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Wheat bran (WB) from Triticum aestivum has many beneficial effects on human health. To the best of our knowledge, very little has been published about its ability to prevent pathogenic bacterial adhesion in the intestine. Here, a WB extract was fractionated using different strategies, and the obtained fractions were tested in different in vitro methodologies to evaluate their interference in the attachment of enterotoxigenic Escherichia coli (ETEC) K88 to intestinal porcine epithelial cells (IPEC-J2) with the aim of identifying the putative anti-adhesive molecules. It was found that a proteinaceous compound in the >300-kDa fraction mediates the recognition of ETEC K88 to IPEC-J2. Further fractionation of the >300-kDa sample by size-exclusion chromatography showed several proteins below 90 kDa, suggesting that the target protein belongs to a high-molecular-weight (MW) multi-component protein complex. The identification of some relevant excised bands was performed by mass spectrometry (MS) and mostly revealed the presence of various protease inhibitors (PIs) of low MW: Serpin-Z2B, Class II chitinase, endogenous alpha-amylase/subtilisin inhibitor and alpha-amylase/trypsin inhibitor CM3. Furthermore, an incubation of the WB extract with ETEC K88 allowed for the identification of a 7S storage protein globulin of wheat, Globulin 3 of 66 kDa, which may be one of the most firmly attached WB proteins to ETEC K88 cells. Further studies should be performed to gain an understanding of the molecular recognition of the blocking process that takes place. All gathered information can eventually pave the way for the development of novel anti-adhesion therapeutic agents to prevent bacterial pathogenesis.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2003., Includes bibliographical references., This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections., EGFR and HER2 expression levels have distinguished themselves as important factors in contributing to various types of cancers including breast and ovarian cancers, but quantitative linkages between receptor expression levels and aberrant cell behaviors are not well understood. The ability to interpret and predict cell responses in a multi-parameter space will be vital in efforts to manipulate cell behavior for therapeutic purposes. HER2 acts as a co-receptor of the EGFR family of receptor tyrosine kinases. HER2 does not bind any known ligand, but plays an active signaling role following heterodimerization with a ligand-bound EGFR family receptor. EGFR family receptors undergo a dynamic process termed trafficking in which receptors and ligands are internalized and then either recycled to the surface or targeted for degradation. Trafficking is intimately connected to cell signaling by controlling the quantity and location of ligand-receptor complexes and is sensitive to disruption via the overexpression of the receptors involved. In this work, we quantitatively establish the role of HER2 and heterodimerization in EGFR trafficking and signaling. A hierarchy of mathematical models describing the trafficking behavior of EGFR and HER2 was developed at various levels of mechanistic detail. At the macroscopic level the trafficking of EGFR and HER2 fall into two regimes, one whose downregulation is sorting-limited (EGFR) and one whose downregulation is internalization-limited (HER2)., (cont.) Subordinate models yield mechanistic detail into the endocytic and endosomal sorting processes supporting the notions that heterodimers internalize as single entities and that HER2 is able to disrupt EGFR sorting through a competitive mechanism. The development of a comprehensive model of EGFR and HER2 trafficking enables the predictions of the quantity and distribution of various receptor species, including homo- and heterodimers as a function of time. Point by point comparison with ERK signaling data for different HER2 expressing cell clones allows the calculation of the signal generated per activated HER2 and per activated EGFR. These results suggest that EGFR and HER2 do not differ significantly in their ERK signaling ability and that HER2-mediated differences in ERK signaling can entirely be explained by interactions at the level of receptor trafficking., by Bart S. Hendriks., Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2003., Includes bibliographical references., This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections., EGFR and HER2 expression levels have distinguished themselves as important factors in contributing to various types of cancers including breast and ovarian cancers, but quantitative linkages between receptor expression levels and aberrant cell behaviors are not well understood. The ability to interpret and predict cell responses in a multi-parameter space will be vital in efforts to manipulate cell behavior for therapeutic purposes. HER2 acts as a co-receptor of the EGFR family of receptor tyrosine kinases. HER2 does not bind any known ligand, but plays an active signaling role following heterodimerization with a ligand-bound EGFR family receptor. EGFR family receptors undergo a dynamic process termed trafficking in which receptors and ligands are internalized and then either recycled to the surface or targeted for degradation. Trafficking is intimately connected to cell signaling by controlling the quantity and location of ligand-receptor complexes and is sensitive to disruption via the overexpression of the receptors involved. In this work, we quantitatively establish the role of HER2 and heterodimerization in EGFR trafficking and signaling. A hierarchy of mathematical models describing the trafficking behavior of EGFR and HER2 was developed at various levels of mechanistic detail. At the macroscopic level the trafficking of EGFR and HER2 fall into two regimes, one whose downregulation is sorting-limited (EGFR) and one whose downregulation is internalization-limited (HER2)., (cont.) Subordinate models yield mechanistic detail into the endocytic and endosomal sorting processes supporting the notions that heterodimers internalize as single entities and that HER2 is able to disrupt EGFR sorting through a competitive mechanism. The development of a comprehensive model of EGFR and HER2 trafficking enables the predictions of the quantity and distribution of various receptor species, including homo- and heterodimers as a function of time. Point by point comparison with ERK signaling data for different HER2 expressing cell clones allows the calculation of the signal generated per activated HER2 and per activated EGFR. These results suggest that EGFR and HER2 do not differ significantly in their ERK signaling ability and that HER2-mediated differences in ERK signaling can entirely be explained by interactions at the level of receptor trafficking., by Bart S. Hendriks., Ph.D.

