Use of reverse phase protein microarrays and reference standard development for molecular network analysis of metastatic ovarian carcinoma

Cancer can be defined as a deregulation or hyperactivity in the ongoing network of intracellular and extracellular signaling events. Reverse phase protein microarray technology may offer a new opportunity to measure and profile these signaling pathways, providing data on post-translational phosphorylation events not obtainable by gene microarray analysis. Treatment of ovarian epithelial carcinoma almost always takes place in a metastatic setting since unfortunately the disease is often not detected until later stages. Thus, in addition to elucidation of the molecular network within a tumor specimen, critical questions are to what extent do signaling changes occur upon metastasis and are there common pathway elements that arise in the metastatic microenvironment. For individualized combinatorial therapy, ideal therapeutic selection based on proteomic mapping of phosphorylation end points may require evaluation of the patient's metastatic tissue. Extending these findings to the bedside will require the development of optimized protocols and reference standards. We have developed a reference standard based on a mixture of phosphorylated peptides to begin to address this challenge.

Combinatorial Design of Secure Lightweight Data Dispersal Schemes (Work in Progress)

Dispersing a data object into a set of data shares is an elemental stage in distributed communication and storage systems. In comparison to data replication, data dispersal with redundancy saves space and bandwidth. Moreover, dispersing a data object to distinct communication links or storage sites limits adversarial access to whole data and tolerates loss of a part of data shares. Existing data dispersal schemes have been proposed mostly based on various mathematical transformations on the data which induce high computation overhead. This paper presents a novel data dispersal scheme where each part of a data object is replicated, without encoding, into a subset of data shares according to combinatorial design theory. Particularly, data parts are mapped to points and data shares are mapped to lines of a projective plane. Data parts are then distributed to data shares using the point and line incidence relations in the plane so that certain subsets of data shares collectively possess all data parts. The presented scheme incorporates combinatorial design theory with inseparability transformation to achieve secure data dispersal at reduced computation, communication and storage costs. Rigorous formal analysis and experimental study demonstrate significant cost-benefits of the presented scheme in comparison to existing methods.

Mass spectrometry and n-in-one analytics in early drug discovery: Combinatorial chemistry libraries, lipophilicity and absorption screening

This thesis describes current and past n-in-one methods and presents three early experimental studies using mass spectrometry and the triple quadrupole instrument on the application of n-in-one in drug discovery. N-in-one strategy pools and mix samples in drug discovery prior to measurement or analysis. This allows the most promising compounds to be rapidly identified and then analysed. Nowadays properties of drugs are characterised earlier and in parallel with pharmacological efficacy. Studies presented here use in vitro methods as caco-2 cells and immobilized artificial membrane chromatography for drug absorption and lipophilicity measurements. The high sensitivity and selectivity of liquid chromatography mass spectrometry are especially important for new analytical methods using n-in-one. In the first study, the fragmentation patterns of ten nitrophenoxy benzoate compounds, serial homology, were characterised and the presence of the compounds was determined in a combinatorial library. The influence of one or two nitro substituents and the alkyl chain length of methyl to pentyl on collision-induced fragmentation was studied, and interesting structurefragmentation relationships were detected. Two nitro group compounds increased fragmentation compared to one nitro group, whereas less fragmentation was noted in molecules with a longer alkyl chain. The most abundant product ions were nitrophenoxy ions, which were also tested in the precursor ion screening of the combinatorial library. In the second study, the immobilized artificial membrane chromatographic method was transferred from ultraviolet detection to mass spectrometric analysis and a new method was developed. Mass spectra were scanned and the chromatographic retention of compounds was analysed using extract ion chromatograms. When changing detectors and buffers and including n-in-one in the method, the results showed good correlation. Finally, the results demonstrated that mass spectrometric detection with gradient elution can provide a rapid and convenient n-in-one method for ranking the lipophilic properties of several structurally diverse compounds simultaneously. In the final study, a new method was developed for caco-2 samples. Compounds were separated by liquid chromatography and quantified by selected reaction monitoring using mass spectrometry. This method was used for caco-2 samples, where absorption of ten chemically and physiologically different compounds was screened using both single and nin- one approaches. These three studies used mass spectrometry for compound identification, method transfer and quantitation in the area of mixture analysis. Different mass spectrometric scanning modes for the triple quadrupole instrument were used in each method. Early drug discovery with n-in-one is area where mass spectrometric analysis, its possibilities and proper use, is especially important.

