Results for “Diversion pathways” — Page 9

DOE OSTI2023

Characterizing and Engineering Trehalose Biosynthesis Pathways to Improve Acetate Tolerance in Pseudomonas putida KT2440

Alkaline pretreatment can depolymerize lignin into a diverse mixture of monomers and smaller compounds, enabling bioconversion of these compounds to value-added chemicals in engineered bacterial hosts such as Pseudomonas putida KT2440. Acetate and salts comprise approximately 8% and 32% of the lignin stream, respectively. High concentrations of these components can cause cell death in P. putida, so lignin-derived streams must be fed in lower amounts to decrease stress. Investigation of the mechanisms of bacterial tolerance to chemicals in lignin-rich substrates is therefore required to overcome this obstacle in lignin bioconversion. Previous work has shown that trehalose, an endogenously produced disaccharide, is involved in tolerance to heat, cold, and osmotic stress, as well as implicated in acid stress in other bacteria. As such, trehalose biosynthesis presents a useful target to increase acetate and osmotic tolerance in P. putida. This work investigates the native TreSA, TreSB, and TreY/TreZ trehalose biosynthesis pathways in this bacterial strain as well as the OtsAB pathway of Sphingobium sp. SYK-6. Overexpression of the OtsAB pathway in P. putida increased tolerance to acetate relative to wild-type. Additionally, functional knockouts of treSA, treSB, treY, and treZ in P. putida showed that interruption of any trehalose biosynthesis pathway, and, in the case of TreY/TreZ, interruption of the pathway at any point, significantly hindered growth in acetate as well as on glucose and LB broth. Each trehalose biosynthesis pathway was then engineered for overexpression in P. putida to determine whether overexpression of these genes conferred additional tolerance to acetate. The TreSA, TreSB, OtsA, and OtsB enzymes were also expressed and purified to determine the reaction rates and kinetics of these pathways. The hypothetical glycoside hydrolase family 15 protein, encoded in the gene located in between otsB and otsA in the Sphingobium operon, was purified as well to investigate its potential involvement in the OtsAB pathway. The findings of this work illuminated the mechanisms of trehalose biosynthesis in P. putida and identified genetic targets to improve strain tolerance to common components of alkaline-pretreated lignin streams. These findings could ultimately improve yields of desired products from lignin in engineered strains of P. putida.

alkaline pretreatment↗

NASA NTRS2001

Effects of different activity and inactivity paradigms on myosin heavy chain gene expression in striated muscle

The goal of this mini-review is to summarize findings concerning the role that different models of muscular activity and inactivity play in altering gene expression of the myosin heavy chain (MHC) family of motor proteins in mammalian cardiac and skeletal muscle. This was done in the context of examining parallel findings concerning the role that thyroid hormone (T(3), 3,5,3'-triiodothyronine) plays in MHC expression. Findings show that both cardiac and skeletal muscles of experimental animals are initially undifferentiated at birth and then undergo a marked level of growth and differentiation in attaining the adult MHC phenotype in a T(3)/activity level-dependent fashion. Cardiac MHC expression in small mammals is highly sensitive to thyroid deficiency, diabetes, energy deprivation, and hypertension; each of these interventions induces upregulation of the beta-MHC isoform, which functions to economize circulatory function in the face of altered energy demand. In skeletal muscle, hyperthyroidism, as well as interventions that unload or reduce the weight-bearing activity of the muscle, causes slow to fast MHC conversions. Fast to slow conversions, however, are seen under hypothyroidism or when the muscles either become chronically overloaded or subjected to intermittent loading as occurs during resistance training and endurance exercise. The regulation of MHC gene expression by T(3) or mechanical stimuli appears to be strongly regulated by transcriptional events, based on recent findings on transgenic models and animals transfected with promoter-reporter constructs. However, the mechanisms by which T(3) and mechanical stimuli exert their control on transcriptional processes appear to be different. Additional findings show that individual skeletal muscle fibers have the genetic machinery to express simultaneously all of the adult MHCs, e.g., slow type I and fast IIa, IIx, and IIb, in unique combinations under certain experimental conditions. This degree of heterogeneity among the individual fibers would ensure a large functional diversity in performing complex movement patterns. Future studies must now focus on 1) the signaling pathways and the underlying mechanisms governing the transcriptional/translational machinery that control this marked degree of plasticity and 2) the morphological organization and functional implications of the muscle fiber's capacity to express such a diversity of motor proteins.

