Characterization of the DNA-binding domain of beta protein, a component of phage lambda Red-pathway by UV catalyzed cross-linking

beta protein, a key component of Red-pathway of phage lambda is necessary for its growth and general genetic recombination in recombination-deficient mutants of Escherichia coli. To facilitate studies on structure-function relationships, we overexpressed beta protein and purified it to homogeneity. A chemical cross-linking reagent, glutaraldehyde, was used to stabilize the physical association of beta protein in solution. A 67-kDa band, corresponding to homodimer, was identified after separation by SDS-polyacrylamide gel electrophoresis. Stoichiometric measurements indicated a site-size of 1 monomer of beta protein/5 nucleotide residues. Electrophoretic gel mobility shift assays suggested that beta protein formed stable nucleoprotein complexes with 36-mer, but not with 27- or 17-mer DNA. Interestingly, the interaction of beta protein with DNA and the stability of nucleoprotein complexes was dependent on the presence of MgCl2, and the binding was abolished by 250 mM NaCl. The K-d of beta protein binding to 36-mer DNA was on the order of 1.8 x 10(-6) M. Photochemical cross-linking of native beta protein or its fragments, generated by chymotrypsin, to 36-mer DNA was performed to identify its DNA-binding domain. Characterization of the cross-linked peptide disclosed that amino acids required for DNA-binding specificity resided within a 20-kDa peptide at the N-terminal end. These findings provide a basis for further understanding oi the structure and function of beta protein.

Analysis of Transverse Shear Strains in Pre-Twisted Thick Beams using Variational Asymptotic Method

The cross-sectional stiffness matrix is derived for a pre-twisted, moderately thick beam made of transversely isotropic materials and having rectangular cross sections. An asymptotically-exact methodology is used to model the anisotropic beam from 3-D elasticity, without any further assumptions. The beam is allowed to have large displacements and rotations, but small strain is assumed. The strain energy is computed making use of the beam constitutive law and kinematical relations derived with the inclusion of geometrical nonlinearities and an initial twist. The energy functional is minimized making use of the Variational Asymptotic Method (VAM), thereby reducing the cross section to a point on the beam reference line with appropriate properties, forming a 1-D constitutive law. VAM is a mathematical technique employed in the current problem to rigorously split the 3-D analysis of beams into two: a 2-D analysis over the beam cross-sectional domain, which provides a compact semi-analytical form of the properties of the cross sections, and a nonlinear 1-D analysis of the beam reference curve. In this method, as applied herein, the cross-sectional analysis is performed asymptotically by taking advantage of a material small parameter and two geometric small parameters. 3-D strain components are derived using kinematics and arranged in orders of the small parameters. Closed-form expressions are derived for the 3-D non-linear warping and stress fields. Warping functions are obtained by the minimization of strain energy subject to certain set of constraints that render the 1-D strain measures well-defined. The zeroth-order 3-D warping field thus yielded is then used to integrate the 3-D strain energy density over the cross section, resulting in the 1-D strain energy density, which in turn helps identify the corresponding cross-sectional stiffness matrix. The model is capable of predicting interlaminar and transverse shear stresses accurately up to first order.

NON-DIMENSIONAL KINETOELASTOSTATIC MAPS FOR COMPLIANT MECHANISMS

How do we assess the capability of a compliant mechanism of given topology and shape? The kinetoelastostatic maps proposed in this paper help answer this question. These maps are drawn in 2D using two non-dimensional quantities, one capturing the nonlinear static response and the other the geometry, material, and applied forces. Geometrically nonlinear finite element analysis is used to create the maps for compliant mechanisms consisting of slender beams. In addition to the topology and shape, the overall proportions and the proportions of the cross-sections of the beam segments are kept fixed for a map. The finite region of the map is parameterized using a non-dimensional quantity defined as the slenderness ratio. The shape and size of the map and the parameterized curves inside it indicate the complete kinetoelastostatic capability of the corresponding compliant mechanism of given topology, shape, and fixed proportions. Static responses considered in this paper include input/output displacement, geometric amplification, mechanical advantage, maximum stress, etc. The maps can be used to compare mechanisms, to choose a suitable mechanism for an application, or re-design as may be needed. The usefulness of the non-dimensional maps is presented with multiple applications of different variety. Non-dimensional portrayal of snap-through mechanisms is one such example. The effect of the shape of the cross-section of the beam segments and the role of different segments in the mechanism as well as extension to 3D compliant mechanisms, the cases of multiple inputs and outputs, and moment loads are also explained. The effects of disproportionate changes on the maps are also analyzed.

Resonant mode analysis in toroidal cavities with elliptic cross-sections

Resonant cavity modes in a torus with elliptical cross section are studied by means of a direct variational method. The nonlinear effects of toroidicity and ellipticity on the frequency of the basic mode are analyzed simply and systematically without the restriction of linear theory. It is shown that the toroidicity effect on the m = 0 transverse magnetic mode is less-than-or-equal-to 11%. The frequency of the mode shifts approximately 11-29% when the elongation of the cross section changes from 1 to 2. The effects of toroidicity and ellipticity differ for each resonant mode.

