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At least 865 records · Page 48
All sourcesNASA NTRSDOE OSTI
NASA NTRS2022

Design of synthetic collagens that assemble into supramolecular banded fibers as a functional biomaterial testbed

Collagens are the most abundant proteins of the extracellular matrix, and the hierarchical folding and supramolecular assembly of collagens into banded fibers is essential for mediating cell-matrix interactions and tissue mechanics. Collagen extracted from animal tissues is a valuable commodity, but suffers from safety and purity issues, limiting its biomaterials applications. Synthetic collagen biomaterials could address these issues, but their construction requires molecular-level control of folding and supramolecular assembly into ordered banded fibers, comparable to those of natural collagens. Here, we show an innovative class of banded fiber-forming synthetic collagens that recapitulate the morphology and some biological properties of natural collagens. The synthetic collagens comprise a functional-driver module that is flanked by adhesive modules that effectively promote their supramolecular assembly. Multiscale simulations support a plausible molecular-level mechanism of supramolecular assembly, allowing precise design of banded fiber morphology. We also experimentally demonstrate that synthetic fibers stimulate osteoblast differentiation at levels comparable to natural collagen. This work thus deepens understanding of collagen biology and disease by providing a ready source of safe, functional biomaterials that bridge the current gap between the simplicity of peptide biophysical models and the complexity of in vivo animal systems.

Jinyuan Hu↗
DOE OSTI2022

Permeability-Engineered Compartmentalization Enables In Vitro Reconstitution of Sustained Synthetic Biology Systems

In nature, biological compartments such as cells rely on dynamically controlled permeability for matter exchange and complex cellular activities. Likewise, the ability to engineer compartment permeability is crucial for in vitro systems to gain sustainability, robustness, and complexity. However, rendering in vitro compartments such a capability is challenging. Here, a facile strategy is presented to build permeability-configurable compartments, and marked advantages of such compartmentalization are shown in reconstituting sustained synthetic biology systems in vitro. Through microfluidics, the strategy produces micrometer-sized layered microgels whose shell layer serves as a sieving structure for biomolecules and particles. In this configuration, the transport of DNAs, proteins, and bacteriophages across the compartments can be controlled an guided by a physical model. Through permeability engineering, a compartmentalized cell-free protein synthesis system sustains multicycle protein production; ≈100 000 compartments are repeatedly used in a five-cycle synthesis, featuring a yield of 2.2 mg mL -1 . Further, the engineered bacteria-enclosing compartments possess near-perfect phage resistance and enhanced environmental fitness. In a complex river silt environment, compartmentalized whole-cell biosensors show maintained activity throughout the 32 h pollutant monitoring. It is anticipated that permeability-engineered compartmentalization should pave the way for practical synthetic biology applications such as green bioproduction, environmental sensing, and bacteria-based therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Nanolatticed Architecture Mitigates Damage in Shark Egg Cases

Structural versatility and multifunctionality of biological materials have resulted in countless bioinspired strategies seeking to emulate the properties of nature. The nanostructured egg case of swell sharks is one of the toughest permeable membranes known and, thus, presents itself as a model system for materials where the conflicting properties, strength and porosity, are desirable. The egg case possesses an intricately ordered structure that is designed to protect delicate embryos from the external environment while enabling respiratory and metabolic exchange, achieving a tactical balance between conflicting properties. Herein, structural analyses revealed an enabling nanolattice architecture that constitutes a Bouligand-like nanoribbon hierarchical assembly. Three distinct hierarchical architectural adaptations enhance egg case survival: Bouligand-like organization for in-plane isotropic reinforcement, noncylindrical nanoribbons maximizing interfacial stress distribution, and highly ordered nanolattices enabling permeability and lattice-governed toughening mechanisms. Furthermore, these discoveries provide fundamental insights for the improvement of multifunctional membranes, fiber-reinforced soft composites, and mechanical metamaterials.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

