SEARCH · Engineering Papers

Results for “pathway analysis”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,477 records · Page 82

All sources NASA NTRS DOE OSTI

DOE OSTI2021

The controlling role of atmosphere in dawsonite versus gibbsite precipitation from tetrahedral aluminate species

In highly alkaline solution, aluminum speciates as the tetrahedrally coordinated aluminate monomer, Al(OH)4- and/or dimer Al2O(OH)62-, yet precipitates as octahedrally coordinated gibbsite (Al(OH)3). This tetrahedral to octahedral transformation governs Al precipitation, which is crucial to worldwide Al production, and to the processing of caustic high-level radioactive wastes. Despite its significance, the transformation pathway remains unknown. Here we explore the roles of atmospheric water and carbon dioxide in mediating the transformation of the tetrahedrally coordinated potassium aluminate dimer salt (K2Al2O(OH)6) to gibbsite versus potassium dawsonite (KAl(CO3)(OH)2). A combination of in-situ attenuated total reflection infrared spectroscopy, ex-situ micro X-ray diffraction, and multivariate curve resolution-alternating least squares chemometrics analysis reveals that humidity plays a key role in the transformation by limiting the amount of alkalinity neutralization by dissolved CO2. Lower humidity favors higher alkalinity and incorporation of carbonate species in the final Al product to form KAl(CO3)(OH)2. Higher humidity enables more acid generation that destabilizes dawsonite and favors gibbsite as the solubility limiting phase. Because the transformation was restricted to occur in thin water films, the results suggest that transition from tetra- to octahedrally coordinated Al does not have to occur in bulk solution, as has often been hypothesized, but may instead appear on the source mineral surface.

Dembowski, Mateusz↗

DOE OSTI2024

Codes and Ordinances for Clean Energy: Highland Park Pathways to Power [Slides]

Through the Communities LEAP (Local Energy Action Program) Pilot, the National Renewable Energy Laboratory (NREL) engaged the Highland Park Stakeholder Coalition to scope four technical assistance work areas to address their energy needs and goals. This slide deck addresses the highlighted tasks under work area "A" related to policy analysis, due diligence, and case studies for removing barriers and providing best practices for local clean energy development.

24 POWER TRANSMISSION AND DISTRIBUTION↗

NASA NTRS2014

Carbon-Temperature-Water Change Analysis for Peanut Production Under Climate Change: A Prototype for the AgMIP Coordinated Climate-Crop Modeling Project (C3MP)

Climate change is projected to push the limits of cropping systems and has the potential to disrupt the agricultural sector from local to global scales. This article introduces the Coordinated Climate-Crop Modeling Project (C3MP), an initiative of the Agricultural Model Intercomparison and Improvement Project (AgMIP) to engage a global network of crop modelers to explore the impacts of climate change via an investigation of crop responses to changes in carbon dioxide concentration ([CO2]), temperature, and water. As a demonstration of the C3MP protocols and enabled analyses, we apply the Decision Support System for Agrotechnology Transfer (DSSAT) CROPGRO-Peanut crop model for Henry County, Alabama, to evaluate responses to the range of plausible [CO2], temperature changes, and precipitation changes projected by climate models out to the end of the 21st century. These sensitivity tests are used to derive crop model emulators that estimate changes in mean yield and the coefficient of variation for seasonal yields across a broad range of climate conditions, reproducing mean yields from sensitivity test simulations with deviations of ca. 2% for rain-fed conditions. We apply these statistical emulators to investigate how peanuts respond to projections from various global climate models, time periods, and emissions scenarios, finding a robust projection of modest (<10%) median yield losses in the middle of the 21st century accelerating to more severe (>20%) losses and larger uncertainty at the end of the century under the more severe representative concentration pathway (RCP8.5). This projection is not substantially altered by the selection of the AgMERRA global gridded climate dataset rather than the local historical observations, differences between the Third and Fifth Coupled Model Intercomparison Project (CMIP3 and CMIP5), or the use of the delta method of climate impacts analysis rather than the C3MP impacts response surface and emulator approach.

