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At least 253 records · Page 14

Structure and function of a flavin-dependent S-monooxygenase from garlic ( Allium sativum )

Allicin is a component of the characteristic smell and flavor of garlic ( Allium sativum ). A flavin-containing monooxygenase (FMO) produced by A. sativum (AsFMO) was previously proposed to oxidize S-allyl- L -cysteine (SAC) to alliin, an allicin precursor. In this paper, we present a kinetic and structural characterization of AsFMO that suggests a possible contradiction to this proposal. Results of steady-state kinetic analyses revealed that AsFMO exhibited negligible activity with SAC; however, the enzyme was highly active with L -cysteine, N-acetyl- L -cysteine, and allyl mercaptan. We found that allyl mercaptan with NADPH was the preferred substrate-cofactor combination. Rapid-reaction kinetic analyses showed that NADPH binds tightly ($K_D$ of ~2 μM) to AsFMO and that the hydride transfer occurs with pro-R stereospecificity. We detected the formation of a long-wavelength band when AsFMO was reduced by NADPH, probably representing the formation of a charge-transfer complex. In the absence of substrate, the reduced enzyme, in complex with NADP + , reacted with oxygen and formed an intermediate with a spectrum characteristic of C4a-hydroperoxyflavin, which decays several orders of magnitude more slowly than the $k$ cat . The presence of substrate enhanced C4a-hydroperoxyflavin formation and, upon hydroxylation, oxidation occurred with a rate constant similar to the $k$ cat . The structure of AsFMO complexed with FAD at 2.08-Å resolution features two domains for binding of FAD and NADPH, representative of class B flavin monooxygenases. These biochemical and structural results are consistent with AsFMO being an S-monooxygenase involved in allicin biosynthesis through direct formation of sulfenic acid and not SAC oxidation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Exploring the Neutron Substructure with Advanced Polarized Helium-3 Targets (Or: How I Learned to Stop Worrying and Love Spectroscopy)

As we seek to understand the smallest, physical aspects of our universe, we cannot simply rely on our senses to probe the world around us as we did in the past. The smallest physical elements of our universe behave in strange, probabilistic ways and are completely invisible to the naked eye/ear/etc. So, we design clever experiments (such as scattering experiments) to probe these minute realms. Then, just as with the larger, observable world, we devise models and equations to describe what we think is happening. Due to the nature of the physical universe at the quantum scale and with the aid of symmetries such as Lorentz invariance, we can write down equations that describe the scattering, but the expressions contain functions, which we call ?form factors? and ?structure functions?, that we cannot compute from first principles. We can, however, formulate models that make predictions for these functions. By comparing our predictions with the observed data, we can gain insight into the validity of our models and thus a better physical understanding of what is happening at these minuscule scales. Studying the constituents inside of the nucleus of an atom adds another layer of difficulty if we can?t remove those components from the nucleus. This is the case with the neutron. When not bound in the nucleus with protons and other neutrons, the neutron will decay into a proton after about 15 minutes. So, we?re forced to study the neutron while it is still bound in the nucleus of an atom such as helium-3 (3He). For the last 1,000 years (rounding up), our group has developed high quality, polarized 3He targets made of an aluminosilicate glass. These targets are made in order to perform experiments at Jefferson Lab (JLab), experiments which let us determine the form factors and structure functions of the neutron by scattering polarized electrons from polarized neutrons (or rather polarized 3He). The specific experiments reported on in this thesis push the bounds of our understanding of the internal structure of the neutron. Good science is often about pushing experimental techniques to a new level. Toward that goal we study our polarized 3He targets both to advance the technology and to choose the best ones for our experiments. We do this using a process called nuclear magnetic resonance (NMR) to gauge the maximum polarization of a target and how fast the polarization decays with time. While these tests primarily provide us information that make analysis of our experimental scattering data possible, they also let us determine whether or not a target-cell is useful or even, dare I say, of spectacular quality. Our latest targets utilize a novel convection design allowing 3He to be polarized and quickly moved in front of the electron-beam, making it possible to use larger targets with higher electron-beam currents than ever before. This means more electrons scatter and we get more data. And by studying our targets in detail prior to using them in our experiments, we have found techniques to take effects which could have been detrimental to target quality and turn them to our advantage! It?s a real case of making lemonade out of lemons. We also use laser spectroscopy to study the absorption lines of alkali-metals in the target (potassium and rubidium, specifically). We add these alkali-metals to our target to facilitate polarizing the 3He. We can use the measurement of these pressure broadened absorption lines to determine the 3He density inside of the target with great precision. Historically, we understood the width of these lines would be dependent on the temperature of the target. Specifically, if I raise the temperature, the width should get bigger. I found that was not the case, which was very confusing at first, though very exciting now that I realize the data are self-consistent and suggestive of unexpected behavior. This thesis details the development of high quality, glass, polarized 3He targets for the 2020 An 1 /dn 2 and 2023 Gn E experiments, which utilized the first 3He convection targets and broke records in target quality. This thesis also covers the initial development of metal windows for the next-generation of 3He target-cells. Finally, this thesis documents the temperature dependence of the width of potassium (K) and rubidium (Rb) absorption lines as measured with laser spectroscopy.