A method of obtaining numerical solutions of a general class of boundary-value problems governed by the two-dimensional diffusion equation is investigated. The method employs a partial discretization of independent variables to reduce the problem of partial differential equations to a sequence of related boundary-value problems governed by a system of linear second-order ordinary differential equations. The generality of the method is demonstrated by applications to example problems involving both regular and irregular boundaries with boundary conditions of a general type. Application of separation of variables techniques to obtain closed-form solutions of a certain class of problems is presented and the results are used to indicate the accuracy of the method. An investigation into the stability characteristics of the resulting system of ordinary differential equations is also presented. It is concluded that the method appears to show promise as an easily implemented numerical method but that the full potential of the approach will not be realized until significant advances have been made in both computing hardware and software. (Author)

A method of determining certain characteristic flexural rigidities and elastic properties of non-linearly elastic materials is presented. A moment curvature relation in the form of a hyperbolic tangent law is introduced. An identification method utilizing quasilinearization and a least squares fitting technique is used to solve the nonlinear differential equation derived from the moment curvature relation, subject to boundary values representing deflections of the bar at discrete points. Deflection data from numerical simulations of a non-linearly elastic prismatic bar are used to demonstrate the identification method. Numerical experiments relating the accuracy of the identification method to the number and accuracy of the boundary values are presented. Conclusions based on the numerical experiments are included. (Author)

The paper is a tutorial discussion of identification problems. The basic principles of one method of identification are discussed. The method of quasilinearization has been developed by Richard Bellman and Robert Kalaba and others. This method is discussed in some detail with emphasis on programming strategies. These strategies are intended to improve the utility of a general quasilinearization program. Specific strategies are concerned with expansion of convergence space, super-position of particular solutions, and convergence criteria. (Author)

A procedure for identification in partial differential equations is described and illustrated by the Laplace equation and the unsteady heat conduction equation. The procedure for solution involves the substitution of difference operators for the partial derivatives with respect to all but one of the independent variables. The linear boundary value problem is solved by superposition of particular solutions. For non-linear boundary value problems which arise from the original form of the equation or from the identification procedure, a Newton-Raphson-Kantorovich expansion in function space is used to reduce the solution to an iterative procedure of solving linear boundary value problems. For the problems considered, this procedure has proven to be effective and results in a reasonable approximation to the solution of the boundary value problem in partial differential equations. For the identification problem, it is shown that the constant parameters are identified to the same accuracy as the supplementary data used in the identification procedure. (Author)

Numerical methods for the solution of the finite difference approximation to the acoustic radiation equation are discussed. For a spherical radiator, the Gauss-Seidel iterative method and the alternating direction implicit method are employed to solve the discrete approximation of the Helmholtz equation in the near field. Emphasis is on the development of the general numerical method and on the extrapolation scheme used to increase the rate of convergence. Measures of the number of calculations needed for various methods of solution are reported. A discussion of the nature of the acoustic radiation problem in numerical computation is also presented. (Author), See also Technical Report no. 4, AD-636 630.