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NASA NTRS2010

Automated Desalting Apparatus

Because salt and metals can mask the signature of a variety of organic molecules (like amino acids) in any given sample, an automated system to purify complex field samples has been created for the analytical techniques of electrospray ionization/ mass spectroscopy (ESI/MS), capillary electrophoresis (CE), and biological assays where unique identification requires at least some processing of complex samples. This development allows for automated sample preparation in the laboratory and analysis of complex samples in the field with multiple types of analytical instruments. Rather than using tedious, exacting protocols for desalting samples by hand, this innovation, called the Automated Sample Processing System (ASPS), takes analytes that have been extracted through high-temperature solvent extraction and introduces them into the desalting column. After 20 minutes, the eluent is produced. This clear liquid can then be directly analyzed by the techniques listed above. The current apparatus including the computer and power supplies is sturdy, has an approximate mass of 10 kg, and a volume of about 20 20 20 cm, and is undergoing further miniaturization. This system currently targets amino acids. For these molecules, a slurry of 1 g cation exchange resin in deionized water is packed into a column of the apparatus. Initial generation of the resin is done by flowing sequentially 2.3 bed volumes of 2N NaOH and 2N HCl (1 mL each) to rinse the resin, followed by .5 mL of deionized water. This makes the pH of the resin near neutral, and eliminates cross sample contamination. Afterward, 2.3 mL of extracted sample is then loaded into the column onto the top of the resin bed. Because the column is packed tightly, the sample can be applied without disturbing the resin bed. This is a vital step needed to ensure that the analytes adhere to the resin. After the sample is drained, oxalic acid (1 mL, pH 1.6-1.8, adjusted with NH4OH) is pumped into the column. Oxalic acid works as a chelating reagent to bring out metal ions, such as calcium and iron, which would otherwise interfere with amino acid analysis. After oxalic acid, 1 mL 0.01 N HCl and 1 mL deionized water is used to sequentially rinse the resin. Finally, the amino acids attached to the resin, and the analytes are eluted using 2.5 M NH4OH (1 mL), and the NH4OH eluent is collected in a vial for analysis.

Spencer, Maegan K.↗

NASA NTRS2003

Tensegrity I. Cell structure and hierarchical systems biology

In 1993, a Commentary in this journal described how a simple mechanical model of cell structure based on tensegrity architecture can help to explain how cell shape, movement and cytoskeletal mechanics are controlled, as well as how cells sense and respond to mechanical forces (J. Cell Sci. 104, 613-627). The cellular tensegrity model can now be revisited and placed in context of new advances in our understanding of cell structure, biological networks and mechanoregulation that have been made over the past decade. Recent work provides strong evidence to support the use of tensegrity by cells, and mathematical formulations of the model predict many aspects of cell behavior. In addition, development of the tensegrity theory and its translation into mathematical terms are beginning to allow us to define the relationship between mechanics and biochemistry at the molecular level and to attack the larger problem of biological complexity. Part I of this two-part article covers the evidence for cellular tensegrity at the molecular level and describes how this building system may provide a structural basis for the hierarchical organization of living systems--from molecule to organism. Part II, which focuses on how these structural networks influence information processing networks, appears in the next issue.

NASA Program Fundamental Space Biology↗

DOE OSTI2022

Photochemical micromotor of eccentric core in isotropic hollow shell exhibiting multimodal motion behavior

Adaptive motion behavior in response to different environmental stimuli is ubiquitous in biology and enables creatures to achieve a diversity of complex tasks, but not typically observed in synthetic systems. In this report we propose a design of chemically-powered micromotors actively performing multimodal motion behaviors with the external stimulus changing. They have isotropic outer surfaces but inherent inner mass asymmetry, such as eccentric core-in-hollow shell TiO 2 (E-TiO 2 ) microspheres. Their motion behavior can be spontaneously transformed among random Brownian propulsion (stochastic walk), negative phototaxis (moving against incident light), and negative photogravitaxis (moving against gravity) when the light intensity, illumination direction, or fuel concentration change. At a low light intensity and/or low H 2 O 2 fuel concentration, the E-TiO 2 micromotors perform directional movement away from light based on the dominated diffusiophoresis by the photocatalytic reaction over the isotropic shell. With the increase of light intensity or fuel concentration, there are more and more photons or fuels to reach the eccentric core and the contribution of the photocatalytic reaction over it to the diffusiophoresis gradually becomes dominant. In this case, the E-TiO 2 micromotors perform stochastic walks near the substrate due to their Brownian random rotational reorientations. The micromotors are single component, have low density, and can be synthesized in a large scale and at a low cost. This work will facilitate the development of multifunctional micro/nanomotors with varying behaviors and functions depending on environmental cues, e.g., enabling efficient search and delivery operations.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Optogenetics and biosensors set the stage for metabolic cybergenetics