climate change↗

DOE OSTI2025

Xylanolytic metabolism is regulated by coordination of transcription factors XynR and XylR in extremely thermophilic Caldicellulosiruptorales

ABSTRACT Global transcription factors (TFs) control metabolic processes in bacteria to efficiently utilize available carbon. The orderCaldicellulosiruptoraleshas drawn interest due to the ability of its members to degrade components of lignocellulosic biomass. Regulatory reconstruction ofAnaerocellum (f. Caldicellulosiruptor) besciiidentified two major global transcription factors for xylan utilization, XynR and XylR, and the corresponding putative transcription factor binding sites. Recombinant versions of XynR (LacI family) and XylR (ROK family) were subjected to fluorescence polarization (FP) and biolayer interferometry (BLI) analysis to confirm the predicted binding sites. Four XynR sites and two XylR sites were validated, accounting for 20 of 26 genes regulated by XynR and six of seven genes regulated by XylR. Bioinformatic analysis of the individual genes controlled by the two regulators showed an inter-dependent scheme for xylan conversion; the transport of xylooligosaccharides (XOS) is dependent on XylR, while enzymes responsible for hydrolysis are controlled by both regulators. For xylose catabolism by the xylose isomerase-xylulose kinase pathway, regulation is also split, with XylR controlling xylose isomerase and XynR controlling xylokinase. The XynR/XylR regulator pair withinA. besciiis conserved in all sequenced species ofCaldicellulosiruptorales, suggesting similarities in regulating linear xylan conversion. In other xylanolytic thermophiles, XylR homologs control xylan degradation, compared to just 6 out of 26 genes forA. bescii. These results show that two separate regulatory schemes (dual repression) are coordinated byA. besciito effectively regulate the hemicellulose inventory and xylan catabolism. IMPORTANCE To take full advantage of extreme thermophiles as platform metabolic engineering microorganisms, the tools for genetic manipulation must be further developed, and strategies that exploit a better understanding of metabolic regulation need to be discerned.Anaerocellum bescii, the most studied of the extremely thermophilic fermentative anaerobic bacteria that can utilize microcrystalline cellulose, can degrade microcrystalline cellulose and hemicellulose and has been metabolically engineered to convert the resulting sugars to products such as ethanol and acetone. For xylan, in particular, two major global transcription factors (TFs), XynR and XylR, play a role in sugar metabolism, although their predicted regulatory interdependence from bioinformatics analysis has not been elucidated experimentally. Here, fluorescence polarization (FP) and biolayer interferometry (BLI) were used to explore this issue to support metabolic engineering efforts aimed at improving carbohydrate processing to industrial chemicals.

Biotechnology & Applied Microbiology↗

DOE OSTI2024

Simulation & Analysis of the Hydronic Shell Retrofit System as a Solution for Deep Energy Retrofits and Electrification of Large Multifamily Housing Communities in Cold Climate

Among 32 million multi-family buildings in the United States, approximately 42% have poor or no insulation. Envelope retrofits of these buildings will provide thermal resiliency and enable a pathway to electrification of space heating systems as a result of improved thermal performance. Hydronic Shell (HS) is a technology which combines an insulated retrofit panel with a heating, ventilation and air-conditioning (HVAC) thus enabling both envelope retrofit and space heating electrification. In this study, we used whole building energy simulation to evaluate energy impact of multi-family building retrofit with hydronic shell system. The simulation was performed for four locations of New York, Syracuse, Chicago and Boston. The results from the simulation showed more than 66% cooling energy reduction and more than 88% heating energy reduction from Hydronic Shell retrofit compared to Baseline building in all four locations. This reduction in energy consumption resulted in up to 219 MT reduction in annual CO2 emission. The cost reduction per floor area achieved from HVAC energy consumption reduction using Hydronic Shell retrofit was 0.66 to 0.99 $\$$/ft 2 . The results also showed higher percentage of heating energy reduction comes from the envelope only retrofit and higher percentage of cooling energy reduction comes from the retrofit HVAC system for the four locations under study.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2023

