Fourier transform infrared (FTIR) microscopy has shown promise as an analytical tool for detecting changes in cells and tissues, such as those due to viral infection, apoptosis induction or malignancy. In many cases, diagnosis via FTIR microscopy can be undertaken on a timescale shorter than that required for other physical or histological techniques. In this work we have used FTIR microscopy to study Vero cells that have been infected with herpes simplex virus (type I) and adenovirus. We have studied cellular samples at various time intervals following exposure to the virus. Several spectral regions were identified that allow discrimination between infected and uninfected Vero cell samples at 24 hours post exposure to both HSV1 and adenovirus. Spectral features were also identified that could be used to discriminate infected cells within 2-6 hours after exposure to both viruses. FTIR microscopy is therefore a useful tool for following the kinetics of viral infection in the 2-24 hours time range, at least at the levels of infection used in this study. In a second type of study, FTIR microscopy was used to study apoptosis induction in acute lymphoblastic leukemia T-cells. Apoptosis was induced in T-cells in three different ways. We show that FTIR microscopy can be used to distinguish T-cells in the early stages of apoptosis from normal cells. We also provide data that may suggest that FTIR microscopy can distinguish cells that have undergone apoptosis via different pathways. For most of the FTIR microscopic studies on cellular samples we have focused on the collection of spectral data in the 1500-800 cm-1 region. Spectra were collected for control cells and variously treated cells. The two sets of cells were then analyzed statistically using: 1) pair-wise comparison, 2) logistic regression, 3) partial least square regression, 4) principle component fed linear discriminant analysis and 5) hierarchical cluster analysis. The statistical analyses rigorously quantify to what extent treated and untreated cells can be distinguished. Since different statistical methods give differing results for the same data, it is important the right statistical method should be applied. The basis for these differences is discussed.

Herpes simplex viruses (HSV) establish latent infections in sensory neurons of their host and are maintained in this state by little understood mechanisms that, at least in part, are regulated by signalling through nerve growth factor (NGF) and its receptor tropomyosin related kinase, trkA. Previous studies have demonstrated that Zhangfei is a transcriptional factor that is expressed in differentiated neurons and is thought to influence HSV replication and latency. Zhangfei, like the HSV trans-activator VP16 and Luman, binds the ubiquitous nuclear protein host cell factor (HCF) inhibiting the ability of VP16 and Luman to initiate HSV replication. <p>Recently, Brn3a, another neuronal factor thought to influence HSV latency and reactivation was found to possess an HCF-binding domain and could potentially require HCF for activity. The neuronal POU IV domain protein, Brn3a, among its many regulatory functions has been described as an enhancer of the NGF receptor trkA, during development in mouse. I therefore investigated the possible link between Brn3a, TrkA, NGF signaling, HCF, Zhangfei and HSV-1 latency and reactivation. I hypothesized that Zhangfei would also suppress the ability of Brn3a to activate the expression of TrkA and that this would have an impact on NGF-TrkA signaling and, consequently on HSV-1 reactivation from latency.<p>My first study determined which Brn3a/trkA promoter interactions were important for trkA transcription. I constructed a plasmid that contains 1043 base pairs of genomic sequences that extend from 30 nucleotides upstream of trkA coding region. In contrast to previous data, a short 190 bp region that lies proximal to the trkA initiation codon was sufficient for Brn3a trans-activation in NGF-differentiated PC12, Vero and human medulloblastoma cells. At least two portions of the 190 bp fragment bind to Brn3a. In addition, Brn3a increased endogenous levels of trkA transcripts in PC12 cells and initiated trkA expression in medulloblastoma cells, which normally do not express trkA. <p>The second step was to determine the effects of HCF and Zhangfei association with Brn3a on trkA trans-activation. I found that Brn3a required HCF for activating the trkA promoter and that Zhangfei has a suppressive effect over Brn3a-trkA activation in non-neuronal cells. In sympathetic neuron-like NGF-treated PC12 cells, Zhangfei did not suppress the ability of Brn3a to activate the TrkA promoter, however, Zhangfei was able capable of inducing the expression of TrkA in the absence of Brn3a. Both Brn3a and Zhangfei induced the expression of endogenous trkA in PC12 cells.<p>Since Vero and PC12 cells are not from human origin I wanted to examine the ability of Zhangfei to induce trkA transcription in medulloblastoma cells, that because of its tumor nature do not express trkA. TrkA transfections in these cells have shown to drive them to cell arrest or apoptosis. Since Zhangfei is not express in medulloblastoma tumors I then used ONS-76 medulloblastoma cells as a model to determine Zhangfeis envolvement in the NGF-trkA signaling pathway.<p> I show herein that in ONS-76 medulloblastoma cells resveratrol, an inducer of apoptosis and differentiation, increased the expression of Zhangfei and trkA as well as Early Growth Response Gene 1 (Egr1), a gene normally activated by NGF-trkA signalling. ONS-76 cells stop growing soon after treatment with resveratrol and a portion of the cell undergo apoptosis. While the induction of Zhangfei in resveratrol-treated cells was modest albeit consistent, the infection of actively growing medulloblastoma cells with an adenovirus vector expressing Zhangfei mimicked the effects of resveratrol. Zhangfei activated the expression of trkA and Egr1 and caused these cells to display markers of apoptosis. The phosphorylation of Erk1, an intermediate kinase in the NGF-trkA signaling critical for differentiation, was observed in Zhangfei infected cells, supporting the hypothesis that Zhangfei is a mediator of trkA-NGF signaling in theses cells leading either to differentiation or apoptosis. Binding of HCF by Zhangfei did not appear to be required for this effect as a mutant of Zhangfei incapable of binding HCF was also able to induce the expression of trkA and Egr1. <p>In in vivo and in vitro models of HSV-1 latency, the virus reactivates when NGF supply to the neuron is interrupted. Based on the above evidence Zhangfei, in HSV-1 latently infected neurons, would have the ability to prolong a state of latency by inducing trkA expression allowing the activation of NGF-trkA signaling pathway. Since NGF is produced by many cell types it is possible that reactivation is triggered not by a decrease in NGF but by a down-regulation of TrkA expression.Therefore, if Zhangfei expression is suppress the trkA signaling could be interrupted or shifted towards apoptosis signaling, this would allow neuronal HCF-binding proteins like Luman, which can activate HSV IE expression, to initiate HSV IE expression and subsequently viral replication.