We report cybergenetic systems use computer interfaces to enable feed-back controls over biological processes in real time. The complex and dynamic nature of cellular metabolism makes cybergenetics attractive for controlling engineered metabolic pathways in microbial fermentations. Cybergenetics would not only create new avenues of research into cellular metabolism, it would also enable unprecedented strategies for pathway optimization and bioreactor operation and automation. Implementation of metabolic cybergenetics, however, will require new capabilities from actuators, biosensors, and control algorithms. The recent application of optogenetics in metabolic engineering, the expanding role of genetically encoded biosensors in strain development, and continued progress in control algorithms for biological processes suggest that this technology will become available in the not so distant future.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Solvation directed morphological control in metal oxide nanostructures

The development of structural hierarchy on various length scales during the crystallization process is ubiquitous in biological systems and minerals and is common in synthetic nanomaterials. The driving forces for the formation of complex architectures range from local interfacial interactions, that modify interfacial speciation, local supersaturation, and nucleation barriers, to macroscopic interparticle forces. Although it is enticing to interpret the formation of hierarchical architectures as the assembly of independently nucleated building blocks, crystallization pathways often follow monomer-by-monomer addition with structural complexity arising from interfacial chemical coupling and strongly correlated fluctuation dynamics in the electric double layers. Here, we show that the development of structural hierarchy through heterogeneous nucleation is driven by dipolar and solvation forces. Specifically, coupled simulations and experimental studies revealed that dipole build-up along the slow growth direction can trigger twinning and the development of branched architectures. Enthalpic solvation interactions were shown to either enhance or reduce the dipole moment of the nanoparticles and, thereby, control crystal morphology and architecture. The systematic studies of chemical coupling between different solvents and undercoordinated surface atoms of the growing nanocrystals revealed the mechanism of dimensionality control and the development of structural hierarchy without ligands or structure-directing agents.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2022

Double and Charge-Transfer Excitations in Time-Dependent Density Functional Theory

Time-dependent density functional theory has emerged as a method of choice for calculations of spectra and response properties in physics, chemistry, and biology, with its system-size scaling enabling computations on systems much larger than otherwise possible. While increasingly complex and interesting systems have been successfully tackled with relatively simple functional approximations, there has also been increasing awareness that these functionals tend to fail for certain classes of approximations. Here I review the fundamental challenges the approximate functionals have in describing double excitations and charge-transfer excitations, which are two of the most common impediments for the theory to be applied in a black-box way. At the same time, I describe the progress made in recent decades in developing functional approximations that give useful predictions for these excitations.

Chemistry↗

DOE OSTI2025

Human Coronavirus-229E Hijacks Key Host-Cell RNA-Processing Complexes for Replication

The recent rise in zoonotic coronavirus outbreaks underscores the urgency to understand virus-host interactions and develop potent antiviral therapeutics. Systems biology approaches, particularly proteomics have been invaluable in providing a global overview of such interactions. However, these conventional approaches rely on measuring protein abundance changes which don’t reflect functional shifts. In this study, we employed a high-throughput structural proteomics approach called limited proteolysis-based mass spectrometry (LiP-MS) to capture conformational changes, which we demonstrate are better proxies for functional alterations. We applied this tool to both immortalized and primary human lung cells following human coronavirus 229E (HCoV-229E) infection. We identified significant infection-induced structural changes within RNA processing complexes such as the spliceosome-C and NOP56-associated complex. These observations emphasize that HCoV-229E infection propagates a multi-pronged effort to obstruct the house keeping RNA processing functions in the host. Finally, we show that HCoV-229E replication can be attenuated by the targeted disruption of these complexes, indicating that the identified cellular factories are viable targets to prevent coronavirus infection.

