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At least 505 records · Page 28

Chuar Group of the Grand Canyon: record of breakup of Rodinia, associated change in the global carbon cycle, and ecosystem expansion by 740 Ma

The Chuar Group (approximately 1600 m thick) preserves a record of extensional tectonism, ocean-chemistry fluctuations, and biological diversification during the late Neoproterozoic Era. An ash layer from the top of the section has a U-Pb zircon age of 742 +/- 6 Ma. The Chuar Group was deposited at low latitudes during extension on the north-trending Butte fault system and is inferred to record rifting during the breakup of Rodinia. Shallow-marine deposition is documented by tide- and wave-generated sedimentary structures, facies associations, and fossils. C isotopes in organic carbon show large stratigraphic variations, apparently recording incipient stages of the marked C isotopic fluctuations that characterize later Neoproterozoic time. Upper Chuar rocks preserve a rich biota that includes not only cyanobacteria and algae, but also heterotrophic protists that document increased food web complexity in Neoproterozoic ecosystems. The Chuar Group thus provides a well-dated, high-resolution record of early events in the sequence of linked tectonic, biogeochemical, environmental, and biological changes that collectively ushered in the Phanerozoic Eon.

NASA Discipline Exobiology↗

Structural Heterogeneity and Hydrodynamics of an Intrinsically Disordered Protein Condensate

Biology demonstrates precise control over the free-energy landscape through the selective partitioning of biomacromolecules into membraneless organelles, enabling essential functions such as biochemical transformations, signaling cascades, and mechanical reinforcement. Although the function of these condensates depends on their underlying structure and hydrodynamics, molecular-scale information on these systems remains sparse. Here, in this study, neutron scattering is used to probe the organization and dynamics of the intrinsically disordered N-terminal domain of Galectin-3, an extracellular lectin responsible for facilitating liquid–liquid phase separation on the cellular surface, in both dilute and condensed phases. Dilute solutions contain isolated protein chains in equilibrium with mesoscopic clusters, whereas the condensed phase adopts a bicontinuous, microemulsion-like morphology. The dilute phase behavior is quantitatively described by coarse-grained polymer models from soft-matter physics, demonstrating their predictive power for complex biological proteins. At elevated concentrations, the proteins self-assemble akin to block copolymers, microphase separating through the aggregation of hydrophobic domains along the protein contour. The resulting condensate remains fluid-like despite a 25-fold increase in concentration; its internal hydrodynamics slow by only a factor of 3 relative to dilute protein chains. These results provide a molecular-level framework for how disordered proteins achieve both the structural complexity and dynamic fluidity of biomolecular condensates.

Carrick, Brian R. [Massachusetts Inst. of Technolo↗

Constructing protein polyhedra via orthogonal chemical interactions

Many proteins exist naturally as symmetrical homooligomers or homopolymers. The emergent structural and functional properties of such protein assemblies have inspired extensive efforts in biomolecular design2–5. As synthesized by ribosomes, proteins are inherently asymmetric. Therefore, they must acquire multiple surface patches that selectively associate to generate the different symmetry elements needed to form higher-order architectures—a daunting task for protein design. Here we address this problem using an inorganic chemical approach, whereby multiple modes of protein–protein interactions and symmetry are simultaneously achieved by selective, ‘one-pot’ coordination of soft and hard metal ions. We show that a monomeric protein (protomer) appropriately modified with biologically inspired hydroxamate groups and zinc-binding motifs assembles through concurrent Fe 3+ and Zn 2+ coordination into discrete dodecameric and hexameric cages. Our cages closely resemble natural polyhedral protein architectures and are, to our knowledge, unique among designed systems in that they possess tightly packed shells devoid of large apertures. At the same time, they can assemble and disassemble in response to diverse stimuli, owing to their heterobimetallic construction on minimal interprotein-bonding footprints. With stoichiometries ranging from [2 Fe:9 Zn:6 protomers] to [8 Fe:21 Zn:12 protomers], these protein cages represent some of the compositionally most complex protein assemblies—or inorganic coordination complexes—obtained by design.

