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At least 397 records · Page 22

Estimating Major Ion and Nutrient Concentrations in Mangrove Estuaries in Everglades National Park Using Leaf and Satellite Reflectance

Coastal mangrove ecosystems are under duress worldwide because of urban development, sea-level rise, and climate change, processes that are capable of changing the salinity and nutrient concentration of the water utilized by the mangroves. This study correlates long-term water chemistry in mangrove environments, located in Everglades National Park,with mangrove spectral reflectance measurements made at both the leaf and canopy scales. Spectral reflectance measurements were collected using a handheld spectrometer for leaf-level measurements and Landsat 5TMdata for regional coverage. Leaf-level reflectance data were collected from three mangrove species (i.e., red, black and white mangroves) across two regions; a tall mangrove (approximately 18m) and dwarf mangrove (1- 2 m) region. The reflectance data were then used to calculate a wide variety of biophysical reflectance indices (e.g., NDVI, EVI, SAVI) to determine signs of stress. Discrete, quarterly water samples from the surface water, groundwater, and pore water (20 and 85 cm depths) and daily autonomous surface water samples were collected at each site and analyzed for major anions (Cl(−) and SO(2(-)/4)), cations (Na(+), K(+), Mg(sup 2(+)), and Ca(sup 2(+)), total nitrogen (TN) and total phosphorus (TP).Mangrove sites that exhibited the highest salinity and ionic concentrations in the surface and subsurface water also had the lowest near-infrared reflectance at both the leaf and satellite levels. Seasonal reflectance responses were measured in the near-infrared (NIR) wavelengths at both the leaf and canopy scales and were strongly correlated with nutrient and ionic concentrations in the surface and subsurface water, even though there was no significant separability between the three mangrove species. Study sites that experienced the greatest variability in surface and subsurface water ionic concentrations also exhibited the greatest fluctuations in NIR spectral reflectance. Landsat 5TM images were able to detect tall and dwarf mangroves by the differences in spectral indices (e.g., NDVI, NDWI, and EVI) because of the variability in the background conditions amongst the environments. In addition, Landsat 5TM images spanning 16 years (1993- 2009) were successfully used to estimate the seasonal variability in ionic concentrations in the surface water across the Florida Coastal mangrove ecotone. This study has shown that water chemistry can be estimated indirectly by measuring the change in spectral response at the leaf- or satellite-scale. Furthermore, the results of this research may be extrapolated to similar coastal mangrove systems throughout the Caribbean and world-wide wherever red, black, and white mangroves occur.

Mangroves↗

Inferring Stochastic Rates from Heterogeneous Snapshots of Particle Positions

Many imaging techniques for biological systems—like fixation of cells coupled with fluorescence microscopy—provide sharp spatial resolution in reporting locations of individuals at a single moment in time but also destroy the dynamics they intend to capture. In this study, these snapshot observations contain no information about individual trajectories, but still encode information about movement and demographic dynamics, especially when combined with a well-motivated biophysical model. The relationship between spatially evolving populations and single-moment representations of their collective locations is well-established with partial differential equations (PDEs) and their inverse problems. However, experimental data is commonly a set of locations whose number is insufficient to approximate a continuous-in-space PDE solution. Here, motivated by popular subcellular imaging data of gene expression, we embrace the stochastic nature of the data and investigate the mathematical foundations of parametrically inferring demographic rates from snapshots of particles undergoing birth, diffusion, and death in a nuclear or cellular domain. Toward inference, we rigorously derive a connection between individual particle paths and their presentation as a Poisson spatial process. Using this framework, we investigate the properties of the resulting inverse problem and study factors that affect quality of inference. One pervasive feature of this experimental regime is the presence of cell-to-cell heterogeneity. Rather than being a hindrance, we show that cell-to-cell geometric heterogeneity can increase the quality of inference on dynamics for certain parameter regimes. Altogether, the results serve as a basis for more detailed investigations of subcellular spatial patterns of RNA molecules and other stochastically evolving populations that can only be observed for single instants in their time evolution.