Imaging plant metabolism in situ

Abstract Mass spectrometry imaging (MSI) has emerged as an invaluable analytical technique for investigating the spatial distribution of molecules within biological systems. In the realm of plant science, MSI is increasingly employed to explore metabolic processes across a wide array of plant tissues, including those in leaves, fruits, stems, roots, and seeds, spanning various plant systems such as model species, staple and energy crops, and medicinal plants. By generating spatial maps of metabolites, MSI has elucidated the distribution patterns of diverse metabolites and phytochemicals, encompassing lipids, carbohydrates, amino acids, organic acids, phenolics, terpenes, alkaloids, vitamins, pigments, and others, thereby providing insights into their metabolic pathways and functional roles. In this review, we present recent MSI studies that demonstrate the advances made in visualizing the plant spatial metabolome. Moreover, we emphasize the technical progress that enhances the identification and interpretation of spatial metabolite maps. Within a mere decade since the inception of plant MSI studies, this robust technology is poised to continue as a vital tool for tackling complex challenges in plant metabolism.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
NASA NTRS2014

HRP's Healthcare Spin-Offs Through Computational Modeling and Simulation Practice Methodologies

Spaceflight missions expose astronauts to novel operational and environmental conditions that pose health risks that are currently not well understood, and perhaps unanticipated. Furthermore, given the limited number of humans that have flown in long duration missions and beyond low Earth-orbit, the amount of research and clinical data necessary to predict and mitigate these health and performance risks are limited. Consequently, NASA's Human Research Program (HRP) conducts research and develops advanced methods and tools to predict, assess, and mitigate potential hazards to the health of astronauts. In this light, NASA has explored the possibility of leveraging computational modeling since the 1970s as a means to elucidate the physiologic risks of spaceflight and develop countermeasures. Since that time, substantial progress has been realized in this arena through a number of HRP funded activates such as the Digital Astronaut Project (DAP) and the Integrated Medical Model (IMM). Much of this success can be attributed to HRP's endeavor to establish rigorous verification, validation, and credibility (VV&C) processes that ensure computational models and simulations (M&S) are sufficiently credible to address issues within their intended scope. This presentation summarizes HRP's activities in credibility of modeling and simulation, in particular through its outreach to the community of modeling and simulation practitioners. METHODS: The HRP requires all M&S that can have moderate to high impact on crew health or mission success must be vetted in accordance to NASA Standard for Models and Simulations, NASA-STD-7009 (7009) [5]. As this standard mostly focuses on engineering systems, the IMM and DAP have invested substantial efforts to adapt the processes established in this standard for their application to biological M&S, which is more prevalent in human health and performance (HHP) and space biomedical research and operations [6,7]. These methods have also generated substantial interest by the broader medical community though institutions like the National Institutes of Health (NIH) and the Food and Drug Administration (FDA) to develop similar standards and guidelines applicable to the larger medical operations and research community. DISCUSSION: Similar to NASA, many leading government agencies, health institutions and medical product developers around the world are recognizing the potential of computational M&S to support clinical research and decision making. In this light, substantial investments are being made in computational medicine and notable discoveries are being realized [8]. However, there is a lack of broadly applicable practice guidance for the development and implementation of M&S in clinical care and research in a manner that instills confidence among medical practitioners and biological researchers [9,10]. In this presentation, we will give an overview on how HRP is working with the NIH's Interagency Modeling and Analysis Group (IMAG), the FDA and the American Society of Mechanical Engineers (ASME) to leverage NASA's biomedical VV&C processes to establish a new regulatory standard for Verification and Validation in Computational Modeling of Medical Devices, and Guidelines for Credible Practice of Computational Modeling and Simulation in Healthcare.