A review of the crayfish fishery of Nigeria with special reference to the Cross River State

The fishery for crayfish is of considerable importance in the maritime region of the Cross River State, Nigeria, where it forms an important occupation of a host of fishermen. Crayfish landings from this State contributed 11% to the national marine fish landings within the period 1980 to 1984 and also in the same period the volume of crayfish alone formed 26% of the marine fish landings within the State. The species exploited as crayfish include Palaemon hastatus; Hippolysmata hastatoides, and Macrobrachium sp; mixed with the larval, and juveniles of pink shrimp Panaeus dourarum. They are generally small in size ranging from 7 cm (maximum) to 2.5 cm. Crayfish are caught all year round along the Niger Delta, but particularly along the river estuaries and littoral waters of the Cross River State with the highest production occurring in March to May. Crayfish are usually smoked, and occasionally sun-dried, and they form an indispensable food item in the diet of the people of the entire southern States in particular and Nigeria in general. It appears that crayfish landings could be substantially increased without depleting the stock, if a proper exploratory survey is undertaken of the Niger delta, and the Cross River estuaries to chart potentially rich grounds of this resource

Optimizations for the uniformity of the non-volatile volume grating in doubly doped LiNbO3 crystals

The formation of the non-uniformity of the non-volatile volume grating in doubly doped LiNbO3 crystals is studied in detail. We find that the non-uniformity of the grating is mainly caused by strong ultraviolet light absorption, and the average saturation space-charge field is small and the diffraction efficiency is low as a result of the non-uniformity of the grating. In order to optimize the uniformity of the grating, we propose the recording scheme by using two sensitizing beams simultaneously from the two opposite sides of the crystals. Theoretical simulations and experimental verifications are performed. Results show that the well uniformed grating with high diffraction efficiency can be obtained by using this optimization scheme. (c) 2004 Elsevier B.V. All rights reserved.

Estimating the girth of fish by applying an elliptic model

A new method for estimating the maximum girth of roundfish is proposed as illustrated; this is based on an elliptic approximation of the cross sections of the fish body. Results derived from a small sample horse mackerel, Trachurus trachurus, suggest that maximum girth estimates based on the elliptic model are more precise than the values estimated by applying a conventional method.

Age and growth of the swordfish (Xiphias gladius L.) in the waters around Taiwan determined from anal-fin rays

Age and growth of the swordfish (Xiphias gladius) in Taiwan waters was studied from counts of growth bands on cross sections of the second ray of the first anal fin. Data on lower jaw fork length and weight, and samples of the anal fin of male and female swordfish were collected from three offshore and coastal tuna longline fishing ports on a monthly basis between September 1997 and March 1999. In total, 685 anal fins were collected and 627 of them (293 males and 334 females) were aged successfully. The lower jaw fork lengths of the aged individuals ranged from 83.4 to 246.6 cm for the females and from 83.3 to 206 cm for the males. The radii of the fin rays and growth bands on the cross sections were measured under a dissecting microscope equipped with an image analysis system. Trends in the monthly marginal increment ratio indicated that growth bands formed once a year. Thus, the age of each fish was deter-mined from the number of visible growth bands. Two methods were used to estimate and compare the standard and the generalized von Bertalanffy growth parameters for both males and females. The nonlinear least square estimates of the generalized von Bertalanffy growth parameters in method II, in which a power function was used to describe the relationship between ray radius and LJFL, were recommended as most acceptable. There were significant differences in growth parameters between males and females. The growth parameters estimated for females were the following: asymptotic length (L∞) = 300.66 cm, growth coefficient (K) = 0.040/yr, age at zero length (t0) = –0.75 yr, and the fitted fourth parameter (m) = –0.785. The growth parameters estimated for males were the following: asymptotic length (L∞) = 213.05 cm, growth coefficient (K) = 0.086/yr, age at zero length (t0) = –0.626 yr, and the fitted fourth parameter (m) = –0.768.

Phenomenological analysis of the double-pion production in nucleon-nucleon collisions up to 2.2 GeV

With an effective Lagrangian approach, we analyze several NN -> NN pi pi channels by including various resonances with mass up to 1.72 GeV. For the channels with the pion pair of isospin zero, we confirm the dominance of N*(1440) -> N sigma in the near-threshold region. At higher energies and for channels with the final pion pair of isospin one, we find large contributions from N*(1440) -> Delta pi, double-Delta, Delta(1600) -> N*(1440)pi, Delta(1600) -> Delta pi and Delta(1620) -> Delta pi. There are also sizable contributions from Delta -> Delta pi, Delta -> N pi, N -> Delta pi, and nucleon pole at energies close to the threshold. We give a good reproduction to the total cross sections up to beam energies of 2.2 GeV except for the pp -> pp pi(0)pi(0) channel at energies around 1.1 GeV and our results agree with the existing data of differential cross sections of pp -> pp pi(+)p pi(-), pp -> nn pi(+)pi(+), and pp -> pp pi(0)pi(0) which are measured at CELSIUS and COSY.

3D refraction correction and extraction of clinical parameters from spectral domain optical coherence tomography of the cornea.

