Point Scattering Theory of X-Ray K-Absorbtion Fine Structure

We calculate the extended X-ray absorption fine structure by treating the ejected photoelectron as a spherical wave which expands in the lattice and is partially scattered by neighbors of the absorbing atom. The neighboring atoms are treated as point scattered and the total scattered wave is summed from the waves scattered by each atom. The fine structure is determined from the dipole transition matrix between the initial K-state and the final photoelectron state. Calculations compare favorably with experimental data.

Analysis of variants and mutations in the human winged helix FOXA3 gene and associations with metabolic traits

BACKGROUND/OBJECTIVES

The forkhead factor Foxa3 is involved in the early transcriptional events controlling adipocyte differentiation and plays a critical function in fat depot expansion in response to high-fat diet regimens and during aging in mice. No studies to date have assessed the potential associations of genetic variants in FOXA3 with human metabolic outcomes.

SUBJECTS/METHODS

In this study, we sequenced FOXA3 in 392 children, adolescents and young adults selected from several cohorts of subjects recruited at the National Institute of Child Health and Human Development of the National Institutes of Health based on the availability of dual-energy X-ray absorptiometry data, magnetic resonance imaging scans and DNA samples. We assessed the association between variants present in these subjects and metabolic traits and performed in vitro functional analysis of two novel FOXA3 missense mutations identified.

RESULTS

Our analysis identified 14 novel variants and showed that the common single-nucleotide polymorphism (SNP) rs28666870 is significantly associated with greater body mass index, lean body mass and appendicular lean mass (P values 0.009, 0.010 and 0.013 respectively). In vitro functional studies showed increased adipogenic function for the FOXA3 missense mutations c.185C>T (p.Ser62Leu) and c.731C>T (p.Ala244Val) compared with FOXA3-WT.

CONCLUSIONS

Our study identified novel FOXA3 variants and mutations, assessed the adipogenic capacity of two novel missense alterations in vitro and demonstrated for the first time the associations between FOXA3 SNP rs28666870 with metabolic phenotypes in humans.

Strain-induced bond buckling and its role in insulating properties of Cr-doped V2O3

Structural transformations around both V and Cr atoms in (V1-xCrx)2O3 across its metal-insulator transition (MIT) at x approximately 0.01 are studied by extended x-ray absorption fine-structure technique. Our new results for Cr made possible by the use of a novel x-ray analyzer that we developed reveal the substitutional mechanism of Cr doping. We find that this system has a buckled structure with short Cr-V and long V-V bonds. This system of bonds is disordered around the average trigonal lattice ascertained by x-ray diffraction. Such local distortions can result in a long range strain field that sets in around dilute Cr atoms in microscopic regions. We suggest that such locally strained regions should be insulating even at small x. The possibility of local insulating regions within a metallic phase, first suggested by Rice and Brinkman in 1972, remains unaccounted for in modern MIT theories.

In vivo multiphoton imaging of a transgenic mouse model of Alzheimer disease reveals marked thioflavine-S-associated alterations in neurite trajectories

Postmortem analyses of senile plaques reveal numerous dystrophic processes in their vicinity. We used in vivo multiphoton microscopy of a transgenic model of Alzheimer disease (AD) to simultaneously image senile plaques and nearby neuronal processes. Plaques were labeled by immunofluorescent staining or thioflavine-S and neuronal processes were labeled with a fluorescent dextran conjugate. Imaging of 3-dimensional volumes in the vicinity of plaques revealed subtle changes in neurite geometry in or near diffuse plaques. By contrast, disruptions in neurite morphology, including dystrophic neurites immediately surrounding plaques as well as major alterations in neurite trajectories, were seen in association with thioflavine-S-positive plaques. Nearly half of all labeled processes that came within 50 microm of a thioflavine-S-positive plaque were altered, suggesting a fairly large "halo" of neuropil alterations that extend beyond the discrete border of a thioflavine-S plaque. These results support the hypothesis that compact thioflavine-S-positive plaques disrupt the neuropil in AD.