NASA Discipline Musculoskeletal↗

DOE OSTI2025

Microbial Pathways for Cost-Effective Low-Carbon Renewable Indigoidine

Indigoidine is a bioadvantaged platform molecule with diverse applications, including use as a textile dye, biotransistor, biosolar cell, biosensor, and food coloring. There are multiple microbial hosts and carbon sources that can be used and optimized for its production, yet there is limited guidance for which options have the greatest commercial potential. Here, we consider five different host microbes and combine genome-scale metabolic models with techno-economic and lifecycle assessment models. Pseudomonas putida currently outperforms synthetic indigo production and other indigoidine-producing hosts, using glucose, xylose, and lignin-derived aromatics to produce indigoidine at a minimum selling price of $2.9/kg and a greenhouse gas (GHG) footprint of 3.5 kgCO 2e /kg. Optimizing pathways-achieving 90% of the theoretical indigoidine yield from sugars and aromatics-can reduce costs 6-7-fold and GHG emissions 3-10-fold. From a cost perspective, microbes that co-utilize aromatics are advantageous, while selecting hosts that coproduce other value-added molecules can reduce GHG emissions. System-wide improvements and the use of a low-cost, low-carbon nitrogen source are crucial for commercial viability in all cases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

The association between vaginal microbiota disorders and early missed abortion: A prospective study

Abstract Introduction The objective of this study was to explore the association between disordered vaginal microbiota and missed abortion to ascertain potential causes of missed abortion related to vaginal microbiology. Material and methods This study was a prospective cohort study with a comparison group (reference group). Vaginal secretions from the posterior fornix of women in the early stages of pregnancy were collected in the Xiangya Third Hospital of Central South University in Changsha, Hunan, China, from November 2018 to November 2019. A total of 54 cases of missed abortion (case group) and 50 cases of normal pregnancy requiring induced abortion (reference group) were analyzed. Bacterial DNA was extracted, hybridized with gene‐specific primers, and then detected using a bacterial chip. The composition and relative abundance of vaginal microbiota in the two groups were compared using α‐diversity analysis, β‐diversity analysis, and the linear discriminant analysis effect size method. Results The α‐diversity analysis showed that the Simpson index of the case group was lower than that of the reference group, whereas the Shannon index in the case group was higher. The relative abundance of Firmicutes in the case group (42.52%) was lower than in the reference group (51.03%, p < 0.05), as was the relative abundance of Lactobacillus (case group 16.51%, reference group 23.00%; p < 0.05). Interestingly, levels of Mycoplasma genitalium and Ureaplasma were lower in the case group ( p < 0.05). The relative abundance of Lactobacillus crispatus , Lactobacillus jensenii , and Lactobacillus gasseri was also significantly lower in the case group than in the reference group ( p < 0.05). The pathways enriched in the case group were predominantly related to metabolism, whereas the genetics‐related pathways were predominantly enriched in the reference group. Conclusions Bacteria are more diverse and unevenly distributed in patients with missed abortion. Decreases in the proportion of vaginal Lactobacillus and changes in Lactobacillus species in these patients may increase the chance of genital tract pathogenic bacterial infection. To our knowledge, our study was the first to observe that a decrease of Firmicutes levels in the vaginal microbiota might impair energy metabolism and have an association with missed abortion.

Sun, Dan↗

DOE OSTI2025

Leveraging data mining, active learning, and domain adaptation for efficient discovery of advanced oxygen evolution electrocatalysts

Developing advanced catalysts for acidic oxygen evolution reaction (OER) is crucial for sustainable hydrogen production. This study presents a multistage machine learning (ML) approach to streamline the discovery and optimization of complex multimetallic catalysts. Our method integrates data mining, active learning, and domain adaptation throughout the materials discovery process. Unlike traditional trial-and-error methods, this approach systematically narrows the exploration space using domain knowledge with minimized reliance on subjective intuition. Then, the active learning module efficiently refines element composition and synthesis conditions through iterative experimental feedback. The process culminated in the discovery of a promising Ru-Mn-Ca-Pr oxide catalyst. Our workflow also enhances theoretical simulations with domain adaptation strategy, providing deeper mechanistic insights aligned with experimental findings. By leveraging diverse data sources and multiple ML strategies, we demonstrate an efficient pathway for electrocatalyst discovery and optimization. This comprehensive, data-driven approach represents a paradigm shift and potentially benchmark in electrocatalysts research.

