The amino acid sequence of Chromatium ferredoxin
Amino acid sequence of Chromatium ferredoxin molecule compared with other ferredoxins concerning structural, functional and evolutionary relationships
Evans, M. C. W.↗
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When Do Band Gap Calculations Agree with Experiments in Monolayer-Protected Cu 14 and Au 20 Atomically Precise Nanoclusters? A (TD)-DFT Comparison of HOMO–LUMO, Fundamental, Optical, and Electrochemical Energy Gaps
In view of the tremendous progress in atomically precise metal nanoclusters where electrochemical and optical energetics are routinely supported by computations to establish structure−function correlations, we explore the relationship between different protocols for measuring and computing band gaps of two distinct organic ligand-protected nanoclusters: [Cu 14 H 10 (MBN) 3 (PPh 3 ) 8 ] + and Au 20 (TBBT) 16 . Through UV/visible spectroscopy and differential pulse voltammetry, we measure optical and electrochemical band gaps in those systems. We then compare these experimentally determined gaps to HOMO−LUMO gaps, fundamental gaps, vertical excitation energies, and E o ox − E o red potentials computed using different density functional theory (DFT) or time-dependent DFT (TDDFT) methods. Specifically, in both copper and gold nanoclusters, we test the effect of truncating inert ligands from the model and compare density functionals with varying degrees of Hartree−Fock (HF) exchange from 0 to 50%, range-separated hybrids with a varying long-range tuning parameter, different correlation functionals, basis sets, and (equilibrium and nonequilibrium) continuum solvation models. Despite having different frontier orbital characters (the copper nanocluster has a metal-to-ligand charge transfer character while the gold nanocluster has metal-centered frontier orbitals), both nanoclusters display a similar sensitivity of the HOMO−LUMO gap to the HF exchange that is partially mitigated when computing the fundamental, optical, and electrochemical gaps. Other factors, such as the nature of the correlation functional, basis set, and geometry relaxation, have a considerably smaller effect on computed band gaps in these systems. Overall, this work provides guidelines for factors of varied importance for correlating computed and experimental band gap values.
Chemical calculations↗
Role of the flocculus of the cerebellum in motor learning of the vestibulo-ocular reflex
Structure-function studies at the systems level are an effective method for understanding the relationship of the central nervous system to behavior. Motor learning or adaptation of the vestibulo-ocular reflex is a clear example wherein this approach has been productive. During a vestibulo-ocular reflex the brain converts a head velocity signal, transduced through the vestibular semicircular canals, into an eye movement command delivered to the extraocular muscles. If the viewed target remains on the fovea of the retina, the reflex is compensatory, and its gain, eye velocity/head velocity, is one. When the image of the viewed object slips across the retina, visual acuity decreases, and the gain of the reflex, which is no longer one, is plastically adapted or adjusted until retinal stability is restored. The anatomic substrate for this plasticity thus involves brain structures in which visual-vestibular interaction can potentially occur, as well as vestibular and visual sensory and oculomotor motor structures. Further, it has been known for many years that removal of the flocculus of the cerebellum permanently precludes further vestibulo-ocular reflex adaptation, demonstrating the involvement of the cerebellum in this behavior. Maekawa and Simpson (J Neurophysiol 1973;36: 649-66) discovered that one visual input to the flocculus involved the accessory optic system and the inferior olive. Ensuing work has demonstrated that the visual signals used to adapt the vestibulo-ocular reflex are transmitted by this accessory optic system to the flocculus and subsequently to brain stem structures involved in vestibulo-ocular reflex plasticity. Presently the inclusive list of anatomic sites involved in vestibulo-ocular reflex circuitry and its adaptive plasticity is small. Our laboratory continues to believe that this behavior should be caused by interactions within this small class of neurons. By studying each class of identified neuron and its interactions with others within the list, we hope to ultimately understand the mechanisms used by the brain in the expression of this behavior.
