Human interleukin-6 (hIL-6) is a multifunctional cytokine that regulates immune and inflammatory responses in addition to metabolic and regenerative processes and cancer. hIL-6 binding to the IL-6 receptor (IL-6Rα) induces homodimerization and recruitment of the glycoprotein (gp130) to form a hexameric signaling complex. Anti-IL-6 and IL-6R antibodies are clinically approved inhibitors of IL-6 signaling pathway for treating rheumatoid arthritis and Castleman's disease, respectively. There is a potential to develop novel small molecule IL-6 antagonists derived from understanding the structural basis for IL-6/IL-6Rα interactions. In this work, we combine homology modeling with extensive molecular dynamics (MD) simulations to examine the association of hIL-6 with IL-6Rα. A comparison with MD of apo hIL-6 reveals that the binding of hIL-6 to IL-6Rα induces structural and dynamic rearrangements in the AB loop region of hIL-6, disrupting intraprotein contacts and increasing the flexibility of residues 48 to 58 of the AB loop. In contrast, due to the involvement of residues 59 to 78 in forming contacts with the receptor, these residues of the AB loop are observed to rigidify in the presence of the receptor. The binary complex is primarily stabilized by two pairs of salt bridges, Arg181 (hIL-6)- Glu182 (IL-6Rα) and Arg184 (hIL-6)- Glu183 (IL-6Rα) as well as hydrophobic and aromatic stacking interactions mediated essentially by Phe residues in both proteins. An interplay of electrostatic, hydrophobic, hydrogen bonding, and aromatic stacking interactions facilitates the formation of the hIL-6/IL-6Rα complex.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

The single-cell transcriptome program of nodule development cellular lineages in Medicago truncatula

Legumes establish a symbiotic relationship with nitrogen-fixing rhizobia by developing nodules. Nodules are modified lateral roots that undergo changes in their cellular development in response to bacteria, but the transcriptional reprogramming that occurs in these root cells remains largely uncharacterized. Here, we describe the cell-type-specific transcriptome response of Medicago truncatula roots to rhizobia during early nodule development in the wild-type genotype Jemalong A17, complemented with a hypernodulating mutant (sunn-4) to expand the cell population responding to infection and subsequent biological inferences. The analysis identifies epidermal root hair and stele sub-cell types associated with a symbiotic response to infection and regulation of nodule proliferation. Trajectory inference shows cortex-derived cell lineages differentiating to form the nodule primordia and, posteriorly, its meristem, while modulating the regulation of phytohormone-related genes. Gene regulatory analysis of the cell transcriptomes identifies new regulators of nodulation, including STYLISH 4, for which the function is validated.

Cell Biology↗

DOE OSTI2024

Preclinical characterization of Pan-NKG2D ligand-binding NKG2D receptor decoys

NKG2D and its ligands are critical regulators of protective immune responses controlling infections and cancer, defining a crucial immune signaling axis. Current therapeutic efforts targeting this axis almost exclusively aim at enhancing NKG2D-mediated effector functions. However, this axis can drive disease processes when dysregulated, in particular, driving stem-like cancer cell reprogramming and tumorigenesis through receptor/ligand self-stimulation on tumor cells. Despite complexities with its structure and biology, we developed multiple novel engineered proteins that functionally serve as axis-blocking NKG2D “decoys” and report biochemical, structural, in vitro , and in vivo evaluation of their functionality.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Structural Insights into the Mechanisms and Pharmacology of K 2P Potassium Channels

