Fast automated energy changes at synchrotron radiation beamlines equipped with transfocator or focusing mirrors.

Algorithms and procedures to fully automate retuning of synchrotron radiation beamlines over wide energy ranges are discussed. The discussion is based on the implementation at the National Institute of General Medical Sciences and the National Cancer Institute Structural Biology Facility at the Advanced Photon Source. When a user selects a new beamline energy, software synchronously controls the beamline monochromator and undulator to maintain the X-ray beam flux after the monochromator, preserves beam attenuation by determining a new set of attenuator foils, changes, as needed, mirror reflecting stripes and the undulator harmonic, preserves beam focal distance of compound refractive lens focusing by changing the In/Out combination of lenses in the transfocator, and, finally, restores beam position at the sample by on-the-fly scanning of either the Kirkpatrick-Baez mirror angles or the transfocator up/down and inboard/outboard positions.

THE ROLE OF SECRETING FUNCTION OF DECIDUA IN THE DEVELOPMENT OF COMPLICATIONS OF GESTATION PROCESS IN PREGNANT WOMEN WITH A PAST HISTORY OF CHRONIC ENDOMETRITIS.

Objective: The aim: To determine the serum FAMG in the I and II trimester of pregnancy in women with a past history of chronic endometritis, and to clarify its impact on the development of pathology of pregnancy.

Patients And Methods: Materials and methods: The level of FAMG was determined at 6-8 and 16-18 weeks of gestation in 135 pregnant women with a past history of chronic endometritis, who received treatment of chronic endometritis at the stage of pregravid preparation and 168 women who became pregnant without its prior treatment. The dependence of the development of pre-eclampsia on the level of FAMG at the early stages of pregnancy has been evaluated.

AOTF-based hyperspectral imaging phase microscopy.

Phase imaging microscopy with incoherent object illumination is convenient and affordable for biomedical research and clinics since it provides easy integration with a variety of bright-field optical microscopes. We report the design of a new hyperspectral imaging system based on a combination of a spatial light modulator (SLM) and an acousto-optic tunable filter (AOTF) for phase imaging microscopy. Contrast of phase-only objects originates from matched spectral and spatial filtering performed by the SLM and the AOTF located in Fourier-conjugate optical planes in the back-end of the optical system.

Optimization of noncollinear AOTF design for laser beam shaping.

Optimization of a wide-angle paratellurite acousto-optic tunable filter (AOTF) is performed for applications in laser beam shaping systems. The AOTF configuration with annular transfer function is analyzed. It is demonstrated that the optimal AOTF design for single-frequency operation as a narrow-band spatial frequency filter is obtained at acoustic propagation angle of 5.

Linear Phase Design of Piezoelectric Transducers for Acousto-Optic Dispersion Delay Lines Using Differential Evolution for Matching Circuit Optimization.

A numerical method for providing linear phase response of bulk acoustic wave (BAW) piezoelectric transducers (PTs) of acousto-optic devices is developed. Our approach is based on the analytic approximation of the phase response of the PT with the matching electrical circuit and optimization with a differential evolution genetic algorithm. Simulations and experiments were performed for two typical BAW excitation schemes: direct and reflective.

Novel protocol of hyperspectral data acquisition by means of an acousto-optical tunable filter with synthesized transmission function.

A new protocol of hyperspectral data acquisition with an acousto-optical tunable filter is proposed and tested experimentally. Correction for the illumination source spectrum and regular spectral sensitivity factors is embedded in the data acquisition routine. The protocol is based on the adaptive electronic setting of the filter transmission passband inversely proportional to the power spectrum of the light source.

Possibility for non-invasive diagnosis of chronic endometritis in women at risk during pregravid preparation.

Objective: Introduction: Detection and treatment of chronic endometritis (CE) is clinically significant, though involves intrauterine intervention to collect endometrium. The aim: To estimate the possibility to use fertility α2-microglobulin (FAMG) as the marker of the high risk for CE.

Patients And Methods: Materials and methods: 70 women with CE who were planning pregnancy were tested for FAMG in menstrual blood.

Role of uterine blood flow disturbances in the development of late gestosis.

Objective: Introduction: Chronic endometritis (CE) associated lesions lessen the implantation potential of endometrium and aggravate the course of invasive processes in the uterine vessels The aim: Study of changes in doplerometric parameters of blood flow in spiral and uterine arteries in 17-18 weeks of pregnancy in women with СE in anamnesis.

Patients And Methods: Materials and methods: Сalculation of systolic/diastolic ratio (SDR), pulse index (PI) and resistive index (RI) has been carried out in 70 pregnant had CE in past history and 10 healthy pregnant women who experienced neither chronic endometritis before pregnancy nor preeclampsia.