59 BASIC BIOLOGICAL SCIENCES↗

Allosteric Mechanisms of Molecular Machines at the Membrane: Transport by Sodium-Coupled Symporters

Solute transport across cell membranes is ubiquitous in biology as an essential physiological process. Secondary active transporters couple the unfavorable process of solute transport against its concentration gradient to the energetically favorable transport of one or several ions. The study of such transporters over several decades indicates that their function involves complex allosteric mechanisms that are progressively being revealed in atomistic detail. We focus on two well-characterized sodium-coupled symporters: the bacterial amino acid transporter LeuT, which is the prototype for the “gated pore” mechanism in the mammalian synaptic monoamine transporters, and the archaeal GltPh, which is the prototype for the “elevator” mechanism in the mammalian excitatory amino acid transporters. We present the evidence for the role of allostery in the context of a quantitative formalism that can reconcile biochemical and biophysical data and thereby connects directly to recent insights into the molecular structure and dynamics of these proteins. We demonstrate that, while the structures and mechanisms of these transporters are very different, the available data suggest a common role of specific models of allostery in their functions. We argue that such allosteric mechanisms appear essential not only for sodium-coupled symport in general but also for the function of other types of molecular machines in the membrane.

Chemistry↗

Highly Basic Clusters in the Herpes Simplex Virus 1 Nuclear Egress Complex Drive Membrane Budding by Inducing Lipid Ordering

During replication of herpesviruses, capsids escape from the nucleus into the cytoplasm by budding at the inner nuclear membrane. This unusual process is mediated by the viral nuclear egress complex (NEC) that deforms the membrane around the capsid by oligomerizing into a hexagonal, membrane-bound scaffold. Here, we found that highly basic membrane-proximal regions (MPRs) of the NEC alter lipid order by inserting into the lipid headgroups and promote negative Gaussian curvature. We also find that the electrostatic interactions between the MPRs and the membranes are essential for membrane deformation. One of the MPRs is phosphorylated by a viral kinase during infection, and the corresponding phosphomimicking mutations block capsid nuclear egress. We show that the same phosphomimicking mutations disrupt the NEC-membrane interactions and inhibit NEC-mediated budding in vitro, providing a biophysical explanation for the in vivo phenomenon. Our data suggest that the NEC generates negative membrane curvature by both lipid ordering and protein scaffolding and that phosphorylation acts as an off switch that inhibits the membrane-budding activity of the NEC to prevent capsid-less budding.

membrane curvature↗

Non-Invasive Biophysical Techniques to Monitor the Structural Plasticity of the Photosynthetic Machinery of Live Diatom Cells

The photosynthetic performance of diatoms depends largely on the organization and structural flexibility of their thylakoid membranes, the densely packed, highly organized membrane vesicles in which light reactions of photosynthesis occur. Different regulatory mechanisms that fine tune the photosynthetic functions affect the organization of the photosynthetic machinery at different levels of structural complexity, from the level of individual protein complexes to the macroarray of membrane proteins and the remodeling of the entire thylakoid membrane system. To monitor these reorganizations, non-invasive techniques are of special value. In this chapter, we focus our attention on three of these techniques, which have been demonstrated to provide unique and useful information on the structure and structural and functional plasticity of live diatom cells: (i) circular dichroism (CD) spectroscopy, which has provided unique information on the chiral (macro-)organization of protein complexes and on their rapid, reversible reorganizations, fine-tuning the light-harvesting processes, as well as on variations in the short-range excitonic interactions in the antenna complexes; (ii) small-angle neutron scattering (SANS), which has been used to determine the periodic organization of the thylakoid membranes and to monitor reversible ultrastructural changes on the time-scale of minutes, induced by variations in the environmental conditions such as changes in temperature or light intensity; and (iii) electrochromic shift absorbance transients (ΔA ECS ), a spectroscopic tool which has been shown to be capable of identifying distinct functional groups of the light-harvesting carotenoid fucoxanthin in different diatoms and in cells exposed to different light intensities. Future use of these techniques will most certainly contribute to the deeper understanding of key regulatory mechanisms of photosynthesis in diatoms.