Leak currents, defined as voltage and time independent flows of ions across cell membranes, are central to cellular electrical excitability control. The K 2P (KCNK) potassium channel class comprises an ion channel family that produces potassium leak currents that oppose excitation and stabilize the resting membrane potential in cells in the brain, cardiovascular system, immune system, and sensory organs. Due to their widespread tissue distribution, K 2P s contribute to many physiological and pathophysiological processes including anesthesia, pain, arrythmias, ischemia, hypertension, migraine, intraocular pressure regulation, and lung injury responses. Structural studies of six homomeric K 2P s have established the basic architecture of this channel family, revealed key moving parts involved in K 2P function, uncovered the importance of asymmetric pinching and dilation motions in the K 2P selectivity filter (SF) C-type gate, and defined two K 2P structural classes based on the absence or presence of an intracellular gate. Further, a series of structures characterizing K 2P :modulator interactions have revealed a striking polysite pharmacology housed within a relatively modestly sized (~70 kDa) channel. Binding sites for small molecules or lipids that control channel function are found at every layer of the channel structure, starting from its extracellular side through the portion that interacts with the membrane bilayer inner leaflet. This framework provides the basis for understanding how gating cues sensed by different channel parts control function and how small molecules and lipids modulate K 2P activity. Such knowledge should catalyze development of new K 2P modulators to probe function and treat a wide range of disorders.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

IFNgamma-inducible CXCL10/CXCR3 axis alters the sensitivity of HEp-2 cells to ionizing radiation

Highlights: • IFNgamma/CXCL10/CXCR3 are necessary for effective IR-induced HEp-2 cell killing. • Local IR showed fewer effects on tumor burden in mice carrying CXCL10-KO xenografts. • Loss of CXCL10 showed blockage in the G0/G1 phase when exposed to a moderate dose of IR. Radiotherapy is a conventional approach for anti-cancer treatment, killing tumor cells through damaging cellular DNA. While increasing studies have demonstrated that tumors generated the tolerance to radiation and tumor immune system was found to be correlated to radiotherapy resistance. Therefore, it is critical to identify potential immune factors associated with the efficacy of radiotherapy. Here in this study, we evaluated the sensitivities of different tumor cells to radiation and determined HEp-2 cells as the radio-resistant tumor cells for further investigation. IFNgamma as a key regulator of host immune response showed the potential to sensitize tumors to ionizing radiation (IR). Besides, IFNgamma-induced CXC chemokine ligand 10 (CXCL10) was found to be necessary for effective IR-induced killing of cultured HEp-2 cells. Increased clonogenic survival was observed in CXCL10-depleted HEp-2 cells and CXCL10-KO cells. Additionally, the loss of CXCL10 in HEp-2 cells showed less progression of the G0/G1 phase to G2/M when exposed to IR (8 Gy). Local IR (20 Gy) to nude mice bearing HEp-2 tumors significantly reduced tumor burden, while fewer effects on tumor burden in mice carrying CXCL10-KO tumors were observed. We furtherly evaluated the possible roles the chemokine receptor CXCR3 plays in mediating the sensitivity of cultured HEp-2 cells to IR. Altered expression of CXCR3 in HEp-2 cells affected IR-induced killing of HEp-2 cells. Our data suggest the IFNgamma-activated CXCL10/CXCR3 axis may contribute to the effective radiation-induced killing of HEp-2 cells in vitro.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

DOE OSTI2021

Impact of vegetation physiology and phenology on watershed hydrology in a semiarid watershed in the Pacific Northwest in a changing climate

