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At least 883 records · Page 49Linked to original sources

Resolution of lexical ambiguity: evidence from an eye movement priming paradigm.

Subjects' eye movements were monitored while they read 2-sentence passages of text. A target-word region was defined in the 2nd sentence of each passage. During the initial 35 ms of a target region eye fixation, an ambiguous word was presented as a prime. A target word subsequently replaced the prime during the fixation. Priming was measured by comparing fixation times on targets preceded by semantically related versus unrelated ambiguous primes. The type of prior context (consistent vs. inconsistent), type of ambiguous prime (biased vs. balanced), and strength of instantiated meaning (dominant vs. subordinate) could all affect priming. Priming effects were only found when the prior context was consistent with the dominant sense of a biased ambiguous prime. The results are discussed in terms of models of ambiguity resolution: The data seem most consistent with a reordered access model.

Eye Movements↗

The nature and origin of interstellar diamond.

Microscopic diamond was recently discovered in oxidized acid residues from several carbonaceous chondrite meteorites (for example, the C delta component of the Allende meteorite). Some of the reported properties of C delta seem in conflict with those expected of diamond. Here we present high spatial resolution analytical data which may help to explain such results. The C delta diamond is an extremely fine-grained (0.5-10 nm) single-phase material, but surface and interfacial carbon atoms, which may comprise as much as 25% of the total, impart an 'amorphous' character to some spectral data. These data support the proposed high-pressure conversion of amorphous carbon and graphite into diamonds due to grain-grain collisions in the interstellar medium although a low-pressure mechanism of formation cannot be ruled out.

Carbon↗

Structural basis for HLA-DQ binding by the streptococcal superantigen SSA.

Streptococcal superantigen (SSA) is a 28,000 Mr toxin originally isolated from a pathogenic strain of Streptococcus pyogenes that has 60% sequence identity with staphylococcal enterotoxin B (SEB). SSA and SEB, however, do not compete for binding on the surfaces of cells expressing MHC class II molecules. This behavior had been ascribed to SSA and SEB binding to distinct sites on, or different subsets of, HLA-DR molecules. Here we demonstrate that SSA binds predominantly to HLA-DQ, rather than to HLA-DR molecules, and present the crystal structure of SSA at 1.85 A resolution. These data provide a structural basis for interpreting the interaction of SSA with HLA-DQ molecules as well as a foundation for understanding bacterial superantigen affinities for distinct MHC isotypes.

Amino Acid Sequence↗

Environments of ethidium binding to allosteric Dna: II. Accessibility, mobility and mode of binding.

DNA binding compounds were previously shown to bind to the right-handed DNA forms and hybrid B-Z forms in a highly cooperative manner and indicate that structural specificity plays a key role in a ligand binding to DNA. In this study, the modes of binding and structural specificity of agents to unusual DNA are examined by a variety of fluorescence techniques (intensity, polarization and quenching, etc.) to explore a reliable method to detect the association environment of ligands to deoxyoligonucleotides initially containing a B-Z junction between the left-handed Z-DNA and right-handed B-DNA. The results of fluorescence energy transfer measurement demonstrated that the ligand molecules bind to the allosterically converted DNA structures by intercalation. In the absence of high-resolution structural data, this fluorescence energy transfer measurement allowed reliable measures and infer the binding environment of ligands to the allosteric DNA structures.

Allosteric Regulation↗

A bacterial dynamin-like protein.

Dynamins form a superfamily of large mechano-chemical GTPases that includes the classical dynamins and dynamin-like proteins (DLPs). They are found throughout the Eukarya, functioning in core cellular processes such as endocytosis and organelle division. Many bacteria are predicted by sequence to possess large GTPases with the same multidomain architecture that is found in DLPs. Mechanistic dissection of dynamin family members has been impeded by a lack of high-resolution structural data currently restricted to the GTPase and pleckstrin homology domains, and the dynamin-related human guanylate-binding protein. Here we present the crystal structure of a cyanobacterial DLP in both nucleotide-free and GDP-associated conformation. The bacterial DLP shows dynamin-like qualities, such as helical self-assembly and tubulation of a lipid bilayer. In vivo, it localizes to the membrane in a manner reminiscent of FZL, a chloroplast-specific dynamin-related protein with which it shares sequence similarity. Our results provide structural and mechanistic insight that may be relevant across the dynamin superfamily. Concurrently, we show compelling similarity between a cyanobacterial and chloroplast DLP that, given the endosymbiotic ancestry of chloroplasts, questions the evolutionary origins of dynamins.