36 MATERIALS SCIENCE↗

Biology IS the Technology: the Microbial Ecology of Space Food Production and the Power of Aquaponics as a Learning Tool

To accomplish the objective of human missions to Mars and/or the long-term colonization of the moon, bioregenerative life support systems and food production systems will be absolutely necessary. Microbes are an essential and unavoidable component of these systems. In fact, these systems are driven by complex microbial communities about which we know very little, a glaring strategic knowledge gap in our ability to support extended human exploration in closed systems. Our laboratory has been working to use molecular ecological methods, including nanopore sequencing technology already deployed on the International Space Station, to understand the microbes in food production systems on Earth. Our ultimate goal is to inform the implementation of food production systems off-world. To date, we have sampled and sequenced the microbiomes of aquaponics systems, hydroponics systems, and fish ponds. Our results have revealed that the microbial communities in these systems are extremely diverse, and highly variable between systems. Along the way, we have discovered the power of aquaponics systems as teaching tools, and the capacity of students to perform high quality citizen science. By designing, constructing, and operating aquaponics systems, students better understand the role of microbes in the cycling of the elements in natural ecosystems, and in the human built environment. In partnership with schools and colleges, contributing new knowledge as citizen scientists, we are now exploring the relationships between the functioning of these systems and their microbial flora.

Bebout, Brad↗

Rational Design of Novel Biomimetic Sequence-Defined Polymers for Mineralization Applications

Silica biomineralization is a naturally occurring process, wherein organisms use proteins and other biological structures to direct the formation of complex, hierarchical nanostructures. Discovery and characterization of such proteins and their underlying mechanisms spurred significant efforts to identify routes for biomimetic mineralization that reproduce the exquisite shapes and size selectivities found in nature. A common strategy has been the use of short peptide sequences with chemistry mimicking those found in natural systems, such as the use of the silaffin-derived R5 peptide. While progress has been made using this approach, there are many limitations that have prevented breakthroughs in biomimicry. To advance our ability to use charged macromolecules for silica formation, we propose to use sequence-defined synthetic polymers known as peptoids, or N-substituted polyglycines, which present significant capability for the precise tuning of sequence and structure beyond what can often be achieved with peptides alone. This study presents a computationally predicted design of these polymers that leads to the controlled formation of silica nanomaterials. We investigate surface adsorption and the mineralization process through analysis of binding mechanisms and energetics of the R5 system. Next, we synthesized two R5-inspired peptoids and validated our prediction in the design of mineralization polymers through characterization using surface plasmon resonance and electron microscopy. Here, this computationally guided study holds great promise for designing new sequences with unprecedented control of the placement of chemical functional groups, thus allowing for further unraveling of silicification mechanisms and the eventual design of sequence-defined synthetic polymers leading to the predictive synthesis of nanostructured functional materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Building a Simplistic Automatic Extruder: Instrument Development Opportunities for the Laboratory

This work presents an automatic extruder as a research experience for undergraduate students. The system offers a user-friendly approach to preparing vesicles, such as liposomes or polymersomes, with a defined size and polydispersity properties crucial for research in biology and macromolecules. It comprises two syringe pumps connected by a membrane filter. The setup is controlled by software. Compared to manual extrusion, this automated system provides advantages, such as precisely controlled variables. The project describes a tool to enhance undergraduate learning in science and engineering laboratories. Building an automatic extruder serves as a simplified model of a complex industrial process. It offers a clear advantage: automating a well-understood manual extrusion process. To make this project accessible, it is broken down into three manageable tasks: software development, hardware assembly, and testing procedures. This breakdown describes the software created, the hardware components used, and the testing procedures conducted for this project. All project data, including software code, testing data, and procedures, are freely available online. This allows undergraduate students to not only begin their own projects but also contribute to this educational instrument’s ongoing development.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Direct Aerobic Generation of a Ferric Hydroperoxo Intermediate Via a Preorganized Secondary Coordination Sphere