DNA Free Energy-Based Promoter Prediction and Comparative Analysis of Arabidopsis and Rice Genomes

The cis-regulatory regions on DNA serve as binding sites for proteins such as transcription factors and RNA polymerase. The combinatorial interaction of these proteins plays a crucial role in transcription initiation, which is an important point of control in the regulation of gene expression. We present here an analysis of the performance of an in silico method for predicting cis-regulatory regions in the plant genomes of Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) on the basis of free energy of DNA melting. For protein-coding genes, we achieve recall and precision of 96% and 42% for Arabidopsis and 97% and 31% for rice, respectively. For noncoding RNA genes, the program gives recall and precision of 94% and 75% for Arabidopsis and 95% and 90% for rice, respectively. Moreover, 96% of the false-positive predictions were located in noncoding regions of primary transcripts, out of which 20% were found in the first intron alone, indicating possible regulatory roles. The predictions for orthologous genes from the two genomes showed a good correlation with respect to prediction scores and promoter organization. Comparison of our results with an existing program for promoter prediction in plant genomes indicates that our method shows improved prediction capability.

Combining indentation and diffusion couple techniques for combinatorial discovery of high temperature shape memory alloys

We demonstrate the possibility of accelerated identification of potential compositions for high-temperature shape memory alloys (SMAs) through a combinatorial material synthesis and analysis approach, wherein we employ the combination of diffusion couple and indentation techniques. The former was utilized to generate smooth and compositionally graded inter-diffusion zones (IDZs) in the Ni-Ti-Pd ternary alloy system of varying IDZ thickness, depending on the annealing time at high temperature. The IDZs thus produced were then impressed with an indenter with a spherical tip so as to inscribe a predetermined indentation strain. Subsequent annealing of the indented samples at various elevated temperatures, T-a, ranging between 150 and 550 degrees C allows for partial to full relaxation of the strain imposed due to the shape memory effect. If T-a is above the austenite finish temperature, A(f), the relaxation will be complete. By measuring the depth recovery, which serves as a proxy for the shape recovery characteristic of the SMA, a three-dimensional map in the recovery temperature composition space is constructed. A comparison of the published Af data for different compositions with the Ta data shows good agreement when the depth recovery is between 70% and 80%, indicating that the methodology proposed in this paper can be utilized for the identification of promising compositions. Advantages and further possibilities of this methodology are discussed.

Combinatorial Exploration of the Structural Landscape of Acid-Pyridine Cocrystals

The structural landscape of acid-pyridine cocrystals is explored by adopting a combinatorial matrix method with 4-substituted benzoic acids and 4-substituted pyridines. The choice of the system restricts the primary synthon to the robust acid-pyridine entity. This methodology accordingly provides hints toward the formation of secondary synthons. The pK(a) rule is validated in the landscape by taking all components of the matrix together and exploring it as a whole. Along with the global features, the exploration of landscapes reveals some local features. Apart from the identification of secondary synthons, it also sheds light on the propensity of hydration in cocrystals, synthon competition, and certain topological similarities. The method described here combines two approaches, namely, database analysis and high throughput crystallography, to extract more information with minimal extra experimental effort.

Analysis of a transcriptional network involving PU.1, Notch, and Gata3 in the lymphomyeloid lineage decision during early T-cell development

Hematopoiesis is a well-established system used to study developmental choices amongst cells with multiple lineage potentials, as well as the transcription factor network interactions that drive these developmental paths. Multipotent progenitors travel from the bone marrow to the thymus where T-cell development is initiated and these early T-cell precursors retain lineage plasticity even after initiating a T-cell program. The development of these early cells is driven by Notch signaling and the combinatorial expression of many transcription factors, several of which are also involved in the development of other cell lineages. The ETS family transcription factor PU.1 is involved in the development of progenitor, myeloid, and lymphoid cells, and can divert progenitor T-cells from the T-lineage to a myeloid lineage. This diversion of early T-cells by PU.1 can be blocked by Notch signaling. The PU.1 and Notch interaction creates a switch wherein PU.1 in the presence of Notch promotes T-cell identity and PU.1 in the absence of Notch signaling promotes a myeloid identity. Here we characterized an early T-cell cell line, Scid.adh.2c2, as a good model system for studying the myeloid vs. lymphoid developmental choice dependent on PU.1 and Notch signaling. We then used the Scid.adh.2c2 system to identify mechanisms mediating PU.1 and Notch signaling interactions during early T-cell development. We show that the mechanism by which Notch signaling is protecting pro-T cells is neither degradation nor modification of the PU.1 protein. Instead we give evidence that Notch signaling is blocking the PU.1-driven inhibition of a key set of T-regulatory genes including Myb, Tcf7, and Gata3. We show that the protection of Gata3 from PU.1-mediated inhibition, by Notch signaling and Myb, is important for retaining a T-lineage identity. We also discuss a PU.1-driven mechanism involving E-protein inhibition that leads to the inhibition of Notch target genes. This is mechanism may be used as a lockdown mechanism in pro-T-cells that have made the decision to divert to the myeloid pathway.

