State Estimation for diffusion systems using a Karhunen-Loeve-Galerkin Reduced-Order Model

This thesis focuses on generating a continuous estimate of state using a small number of sensors for a process modeled by the diffusion partial differential equation(PDE). In biological systems the diffusion of oxygen in tissue is well described by the diffusion equation, also known by biologists as Fick\u27s first law. Mass transport of many other materials in biological systems are modeled by the diffusion PDE such as CO2, cell signaling factors, glucose and other biomolecules. Estimating the state of a PDE is more formidable than that of a system described by ordinary differential equations (ODEs). While the state variables of the ODE system are finite in number, the state variables of the PDE are distributed in the spatial domain and infinite in number. Reduction of the number of state variables to a finite small number which is tractable for estimation will be accomplished through use of the Karhunen-Loeve-Galerkin method for model order reduction. The model order reduction is broken into two steps, (i) determine an appropriate set of basis functions and (ii) project the PDE onto the set of candidate basis functions. The Karhunen-Loeve expansion is used to decompose a set of observations of the system into the principle modes composing the system dynamics. The observations may be obtained through numerical simulation or physical experiments that encompass all dynamics that the reduced-order model will be expected to reproduce. The PDE is then projected onto a small number of basis functions using the linear Galerkin method, giving a small set of ODEs which describe the system dynamics. The reduced-order model obtained from the Karhunen-Loeve-Galerkin procedure is then used with a Kalman filter to estimate the system state. Performance of the state estimator will be investigated using several numerical experiments. Fidelity of the reduced-order model for several different numbers of basis functions will be compared against a numerical solution considered to be the true solution of the continuous problem. The efficiency of the empirical basis compared to an analytical basis will be examined. The reduced-order model will then be used in a Kalman filter to estimate state for a noiseless system and then a noisy system. Effects of sensor placement and quantity are evaluated. A test platform was developed to study the estimation process to track state variables in a simple non-biological system. The platform allows the diffusion of dye through gelatin to be monitored with a camera. An estimate of dye concentration throughout the entire volume of gelatin will be accomplished using a small number of point sensors, i.e. pixels selected from the camera. The estimate is evaluated against the actual diffusion as captured by the camera. This test platform will provide a means to empirically study the dynamics of diffusion-reaction systems and associated state estimators

The Radioresistance of Deinococcus Radiodurans.

Deinococcus radiodurans is a remarkably ionizing radiation resistant bacterium. As a vegetative cell it is capable of withstanding 5,000 Gy ionizing radiation without evidence of death or mutation. D. radiodurans survives irradiation by repairing DNA damage via an extremely efficient DNA repair system. However, this DNA repair system has not been completely defined. In addition, the selective process allowing the evolution of high level radioresistance has remained a question. This dissertation bolsters the understanding of the DNA repair system of D. radiodurans by characterizing a collection of ionizing radiation sensitive (IRS) mutants. The level of radioresistance is quantified and transformation ability is assessed for each IRS mutant. A new subset of mutants slow to recover from irradiation is identified. The IRS mutant collection is organized into sixteen linkage groups. Using linkage group data, the order of mutations within the pol linkage group is determined and the distance between cotransformed markers is found to be unusually small. The irrI mutant within linkage group I is observed using pulsed-field gel electrophoresis (PFGE) to examine mutant DNA during a post-irradiation recovery time course. This information in conjunction with survival data provides evidence that the irrI gene product inhibits DNA degradation at DNA gaps or double-strand breaks (dsbs). This dissertation also provides evidence which indicates a selection process by which extreme radioresistance mechanisms could have evolved. A correlation is found between desiccation sensitivity and ionizing radiation sensitivity within the IRS mutant collection. PFGE observation of desiccated and ionizing radiation irradiated cell samples demonstrate that the DNA within these cell samples contains multiple dsbs. Because desiccation and ionizing radiation cause a similar pattern of DNA damage in the form of dsbs, the DNA repair mechanism used to survive ionizing radiation exposure could have evolved in response to periods of desiccation

Genome structure of bdelloid rotifers : shaped by asexuality or desiccation?