No description available.

This paper discusses the approximate and the exact n-point D-optimal design problems for the common multivariate linear and quadratic polynomial regression on some convex design spaces. For the linear polynomial regression, the design space considered are q-simplex, q-ball and convex hull of a set of finite points. It is shown that the approximate and the exact n-point D-optimal designs are concentrated on the extreme points of the design space. The structure of the optimal designs on regular polygons or regular polyhedra is also discussed. For the quadratic polynomial regression, the design space considered is a q-ball. The configuration of the approximate and the exact n-point D-optimal designs for quadratic model in two variables on a disk are investigated.

<p>Is it possible for a minimal model of anaerobic muscle contraction to describe measured data? There have been many models trying to describe separate parts of the human body with various results. In this thesis a model has been created to describe all the essential biochemical reactions of anaerobic muscle metabolism during contraction but with as few states and parameters as possible. A toolbox in Matlab was used for simulation and also for parameter estimation. The best model eventually got validated to see statistically how well it can describe the measured data. During the simulations an unnecessary assumption got revealed which helped us to understand the system better. The vision of a whole-body model may not be so far into the future as many think and the first step is to understand smaller biochemical systems like muscle contraction.</p>

Thesis (Ph. D.)--University of Missouri--Columbia, 2002. / Typescript. Vita. Includes bibliographical references (leaves 89-103). Also available on the Internet.

Viruses are obligate parasites that use the host cellular machinery to produce progeny virions. The host responds to this invading pathogen by induction of the immune system; however, the virus employs a variety of strategies to overcome these attacks. The complexity of the virus-host interaction is of great interest to researchers with aims to both characterize the relationship and target steps of the viral life cycle to hinder infection. Many targeted tactics employ single protein analysis; however, approaches that examine the whole set of virus/host interactions are available. Transcriptional alterations within host cells have been determined for many virus- host interactions by micro-array techniques; however little is known about the effects on cellular proteins. This study uses a quantitative mass spectrometric-based method, SILAC, to study differences in a host cell's proteome with infection by a virus. Mammalian reoviruses and herpes simplex viruses are prototypical viruses commonly studied to determine virus life cycle and interactions with hosts. Using three strains of reoviruses and one HSV1 strain, cells were infected to identify differentially regulated proteins at different times. Thousands of proteins were identified for each virus type, some up or down regulated after infection. Biological functions and network analyses were performed using online networking tools. These pathway analyses indicated numerous processes including cell death and inflammatory response are affected by T1L reovirus infection. Comparing reovirus strains revealed a greater overall proteomic change in host function when infected with the more pathogenic T3DC strain. For the HSV infection, host proteins altered during the different immediate early, earlyand late phases of infection helped characterize the host-virus interaction parallel to the virus life cycle. Overall, my study has characterized proteomic changes in different virus infection systems, identifying numerous novel cellular functional pathways and specific proteins altered during virus infections, specifically the secretogranin II protein that had opposite types of regulation in reoviruses and HSV and was examined for its effects on virus replication. Further studies on the novel proteomic characteristics may provide greater understanding to the complex virus-host interactome, leading to possible antiviral targets. / October 2015