coronavirus↗

DOE OSTI2025

BCARS Simulated Phantom Dataset for Evaluation of Processing Pipelines

Broadband coherent anti-Stokes Raman scattering (BCARS) microscopy is a powerful label-free biological imaging technique, but the raw signal requires careful processing. The vibrationally resonant (Raman) fingerprint signal is usually small compared with instrumental noise sources and the nonresonant background (NRB) inherent in the BCARS signal. Fortunately, the NRB exhibits a systematic phase relationship with the coherent Raman response, acting as a heterodyne amplifier for the weak fingerprint signal. Due to this heterodyne effect, the Raman response can be recovered quantitatively and invariantly across different instruments, provided the NRB shape is known. Even with heterodyne amplification, the amplitudes of fingerprint signal components are often comparable to system noise. Singular value decomposition (SVD), which utilizes spatial information, is often employed for additional noise filtering. Consequently, finding optimal processing parameters to properly distinguish the NRB and Raman responses and suppress noise in the complex BCARS signal requires a reference system that realistically represents the spectral and spatial properties of BCARS signals obtained from biological samples. We present a digital tissue phantom that meets these criteria as a tool for testing candidate signal processing pipelines. The digital phantom is generated with simulated hyperspectral Raman images having system-specific noise and background characteristics. Here, we analyze phantom datasets with differing background and signal-to-noise conditions to evaluate their impact on the performance of multiple signal processing pipelines. Specifically, we investigate the application of a Butterworth filter-based routine to directly estimate the NRB from the BCARS signal. Additionally, we evaluate a Lorentzian wavelet transform as an alternative to the Hilbert transform for extracting the Raman spectrum from the BCARS signal. While we demonstrate this phantom for BCARS, it can be used for any spectroscopic Raman imaging approach.

Dixon, Jessica Z. [Georgia Institute of Technology↗

DOE OSTI2020

A Bioinspired Multicomponent Catalytic System for Converting Carbon Dioxide into Methanol Autocatalytically

Nature utilizes multicomponent catalyst systems to convert simple, abundant starting materials to complex molecules that are essential for life. In contrast, synthetic chemical transformations rarely adopt this strategy because the sophisticated supramolecular assemblies used by biology for active site separation and substrate trafficking are difficult to replicate. Herein, a method is described for multicomponent catalyst separation that involves encapsulating transition metal complexes in nanoporous materials called metal-organic frameworks. The multicomponent catalyst system was highly active for converting hydrogen and carbon dioxide to methanol, and it could be formulated so that it is readily recyclable. Moreover, an autocatalytic feature was uncovered that was only made possible by utilizing the multicomponent catalyst strategy employed. Furthermore, these results open avenues for obtaining fuel from abundant and renewable resources.

08 HYDROGEN↗

DOE OSTI2023

Influence of aluminum incorporation and aqueous conditions on metal ion release of high-Ni transition metal oxide nanomaterials

Developing a materials perspective of how to control the degradation and negative impact of complex metal oxides requires an integrated understanding of how these nanomaterials transform in the environment and interact with biological systems. Doping with aluminum is known to stabilize oxide materials, but has not been assessed cohesively from synthesis to environmental fate and biological impact. In the present study, the influence of aluminum doping on metal ion release from transition metal oxides was investigated by comparing aqueous transformations of lithium nickel cobalt aluminum oxide (LiNi 0.82 Co 0.15 Al 0.03 O 2 ; NCA) and lithium nickel cobalt oxide (LiNi 0.80 Co 0.20 O 2 ; NC) nanoparticles and by calculating the energetics of metal release using a density functional theory (DFT) and thermodynamics method. Two model environmental organisms were used to assess biological impact, and metal ion release was compared for NCA and NC nanoparticles incubated in their respective growth media: moderately hard reconstituted water (MHRW) for the freshwater invertebrate Daphnia magna (D. magna) and minimal growth medium for the Gram-negative bacterium Shewanella oneidensis MR-1 (S. oneidensis). Further, the amount of metal ions released was reduced for NCA compared to NC in MHRW, which correlated to changes in the modeled energetics of release upon Al substitution in the lattice. In minimal medium, metal ion release was approximately an order of magnitude higher compared to MHRW and was similar to the stoichiometry of the bulk nanoparticles for both NCA and NC. Interpretation of the release profiles and modeling indicated that the increase in total metal ion release and the reduced influence of Al doping arises from lactate complexation of metal ions in solution. The relative biological impacts of NC and NCA exposure for both S. oneidensis and D. magna were consistent with the metal release trends observed for minimal medium and MHRW, respectively. Together, these results demonstrate how a combined experimental and computational approach provides valuable insight into the aqueous transformations and biological impacts of complex metal oxide nanoparticles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Structural insights into the assembly and the function of the plant oxidative phosphorylation system