Szabo, Milan↗

Biophysical characterization of actin bundles generated by the Chlamydia trachomatis Tarp effector

Highlights: • The F-actin binding domain of Tarp is sufficient to bundle filamentous actin. • Actin bundles formed by Tarp are more flexible than that of α-actinin and fascin. • Tarp mediated actin bundling is independent of actin nucleation. Chlamydia trachomatis entry into host cells is mediated by pathogen-directed remodeling of the actin cytoskeleton. The chlamydial type III secreted effector, translocated actin recruiting phosphoprotein (Tarp), has been implicated in the recruitment of actin to the site of internalization. Tarp harbors G-actin binding and proline rich domains required for Tarp-mediated actin nucleation as well as unique F-actin binding domains implicated in the formation of actin bundles. Little is known about the mechanical properties of actin bundles generated by Tarp or the mechanism by which Tarp mediates actin bundle formation. In order to characterize the actin bundles and elucidate the role of different Tarp domains in the bundling process, purified Tarp effectors and Tarp truncation mutants were analyzed using Total Internal Reflection Fluorescence (TIRF) microscopy. Our data indicate that Tarp mediated actin bundling is independent of actin nucleation and the F-actin binding domains are sufficient to bundle actin filaments. Additionally, Tarp-mediated actin bundles demonstrate distinct bending stiffness compared to those crosslinked by the well characterized actin bundling proteins fascin and alpha-actinin, suggesting Tarp may employ a novel actin bundling strategy. The capacity of the Tarp effector to generate novel actin bundles likely contributes to chlamydia's efficient mechanism of entry into human cells.

60 APPLIED LIFE SCIENCES↗

Capillary electrophoresis: Imaging of electroosmotic and pressure driven flow profiles in fused silica capillaries

This study is a continuation of the summer of 1994 NASA/ASEE Summer Faculty Fellowship Program. This effort is a portion of the ongoing work by the Biophysics Branch of the Marshall Space Flight Center. The work has focused recently on the separation of macromolecules using capillary electrophoresis (CE). Two primary goals were established for the effort this summer. First, we wanted to use capillary electrophoresis to study the electrohydrodynamics of a sample stream. Secondly, there was a need to develop a methodology for using CE for separation of DNA molecules of various sizes. In order to achieve these goals we needed to establish a procedure for detection of a sample plug under the influence of an electric field Detection of the sample with the microscope and image analysis system would be helpful in studying the electrohydrodynamics of this stream under load. Videotaping this process under the influence of an electric field in real time would also be useful. Imaging and photography of the sample/background electrolyte interface would be vital to this study. Finally, detection and imaging of electroosmotic flow and pressure driven flow must be accomplished.

Williams, George O., Jr.↗

Cryo-EM structures of PP2A:B55–FAM122A and PP2A:B55–ARPP19

Progression through the cell cycle is controlled by regulated and abrupt changes in phosphorylation. Mitotic entry is initiated by increased phosphorylation of mitotic proteins, a process driven by kinases, whereas mitotic exit is achieved by counteracting dephosphorylation, a process driven by phosphatases, especially PP2A:B55. Although the role of kinases in mitotic entry is well established, recent data have shown that mitosis is only successfully initiated when the counterbalancing phosphatases are also inhibited. Inhibition of PP2A:B55 is achieved by the intrinsically disordered proteins ARPP19 and FAM122A. Despite their critical roles in mitosis, the mechanisms by which they achieve PP2A:B55 inhibition is unknown. Here, we report the single-particle cryo-electron microscopy structures of PP2A:B55 bound to phosphorylated ARPP19 and FAM122A. Consistent with our complementary NMR spectroscopy studies, both intrinsically disordered proteins bind PP2A:B55, but do so in highly distinct manners, leveraging multiple distinct binding sites on B55. Our extensive structural, biophysical and biochemical data explain how substrates and inhibitors are recruited to PP2A:B55 and provide a molecular roadmap for the development of therapeutic interventions for PP2A:B55-related diseases.