Science & Technology - Other Topics↗

DOE OSTI2020

Sequencing and Analysis of the Sex Determination Region of Populus trichocarpa

The ages and sizes of a sex-determination region (SDR) are difficult to determine in non-model species. Due to the lack of recombination and enrichment of repetitive elements in SDRs, the quality of assembly with short sequencing reads is universally low. Unique features present in the SDRs help provide clues about how SDRs are established and how they evolve in the absence of recombination. Several Populus species have been reported with a male heterogametic configuration of sex (XX/XY system) mapped on chromosome 19, but the exact location of the SDR has been inconsistent among species, and thus far, none of these SDRs has been fully assembled in a genomic context. Here we identify the Y-SDR from a Y-linked contig directly from a long-read PacBio assembly of a Populus trichocarpa male individual. We also identified homologous gene sequences in the SDR of P. trichocarpa and the SDR of the W chromosome in Salix purpurea. We show that inverted repeats (IRs) found in the Y-SDR and the W-SDR are lineage-specific. We hypothesize that, although the two IRs are derived from the same orthologous gene within each species, they likely have independent evolutionary histories. Furthermore, the truncated inverted repeats in P. trichocarpa may code for small RNAs that target the homologous gene for RNA-directed DNA methylation. These findings support the hypothesis that diverse sex-determining systems may be achieved through similar evolutionary pathways, thereby providing a possible mechanism to explain the lability of sex-determination systems in plants in general.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Revising the Role of Cortical Cytoskeleton during Secretion: Actin and Myosin XI Function in Vesicle Tethering

In plants, secretion of cell wall components and membrane proteins plays a fundamental role in growth and development as well as survival in diverse environments. Exocytosis, as the last step of the secretory trafficking pathway, is a highly ordered and precisely controlled process involving tethering, docking, and fusion of vesicles at the plasma membrane (PM) for cargo delivery. Although the exocytic process and machinery are well characterized in yeast and animal models, the molecular players and specific molecular events that underpin late stages of exocytosis in plant cells remain largely unknown. Here, by using the delivery of functional, fluorescent-tagged cellulose synthase (CESA) complexes (CSCs) to the PM as a model system for secretion, as well as single-particle tracking in living cells, we describe a quantitative approach for measuring the frequency of vesicle tethering events. Genetic and pharmacological inhibition of cytoskeletal function, reveal that the initial vesicle tethering step of exocytosis is dependent on actin and myosin XI. In contrast, treatments with the microtubule inhibitor, oryzalin, did not significantly affect vesicle tethering or fusion during CSC exocytosis but caused a minor increase in transient or aborted tethering events. With data from this new quantitative approach and improved spatiotemporal resolution of single particle events during secretion, we generate a revised model for the role of the cortical cytoskeleton in CSC trafficking.

Zhang, Weiwei↗

NASA NTRS2021

Geological Factors Impacted Cadmium Availability and use as an Alternative Cofactor for Zinc in the Carbon Fixation Pathways of Marine Diatoms

Transition metal cofactors are crucial for many biological processes. Despite being primarily considered to be toxic, the transition metal cadmium (Cd) was discovered to be a substitute cofactor for zinc (Zn) in photosynthetic carbon fixation pathways of marine diatoms. However, it is not known how conditions in the geosphere impacted Cd availability and its incorporation as an alternative metal cofactor for phytoplankton. We employed mineral chemistry network analysis to investigate which geochemical factors may have influenced the availability of Cd and Zn during the putative time period that the alternative Cd-based pathway evolved. Our results show that Zn minerals are more chemically diverse than are Cd minerals, but Zn- and Cd-containing minerals have similar network centrality values when specifically considering sulfur (S)-containing species. Cadmium and Zn sulfides are the most common Cd- and Zn-containing mineral species over the past 500 million years. In particular, the Cd and Zn sulfides, respectively greenockite and sphalerite, were highly abundant during this time period. Furthermore, S-containing Cd and Zn minerals are commonly co-located in geologic time, allowing them to be weathered and transported to the ocean in tandem, rather than from separate sources. We suggest that the simultaneous weathering of Cd and Zn sulfides allowed for Cd to be a bioavailable direct substitute for Zn in protein complexes during periods of Zn depletion. The biogeochemical cycles of Zn and Cd exemplify the importance of the coevolution of the geosphere and biosphere in shaping primary production in the modern ocean.