Jantzi, Christopher↗

Application of a data-mining method based on Bayesian networks to lesion-deficit analysis

Although lesion-deficit analysis (LDA) has provided extensive information about structure-function associations in the human brain, LDA has suffered from the difficulties inherent to the analysis of spatial data, i.e., there are many more variables than subjects, and data may be difficult to model using standard distributions, such as the normal distribution. We herein describe a Bayesian method for LDA; this method is based on data-mining techniques that employ Bayesian networks to represent structure-function associations. These methods are computationally tractable, and can represent complex, nonlinear structure-function associations. When applied to the evaluation of data obtained from a study of the psychiatric sequelae of traumatic brain injury in children, this method generates a Bayesian network that demonstrates complex, nonlinear associations among lesions in the left caudate, right globus pallidus, right side of the corpus callosum, right caudate, and left thalamus, and subsequent development of attention-deficit hyperactivity disorder, confirming and extending our previous statistical analysis of these data. Furthermore, analysis of simulated data indicates that methods based on Bayesian networks may be more sensitive and specific for detecting associations among categorical variables than methods based on chi-square and Fisher exact statistics.

NASA Discipline Neuroscience↗

Statistics of pressure fluctuations in turbulent kinetic plasmas

ABSTRACT In this study, we explore the statistics of pressure fluctuations in kinetic collisionless turbulence. A 2.5D kinetic particle-in-cell simulation of decaying turbulence is used to investigate pressure balance via the evolution of thermal and magnetic pressure in a plasma with β of order unity. We also discuss the behaviour of thermal, magnetic, and total pressure structure functions and their corresponding wavenumber spectra. The total pressure spectrum exhibits a slope of −7/3 extending for about a decade in the ion-inertial range. In contrast, shallower −5/3 spectra are characteristic of the magnetic pressure and thermal pressure. The steeper total pressure spectrum is a consequence of cancellation caused by density-magnetic field magnitude anti-correlation. Further, we evaluate higher order total pressure structure functions in an effort to discuss intermittency and compare the power exponents with higher order structure functions of velocity and magnetic fluctuations. Finally, applications to astrophysical systems are also discussed.

Astronomy & Astrophysics↗

Granal thylakoid structure and function: explaining an enduring mystery of higher plants

Summary In higher plants, photosystems II and I are found in grana stacks and unstacked stroma lamellae, respectively. To connect them, electron carriers negotiate tortuous multi‐media paths and are subject to macromolecular blocking. Why does evolution select an apparently unnecessary, inefficient bipartition? Here we systematically explain this perplexing phenomenon. We propose that grana stacks, acting like bellows in accordions, increase the degree of ultrastructural control on photosynthesis through thylakoid swelling/shrinking induced by osmotic water fluxes. This control coordinates with variations in stomatal conductance and the turgor of guard cells, which act like an accordion's air button. Thylakoid ultrastructural dynamics regulate macromolecular blocking/collision probability, direct diffusional pathlengths, division of function of Cytochrome b 6 f complex between linear and cyclic electron transport, luminal pH via osmotic water fluxes, and the separation of pH dynamics between granal and lamellar lumens in response to environmental variations. With the two functionally asymmetrical photosystems located distantly from each other, the ultrastructural control, nonphotochemical quenching, and carbon‐reaction feedbacks maximally cooperate to balance electron transport with gas exchange, provide homeostasis in fluctuating light environments, and protect photosystems in drought. Grana stacks represent a dry/high irradiance adaptation of photosynthetic machinery to improve fitness in challenging land environments. Our theory unifies many well‐known but seemingly unconnected phenomena of thylakoid structure and function in higher plants.