Comparing Parallel Plastic‐to‐X Pathways and Their Role in a Circular Economy for PET Bottles

Abstract The United States generates the most plastic waste of any country and is a top contributor to global plastic pollution. Multiple 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 lifetimes and utilities. Herein, they present a material flow model equipped with consequential life cycle assessment, cost analysis, and a plastic circularity indicator that considers product quality and lifetime. The model is used to estimate the greenhouse gas (GHG) emissions, circularity, and cost of polyethylene terephthalate (PET) bottle mechanical downcycling to lower‐quality resin, closed‐loop glycolysis to food‐grade PET, upcycling to glass fiber‐reinforced plastic, and conversion to non‐plastic products (electricity, oil) on a United States economy‐wide basis for the year 2020. A brute force algorithm suggests that a combination of 68% glycolysis, 11% mechanical recycling, 6% upcycling, 9% landfilling, and 5% incineration can minimize the cost and GHG emissions and maximize the circularity of the current PET economy. However, uncertainty around transportation distances, materials recovery facility efficiencies, and recycling yields can result in different “optimal” pathway mixes. This flexible framework enables informed decision‐making to move toward a cost‐ and environment‐conscious circular economy for plastic.

09 BIOMASS FUELS↗

DOE OSTI2021

Exploring the Role of Humidity, Temperature, and Mixed Ionic and Electronic Conductivity on SOFC Anode Electrocatalysis

Infiltration of nanoscale electrocatalysts into Ni/yttria-stabilized zirconia (Ni-YSZ) cermets has been shown to improve the electrochemical performance of solid oxide fuel cell (SOFC) anodes. While infiltrated electrodes in SOFCs result in improved cell performance, long-term operation leads to coarsening of the infiltrated nanoparticles and negates the short-term performance improvements. This study explores the roles of humidity, temperature, and number of cycles of nanocatalyst infiltration in improving mixed conduction within the Ni-YSZ electrode. Two mixed conduction phases were studied: Gd 0.1 Ce 0.9 O 2-δ (GDC) as an infiltrant into Ni-YSZ electrodes, and Ni/transition metal doped-YSZ electrodes infiltrated with Ni. Analysis of impedance data from these cells shows improved electrochemical performance in infiltrated cells with mixed conduction compared with infiltrated cells containing purely ionic and electronic conducting phases. Improved anode performance is attributed to the availability of electronic pathways through predominantly ionic-conducting phases to connect distant Ni nanoparticles and/or Ni grains.

25 ENERGY STORAGE↗

DOE OSTI2025

Single cell RNA sequencing reveals shifts in cell maturity and function of endogenous and infiltrating cell types in response to acute intervertebral disc injury

Intervertebral disc (IVD) degeneration contributes to disabling back pain. Degeneration can be initiated by injury and progressively leads to an irreversible loss of cells and function. IVD function restoration through cell replacement therapies have had limited success due to knowledge gaps in the critical cell populations important for repair. Here, in this study, we used single cell RNA sequencing to identify the transcriptional changes of IVD resident and infiltrating cell populations from Control and Injured coccygeal IVDs extracted from 12-week-old female C57BL/6J mice 7 days post injury. Clustering, gene ontology, and pseudotime trajectory analyses determined transcriptomic divergences with injury, flow cytometry identified they types of infiltrating immune cells, and immunofluorescence was utilized to define mesenchymal stem cell (MSC) localization. We identified 11 distinct clusters that included IVD, immune, vascular cells, and MSCs. Differential gene expression analysis determined that Outer Annulus Fibrosus, Neutrophils, Saa2-High MSCs, Macrophages, and Krt18 + Nucleus Pulposus (NP) cells were the major drivers of transcriptomic differences between Control and Injured cells. Gene ontology revealed that the most upregulated biological pathways were angiogenesis and T cell-related while wound healing and ECM regulation were downregulated. Pseudotime trajectory analyses revealed that IVD injury directed cells towards increased differentiation in all clusters, except for Krt18 + NP cells which remained in a less mature cell state. Saa2-High and Grem1-High MSCs populations shifted towards more differentiated IVD cells profiles with injury and localized distinctly within the IVD. This study revealed novel MSC populations with the potential to be leveraged for future IVD repair studies.

