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At least 379 records · Page 21

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DOE OSTI2023

Genetically Encoded Crosslinking Enables Identification of Multivalent Ubiquitin‐Deubiquitylating Enzyme Interactions

Abstract Ubiquitin (Ub) proteoforms control nearly every aspect of eukaryotic cell biology through their diversity. Inspired by the widely used Ub C‐terminal electrophiles (Ub−E), here we report the identification of multivalent binding of Ub with deubiquitylating enzymes (Dubs) using genetic code expansion (GCE) and crosslinking mass spectrometry. While the Ub−Es only gather structural information with the S1 Dub sites, we demonstrate that GCE of Ub with p‐benzoyl‐L‐phenylalanine enables identification of interaction modes beyond the S1 site with a panel of Dubs of both eukaryotic and prokaryotic origin. Collectively, this represents the next generation of Ub‐based affinity probes with a unique ability to unravel Ub interaction landscapes beyond what is afforded by cysteine‐based chemistries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Design of Chiral Domains by Surface Confinement of Liquid Crystals

Chirality, or absence of mirror symmetry, is a fascinating attribute of inanimate and living objects, which inspires artists and fascinates scientists in various disciplines, from physics to mathematics, biology to chemistry and crystallography. Producing and controlling the sense of handedness in systems formed by mirror-symmetric elements or containing an equal amount of left- and right-twisted elements is usually a nontrivial task. In this issue of ACS Central Science, Geonhyeong Park et al [1] demonstrate that a slab of a lyotropic chromonic liquid crystal (LCLC), formed by achiral molecules dispersed in water, can produce a periodic array of domains with left- and right-handed twists of the orientation of molecular aggregates. The twist develops over macroscopic regions of tens of microns in size and is caused by a balance of two facets of the orientational order pertinent to liquid crystals: the elastic response to deformations of orientation and anisotropy of surface interactions at confining boundaries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Conceptualizing Biogeochemical Reactions With an Ohm's Law Analogy

Abstract In studying problems like plant‐soil‐microbe interactions in environmental biogeochemistry and ecology, one usually has to quantify and model how substrates control the growth of, and interaction among, biological organisms (and abiotic factors, e.g., adsorptive mineral soil surfaces). To address these substrate‐consumer relationships, many substrate kinetics and growth rules have been developed, including the famous Monod kinetics for single‐substrate‐based growth and Liebig's law of the minimum for multiple‐nutrient‐colimited growth. However, the mechanistic basis that leads to these various concepts and mathematical formulations and the implications of their parameters are often quite uncertain. Here, we show that an analogy based on Ohm's law in electric circuit theory is able to unify many of these different concepts and mathematical formulations. In this Ohm's law analogy, a resistor is defined by a combination of consumers’ and substrates’ kinetic traits. In particular, the resistance is equal to the mean first passage time that has been used to derive the Michaelis‐Menten kinetics under substrate replete conditions for a single substrate as well as the predation rate of individual organisms. We further show that this analogy leads to important insights on various biogeochemical problems, such as (a) multiple‐nutrient‐colimited biological growth, (b) denitrification, (c) fermentation under aerobic conditions, (d) metabolic temperature sensitivity, and (e) the legitimacy of Monod kinetics for describing bacterial growth. We expect that our approach will help both modelers and nonmodelers to better understand and formulate hypotheses when studying certain aspects of environmental biogeochemistry and ecology.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Exploring the environmental drivers of human blastomycosis cases in the Midwestern United States

Blastomycosis is a fungal infection endemic to the eastern United States (US) and Canada caused by the inhalation of the fungi Blastomyces spp. Currently, the environmental drivers of disease dynamics are poorly understood. The goal of our work was to explore what environmental conditions are associated with the annual presence of blastomycosis cases, and therefore are potentially explanatory of the ecological niche of Blastomyces. We examined the relationships between reported cases of blastomycosis in three Midwestern US states (Michigan, Minnesota, and Wisconsin) from 2007–2017 in relation to eleven hypothesized environmental conditions, including climate, stream and soil mineral content, and land cover variables. Then, we fit logistic regression models to explore the relationships between the environmental variables and yearly blastomycosis case occurrence. Mean soil moisture, stream sediment mercury content, percent of water within the county, and woody wetlands land cover were all positively associated with the presence of annual cases, with woody wetlands having the most consistent signal across the three states. We also found significant differences in the likelihood of case presence between US states that were not explained by the variables in our model, suggesting state-level differences in case reporting and disease awareness. Our results provide a perspective on potential biological hypotheses to further test regarding environmental controls on the life cycle and ecological niche of Blastomyces.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Small-scale roughness entraps water and controls underwater adhesion

