Structure-oriented rational design of chymotrypsin inhibitor models

Three peptides modelling a highly potent, 35-residue chymotrypsininhibitor (Schistocerca gregaria chymotrypsin inhibitor) weredesigned and synthesized by convergent peptide synthesis. Foreach model peptide, the inhibitory constant (K_i) on chymotrypsinand the solution structure were determined. In addition, moleculardynamics calculations were performed for all of them. Two modelscontaining approximately half of the parent inhibitor (17 of35 residues) were designed and subsequently found to have nosubstantial inhibitory activity (K_i values in the mM range).The third model composed of 24 amino acid residues proved tobe an effective (K_i 10^–7) inhibitor of bovine chymotrypsin.Both the solution structure properties determined by NMR spectroscopyand the dynamic behaviour of the latter model system are comparableto the native inhibitor. In contrast, the structure and dynamicsof the first two related model peptides show characteristicdifferences. We suggest that the conformation and flexibilityof the modelled protease inhibitor are crucial for its biologicalefficiency. Moreover, the structural and dynamic features ofthe binding loop (28–33) and those of the rest of themolecule appear to be interdependent. Most importantly, thesestructural characteristics can be rationally modified, at leastpartially, by peptide design. Received March 7, 2003; revised August 25, 2003; accepted August 26, 2003.     

Adenosine triphosphate (ATP) and other nucleotides stimulate the hydrolysis of phosphatidylethanolamine in intact fibroblasts

Addition of adenosine triphosphate (ATP) to [¹⁴C]ethanolamine-prelabeled NIH 3T3 fibroblasts resulted in rapid formation of [¹⁴C]ethanolamine from the prelabeled cellular phosphatidylethanolamine (PtdEtn) pool. After 2-min exposure, 10 μM ATP had near maximal effects on PtdEtn hydrolysis. Several other nucleotides, including UTP, ITP, and the stable ATP analog adenosine 5′-O-(3-thiotriphosphate) (ATPγS), also had stimulatory effects on PtdEtn hydrolysis with a potency comparable to that observed with ATP. The same nucleotides which acted on PtdEtn hydrolysis also had similar stimulatory effects on the hydrolysis of phosphatidylcholine (PtdCho) in [¹⁴C]choline-labeled cells. In isolated membranes, Mg²⁺ greatly enhanced the stimulatory effects of ATP and ATPγS, but not of other nucleotides, on the hydrolysis of PtdEtn and PtdCho. Results indicate that in isolated membranes, both ATP and ATPγS stimulate phospholipid hydrolysis by two different mechanisms, but in intact cells only one of these mechanisms appears to be responsive to externally added nucleotides.     

Determination of trace manganese and Ni in neem oil by ETA-AAS with emulsion sample introduction

An emulsion-based method was developed as an alternative for the introduction of oil-based samples into a graphite furnace to produce a more rapid, precise, and accurate method of analysis. The combination of emulsion sampling and electrothermal atomization for atomic absorption spectroscopy was developed and then applied to the determination of Ni and manganese in neem oil from Venezuela. The optimal concentration of neem oil in the emulsion was 30 and 4% for Ni and Mn, respectively, based on the metal concentration of the neem oil. The stability of the emulsion as a function of time was evaluated. The use of aqueous calibration solutions and the accuracy attained using this method make it attractive for the analysis of oil samples. The metal recovery was between 97 and 101%. Based on the emulsion method, the neem oil samples had 1.39 and 0.21 mg of Mn and Ni per kg of oil, respectively. The wet digestion method indicated a Mn and Ni concentration in the neem oil sample of 1.42 and 0.24 mg/kg, respectively.     

Parametric estimation of affine deformations of planar shapes

We consider the estimation of affine transformations aligning a known 2D shape and its distorted observation. The classical way to solve this registration problem is to find correspondences between the shapes and then compute the transformation parameters from these landmarks. Here we propose a novel approach where the exact transformation is obtained as the solution of a polynomial system of equations. The method has been tested on synthetic as well as on real images and its robustness in the presence of segmentation errors and additive geometric noise has also been demonstrated. We have successfully applied the method for the registration of hip prosthesis X-ray images. The advantage of the proposed solution is that it is fast, easy to implement, has linear time complexity, works without established correspondences and provides an exact solution regardless of the magnitude of transformation.     