59 BASIC BIOLOGICAL SCIENCES↗

Optimal arrangements of 1,3-diphenylisobenzofuran molecule pairs for fast singlet fission

A simplified version of the frontier orbital model has been applied to pairs of C 2 , C 2v , C s , and C 1 symmetry 1,3-diphenylisobenzofuran rotamers to determine their best packing for fast singlet fission (SF). For each rotamer the square of the electronic matrix element for SF was calculated at 2.2 × 10 9 pair geometries and a few thousand most significant physically accessible local maxima were identified in the six-dimensional space of mutual arrangements. At these pair geometries, SF energy balance was evaluated, relative SF rate constants were approximated using Marcus theory, and the SF rate constant k SF was maximized by further optimization of the geometry of the molecular pair. The process resulted in 142, 67, 214, and 291 unique geometries for the C 2 , C 2v , C s , and C 1 symmetry molecular pairs, respectively, predicted to be superior to the C 2 symmetrized known crystal pair structure. Furthermore, these optimized pair geometries and their triplet biexciton binding energies are reported as targets for crystal engineering and/or covalent dimer synthesis, and as possible starting points for high-level pair geometry optimizations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The photophysics of monomeric bacteriochlorophylls c and d and their derivatives: properties of the triplet state and singlet oxygen photogeneration and quenching

Measurements of pigment triplet-triplet absorption, pigment phosphorescence and photosensitized singlet oxygen luminescence were carried out on solutions containing monomeric bacteriochlorophylls (Bchl) c and d, isolated from green photosynthetic bacteria, and their magnesium-free and farnesyl-free analogs. The energies of the pigment triplet states fell in the range 1.29-1.34 eV. The triplet lifetimes in aerobic solutions were 200-250 ns; they increased to 280 +/- 70 microseconds after nitrogen purging in liquid solutions and to 0.7-2.1 ms in a solid matrix at ambient or liquid nitrogen temperatures. Rate constants for quenching of the pigment triplet state by oxygen were (2.0-2.5) x 10(9) M-1 s-1, which is close to 1/9 of the rate constant for diffusion-controlled reactions. This quenching was accompanied by singlet oxygen formation. The quantum yields for the triplet state formation and singlet oxygen production were 55-75% in air-saturated solutions. Singlet oxygen quenching by ground-state pigment molecules was observed. Quenching was the most efficient for magnesium-containing pigments, kq = (0.31-1.2) x 10(9) M-1 s-1. It is caused mainly by a physical process of singlet oxygen (1O2) deactivation. Thus, Bchl c and d and their derivatives, as well as chlorophyll and Bchl a, combine a high efficiency of singlet oxygen production with the ability to protect photochemical and photobiological systems against damage by singlet oxygen.

NASA Discipline Number 52-30↗

Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core

The molecular events that permit the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to bind and enter cells are important to understand for both fundamental and therapeutic reasons. Spike proteins consist of S1 and S2 domains, which recognize angiotensin-converting enzyme 2 (ACE2) receptors and contain the viral fusion machinery, respectively. Ostensibly, the binding of spike trimers to ACE2 receptors promotes dissociation of the S1 domains and exposure of the fusion machinery, although the molecular details of this process have yet to be observed. We report the development of bottom-up coarse-grained (CG) models consistent with cryo-electron tomography data, and the use of CG molecular dynamics simulations to investigate viral binding and S2 core exposure. We show that spike trimers cooperatively bind to multiple ACE2 dimers at virion-cell interfaces in a manner distinct from binding between soluble proteins, which processively induces S1 dissociation. We also simulate possible variant behavior using perturbed CG models, and find that ACE2-induced S1 dissociation is primarily sensitive to conformational state populations and the extent of S1/S2 cleavage, rather than ACE2 binding affinity. These simulations reveal an important concerted interaction between spike trimers and ACE2 dimers that primes the virus for membrane fusion and entry.

59 BASIC BIOLOGICAL SCIENCES↗

Correspondence between discrete and continuous models of excitable media: trigger waves

We present a theoretical framework for relating continuous partial differential equation (PDE) models of excitable media to discrete cellular automata (CA) models on a randomized lattice. These relations establish a quantitative link between the CA model and the specific physical system under study. We derive expressions for the CA model's plane wave speed, critical curvature, and effective diffusion constant in terms of the model's internal parameters (the interaction radius, excitation threshold, and time step). We then equate these expressions to the corresponding quantities obtained from solution of the PDEs (for a fixed excitability). This yields a set of coupled equations with a unique solution for the required CA parameter values. Here we restrict our analysis to "trigger" wave solutions obtained in the limiting case of a two-dimensional excitable medium with no recovery processes. We tested the correspondence between our CA model and two PDE models (the FitzHugh-Nagumo medium and a medium with a "sawtooth" nonlinear reaction source) and found good agreement with the numerical solutions of the PDEs. Our results suggest that the behavior of trigger waves is actually controlled by a small number of parameters.