Physiology and morphology of intratelencephalically projecting corticostriatal-type neurons in pigeons as revealed by intracellular recording and cell filling

Much of the Wulst and dorsal ventricular ridge (DVR) in birds, which together make up the part of the avian telencephalon functionally resembling mammalian cerebral cortex, projects to the striatum. Those connections arise from neurons projecting additionally to the brainstem as well as from neurons projecting only within the telencephalon. As part of an effort to further characterize corticostriatal-type projection neurons in birds, we recorded intracellularly from neurons of the outer DVR, identified neurons projecting to the striatum by antidromic stimulation from the ipsilateral rostromedial striatum or subsequently by their axonal projection, characterized these neurons physiologically and then filled them with biocytin. As neurons in the outer DVR only project within telencephalon, neurons within it projecting to the striatum are of the intratelencephalically projecting (IT) type. Our studies suggest that: (1) the membrane potentials of avian IT-type neurons fluctuate between two preferred subthreshold values, and action potentials occur only in the 'up' state, (2) avian IT-type neurons show a time-dependent inward rectification in response to hyperpolarization and regular firing in response to constant current injection, (3) the conduction velocity of avian IT-type neurons is slow (about 0.2 m/s), (4) avian IT-type neurons possess radially disposed densely spiny dendrites but no apical dendrite, (5) avian IT-type neurons have local and distant collateral projections within the DVR, and (6) individual avian IT-type neurons give rise to an extensive terminal field within the striatum. Aside from the shape of their dendritic tree, IT-type neurons in birds closely resemble IT-type corticostriatal neurons in mammals in these various aspects, although it is presently uncertain whether this neuron type has been inherited in common by birds and mammals from stem amniotes.

Rapid development and plasticity of layer 2/3 maps in rat barrel cortex in vivo

Cortical synaptic circuitry develops rapidly in the second postnatal week, simultaneous with experience-dependent turnover of dendritic spines. To relate the emergence of sensory maps to synaptogenesis, we recorded synaptic potentials evoked by whisker deflection in layer 2/3 neurons from postnatal day (P) 12 to 20. At P12, synaptic responses were undetectable. Only 2 days later in life (P14), receptive fields had mature organization. Sensory deprivation, if initiated before P14, disrupted receptive field structure. In layer 4, responses and maps were already mature by P12 and insensitive to deprivation, implying that barrel cortex develops from layer 4 to layer 2/3. Thus, P12-14 is a critical period shared by layer 2/3 synapses and their spines, suggesting that spine plasticity is involved in the refinement of maps.

Dredged material decontamination demonstration for the port of New York/New Jersey

Management of contaminated dredged material is a significant challenge in the Port of New York and New Jersey as a result of more stringent regional ocean placement regulations with escalating costs for upland placement. One component of an overall management plan can be the application of a decontamination technology followed by creation of a product suitable for beneficial use. This concept is the focus of a project now being carried out by the US Environmental Protection Agency, Region 2, the US Army Corps of Engineers, New York District, the US Department of Energy, Brookhaven National Laboratory, and regional university groups that have included Rensselaer Polytechnic Institute, Rutgers University, New Jersey Institute of Technology, and Stevens Institute of Technology. The project has progressed through phased testing of commercial technologies at the bench scale (15 liters) (Marcor, Metcalf & Eddy, Gas Technology Institute, Westinghouse Science & Technology, BioGenesis, International Technology, and BioSafe) and pilot-scale (1.5-500m(3)) (BioGenesis, Gas Technology Institute, and Westinghouse Science & Technology) levels. The technologies developed by Gas Technology Institute and BioGenesis are now going forward to commercial demonstration facilities that are intended to treat from 23000 to 60000m(3) of dredged material during their first operational period in 2001-2002. Beneficial use products are soils and cement. Treatment costs for the final commercial facilities are estimated at US$ 39 per m(3). Selection of the technologies was made based on the effectiveness of the treatment process, evaluation of the possible beneficial use of the treated materials, and other factors. Major elements of the project are summarized here.

Dopant structural distortions in high-temperature superconductors: anactive or a passive role?

The parent compounds of high-temperature superconductors, such as YBa2Cu3O6 and La2CuO4, are strongly interacting electron systems, rendering them insulators with Mott-Hubbard gaps of a few electronvolts. Charge carriers (holes) are introduced by chemical doping, causing an insulator-metal (IM) transition and, at low temperatures, superconductivity. The role of dopants is widely seen as limited to the introduction of holes into the CuO2 planes (i.e. occupying electronic states derived from Cu 3d(x2-y2) and O 2p(x,y) atomic orbitals). Most theories of high-Tc superconductivity deal with pairing interactions between these planar holes. Local distortions around dopants are poorly understood, because of the experimental difficulty in obtaining such information, particularly at low doping. This has resulted in the neglect, in most theories, of the effect of such distortions on the chemical and electronic structure of high-Tc superconductors. Angular-resolved X-ray absorption fine structure (XAFS) spectroscopy on oriented samples is an ideal technique to elucidate the dopant distortions. Element specificity, together with a large orientation dependence of the XAFS signal in these layered structures, allows the local structure around dopants to be resolved. Results are presented here on (Sr, Ba) and Ni dopants, which substitute at the La and Cu sites, respectively, of insulating La2CuO4. The relevance of the measured local distortions for a complete understanding of the normal and superconducting properties of cuprates is discussed.