Animals↗

Reconstruction of firing rate changes across neuronal populations by temporally deconvolved Ca2+ imaging.

Methods to record action potential (AP) firing in many individual neurons are essential to unravel the function of complex neuronal circuits in the brain. A promising approach is bolus loading of Ca(2+) indicators combined with multiphoton microscopy. Currently, however, this technique lacks cell-type specificity, has low temporal resolution and cannot resolve complex temporal firing patterns. Here we present simple solutions to these problems. We identified neuron types by colocalizing Ca(2+) signals of a red-fluorescing indicator with genetically encoded markers. We reconstructed firing rate changes from Ca(2+) signals by temporal deconvolution. This technique is efficient, dramatically enhances temporal resolution, facilitates data interpretation and permits analysis of odor-response patterns across thousands of neurons in the zebrafish olfactory bulb. Hence, temporally deconvolved Ca(2+) imaging (TDCa imaging) resolves limitations of current optical recording techniques and is likely to be widely applicable because of its simplicity, robustness and generic principle.

Action Potentials↗

Human and mouse adrenal glands are characterized by species-specific steroidogenic states and tissue turnover.

The adult adrenal cortex undergoes constant renewal, yet underlying human-specific mechanisms remain poorly understood. Here we generated single-cell and spatial transcriptomic atlases of adult human and mouse adrenal glands, leveraging single-cell-resolution spatial data and a rare clonal mosaic case for lineage inference. In humans, we identified age-associated zona glomerulosa (ZG) cell states with direct cortisol synthesis capacity and sex-specific differences in inferred cholesterol balance. Cross-species comparison revealed conserved aldosterone-producing ZG but notable divergence in zona fasciculata markers, absence of zona reticularis homologs in mice and differential SHH-WNT4 signaling in proliferating cells. We uncovered human WT1- capsule-to-ZG transition and vascular smooth muscle cell-to-steroidogenic transitions supported by mosaic lineage evidence. We revealed dispersed proliferating cortical SF1+EZH2+ cells throughout the human cortex in contrast with ZG restriction in mice. Taken together, our data expand the centripetal renewal model and establish a comparative framework for human adrenocortical biology.

Animals↗

Structure of the conserved domain of ANAC, a member of the NAC family of transcription factors.

The structure of the DNA-binding NAC domain of Arabidopsis ANAC (abscisic-acid-responsive NAC) has been determined by X-ray crystallography to 1.9A resolution (Protein Data Bank codes 1UT4 and 1UT7). This is the first structure determined for a member of the NAC family of plant-specific transcriptional regulators. NAC proteins are characterized by their conserved N-terminal NAC domains that can bind both DNA and other proteins. NAC proteins are involved in developmental processes, including formation of the shoot apical meristem, floral organs and lateral shoots, as well as in plant hormonal control and defence. The NAC domain does not possess a classical helix-turn-helix motif; instead it reveals a new transcription factor fold consisting of a twisted beta-sheet surrounded by a few helical elements. The functional dimer formed by the NAC domain was identified in the structure, which will serve as a structural template for understanding NAC protein function at the molecular level.

Amino Acid Sequence↗

The state of the filament.

Movement is a defining characteristic of life. Macroscopic motion is driven by the dynamic interactions of myosin with actin filaments in muscle. Directed polymerization of actin behind the advancing membrane of a eukaryotic cell generates microscopic movement. Despite the fundamental importance of actin in these processes, the structure of the actin filament remains unknown. The Holmes model of the actin filament was published 15 years ago, and although it has been widely accepted, no high-resolution structural data have yet confirmed its veracity. Here, we review the implications of recently determined structures of F-actin-binding proteins for the structure of the actin filament and suggest a series of in silico tests for actin-filament models. We also review the significance of these structures for the arp2/3-mediated branched filament.

Actin Cytoskeleton↗

Analysis of the H + D2 reaction mechanism through consideration of the intrinsic reactant polarisation.

The effect of reactant polarisation on the dynamics of the title reaction at collision energies up to 1.6 eV is analysed in depth. The analysis takes advantage of two novel theoretical concepts: intrinsic reaction properties and stereodynamical portraits. Exact quantum methods are used to determine the polarisation moments that quantify the intrinsic reactant polarisation at various levels of detail, including or not product state and/or scattering angle resolution. The data is then examined with the aid of stereodynamical portraits, which facilitate the rationalisation of the stereochemical effects that are relevant for the reaction dynamics. This allows for detailed characterisations of the so-called direct and delayed reaction mechanisms.