Cartilage↗

DOE OSTI2026

Atomic Evolution of Hydrogen Intercalation Wave Dynamics in Palladium Nanocrystals Revealed by Liquid-Phase Transmission Electron Microscopy

Solute-intercalation-induced phase separation creates spatial heterogeneities in host materials, a phenomenon ubiquitous in batteries, hydrogen storage, and other energy devices. Despite many efforts, probing intercalation processes at the atomic scale has been a significant challenge. By utilizing liquid-phase transmission electron microscopy (TEM), we study hydrogen (de)intercalation in palladium nanocrystals as a model system and have achieved unprecedented atomic-resolution imaging of hydrogen intercalation wave dynamics. Our observations reveal that intercalation wave mechanisms, instead of shrinking-core mechanisms, prevail at ambient temperature for palladium nanocubes ranging from ∼60 nm down to ∼10 nm. Systematic image analysis uncovers the atomic evolution of the hydrogen intercalation wave, transitioning from nonplanar and inclined boundaries to those closely aligned with {100} planes. Our kinetic Monte Carlo simulations demonstrate that the observed intercalation wave dynamics correspond to sorption pathways minimizing the lattice mismatch strain at the phase boundary. In conclusion, unveiling the atomic intercalation pathways holds profound implications for engineering intercalation-mediated devices and advancements in energy sciences.

Lee, Daewon [Lawrence Berkeley National Laboratory↗

DOE OSTI2025

Isothermal solidification for high-entropy alloy synthesis

Kinetically trapping the high-temperature states through rapid cooling solidification is widely used for the synthesis of high-entropy alloys (HEAs), especially those with intrinsically immiscible elemental combinations. However, strategies need to be developed to overcome the fundamental limitations of rapid cooling solidification in controlling the crystallinity, structure and morphology of HEAs. Here, in this study, we introduce an isothermal solidification strategy for the synthesis of HEAs by rapidly altering the metal alloy composition through liquid–liquid interface reactions at low temperatures, for example, from 25 °C to 80 °C. We use gallium (Ga)-based metal as the sacrificial reagent and mixing medium. By directing the reactions to the interfaces between the Ga-based liquid metal and an aqueous metal ion solution, the foreign metal ions can be reduced at the interfaces and incorporated into the liquid metal quickly. HEAs with various crystallinity (single crystal, mesocrystal, polycrystal and amorphous), morphology (zero, two and three dimensions) and compositions can be achieved through the isothermal solidification. Ga can be completely consumed, resulting in Ga-free HEAs. If desired, Ga can be one of the metal elements in the final products. In situ liquid phase transmission electron microscopy (TEM) studies and theoretical analysis show the isothermal solidification mechanisms. Our direct observations show the enhanced mixing of liquid metal elements and the solidification process with fluctuating nucleation dynamics. The isothermal solidification marks a powerful strategy for HEA synthesis through an unexplored pathway of kinetically trapping the high-entropy states.