One of the key functions of mitochondria is the production of ATP to support cellular metabolism and growth. The last step of mitochondrial ATP synthesis is performed by the oxidative phosphorylation (OXPHOS) system, an ensemble of protein complexes embedded in the inner mitochondrial membrane. In the last 25 yr, many structures of OXPHOS complexes and supercomplexes have been resolved in yeast, mammals, and bacteria. However, structures of plant OXPHOS enzymes only became available very recently. In this review, we highlight the plant-specific features revealed by the recent structures and discuss how they advance our understanding of the function and assembly of plant OXPHOS complexes. Here we also propose new hypotheses to be tested and discuss older findings to be re-evaluated. Further biochemical and structural work on the plant OXPHOS system will lead to a deeper understanding of plant respiration and its regulation, with significant agricultural, environmental, and societal implications.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRSDate not supplied

The Search for Chiral Asymmetry as a Potential Biosignature in Samples from Mars

The search for evidence of extraterrestrial life in our solar system is currently guided by our understanding of terrestrial biology and its associated biosignatures. The observed homochirality in all life on Earth, that is, the predominance of “left-handed” or L-amino acids and “right-handed” or D-sugars, is a unique property of life that is crucial for molecular recognition, enzymatic function, information storage and structure and is thought to be a prerequisite for the origin or early evolution of life. Therefore, the detection of L- or D-enantiomeric excesses of chiral amino acids and sugars could be a powerful indicator of extant or extinct life on Mars or other habitable environments in our solar system. The exploration of habitable environments on Mars, including an assessment of the preservation potential for complex organics of either abiotic or biological origin, remains a key goal of both current and future Mars missions. Now with the unambiguous detection of indigenous organic matter in sedimentary rocks on Mars [1-3], NASA’s Curiosity rover has significantly advanced our understanding of the preservation of potential chemical biosignatures in the martian near surface. Although amino acids have not yet been identified by in situ measurements on Mars, if they were present, it is expected that amino acid hydrolysis and racemization would be very slow and any chiral or isotopic signatures from an extinct martian biota could be preserved for billions of years, given the extremely cold and dry surface conditions [4]. One of ESA’s Rosalind Franklin rover payload instruments called the Mars Organic Molecule Analyzer (MOMA) includes a wet chemistry package capable of measuring the enantiomeric ratios of any chiral amino acids present at part-per-million concentrations or higher [5]. The complexity and limited duration of spaceflight operations and the known analytical challenges associated with in situ extraction and characterization of trace reduced organic compounds in ancient rocks make it challenging to determine the origins of martian organic matter found to date. Coordinated state-of-the-art laboratory measurements of returned samples from Mars that include spatially resolved chemical, mineralogical, and isotopic studies and molecule-specific isotopic and enantiomeric measurements will be required to firmly establish whether the complex organic matter detected on Mars comes from biotic or abiotic sources. Ultimately, sample return may be our best chance of identifying chemical biosignatures from a past or present martian biota, if one ever existed on Mars. NASA’s Perseverance rover will collect dozens of surface sample cores for possible future return to Earth by NASA and ESA. Here we review our current knowledge of the distributions and enantiomeric and isotopic compositions of non-biological amino acids found in meteorites compared to terrestrial biochemistry and propose a set of measurement criteria that should be used to help establish the origin of any chiral asymmetry detected in samples from Mars [6].

Daniel P Glavin↗

NASA NTRS1993

Measuring the dynamics of structural changes in biological macromolecules from light scattering data

Examining techniques to study the dynamics of structural changes in various molecules has been an ongoing goal of the space program. Knowing how these phenomena occur in biological systems is fundamental to understanding what is necessary for life to remain functional in the space environment. A hierarchy of biological organization is functionally described when cells join together small organic molecules to form larger and more complex molecules. Characterizing the architecture of a particular macromolecule helps determine how that molecule works in the living cell and is basic to the diversity of life. Understanding this arrangement involves the correlation of the structure of macromolecules with their functions. A light scattering photometer was developed for detecting continuous measurement of the angular spectrum of light scattered by dynamically changing systems. The analysis of light scattered by biological macromolecules can be used to determine concentration, size, shape, molecular weight, and structural changes of cells, such as erythrocytes. Some light scattering photometers can collect and store 120 angular scattering spectra per minute, with an angular resolution of 0.2 deg which can be displayed with computer graphics. The light scattering photometer does the following: functions to produce and detect scattered light; determines scatter angles; and collects, stores, and analyzes data.

