The plant blue light receptor, phot1, a member of the phototropin family (1), is a plasma membrane-associated flavoprotein that contains two (ϳ110 amino acids) flavinbinding domains, LOV1 and LOV2, within its N terminus and a typical serine-threonine protein kinase domain at its C terminus. The LOV (light, oxygen, and voltage) domains belong to the PAS domain superfamily of sensor proteins. In response to blue light, phototropins undergo autophosphorylation. E. coli-expressed LOV domains bind riboflavin-5-monophosphate, are photochemically active, and have major absorption peaks at 360 and 450 nm, with the 450 nm peak having vibronic structure at 425 and 475 nm. These spectral features correspond to the action spectrum for phototropism in higher plants. Near-UV blue light regulates a variety of different responses in higher plants. These include phototropism, the inhibition of hypocotyl elongation, the expression of various genes, and stomatal opening. Phot1 (nph1), the recently discovered blue light receptor, is a member of the phototropin receptor family (1). Phot1 is a plasma membrane-associated flavoprotein that functions as the primary photoreceptor mediating phototropic plant movement (2-4). Phot1 has two 12.1-kDa flavin-binding domains, LOV1 and LOV2, within its N-terminal region and a typical serinethreonine protein kinase domain at the C-terminal region. Heterologous expression studies have shown that phot1 binds FMN 1 as a chromophore and undergoes autophosphorylation in response to light treatment. It has therefore been proposed that this receptor functions as a light-activated serine/threonine kinase (4). The isolated LOV domains from oat phot1 expressed in Escherichia coli have been shown to undergo a cyclic photoreaction upon the absorption of light; LOV1 recovers with a half-time of 11.5 s, whereas LOV2 recovers with a half-time of 27 s (5). In addition, the quantum efficiencies for photoproduct (adduct) formation for LOV1 and LOV2 are ϳ0.045 and 0.44, respectively (5). The ground forms of the LOV domains have major absorption peaks at 360 and 450 nm with the 450 peak having vibronic structure at 425 and 475 nm. Upon absorption of light, the chromophore bleaches 2 in the 450 nm region generating a species that absorbs maximally at 390 nm. This intermediate has been assigned as a flavin-cysteinyl adduct between the protein and the C(4a) carbon of the FMN chromophore. This adduct breaks down spontaneously, returning the protein to its ground form. A LOV2 mutant (LOV2C39A) in which the cysteine that forms the adduct has been mutated to alanine does not undergo this photoreaction (5).Recently the crystal structure of the LOV2 domain from the fern Adiantum capillus-veneris phy3 (6) was solved to 2.7-Å resolution (7). Phy3 is a chimeric photoreceptor with homology to phytochrome at its N-terminal end and an almost complete phototropin at its C-terminal end. Its LOV2 domain shares a 70% sequence homology to the oat phot1 LOV2 (6). The structure indicates that the FMN molecule is held noncovalently within...

With the advent of the Heliophysics/Geospace System Observatory (H/GSO), a complement of multi-spacecraft missions and ground-based observatories to study the space environment, data retrieval, analysis, and visualization of space physics data can be daunting. The Space Physics Environment Data Analysis System (SPEDAS), a grass-roots software development platform ( www.spedas.org ), is now officially supported by NASA Heliophysics as part of its data environment infrastructure. It serves more than a dozen space missions and ground observatories and can integrate the full complement of past and upcoming space physics missions with minimal resources, following clear, simple, and well-proven guidelines. Free, modular and configurable to the needs of individual missions, it works in both command-line (ideal for experienced users) and Graphical User Interface (GUI) mode (reducing the learning curve for first-time users). Both options have “crib-sheets,” user-command sequences in ASCII format that can facilitate record-and-repeat actions, especially for complex operations and plotting. Crib-sheets enhance scientific interactions, as users can move rapidly and accurately from exchanges of technical information on data processing to efficient discussions regarding data interpretation and science. SPEDAS can readily query and ingest all International Solar Terrestrial Physics (ISTP)-compatible products from the Space Physics Data Facility (SPDF), enabling access to a vast collection of historic and current mission data. The planned incorporation of Heliophysics Application Programmer’s Interface (HAPI) standards will facilitate data ingestion from distributed datasets that adhere to these standards. Although SPEDAS is currently Interactive Data Language (IDL)-based (and interfaces to Java-based tools such as Autoplot), efforts are under-way to expand it further to work with python (first as an interface tool and potentially even receiving an under-the-hood replacement). We review the SPEDAS development history, goals, and current implementation. We explain its “modes of use” with examples geared for users and outline its technical implementation and requirements with software developers in mind. We also describe SPEDAS personnel and software management, interfaces with other organizations, resources and support structure available to the community, and future development plans. Electronic Supplementary Material The online version of this article (10.1007/s11214-018-0576-4) contains supplementary material, which is available to authorized users.