While controlling underwater adhesion is critical for designing biological adhesives and in improving the traction of tires, haptics, or adhesives for health monitoring devices, it is hindered by a lack of fundamental understanding of how the presence of trapped water impedes interfacial bonding. Here, by using well-characterized polycrystal diamond surfaces and soft, nonhysteretic, low–surface energy elastomers, we show a reduction in adhesion during approach and four times higher adhesion during retraction as compared to the thermodynamic work of adhesion. Our findings reveal how the loading phase of contact is governed by the entrapment of water by ultrasmall (10-nanometer-scale) surface features. In contrast, the same nanofeatures that reduce adhesion during approach serve to increase adhesion during separation. The explanation for this counterintuitive result lies in the incompressibility-inextensibility of trapped water and the work needed to deform the polymer around water pockets. Unlike the well-known viscoelastic contribution to adhesion, this science unlocks strategies for tailoring surface topography to enhance underwater adhesion.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

A New Theoretical Framework for Designing Ion Transport Pathways

The rapid transport of specific ions through matter is critical to energy storage, membrane separations, and health. However, commercial materials resist ion transport, lack specificity, or both, making ion transport costly and ineffective. Inspiration for new material designs can be taken from biology, where membrane transport proteins exert exquisite control over the specificity and rate of ion transport. The challenge in understanding and designing transport pathways is that ions often exchange their hydrating waters for direct contacts with atoms in the transport pathway. Despite intense study over decades, no theory exists to explain local ion binding and transport mechanisms and experiments cannot differentiate reliably between ions and water in binding sites. Here, we developed a new approach, based on quantum methods and extension of the quasi-chemical free energy theory, to understand and design pathways through materials for rapid transport of specific ions. Understanding ion transport mechanisms will significantly advance our nation’s ability to develop cost-effective materials for energy sustainability and therapeutics for health.

36 MATERIALS SCIENCE↗

NASA NTRS1976

Potential biomedical applications of ion beam technology

Electron bombardment ion thrusters used as ion sources have demonstrated a unique capability to vary the surface morphology of surgical implant materials. The microscopically rough surface texture produced by ion beam sputtering of these materials may result in improvements in the biological response and/or performance of implanted devices. Control of surface roughness may result in improved attachment of the implant to soft tissue, hard tissue, bone cement, or components deposited from blood. Potential biomedical applications of ion beam texturing discussed include: vascular prostheses, artificial heart pump diaphragms, pacemaker fixation, percutaneous connectors, orthopedic pros-thesis fixtion, and dental implants.

Banks, B. A.↗

NASA NTRS1976

Potential biomedical applications of ion beam technology

Banks, B. A.↗

NASA NTRS1995

Influence of spaceflight on the production of interleukin-3 and interleukin-6 by rat spleen and thymus cells

Six adult male Sprague-Dawley rats were flown on the 7-day US space shuttle mission STS-54. After flight, the spleen and thymus from each animal were assayed for the capacity to secrete the cytokines interleukin-3 (IL-3) and IL-6. Spleen and thymus cells were incubated for 48 h in the presence of 5 microgram/ml of concanavalin A or 2 microgram/ml of bacterial lipopolysaccharide to stimulate the production of IL-3 and IL-6. IL-3 activity was measured using the IL-3/colony-stimulating-factor-dependent cell line 32D. IL-6 activity was measured using the IL-6-dependent cell line 7TD1. Spleen and thymus cells harvested from flown rats secreted significantly higher titers of biologically active IL-3 compared with ground control rats. Spaceflight significantly enhanced IL-6 production by thymus, but not spleen, cells. The results of this study demonstrate that spaceflight can enhance the production of certain cytokines by cells of the immune system.

Miller, Edwin S.↗

NASA NTRS1998

SSBRP Communication & Data System Development using the Unified Modeling Language (UML)

The Unified Modeling Language (UML) is the standard method for specifying, visualizing, and documenting the artifacts of an object-oriented system under development. UML is the unification of the object-oriented methods developed by Grady Booch and James Rumbaugh, and of the Use Case Model developed by Ivar Jacobson. This paper discusses the application of UML by the Communications and Data Systems (CDS) team to model the ground control and command of the Space Station Biological Research Project (SSBRP) User Operations Facility (UOF). UML is used to define the context of the system, the logical static structure, the life history of objects, and the interactions among objects.