Naman Srivastava↗

DOE OSTI2023

Towards a Circular Economy for PET Bottles in the US

The United States generates the most plastic waste of any country. Along with that GHG emissions from the global plastic economy are expected to increase to 15% of the global carbon budget by 2050. It is imperative that plastic recycling is made a reality to reduce both plastic pollution in the environment and GHG emissions. A portfolio of end-of-life strategies must be implemented to minimize environmental impacts and retain valuable plastic material, but it is challenging to compare options that generate products with different utility and lifetime. Plastic use reduction, reuse and recycling are thus increasingly important, but making informed policy and research decisions within this space can be challenging given the diverse range of available solutions. The novel analysis framework, Plastic Parallel Pathways Platform (4P) has been equipped with consequential life cycle assessment, techno-economic analysis, and a plastic circularity indicator to estimate the greenhouse gas (GHG) emissions, circularity, and cost of polyethylene terephthalate (PET) down-cycling to lower-quality resin, closed-loop recycling to food-grade PET bottles, up-cycling to fiber-reinforced plastic (FRP), and conversion to non-plastic products (electricity, oil) on a United States economy-wide basis. Integrating system dynamics into this robust plastics model that already incorporates techno-economics, circularity, and environmental impacts will enable identification of key bottlenecks between manufacturers, waste sorters, and reclaimers that currently prevent rapid decarbonization of the plastics economy. System dynamics (SD) explore the evolution of activities and technologies based on changed macro parameters such as plastic demand and supply, market shifts, and cross-sectoral interactions. This project particularly aims to explore the interplay between, waste collection, plastic waste sorting, recycling, and manufacturing, as well as the effect of plastic bale quality and plastic reuse initiatives on the surrounding process stages. This functionality will facilitate combinatory analysis in which a portfolio of end-of-life pathways are assessed simultaneously, with the exact makeup of that portfolio affected by parameters such as technology scales, resource constraints, and waste mitigation efforts. Integrating SD with the 4P framework enables analyzing the effect of increased revenue and reinvestment into improving process efficiencies, sorting and collection quantities. Through that, market effects of increased recycled resin availability can be studied for the plastics systems model for the US. The results will help identify technical or economic bottlenecks that currently limit efforts to decarbonize the U.S. plastics economy.

circular economy↗

DOE OSTI2024

Towards a Circular Economy for PET Bottles in the U.S. - 4P Model

The United States generates the most plastic waste of any country. Along with that GHG emissions from the global plastic economy are expected to increase to 15% of the global carbon budget by 2050. It is imperative that plastic recycling is made a reality to reduce both plastic pollution in the environment and GHG emissions. A portfolio of end-of-life strategies must be implemented to minimize environmental impacts and retain valuable plastic material, but it is challenging to compare options that generate products with different utility and lifetime. Plastic use reduction, reuse and recycling are thus increasingly important, but making informed policy and research decisions within this space can be challenging given the diverse range of available solutions. The novel analysis framework, Plastic Parallel Pathways Platform (4P) has been equipped with consequential life cycle assessment, techno-economic analysis, and a plastic circularity indicator to estimate the greenhouse gas (GHG) emissions, circularity, and cost of polyethylene terephthalate (PET) down-cycling to lower-quality resin, closed-loop recycling to food-grade PET bottles, up-cycling to fiber-reinforced plastic (FRP), and conversion to non-plastic products (electricity, oil) on a United States economy-wide basis. Integrating system dynamics into this robust plastics model that already incorporates techno-economics, circularity, and environmental impacts will enable identification of key bottlenecks between manufacturers, waste sorters, and reclaimers that currently prevent rapid decarbonization of the plastics economy. System dynamics (SD) explore the evolution of activities and technologies based on changed macro parameters such as plastic demand and supply, market shifts, and cross-sectoral interactions. This project particularly aims to explore the interplay between, waste collection, plastic waste sorting, recycling, and manufacturing, as well as the effect of plastic bale quality and plastic reuse initiatives on the surrounding process stages. This functionality will facilitate combinatory analysis in which a portfolio of end-of-life pathways are assessed simultaneously, with the exact makeup of that portfolio affected by parameters such as technology scales, resource constraints, and waste mitigation efforts. Integrating SD with the 4P framework enables analyzing the effect of increased revenue and reinvestment into improving process efficiencies, sorting and collection quantities. Through that, market effects of increased recycled resin availability can be studied for the plastics systems model for the US. The results will help identify technical or economic bottlenecks that currently limit efforts to decarbonize the U.S. plastics economy.