1. We studied the responses of 103 neurons in visual area V4 of anesthetized macaque monkeys to two novel classes of visual stimuli, polar and hyperbolic sinusoidal gratings. We suspected on both theoretical and experimental grounds that these stimuli would be useful for characterizing cells involved in intermediate stages of form analysis. Responses were compared with those obtained with conventional Cartesian sinusoidal gratings. Five independent, quantitative analyses of neural responses were carried out on the entire population of cells. 2. For each cell, responses to the most effective Cartesian, polar, and hyperbolic grating were compared directly. In 18 of 103 cells, the peak response evoked by one stimulus class was significantly different from the peak response evoked by the remaining two classes. Of the remaining 85 cells, 74 had response peaks for the three stimulus classes that were all within a factor of 2 of one another. 3. An information-theoretic analysis of the trial-by-trial responses to each stimulus showed that all but two cells transmitted significant information about the stimulus set as a whole. Comparison of the information transmitted about each stimulus class showed that 23 of 103 cells transmitted a significantly different amount of information about one class than about the remaining two classes. Of the remaining 80 cells, 55 had information transmission rates for the three stimulus classes that were all within a factor of 2 of one another. 4. To identify cells that had orderly tuning profiles in the various stimulus spaces, responses to each stimulus class were fit with a simple Gaussian model. Tuning curves were successfully fit to the data from at least one stimulus class in 98 of 103 cells, and such fits were obtained for at least two classes in 87 cells. Individual neurons showed a wide range of tuning profiles, with response peaks scattered throughout the various stimulus spaces; there were no major differences in the distributions of the widths or positions of tuning curves obtained for the different stimulus classes. 5. Neurons were classified according to their response profiles across the stimulus set with two objective methods, hierarchical cluster analysis and multidimensional scaling. These two analyses produced qualitatively similar results. The most distinct group of cells was highly selective for hyperbolic gratings. The majority of cells fell into one of two groups that were selective for polar gratings: one selective for radial gratings and one selective for concentric or spiral gratings. There was no group whose primary selectivity was for Cartesian gratings. 6. To determine whether cells belonging to identified classes were anatomically clustered, we compared the distribution of classified cells across electrode penetrations with the distribution that would be expected if the cells were distributed randomly. Cells with similar response profiles were often anatomically clustered. 7. A position test was used to determine whether response profiles were sensitive to pre...

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Early photolysis intermediates of native bovine rhodopsin (RHO) are investigated by nanosecond laser photolysis near physiological temperature. Absorption difference spectra are collected after excitation with 477-, 532-, and 560-nm laser pulses of various energies and with 477-nm laser excitation at 5, 12, 17, 21, and 32 degrees C. The data are analyzed by using singular-value decomposition (SVD) and a global exponential fitting routine. Two rate constants associated with distinct spectral changes are observed during the time normally associated with the decay of bathorhodopsin to lumirhodopsin. Various models consistent with this observation are considered. A sequential model in which there is a reversible step between a bathorhodopsin intermediate and a new intermediate (BSI), which is blue-shifted relative to lumirhodopsin, is shown to best fit the data. The temperature dependence of the observed and calculated rate constants leads to linear Arrhenius plots. Extrapolation of the temperature dependence suggests that BSI should not be observable after rhodopsin photolysis at temperatures below -100 degrees C. The results are discussed with regard to the artificial visual pigments cis-5,6-dihydroisorhodopsin and 13-demethylrhodopsin. It is proposed that the rate of the BATHO to BSI transition is limited by the relaxation of the strained all-trans-retinal chromophore within a tight protein environment. The transition to LUMI involves chromophore relaxation concurrent with protein relaxation. While the first process is strongly affected by changes in the chromophore, the second transition seems to be determined more by protein relaxation.