Biotechnologies for cancer diagnostics : cell sorting, protein analysis and imaging of cellular metabolism

This thesis presents the development of chip-based technology for informative in vitro cancer diagnostics. In the first part of this thesis, I will present my contribution in the development of a technology called “Nucleic Acid Cell Sorting (NACS)”, based on microarrays composed of nucleic acid encoded peptide major histocompatibility complexes (p/MHC), and the experimental and theoretical methods to detect and analyze secreted proteins from single or few cells.

Secondly, a novel portable platform for imaging of cellular metabolism with radio probes is presented. A microfluidic chip, so called “Radiopharmaceutical Imaging Chip” (RIMChip), combined with a beta-particle imaging camera, is developed to visualize the uptake of radio probes in a small number of cells. Due to its sophisticated design, RIMChip allows robust and user-friendly execution of sensitive and quantitative radio assays. The performance of this platform is validated with adherent and suspension cancer cell lines. This platform is then applied to study the metabolic response of cancer cells under the treatment of drugs. Both cases of mouse lymphoma and human glioblastoma cell lines, the metabolic responses to the drug exposures are observed within a short time (~ 1 hour), and are correlated with the arrest of cell-cycle, or with changes in receptor tyrosine kinase signaling.

The last parts of this thesis present summaries of ongoing projects: development of a new agent as an in vivo imaging probe for c-MET, and quantitative monitoring of glycolytic metabolism of primary glioblastoma cells. To develop a new agent for c-MET imaging, the one-bead-one-compound combinatorial library method is used, coupled with iterative screening. The performance of the agent is quantitatively validated with cell-based fluorescent assays. In the case of monitoring the metabolism of primary glioblastoma cell, by RIMChip, cells were sorting according to their expression levels of oncoprotein, or were treated with different kinds of drugs to study the metabolic heterogeneity of cancer cells or metabolic response of glioblastoma cells to drug treatments, respectively.

Design and analysis of nucleic acid reaction pathways

Nucleic acids are a useful substrate for engineering at the molecular level. Designing the detailed energetics and kinetics of interactions between nucleic acid strands remains a challenge. Building on previous algorithms to characterize the ensemble of dilute solutions of nucleic acids, we present a design algorithm that allows optimization of structural features and binding energetics of a test tube of interacting nucleic acid strands. We extend this formulation to handle multiple thermodynamic states and combinatorial constraints to allow optimization of pathways of interacting nucleic acids. In both design strategies, low-cost estimates to thermodynamic properties are calculated using hierarchical ensemble decomposition and test tube ensemble focusing. These algorithms are tested on randomized test sets and on example pathways drawn from the molecular programming literature. To analyze the kinetic properties of designed sequences, we describe algorithms to identify dominant species and kinetic rates using coarse-graining at the scale of a small box containing several strands or a large box containing a dilute solution of strands.

High-throughput characterization of heterogeneous catalysts by temperature-programmed analysis method

A multistream reactor for high-throughput examining the surface acidity by NH3-TPD method by application of multistream mass spectrometer screening (MSMSS) technique has been developed. This method allows for examining the surface acidity of 10 catalyst samples in about 6 h, which is an improvement over the traditional process. The demonstration of the feasibility of high-throughput TPD can be significant in convincing the hardened traditionalists in the heterogeneous catalysis community that, combinatorial methods indeed should have an important place in scientific catalyst research and development. The developed method could also be used for almost all the temperature-programmed analysis theoretically with careful designed multistream reactors. (C) 2003 Elsevier B.V. All rights reserved.

Characterisation of pavement profile heights using accelerometer readings and a combinatorial optimisation technique

Pavement surface profiles induce dynamic ride responses in vehicles which can potentially be used to classify road surface roughness. A novel method is proposed for the characterisation of pavement roughness through an analysis of vehicle accelerations. A combinatorial optimisation technique is applied to the determination of pavement profile heights based on measured accelerations at and above the vehicle axle. Such an approach, using low-cost inertial sensors, would provide an inexpensive alternative to the costly laser-based profile measurement vehicles. The concept is numerically validated using a half-car roll dynamic model to infer measurements of road profiles in both the left and right wheel paths.