Capable of three-dimensional imaging of the cornea with micrometer-scale resolution, spectral domain-optical coherence tomography (SDOCT) offers potential advantages over Placido ring and Scheimpflug photography based systems for accurate extraction of quantitative keratometric parameters. In this work, an SDOCT scanning protocol and motion correction algorithm were implemented to minimize the effects of patient motion during data acquisition. Procedures are described for correction of image data artifacts resulting from 3D refraction of SDOCT light in the cornea and from non-idealities of the scanning system geometry performed as a pre-requisite for accurate parameter extraction. Zernike polynomial 3D reconstruction and a recursive half searching algorithm (RHSA) were implemented to extract clinical keratometric parameters including anterior and posterior radii of curvature, central cornea optical power, central corneal thickness, and thickness maps of the cornea. Accuracy and repeatability of the extracted parameters obtained using a commercial 859nm SDOCT retinal imaging system with a corneal adapter were assessed using a rigid gas permeable (RGP) contact lens as a phantom target. Extraction of these parameters was performed in vivo in 3 patients and compared to commercial Placido topography and Scheimpflug photography systems. The repeatability of SDOCT central corneal power measured in vivo was 0.18 Diopters, and the difference observed between the systems averaged 0.1 Diopters between SDOCT and Scheimpflug photography, and 0.6 Diopters between SDOCT and Placido topography.

The electron impact ionization of magnesium (2p)

A systematic study of the triple differential cross section for the electron impact ionization of magnesium is presented. Complete sets of theoretical results using both the first Born and the distorted wave Bom approximation are given for a range of asymmetric kinematical regimes. How the physical significance of the different approximations enter the character of the cross sections will be explicitly demonstrated. Comparison is made with experiments of the Maryland group and suggestions are made for new experiments.

Highly resolved absolute cross-sections for dissociative electron attachment to SF5CF3

Using two complementary experimental methods, we have measured partial (mass-resolved) cross-sections for dissociative electron attachment to the molecule trifluoromethyl sulfurpentafluoride (SF5CF3) at the gas temperature T-G = 300 K over a broad range of electron energies (E = 0.001-12 eV). The absolute scale for these cross-sections was obtained with reference to the thermal (T = 300 K) rate coefficient for anion formation (8.0(3) x 10(-8) cm(3) s(-1)). Below 1 eV, SF5- is the dominant product anion and formed through the lowest anion state which cuts the neutral SF5CF3 potential close to the S-C equilibrium distance. The highly resolved laser photoelectron attachment data exhibit a downward Wigner cusp at 86meV, indicating that the nu(4)(alpha(1)) vibrational mode is important for the primary attachment dynamics. Both SF5- and F- anions are formed with similar yields through the first excited resonance located near 3.6eV. Towards higher energies, the anions CF3-, SF4-, and SF3- are also produced. Summation of the partial cross-sections yields a total absolute cross-section for anion formation over the energy range 0.001-12 eV. This is used to calculate the dependence of the rate coefficient for dissociative electron attachment over a broad range of electron temperatures for the fixed gas temperature T-G = 300 K; good agreement is found between the calculated values and those obtained in a drift tube experiment. In addition to the experimental work, semiempirical R-matrix calculations have been Carried out for the energy dependence of the cross-section for SF5- formation. The experimental findings are semi-quantitatively recovered. (C) 2008 Elsevier B.V. All rights reserved.

Effect of a finite energy spread of the positron beam on the threshold behaviour of the positron annihilation cross section

In a recent paper [Phys. Rev. Lett. 88, 163202 (2002)] we established the threshold behavior of the cross section of positron-atom annihilation into two gamma quanta near the positronium (Ps)-formation threshold. Here, the near-threshold behavior of the positron 3 gamma annihilation cross section and its relation to the ortho-Ps-formation cross section are determined. We also analyze the feasibility of observing these effects by examining the effect of the ?nite-energy resolution of a positron beam on the threshold behavior.

Reproducibility of optic disk topographic measurements with the Topcon ImageNet and the Heidelberg Retina Tomograph

Objective: To compare the reproducibility of optic disk measurements provided by an image analyzer and a scanning laser tomograph. Methods: Ten images of the same eye of 10 normal volunteers were taken with the Heidelberg Retina Tomograph and with the Topcon ImageNet. Intraclass correlation coefficient (ICC) and coefficient of variation (CV) were used to evaluate the reproducibility of the measurements. Results: Eleven parameters were analyzed with the Topcon ImageNet. Six parameters (55%) had ICC greater than 90%. Four parameters (36%) had CV less than 10%. Twelve parameters were evaluated with the Heidelberg Retina Tomograph. Nine parameters (75%) had ICC over 90%. Nine parameters (75%) had CV less than 10%. Conclusion: Both systems provided reproducible data. The optic disk parameters provided by the Heidelberg Retina Tomograph had a better reproducibility than those obtained from the Topcon ImageNet.

Photoionization cross-sections for Fe II

The LS R-matrix method was used to compute new photoionization cross sections for Fe II. Results are compared with available experimental data and with previous calculations of the cross section. We also present the first fine-structure photoionization data for this ion obtained with the fully-relativistic DARC codes.