Fast Structure-Based Assignment of 15N HSQC Spectra of Selectively 15N-Labeled Paramagnetic Proteins

A novel strategy for fast NMR resonance assignment of N-15 HSQC spectra of proteins is presented. It requires the structure coordinates of the protein, a paramagnetic center, and one or more residue-selectively N-15-labeled samples. Comparison of sensitive undecoupled N-15 HSQC spectra recorded of paramagnetic and diamagnetic samples yields data for every cross-peak on pseudocontact shift, paramagnetic relaxation enhancement, cross-correlation between Curie-spin and dipole-dipole relaxation, and residual dipolar coupling. Comparison of these four different paramagnetic quantities with predictions from the three-dimensional structure simultaneously yields the resonance assignment and the anisotropy of the susceptibility tensor of the paramagnetic center. The method is demonstrated with the 30 kDa complex between the N-terminal domain of the epsilon subunit and the theta subunit of Escherichia Coll DNA polymerase III. The program PLATYPUS was developed to perform the assignment, provide a measure of reliability of the assignment, and determine the susceptibility tensor anisotropy.

Triple objective team mentoring: achieving learning objectives with chemical engineering students

A sophisticated style of mentoring has been found to be essential to support engineering student teams undertaking technically demanding, real-world problems as part of a Project-Centred Curriculum (PCC) at The University of Queensland. The term ‘triple-objective’ mentoring was coined to define mentoring that addresses not only the student’s technical goal achievement but also their time and team management. This is achieved through a number of formal mentor meetings that are informed by a confidential instrument which requires students to individually reflect on team processes prior to the meeting, and a checklist of technical requirements against which the interim student team progress and achievements are assessed. Triple-objective mentoring requires significant time input and coordination by the academic but has been shown to ensure effective student team work and learning undiminished by team dysfunction. Student feedback shows they value the process and agree that the tools developed to support the process are effective in developing and assessing team work and skills with average scores mostly above 3 on a four point scale.

A shift from passive teaching at medical conferences to more interactive methods improves physician learning

Conferences that deliver interactive sessions designed to enhance physician participation, such as role play, small discussion groups, workshops, hands-on training, problem- or case-based learning and individualised training sessions, are effective for physician education.

Chemical treatment of Escherichia coli. II. Direct extraction of recombinant protein from cytoplasmic inclusion bodies in intact cells

A method is presented for the direct extraction of the recombinant protein Long-R-3-IGF-I from inclusion bodies located in the cytoplasm of intact Escherichia coli cells. Chemical treatment with 6M urea, 3 mM EDTA, and 20 mM dithiothreitol (DTT) at pH 9.0 proved an effective combination for extracting recombinant protein from intact cells. Comparable levels of Long-R-3-IGF-I were recovered by direct extraction as achieved by in vitro dissolution following mechanical disruption. However, the purity of directly extracted recombinant protein was lower due to contamination by bacterial cell components. The kinetics of direct extraction are described using a first-order equation with the time constant of 3 min. Urea appears important for permeabilization of the cell and dissolution of the inclusion body. Conversely, EDTA is involved in permeabilization of the cell wall and DTT enhances protein release. pH proved to be important with lower levels of protein release achieved at low pH values (

Matrix elements of U(2n) generators in a multishell spin-orbit basis. I. The del-operator MEs in a two-shell composite Gelfand-Paldus basis

This is the first in a series of three articles which aimed to derive the matrix elements of the U(2n) generators in a multishell spin-orbit basis. This is a basis appropriate to many-electron systems which have a natural partitioning of the orbital space and where also spin-dependent terms are included in the Hamiltonian. The method is based on a new spin-dependent unitary group approach to the many-electron correlation problem due to Gould and Paldus [M. D. Gould and J. Paldus, J. Chem. Phys. 92, 7394, (1990)]. In this approach, the matrix elements of the U(2n) generators in the U(n) x U(2)-adapted electronic Gelfand basis are determined by the matrix elements of a single Ll(n) adjoint tensor operator called the del-operator, denoted by Delta(j)(i) (1 less than or equal to i, j less than or equal to n). Delta or del is a polynomial of degree two in the U(n) matrix E = [E-j(i)]. The approach of Gould and Paldus is based on the transformation properties of the U(2n) generators as an adjoint tensor operator of U(n) x U(2) and application of the Wigner-Eckart theorem. Hence, to generalize this approach, we need to obtain formulas for the complete set of adjoint coupling coefficients for the two-shell composite Gelfand-Paldus basis. The nonzero shift coefficients are uniquely determined and may he evaluated by the methods of Gould et al. [see the above reference]. In this article, we define zero-shift adjoint coupling coefficients for the two-shell composite Gelfand-Paldus basis which are appropriate to the many-electron problem. By definition, these are proportional to the corresponding two-shell del-operator matrix elements, and it is shown that the Racah factorization lemma applies. Formulas for these coefficients are then obtained by application of the Racah factorization lemma. The zero-shift adjoint reduced Wigner coefficients required for this procedure are evaluated first. All these coefficients are needed later for the multishell case, which leads directly to the two-shell del-operator matrix elements. Finally, we discuss an application to charge and spin densities in a two-shell molecular system. (C) 1998 John Wiley & Sons.