Zhang, Qiubo [Lawrence Berkeley National Laborator↗

DOE OSTI2026

Carbon source–driven metabolic and regulatory remodeling defines phenomic states in Lipomyces starkeyi

Lipomyces is a genus of oleaginous yeasts with potential for contributing to reliable biomanufacturing supply chains. However, progress in advanced strain designs and engineering efforts are still constrained by a lack of understanding of the underlying molecular drivers of Lipomyces phenotypes. To address this gap, we collected a suite of multi-omic data to dissect how carbon source availability reshapes the metabolic network, lipid allocation, and regulatory architecture of Lipomyces starkeyi. We observed that glucose promotes biosynthetic and proliferative processes supported by abundant energy and carbon intermediates, xylose enhances redox-balancing mechanisms centered on the pentose phosphate pathway, and glycerol activates respiratory metabolism, ß-oxidation, and the glyoxylate cycle. Lipid species distributions remained consistent in both nitrogen replete and depleted conditions across the carbon sources, indicating robust production mechanisms. Regulatory protein identification and network analysis revealed glycerol-driven respiratory growth favors regulatory programs integrating stress tolerance, redox balance, and lipid-associated metabolism, whereas xylose growth activates compensatory transcriptional responses aimed at maintaining mitochondrial function. Nitrogen limitation modulates the strength of these responses but does not fundamentally alter their direction, reinforcing carbon source as the dominant driver of regulatory architecture. Taken together, this data enhances the understanding of Lipomyces molecular rearrangements and provides a foundation for further development of predictive phenotypic tools in this genus.

Biotechnology↗

DOE OSTI2022

Co-sputtering of lithium vanadium oxide thin films with variable lithium content to enable advanced solid-state batteries

Advanced solid-state batteries most likely will entail aggressive structures or architectures with constraints that typically limit processing temperatures. Considering this, we have identified the importance of providing lithiated electrode materials at a modest processing temperature. Here we describe a pathway to meet this by the development of a co-sputtering process using lithium oxide and vanadium oxide targets which enables the growth of lithiated vanadium oxide (LVO) thin films for application in solid-state batteries. Analysis of the structure and film composition of samples deposited with different co-sputtering rate ratios and post-annealing shows that multiple phases of Li x V 2 O 5 likely coexist (i.e. α-, ε-, δ-, and γ-V 2 O 5 ), and that this is unchanged after electrochemical cycling. The co-sputtering process can tune the lithium content up to a highly lithiated state of at least Li 2 V 2 O 5 . Electrochemical half-cells showed a significant amount of lithium available on the first charge (delithiation of LVO). LVO samples post-annealed at 300 °C showed typical redox peaks for Li x V 2 O 5 for both one and two lithium insertion reactions, which were highly reversible in most cases. A thin-film solid-state battery prototype using LVO as a cathode had 20% of the expected capacity, although the coulombic efficiency is near 100% at a fast rate (22C). As a result, this co-sputtering technique represents an opportunity for low temperature synthesis of pre-lithiated cathodes for thin film batteries, and introduces a broader methodology of depositing metal oxides with different alkali metal contents.

25 ENERGY STORAGE↗

DOE OSTI2026

Hydrogen defects in LaBi 2 O 4 X (X = Cl, Br, and I) Sillén oxyhalide phases and their impacts on ionic transport

Sillén oxyhalides have recently emerged as promising materials for both photocatalytic and ionic transport applications, yet the role of likely-ubiquitous hydrogen-related defects in these layered compounds remains largely unexplored. Here, we employ first-principles defect calculations to investigate incorporation energetics for hydrogen- and oxygen-related defects, as well as their migration barriers in LaBi 2 O 4 X (X = Cl, Br, I) phases. We find that hydrogen interstitials, particularly protonic species (H i + ), are readily accommodated within the open Bi–O layers. Protons compete with oxygen vacancy donors (V O 2+ ) and charge-compensate with oxygen interstitial acceptors (O i 2− ). By linking hydrogen defect formation to water- and oxygen-related redox equilibria, we reveal that V O 2+ facilitates H i + incorporation, while O i 2− promotes interstitial hydroxide formation, establishing a direct connection between proton and oxide-ion transport. Calculated migration barriers indicate that ionic diffusion is confined to Bi–O layers with low barriers of 0.20–0.25 eV for H i + and 0.14–0.25 eV for V O 2+ , suggesting that the materials contain intrinsic pathways for mixed ionic conduction. These results provide a microscopic picture of hydrogen behavior in Sillén oxyhalides and point to design strategies for integrating protonic and oxide-ion transport in layered oxyhalide electrolytes. Band-edge alignment analysis shows that LaBi 2 O 4 I provides the optimal combination of hydrogen solubility, oxygen defect stability, and mixed ionic conductivity, highlighting its potential for low-temperature electrochemical and energy-conversion applications. Overall, this work establishes the defect-driven origin of hydrogen transport in Sillén oxyhalides and expands their applicability beyond photocatalysis to mixed ionic conduction and hydrogen electrochemistry.