Musings about the development of XAFS

A personal recollection of the development of X-ray absorption fine structure (XAFS) into a structure-determination technique is presented. Because of confusion in the theoretical explanation of the 'Kronig structure', now called EXAFS, the extended XAFS, its explanation remained unresolved for about 40 years. As I was introduced to the EXAFS phenomenon by Farrel Lytle and saw his impressive data, the thought came to me that scattering of the photoelectron from surrounding atoms could be the mechanism of the effect. My graduate student, Dale Sayers, agreed to work on developing the theory under my supervision and to make EXAFS measurements under Lytle's supervision as his PhD thesis. The theory led to the idea of a Fourier transform of the EXAFS, which showed peaks from surrounding atoms, proving the validity of the theory and suggesting the method of structure determination by using standards from known structures. Within a few years, facilities at synchrotron sources were developed to measure XAFS, opening up the technique to the general scientific community. In spite of some initial growing pains, XAFS has matured into a powerful technique for local structure and has been applied to obtain magnetic structure, in addition to distribution of atoms. Other related techniques have been spawned from XAFS, expanding the impact of the original phenomenon.

Determining crystalline atomic positions using XAFS, a new addition to the UWXAFS analysis package

XAFS and x-ray diffraction (XRD) are complementary structure determination techniques. The combination of XAFS and XRD can be used to determine the complete crystal structure when diffraction can not be refined. This is often the case at high pressures or high temperatures where there is limited access to the samples and energy dispersive x-ray diffraction is used. A new method to determine the atomic positions within the unit cell using EXAFS data with the programs RUNFIT and MKFIT is described. These programs systematically produce and test models for the XAFS data that are consistent with the diffraction results. The programs were written to solve the structure of two intermediate high pressure phases of AgCl, and are distributed with a working example.

Experience-dependent plasticity of dendritic spines in the developing rat barrel cortex in vivo

Do changes in neuronal structure underlie cortical plasticity? Here we used time-lapse two-photon microscopy of pyramidal neurons in layer 2/3 of developing rat barrel cortex to image the structural dynamics of dendritic spines and filopodia. We found that these protrusions were highly motile: spines and filopodia appeared, disappeared or changed shape over tens of minutes. To test whether sensory experience drives this motility we trimmed whiskers one to three days before imaging. Sensory deprivation markedly (approximately 40%) reduced protrusive motility in deprived regions of the barrel cortex during a critical period around postnatal days (P)11-13, but had no effect in younger (P8-10) or older (P14-16) animals. Unexpectedly, whisker trimming did not change the density, length or shape of spines and filopodia. However, sensory deprivation during the critical period degraded the tuning of layer 2/3 receptive fields. Thus sensory experience drives structural plasticity in dendrites, which may underlie the reorganization of neural circuits.

Selective removal of organic contaminants from sediments: a methodology for toxicity identification evaluations (TIEs)

Aqueous slurries of a test sediment spiked with dibenz[a,h]anthracene, 2,4,5,2',4',5'-hexachlorobiphenyl, p,p'-DDE, or phenanthrene were subjected to decontamination experimentation. The spiked sediments were agitated at elevated temperatures for at least 96 h in the presence of either of the two contaminant-absorbing media: clusters of polyethylene membrane or lipid-containing semipermeable membrane devices (SPMDs). The effects of treatment temperature and surface area of media on the removal of contaminants were explored. This work is part of a larger methodology for whole-sediment toxicity identification evaluation (TIE). A method is being sought that is capable of detoxifying sediments with respect to organic contaminants while leaving toxicity attributable to inorganic contaminants unaffected.