Non-NASA Center↗

Development of Graphical User Interface for ARRBOD (Acute Radiation Risk and BRYNTRN Organ Dose Projection)

The space radiation environment, particularly solar particle events (SPEs), poses the risk of acute radiation sickness (ARS) to humans; and organ doses from SPE exposure may reach critical levels during extra vehicular activities (EVAs) or within lightly shielded spacecraft. NASA has developed an organ dose projection model using the BRYNTRN with SUMDOSE computer codes, and a probabilistic model of Acute Radiation Risk (ARR). The codes BRYNTRN and SUMDOSE, written in FORTRAN, are a Baryon transport code and an output data processing code, respectively. The ARR code is written in C. The risk projection models of organ doses and ARR take the output from BRYNTRN as an input to their calculations. BRYNTRN code operation requires extensive input preparation. With a graphical user interface (GUI) to handle input and output for BRYNTRN, the response models can be connected easily and correctly to BRYNTRN in friendly way. A GUI for the Acute Radiation Risk and BRYNTRN Organ Dose (ARRBOD) projection code provides seamless integration of input and output manipulations, which are required for operations of the ARRBOD modules: BRYNTRN, SUMDOSE, and the ARR probabilistic response model. The ARRBOD GUI is intended for mission planners, radiation shield designers, space operations in the mission operations directorate (MOD), and space biophysics researchers. The ARRBOD GUI will serve as a proof-of-concept example for future integration of other human space applications risk projection models. The current version of the ARRBOD GUI is a new self-contained product and will have follow-on versions, as options are added: 1) human geometries of MAX/FAX in addition to CAM/CAF; 2) shielding distributions for spacecraft, Mars surface and atmosphere; 3) various space environmental and biophysical models; and 4) other response models to be connected to the BRYNTRN. The major components of the overall system, the subsystem interconnections, and external interfaces are described in this report; and the ARRBOD GUI product is explained step by step in order to serve as a tutorial.

Kim, Myung-Hee↗

Laser speckle-imaging of blood microcirculation in the brain cortex of laboratory rats in stress

The results of experimental approbation of the method of laser full-field speckle-imaging for monitoring the changes in blood microcirculation state of the brain cortex of laboratory rats under the conditions of developing stroke and administration of vasodilating and vasoconstrictive agents are presented. The studies aimed at the choice of the optimal conditions of speckle-image formation and recording were performed and the software implementing an adaptive algorithm for processing the data of measurements was created. The transfer of laser radiation to the probed region of the biotissue was implemented by means of a silica-polymer optical fibre. The problems and prospects of speckle-imaging of cerebral microcirculation of blood in laboratory and clinical conditions are discussed.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

ZMPY3D: accelerating protein structure volume analysis through vectorized 3D Zernike moments and Python-based GPU integration

Abstract Motivation Volumetric 3D object analyses are being applied in research fields such as structural bioinformatics, biophysics, and structural biology, with potential integration of artificial intelligence/machine learning (AI/ML) techniques. One such method, 3D Zernike moments, has proven valuable in analyzing protein structures (e.g., protein fold classification, protein–protein interaction analysis, and molecular dynamics simulations). Their compactness and efficiency make them amenable to large-scale analyses. Established methods for deriving 3D Zernike moments, however, can be inefficient, particularly when higher order terms are required, hindering broader applications. As the volume of experimental and computationally-predicted protein structure information continues to increase, structural biology has become a “big data” science requiring more efficient analysis tools. Results This application note presents a Python-based software package, ZMPY3D, to accelerate computation of 3D Zernike moments by vectorizing the mathematical formulae and using graphical processing units (GPUs). The package offers popular GPU-supported libraries such as CuPy and TensorFlow together with NumPy implementations, aiming to improve computational efficiency, adaptability, and flexibility in future algorithm development. The ZMPY3D package can be installed via PyPI, and the source code is available from GitHub. Volumetric-based protein 3D structural similarity scores and transform matrix of superposition functionalities have both been implemented, creating a powerful computational tool that will allow the research community to amalgamate 3D Zernike moments with existing AI/ML tools, to advance research and education in protein structure bioinformatics. Availability and implementation ZMPY3D, implemented in Python, is available on GitHub (https://github.com/tawssie/ZMPY3D) and PyPI, released under the GPL License.