Enzymes exert control over the reactivity of metal centers with precise tuning of the secondary coordination sphere of active sites. One particularly elegant illustration of this principle is in the controlled delivery of proton and electron equivalents in order to activate abundant but kinetically inert oxidants such as O 2 for oxidative chemistry. Chemists have drawn inspiration from biology in designing molecular systems where the secondary coordination sphere can shuttle protons or electrons to substrates. However, a biomimetic activation of O 2 requires the transfer of both protons and electrons, and molecular systems where ancillary ligands are designed to provide both of these equivalents are comparatively rare. Here, we report the use of a dihydrazonopyrrole (DHP) ligand complexed to Fe to perform exactly such a biomimetic activation of O 2 . In the presence of O 2 , this complex directly generates a high spin Fe(III)-hydroperoxo intermediate which features a DHP• ligand radical via ligand-based transfer of an H atom. This system displays oxidative reactivity and ultimately releases hydrogen peroxide, providing insight on how secondary coordination sphere interactions influence the evolution of oxidizing intermediates in Fe-mediated aerobic oxidations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Bioregenerative Planetary Life Support Systems Test Complex (BIO-Plex): NASA's Next Human-Rated Testing Facility

As a key component in its ground test bed capability, NASA's Advanced Life Support Program has been developing a large-scale advanced life support test facility capable of supporting long-duration evaluations of integrated bioregenerative life support systems with human test crews. This facility-targeted for evaluation of hypogravity compatible life support systems to be developed for use on planetary surfaces such as Mars or the Moon-is called the Bioregenerative Planetary Life Support Systems Test Complex (BIO-Plex) and is currently under development at the Johnson Space Center. This test bed is comprised of a set of interconnected chambers with a sealed internal environment which are outfitted with systems capable of supporting test crews of four individuals for periods exceeding one year. The advanced technology systems to be tested will consist of both biological and physicochemical components and will perform all required crew life support functions. This presentation provides a description of the proposed test "missions" to be supported by the BIO-Plex and the planned development strategy for the facility.

Tri, Terry O.↗

Automated Symbolic Upscaling: 2. Model Generation for Extended Applicability Regimes

Abstract In this second part of the two paper series, we detail an algorithmic procedure for systematically implementing the generalized closure form strategy presented in Part 1. This strategy extends the applicability of homogenized models with respect to classical homogenization theory, as demonstrated in Part 1 where upscaled models are rigorously derived in moderately reactive physical regimes. After encoding the algorithm into Symbolica, an automated upscaling framework, we upscale two reactive mass transport problems and numerically validate the resulting nonlinear homogenized models by showing the absolute error estimates predicted by homogenization theory are satisfied. In both problems, nontrivial closure forms and closure problems are automatically formulated using the encoded strategy with no human interaction, nor prior knowledge regarding the closure required for the systems. We hope these demonstrations spark further interest in automated analytical frameworks for multiscale modeling, as such capabilities are invaluable for generating rigorous multiscale models of complex phenomena in porous media.

Pietrzyk, Kyle↗

Transient absorption spectroscopy to explore cellular pathways to photobiomodulation

Photobiomodulation (PBM) describes the use of low irradiance light in the red to near-infrared wavelength range to stimulate biological effects in tissue, and many biological and spectroscopic techniques are used to study PBM. However, these techniques focus on the products or downstream effects rather than the electronic transitions that initiate the PBM processes. This study presents a novel approach to studying low irradiance light exposures on individual proteins and/or protein complexes by combining a continuous wave (CW) laser diode with femtosecond transient absorption spectroscopy (TAS), coined here as CW-TAS, and tests the system on reduced cytochrome c (Cyt c) for proof of principle. TAS was conducted using a 532-nm excitation pump beam and a 350-600 nm supercontinuum probe. In this work, CW laser diodes with wavelengths of 450 nm, 635 nm, and 808 nm were interchangeably fiber coupled into the HELIOS Fire. Samples of Cyt c were tested by TAS using a pump power of 15 µW, both with and without CW exposure. CW exposures were carried out with irradiances of 1.60 and 3.20 mW/cm 2 , except for 808 nm, which was only tested at 1.60 mW/cm 2 . Both kinetic and global analyses were performed on the TAS data and the time constants for sets with and without CW exposures were compared. The TAS data for Cyt c with the full dosage of CW exposures did not alter the TAS data distinguishably from the control data. No new electronic transient signals were observed beyond the background when testing Cyt c with the CW exposures. Kinetic analysis confirmed that existing transients did not deviate beyond uncertainty. Global time constants for Cyt c were calculated to be 0.25 ± 0.03 ps and 5.1 ± 0.3 ps for the control study, and the time constants for the CW exposed Cyt c were not significantly different. This study concludes that CW irradiation, at doses delivered, does not alter the transient absorption data of Cyt c. The CW-TAS method provides a new tool for studying PBM effects in other proteins and protein complexes, such as Complex IV, in future studies.

