Diversity Arrays: a solid state technology for sequence information independent genotyping

Here we present the successful application of the microarray technology platform to the analysis of DNA polymorphisms. Using the rice genome as a model, we demonstrate the potential of a high-throughput genome analysis method called Diversity Array Technology, DArT‘. In the format presented here the technology is assaying for the presence (or amount) of a specific DNA fragment in a representation derived from the total genomic DNA of an organism or a population of organisms. Two different approaches are presented: the first involves contrasting two representations on a single array while the second involves contrasting a representation with a reference DNA fragment common to all elements of the array. The Diversity Panels created using this method allow genetic fingerprinting of any organism or group of organisms belonging to the gene pool from which the panel was developed. Diversity Arrays enable rapid and economical application of a highly parallel, solid-state genotyping technology to any genome or complex genomic mixtures.

Three-dimensional tracking of motile bacteria near a solid planar surface.

Knowing how motile bacteria move near and along a solid surface is crucial to understanding such diverse phenomena as the migration of infectious bacteria along a catheter, biofilm growth, and the movement of bacteria through the pore spaces of saturated soil, a critical step in the in situ bioremediation of contaminated aquifers. In this study, a tracking microscope is used to record the three-dimensional motion of Escherichia coli near a planar glass surface. Data from the tracking microscope are analyzed to quantify the effects of bacteria-surface interactions on the swimming behavior of bacteria. The speed of cells approaching the surface is found to decrease in agreement with the mathematical model of Ramia et al. [Ramia, M., Tullock, D. L. & Phan-Tien, N. (1993) Biophys J. 65,755-778], which represents the bacteria as spheres with a single polar flagellum rotating at a constant rate. The tendency of cells to swim adjacent to the surface is shown in computer-generated reproductions of cell traces. The attractive interaction potential between the cells and the solid surface is offered as one of several possible explanations for this tendency.

The Identification of Best Management Practices in a Materials Recovery Facility to Increase Solid Waste Diversion in the Department of Defense (DoD) Installations along the Front Range of Colorado to Satisfy the DoD Solid Waste Diversion Goal of 40 Percent

The five installations operated by the Department of Defense (DoD) in the Front Range region of Colorado do not meet the DoD non-hazardous solid waste diversion goal of 40 percent, further impacting landfills and generating greenhouse gases. This applied capstone project identifies and evaluates best management practices of a Materials Recovery Facility (MRF), qualitatively and quantitatively, to increase solid waste diversion at a DoD MRF. An environmental benefits model quantified the externalities of increasing solid waste diversion at the installations. By implementing best management practices at a MRF, the DoD would divert an additional 1,400 tons of solid waste per year, resulting in the equivalent of 1,502,567 gallons of gasoline being saved, among many benefits presented in this capstone.

Building International CSR on Solid Foundations: Location and Network Aspects of Nonmarket Environments in Europe and Non-Europe Markets. ACES Working Papers, 2011

Multinational companies' (MNCs) corporate social responsibility (CSR) programs frequently comprise a portfolio of disconnected country-level programs or, alternatively, consist of blanket corporate policies that apply in the same way across the geographies where the company operates. Yet, the international nonmarket environment in which CSR programs operate is neither a completely fragmented nor a perfectly homogeneous one. Building on the concept of stakeholder-issue-networks, we develop a model that explicitly takes into consideration the role of geography in the characterization of a firm's nonmarket environment. This allows us to develop a taxonomy of nonmarket environments on the basis of their geographic spread and their degree of cross-border connectedness. We then explore the strategic and organizational implications that different ideal types of (cross-border) nonmarket environments have for the development of international CSR policies.

