IPO Tech Transfer Annual Report FY25 Content Final 7.29.26
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Administration and management↗
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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.
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Near-adjacent heavy lanthanide separation and sensing using dimerizing lanmodulins
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Biological and medical sciences↗
Development of a Gut-on-a-Chip Microfluidic Device with Three-Dimensionally Printed Human Intestinal Tissue for Studying Human-Microbe Interactions
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Biological and medical sciences↗
Small-molecule modulation of β-arrestins
β-Arrestins are multifunctional regulators of G-protein-coupled receptor (GPCR) signalling and orchestrate diverse downstream signalling events and physiological responses across the GPCR superfamily. Although GPCR pharmacology has advanced to target orthosteric and allosteric sites, as well as G proteins and GPCR kinases, direct chemical tools to modulate β-arrestin activities have remained conspicuously absent. Here we report the identification of small-molecule inhibitors that selectively target β-arrestins and delineate their mechanism of action through integrated pharmacological, biochemical, biophysical and structural analyses. These inhibitors disrupt β-arrestin engagement with agonist-activated GPCRs, impairing desensitization, internalization and β-arrestin-dependent physiological functions while sparing G protein–receptor coupling. Cryo-electron microscopy, molecular dynamics simulations and structure-guided mutagenesis reveal that one modulator, Cmpd-5, engages a pocket within the central crest of β-arrestin1 formed by the middle, C and lariat loops, a critical receptor-binding interface, stabilizing a distinct conformation that is incompatible with full β-arrestin–receptor engagement. Together, these findings establish a mechanistic framework for β-arrestin modulation, reveal a novel allosteric site for structure-based drug design, and open new avenues for transducer-targeted, pathway-specific GPCR therapeutic agents.
Kahsai, Alem W. [Duke University, Durham, NC (Unit↗
Molecular origin of anisotropic shear elastoplasticity in chitin
Chitin nano- and mesoscale structures present in the exoskeleton of crustaceans exhibit exceptional longitudinal stiffness and toughness, rivaling or even exceeding that of many synthetic polymer architectures. Here, we reveal the origin of the asymmetric shear response in chitin multiscale architectures, marked by pronounced anisotropy in deformation. Under shear aligned with the molecular axis, chitin accommodates strain through coherent atomic rearrangements that enable elastic recovery. In contrast, shear applied perpendicular to this axis induces liquid-like plasticity via localized sliding. These results demonstrate the intrinsic mechanical anisotropy of chitin, underpinning a dual function in resisting repetitive loading while dissipating internal stress during high-strain events. Our findings establish the molecular basis of shear elastoplasticity in multiscale chitin structures, wherein axial elasticity supports energy storage in load-bearing regions, whereas transverse plasticity enables controlled energy dissipation. These atomic-scale insights lay a foundation for the predictive design of chitin-based materials with tunable strength-toughness profiles.
Wan, Zhangmin [University of British Columbia, Van↗
De Novo Design of High‐Affinity Miniprotein Binders Targeting Francisella Tularensis Virulence Factor
Abstract Francisella tularensis poses considerable public health risk due to its high infectivity and potential for bioterrorism. Francisella‐like lipoprotein (Flpp3), a key virulence factor unique to Francisella, plays critical roles in infection and immune evasion, making it a promising target for therapeutic development. However, the lack of well‐defined binding pockets and structural information on native interactions has hindered structure‐guided ligand discovery against Flpp3. Here, we used a combination of physics‐based and deep‐learning methods to design high‐affinity miniprotein binders targeting two distinct sites on Flpp3. We identified four binders for site I with binding affinities ranging between 24–110 nM. For the second site, an initial binder showed a dissociation constant ( K D ) of 81 nM, and subsequent site saturation mutagenesis yielded variants with sub‐nanomolar affinities. Circular dichroism confirmed the topology of designed miniproteins. The X‐ray crystal structure of Flpp3 in complex with a site I binder is nearly identical to the design model (Cα root‐mean‐square deviation (RMSD): 0.9 Å). These designed miniproteins provide research tools to explore the roles of Flpp3 in tularemia and should enable the development of new therapeutic candidates.