Results: Results: SDR in SA patients with CE in history and follow-up development of preeclampsia is by 19& higher the control values (р<0,05); PI was 85& higher than the similar one in the control group and RI was 86& higher (р<0,01).

Risk markers of reproductive loss in women with hyperandrogenism.

Objective: Introduction: The frequency of the pathological course of pregnancy with hyperandrogenism ranges from 21 to 48%. With the predominance of androgens against the background of lowering the normal products of steroidogenesis, a pro-inflammatory immune imbalance is formed, which causes a premature termination of the development of pregnancy. Many studies indicate that hyperandrogenism is a factor in the development of obstetric pathology, including placental dysfunction.

The degradation of three-ringed polycyclic aromatic hydrocarbons by wood-inhabiting fungus Pleurotus ostreatus and soil-inhabiting fungus Agaricus bisporus.

The degradation of two isomeric three-ringed polycyclic aromatic hydrocarbons by the white rot fungus Pleurotus ostreatus D1 and the litter-decomposing fungus Agaricus bisporus F-8 was studied. Despite some differences, the degradation of phenanthrene and anthracene followed the same scheme, forming quinone metabolites at the first stage. The further fate of these metabolites was determined by the composition of the ligninolytic enzyme complexes of the fungi.

High-throughput in situ X-ray screening of and data collection from protein crystals at room temperature and under cryogenic conditions.

Protein crystallography has significantly advanced in recent years, with in situ data collection, in which crystals are placed in the X-ray beam within their growth medium, being a major point of focus. In situ methods eliminate the need to harvest crystals, a previously unavoidable drawback, particularly for often small membrane-protein crystals. Here, we present a protocol for the high-throughput in situ X-ray screening of and data collection from soluble and membrane-protein crystals at room temperature (20-25°C) and under cryogenic conditions.

Degradation of phenanthrene by the rhizobacterium Ensifer meliloti.

The biodegradation of the polycyclic aromatic hydrocarbon phenantherene by the rhizobacterial strain Ensifer meliloti P221, isolated from the root zone of plant grown in PAH-contaminated soil was studied. Bacterial growth and phenanthrene degradation under the influence of root-exuded organic acids were also investigated. Analysis of the metabolites produced by the strain by using thin-layer chromatography, gas chromatography, high-pressure liquid chromatography, and mass-spectrometry revealed that phenanthrene is bioconverted via two parallel pathways.

Integrated nonlinear optical imaging microscope for on-axis crystal detection and centering at a synchrotron beamline.

Nonlinear optical (NLO) instrumentation has been integrated with synchrotron X-ray diffraction (XRD) for combined single-platform analysis, initially targeting applications for automated crystal centering. Second-harmonic-generation microscopy and two-photon-excited ultraviolet fluorescence microscopy were evaluated for crystal detection and assessed by X-ray raster scanning. Two optical designs were constructed and characterized; one positioned downstream of the sample and one integrated into the upstream optical path of the diffractometer.

Isolation and characterization of a glyphosate-degrading rhizosphere strain, Enterobacter cloacae K7.

Plant-growth-promoting rhizobacteria exert beneficial effects on plants through their capacity for nitrogen fixation, phytohormone production, phosphate solubilization, and improvement of the water and mineral status of plants. We suggested that these bacteria may also have the potential to express degradative activity toward glyphosate, a commonly used organophosphorus herbicide. In this study, 10 strains resistant to a 10 mM concentration of glyphosate were isolated from the rhizoplane of various plants.

Predicted optical performance of the GM/CA@APS micro-focus beamline.

GM/CA at the APS has developed microcrystallography capabilities for structural biology applications. The robust, quad, mini-beam collimators, which enable users to rapidly select between a 5, 10 or 20 micron diameter beam or a scatter guard for the full focused beam, are coupled with several powerful automated software tools that are built into the beamline control system JBluIce-EPICS. Recent successes at beamlines around the world in solving structures from microcrystals (2 - 10 microns) have led to increased demand for high-intensity micro-focus beams.

Versatile peroxidase of Bjerkandera fumosa: substrate and inhibitor specificity.

The inhibitor and substrate specificities of versatile peroxidase from Bjerkandera fumosa (VPBF) were studied. Two different effects were found: NaN(3), Tween-80, anthracene, and fluorene decreased the activity of VPBF, but p-aminobenzoic acid increased it. A mixed mechanism of effector influence on the activity of this enzyme was shown.

Gas-liquid chromatography-obtained differences in the dissolution enthalpy between two positional isomers in a polar stationary phase: a measure of the inter- or intramolecular hydrogen bond energy?