Mulugeta, Lealem↗
DOE OSTI2020

The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering

The Synthetic Biology Open Language (SBOL) is a community-developed data standard that allows knowledge about biological designs to be captured using a machine-tractable, ontology-backed representation that is built using Semantic Web technologies. While early versions of SBOL focused only on the description of DNA-based components and their sub-components, SBOL can now be used to represent knowledge across multiple scales and throughout the entire synthetic biology workflow, from the specification of a single molecule or DNA fragment through to multicellular systems containing multiple interacting genetic circuits. The third major iteration of the SBOL standard, SBOL3, is an effort to streamline and simplify the underlying data model with a focus on real-world applications, based on experience from the deployment of SBOL in a variety of scientific and industrial settings. Here, we introduce the SBOL3 specification both in comparison to previous versions of SBOL and through practical examples of its use.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Statistical Uncertainty of Inhalation Dose Coefficients: Impact of Particle Deposition in ICRP 66 Human Respiratory Tract Model

Inhaled radioactive materials can pose a long-term health concern, as the material can be incorporated into the body’s metabolic pathways and remain in organs and tissues for extended durations. During the retention period, the radioactive material may localize in a source organ and irradiate adjacent target organs and tissues. Distribution of these materials changes over time, requiring biokinetic modeling to evaluate their movement through various tissues and organs. The evolving distribution depends on multiple inputs characterizing the inhaled material, such as particle size and size distribution, particle density, aspect ratio, specific radionuclide, the chemical form, and solubility. In addition, biological parameters such as breathing rate, breathing type (nasal or nasal/oral), respiratory system morphometry, tidal volume, functional residual capacity, and anatomical dead space all influence material transport. These aerosol properties and physiological characteristics of the respiratory tract jointly define a range of initial conditions that influence the time-dependent distribution of radioactive material. To evaluate both uncertainty in the initial conditions of inhalation exposure and the final output (committed effective dose) from biokinetic models, a Python-based software tool, Radiological Exposure Dose Calculator (REDCAL), was developed to propagate uncertainty within the human respiratory tract model. Focusing on deposition fraction uncertainty, the primary objective was to characterize the initial activity distribution across respiratory regions as a function of anticipated particle sizes and distributions. The impact of the deposition fraction uncertainty was propagated to committed effective dose coefficients for selected radionuclides in a companion publication. For each particle size, a lognormal distribution, characterized by its geometric mean as defined within ICRP Publication 66, serves as the basis for introducing uncertainty into the physical processes governing deposition in various lung regions. Finally, this study addresses the deposition process and examines how uncertainty in deposition mechanisms affects activity distribution in the airways, ultimately presenting the expected range and standard deviation of deposited activity as a function of particle size.

International Commission on Radiological Protectio↗
NASA NTRS1997

Gravitational Biology: The Rat Model

In this session, Session JP3, the discussion focuses on the following topics: Morphology of brain, pituitary and thyroid in the rats exposed to altered gravity; Biochemical Properties of B Adrenoceptors After Spaceflight (LMS-STS78) or Hindlimb Suspension in Rats; Influence of Hypergravity on the Development of Monoaminergic Systems in the Rat Spinal Cord; A Vestibular Evoked Potentials (VsEPs) Study of the Function of the Otolith Organs in Different Head Orientations with respect to Earth Gravity Vector in the Rat; Quantitative Observations on the Structure of Selected Proprioceptive Components in Adult Rats that Underwent About Half of their Fetal Development in Space; Effects of a Nine-Day Shuttle Mission on the Development of the Neonatal Rat Nervous System, A Behavioral Study; Muscle Atrophy Associated to Microgravity in Rat, Basic Data For Countermeasures; Simulated Weightlessness by Unloading in the Rat, Results of a Time Course Study of Biochemical Events Occurring During Unloading and Lack of Effect of a rhBNP-2 Treatment on Bone Formation and Bone Mineral Content in Unloading Rats; and Cytological Mechanism of the Osteogenesis Under Microgravity Conditions.