Is it possible for a minimal model of anaerobic muscle contraction to describe measured data? There have been many models trying to describe separate parts of the human body with various results. In this thesis a model has been created to describe all the essential biochemical reactions of anaerobic muscle metabolism during contraction but with as few states and parameters as possible. A toolbox in Matlab was used for simulation and also for parameter estimation. The best model eventually got validated to see statistically how well it can describe the measured data. During the simulations an unnecessary assumption got revealed which helped us to understand the system better. The vision of a whole-body model may not be so far into the future as many think and the first step is to understand smaller biochemical systems like muscle contraction.

Analysis of simplex search and design of algorithmic system synthesis methods is performed in the current PhD thesis. The main objective is to create algorithmic methods for stochastic automatic control system synthesis, filter synthesis and algorithmic methods of variational calculus. Algorithmic methods allow solving system synthesis problems in cases when mathematical object is complex or it does not exist, when statistical characteristics of operating signals are unknown, i.e. when application of classical system synthesis methods is impossible. / Disertacijoje atliekami simpleksinės paieškos tyrimai ir nagrinėjama algoritminės sistemų sintezės metodų sudarymo problema. Pagrindinis disertacijos tikslas yra sukurti algoritminius stochastinių automatinio valdymo sistemų, filtrų sintezės bei variacinio skaičiavimo metodus. Algoritminiai metodai leidžia spręsti sistemų sintezės uždavinius, kuomet objekto matematinis modelis sudėtingas arba jo išvis nėra, kai nežinomos stochastines sistemas veikiančių signalų statistinės charakteristikos, t. y. kai klasikinių sistemų sintezės metodų taikymas yra neįmanomas.

Disertacijoje atliekami simpleksinės paieškos tyrimai ir nagrinėjama algoritminės sistemų sintezės metodų sudarymo problema. Pagrindinis disertacijos tikslas yra sukurti algoritminius stochastinių automatinio valdymo sistemų, filtrų sintezės bei variacinio skaičiavimo metodus. Algoritminiai metodai leidžia spręsti sistemų sintezės uždavinius, kuomet objekto matematinis modelis sudėtingas arba jo išvis nėra, kai nežinomos stochastines sistemas veikiančių signalų statistinės charakteristikos, t. y. kai klasikinių sistemų sintezės metodų taikymas yra neįmanomas. Disertaciją sudaro septyni skyriai, iš kurių paskutinis – rezultatų apibendrinimas. Pirmajame (įvadiniame) skyriuje nagrinėjamas problemos aktualumas, formuluojamas darbo tikslas bei uždaviniai, aprašomas mokslinis darbo naujumas, pristatomi autoriaus pranešimai ir publikacijos, disertacijos struktūra. Antrasis skyrius skirtas literatūros apžvalgai. Jame analizuojami paieškinio optimizavimo, optimalaus valdymo, AVS optimizavimo uždaviniai, optimizavimo objektų savybės, pateikta paieškinio optimizavimo metodų charakteristika, aprašyti kintamos struktūros valdymo sistemų sintezės principai, variacinio skaičiavimo metodai ir simpleksinės paieškos savybės. Trečiajme disertacijos skyriuje pateiktos stačiakampio simplekso taisyklės, paieškos statistinių charakteristikų skaičiavimo metodika, charakteristikų skaičiavimo teoriniai ir modeliavimo eksperimentiniai rezultatai. Ketvirtajame disertacijos skyriuje pateikti stochastinių... [toliau žr. visą tekstą] / Analysis of simplex search and design of algorithmic system synthesis methods is performed in the current PhD thesis. The main objective is to create algorithmic methods for stochastic automatic control system synthesis, filter synthesis and algorithmic methods of variational calculus. Algorithmic methods allow solving system synthesis problems in cases when mathematical object is complex or it does not exist, when statistical characteristics of operating signals are unknown, i. e. when application of classical system synthesis methods is impossible. The thesis is divided into seven chapters including the conclusion’s chapter. First chapter is dedicated for an introduction to the problem and its topicality. There are also formulated purposes and tasks of the work; the used methods and novelty of solutions are described; author‘s publications and structure of the thesis are presented. Second chapter covers an analysis of existing publications related with problems of the thesis. Search optimization algorithms, optimal control, automatic system optimization problems are analyzed, characteristics of search optimization algorithms are presented, the principles of variable structure system synthesis, variational calculus methods and simplex search characteristics are described. In the third chapter the rules of rectangular simplex search, the methods to calculate statistical characteristics of search, the results of characteristics calculation and experimental results of... [to full text]