Concurrent with changes in climate conditions, increases in atmospheric composition and transport can affect land surface processes by regulating physiological and phenological responses of plants, and consequently perturb water, carbon, and nitrogen (N) dynamics at multiple scales. Howerver, the relationships bwtween plants physiological and phenological and land surface processes in a changing climate are less well known due to the limitation of representing palnts properties in traditional hydrological models. In this study, we use the Community Land Model version 5 (CLM5) to investigate how projected changes in large scale atmospheric conditions can affect hydrologic and biogeochemical dynamics in the Upper Columbia-Priest Rapids (UCPR) watershed, a typical semi-arid watershed located in the north-western United States dominated by croplands. Six numerical experiments considering climate change, CO2 concentration, and N deposition consistent with the Representative Concentration Pathways (RCPs) 4.5 and 8.5 are performed at 1-km resolution over the period of 2015-2099. Our results show that, compared with historical results (1985-2014), the elevated CO2 directly increases plants N uptake rates that provide additional leaf N to enhance photosynthesis by the end of 21st century (2070-2099). The higher GPP leads to changes in stomatal resistance and increased leaf area index (LAI) that affect evaporatranspiration (ET) and its components. As a result of stomatal responses to a higher CO2 concentration, ET over corn fields declines by 24.6 mm yr-1 under RCP4.5, and by 64.0 mm yr-1 under RCP8.5, respectively by the end of the century from its historical mean of 428 mm yr-1. Meanwhile, ET over soybean fields increases by 27.7 mm yr-1 under RCP4.5 and 9.98 mm yr-1 under RCP8.5 from its historical mean of 507 mm yr-1 as a result of CO2 fertilization as soybeans are able to uptake more N to increase LAI significantly. Furtherfore, the changes in physiological and phenological in corn and soybean can strongly modulate water budget terms over the watershed in response to expected changes in greenhouse gas concentrations and atmospheric composition. Additionally, increases in CO2 concentration and N deposition are beneficial for improving water use efficiency of corn and soybean, therefore lead to less water consumption per unit gram of carbon produced from these crops. Our study elucidates the need to jointly consider effects of surface climate and atmospheric composition and transport in understanding and predicting watershed hydrologic and biogeochemical responses, especially for an agricultural watershed.

Zhu, Bowen↗

DOE OSTI2022

ssDNA is an allosteric regulator of the C. crescentus SOS-independent DNA damage response transcription activator, DriD

DNA damage repair systems are critical for genomic integrity. However, they must be coordinated with DNA replication and cell division to ensure accurate genomic transmission. In most bacteria, this coordination is mediated by the SOS response through LexA, which triggers a halt in cell division until repair is completed. Recently, an SOS-independent damage response system was revealed in Caulobacter crescentus. This pathway is controlled by the transcription activator, DriD, but how DriD senses and signals DNA damage is unknown. To address this question, we performed biochemical, cellular, and structural studies. We show that DriD binds a specific promoter DNA site via its N-terminal HTH domain to activate transcription of genes, including the cell division inhibitor didA. A structure of the C-terminal portion of DriD revealed a WYL motif domain linked to a WCX dimerization domain. Strikingly, we found that DriD binds ssDNA between the WYL and WCX domains. Comparison of apo and ssDNA-bound DriD structures reveals that ssDNA binding orders and orients the DriD domains, indicating a mechanism for ssDNA-mediated operator DNA binding activation. Biochemical and in vivo studies support the structural model. Our data thus reveal the molecular mechanism underpinning an SOS-independent DNA damage repair pathway.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

KIN3 impacts arbuscular mycorrhizal symbiosis and promotes fungal colonisation in Medicago truncatula

Summary Arbuscular mycorrhizal fungi help their host plant in the acquisition of nutrients, and this association is itself impacted by soil nutrient levels. High phosphorus levels inhibit the symbiosis, whereas high nitrogen levels enhance it. The genetic mechanisms regulating the symbiosis in response to soil nutrients are poorly understood. Here, we characterised the symbiotic phenotypes in four Medicago truncatula Tnt1 ‐insertion mutants affected in arbuscular mycorrhizal colonisation. We located their Tnt1 insertions and identified alleles for two genes known to be involved in mycorrhization, RAM1 and KIN3 . We compared the effects of the kin3‐2 and ram1‐4 mutations on gene expression, revealing that the two genes alter the expression of overlapping but not identical gene sets, suggesting that RAM1 acts upstream of KIN3. Additionally, KIN3 appears to be involved in the suppression of plant defences in response to the fungal symbiont. KIN3 is located on the endoplasmic reticulum of arbuscule‐containing cortical cells, and kin3‐2 mutants plants hosted significantly fewer arbuscules than the wild type. KIN3 plays an essential role in the symbiotic response to soil nitrogen levels, as, contrary to wild‐type plants, the kin3‐2 mutant did not exhibit increased root colonisation under high nitrogen.

Irving, Thomas B.↗