Routine histological technique applied to a biological model for environmental studies

Introduction and aim Earthworms are an important test organisms used in several standard ecotoxicological tests (e.g. ISO, 2008, 2012; OECD, 2004, 1094) and they are also model organisms to test soil structure and permeability, as well as for important soil services as the degradation organic matter. Although histopathological changes have been demonstrated to be good biomarkers to assess the exposure of these animals to different physical and chemical stress agents, studies with clear and high quality images describing normal tissue conditions are scarce in the literature, so the aim of this work was to better characterize this biological model. Material and Methods Eight adult earthworms exposed to an artificial standard soil (OECD, 2004) for 28 days, were extracted and placed in a plastic box to depurate their gut content, fixed in 10% neutral-buffered formalin and processed for routine histopathological diagnosis. Results and discussion Satisfactory histological sections were obtained. Some difficulties were faced related with microtome sectioning, resulting in artefacts, namely lines across sections produced by a nick in the cutting edge of the microtome knife cutting tear, motivated by the presence of sand and other solid particles that persisted in the gut of earthworms. Nevertheless, it was possible to obtain representative figures from different earthworm sections. Conclusion Routine histological technique was effective for obtaining satisfactory histological sections and the knowledge of the histology of earthworms could be very useful for future application in environmental studies, using this biological model.

Dissolved organic carbon concentrations, amino sugar concentrations and highly significantly correlating FT-ICR mass peak magnitudes obtained from solid phase extracted marine dissolved organic matter during POLARSTERN cruise ANT-XXV/1

Dissolved organic matter (DOM) was extracted with solid phase extraction (SPE) from 137 water samples from different climate zones and different depths along an Eastern Atlantic Ocean transect. The extracts were analyzed with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) with electrospray ionization (ESI). D14C analyses were performed on subsamples of the SPE-DOM. In addition, the amount of dissolved organic carbon was determined for all water and SPE-DOM samples as well as the yield of amino sugars for selected samples. Linear correlations were observed between the magnitudes of 43% of the FT-ICR mass peaks and the extract D14C values. Decreasing SPE-DOM D14C values went along with a shift in the molecular composition to higher average masses (m/z) and lower hydrogen/carbon (H/C) ratios. The correlation was used to model the SPE-DOM D14C distribution for all 137 samples. Based on single mass peaks a degradation index was developed to compare the degradation state of marine SPE-DOM samples analyzed with FT-ICR MS. A correlation between D14C, degradation index, DOC values and amino sugar yield supports that SPE-DOM analyzed with FT-ICR MS reflects trends of bulk DOM. A relative mass peak magnitude ratio was used to compare aged SPE-DOM and fresh SPE-DOM regarding single mass peaks. The magnitude ratios show a continuum of different reactivities for the single compounds. Only few of the compounds present in the FT-ICR mass spectra are expected to be highly degraded in the oldest water masses of the Pacific Ocean. All other compounds should persist partly thermohaline circulation. Prokaryotic (bacterial) production, transformation and accumulation of this very stable DOM occurs probably primarily in the upper ocean. This DOM is an important contribution to very old DOM, showing that production and degradation are dynamic processes.

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Includes index.

Characterization of the Structure and Dynamics of Biomimetic Peptides by Solid-State NMR

Thesis (Ph.D.)--University of Washington, 2016-05

Synthesis of acetoxy stabilised indolequinones as precursors to model eumelanin polymers

We report an efficient synthetic route to obtaining a stable analogue of 5,6-dihydroxyindole. These analogues can be used to build controlled composition model melanin biopolymers for solid state and spectroscopic studies of this important biomolecule.

Electromagnetic modeling of conformal wideband and multi-band patch antennas by bridging a solid-object modeler with MoM software

The advantages of antennas that can resemble the shape of the body to which they are attached are obvious. However, electromagnetic modeling of such unusually shaped antennas can be difficult. In this paper, the commercially available software SolidWorks(TM) is used for accurately drawing complex shapes in conjunction with the electromagnetic software FEKO(TM) to model the EM behavior of conformal antennas. The application of SolidWorks and custom-written software allows all the required information that forms the analyzed structure to be automatically inserted into FEKO, and gives the user complete control over the antenna being modeled. This approach is illustrated by a number of simulation examples of single, wideband, multi-band planar and curved patch antennas.