Non-NASA Center↗
A simulator for evaluating methods for the detection of lesion-deficit associations
Although much has been learned about the functional organization of the human brain through lesion-deficit analysis, the variety of statistical and image-processing methods developed for this purpose precludes a closed-form analysis of the statistical power of these systems. Therefore, we developed a lesion-deficit simulator (LDS), which generates artificial subjects, each of which consists of a set of functional deficits, and a brain image with lesions; the deficits and lesions conform to predefined distributions. We used probability distributions to model the number, sizes, and spatial distribution of lesions, to model the structure-function associations, and to model registration error. We used the LDS to evaluate, as examples, the effects of the complexities and strengths of lesion-deficit associations, and of registration error, on the power of lesion-deficit analysis. We measured the numbers of recovered associations from these simulated data, as a function of the number of subjects analyzed, the strengths and number of associations in the statistical model, the number of structures associated with a particular function, and the prior probabilities of structures being abnormal. The number of subjects required to recover the simulated lesion-deficit associations was found to have an inverse relationship to the strength of associations, and to the smallest probability in the structure-function model. The number of structures associated with a particular function (i.e., the complexity of associations) had a much greater effect on the performance of the analysis method than did the total number of associations. We also found that registration error of 5 mm or less reduces the number of associations discovered by approximately 13% compared to perfect registration. The LDS provides a flexible framework for evaluating many aspects of lesion-deficit analysis.
NASA Program Biomedical Research and Countermeasur↗
Evidence for turbulence in H II regions
The results of extensive velocity mapping across the face of Galactic H II regions are used to make an accurate determination of velocity dispersions and structure functions for a number of nebulae. A dependence of random velocities upon scale, indicating the presence of turbulence, is found. These relationships are compared with the predictions of models for Kolmogorov turbulence in H II regions, and poor agreement is found. A more general formulation shows that there is no single power law for the velocity-distance relation that fits the observations. From the variations in the shape of the observed structure function, it is concluded that the turbulent energy enters the nebulae at several different scales. It is also found that velocity broadening of the observed lines is significantly greater than would be inferred from the velocity scatter across the face of the nebulae.
O'Dell, C. R.↗
An evaluation of satellite-derived humidity and its relationship to convective development
An aircraft prototype of the High-Resolution Interferometer Sounder (HIS) was flown over Tennessee and northern Alabama during summer 1986. The HIS temperature and dewpoint soundings were examined on two flight days to determine their error characteristics and utility in mesoscale analyses. Random errors were calculated from structure functions while total errors were obtained by pairing the HIS soundings with radiosonde-derived profiles. Random temperature errors were found to be less than 1 C at most levels, but random dewpoint errors ranged from 1 to 5 C. Total errors of both parameters were considerably greater, with dewpoint errors especially large on the day having a pronounced subsidence inversion. Cumulus cloud cover on 15 June limited HIS mesoscale analyses on that day. Previously undetected clouds were found in many HIS fields of view, and these probably produced the low-level horizontal temperature and dewpoint variations observed in the retrievals. HIS dewpoints at 300 mb indicated a strong moisture gradient that was confirmed by GOES 6.7-micron imagery. HIS mesoscale analyses on 19 June revealed a tongue of humid air stretching across the study area. The moist region was confirmed by radiosonde data and imagery from the Multispectral Atmospheric Mapping Sensor (MAMS). Convective temperatures derived from HIS retrievals helped explain the cloud formation that occurred after the HIS overflights. Crude estimates of Bowen ratio were obtained from HIS data using a mixing-line approach. Values indicated that areas of large sensible heat flux were the areas of first cloud development. These locations were also suggested by GOES visible and infrared imagery. The HIS retrievals indicated that areas of thunderstorm formation were regions of greatest instability. Local landscape variability and atmospheric temperature and humidity fluctuations were found to be important factors in producing the cumulus clouds on 19 June. HIS soundings were capable of detecting some of this variability. The authors were impressed by HIS's performance on the two study days.