Windrem, May↗

NASA NTRS2019

Design, Prototyping, and Testing of a Novel Flowpath with an Array of Six 3D Matrix Vitvo Bioreactors for the NASA Bioculture System

The NASA Bioculture System is an advanced cell culture closed-loop system containing highly automated flowpaths designed to conduct long term biology experiments on ISS with earth remote controllable medium flow, temperature, gas composition, medium exchange, cell sampling and fixation. This technology was already demonstrated with successful cardiomyocyte and osteocyte cultures experiments onboard the ISS and is now supporting NASA PI science. The Bioculture System, however, can only support 10 cassettes with disposable flowpaths, each containing a single hollow fiber bioreactor with a culture capacity of about 2ml. This constraint not only severely limits the number of investigators that can conduct experiments in space, but also subjects the experiments to limitations in the number of replicates and conditions that can be studied. To address these limitations, we sought a novel design solution to maximize the number of separate bioreactor cultures and volume that can be conducted simultaneously. To this end we designed, prototyped, and are now testing a six-Vitvo 3D Matrix 2ml bioreactor insert that replaces the conventional Bioculture System hollow fiber bioreactor. This design will allow the Bioculture System to support up to 60 different bioreactors and samples at once. Specifically, the novel gas-tight containment housing insert contains six COTS Rigenerand VITVO bioreactors stacked on each side of a heat sink powered by the existing heating element and pair of temperature sensors. Medium will be distributed into each bioreactor's cell-free chamber via its built-in Luer connector, then across the 3D matrix to the cell chamber, dissipating laminar flow and limiting fluid shear stresses that might mechanostimulate cell cultures. Gas (5% CO2 in air) will be supplied directly to the bioreactor gas-tight housing for exchange via the bioreactor flat-surface gas-permeable membranes, eliminating the need for the existing Bioculture System cassette oxygenator. If successfully implemented on ISS, this new multi-bioreactor insert for the Bioculture System has the potential to make real-time cell science experimentation in space more efficient and accessible to more investigators.

Ma, Kristin R.↗

NASA NTRSDate not supplied

KSC to EDEN ISS: Outredgeous Lettuce Growth on the Passive Porous Tube Nutrient Delivery System (PPTNDS)

EDEN ISS is a controlled environment greenhouse established near the Neumayer Station III in Antarcticawith the mission to enable fresh crop production for the crew who are working in this remote location. EDEN provides a space to conduct plant biology and related research in a unique and isolated controlled environment (CE), while providing a platform to test developing methods relevant to long duration manned space missions. In 2021, Kennedy Space Center (KSC) scientist Jess Bunchek fulfilled a one-year mission at EDEN. During that time a variety of fresh crops were grown to record horticultural and microbiological data as well as provide the crew with fresh food to eat. One method for crop growth included an experimental irrigation system called the Passive Porous Tube Nutrient Delivery System (PPTNDS) which was developed at KSC as a microgravity-capable plant irrigation system designed to support Space Plant Biology investigations and/or crop growth during space missions. The PPTNDS was employed to grow Outredgeous Lettuce (OL) during two growouts at EDEN, (harvesting at Day After Planting (DAP) 61 and 63) and two growouts at KSC where plant growth and micro sample data were captured. This paper presents the data collected from the PPTNDS and compares it to growth on a Nutrient Film Technique (NFT) hydroponic system operated in the same environment. The result shows a system that grows OL at a reduced rate compared to the NFT system but uses less water and crew interaction to operate.

Jacob Torres↗

DOE OSTI2022

Allosteric regulation of glycogen breakdown by the second messenger cyclic di-GMP

Streptomyces are our principal source of antibiotics, which they generate concomitant with a complex developmental transition from vegetative hyphae to spores. c-di-GMP acts as a linchpin in this transition by binding and regulating the key developmental regulators, BldD and WhiG. Here we show that c-di-GMP also binds the glycogen-debranching-enzyme, GlgX, uncovering a direct link between c-di-GMP and glycogen metabolism in bacteria. Further, we show c-di-GMP binding is required for GlgX activity. We describe structures of apo and c-di-GMP-bound GlgX and, strikingly, their comparison shows c-di-GMP induces long-range conformational changes, reorganizing the catalytic pocket to an active state. Glycogen is an important glucose storage compound that enables animals to cope with starvation and stress. Our in vivo studies reveal the important biological role of GlgX in Streptomyces glucose availability control. Overall, we identify a function of c-di-GMP in controlling energy storage metabolism in bacteria, which is widespread in Actinobacteria.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2002