59 BASIC BIOLOGICAL SCIENCES↗

Ballistic Puncture Self-Healing Polymeric Materials

Space exploration launch costs on the order of $10,000 per pound provide an incentive to seek ways to reduce structural mass while maintaining structural function to assure safety and reliability. Damage-tolerant structural systems provide a route to avoiding weight penalty while enhancing vehicle safety and reliability. Self-healing polymers capable of spontaneous puncture repair show promise to mitigate potentially catastrophic damage from events such as micrometeoroid penetration. Effective self-repair requires these materials to quickly heal following projectile penetration while retaining some structural function during the healing processes. Although there are materials known to possess this capability, they are typically not considered for structural applications. Current efforts use inexpensive experimental methods to inflict damage, after which analytical procedures are identified to verify that function is restored. Two candidate self-healing polymer materials for structural engineering systems are used to test these experimental methods.

Gordon, Keith L.↗

Fungal community structure and function shifts with atmospheric nitrogen deposition

Fungal decomposition of soil organic matter depends on soil nitrogen (N) availability. This ecosystem process is being jeopardized by changes in N inputs that have resulted from a tripling of atmospheric N deposition in the last century. Soil fungi are impacted by atmospheric N deposition due to higher N availability, as soils are acidified, or as micronutrients become increasingly limiting. Fungal communities that persist with chronic N deposition may be enriched with traits that enable them to tolerate environmental stress, which may trade-off with traits enabling organic matter decomposition. We hypothesized that fungal communities would respond to N deposition by shifting community composition and functional gene abundances toward those that tolerate stress but are weak decomposers. We sampled soils at seven eastern US hardwood forests where ambient N deposition varied from 3.2 to 12.6 kg N ha -1 year -1 , five of which also have experimental plots where atmospheric N deposition was simulated through fertilizer application treatments (25–50 kg N ha -1 year -1 ). Fungal community and functional responses to fertilizer varied across the ambient N deposition gradient. Fungal biomass and richness increased with simulated N deposition at sites with low ambient deposition and decreased at sites with high ambient deposition. Fungal functional genes involved in hydrolysis of organic matter increased with ambient N deposition while genes involved in oxidation of organic matter decreased. One of four genes involved in generalized abiotic stress tolerance increased with ambient N deposition. In summary, we found that the divergent response to simulated N deposition depended on ambient N deposition levels. Fungal biomass, richness, and oxidative enzyme potential were reduced by N deposition where ambient N deposition was high suggesting fungal communities were pushed beyond an environmental stress threshold. Fungal community structure and function responses to N enrichment depended on ambient N deposition at a regional scale.

59 BASIC BIOLOGICAL SCIENCES↗

More is definitely different: the zebrafish as witness: Comment on ”Structure and function in artificial, zebrafish and human neural networks” by Peng Ji et al.

We report half a century ago, in his foundation paper More is different, Anderson stated the relevance of including multiple scales of interaction, instead of trying to reduce everything to fundamental principles. By doing so, one may witness phenomena that were not expected by looking at each individual components separately. This idea finds indeed numerous realizations such as the synchronization phenomenon, where a multitude of dynamical systems suddenly start to behave coherently together, or the spreading of diseases over entire populations, to name only two examples. But if one would have to give a single example of a system where the multiplicity of interaction scales is of utmost importance, it would probably be the brain. In their review, Ji et al. give a comprehensive overview of the multiple scales of science required in the investigation of structural and functional brain networks, as well as their interplay.

59 BASIC BIOLOGICAL SCIENCES↗

Influence of cellular redox reactions on the structure and function of light harvesting and photosystems

Photosynthesis enables the conversion of one of the most abundant and free forms of energy, sunlight, into chemical bonds through the utilization of highly tailored protein complexes. These enzymes work in unison to absorb, convert, and transform light into high-energy electrons which are used for various functions important to metabolism and cellular protection. Over the last ∼50 years, photosynthetic organisms, such as cyanobacteria, have been adapted and engineered to produce valuable compounds like hydrogen and ethylene, among others. Often this is performed by removing native and/or adding in exogenous energy utilization pathways so that light energy is re-directed towards the synthesis of desired compounds. However, the interplay between primary light capture, conversion reactions, and the downstream electron utilization sinks is not fully understood. Further complicating these strategies are the plethora of compensatory mechanisms that facilitate steady electron flow and the maintenance of photosynthesis under dynamic conditions. This manifests as structural and functional plasticity of the photosynthetic machinery, often seen in modulations of oligomeric compositions or changes in protein-protein interactions and coupling with redox enzymes. Understanding these mechanisms is crucial to biotechnology applications because re-engineering electron utilization sinks has profoundly different effects on the light capture and conversion reactions of photosynthesis. Optimization requires a molecular-level understanding of the functional interrelationships between electron sinks and photosynthetic components that influence photosynthetic efficiencies to realize potential improvements in product yields. Here, we aim to highlight how perturbation of reductive reactions is revealing the functional plasticity in key components of the photosynthetic energy transduction pathway.