A cross-linked histidine-phenol compound was synthesized as a chemical analogue of the active site of cytochrome c oxidase. The structure of the cross-linked compound (compound 1) was verified by IR, (1)H and (13)C NMR, mass spectrometry, and single-crystal X-ray analysis. Spectrophotometric titrations indicated that the pK(a) of the phenolic proton on compound 1 (8.34) was lower than the pK(a) of tyrosine (10.1) or of p-cresol (10.2). This decrease in pK(a) is consistent with the hypothesis that a cross-linked histidine-tyrosine may facilitate proton delivery to the binuclear site in cytochrome c oxidase. Time-resolved optical absorption spectra of compound 1 at room temperature, generated by excitation at 266 nm in the presence and absence of dioxygen, indicated a species with absorption maxima at approximately 330 and approximately 500 nm, which we assign to the phenoxyl radical of compound 1. The electron paramagnetic resonance (EPR) spectra of compound 1, obtained after UV photolysis, confirmed the generation of a paramagnetic species at low temperature. Because the cross-linked compound lacks beta-methylene protons, the EPR line shape was dramatically altered when compared to that of the tyrosyl radical. However, simulation of the EPR line shape and measurement of the isotropic g value was consistent with a small coupling to the imidazole nitrogen and with little spin density perturbation in the phenoxyl ring. The ground-state Fourier transform infrared (FT-IR) spectrum of compound 1 showed that addition of the imidazole ring perturbs the frequency of the tyrosine ring stretching vibrations. The difference FT-IR spectrum, associated with the oxidation of the cross-linked compound, detected significant perturbations of the phenoxyl radical vibrational bands. We postulate that phenol oxidation produces a small delocalization of spin density onto the imidazole nitrogen of compound 1, which may explain its unique optical spectral properties.

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The phototropins are a family of membrane-associated flavoproteins that function as the primary blue light receptors regulating phototropism, chloroplast movements, stomatal opening, and leaf expansion in plants. Phot1, a member of this family, contains two FMN-binding domains, LOV1 and LOV2, within the Nterminal region and a C-terminal serine-threonine protein kinase domain. Light irradiation of oat phot1 LOV2 produces a cysteinyl adduct (Cys-39) at the flavin C(4a) position, which decays thermally back to the dark state. We measured pH and isotope effects on the photocycle. Between pH 3.7 and 9.5, adduct formation showed minimal pH dependence, and adduct decay showed only slight pH dependence, indicating that the pK values of mechanistically relevant groups are outside this range. LOV2 showed a nearly 5-fold slowing of adduct formation in D 2 O relative to H 2 O, indicating that the ratelimiting step involves proton transfer(s). Light-induced changes in the far UV CD spectrum of LOV2 revealed putative protein structural perturbations. The light minus dark CD difference spectrum resembles an inverted ␣-helix spectrum, suggesting that ␣-helicity is reversibly lost upon light irradiation. Decay kinetics for CD spectral changes in the far UV region occur at the same rate as those in the visible region, indicating synchronous relaxation of protein and chromophore structures.The phototropins are a family of blue light receptors that are responsible for phototropism (1, 2) and are involved in lightinduced chloroplast movements (3) as well as blue light-stimulated stomatal opening (4) and leaf expansion in higher plants (5). Phototropin-like proteins have recently been identified in the green alga Chlamydomonas reinhardtii (6, 7) and in bacteria (8). The physiological roles of such proteins in these latter systems are not yet elucidated.The phototropin phot1 (9, 10), which becomes autophosphorylated in response to blue light, is a membrane-associated protein that contains two 12-kDa, FMN-binding LOV (light, oxygen, voltage) (11, 12) domains (LOV1 and LOV2) in its N-terminal region and a typical serine-threonine kinase domain in its C-terminal region (11). LOV domains belong to the PAS domain superfamily, which are found in a variety of sensor proteins in organisms ranging from archaea to eukaryotes (13).Upon light excitation, the isolated LOV2 domain of phot1 undergoes a cyclic photoreaction (14). The photocycle of phot1 LOV2 has been elucidated in part (15). Blue light irradiation excites the FMN chromophore to a triplet state that absorbs maximally around 660 nm (designated LOV2 Despite the above progress made in understanding the phot1 LOV2 photochemistry, specific mechanistic and conformational steps of the photocycle remain to be elucidated. Adduct decay for the LOV2 domain of oat phot1 has been shown to be 3 times slower in D 2 O than in H 2 O (15), indicating that proton transfer reactions, probably involving at least N-5, are rate-limiting components of the back reaction. To date, no comparable information has...