Fuelberg, Henry E.↗
An ecological framework for microbial metabolites in the ocean ecosystem
The ocean microbe‐metabolite network involves thousands of individual metabolites that encompass a breadth of chemical diversity and biological functions. These microbial metabolites mediate biogeochemical cycles, facilitate ecological relationships, and impact ecosystem health. While analytical advancements have begun to illuminate such roles, a challenge in navigating the deluge of marine metabolomics information is to identify a subset of metabolites that have the greatest ecosystem impact. Here, we present an ecological framework to distill knowledge of fundamental metabolites that underpin marine ecosystems. We borrow terms from macroecology that describe important species, namely “dominant,” “keystone,” and “indicator” species, and apply these designations to metabolites within the ocean microbial metabolome. These selected metabolites may shape marine community structure, function, and health and provide focal points for enhanced study of microbe‐metabolite networks. Applying ecological concepts to marine metabolites provides a path to leverage metabolomics data to better describe and predict marine microbial ecosystems.
microbial metabolites↗
Characteristic Ultraviolet/Optical Timescales in Active Galactic Nuclei
The UV/optical light curves of active galactic nuclei (AGNs) may be roughly characterized by a periodic fractional flux variations of approx. 10% on timescales of 1 month. The physical mechanism(s) responsible remain ill defined. We present a structure function analysis, i.e., measure the power distribution over a range of timescales tau, of 13 AGNs to constrain the origin of UV/optical emission. On timescales tau approx. 5- 60 days, the mean UV and optical power density spectra (PDS) are equivalent. This may suggest that the underlying energy generating mechanism is identical. The combined W/optical PDS is P(f) proportional to f(sup -alpha)- with alpha = 2.13(sup +0.22, sub -0.06). For sources with measured X-ray PDS indices, we find they are indistinguishable from their UV/optical counterparts. This supports scenarios whereby X-rays are generated via Compton upscattering of UV photons, to later radiatively drive optical variations. At the same time, we present evidence for characteristic variability timescales tau(sub char) of approx. 5-100 days in 10 sources. These variability timescales combined with reverberation based masses M suggest a M - tau(sub char) relationship; higher mass systems have larger characteristic timescales. The UV tau(sub char) may possibly reflect dynamical or accretion disk thermal timescales. We find suggestive evidence for a dichotomy, at tau approx. 30 days and M approx. l0(exp 7) solar mass, between short- and long-time scale optical variations. These optical variations may be attributable to dynamical and accretion disk thermal or starburst activity timescales, respectively.
Collier, Stefan↗
Structural, functional, and regulatory evaluation of a cysteine post-translationally modified Gcn5-related N -acetyltransferase
Polyamines within the cell are tightly regulated by spermidine/spermine N-acetyltransferase (SSAT) enzymes. While several SSATs have been investigated in different bacterial species, there is still a significant gap in knowledge about which proteins are functional SSATs in many organisms. For example, while it is known that Pseudomonas aeruginosa synthesizes the polyamine spermidine, the SSAT that acetylates this molecule and its importance in regulating intracellular polyamines remains unknown. We previously identified a candidate Gcn5-related N-acetyltransferase (GNAT) protein from P. aeruginosa (PA2271) that could fulfill this role since it acetylates spermidine, but no further studies were conducted. Here, we explored the structure/function relationship of the PA2271 protein by determining its X-ray crystal structure and performing enzyme kinetics assays. We also identified active site residues that are essential for catalysis and substrate binding. As the study progressed, we encountered results that led us to explore the importance of four cysteine residues on enzyme activity and disulfide bond formation or modification of cysteine residues. We found these cysteine residues in PA2271 are important for protein solubility and activity, and there is an interrelationship between cysteine residues that contribute to these effects. Furthermore, we also found disulfide bonds could form between C 121 and C 165 and speculate that these residues may contribute to redox regulation of PA2271 protein activity.