carbon↗

DOE OSTI2024

Towards a Circular Economy for PET Bottles in the U.S. - 4P Framework

The United States generates the most plastic waste of any country. Along with that GHG emissions from the global plastic economy are expected to increase to 15% of the global carbon budget by 2050. It is imperative that plastic recycling is made a reality to reduce both plastic pollution in the environment and GHG emissions. A portfolio of end-of-life strategies must be implemented to minimize environmental impacts and retain valuable plastic material, but it is challenging to compare options that generate products with different utility and lifetime. Plastic use reduction, reuse and recycling are thus increasingly important, but making informed policy and research decisions within this space can be challenging given the diverse range of available solutions. The novel analysis framework, Plastic Parallel Pathways Platform (4P) has been equipped with consequential life cycle assessment, techno-economic analysis, and a plastic circularity indicator to estimate the greenhouse gas (GHG) emissions, circularity, and cost of polyethylene terephthalate (PET) down-cycling to lower-quality resin, closed-loop recycling to food-grade PET bottles, up-cycling to fiber-reinforced plastic (FRP), and conversion to non-plastic products (electricity, oil) on a United States economy-wide basis. Integrating system dynamics into this robust plastics model that already incorporates techno-economics, circularity, and environmental impacts will enable identification of key bottlenecks between manufacturers, waste sorters, and reclaimers that currently prevent rapid decarbonization of the plastics economy. System dynamics (SD) explore the evolution of activities and technologies based on changed macro parameters such as plastic demand and supply, market shifts, and cross-sectoral interactions. This project particularly aims to explore the interplay between, waste collection, plastic waste sorting, recycling, and manufacturing, as well as the effect of plastic bale quality and plastic reuse initiatives on the surrounding process stages. This functionality will facilitate combinatory analysis in which a portfolio of end-of-life pathways are assessed simultaneously, with the exact makeup of that portfolio affected by parameters such as technology scales, resource constraints, and waste mitigation efforts. Integrating SD with the 4P framework enables analyzing the effect of increased revenue and reinvestment into improving process efficiencies, sorting and collection quantities. Through that, market effects of increased recycled resin availability can be studied for the plastics systems model for the US. The results will help identify technical or economic bottlenecks that currently limit efforts to decarbonize the U.S. plastics economy.

circular economy↗

DOE OSTI2024

An Autonomous Critical Data Extrapolator for the AGN-201m

Nuclear nonproliferation serves as a key goal, being undertaken by the International Atomic Energy Agency (IAEA). To recognize proliferation there are two pathways that states, who intend to use nuclear material for malicious purposes can take, diversion can misuse. Diversion is when fissile nuclear material is declared to the IAEA for non-weapon purposes, but then covertly removed. If the source of nuclear material, that is not declared and not fissionable, is placed inside the reactor core to create fissile material used to create weapons then the state is using the second pathway of proliferation, misuse. With the emerging development in areas of simulation and machine learning the creation of virtual models of reactor systems, digital twins, serve as a potential method to identify proliferation through detecting anomalous behavior in the reactor. A digital twin for a physical nuclear reactor has never been developed, as digital twins serve as an emerging technology. To investigate the process for development and use of a digital twin for a nuclear reactor Idaho State University’s AGN-201m serves as the nuclear reactor used for development of this digital twin. A data acquisition system has been installed to the reactor system allowing for the transfer of collected data from a reactor operation to Idaho National Laboratory’s Deeplynx data warehouse. When utilizing data to train reactor physics and machine learning models, a significant challenge encountered is the initial state of the data. Nuclear proliferation will have the capacity to be detected when the reactor immediately starts up, nor will it occur after the reactor shuts down. Generally, it will be detected when the reactor is operating at some desired power over a sufficient period for that specific reactor design. For the AGN-201m this will be when the reactor is critical (generally 1 mW or above) for a timespan that is within or less than the range of a regular business day. Datasets sent to Deeplynx have had to be manually cut to when the reactor is critical based on plots of power levels. This method is inefficient and laborious, especially when using multiple datasets at once to train a model. To provide a more streamlined approach an automated critical data extrapolator is developed, with capabilities of recognizing when the reactor operation first reaches criticality, and when the reactor undergoes a SCRAM and is shutdown.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2026

Gene and genome duplications have contrasting impacts on biosynthetic and flower developmental pathways in California poppy