59 BASIC BIOLOGICAL SCIENCES↗

Low-gravity Orbiting Research Laboratory Environment Potential Impact on Space Biology Research

One of the major objectives of any orbital space research platform is to provide a quiescent low gravity, preferably a zero gravity environment, to perform fundamental as well as applied research. However, small disturbances exist onboard any low earth orbital research platform. The impact of these disturbances must be taken into account by space research scientists during their research planning, design and data analysis in order to avoid confounding factors in their science results. The reduced gravity environment of an orbiting research platform in low earth orbit is a complex phenomenon. Many factors, among others, such as experiment operations, equipment operation, life support systems and crew activity (if it is a crewed platform), aerodynamic drag, gravity gradient, rotational effects as well as the vehicle structural resonance frequencies (structural modes) contribute to form the overall reduced gravity environment in which space research is performed. The contribution of these small disturbances or accelerations is precisely why the environment is NOT a zero gravity environment, but a reduced acceleration environment. This paper does not discuss other factors such as radiation, electromagnetic interference, thermal and pressure gradient changes, acoustic and CO2 build-up to name a few that affect the space research environment as well, but it focuses solely on the magnitude of the acceleration level found on orbiting research laboratory used by research scientists to conduct space research. For ease of analysis this paper divides the frequency spectrum relevant to most of the space research disciplines into three regimes: a) quasi-steady, b) vibratory and c) transient. The International Space Station is used as an example to illustrate the point. The paper discusses the impact of these three regimes on space biology research and results from space flown experiments are used to illustrate the potential negative impact of these disturbances (accelerations) on space biology research.

Jules, Kenol↗

Non-traditional stable isotope measurements using laser desorption Orbitrap mass spectrometry: Implications for planetary missions.

Isotopic fractionation recorded in planetary materials provides insights into physical, chemical, and/or potential biological processes occurring on Solar System bodies. As we enter into the next decades of planetary exploration, the crucial information revealed by isotopic compositions of rocky and icy samples mandates that next generation spaceflight instrumentation possess the capability to measure isotope ratios in situ with sufficient precision/accuracy to distinguish between such processes. Here, in addition to identifying and fingerprinting complex organic materials with high accuracy and ultrahigh mass resolutions, laser desorption Orbitrap™ mass spectrometry (LD-O-MS) has the capability to determine the elemental and isotopic composition of solid planetary materials such as rock, regolith, organics, ice, etc. Here, we use a space-qualified LD-O-MS instrument comprising a 266 nm ultraviolet (UV) laser and Orbitrap mass analyzer ruggedized for planetary applications to investigate the stable isotopic composition of Ti and Zn metal plates. Based on the isotopic analyses, we constrain the performance of the CORALS instrument to sub per mille (‰) level accuracy and precision for Ti and at the per mille (‰) level for Zn. An LD-O-MS instrument is a versatile instrument capable of measuring isotopic composition of a variety of planetary samples and would constitute a critical instrument in the exploration of various planetary bodies including but not limited to Moon, Mars, Enceladus and other ocean or icy worlds, Ceres and other asteroids, and comets, thereby answering several high-priority questions pertaining to the formation and evolution of our Solar System.