59 BASIC BIOLOGICAL SCIENCES↗
Defining the Relationship Between Biomarkers of Oxidative and Inflammatory Stress and the Risk for Atherosclerosis in Astronauts During and After Long-Duration Spaceflight
Future human space travel will primarily consist of long-duration missions aboard the International Space Station (ISS) or exploration class missions to Mars, its moons, or nearby asteroids. These missions will expose astronauts to increased risk of oxidative and inflammatory damage primarily from radiation, but also from psychological stress, reduced physical activity, diminished nutritional status, and, in the case of extravehicular activity, hyperoxic exposure. There is evidence that increased oxidative damage and inflammation can accelerate the development of atherosclerosis. PURPOSE The purpose of this proposal is to identify biomarkers of oxidative and inflammatory stress and to correlate them to indices of atherosclerosis risk before, during, and after long-duration spaceflight. METHODS To meet the objectives of the study, we will study astronauts before, during, and up to 5 years after long-duration missions aboard ISS. Biomarkers of oxidative and inflammatory stress, some of which we have previously shown to be elevated with spaceflight, will be measured before, during, and after spaceflight. Arterial structure will be monitored using ultrasound to measure carotid intima-medial thickness before, during, and after weightlessness. Carotid intima-medial thickness has been shown to be a better indicator than Framingham Risk scores for prediction of atherosclerosis. Arterial function will be monitored using brachial flow-mediated dilation before flight and after landing. Brachial flow-mediated dilation is a good index of endothelium-dependent vasodilation, which is a sensitive predictor of atherosclerotic risk. This is the first study to propose assessing atherosclerotic risk using biochemical, structural, and functional measures before, during, and immediately after spaceflight and structural functional measures for up to 5 years after landing. EXPECTED RESULTS We hypothesize that these biomarkers of oxidative and inflammatory stress will be increased with spaceflight and will correlate with increased carotid intima-medial thickness in- and postflight and with decreased flow-mediated dilation after the mission. Furthermore, we hypothesize that measures of oxidative stress will return to baseline after flight, but that biomarkers of inflammatory stress and vascular indices of atherosclerosis risk will remain elevated.
Lee, Stuart M. C.↗
The Effects of Long Duration Head Down Tilt Bed Rest on Neurocognitive Performance: The Effects of Exercise Interventions
We are conducting ongoing experiments in which we are performing structural and functional magnetic resonance brain imaging to identify the relationships between changes in neurocognitive function and neural structural alterations following a six month International Space Station mission and following 70 days exposure to a spaceflight analog, head down tilt bedrest. Our central hypothesis is that measures of brain structure, function, and network integrity will change from pre to post intervention (spaceflight, bedrest). Moreover, we predict that these changes will correlate with indices of cognitive, sensory, and motor function in a neuroanatomically selective fashion. Our interdisciplinary approach utilizes cutting edge neuroimaging techniques and a broad ranging battery of sensory, motor, and cognitive assessments that will be conducted pre flight, during flight, and post flight to investigate potential neuroplastic and maladaptive brain changes in crewmembers following long-duration spaceflight. Success in this endeavor would 1) result in identification of the underlying neural mechanisms and operational risks of spaceflight-induced changes in behavior, and 2) identify whether a return to normative behavioral function following re-adaptation to Earth's gravitational environment is associated with a restitution of brain structure and function or instead is supported by substitution with compensatory brain processes. Our ongoing bed rest participants are also engaging in exercise studies directed by Dr. Lori Ploutz Snyder. In this presentation, I will briefly highlight the existing literature linking exercise and fitness to brain and behavioral functions. I will also overview the metrics from my study that could be investigated in relation to the exercise and control subgroups.
Seidler, R. D.↗
The Effects of Spaceflight and a Spaceflight Analog on Neurocognitive Perfonnance: Extent, Longevity, and Neural Bases
We are conducting ongoing experiments in which we are performing structural and functional magnetic resonance brain imaging to identify the relationships between changes in neurocognitive function and neural structural alterations following a six month International Space Station mission and following 70 days exposure to a spaceflight analog, head down tilt bedrest. Our central hypothesis is that measures of brain structure, function, and network integrity will change from pre to post intervention (spaceflight, bedrest). Moreover, we predict that these changes will correlate with indices of cognitive, sensory, and motor function in a neuroanatomically selective fashion. Our interdisciplinary approach utilizes cutting edge neuroimaging techniques and a broad ranging battery of sensory, motor, and cognitive assessments that will be conducted pre flight, during flight, and post flight to investigate potential neuroplastic and maladaptive brain changes in crewmembers following long-duration spaceflight. Success in this endeavor would 1) result in identification of the underlying neural mechanisms and operational risks of spaceflight-induced changes in behavior, and 2) identify whether a return to normative behavioral function following re-adaptation to Earth's gravitational environment is associated with a restitution of brain structure and function or instead is supported by substitution with compensatory brain processes. With the bedrest study, we will be able to determine the neural and neurocognitive effects of extended duration unloading, reduced sensory inputs, and increased cephalic fluid distribution. This will enable us to parse out the multiple mechanisms contributing to any spaceflight-induced neural structural and behavioral changes that we observe in the flight study. In this presentation I will discuss preliminary results from six participants who have undergone the bed rest protocol. These individuals show decrements in balance and functional mobility, and alterations in brain structure and function, in association with extended bed rest.