Author Posting. © The Author(s), 2010. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Journal of Heredity 101 (2010): S85-S93, doi:10.1093/jhered/esq008.Bdelloid rotifers are microscopic invertebrate animals best known for their ancient asexuality and the ability to survive desiccation at any life stage. Both factors are expected to have a profound influence on their genome structure. Recent molecular studies demonstrated that, while the gene-rich regions of bdelloid genomes are organized as co-linear pairs of closely related sequences and depleted in repetitive DNA, subtelomeric regions harbor diverse transposable elements and horizontally acquired genes of foreign origin. While asexuality is expected to result in depletion of deleterious transposons, only desiccation appears to have the power to produce all of the uncovered genomic peculiarities. Repair of desiccation-induced DNA damage would require the presence of a homologous template, maintaining co-linear pairs in gene-rich regions, and selecting against insertion of repetitive DNA which might cause chromosomal rearrangements. Desiccation may also induce a transient state of competence in recovering animals, allowing them to acquire environmental DNA. Even if bdelloids engage in rare or obscure forms of sexual reproduction, all these features could still be present. The relative contribution of asexuality and desiccation to genome organization may be clarified by analyzing whole-genome sequences and comparing foreign gene and transposon content in species which lost the ability to survive desiccation.This work was supported by the National Science Foundation (grant MCB-0821956 to I.A.)

Structure and function of the regulatory C-terminal HRDC domain from Deinococcus radiodurans RecQ

RecQ helicases are critical for maintaining genome integrity in organisms ranging from bacteria to humans by participating in a complex network of DNA metabolic pathways. Their diverse cellular functions require specialization and coordination of multiple protein domains that integrate catalytic functions with DNA–protein and protein–protein interactions. The RecQ helicase from Deinococcus radiodurans (DrRecQ) is unusual among RecQ family members in that it has evolved to utilize three ‘Helicase and RNaseD C-terminal’ (HRDC) domains to regulate its activity. In this report, we describe the high-resolution structure of the C-terminal-most HRDC domain of DrRecQ. The structure reveals unusual electrostatic surface features that distinguish it from other HRDC domains. Mutation of individual residues in these regions affects the DNA binding affinity of DrRecQ and its ability to unwind a partial duplex DNA substrate. Taken together, the results suggest the unusual electrostatic surface features of the DrRecQ HRDC domain may be important for inter-domain interactions that regulate structure-specific DNA binding and help direct DrRecQ to specific recombination/repair sites

Appearance of Membrane Compromised, Viable But Not Culturable and Culturable Rhizobial Cells as a Consequence of Desiccation

For agricultural purposes, drought related stresses negatively affect the Rhizobiaceae in at least three ways. Firstly, rhizobial populations are affected by desertification of agricultural soils. Secondly, the quality of dry-base inocula, also called formula, is negatively affected by a drying step, and thirdly, rhizosphere bacteria protect crop-plants against drought. Although survival of cultivatable bacteria has been studied intensively in dry-base seed inocula and in-vitro, thus far research has only marginally addressed the bacterial cell, its cellular structures and physiology. Many questions remain regarding the sensing of and physiological response of rhizobia to desiccation. This review will focus on the three different fractions of cells after desiccation, the membrane compromised cells, the viable but not culturable cells and the culturable cells

Irradiation-Induced Deinococcus radiodurans Genome Fragmentation Triggers Transposition of a Single Resident Insertion Sequence

Stress-induced transposition is an attractive notion since it is potentially important in creating diversity to facilitate adaptation of the host to severe environmental conditions. One common major stress is radiation-induced DNA damage. Deinococcus radiodurans has an exceptional ability to withstand the lethal effects of DNA–damaging agents (ionizing radiation, UV light, and desiccation). High radiation levels result in genome fragmentation and reassembly in a process which generates significant amounts of single-stranded DNA. This capacity of D. radiodurans to withstand irradiation raises important questions concerning its response to radiation-induced mutagenic lesions. A recent study analyzed the mutational profile in the thyA gene following irradiation. The majority of thyA mutants resulted from transposition of one particular Insertion Sequence (IS), ISDra2, of the many different ISs in the D. radiodurans genome. ISDra2 is a member of a newly recognised class of ISs, the IS200/IS605 family of insertion sequences