Gokce‐Alpkilic, Gizem [Molecular Engineering and S↗
Conformer-Specific Dissociation Dynamics in Dimethyl Methylphosphonate Radical Cation
The dynamics of the dimethyl methylphosphonate (DMMP) radical cation after production by strong field adiabatic ionization have been investigated. Pump-probe experiments using strong field 1300 nm pulses to adiabatically ionize DMMP and a 800 nm non-ionizing probe induce coherent oscillations of the parent ion yield with a period of about 45 fs. The yields of two fragments, PO 2 C 2 H 7 + and PO 2 CH 4 + , oscillate approximately out of phase with the parent ion, but with a slight phase shift relative to each other. We use electronic structure theory and nonadiabatic surface hopping dynamics to understand the underlying dynamics. The results show that while the cation oscillates on the ground state along the P=O bond stretch coordinate, the probe excites population to higher electronic states that can lead to fragments PO 2 C 2 H 7 + and PO 2 CH 4 + . The computational results combined with the experimental observations indicate that the two conformers of DMMP that are populated under experimental conditions exhibit different dynamics after being excited to the higher electronic states of the cation leading to different dissociation products. These results highlight the potential usefulness of these pump-probe measurements as a tool to study conformer-specific dynamics in molecules of biological interest.
59 BASIC BIOLOGICAL SCIENCES↗
Evaluation of Howard A. Hanson Dam Juvenile Fish Passage and Survival Study: Downstream Passage and Survival (Acoustic Telemetry) (Task Final Report)
The Downstream Passage and Survival (Acoustic Telemetry) task was one of several tasks for the Evaluation of Howard A. Hanson Dam (HAHD) Juvenile Fish Passage and Survival study. For this task, a juvenile fish passage and survival study was conducted at HAHD from March 10, 2024 through June 27, 2024 for arrays in the HAHD Reservoir and Green River, and through July 9, 2024 for the arrays in the Duwamish River. Fish releases occurred over four times from March through May. Active tag (acoustic telemetry) technology was used to provide biological baseline information for the passage and survival of juvenile Puget Sound (PS) Chinook salmon (Oncorhynchus tshawytscha). Results will be used by biologists, engineers, resource managers, and regional decision-makers to inform the engineering design of the new fish passage facility (FPF) at HAHD. However, hatchery sub-yearling PS Chinook salmon of the appropriate size for tag implantation during the study period (> 95 mm in fork length, Geist et al. 2018) were unavailable. Therefore, yearling Coho salmon (O. kisutch) were used as a surrogate species for this acoustic telemetry study.
13 HYDRO ENERGY↗
Light-triggered electrochemical biosensor using singlet oxygen for self-powered operation and glucose detection
This study introduces a light-activated sensing strategy that integrates photosensitization with electrochemical detection. The sensor employs Eosin Y, a photosensitizer that generates singlet oxygen ( 1 O 2 ) via type II photosensitization. Immobilized within a thin polymer matrix on a carbon working electrode, Eosin Y produces 1 O 2 , under green light (520 nm) illumination, initiating a redox process that yields a measurable current. To incorporate biosensing capabilities and enable self-powered operation, this 1 O 2 – mediated process was coupled with glucose oxidase (GOx) to construct a fully operational glucose biosensor. The addition of glucose reverses the current flow by causing GOx to compete for electrons, with the resulting current magnitude correlating with glucose concentration providing a sensitive measure of glucose. The biosensor, as proof-of-principle, demonstrated excellent performance over a range of glucose concentrations (0–73 mM), achieving a detection limit (LOD) of 2.8 mM for steady state photocurrent under oxygen-saturated conditions. This platform leverages light and 1 O 2 as stimuli for tunable, on-demand signal control, offering a novel approach for adaptive, real-time biosensing technologies.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Dust and Primary Biological Aerosol Particles (PBAP) Effects on Sea Breeze Systems Over Houston
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Du, Qiuyan↗
U.S. Pacific Coast Workshop Report on Preconstruction Research Recommendations (U.S. Offshore Wind Synthesis of Environmental Effects Research (SEER) Project)