Seidler, R. D.↗
Proteins with Novel Structure, Function and Dynamics
Recently, a small enzyme that ligates two RNA fragments with the rate of 10(exp 6) above background was evolved in vitro (Seelig and Szostak, Nature 448:828‐831, 2007). This enzyme does not resemble any contemporary protein (Chao et al., Nature Chem. Biol. 9:81‐83, 2013). It consists of a dynamic, catalytic loop, a small, rigid core containing two zinc ions coordinated by neighboring amino acids, and two highly flexible tails that might be unimportant for protein function. In contrast to other proteins, this enzyme does not contain ordered secondary structure elements, such as alpha‐helix or beta‐sheet. The loop is kept together by just two interactions of a charged residue and a histidine with a zinc ion, which they coordinate on the opposite side of the loop. Such structure appears to be very fragile. Surprisingly, computer simulations indicate otherwise. As the coordinating, charged residue is mutated to alanine, another, nearby charged residue takes its place, thus keeping the structure nearly intact. If this residue is also substituted by alanine a salt bridge involving two other, charged residues on the opposite sides of the loop keeps the loop in place. These adjustments are facilitated by high flexibility of the protein. Computational predictions have been confirmed experimentally, as both mutants retain full activity and overall structure. These results challenge our notions about what is required for protein activity and about the relationship between protein dynamics, stability and robustness. We hypothesize that small, highly dynamic proteins could be both active and fault tolerant in ways that many other proteins are not, i.e. they can adjust to retain their structure and activity even if subjected to mutations in structurally critical regions. This opens the doors for designing proteins with novel functions, structures and dynamics that have not been yet considered.
Proteins↗
Long Duration Head Down Tilt Bed Rest and Spaceflight Effects on Neurocognitive Performance: Extent, Longevity and Neural Bases
We have recently completed a long duration head down tilt bed rest (HDBR) study in which we performed structural and functional magnetic resonance brain imaging to identify the relationships between changes in neurocognitive function and neural structural alterations in a spaceflight analog environment. We are also collecting the same measures in crewmembers prior to and following a six month International Space Station mission. We will present data demonstrating that bed rest resulted in functional mobility and balance deterioration with recovery post-HDBR. We observed numerous changes in brain structure, function, and connectivity relative to a control group which were associated with pre to post bed rest changes in sensorimotor function. For example, gray matter volume (GMv) increased in posterior parietal areas and decreased in frontal regions. GMv increases largely overlapped with fluid decreases and vice versa. Larger increases in precentral gyrus (M1)/ postcentral gyrus (S1+2) GMv and fluid decreases were associated with smaller balance decrements. Vestibular activation in the bilateral insular cortex increased with bed rest and subsequently recovered. Larger increases in vestibular activation in multiple brain regions were associated with greater decrements in balance and mobility. We found connectivity increases between left M1 with right S1+2 and the superior parietal lobule, and right vestibular cortex with the cerebellum. Decreases were observed between right Lobule VIII with right S1+2 and the supramarginal gyrus, right posterior parietal cortex (PPC) with occipital regions, and the right superior posterior fissure with right Crus I and II. Connectivity strength between left M1 and right S1+2/superior parietal lobule increased the most in individuals that exhibited the least balance impairments. In sum, we observed HDBR-related changes in measures of brain structure, function, and network connectivity, which correlated with indices of sensorimotor function. Recovery was observed post HDBR but remained incomplete at 12 days post-HDBR. Preliminary findings from our parallel ongoing flight study will be compared and contrasted with bed rest results during this presentation.