Benzylisoquinoline alkaloids (BIAs) represent a vast group of specialized plant metabolites with diverse pharmaceutical applications, synthesized by a variety of gene families. Among the multiple plant lineages that produce BIAs, the most notable is the poppy family (Papaveraceae), with California poppy (Eschscholzia californica) emerging as a model organism. Here, we report a haplotype-resolved genome assembly, in combination with a high-density expression atlas, for California poppy. Genome analyses reveal recent diversification of BIA biosynthesis genes in poppy through localized duplications. Furthermore, we demonstrate that the degree of phylogenetic relatedness among paralogs within BIA biosynthesis-associated gene families correlates with similarities in gene expression. In contrast, gene families involved in carotenoid biosynthesis, which contributes to the intense orange petal pigmentation, are not phylogenetically clustered, and floral developmental regulators exhibit a high degree of retention of gene duplicates associated with ancient polyploidy events. These findings illustrate alternative roles for gene and genome duplications as drivers of trait evolution. Given the position of California poppy in the angiosperm phylogeny, the high-quality genomic resources generated for this work constitute a valuable resource for comparative genomic and transcriptomic analyses for poppies and flowering plants more generally.

Rössner, Le-Han [Justus-Liebig University, Giessen↗

DOE OSTI2024

Effects of Eimeria acervulina infection on the luminal and mucosal microbiota of the cecum and ileum in broiler chickens

Coccidiosis, an intestinal disease caused by Eimeria parasites, is responsible for major losses in the poultry industry by impacting chicken health. The gut microbiota is associated with health factors, such as nutrient exchange and immune system modulation, requiring understanding on the effects of Eimeria infection on the gut microbiota. This study aimed to determine the effects of Eimeria acervulina infection on the luminal and mucosal microbiota of the cecum (CeL and CeM) and ileum (IlL and IlM) at multiple time points (days 3, 5, 7, 10, and 14) post-infection. E. acervulina infection decreased evenness in CeL microbiota at day 10, increased richness in CeM microbiota at day 3 before decreasing richness at day 14, and decreased richness in IlL microbiota from day 3 to 10. CeL, CeM, and IlL microbiota differed between infected and control birds based on beta diversity at varying time points. Infection reduced relative abundance of bacterial taxa and some predicted metabolic pathways known for short-chain fatty acid production in CeL, CeM, and IlL microbiota, but further understanding of metabolic function is required. Despite E. acervulina primarily targeting the duodenum, our findings demonstrate the infection can impact bacterial diversity and abundance in the cecal and ileal microbiota.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Juvenile life history diversity is associated with lifetime individual heterogeneity in a migratory fish

Abstract Differences in the life history pathways (LHPs) of juvenile animals are often associated with differences in demographic rates in later life stages. For migratory animals, different LHPs often result in animals from the same population occupying distinct habitats subjected to different environmental drivers. Understanding how demographic rates differ among animals expressing different LHPs may reveal fitness trade‐offs that drive the expression of alternative LHPs and enable better prediction of population dynamics in a changing environment. To understand how demographic outcomes and their relationships with environmental variables differ among animals with different LHPs, we analyzed a long‐term (2006–2021) mark–recapture dataset for Chinook salmon ( Oncorhynchus tshawytscha ) from the Wenatchee River, Washington, USA. Distinct LHPs represented in this population include either remaining in the natal stream until emigrating to the ocean as a 1‐year‐old (natal‐reach rearing) or emigrating from the natal stream and rearing in downstream habitats for several months before completing the emigration to the ocean as a 1‐year‐old (downstream rearing). We found that downstream‐rearing fish emigrated to the ocean 19 days earlier on average and returned as adults from the ocean at higher rates. We detected a positive correlation between rate of return from the ocean by downstream‐rearing fish and coastal upwelling in their spring of outmigration, whereas for natal‐reach‐rearing fish we detected a positive correlation with sea surface temperature during their first marine summer. Different responses to environmental variability should lead to asynchrony in adult abundance among juvenile LHPs. A higher proportion of downstream‐rearing fish returned at younger ages compared with natal‐reach‐rearing fish, which contributed to variability in age at reproduction and greater mixing across generations. Our results demonstrate how diversity in juvenile LHPs is associated with heterogeneity in demographic rates during subsequent life stages, which can in turn affect variance in aggregate population abundance and response to environmental change. Our findings underscore the importance of considering life history diversity in demographic analyses and provide insights into the effects of life history diversity on population dynamics and trade‐offs that contribute to the maintenance of life history diversity.