Energy - Conversion↗

DOE OSTI2022

Evaluating Contributions of Pitch-Carbon Coating to Improved Stability of Si Anodes Through Voltage-Resolved Multi-Phase Characterization

Silicon nanoparticles have emerged as a promising alternative to graphite to improve the energy density of next-generation lithium-ion battery anodes. Nano-sized Si domains facilitate rapid ion transport and minimize particle-scale mechanical degradation, but also exhibit increased (electro)chemical reactivity with Li-ion electrolyte components due to their high surface area. We have previously demonstrated that surface modification of Si nanoparticles with pitch-carbon is an effective strategy to reduce these parasitic reactions. In the present work, we holistically evaluate the mechanistic contribution of pitch-carbon coating to the observed stability improvement over uncoated Si. We utilize coupled in situ and ex situ methods to probe changes to solid-surface, volatile headspace, and gas-phase chemistry occurring during initial cycling. Measurements taken at targeted potentials associated with electrolyte species reduction enables the decoupling of specific reaction pathways tied to interfacial stability. Further, we demonstrate the non-trivial role of gas reconsumption in dictating the nature of the passivating surface layer evolved on both uncoated and pitch-coated Si. This multi-phase analysis offers insights into the mechanism of effective surface passivation, which may be applied to inform future Si material development.

ENERGY STORAGE↗

DOE OSTI2021

Achieving Integrated Daylighting and Electric Lighting Systems: Current State of the Art and Needed Research

This paper presents the results of a multi-disciplinary scoping study, the goals of which were to see the seamless integration and application of light in buildings, regardless of source, that is purposely modulated to illuminate surfaces and designed in a way that is comfortable, healthy, pleasing, cost effective, and energy efficient. The scoping study was performed in order to set the stage for transforming the design and realization of lighting systems integration (daylight and electric). This, in turn, will support achieving the the U.S. Department of Energy’s (DOE) Building Technologies Office (BTO) long-term energy savings goals. Holistic lighting systems of the future should include components that are adaptable to change, resilient to disruption, and robust. The system of codes, standards, guidelines, and contracts employed to design and implement lighting systems should be structured to help them to flourish, rather than being barriers to realization. Finally, the research thrusts and mechanisms should be engaged with these goals in mind. While integrated lighting systems may reduce lighting energy use in buildings, a broader web of non-energy impacts affecting occupant’s overall health, comfort, and satisfaction may also guide technology investment goals when the entire lighting systems lifecycle is considered. Daylighting systems are separated from electric lighting systems, and both are characteristically detached from other systems such as safety, security, communications, and information systems. Being disconnected from the inputs and outputs of other building systems precludes the ability to acquire and utilize information about occupation, status of systems, and interior and exterior environmental conditions. The outcome of this separation is that the standard building is not fulfilling the potential for creating dynamic and holistic lighting for building occupants.

Davis, Robert G.↗

NASA NTRS2001

Combining Flux Balance and Energy Balance Analysis for Large-Scale Metabolic Network: Biochemical Circuit Theory for Analysis of Large-Scale Metabolic Networks

Predicting behavior of large-scale biochemical metabolic networks represents one of the greatest challenges of bioinformatics and computational biology. Approaches, such as flux balance analysis (FBA), that account for the known stoichiometry of the reaction network while avoiding implementation of detailed reaction kinetics are perhaps the most promising tools for the analysis of large complex networks. As a step towards building a complete theory of biochemical circuit analysis, we introduce energy balance analysis (EBA), which compliments the FBA approach by introducing fundamental constraints based on the first and second laws of thermodynamics. Fluxes obtained with EBA are thermodynamically feasible and provide valuable insight into the activation and suppression of biochemical pathways.