Membrane potential synchrony of simultaneously recorded striatal spiny neurons in vivo

The basal ganglia are an interconnected set of subcortical regions whose established role in cognition and motor control remains poorly understood. An important nucleus within the basal ganglia, the striatum, receives cortical afferents that convey sensorimotor, limbic and cognitive information. The activity of medium-sized spiny neurons in the striatum seems to depend on convergent input within these information channels. To determine the degree of correlated input, both below and at threshold for the generation of action potentials, we recorded intracellularly from pairs of spiny neurons in vivo. Here we report that the transitions between depolarized and hyperpolarized states were highly correlated among neurons. Within individual depolarized states, some significant synchronous fluctuations in membrane potential occurred, but action potentials were not synchronized. Therefore, although the mean afferent signal across fibres is highly correlated among striatal neurons, the moment-to-moment variations around the mean, which determine the timing of action potentials, are not. We propose that the precisely timed, synchronous component of the membrane potential signals activation of cell assemblies and enables firing to occur. The asynchronous component, with low redundancy, determines the fine temporal pattern of spikes.

Spontaneous subthreshold membrane potential fluctuations and action potential variability of rat corticostriatal and striatal neurons in vivo

We measured the timing of spontaneous membrane potential fluctuations and action potentials of medial and lateral agranular corticostriatal and striatal neurons with the use of in vivo intracellular recordings in urethan-anesthetized rats. All neurons showed spontaneous subthreshold membrane potential shifts from 7 to 32 mV in amplitude, fluctuating between a hyperpolarized down state and depolarized up state. Action potentials arose only during the up state. The membrane potential state transitions showed a weak periodicity with a peak frequency near 1 Hz. The peak of the frequency spectra was broad in all neurons, indicating that the membrane potential fluctuations were not dominated by a single periodic function. At frequencies >1 Hz, the log of magnitude decreased linearly with the log of frequency in all neurons. No serial dependence was found for up and down state durations, or for the time between successive up or down state transitions, showing that the up and down state transitions are not due to superimposition of noisy inputs onto a single frequency. Monte Carlo simulations of stochastic synaptic inputs to a uniform finite cylinder showed that the Fourier spectra obtained for corticostriatal and striatal neurons are inconsistent with a Poisson-like synaptic input, demonstrating that the up state is not due to an increase in the strength of an unpatterned synaptic input. Frequency components arising from state transitions were separated from those arising from the smaller membrane potential fluctuations within each state. A larger proportion of the total signal was represented by the fluctuations within states, especially in the up state, than was predicted by the simulations. The individual state spectra did not correspond to those of random synaptic inputs, but reproduced the spectra of the up and down state transitions. This suggests that the process causing the state transitions and the process responsible for synaptic input may be the same. A high-frequency periodic component in the up states was found in the majority of the corticostriatal cells in the sample. The average size of the component was not different between neurons injected with QX-314 and control neurons. The high-frequency component was not seen in any of our sample of striatal cells. Corticostriatal and striatal neurons' coefficients of variation of interspike intervals ranged from 1.0 to 1.9. When interspike intervals including a down state were subtracted from the calculation, the coefficient of variation ranged from 0.4 to 1.1, indicating that a substantial proportion of spike interval variance was due to the subthreshold membrane potential fluctuations.

Development and validation of an emergency department screening and referral protocol for victims of domestic violence

STUDY OBJECTIVE

To describe the development, design, and validation of an emergency department protocol for the identification, documentation, and referral of victims of domestic violence.

METHODS

We based protocol development and design on a departmental needs assessment. The validation component involved the screening of women 16 years and older treated in the ED during a 2-week period at both triage (stage 1) and nursing assessment (stage 2). Sensitivity and specificity of the triage screen were determined.

RESULTS

The departmental needs assessment revealed several important limiting factors that motivated the design of the protocol. In response, the protocol design included a two-stage screening process, stage 1 taking place at triage and stage 2 as part of the nursing assessment. During the 2-week validation study, 595 women 16 years and older were treated in the ED, but complete two-stage screening data were obtained for only 114 (19%). Of the patients who were appropriately screened, eight screened positive at stage 1 and two of the eight were confirmed at stage 2. Two additional cases were identified at stage 2 in whom violence had not been suspected at stage 1. Triage screen sensitivity was 50%, specificity 95%. Of the women properly screened at both stages, 3.5% were identified as victims of domestic violence.

CONCLUSION

We identified many obstacles to implementation of an ED domestic violence screening and referral protocol, demonstrating that evaluation is imperative in determining actual clinical impact.