58 GEOSCIENCES↗

Nuclear–Electronic Orbital QM/MM Approach: Geometry Optimizations and Molecular Dynamics

Hybrid quantum mechanical/molecular mechanical (QM/MM) methods allow simulations of chemical reactions in atomistic solvent and heterogeneous environments such as proteins. Herein, the nuclear–electronic orbital (NEO) QM/MM approach is introduced to enable the quantization of specified nuclei, typically protons, in the QM region using a method such as NEO-density functional theory (NEO-DFT). This approach includes proton delocalization, polarization, anharmonicity, and zero-point energy in geometry optimizations and dynamics. Expressions for the energies and analytical gradients associated with the NEO-QM/MM method, as well as the previously developed polarizable continuum model (NEO-PCM), are provided. Geometry optimizations of small organic molecules hydrogen bonded to water in either dielectric continuum solvent or explicit atomistic solvent illustrate that aqueous solvation can strengthen hydrogen-bonding interactions for the systems studied, as indicated by shorter intermolecular distances at the hydrogen-bond interface. We then performed a real-time direct dynamics simulation of a phenol molecule in explicit water using the NEO-QM/MM method. Furthermore, these developments and initial examples provide the foundation for future studies of nuclear–electronic quantum dynamics in complex chemical and biological environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Identifying microbial functional guilds performing cryptic organotrophic and lithotrophic redox cycles in anaerobic granular biofilms

Granular biofilms used in anaerobic digester systems contain diverse microbial populations that interact to hydrolyze organic matter and produce methane within controlled environments. Prior research investigated the feasibility of utilizing granular biofilms obtained from an anaerobic digester to remove nitrate without the addition of exogenous electron donors. These granules possessed a unique structure of alternating light and dark iron sulfide and pyrite rich layers that potentially served as both an electron source and sink, linking carbon, nitrogen, sulfur, and iron cycles. To characterize the functional roles of diverse microbial populations enriched within these layered biofilms, we analyzed metagenomes obtained from three different granules. Comparisons between the functional gene content of forty metagenome assembled genomes (MAGs) identified phylogenetically cohesive functional guilds. Each of these functional MAG clusters was assigned to specific steps in anaerobic digestion (hydrolysis, acidogenesis, acetogenesis, and methanogenesis) and anaerobic respiration (denitrification and sulfate reduction). Comparisons with metagenomes derived from a variety of natural and engineered ecosystems confirmed that the enriched denitrifying bacteria were similar to populations typically found in wetlands and biological nitrogen removal systems. Analysis of read alignments to individual genes within the forty MAGs identified conserved genomic features that were representative of the functions that distinguished functional guilds. Overall, this research illustrates the utility of functional based classification of microorganisms for characterizing ecosystem functions and highlights the potential application of engineered ecosystems to serve as experimental models for complex natural ecosystems.

Ecosystem engineering↗

Natural evidence for chemical and early biological evolution

Oparin (1924) and Haldane (1929) have independently hypothesized that life arose under reducing conditions through an evolutionary sequence of events involving increasingly complex organic substances. The natural evidence for this hypothesis of chemical evolution is considered, giving particular attention to tangible samples which have been chemically analyzed in earth-bound laboratories. It is found that meteorites provide naturally occurring evidence in support of chemical evolution, but not of biological evolution. Studies on the early Precambrian Swaziland Sequence and the Bulawayan System of southern Africa provide evidence for very early biological evolution.

Kvenvolden, K. A.↗

Light weight escape capsule for fighter aircraft

Emergency crew escape capabilities have been less than adequate for fighter aircraft since before WW II. From the over-the-side bailout of those days through the current ejection seat with a rocket catapult, escaping from a disabled aircraft has been risky at best. Current efforts are underway toward developing a high-tech, smart ejection seat that will give fighter pilots more room to live in the sky, but an escape capsule is needed to meet current and future fighter envelopes. Escape capsules have a bad reputation due to past examples of high weight, poor performance and great complexity. However, the advantages available demand that a capsule be developed. This capsule concept will minimize the inherent disavantages and incorporate the benefits while integrating all aspects of crew station design. The resulting design is appropriate for a crew station of the year 2010 and includes improved combat acceleration protection, chemical or biological combat capability, improved aircraft to escape system interaction, and the highest level of escape performance achievable. The capsule is compact, which can allow a reduced aircraft size and weighs only 1200 lb. The escape system weight penalty is only 120 lb higher than that for the next ejection seat and the capsule has a corresponding increase in performance.