Seidler, R. D.↗
Spaceflight Effects on Neurocognitive Performance: Extent, Longevity and Neural Bases
We are conducting ongoing experiments in which we are performing structural and functional magnetic resonance brain imaging to identify the relationships between changes in neurocognitive function and neural structural alterations following a six month International Space Station mission. Our central hypothesis is that measures of brain structure, function, and network integrity will change from pre to post spaceflight. Moreover, we predict that these changes will correlate with indices of cognitive, sensory, and motor function in a neuroanatomically selective fashion. Our interdisciplinary approach utilizes cutting edge neuroimaging techniques and a broad ranging battery of sensory, motor, and cognitive assessments that are conducted pre flight, during flight, and post flight to investigate potential neuroplastic and maladaptive brain changes in crewmembers following long-duration spaceflight. Success in this endeavor would 1) result in identification of the underlying neural mechanisms and operational risks of spaceflight-induced changes in behavior, and 2) identify whether a return to normative behavioral function following re-adaptation to Earth's gravitational environment is associated with a restitution of brain structure and function or instead is supported by substitution with compensatory brain processes. We have collected data on several crewmembers and preliminary findings will be presented. Eventual comparison to results from our parallel bed rest study will enable us to parse out the multiple mechanisms contributing to any spaceflight-induced neural structural and behavioral changes that we observe.
Seidler, R. D.↗
Effects of One Year of Spaceflight on Neurocognitive Function
It is known that spaceflight adversely affects human sensorimotor function. With interests in longer duration deep space missions it is important to understand microgravity dose-response relationships. NASA's One Year Mission project allows for comparison of the effects of one year in space with those seen in more typical six month missions to the International Space Station. In the Neuromapping project we are performing structural and functional magnetic resonance brain imaging to identify the relationships between changes in neurocognitive function and neural structural alterations following a six month International Space Station mission. Our central hypothesis is that measures of brain structure, function, and network integrity will change from pre- to post-spaceflight. Moreover, we predict that these changes will correlate with indices of cognitive, sensory, and motor function in a neuroanatomically selective fashion. Our interdisciplinary approach utilizes cutting edge neuroimaging techniques and a broad-ranging battery of sensory, motor, and cognitive assessments that are conducted pre-flight, during flight, and post-flight to investigate potential neuroplastic and maladaptive brain changes in crewmembers following long-duration spaceflight. With the one year mission we had one crewmember participate in all of the same measures pre-, per- and post-flight as in our ongoing study. During this presentation we will provide an overview of the magnitude of changes observed with our brain and behavioral assessments for the one year crewmember in comparison to participants that have completed our six month study to date.
Seidler, R. D.↗
The Effects of Spaceflight and Head Down Tilt Bed Rest on Neurocognitive Performance: Extent, Longevity, and Neural Bases
Spaceflight effects on gait, balance, & manual motor control have been well studied; some evidence for cognitive deficits. Rodent cortical motor & sensory systems show neural structural alterations with spaceflight. specific Aims: Aim 1-Identify changes in brain structure, function, and network integrity as a function of head down tilt bed rest and spaceflight, and characterize their time course. Aim 2-Specify relationships between structural and functional brain changes and performance and characterize their time course.
Seidler, Rachael D.↗
The Effects of Spaceflight on Neurocognitive Performance: Extent, Longevity, and Neural Bases
Spaceflight effects on gait, balance, & manual motor control have been well studied; some evidence for cognitive deficits. Rodent cortical motor & sensory systems show neural structural alterations with spaceflight. We found extensive changes in behavior, brain structure & brain function following 70 days of HDBR. Specific Aim: Aim 1-Identify changes in brain structure, function, and network integrity as a function of spaceflight and characterize their time course. Aim 2-Specify relationships between structural and functional brain changes and performance and characterize their time course.
Seidler, Rachael D.↗