Microsecond-resolved XAFS of the triplet excited state of Pt2(P2O5H2)4(4-)

Little is known about the excited-state structures of most inorganic compounds. Time-resolved resonance Raman and time-resolved infrared spectroscopies can provide only indirect structural information for short-lived excited species in solution at room temperature. Time-resolved X-ray diffraction has the potential to give more direct information, but no excited-state structures have yet been reported; picosecond gas-phase electron diffraction has been proposed recently, but not yet demonstrated. Here we report a technique that combines the X-ray absorption fine-structure (XAFS) method with rapid-flow laser spectroscopy to measure structural changes in a solution-phase excited-state transition-metal complex with microsecond resolution. We find that the triplet excited state of Pt2(P2O5H2)4(4-), with a lifetime of about 4 microseconds, undergoes a contraction in the Pt-Pt distance of 0.52 +/- 0.13 A relative to the ground state. We anticipate that time-resolved XAFS will have broad applications in chemistry and biology.

Guiding and concentrating hard x-rays by using a flexible hollow-core tapered glass fiber

A 1.6-m-long, flexible, hollow glass fiber with a gradually diminishing bore diameter has been used efficiently to compress the size of an x-ray beam as it reflects from the inside walls of the fiber by total external reflection. The transmission characteristics of the fiber are reported for monochromatic synchrotron radiation of 8.04, 13, and 20 keV, as well as for CuKalpha radiation from a conventional x-ray tube. Intensity enhancements as large as 10 that correspond to a transmission efficiency of 54% were observed. The high efficiency of this prototype fiber supports the idea that this confinement technique should yield intensity gains of many orders of magnitude as the optimal fiber design is achieved.

Comparison of the effects of saccharide binding and crystallization on the zinc transition-metal site of concanavalin A

The Zn site in concanavalin A solution was studied by X-ray absorption fine structure spectroscopy (XAFS) with and without the saccharide methyl alpha-D-glucoside (aMG) bound to the protein. No structural change occurs in the metal-binding site when the saccharide is bound to the protein. There is, however, evidence for structural change remote from the metal site. This is in contrast to the significant changes that we have previously found to occur in the near neighborhood of the Zn atom when an aqueous solution of Zn concanavalin A crystallizes. We propose a structural explanation of these facts based on the known crystal structure of concanavalin A.

Structural differences in solution and crystalline forms of met-myoglobin

For several decades X-ray diffraction studies have been the paragon of biological structure studies at atomic resolution. Diffraction provides three-dimensional structure information, which is essential to our fundamental understanding of protein function. However, since X-ray diffraction cannot be done to atomic resolution on proteins in their native solution or membrane-bound state, the possibility exists that the conformations of the protein in crystals are slightly different from the conformations in solution, and attempts to interpret details of the structure may be misleading and without physiological relevance. In this paper, we show that this concern is justified for a familiar protein, myoglobin. Performing X-ray absorption fine structure experiments on both solution and crystalline met-myoglobin (met-Mb), we find significant differences in the local environment of the iron between the two states. Specifically, the average iron-nearest neighbor atom distance in the crystalline form is 0.05 A shorter than that in the solution form, and the iron-nearest neighbor bond is more rigid in the crystalline met-Mb. Possible artifactual explanations for the differences have been ruled out.

X-ray absorption fine structure investigation of the zinc transition metal binding site of Zn concanavalin A in solution and in the crystal

We report details on measurements by the X-ray absorption fine structure (XAFS) technique of the conformational changes around the transition metal binding site (S1) of the protein concanavalin A induced by crystallization when that site is occupied by Zn. A change from hexa- to tetracoordination occurs at the S1 site on crystallization when the calcium-binding site (S2) is occupied by a calcium atom. When the S2 site is unoccupied, the Zn is pentacoordinated both in solution and in the crystal. The average distance to the coordination shell increases with coordination number as expected. Conformational changes are detected up to 4.5 A from the Zn, the limit of sensitivity of the XAFS technique. When the Zn is hexacoordinated, the ligands around the Zn, as determined by XAFS, are consistent with the crystal structure determination results of five oxygens and one nitrogen. The atom that is released in the tetracoordinated Zn. decreases to five is an oxygen atom, and, in addition, the nitrogen is released in the tetracoordinated Zn. Thus, when S2 is emptied, the protein gains a ligand about the Zn site in the crystal and loses one in solution. These results provide direct evidence that the protein conformation can be altered by the intermolecular forces of crystallization.