59 BASIC BIOLOGICAL SCIENCES↗

Functional Janus structured liquids and aerogels

Janus structures have unique properties due to their distinct functionalities on opposing faces, but have yet to be realized with flowing liquids. We demonstrate such Janus liquids with a customizable distribution of nanoparticles (NPs) throughout their structures by joining two aqueous streams of NP dispersions in an apolar liquid. Using this anisotropic integration platform, different magnetic, conductive, or non-responsive NPs can be spatially confined to opposite sides of the original interface using magnetic graphene oxide (mGO)/GO, Ti 3 C 2 T x /GO, or GO suspensions. The resultant Janus liquids can be used as templates for versatile, responsive, and mechanically robust aerogels suitable for piezoresistive sensing, human motion monitoring, and electromagnetic interference (EMI) shielding with a tuned absorption mechanism. The EMI shields outperform their current counterparts in terms of wave absorption, i.e., SE T ≈ 51 dB, SE R ≈ 0.4 dB, and A = 0.91, due to their high porosity ranging from micro- to macro-scales along with non-interfering magnetic and conductive networks imparted by the Janus architecture.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Overexpression of neurofilament H disrupts normal cell structure and function

Studying exogenously expressed tagged proteins in live cells has become a standard technique for evaluating protein distribution and function. Typically, expression levels of experimentally introduced proteins are not regulated, and high levels are often preferred to facilitate detection. However, overexpression of many proteins leads to mislocalization and pathologies. Therefore, for normative studies, moderate levels of expression may be more suitable. To understand better the dynamics of intermediate filament formation, transport, and stability in a healthy, living cell, we inserted neurofilament heavy chain (NFH)-green fluorescent protein (GFP) fusion constructs in adenoviral vectors with tetracycline (tet)-regulated promoters. This system allows for turning on or off the synthesis of NFH-GFP at a selected time, for a defined period, in a dose-dependent manner. We used this inducible system for live cell imaging of changes in filament structure and cell shape, motility, and transport associated with increasing NFH-GFP expression. Cells with low to intermediate levels of NFH-GFP were structurally and functionally similar to neighboring, nonexpressing cells. In contrast, overexpression led to pathological alterations in both filament organization and cell function. Copyright 2002 Wiley-Liss, Inc.

Non-NASA Center↗

The Influence of Ecological Isolation on the Structural and Functional Stability of Complex Microbial Communities

To help understand how the behavior of microorganisms and microbial communities in insular space habitats may differ from the behavior of these groups on Earth, long-term incubations (100+ days) were conducting using wastewater bioreactors (batch fed) designed to mimic "closed" and "open" ecological systems. The issue of immigration was considered, and the goal of the research was to determine whether the stability of microbial communities in space is reduced due to their prolonged isolation. Bioreactors were established by inoculating flasks of sterile synthetic wastewater with the microbial community obtained from a local treatment facility; each day, one-third of the medium in the flask was replaced with an equal volume of sterile artificial wastewater. Flasks were divided into two treatments: "closed" and "open" to recruitment of additional microorganisms. "Closed" flasks were maintained as described above, while the medium used to feed the "open" flasks was supplemented daily with a small amount of raw sewage (which provided a continuous source of new potential community members). Significant differences in microbial community structure and function developed in the two sets of communities, and the results suggest that the open community was more stable and better able to adjust to changing environmental conditions. Each community's resistance to environmental (temperature fluctuations) and biological stresses (starvation and invasion by an opportunistic pathogen Pseudomonas aeruginosa) was monitored. Experiments were also conducted to determine whether the effect of isolation changes depending on the microbial communities' initial diversity or composition; communities with a low(er) initial diversity were less stable. Overall, the results indicate that isolation will be an important factor influencing the activity of microbial communities on board spacecraft. A possible way of mitigating these effects would be to include communities with high initial diversity or to periodically re-inoculate the systems using diverse inocula transported from Earth.