Deuterium↗

Observation of a tetrahedral reaction intermediate in the HIV-1 protease-substrate complex.

HIV-1 protease is an effective target for the design of drugs against AIDS. To help this process of drug design, three-dimensional structures have been determined of complexes between HIV-1 protease and a variety of transition-state analogue inhibitors. The true transition state, however, has not been structurally characterized. The crystal structure of the C95M/C1095A HIV-1 protease tethered dimer shows a distinctive feature in which the two flaps of the enzyme are in a 'closed conformation' even in the unliganded state. This unique feature has been utilized here to study the structure of HIV-1 protease complexed to an oligopeptide substrate of amino acid sequence His-Lys-Ala-Arg-Val-Leu*NPhe-Glu-Ala-Nle-Ser (where * denotes the cleavage site, and NPhe and Nle denote p-nitrophenylalanine and norleucine residues respectively). The X-ray structure of the complex refined against 2.03 A (0.203 nm) resolution synchrotron data shows that the substrate is trapped as a tetrahedral reaction intermediate in the crystal. The hydrogen-bonding interactions between the reaction intermediate and the catalytic aspartates are different from those observed previously using transition-state analogues. The reaction intermediate did not dissociate to release the products, possibly due to the inflexibility introduced in the flaps when the enzyme is packed inside crystals.

Binding Sites↗

Ammonium ion transport by the AMT/Rh homologue LeAMT1;1.

AMT (ammonium transporter)/Rh (Rhesus) ammonium transporters/channels are identified in all domains of life and fulfil contrasting functions related either to ammonium acquisition or excretion. Based on functional and crystallographic high-resolution structural data, it was recently proposed that the bacterial AmtB (ammonium transporter B) is a gas channel for NH3 [Khademi, O'Connell, III, Remis, Robles-Colmenares, Miercke and Stroud (2004) Science 305, 1587-1594; Zheng, Kostrewa, Berneche, Winkler and Li (2004) Proc. Natl. Acad. Sci. U.S.A. 101, 17090-17095]. Key residues, proposed to be crucial for NH3 conduction, and the hydrophobic, but obstructed, pore were conserved in a homology model of LeAMT1;1 from tomato. Transport by LeAMT1;1 was affected by mutations of residues that were predicted to constitute the aromatic recruitment site for NH4+ at the external pore entrance. Despite the structural similarities, LeAMT1;1 was shown to transport only the ion; each transported 14C-methylammonium molecule carried a single positive elementary charge. Similarly, NH4+ (or H+/NH3) was transported, but NH3 conduction was excluded. It is concluded that related proteins and a similar molecular architecture can apparently support contrasting transport mechanisms.

Animals↗

[Determination of visual acuity by the visually evoked cortical potential (author's transl)].

Monocularly evoked cortical potentials were recorded monopolarly (3 cm above Prot. occ. ext. sup.) to steady-state checkerboard stimuli (check sizes 1.4 to 26 min, rev. freq. 7/s, mean luminance 10.8 cd/m2, field diameter 4.5 deg., centr. fix.). For a number of visual acuities (obtained by inserting plus lenses up to 3.0 dpt) the smallest check size evoking reliable VECPs was related to the visual acuities obtained at a visual test chart. The use of 20 instead of 100 per cent contrast stimuli provided a significant decrease of slope of threshold check size versus visual acuity, resulting in a three-fold increase in the resolution of data. The method permits the evaluation of visual acuities between 0.1 and 1.0 in normals and patients within limits of +/- log 0.1 (1 sigma) and +/- log 0.2 visual acuity (2 sigma).

Adult↗

Level-crossing statistics of the horizontal wind speed in the planetary surface boundary layer.

The probability density of the times for which the horizontal wind remains above or below a given threshold speed is of some interest in the fields of renewable energy generation and pollutant dispersal. However there appear to be no analytic or conceptual models which account for the observed power law form of the distribution of these episode lengths over a range of over three decades, from a few tens of seconds to a day or more. We reanalyze high resolution wind data and demonstrate the fractal character of the point process generated by the wind speed level crossings. We simulate the fluctuating wind speed by a Markov process which approximates the characteristics of the real (non-Markovian) wind and successfully generates a power law distribution of episode lengths. However, fundamental questions concerning the physical basis for this behavior and the connection between the properties of a continuous-time stochastic process and the fractal statistics of the point process generated by its level crossings remain unanswered. (c) 2001 American Institute of Physics.