Source record↗
DOE OSTI2026

Soil metagenomics umbrella narrative

Implementing accessible, authentic research experiences in introductory courses is challenging, particularly at institutions serving diverse student populations. To address this gap, we developed and deployed a Course-based Undergraduate Research Experience (CURE) focused on plant-microbe interactions in General Biology II at Northeastern Illinois University (NEIU), a minority-serving institution with a diverse student body. Students grew sugar beets (Beta vulgaris), extracted DNA from the rhizoplane, and used the Department of Energy Systems Biology Knowledgebase (KBase) for bioinformatic analysis to compare microbial relative abundance in fertilized versus unfertilized soil. Over five semesters, the CURE engaged 103 students and leveraged the intuitive KBase platform to make complex sequencing data accessible. Pre/post-course survey data revealed significant increases in student self-assessed research skills, including the ability to explain results and determine the types of data to collect. Furthermore, students reported significant gains in confidence related to experimental design and hypothesis development, alongside a strong increase in familiarity with KBase. Informal faculty feedback indicated high student engagement and appreciation for the real-world connections (e.g. food systems, agriculture, and health). This scalable, low-cost model effectively integrates data science tools into the foundational curriculum, demonstrating a potent strategy for boosting research skills and broadening participation in authentic scientific inquiry among diverse undergraduate students.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Task 2.1: Adsorption-Based ISPR for BETO-Relevant Bioproducts

This task focuses on the development of adsorption-based in situ product recovery (ISPR) integrated with simulated moving bed chromatography for the recovery and purification of carboxylate products that are relevant to BETO. ISPR has been pursued previously in the Separations Consortium to recover carboxylic acids near or below their pKa values with liquid-liquid extraction coupled to downstream distillation. However, there are many acid products in the BETO portfolio that require neutralization well above their pKa values wherein ISPR could still be a major benefit to the bioprocess performance, including muconic acid, beta-ketoadipic acid, 3-hydroxypropionic acid, itaconic acid, butyric acid, and others. In this task, we are combining dynamic filtration with a rotating ceramic disk, resin capacity measurements, tailored resin synthesis, and simulated moving bed chromatography into an ISPR system that can be used to recover BETO-relevant carboxylates from bioreactor cultivations. We are working across process scales and using computational modeling where applicable alongside techno-economic analysis and life cycle assessment to understand major cost, energy, and GHG emissions drivers. The impact of this project will be a bench-scale integrated approach to recover carboxylate products in situ, which will reduce the waste generation from biological carboxylate production processes and improve the productivities of biological systems.

bio-based acid↗
DOE OSTI2023

Establishment of a genome editing tool using CRISPR-Cas9 ribonucleoprotein complexes in the non-model plant pathogen Sphaerulina musiva

CRISPR-Cas9 is a versatile genome editing system widely used since 2013 to introduce site-specific modifications into the genomes of model and non-model species. This technology is used in various applications, from gene knock-outs, knock-ins, and over-expressions to more precise changes, such as the introduction of nucleotides at a targeted locus. CRISPR-Cas9 has been demonstrated to be easy to establish in new species and highly efficient and specific compared to previous gene editing strategies such as Zinc finger nucleases and transcription activator-like effector nucleases. Grand challenges for emerging CRISPR-Cas9 tools in filamentous fungi are developing efficient transformation methods for non-model organisms. In this paper, we have leveraged the establishment of CRISPR-Cas9 genome editing tool that relies on Cas9/sgRNA ribonucleoprotein complexes (RNPs) in the model species Trichoderma reesei and developed the first protocol to efficiently transform the non-model species, Sphaerulina musiva. This fungal pathogen constitutes a real threat to the genus Populus, a foundational bioenergy crop used for biofuel production. Herein, we highlight the general considerations to design sgRNAs and their computational validation. We also describe the use of isolated protoplasts to deliver the CRISPR-Cas9 RNP components in both species and the screening for targeted genome editing events. The development of engineering tools in S. musiva can be used for studying genes involved in diverse processes such as secondary metabolism, establishment, and pathogenicity, among many others, but also for developing genetic mitigation approaches. The approach described here provides guidance for potential development of transformation systems in other non-model spore-bearing ascomycetes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Leaf angle as a leaf and canopy trait: Rejuvenating its role in ecology with new technology