Combinatorial Frequency Generation in Quasi-Periodic Stacks of Nonlinear Dielectric Layers

Three-wave mixing in quasi-periodic structures (QPSs) composed of nonlinear anisotropic dielectric layers, stacked in Fibonacci and Thue-Morse sequences, has been explored at illumination by a pair of pump waves with dissimilar frequencies and incidence angles. A new formulation of the nonlinear scattering problem has enabled the QPS analysis as a perturbed periodic structure with defects. The obtained solutions have revealed the effects of stack composition and constituent layer parameters, including losses, on the properties of combinatorial frequency generation (CFG). The CFG features illustrated by the simulation results are discussed. It is demonstrated that quasi-periodic stacks can achieve a higher efficiency of CFG than regular periodic multilayers.

Numerical and combinatorial applications of generalized Appell polynomials

This thesis studies properties and applications of different generalized Appell polynomials in the framework of Clifford analysis. As an example of 3D-quasi-conformal mappings realized by generalized Appell polynomials, an analogue of the complex Joukowski transformation of order two is introduced. The consideration of a Pascal n-simplex with hypercomplex entries allows stressing the combinatorial relevance of hypercomplex Appell polynomials. The concept of totally regular variables and its relation to generalized Appell polynomials leads to the construction of new bases for the space of homogeneous holomorphic polynomials whose elements are all isomorphic to the integer powers of the complex variable. For this reason, such polynomials are called pseudo-complex powers (PCP). Different variants of them are subject of a detailed investigation. Special attention is paid to the numerical aspects of PCP. An efficient algorithm based on complex arithmetic is proposed for their implementation. In this context a brief survey on numerical methods for inverting Vandermonde matrices is presented and a modified algorithm is proposed which illustrates advantages of a special type of PCP. Finally, combinatorial applications of generalized Appell polynomials are emphasized. The explicit expression of the coefficients of a particular type of Appell polynomials and their relation to a Pascal simplex with hypercomplex entries are derived. The comparison of two types of 3D Appell polynomials leads to the detection of new trigonometric summation formulas and combinatorial identities of Riordan-Sofo type characterized by their expression in terms of central binomial coefficients.

Bounds on edit metric codes with combinatorial DNA constraints

The design of a large and reliable DNA codeword library is a key problem in DNA based computing. DNA codes, namely sets of fixed length edit metric codewords over the alphabet {A, C, G, T}, satisfy certain combinatorial constraints with respect to biological and chemical restrictions of DNA strands. The primary constraints that we consider are the reverse--complement constraint and the fixed GC--content constraint, as well as the basic edit distance constraint between codewords. We focus on exploring the theory underlying DNA codes and discuss several approaches to searching for optimal DNA codes. We use Conway's lexicode algorithm and an exhaustive search algorithm to produce provably optimal DNA codes for codes with small parameter values. And a genetic algorithm is proposed to search for some sub--optimal DNA codes with relatively large parameter values, where we can consider their sizes as reasonable lower bounds of DNA codes. Furthermore, we provide tables of bounds on sizes of DNA codes with length from 1 to 9 and minimum distance from 1 to 9.

Combinatorial peptide ligand libraries and plant proteomics: a winning strategy at a price

The mechanism of action and properties of a solid-phase ligand library made of hexapeptides (combinatorial peptide ligand libraries or CPLL), for capturing the "hidden proteome", i.e. the low- and very low-abundance proteins constituting the vast majority of species in any proteome, as applied to plant tissues, are reviewed here. Plant tissues are notoriously recalcitrant to protein extraction and to proteome analysis. Firstly, rigid plant cell walls need to be mechanically disrupted to release the cell content and, in addition to their poor protein yield, plant tissues are rich in proteases and oxidative enzymes, contain phenolic compounds, starches, oils, pigments and secondary metabolites that massively contaminate protein extracts. In addition, complex matrices of polysaccharides, including large amount of anionic pectins, are present. All these species compete with the binding of proteins to the CPLL beads, impeding proper capture and identification / detection of low-abundance species. When properly pre-treated, plant tissue extracts are amenable to capture by the CPLL beads revealing thus many new species among them low-abundance proteins. Examples are given on the treatment of leaf proteins, of corn seed extracts and of exudate proteins (latex from Hevea brasiliensis). In all cases, the detection of unique gene products via CPLL capture is at least twice that of control, untreated sample.