An Analytical Method for Predicting the Performance of Parallel Image Processing Operations

This paper presents an analytical performance prediction model and methodology that can be used to predict the execution time, speedup, scalability and similar performance metrics of a large set of image processing operations running on a p-processor parallel system. The model which requires only a few parameters obtainable on a minimal system can help in the systematic design, evaluation and performance tuning of parallel image processing systems. Using the model one can reason about the performance of a parallel image processing system prior to implementation. The method can also support programmers in detecting critical parts of an implementation and system designers in predicting hardware performance and the effect of hardware parameter changes on performance. The execution of parallel image processing operations was studied and operations were arranged in three main problem classes based on data locality and the communication patterns of the algorithms. The core of the method is the derivation of the overhead function, as it is the overhead that determines the achievable speedup. The overheads were examined and modelled for each class. The use of the method is illustrated by four class-representative image processing algorithms: image-scalar addition, convolution, histogram calculation and the Fast Fourier Transform. The developed performance model has been validated on a 16-node parallel machine and it has been shown that the model is able to predict the parallel run-time and other performance metrics of parallel image processing operations accurately.     

Effects of Sulforaphane-Induced Cell Death upon Repeated Passage of Either P-Glycoprotein-Negative or P-Glycoprotein-Positive L1210 Cell Variants

The expression of the membrane ABCB1 transporter in neoplastic cells is one of the most common causes of reduced sensitivity to chemotherapy. In our previous study, we investigated the effect of a single culture of ABCB1-negative (S) and ABCB1-positive variants of L1210 cells (R and T) in the presence of sulforaphane (SFN). We demonstrated that SFN induces the onset of autophagy more markedly in S cells than in R or T cells. In the current study, we focused on the effect of the repeated culture of S, R and T cells in SFN-containing media. The repeated cultures increased the onset of autophagy compared to the simple culture, mainly in S cells and to a lesser extent in R and T cells, as indicated by changes in the cellular content of 16 and 18 kDa fragments of LC3B protein or changes in the specific staining of cells with monodansylcadaverine. We conclude that SFN affects ABCB1-negative S cells more than ABCB1-positive R and T cells during repeated culturing. Changes in cell sensitivity to SFN appear to be related to the expression of genes for cell-cycle checkpoints, such as cyclins and cyclin-dependent kinases.     

Kinetic parameter estimation for cooling crystallization process based on cell average technique and automatic differentiation

In this paper, a cell average technique(CAT) based parameter estimation method is proposed for cooling crystallization involved with particle growth, aggregation and breakage, by establishing a more efficient and accurate solution in terms of the automatic differentiation(AD) algorithm. To overcome the deficiency of CAT that demands high computation cost for implementation, a set of ordinary differential equations(ODEs) entailed from CAT based discretized population balance equation(PBE) are solved by using the AD based high-order Taylor expansion. Moreover, an AD based trust-region reflective(TRR) algorithm and another interior-point(IP) algorithm are established for estimating the kinetic parameters associated with particle growth, aggregation and breakage. As a result, the estimation accuracy can be further improved while the computation cost can be significantly reduced, compared to the existing algorithms. Benchmark examples from the literature are used to illustrate the accuracy and efficiency of the AD-based CAT, TRR and IP algorithms in comparison with the existing algorithms. Moreover, seeded batch cooling crystallization experiments of β form L-glutamic acid are performed to validate the proposed method.     

Peculiarities in thermal evolution of precipitated amorphous calcium phosphates with an initial Ca/P ratio of 1:1

Thermal evolution of amorphous calcium phosphate (ACP) powder from a fast nitrate synthesis with a Ca/P ratio of 1:1 were studied in the range of 20–980?°C. The powder consisted of amorphous dicalcium phosphate anhydrate (CaHPO₄) after heating to 200?°C. CaHPO₄ gradually condensed to amorphous calcium pyrophosphate Ca₂P₂O₇ (CPP) between 200 to 620?°C. Amorphous CPP crystallized at 620–740?°C to a metastable polymorph α′-CPP of the high-temperature phase α-CPP and β-CPP. The α′-CPP/ β-CPP phase ratio reached a maximum at 800?°C (60?wt% α′-CPP/40?wt% β-CPP), and α′-CPP gradually transformed to β-CPP at a higher temperature. Some β-TCP occurred at 900?°C, so that a three-phasic mixture was obtained in the powder heated to 980?°C. The occurrence of metastable α′-CPP is attributed to Ostwald’s step rule, and a mechanism for β-TCP formation is proposed. The advantages of prospective biomaterials from these powders are discussed.