Abstract Life on Earth depends on the conversion of solar energy to chemical energy by plants through photosynthesis. A fundamental challenge in optimizing photosynthesis is to adjust leaf angles to efficiently use the intercepted sunlight under the constraints of heat stress, water loss and competition. Despite the importance of leaf angle, until recently, we have lacked data and frameworks to describe and predict leaf angle dynamics and their impacts on leaves to the globe. We review the role of leaf angle in studies of ecophysiology, ecosystem ecology and earth system science, and highlight the essential yet understudied role of leaf angle as an ecological strategy to regulate plant carbon–water–energy nexus and to bridge leaf, canopy and earth system processes. Using two models, we show that leaf angle variations have significant impacts on not only canopy‐scale photosynthesis, energy balance and water use efficiency but also light competition within the forest canopy. New techniques to measure leaf angles are emerging, opening opportunities to understand the rarely‐measured intraspecific, interspecific, seasonal and interannual variations of leaf angles and their implications to plant biology and earth system science. We conclude by proposing three directions for future research.

Yang, Xi↗
NASA NTRS2019

Using the NASA GeneLab Data System to Study the Metagenomes of Spaceships and Their Occupants

With humans pushing to live further off Earth for longer periods of time, it is increasingly important to understand the changes that occur in biological systems during spaceflight whether these be astronauts, their microbial commensals, or their plant-based life support systems. In a three-part presentation, we discuss GeneLab and recent discoveries regarding the microbiota of spacecrafts and space-flown animals. Part 1: GeneLab: Open Science for Life in Space, Jonathan Galazka, NASA Ames Research Center To accelerate the pace of discovery from precious spaceflight biological experiments, NASA as develop the GeneLab data system (genelab.nasa.gov), which allows unfettered access to omics data from spaceflight and spaceflight relevant experiments. GeneLab houses metagenomic datasets from spacecraft and relevant spacecraft models. Users can download this data and associated metadata to make new discoveries about how microbial communities may change and adapt to spaceflight.

Galazka, Jonathan M.↗
DOE OSTI2021

Diazotrophic Bacteria and Their Mechanisms to Interact and Benefit Cereals

Plant-growth-promoting bacteria (PGPB) stimulate plant growth through diverse mechanisms. In addition to biological nitrogen fixation, diazotrophic PGPB can improve nutrient uptake efficiency from the soil, produce and release phytohormones to the host, and confer resistance against pathogens. The genetic determinants that drive the success of biological nitrogen fixation in nonlegume plants are understudied. These determinants include recognition and signaling pathways, bacterial colonization, and genotype specificity between host and bacteria. This review presents recent discoveries of how nitrogen-fixing PGPB interact with cereals and promote plant growth. We suggest adopting an experimental model system, such as the Setaria–diazotrophic bacteria association, as a reliable way to better understand the associated mechanisms and, ultimately, increase the use of PGPB inoculants for sustainable agriculture. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Biochemistry & Molecular Biology↗
DOE OSTI2021

Searching for fat tails in CRISPR-Cas systems: Data analysis and mathematical modeling

Understanding CRISPR-Cas systems—the adaptive defence mechanism that about half of bacterial species and most of archaea use to neutralise viral attacks—is important for explaining the biodiversity observed in the microbial world as well as for editing animal and plant genomes effectively. The CRISPR-Cas system learns from previous viral infections and integrates small pieces from phage genomes called spacers into the microbial genome. The resulting library of spacers collected in CRISPR arrays is then compared with the DNA of potential invaders. One of the most intriguing and least well understood questions about CRISPR-Cas systems is the distribution of spacers across the microbial population. Here, using empirical data, we show that the global distribution of spacer numbers in CRISPR arrays across multiple biomes worldwide typically exhibits scale-invariant power law behaviour, and the standard deviation is greater than the sample mean. We develop a mathematical model of spacer loss and acquisition dynamics which fits observed data from almost four thousand metagenomes well. In analogy to the classical ‘rich-get-richer’ mechanism of power law emergence, the rate of spacer acquisition is proportional to the CRISPR array size, which allows a small proportion of CRISPRs within the population to possess a significant number of spacers. Our study provides an alternative explanation for the rarity of all-resistant super microbes in nature and why proliferation of phages can be highly successful despite the effectiveness of CRISPR-Cas systems.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2001