In May 2022, the U.S. Offshore Wind Synthesis of Environmental Effects Research (SEER) project team hosted a stakeholder workshop focused on preconstruction (baseline) research needs for potential floating offshore wind (OSW) energy development on the U.S. Pacific Coast, including California, Oregon, and Washington. Prior to the workshop, the SEER team developed a set of initial synthesized research recommendations that were identified based on a review of relevant, publicly available resources and with advisory group input. The workshop covered three marine life breakout groups on subsequent days to discuss research recommendations related to 1) marine mammals and sea turtles, 2) fish and invertebrates, and 3) birds and bats. As part of the workshop, over a hundred participants from the public and private sectors provided feedback on various aspects of the initial research recommendations, including associated data and knowledge gaps, benefits/limitations of available methods and technologies, and technological advancements or infrastructure needed to address the recommendation. Approximately 1,000 total comments were received on the workshop MURAL boards and were synthesized in this report. Based on workshop feedback, SEER developed a final database of over 500 specific research recommendations based on more than 40 resources. In Fall 2022, the full database and a tool with updated synthesized research recommendations were disseminated on Tethys (https://tethys.pnnl.gov) to assist with informing future funding opportunities and research programming. There is a continued need to improve awareness of the potential environmental effects, monitoring technologies, and management strategies for floating OSW energy development on the U.S. Pacific Coast. Coordination of these activities will require the sustained involvement of multiple stakeholders from across sectors. Beyond the baseline considerations discussed in this workshop, future state-of-the-science activities should be planned to consider research needs across wind energy life cycle phases for all relevant wildlife taxa and associated habitat and ecosystem processes.
17 WIND ENERGY↗
Proteome-wide analysis of protein stability in Escherichia coli under acid stress
Knowledge of protein acid sensitivity remains sparse and is largely derived from low-throughput, enzyme-specific assays. We used a scalable framework to map acid stability across the Escherichia coli proteome to assess the acid stability of 1,675 unique proteins, estimating pH 50 values for over 90% of them. The parameter pH50 was defined as the pH value at which only 50% of the initial protein remains in solution following acid treatment. Proteome-wide pH 50 values ranged from 2.28 to 6.33 (median 5.11). Approximately 9% of detected proteins remained stable across all tested pH conditions. Our results align with published data and the assay of citrate synthase (GltA) performed here. Protein acid stability differed significantly by subcellular localization: periplasmic proteins were relatively more abundant in the acid-stable group, cytoplasmic proteins were abundant at pH 50 values 4.5–5.5, and inner membrane proteins at higher pH 50 between 5.5 and 6.0. Outer membrane proteins were too few to draw strong conclusions regarding enrichment within specific pH 50 groups. Notably, the periplasmic binding protein of the molybdate ABC transporter (ModA), was enriched after incubation at low pH. Estimated pH 50 values showed no correlation with protein isoelectric point and molecular weight. Together, this work provides the first proteome-wide map of protein acid stability and establishes a general framework for studying different chemical stressors.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Osmotic and phoretic competition explains chemotaxic assembly and sorting
Microscale objects responding to chemical gradients by migrating toward or away from a preferred species is a simple yet constitutive mechanism by which transport occurs in biological organisms. Synthetic chemotaxis provides key physical descriptions of simplified systems that can be used in biological models, or in the creation of advanced responsive material systems. In this article, we provide a quantitative framework for understanding synthetic chemotaxis of microparticles which involves a competition between phoresis and osmosis. We present separate quantitative measurements of phoresis and osmosis acting on individual taxing particles, finding that phoresis follows the long-predicted v ∼ 1 / r 2 scaling while the osmotic contribution depends on the geometry and details of the system, and must be solved on a case-by-case basis. Through this, we are able to develop a more accurate picture of particle transport at the single particle level. Equipped with this approach, we go on to describe how high concentrations of particles in a symmetric chemical gradient grow close-packed hives that reach a steady-state size tunable through light intensity or particle size. Last, we demonstrate that mixed particles experiencing the same chemical gradient will selectively migrate toward or away depending on the nature of the particle surface, thereby locally sorting out a particular species. We anticipate these results will be important in describing both biological and synthetic chemotaxis in phoretic systems and should bring a wealth of studies that take advantage of competing osmotic flows to illicit unexpected dynamic active behavior.