Matrix elements of U(2n) generators in a multishell spin-orbit basis. III. General formulas

This is the third and final article in a series directed toward the evaluation of the U(2n) generator matrix elements (MEs) in a multishell spin/orbit basis. Such a basis is required for many-electron systems possessing a partitioned orbital space and where spin-dependence is important. The approach taken is based on the transformation properties of the U(2n) generators as an adjoint tensor operator of U(n) x U(2) and application of the Wigner-Eckart theorem. A complete set of adjoint coupling coefficients for the two-shell composite Gelfand-Paldus basis (which is appropriate to the many-electron problem) were obtained in the first and second articles of this series. Ln the first article we defined zero-shift coupling coefficients. These are proportional to the corresponding two-shell del-operator matrix elements. See P. J. Burton and and M. D. Gould, J. Chem. Phys., 104, 5112 (1996), for a discussion of the del-operator and its properties. Ln the second article of the series, the nonzero shift coupling coefficients were derived. Having obtained all the necessary coefficients, we now apply the formalism developed above to obtain the U(2n) generator MEs in a multishell spin-orbit basis. The methods used are based on the work of Gould et al. (see the above reference). (C) 1998 John Wiley & Sons, Inc.

Evaluation of multifrequency bioelectrical impedance data for predicting lean tissue mass in beef cattle

Multifrequency bioimpedance analysis has the potential to provide a non-invasive technique for determining body composition in live cattle. A bioimpedance meter developed for use in clinical medicine was adapted and evaluated in 2 experiments using a total of 31 cattle. Prediction equations were obtained for total body water, extracellular body water, intracellular body water, carcass water and carcass protein. There were strong correlations between the results obtained through chemical markers and bioimpedance analysis when determined in cattle that had a wide range of liveweights and conditions. The r(2) values obtained were 0.87 and 0.91 for total body water and extracellular body water respectively. Bioimpedance also correlated with carcass water, measured by chemical analysis (r(2) = 0.72), but less well with carcass protein (r(2) = 0.46). These correlations were improved by inclusion of liveweight and sex as variables in multiple regression analysis. However, the resultant equations were poor predictors of protein and water content in the carcasses of a group of small underfed beef cattle, that had a narrow range of liveweights. In this case, although there was no statistical difference between the predicted and measured values overall, bioimpedance analysis did not detect the differences in carcass protein between the 2 groups that were apparent following chemical analysis. Further work is required to determine the sensitivity of the technique in small underfed cattle, and its potential use in heavier well fed cattle close to slaughter weight.

Sensitive detection of nitric oxide using seeded parametric four-wave mixing

A sensitive near-resonant four-wave mixing technique based on two-photon parametric four-wave mixing has been developed. Seeded parametric four-wave mixing requires only a single laser as an additional phase matched seeder field is generated via parametric four-wave mixing of the pump beam in a high gain cell. The seeder field travels collinearly with the pump beam providing efficient nondegenerate four-wave mixing in a second medium. This simple arrangement facilitates the detection of complex molecular spectra by simply scanning the pump laser. Seeded parametric four-wave mixing is demonstrated in both a low pressure cell and an air/acetylene flame with detection of the two-photon C (2) Pi(upsilon'=0)<--X (2) Pi(upsilon =0) spectrum of nitric oxide. From the cell data a detection limit of 10(12) molecules/cm(3) is established. A theoretical model of seeded parametric four-wave mixing is developed from existing parametric four-wave mixing theory. The addition of the seeder field significantly modifies the parametric four-wave mixing behaviour such that in the small signal regime, the signal intensity can readily be made to scale as the cube of the laser pump power while the density dependence follows a more familiar square law dependence, In general, we find excellent agreement between theory and experiment. Limitations to the process result from an ac Stark shift of the two-photon resonance in the high pressure seeder cell caused by the generation of a strong seeder field, as well as a reduction in phase matching efficiency due to the presence of certain buffer species. Various optimizations are suggested which should overcome these limitations, providing even greater detection sensitivity. (C) 1998 American Institute of Physics, [S0021-9606(98)01014-9].

Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network

Motivation: Prediction methods for identifying binding peptides could minimize the number of peptides required to be synthesized and assayed, and thereby facilitate the identification of potential T-cell epitopes. We developed a bioinformatic method for the prediction of peptide binding to MHC class II molecules. Results: Experimental binding data and expert knowledge of anchor positions and binding motifs were combined with an evolutionary algorithm (EA) and an artificial neural network (ANN): binding data extraction --> peptide alignment --> ANN training and classification. This method, termed PERUN, was implemented for the prediction of peptides that bind to HLA-DR4(B1*0401). The respective positive predictive values of PERUN predictions of high-, moderate-, low- and zero-affinity binder-a were assessed as 0.8, 0.7, 0.5 and 0.8 by cross-validation, and 1.0, 0.8, 0.3 and 0.7 by experimental binding. This illustrates the synergy between experimentation and computer modeling, and its application to the identification of potential immunotheraaeutic peptides.

Modeling ex vivo hematopoiesis using chemical engineering metaphors

Ex vivo hematopoiesis is increasingly used for clinical applications. Models of ex vivo hematopoiesis are required to better understand the complex dynamics and to optimize hematopoietic culture processes. A general mathematical modeling framework is developed which uses traditional chemical engineering metaphors to describe the complex hematopoietic dynamics. Tanks and tubular reactors are used to describe the (pseudo-) stochastic and deterministic elements of hematopoiesis, respectively. Cells at any point in the differentiation process can belong to either an immobilized, inert phase (quiescent cells) or a mobile, active phase (cycling cells). The model describes five processes: (1) flow (differentiation), (2) autocatalytic formation (growth),(3) degradation (death), (4) phase transition from immobilized to mobile phase (quiescent to cycling transition), and (5) phase transition from mobile to immobilized phase (cycling to quiescent transition). The modeling framework is illustrated with an example concerning the effect of TGF-beta 1 on erythropoiesis. (C) 1998 Published by Elsevier Science Ltd. All rights reserved.

Shift of the subharmonic resonances and suppression of fluorescence in a two-level atom driven by a bichromatic field

We study the behavior of a two-level atom that is driven by a bichromatic field consisting of a strong resonant component and a weaker tunable component. In addition to the splitting of the energy levels (the multiphoton AC Stark effect), we find that the weaker component also shifts the subharmonic resonances, an effect we attribute to a dynamic Stark shift. When the weaker component is tuned to a shifted resonance, no fluorescence occurs at either the frequency of the strong component or the three-photon mixing frequency. Results are obtained with numerical techniques and explained in terms of the dressed-atom model of the system. (C) 1998 Optical Society of America [S0740-3224(98)01508-2] OCIS codes: 270.4180, 270.6620, 270.0270.

Homodyne measurements on a Bose-Einstein condensate

We investigate a nondestructive measurement technique to monitor Josephson-like oscillations between two spatially separated neutral atom Bose-Einstein condensates. One condensate is placed in an optical cavity, which is strongly driven by a coherent optical field. The cavity output field is monitored using a homodyne detection scheme. The cavity field is well detuned from an atomic resonance, and experiences a dispersive phase shift proportional to the number of atoms in the cavity. The detected current is modulated by the coherent tunneling oscillations of the condensate. Even when there is an equal number of atoms in each well initially, a phase is established by the measurement process and Josephson-like oscillations develop due to measurement backaction noise alone.

Effects of coping strategies, social support and work-nonwork conflict on shift worker's health

Objectives This study examines the direct and mediated effects of shift workers' coping strategies and social support on structural work-nonwork conflict and subjective health. Methods The participants were 172 registered female nurses, aged 21 to 40 years. They all worked full-time, on rapidly rotating, 8-hour shifts in metropolitan general hospitals. All the respondents completed a self-administered questionnaire requesting demographic information and data on sources of social support, work-nonwork conflict, and coping strategies. Results A path model with good fit (chi(2)=28.88, df=23, P>.23, CFI=0.97) demonstrated complex effects of social support and coping on structural work-nonwork conflict and health. Conclusions Structural work-nonwork conflict mediated the effects of social support from supervisors and emotionally expressive coping on psychological symptoms. Control of shifts mediated the effect of social support from supervisors on structural work-nonwork conflict. Disengagement coping had direct and mediated effects on psychological and physical health. However, it also had mediated effects, with the effect on psychological health being mediated by support from co-workers and the effect on physical symptoms being mediated by family support. Go-worker support mediated the effect of social support from supervisors on psychological symptoms. Overall, these findings support previous research and clarify the process by which coping strategies and social support affect structural work-nonwork conflict and health in shift work.