Neuroprotection for the new millennium. Matchmaking pharmacology and technology

A major theme of the 1990s in the pathophysiology of nervous system injury has been the multifactorial etiology of irreversible injury. Multiple causes imply multiple opportunities for therapeutic intervention--hence the abandonment of the "magic bullet" single pharmacologic agent for neuroprotection in favor of pharmacologic "cocktails". A second theme of the 1990s has been the progress in technology for neuroprotection, minimally- or non-invasive monitoring as well as treatment. Cardiac stenting has eliminated the need, in many cases, for open heart surgery; deep brain stimulation for Parkinson's disease has offered significant improvement in quality of life for many who had exhausted cocktail drug treatment for their disease. Deep brain stimulation of the subthalamic nucleus offers a novel treatment for Parkinson's disease where a technological advance may actually be an intervention with effects that are normally expected from pharmacologic agents. Rather than merely "jamming" the nervous system circuits involved in Parkinson's disease, deep brain stimulation of the subthalamic nucleus appears to improve the neurotransmitter imbalance that lies at the heart of Parkinson's disease. It may also slow the progression of the disease. Given the example of deep brain stimulation of the subthalamic nucleus for Parkinson's disease, in future one may expect other technological or "hardware" interventions to influence the programming or "software" of the nervous system's physiologic response in certain disease states.

Review Literature↗
NASA NTRS2003

Tensegrity II. How structural networks influence cellular information processing networks

The major challenge in biology today is biocomplexity: the need to explain how cell and tissue behaviors emerge from collective interactions within complex molecular networks. Part I of this two-part article, described a mechanical model of cell structure based on tensegrity architecture that explains how the mechanical behavior of the cell emerges from physical interactions among the different molecular filament systems that form the cytoskeleton. Recent work shows that the cytoskeleton also orients much of the cell's metabolic and signal transduction machinery and that mechanical distortion of cells and the cytoskeleton through cell surface integrin receptors can profoundly affect cell behavior. In particular, gradual variations in this single physical control parameter (cell shape distortion) can switch cells between distinct gene programs (e.g. growth, differentiation and apoptosis), and this process can be viewed as a biological phase transition. Part II of this article covers how combined use of tensegrity and solid-state mechanochemistry by cells may mediate mechanotransduction and facilitate integration of chemical and physical signals that are responsible for control of cell behavior. In addition, it examines how cell structural networks affect gene and protein signaling networks to produce characteristic phenotypes and cell fate transitions during tissue development.

Review↗
DOE OSTI2021

Characterizing Machine Learning I/O Workloads on Leadership Scale HPC Systems

High performance computing (HPC) is no longer solely limited to traditional workloads such as simulation and modeling. With the increase in the popularity of machine learning (ML) and deep learning (DL) technologies, we are observing that an increasing number of HPC users are incorporating ML methods into their workflow and scientific discovery processes, across a wide spectrum of science domains such as biology, earth science, and physics. This gives rise to a diverse set of I/O patterns than the traditional checkpoint/restart-based HPC I/O behavior. The details of the I/O characteristics of such ML I/O workloads have not been studied extensively for large-scale leadership HPC systems. This paper aims to fill that gap by providing an in-depth analysis to gain an understanding of the I/O behavior of ML I/O workloads using darshan - an I/O characterization tool designed for lightweight tracing and profiling. We study the darshan logs of more than 23, 000 HPC ML I/O jobs over a time period of one year running on Summit - the second-fastest supercomputer in the world. This paper provides a systematic I/O characterization of ML I/O jobs running on a leadership scale supercomputer to understand how the I/O behavior differs across science domains and the scale of workloads, and analyze the usage of parallel file system and burst buffer by ML I/O workloads.

Paul, Arnab↗