Robert, James A.↗

Interactions of the SAP Domain of Human Ku70 with DNA Substrate: A Molecular Dynamics Study

NASA is developing a systems biology approach to improve the assessment of health risks associated with space radiation. The primary toxic and mutagenic lesion following radiation exposure is the DNA double strand break (DSB), thus a model incorporating proteins and pathways important in response and repair of this lesion is critical. One key protein heterodimer for systems models of radiation effects is the Ku70/80 complex. The Ku70/80 complex is important in the initial binding of DSB ends following DNA damage, and is a component of nonhomologous end joining repair, the primary pathway for DSB repair in mammalian cells. The SAP domain of Ku70 (residues 556-609), contains an a helix-extended strand-helix motif and similar motifs have been found in other nucleic acid-binding proteins critical for DNA repair. However, the exact mechanism of damage recognition and substrate specificity for the Ku heterodimer remains unclear in part due to the absence of a high-resolution structure of the SAP/DNA complex. We performed a series of molecular dynamics (MD) simulations on a system with the SAP domain of Ku70 and a 10 base pairs DNA duplex. Large-scale conformational changes were observed and some putative binding modes were suggested based on energetic analysis. These modes are consistent with previous experimental investigations. In addition, the results indicate that cooperation of SAP with other domains of Ku70/80 is necessary to explain the high affinity of binding as observed in experiments.

Hu, Shaowen↗

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

The search for evidence of extraterrestrial life in our solar system has been guided by our under-standing 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-excesses of chiral amino acids or sugars could be a powerful indicator of extant or extinct life on Mars or other habitable environments in our solar system. However, studies of primitive meteorites have revealed that they contain extraterrestrial amino acids and sugar acids with large enantiomeric excesses (60% and higher) that resulted from non-biological processes [1], complicating the use of chiral asymmetry by itself as a definitive biosignature. The exploration of habitable environments on Mars, including an assessment of the preservation potential for complex organics of either abiotic or biological origin, is an objective of both current and future Mars missions. Now with the unambiguous detection of indigenous organic matter in sedimentary rocks by the Sample Analysis at Mars (SAM) instrument suite on Mars [2-5], NASA’s Curiosity rover has found evidence 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 [5], indigenous achiral amino acids have been identified in one martian meteorite [6]. It is expected that amino acid 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 [7]. The ESA/Roscosmos ExoMars mission scheduled for launch next year includes the Rosalind Franklin rover designed to acquire samples from a depth of ~2 m and deliver them to a suite of instruments, including the Mars Organic Molecule Analyzer (MOMA). The MOMA instrument contains a wet chemistry experiment designed specifically for the detection of amino acids and measurement of their enantiomeric compositions [8]. The complexity and limited duration of spaceflight operations, and the known analytical challenges associated with in situ extraction and characterization of trace reduced organic com-pounds 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, bulk and molecule-specific isotopic, and enantiomeric measurements will be required to firmly establish whether the complex organic matter detected on Mars derives from bio-tic or abiotic processes. Ultimately, Mars Sample Return of rock cores collected by NASA’s Perseverance rover may be our best chance of identifying chemical biosignatures, including any chiral amino acid asymmetry resulting from a past or present martian biota, if one ever existed on Mars. Here we review our current knowledge of the distributions, and enantiomeric and isotopic com-positions of amino acids found in meteorites compared to terrestrial biochemistry. We also propose a set of measurement criteria that should be used to help establish the sources of any amino acids detected in samples returned from Mars using state-of-the-art gas and liquid chromatography mass spectrometry techniques [1].

D P Glavin↗