Clinical pharmacokinetics and pharmacodynamics of tacrolimus in solid organ transplantation

The aim of this review is to analyse critically the recent literature on the clinical pharmacokinetics and pharmacodynamics of tacrolimus in solid organ transplant recipients. Dosage and target concentration recommendations for tacrolimus vary from centre to centre, and large pharmacokinetic variability makes it difficult to predict what concentration will be achieved with a particular dose or dosage change. Therapeutic ranges have not been based on statistical approaches. The majority of pharmacokinetic studies have involved intense blood sampling in small homogeneous groups in the immediate post-transplant period. Most have used nonspecific immunoassays and provide little information on pharmacokinetic variability. Demographic investigations seeking correlations between pharmacokinetic parameters and patient factors have generally looked at one covariate at a time and have involved small patient numbers. Factors reported to influence the pharmacokinetics of tacrolimus include the patient group studied, hepatic dysfunction, hepatitis C status, time after transplantation, patient age, donor liver characteristics, recipient race, haematocrit and albumin concentrations, diurnal rhythm, food administration, corticosteroid dosage, diarrhoea and cytochrome P450 (CYP) isoenzyme and P-glycoprotein expression. Population analyses are adding to our understanding of the pharmacokinetics of tacrolimus, but such investigations are still in their infancy. A significant proportion of model variability remains unexplained. Population modelling and Bayesian forecasting may be improved if CYP isoenzymes and/or P-glycoprotein expression could be considered as covariates. Reports have been conflicting as to whether low tacrolimus trough concentrations are related to rejection. Several studies have demonstrated a correlation between high trough concentrations and toxicity, particularly nephrotoxicity. The best predictor of pharmacological effect may be drug concentrations in the transplanted organ itself. Researchers have started to question current reliance on trough measurement during therapeutic drug monitoring, with instances of toxicity and rejection occurring when trough concentrations are within 'acceptable' ranges. The correlation between blood concentration and drug exposure can be improved by use of non-trough timepoints. However, controversy exists as to whether this will provide any great benefit, given the added complexity in monitoring. Investigators are now attempting to quantify the pharmacological effects of tacrolimus on immune cells through assays that measure in vivo calcineurin inhibition and markers of immuno suppression such as cytokine concentration. To date, no studies have correlated pharmacodynamic marker assay results with immunosuppressive efficacy, as determined by allograft outcome, or investigated the relationship between calcineurin inhibition and drug adverse effects. Little is known about the magnitude of the pharmacodynamic variability of tacrolimus.

Hanging-drop multicellular spheriods as a model of tumour angiogenesis

The establishment of a vascular network within tumours is a key step in the progression towards an aggressive, metastatic state, with poor prognosis. We have developed a novel in vitro model to specifically capture the interaction between endothelial cells and solid tumours. Micro-vascularised in vitro tumour constructs were produced by introducing endothelial cells to multicellular spheroids formed in hanging drops. Upon introduction, the endothelial cells migrated into the tumour spheroid, establishing tubular networks and luminal structures. This system relies on the natural pro-angiogenic capacity of multicellular spheroids, and does not require the addition of exogenous angiogenic factors, or use of extracellular-matrix substitutes.

Quantum trajectories for the realistic measurement of a solid-state charge qubit

We present a new model for the continuous measurement of a coupled quantum dot charge qubit. We model the effects of a realistic measurement, namely adding noise to, and filtering, the current through the detector. This is achieved by embedding the detector in an equivalent circuit for measurement. Our aim is to describe the evolution of the qubit state conditioned on the macroscopic output of the external circuit. We achieve this by generalizing a recently developed quantum trajectory theory for realistic photodetectors [P. Warszawski, H. M. Wiseman, and H. Mabuchi, Phys. Rev. A 65, 023802 (2002)] to treat solid-state detectors. This yields stochastic equations whose (numerical) solutions are the realistic quantum trajectories of the conditioned qubit state. We derive our general theory in the context of a low transparency quantum point contact. Areas of application for our theory and its relation to previous work are discussed.