Lai, Jhih-Siang (ORCID:0000000156775890)↗

Physiological principles of vestibular function on earth and in space

Physiological mechanisms underlying vestibular function have important implications for our ability to understand, predict, and modify balance processes during and after spaceflight. The microgravity environment of space provides many unique opportunities for studying the effects of changes in gravitoinertial force on structure and function of the vestibular system. Investigations of basic vestibular physiology and of changes in reflexes occurring as a consequence of exposure to microgravity have important implications for diagnosis and treatment of vestibular disorders in human beings. This report reviews physiological principles underlying control of vestibular processes on earth and in space. Information is presented from a functional perspective with emphasis on signals arising from labyrinthine receptors. Changes induced by microgravity in linear acceleration detected by the vestibulo-ocular reflexes. Alterations of the functional requirements for postural control in space are described. Areas of direct correlation between studies of vestibular reflexes in microgravity and vestibular disorders in human beings are discussed.

Non-NASA Center↗

Farming in space: environmental and biophysical concerns

The colonization of space will depend on our ability to routinely provide for the metabolic needs (oxygen, water, and food) of a crew with minimal re-supply from Earth. On Earth, these functions are facilitated by the cultivation of plant crops, thus it is important to develop plant-based food production systems to sustain the presence of mankind in space. Farming practices on earth have evolved for thousands of years to meet both the demands of an ever-increasing population and the availability of scarce resources, and now these practices must adapt to accommodate the effects of global warming. Similar challenges are expected when earth-based agricultural practices are adapted for space-based agriculture. A key variable in space is gravity; planets (e.g. Mars, 1/3 g) and moons (e.g. Earth's moon, 1/6 g) differ from spacecraft orbiting the Earth (e.g. Space stations) or orbital transfer vehicles that are subject to microgravity. The movement of heat, water vapor, CO2 and O2 between plant surfaces and their environment is also affected by gravity. In microgravity, these processes may also be affected by reduced mass transport and thicker boundary layers around plant organs caused by the absence of buoyancy dependent convective transport. Future space farmers will have to adapt their practices to accommodate microgravity, high and low extremes in ambient temperatures, reduced atmospheric pressures, atmospheres containing high volatile organic carbon contents, and elevated to super-elevated CO2 concentrations. Farming in space must also be carried out within power-, volume-, and mass-limited life support systems and must share resources with manned crews. Improved lighting and sensor technologies will have to be developed and tested for use in space. These developments should also help make crop production in terrestrial controlled environments (plant growth chambers and greenhouses) more efficient and, therefore, make these alternative agricultural systems more economically feasible food production systems. c2002 COSPAR. Published by Elsevier Science Ltd. All rights reserved.

Review↗

Plasmon-Enhanced Light Harvesting of Chlorophylls on Near-Percolating Silver Films via One-Photon Anti-Stokes Upconversion

There exists a wealth of means of efficient utilization of solar energy in nature, with photosynthesis of chlorophylls as a prime example. Separately, artificially structured plasmonic materials are versatile in light harvesting and energy conversion. Using a simple and scalable design of near-percolating silver nanostructures, we demonstrate that the light-harvesting efficiency of chlorophylls can be drastically enhanced by tuning the plasmon frequency of the constituent silver nanoparticles to coincide with the maximal photon flux of sunlight. In particular, we show that the photon upconversion efficiency can be readily enhanced by over 20 folds, with the room-temperature fluorescence quantum yield increased by a factor of 2.63. The underlying mechanism for the upconversion enhancement is attributed to a one-electron-per-photon anti-Stokes process, involving absorption of a characteristic phonon mode of the chlorophylls. These findings suggest that chlorophylls can serve as molecular building blocks for high-efficiency light harvesting and solar energy conversion.

14 SOLAR ENERGY↗