Modeling and control for closed environment plant production systems

A computer program was developed to study multiple crop production and control in controlled environment plant production systems. The program simulates crop growth and development under nominal and off-nominal environments. Time-series crop models for wheat (Triticum aestivum), soybean (Glycine max), and white potato (Solanum tuberosum) are integrated with a model-based predictive controller. The controller evaluates and compensates for effects of environmental disturbances on crop production scheduling. The crop models consist of a set of nonlinear polynomial equations, six for each crop, developed using multivariate polynomial regression (MPR). Simulated data from DSSAT crop models, previously modified for crop production in controlled environments with hydroponics under elevated atmospheric carbon dioxide concentration, were used for the MPR fitting. The model-based predictive controller adjusts light intensity, air temperature, and carbon dioxide concentration set points in response to environmental perturbations. Control signals are determined from minimization of a cost function, which is based on the weighted control effort and squared-error between the system response and desired reference signal.

NASA Discipline Life Support Systems↗

DOE OSTI2026

Multiphasic droplet microfluidics platform for controlled bacteria and mammalian cell co-culture

Microfluidics has revolutionized high-throughput miniaturized biological assays. However, co-culture of mammalian cells and bacteria remains challenging in microfluidic systems due to incompatible growth requirements, limited spatial control, and the requirement for a mammalian cell adhesion matrix. Here, we present a microfluidic platform that generates multiphasic droplets which encapsulate mammalian and bacterial cells, enabling their direct and indirect co-culture. By combining photopolymerizable hydrogels with polymer phase separation, we generate core–shell droplets composed of a liquid and a hydrogel compartment. The hydrogel compartment supports mammalian cell adhesion and culture, while the liquid compartment sustains bacterial growth. We demonstrate two droplet architectures that allow physical bacteria–mammalian cell contacts or enforce complete physical separation, representing direct and indirect co-culture. Our multiphasic droplets are stable, customizable, able to sustain co-culture for over 24 hours, and compatible with fluorescence-based cell sorting technologies. Overall, our multiphasic droplet microfluidic platform provides a scalable and versatile tool for high-throughput co-culture and screening of host–microbe interactions.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1966

Marine Biology, volume II

Symposium on marine biology - growth rate, cycles, transportation, photosynthesis, distribution, sampling, nutrition, and light control of natural phytoplankton ecological systems

CONFERENCE↗

DOE OSTI2021

Dynamic control over feedback regulatory mechanisms improves NADPH flux and xylitol biosynthesis in engineered E. coli

We report improved NADPH flux and xylitol biosynthesis in engineered E. coli. Xylitol is produced from xylose via an NADPH dependent reductase. We utilize 2-stage dynamic metabolic control to compare two approaches to optimize xylitol biosynthesis, a stoichiometric approach, wherein competitive fluxes are decreased, and a regulatory approach wherein the levels of key regulatory metabolites are reduced. The stoichiometric and regulatory approaches lead to a 20-fold and 90-fold improvement in xylitol production, respectively. Strains with reduced levels of enoyl-ACP reductase and glucose-6-phosphate dehydrogenase, led to altered metabolite pools resulting in the activation of the membrane bound transhydrogenase and an NADPH generation pathway, consisting of pyruvate ferredoxin oxidoreductase coupled with NADPH dependent ferredoxin reductase, leading to increased NADPH fluxes, despite a reduction in NADPH pools. Furthermore, these strains produced titers of 200 g/L of xylitol from xylose at 86% of theoretical yield in instrumented bioreactors. We expect dynamic control over the regulation of the membrane bound transhydrogenase as well as NADPH production through pyruvate ferredoxin oxidoreductase to broadly enable improved NADPH dependent bioconversions or production via NADPH dependent metabolic pathways.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

DOE Early Career Project Annual Report: Disentangling the factors controlling the emission of bioparticles that act as ice nucleating particles

This report describes the accomplishments, progress, and obstacles encountered during the first project year of the U.S. Department of Energy Biological and Environmental Research program Early Career project, “Disentangling the factors controlling the emission of bioparticles that act as ice nucleating particles.”

54 ENVIRONMENTAL SCIENCES↗