Franklin, R. B.↗

On the Use of 3dB Qualification Margin for Structural Parts on Expendable Launch Vehicles

The standard random vibration qualification test used for Expendable Launch Vehicle components is Maximum Predicted Environment (MPE) + 6dB for a duration of 4 times the service life of the part. This can be a severe qualification test for these fatigue-sensitive structures. This paper uses flight data from several launch vehicles to establish that reducing the qualification approach to MPE+3dB for the duration of the peak environment (1x life) is valid for fatigue-sensitive structural components. Items that can be classified as fatigue-sensitive are probes, ducts, tubing, bellows, hoses, and any non-functional structure. Non-functional structure may be flight critical or carry fluid, but it cannot include any moving parts or electronics. This reduced qualification approach does not include primary or secondary structure which would be exclusively designed by peak loads, either transient or quasi-static, that are so large and of so few cycles as to make fatigue a moot point.

Yunis, Isam↗

Mapping the Gas Turbulence in the Coma Cluster: Predictions for Astro-H

Astro-H will be able for the first time to map gas velocities and detect turbulence in galaxy clusters. One of the best targets for turbulence studies is the Coma cluster, due to its proximity, absence of a cool core, and lack of a central active galactic nucleus. To determine what constraints Astro-H will be able to place on the Coma velocity field, we construct simulated maps of the projected gas velocity and compute the second-order structure function, an analog of the velocity power spectrum. We vary the injection scale, dissipation scale, slope, and normalization of the turbulent power spectrum, and apply measurement errors and finite sampling to the velocity field. We find that even with sparse coverage of the cluster, Astro-H will be able to measure the Mach number and the injection scale of the turbulent power spectrum-the quantities determining the energy flux down the turbulent cascade and the diffusion rate for everything that is advected by the gas (metals, cosmic rays, etc.). Astro-H will not be sensitive to the dissipation scale or the slope of the power spectrum in its inertial range, unless they are outside physically motivated intervals. We give the expected confidence intervals for the injection scale and the normalization of the power spectrum for a number of possible pointing configurations, combining the structure function and velocity dispersion data. Importantly, we also determine that measurement errors on the line shift will bias the velocity structure function upward, and show how to correct this bias.

clusters: intracluster medium↗

Cell fine structure and function - Past and present

Electron microscopic studies of nerve membrane fine structure, discussing cell membrane multienzyme and macromolecular energy and information transduction, protein synthesis and nucleic acids interrelations

Fernandez-Moran, H.↗

Structure and function of an inorganic-organic separator for electrochemical cells: Preliminary study

The structure of a new separator material for electrochemical cells has been investigated. Investigation into details of the separator structure showed it to be multilayered and to consist mainly of a quasi-impervious organic skin, a porous region of mixed organic and inorganic material, and an area of nonuniformly treated substrate. The essential feature of the coating (slurry) is believed to be interconnected pores which allow ionic conductivity. The interconnected pores are believed to be formed by the interaction of the plasticizer and inorganic fibers. The major failure mode of silver zinc cells using such a separator (zinc nodules shorting adjacent plates) was investigated.

Bozek, J. M.↗

Structural and functional remodeling of skeletal muscle microvasculature is induced by simulated microgravity

Hindlimb unloading of rats results in a diminished ability of skeletal muscle arterioles to constrict in vitro and elevate vascular resistance in vivo. The purpose of the present study was to determine whether alterations in the mechanical environment (i.e., reduced fluid pressure and blood flow) of the vasculature in hindlimb skeletal muscles from 2-wk hindlimb-unloaded (HU) rats induces a structural remodeling of arterial microvessels that may account for these observations. Transverse cross sections were used to determine media cross-sectional area (CSA), wall thickness, outer perimeter, number of media nuclei, and vessel luminal diameter of feed arteries and first-order (1A) arterioles from soleus and the superficial portion of gastrocnemius muscles. Endothelium-dependent dilation (ACh) was also determined. Media CSA of resistance arteries was diminished by hindlimb unloading as a result of decreased media thickness (gastrocnemius muscle) or reduced vessel diameter (soleus muscle). ACh-induced dilation was diminished by 2 wk of hindlimb unloading in soleus 1A arterioles, but not in gastrocnemius 1A arterioles. These results indicate that structural remodeling and functional adaptations of the arterial microvasculature occur in skeletal muscles of the HU rat; the data suggest that these alterations may be induced by reductions in transmural pressure (gastrocnemius muscle) and wall shear stress (soleus muscle).

Non-NASA Center↗