Science & Technology - Other Topics↗
Direct comparison of gamma, electron beam and X-ray radiation effects on the polymers of a pulsed lavage device
Gamma radiation used for sterilization of medical devices is challenged by cobalt-60 supply and commercial capacity. To maintain a robust radiation sterilization marketplace for the rapidly growing single-use medical device industry, investigation of potential alternatives to gamma technology, such as electron beam (e-beam) and X-ray technology, is critical. In this work, we directly compare the effects of radiation source and absorbed dose level on the polymeric materials and function of a commercial pulsed lavage device used for wound care. Product functionality, polymer mechanical, and polymer optical properties were evaluated using standard methods and input from the device manufacturer. Test results show that functionality of the product was not inhibited by radiation although the battery in the device exposed to X-ray exhibited greater voltage loss compared to batteries in products exposed to gamma or e-beam. Statistically significant differences between gamma and e-beam exposure and between gamma and X-ray exposure were also observed for product appearance in terms of yellowness index of several of the polymers considered. Overall, the results of this study support the viability of e-beam and X-ray radiation technologies as alternatives to cobalt-60 gamma technology for sterilization of the single-use pulsed lavage medical device investigated.
Electron beam↗
Connectivity, Pathology, and ApoE4 Interactions Predict Longitudinal Tau Spatial Progression and Memory
ABSTRACT Tau pathology spread into neocortex indicates a transition from healthy aging to Alzheimer's disease (AD). Connectivity between tau epicenters and later accumulating regions of cortex has been proposed as a mechanism of tau spread, but how this relationship changes with greater AD pathology burden or genotype is not understood. We investigated tau accumulation in two key regions, precuneus and inferior temporal cortex, using resting state functional connectivity (rsFC) and longitudinal PET imaging from a multicohort sample of cognitively unimpaired older adults. We examined how baseline tau PET, Aβ PET, and ApoE4 genotype status interact with rsFC between hippocampus and these downstream regions to predict rate of tau accumulation in neocortex. We found that the 3‐way interaction between connectivity, baseline tau, and baseline Aβ or ApoE4 status was associated with neocortical tau accumulation in precuneus and inferior temporal cortex. In addition, baseline tau, Aβ, and ApoE4 status also moderated the association between connectivity and rate of memory decline. Together, these results suggest that the extent and distribution of future tau accumulation may be predicted by the interaction of baseline connectivity, AD pathology, and genetic risk.
Neurosciences & Neurology↗
Divergent carbon use efficiency-growth rate tradeoff in popular biological growth models
Carbon use efficiency (CUE) is an important trait emerging from processes regulating biological growth. CUE can be computed either based on the growth of structural biomass or total biomass divided by substrate uptake rate. Nonequilibrium thermodynamics and observations suggest that, for an exponentially growing population of cells, structural biomass CUE should first increase, then peak, and finally decrease with specific growth rate; meanwhile, total biomass CUE increases asymptotically with specific growth rate. We compared predictions from six popular models that are often used for plant and microbial growth in existing ecosystem models. We found that, for an exponentially growing population of biological cells, (1) the source-driven Pirt and Compromise models predict that structural biomass CUE increase asymptotically with growth rate; (2) the apparent sink-driven modified Droop model predicts that structural biomass CUE decreases with growth rate; and (3) the sink-driven variable internal storage model and two dynamic energy budget models predict that structural biomass CUE first increases, then peaks, and finally decreases with growth rate. Moreover, the modified Droop model predicts that total biomass CUE is constant with growth rate, while all other five models predict that total biomass CUE increases with growth rate asymptotically. For non-exponential biological growth, we show that there is no static relationship between total biomass CUE or structural biomass CUE with respect to either growth rate or temperature. Therefore, we contend that biological growth models should explicitly represent interactions between substrate acquisition, substate transformation, and maintenance respiration to better capture observed CUE dynamics, and the sink-driven model should be preferred for general ecosystem biogeochemistry modeling.