Johnson, Adriel D.↗

DOE OSTI2021

Designing Sequence-Defined Peptoids for Biomimetic Control over Inorganic Crystallization

Crystallization defines what the world is all about, ranging from biomineralization in living organisms to various materials in our lives. During these processes, biomineralization set a superexcellent example of the additive-controlled crystallization. However, the high complexity and low stability of peptides and proteins preclude their wide applications in controlling inorganic crystallization beyond the biological systems. Peptoids are one type of sequence-defined biomimetic polymers with a simple structure, high stability, protein-like molecular recognition, and distinctive self-assembly properties. They provide a promising alternative to mimic peptides and proteins for controlling inorganic crystallization and extend its application to predictive materials synthesis. In this review article, we extract the main concepts of peptoid engineering and highlight the recent advances in peptoid-controlled inorganic crystallization. Our focus is to understand the principles of sequence engineering that lead to the predictable physiochemical properties of these substances, which will give insights into other inorganic systems.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Design, tuning, and blackbox optimization of laser systems

Chirped pulse amplification (CPA) and subsequent nonlinear optical (NLO) systems constitute the backbone of myriad advancements in semiconductor manufacturing, communications, biology, defense, and beyond. Accurately and efficiently modeling CPA+NLO-based laser systems is challenging because of the complex coupled processes and diverse simulation frameworks. Our modular start-to-end model unlocks the potential for exciting new optimization and inverse design approaches reliant on data-driven machine learning methods, providing a means to create tailored CPA+NLO systems unattainable with current models. To demonstrate this new, to our knowledge, technical capability, we present a study on the LCLS-II photo-injector laser, representative of a high-power and spectro-temporally non-trivial CPA+NLO system.

47 OTHER INSTRUMENTATION↗

NASA NTRS1981

Membrane lipids and the origin of life

The current state of knowledge regarding the development of biological systems is briefly reviewed. At a crucial stage concerning the evolution of such systems, the mechanisms leading to more complex structures must have evolved within the confines of a protected microenvironment, similar to those provided by the contemporary cell membranes. The major components found normally in biomembranes are phospholipids. The structure of the biomembrane is examined, and attention is given to questions concerning the availability of the structural components which are necessary in the formation of primitive lipid membranes. Two approaches regarding the study of protomembranes are discussed. The probability of obtaining ether lipids under prebiotic conditions is considered, taking into account the formation of cyclic and acyclic isoprenoids by the irradiation of isoprene with UV.

Oro, J.↗

NASA NTRS1977

The capuchin monkey as a flight candidate

The highly evolved nervous system and associated complex behavioral capabilities of the nonhuman primates make them good candidates for certain studies in the space environment since deleterious changes in these more complex aspects of a biological status can only be demonstrated by species which share such highly evolved features with man. Important assets which urge the selection of the capuchin monkey for space experiments include his small size, high intelligence, relative disease resistance, nutritional requirements, and lower volume life support systems. The species is particularly suited for experiments on the nervous system or on process under neural control because of the similarity of capuchin and human blood chemistry profiles and endocrine systems involved in the maintenance of homeostasis and vasomotor tone.

Winget, C. M.↗

DOE OSTI2021

A near-infrared optical nanosensor for measuring aerobic respiration in microbial systems

We developed a ratiometric oxygen-sensitive nanosensor and demonstrated application in monitoring metabolic oxygen consumption in microbial samples over time. Based on a near-infrared (NIR) emitting oxygen-quenched luminophore, platinum(II) octaethylporphine ketone (PtOEPK), along with a stable dioctadecyl dicarbocyanine reference dye (DiD), this nanosensor system provides an advantageous approach for overcoming imaging issues in biological systems, such as autofluorescence and optical scattering in the visible wavelength region. The dyes are encapsulated within a polymer-based nanoparticle matrix to maintain them at a constant ratio in biological samples, precluding the need for complex synthetic approaches. With this constant ratio of the two dyes, the nanosensor response can be measured as a ratio of their two signals, accounting for nanosensor concentration artifacts in measurements. The nanosensors are reversible, which enabled us to temporally monitor systems in which dissolved oxygen concentrations both increase and decrease. These sensors were applied for the monitoring of oxygen in samples of Saccharomyces cerevisiae (brewing yeast) in a 96-well optical fluorescence plate reader format over 60 h. By mixing the nanosensors directly into the sample well with the yeast, we were able to dynamically track metabolic activity changes over time due to varying cell concentration and exposure to an antimicrobial agent. As a result, this system could be a potential platform for high-throughput screening of various species or variants of microbes with unknown metabolic rates in response to external stimuli (antimicrobials, metabolites, etc.).

59 BASIC BIOLOGICAL SCIENCES↗