Beard, Daniel A.↗

NASA NTRS2002

A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo

We present the current form of a provisional DNA sequence-based regulatory gene network that explains in outline how endomesodermal specification in the sea urchin embryo is controlled. The model of the network is in a continuous process of revision and growth as new genes are added and new experimental results become available; see http://www.its.caltech.edu/~mirsky/endomeso.htm (End-mes Gene Network Update) for the latest version. The network contains over 40 genes at present, many newly uncovered in the course of this work, and most encoding DNA-binding transcriptional regulatory factors. The architecture of the network was approached initially by construction of a logic model that integrated the extensive experimental evidence now available on endomesoderm specification. The internal linkages between genes in the network have been determined functionally, by measurement of the effects of regulatory perturbations on the expression of all relevant genes in the network. Five kinds of perturbation have been applied: (1) use of morpholino antisense oligonucleotides targeted to many of the key regulatory genes in the network; (2) transformation of other regulatory factors into dominant repressors by construction of Engrailed repressor domain fusions; (3) ectopic expression of given regulatory factors, from genetic expression constructs and from injected mRNAs; (4) blockade of the beta-catenin/Tcf pathway by introduction of mRNA encoding the intracellular domain of cadherin; and (5) blockade of the Notch signaling pathway by introduction of mRNA encoding the extracellular domain of the Notch receptor. The network model predicts the cis-regulatory inputs that link each gene into the network. Therefore, its architecture is testable by cis-regulatory analysis. Strongylocentrotus purpuratus and Lytechinus variegatus genomic BAC recombinants that include a large number of the genes in the network have been sequenced and annotated. Tests of the cis-regulatory predictions of the model are greatly facilitated by interspecific computational sequence comparison, which affords a rapid identification of likely cis-regulatory elements in advance of experimental analysis. The network specifies genomically encoded regulatory processes between early cleavage and gastrula stages. These control the specification of the micromere lineage and of the initial veg(2) endomesodermal domain; the blastula-stage separation of the central veg(2) mesodermal domain (i.e., the secondary mesenchyme progenitor field) from the peripheral veg(2) endodermal domain; the stabilization of specification state within these domains; and activation of some downstream differentiation genes. Each of the temporal-spatial phases of specification is represented in a subelement of the network model, that treats regulatory events within the relevant embryonic nuclei at particular stages. (c) 2002 Elsevier Science (USA).

Non-NASA Center↗

NASA NTRS2002

Distinct requirements for TrkB and TrkC signaling in target innervation by sensory neurons

Signaling by brain-derived neurotrophic factor (BDNF) via the TrkB receptor, or by neurotrophin-3 (NT3) through the TrkC receptor support distinct populations of sensory neurons. The intracellular signaling pathways activated by Trk (tyrosine kinase) receptors, which in vivo promote neuronal survival and target innervation, are not well understood. Using mice with TrkB or TrkC receptors lacking the docking site for Shc adaptors (trkB(shc/shc) and trkC(shc/shc) mice), we show that TrkB and TrkC promote survival of sensory neurons mainly through Shc site-independent pathways, suggesting that these receptors use similar pathways to prevent apoptosis. In contrast, the regulation of target innervation appears different: in trkB(shc/shc) mice neurons lose target innervation, whereas in trkC(shc/shc) mice the surviving TrkC-dependent neurons maintain target innervation and function. Biochemical analysis indicates that phosphorylation at the Shc site positively regulates autophosphorylation of TrkB, but not of TrkC. Our findings show that although TrkB and TrkC signals mediating survival are largely similar, TrkB and TrkC signals required for maintenance of target innervation in vivo are regulated by distinct mechanisms.

Non-NASA Center↗