Tang, Jinyun [Lawrence Berkeley National Laborator↗
Physicochemical and biological characterization of a bispecific antibody in a CrossMab/KIH format that targets EGFR and VEGF-A
Introduction Bispecific antibodies (BsAbs) are a class of antibody therapeutics engineered in various molecular formats to bind two distinct antigens and potentially mediate multiple biological effects. These molecular formats are tailored to mediate specific mechanisms of action and possess unique physicochemical and biological properties that are necessary to assure product quality. In ovarian cancer (OC), both EGFR- and VEGF-A-mediated signaling pathways are often upregulated and cooperate to promote tumor growth and angiogenesis. Thus, inhibiting of EGFR- and VEGF-A pathways with a BsAb may provide synergistic anti-tumor activity. Methods Using publicly available sequences and applying immunoglobulin domain crossover (CrossMab) and knobs-into-holes (KIH) technologies, we generated a BsAb to simultaneously bind EGFR and VEGF-A (designated as anti-EGFR/VEGF-A BsAb). This BsAb served as a model for physiochemical and biological characterization of quality attributes that would be critical for the BsAb’s mechanisms of action. Our goal was to gain fundamental insights into BsAbs designed to target a receptor with one arm and a soluble ligand with the other, to support bioassay development and inform quality control strategies. Results Our data demonstrated that the CrossMab/KIH platform successfully produced a correctly assembled BsAb during cell culture. Characterization confirmed that the anti-EGFR/VEGF-A BsAb bound both EGFR and VEGF-A with comparable activity and affinity to the respective parental monoclonal antibodies. Functionally, the BsAb disrupted both EGF/EGFR and VEGF-A/VEGFR2 signaling pathways in OC and human umbilical vein endothelial cell (HUVEC) models. Furthermore, the BsAb effectively blocked angiogenic signaling driven by VEGF-A secreted from OC cells in a paracrine manner. Discussion Based on the combinatorial mechanism of action and our characterization findings, we concluded that two or more bioassays may be needed to accurately assess the activity of both arms of this type of BsAb.
Immunology↗
Knowledge-guided learning with curated prior genetic biomarkers for robust model interpretation
Abstract Motivation Knowledge-guided learning offers effective and robust model training strategies in data-scarce settings by incorporating established domain knowledge, thereby enhancing generalization, robustness, and interpretability. By contrast, conventional deep learning approaches rely purely on data-driven learning, which can limit robust model interpretability, particularly in high-dimensional settings with limited size samples. In computational biology, knowledge-guided learning has primarily leveraged network- and structural-based knowledge, leading to biologically interpretable representations and enhanced predictive performance compared to conventional approaches. However, curated biomarkers, one of the most accessible forms of biological knowledge, remain largely unexplored within knowledge-guided paradigms. Results In this study, we propose a model-agnostic training paradigm, Biomarker-driven Explainable Prior-guided Learning (BioExPL), that can be applied to any neural networks that incorporates curated prior knowledge. BioExPL enforces neural networks to reflect curated biomarker priors in their latent representations through a novel knowledge-alignment loss. BioExPL consistently demonstrated significantly improved predictive performance and enhanced model interpretability with minimized computational overhead in simulation studies and intensive experiments on multiple cancer datasets. BioExPL not only integrates prior curated knowledge into the model but also accurately identifies unknown associated signals additionally. BioExPL is model-agnostic and domain-independent, enabling its integration into diverse neural network architectures. Availability and implementation The open-source is publicly available at: https://github.com/datax-lab/BioExPL.
Baek, Beomsu [Department of Computer Science, Univ↗