Sorel, Mark H.↗

DOE OSTI2022

MEP pathway products allosterically promote monomerization of deoxy-D-xylulose-5-phosphate synthase to feedback-regulate their supply

Isoprenoids are a very large and diverse family of metabolites required by all living organisms. All isoprenoids derive from the double-bond isomers isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), which are produced by the methylerythritol 4-phosphate (MEP) pathway in bacteria and plant plastids. It has been reported that IPP and DMAPP feedback-regulate the activity of deoxyxylulose 5-phosphate synthase (DXS), a dimeric enzyme that catalyzes the main flux-controlling step of the MEP pathway. Here we provide experimental insights into the underlying mechanism. Isothermal titration calorimetry and dynamic light scattering approaches showed that IPP and DMAPP can allosterically bind to DXS in vitro, causing a size shift. In silico ligand binding site analysis and docking calculations identified a potential allosteric site in the contact region between the two monomers of the active DXS dimer. Modulation of IPP and DMAPP contents in vivo followed by immunoblot analyses confirmed that high IPP/DMAPP levels resulted in monomerization and eventual aggregation of the enzyme in bacterial and plant cells. Loss of the enzymatically active dimeric conformation allows a fast and reversible reduction of DXS activity in response to a sudden increase or decrease in IPP/DMAPP supply, whereas aggregation and subsequent removal of monomers that would otherwise be available for dimerization appears to be a more drastic response in the case of persistent IPP/DMAPP overabundance (e.g., by a blockage in their conversion to downstream isoprenoids). Our results represent an important step toward understanding the regulation of the MEP pathway and rational design of biotechnological endeavors aimed at increasing isoprenoid contents in microbial and plant systems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Comprehensive characterization of the structure of Zr-based metallic glasses

Structure of metallic glasses fascinates as the generic amorphous structural template for ubiquitous systems. Its specification necessitates determination of the complete hierarchical structure, starting from short-range-order (SRO) → medium-range-order (MRO) → bulk structure and free volume (FV) distribution. This link has largely remained elusive since previous investigations adopted one-technique-at-a-time approach, focusing on limited aspects of any one domain. Reconstruction of structure from experimental data inversion is non-unique for many of these techniques. As a result, complete and precise structural understanding of glass has not emerged yet. In this work, we demonstrate the first experimental pathway for reconstruction of the integrated structure, for and glasses. Our strategy engages diverse (×7) multi-scale techniques [XAFS, 3D-APT, ABED/NBED, FEM, XRD, PAS, FHREM] on the same glass. This strategy complemented mutual limitations of techniques and corroborated common parameters to generate complete, self-consistent and precise parameters. Further, MRO domain size and inter-void separation were correlated to identify the presence of FV at MRO boundaries. This enabled the first experimental reconstruction of hierarchical subset: SRO → MRO → FV → bulk structure. The first ever image of intermediate region between MRO domains emerged from this link. We clarify that determination of all subsets is not our objective; the essence and novelty of this work lies in directing the pathway towards finite solution, in the most logical and unambiguous way.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Temperature- and Rate-Dependent Pathways in Formation of Metastable Silicon Phases under Rapid Decompression

High-pressure metallic beta-Sn silicon (Si-II), depending on temperature, decompression rate, stress, etc., may transform to diverse metastable forms with promising semiconducting properties under decompression. However, the underlying mechanisms governing the different transformation paths are not well understood. Here, two distinctive pathways, viz., a thermally activated crystal-crystal transition and a mechanically driven amorphization, were characterized under rapid decompression of Si-II at various temperatures using in situ time-resolved x-ray diffraction. Under slow decompression, Si-II transforms to a crystalline bc8/r8 phase in the pressure range of 4.3-9.2 GPa through a thermally activated process where the overdepressurization and the onset transition strain are strongly dependent on decompression rate and temperature. In comparison, Si-II collapses structurally to an amorphous form at around 4.3 GPa when the volume expansion approaches a critical strain via rapid decompression beyond a threshold rate. The occurrence of the critical strain indicates a limit of the structural metastability of Si-II, which separates the thermally activated and mechanically driven transition processes. The results show the coupled effect of decompression rate, activation barrier, and thermal energy on the adopted transformation paths, providing atomistic insight into the competition between equilibrium and nonequilibrium pathways and the resulting metastable phases.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