Previous GLC work with several 2- and 4-substituted phenols and anilines, as well as with a pyrrolizidine alcohol, had determined the difference between the heats of dissolution of two positional isomers in a strong polar stationary liquid phase; one of these isomers forms an intramolecular hydrogen bond (intra-HB) and the other has no such bond for steric reasons. The energies of the intermolecular hydrogen bonds (inter-HBs), ΔH(inter-HB), formed by the 1,2- and 1,4-isomers with the molecules of a polar phase had been assumed approximately equal, so the difference between them could be ignored. The same assumption had been made for the energies of nonspecific interactions (NSIs), ΔH(NSI).

Automated sample-scanning methods for radiation damage mitigation and diffraction-based centering of macromolecular crystals.

Automated scanning capabilities have been added to the data acquisition software, JBluIce-EPICS, at the National Institute of General Medical Sciences and the National Cancer Institute Collaborative Access Team (GM/CA CAT) at the Advanced Photon Source. A `raster' feature enables sample centering via diffraction scanning over two-dimensional grids of simple rectangular or complex polygonal shape. The feature is used to locate crystals that are optically invisible owing to their small size or are visually obfuscated owing to properties of the sample mount.

Fast fluorescence techniques for crystallography beamlines.

This paper reports on several developments of X-ray fluorescence techniques for macromolecular crystallography recently implemented at the National Institute of General Medical Sciences and National Cancer Institute beamlines at the Advanced Photon Source. These include (i) three-band on-the-fly energy scanning around absorption edges with adaptive positioning of the fine-step band calculated from a coarse pass; (ii) on-the-fly X-ray fluorescence rastering over rectangular domains for locating small and invisible crystals with a shuttle-scanning option for increased speed; (iii) fluorescence rastering over user-specified multi-segmented polygons; and (iv) automatic signal optimization for reduced radiation damage of samples.

Radiation damage in protein crystals is reduced with a micron-sized X-ray beam.

Radiation damage is a major limitation in crystallography of biological macromolecules, even for cryocooled samples, and is particularly acute in microdiffraction. For the X-ray energies most commonly used for protein crystallography at synchrotron sources, photoelectrons are the predominant source of radiation damage. If the beam size is small relative to the photoelectron path length, then the photoelectron may escape the beam footprint, resulting in less damage in the illuminated volume.

JBluIce-EPICS control system for macromolecular crystallography.

The trio of macromolecular crystallography beamlines constructed by the General Medicine and Cancer Institutes Collaborative Access Team (GM/CA-CAT) in Sector 23 of the Advanced Photon Source (APS) have been in growing demand owing to their outstanding beam quality and capacity to measure data from crystals of only a few micrometres in size. To take full advantage of the state-of-the-art mechanical and optical design of these beamlines, a significant effort has been devoted to designing fast, convenient, intuitive and robust beamline controls that could easily accommodate new beamline developments. The GM/CA-CAT beamline controls are based on the power of EPICS for distributed hardware control, the rich Java graphical user interface of Eclipse RCP and the task-oriented philosophy as well as the look and feel of the successful SSRL BluIce graphical user interface for crystallography.

Adaptive acousto-optic technique for femtosecond laser pulse shaping.

We discuss the theoretical and experimental investigation of acousto-optic dispersive tunable filters, based on quasi-collinear geometry of light-sound interaction in a tellurium dioxide single crystal. The geometry uses the effect of strong acoustic anisotropy in the paratellurite as well as peculiarities of acoustic wave reflections at the free boundary of the crystal. A mathematical concept for determination of optical, electrical, and constructional parameters of the filters is developed.

Mini-beam collimator enables microcrystallography experiments on standard beamlines.

The high-brilliance X-ray beams from undulator sources at third-generation synchrotron facilities are excellent tools for solving crystal structures of important and challenging biological macromolecules and complexes. However, many of the most important structural targets yield crystals that are too small or too inhomogeneous for a ;standard' beam from an undulator source, approximately 25-50 microm (FWHM) in the vertical and 50-100 microm in the horizontal direction. Although many synchrotron facilities have microfocus beamlines for other applications, this capability for macromolecular crystallography was pioneered at ID-13 of the ESRF.

Oxidoreductase activity of Sorghum root exudates in a phenanthrene-contaminated environment.

The effect of the polycyclic aromatic hydrocarbon (PAH) phenanthrene on the enzymatic activity of root exudates of the phytoremediating plant Sorghum bicolor (L.) Moench was studied. Analysis of sorghum root exudates allowed us to reveal the activities of oxidase, peroxidase, and tyrosinase.

Acute phase serum amyloid A in ovarian cancer as an important component of proteome diagnostic profiling.

In the context of serum amyloid A (SAA) identification as ovarian cancer marker derived by SELDI-MS, its serum levels were measured by immunoassay in different stages of ovarian cancer, in benign gynecological tumors, and in healthy controls. In addition, SELDI-TOF-MS spectra were obtained by protocol optimized for the SAA peak intensity. SELDI data on small proteins (5.