Journal Article↗

Vibrational excitation and relaxation of five polyatomic molecules in an electrical discharge.

Vibrational excitation and relaxation of five linear polyatomic molecules, OCS, OC3S, HC3N, HC5N, and SiC2S, have been studied by Fourier transform microwave spectroscopy in a supersonic expansion after the application of a low-current dc electric discharge. For each chain, the populations in bending and stretching modes have been characterized as a function of the applied discharge current; for stable OCS and HC3N, vibrational populations were studied as well in the absence of a discharge. With no discharge present the derived vibrational temperatures are slightly below T, the temperature of the gas before the supersonic expansion (i.e., 300 K). In the presence of the discharge, vibrational excitation occurs via inelastic collisions with the electrons and the vibrational temperatures rise as the applied current increases. Global vibrational relaxation is governed by rapid vibration-vibration (VV) energy transfer and slow vibration-translation (VT) energy transfer. The latter process is rate-determining and depends primarily on the wave number of the vibration. Vibrational modes with wave numbers near and below kT/hc (where T = 300 K and kT/hc-210 cm(-1)) are efficiently cooled by VT transfer because a sufficient number of collisions occur in the initial stages of the supersonic expansion. Vibrational modes with wave numbers around 450 cm(-l) appear to be inefficiently cooled in the molecular beam; at these energies VV and VT rates are probably comparable. For high-frequency vibrations, VV energy transfer dominates. For the longer chains OC3S and HC5N, higher-lying modes are generally not detectable and vibrational temperatures of most lower-lying modes were found to be lower than those of OCS and HC3N, suggesting that as the size of the molecules increases, intermode VV transfer becomes more efficient, plausibly due to the higher density of vibrational levels. New high resolution spectroscopic data have been obtained for several vibrationally excited states of OC3S, HC3N, and HC5N. Rotational lines of the 13C and 15N isotopic species of HC5N have been measured, yielding improved rotational and centrifugal distortion constants; 14N nitrogen quadrupole coupling constants for the isotopic species of HC5N with 13C have been determined for the first time.

Journal Article↗

A new action photoelectron spectroscopy for anions.

We present a new experimental approach, in which anion photodetachment spectroscopy is recorded with electrons of fixed kinetic energy. This approach circumvents some shortcomings of the zero electron kinetic energy method. Our method is based on a modified magnetic bottle photoelectron spectrometer (MBPES). A tunable laser is used to detach electrons from mass selected anions, drifting collinearly with the 40 cm MBPES drift tube. To avoid Doppler broadening, a low voltage pulse removes the velocity component of anions from the detached electrons. Spectra are recorded by collecting the wavelength dependence of electron-signal at a predetermined TOF window, corresponding to a specific electron-kinetic energy. We call this approach PEACE, denoting photoelectron action spectroscopy at constant kinetic energy. Our best resolution is 0.65 meV for 1.5 meV electrons. We present a PEACE spectrum of HgCl(-) together with the corresponding simulated theoretical spectrum. The method is similar in resolution and data collection rates to the slow electron velocity map imaging technique recently introduced by Neumark and co-workers.

Journal Article↗

Near-edge electronic structure in NbS2.

The near-edge electronic and structural properties of 2H-NbS(2) were investigated using scanning tunneling microscopy (STM) and density-functional calculations. Geometry optimization of the near-edge structure using density-functional calculations was performed on [1010]- and [1010]-terminated layer edges. Ribbon model systems also included variation of the number of bound sulfur atoms at the edges. Atomic resolution STM data exhibit a pronounced electronic density of states at the outermost edge atomic sites but are otherwise bulk-like in the near-edge region. Optimized NbS2 ribbon structures confirm the STM results indicating that minimal reconstruction occurs and that the edge electronic structure exhibits a significant increase in local density of states compared to bulk. Simulated STM images using extended Hückel tight-binding calculations based on optimized ribbon structures successfully modeled the experimental STM results. The results indicate that the [1010] "Nb" edges are preferentially observed compared to the [1010] "S" edge possibly due to differences in stability.

Journal Article↗