Human intestinal maltase-glucoamylase: crystal structure of the N-terminal catalytic subunit and basis of inhibition and substrate specificity

Human maltase-glucoamylase (MGAM) is one of the two enzymes responsible for catalyzing the last glucose-releasing step in starch digestion. MGAM is anchored to the small-intestinal brush-border epithelial cells and contains two homologous glycosyl hydrolase family 31 catalytic subunits: an N-terminal subunit (NtMGAM) found near the membrane-bound end and a C-terminal luminal subunit (CtMGAM). In this study, we report the crystal structure of the human NtMGAM subunit in its apo form (to 2.0 A) and in complex with acarbose (to 1.9 A). Structural analysis of the NtMGAM-acarbose complex reveals that acarbose is bound to the NtMGAM active site primarily through side-chain interactions with its acarvosine unit, and almost no interactions are made with its glycone rings. These observations, along with results from kinetic studies, suggest that the NtMGAM active site contains two primary sugar subsites and that NtMGAM and CtMGAM differ in their substrate specificities despite their structural relationship. Additional sequence analysis of the CtMGAM subunit suggests several features that could explain the higher affinity of the CtMGAM subunit for longer maltose oligosaccharides. The results provide a structural basis for the complementary roles of these glycosyl hydrolase family 31 subunits in the bioprocessing of complex starch structures into glucose.

Simulating dioxane transport in a heterogeneous glacial aquifer system (Washtenaw County, Michigan) using publicly available models and data

The primary challenge in groundwater and contaminant transport modeling is obtaining the data needed for constructing, calibrating and testing the models. Large amounts of data are necessary for describing the hydrostratigraphy in areas with complex geology. Increasingly states are making spatial data available that can be used for input to groundwater flow models. The appropriateness of this data for large-scale flow systems has not been tested. This study focuses on modeling a plume of 1,4-dioxane in a heterogeneous aquifer system in Scio Township, Washtenaw County, Michigan. The analysis consisted of: (1) characterization of hydrogeology of the area and construction of a conceptual model based on publicly available spatial data, (2) development and calibration of a regional flow model for the site, (3) conversion of the regional model to a more highly resolved local model, (4) simulation of the dioxane plume, and (5) evaluation of the model's ability to simulate field data and estimation of the possible dioxane sources and subsequent migration until maximum concentrations are at or below the Michigan Department of Environmental Quality's residential cleanup standard for groundwater (85 ppb). MODFLOW-2000 and MT3D programs were utilized to simulate the groundwater flow and the development and movement of the 1, 4-dioxane plume, respectively. MODFLOW simulates transient groundwater flow in a quasi-3-dimensional sense, subject to a variety of boundary conditions that can simulate recharge, pumping, and surface-/groundwater interactions. MT3D simulates solute advection with groundwater flow (using the flow solution from MODFLOW), dispersion, source/sink mixing, and chemical reaction of contaminants. This modeling approach was successful at simulating the groundwater flows by calibrating recharge and hydraulic conductivities. The plume transport was adequately simulated using literature dispersivity and sorption coefficients, although the plume geometries were not well constrained.

Discrete element methods for asphalt concrete : development and application of user-defined microstructural models and a viscoelastic micromechanical model

As an important Civil Engineering material, asphalt concrete (AC) is commonly used to build road surfaces, airports, and parking lots. With traditional laboratory tests and theoretical equations, it is a challenge to fully understand such a random composite material. Based on the discrete element method (DEM), this research seeks to develop and implement computer models as research approaches for improving understandings of AC microstructure-based mechanics. In this research, three categories of approaches were developed or employed to simulate microstructures of AC materials, namely the randomly-generated models, the idealized models, and image-based models. The image-based models were recommended for accurately predicting AC performance, while the other models were recommended as research tools to obtain deep insight into the AC microstructure-based mechanics. A viscoelastic micromechanical model was developed to capture viscoelastic interactions within the AC microstructure. Four types of constitutive models were built to address the four categories of interactions within an AC specimen. Each of the constitutive models consists of three parts which represent three different interaction behaviors: a stiffness model (force-displace relation), a bonding model (shear and tensile strengths), and a slip model (frictional property). Three techniques were developed to reduce the computational time for AC viscoelastic simulations. It was found that the computational time was significantly reduced to days or hours from years or months for typical three-dimensional models. Dynamic modulus and creep stiffness tests were simulated and methodologies were developed to determine the viscoelastic parameters. It was found that the DE models could successfully predict dynamic modulus, phase angles, and creep stiffness in a wide range of frequencies, temperatures, and time spans. Mineral aggregate morphology characteristics (sphericity, orientation, and angularity) were studied to investigate their impacts on AC creep stiffness. It was found that aggregate characteristics significantly impact creep stiffness. Pavement responses and pavement-vehicle interactions were investigated by simulating pavement sections under a rolling wheel. It was found that wheel acceleration, steadily moving, and deceleration significantly impact contact forces. Additionally, summary and recommendations were provided in the last chapter and part of computer programming codes wree provided in the appendixes.

STATISTICAL METHODS FOR RARE AND COMMON VARIANT ASSOCIATION STUDIES

Complex human diseases are a major challenge for biological research. The goal of my research is to develop effective methods for biostatistics in order to create more opportunities for the prevention and cure of human diseases. This dissertation proposes statistical technologies that have the ability of being adapted to sequencing data in family-based designs, and that account for joint effects as well as gene-gene and gene-environment interactions in the GWA studies. The framework includes statistical methods for rare and common variant association studies. Although next-generation DNA sequencing technologies have made rare variant association studies feasible, the development of powerful statistical methods for rare variant association studies is still underway. Chapter 2 demonstrates two adaptive weighting methods for rare variant association studies based on family data for quantitative traits. The results show that both proposed methods are robust to population stratification, robust to the direction and magnitude of the effects of causal variants, and more powerful than the methods using weights suggested by Madsen and Browning [2009]. In Chapter 3, I extended the previously proposed test for Testing the effect of an Optimally Weighted combination of variants (TOW) [Sha et al., 2012] for unrelated individuals to TOW &ndash F, TOW for Family &ndash based design. Simulation results show that TOW &ndash F can control for population stratification in wide range of population structures including spatially structured populations, is robust to the directions of effect of causal variants, and is relatively robust to percentage of neutral variants. In GWA studies, this dissertation consists of a two &ndash locus joint effect analysis and a two-stage approach accounting for gene &ndash gene and gene &ndash environment interaction. Chapter 4 proposes a novel two &ndash stage approach, which is promising to identify joint effects, especially for monotonic models. The proposed approach outperforms a single &ndash marker method and a regular two &ndash stage analysis based on the two &ndash locus genotypic test. In Chapter 5, I proposed a gene &ndash based two &ndash stage approach to identify gene &ndash gene and gene &ndash environment interactions in GWA studies which can include rare variants. The two &ndash stage approach is applied to the GAW 17 dataset to identify the interaction between KDR gene and smoking status.

Numerical investigation of effects of addition of ethanol to gasoline on Laminar Flame Speed (LFS), autoignition, and wall quenching

Since the advent of automobiles, alcohol has been considered a possible engine fuel1,2. With the recent increased concern about the high price of crude oil due to fluctuating supply and demand and environmental issues, interest in alcohol based fuels has increased2,3. However, using pure alcohols or blends with conventional fuels in high percentages requires changes to the engine and fuel system design2. This leads to the need for a simple and accurate conventional fuels-alcohol blends combustion models that can be used in developing parametric burn rate and knock combustion models for designing more efficient Spark Ignited (SI) engines. To contribute to this understanding, numerical simulations were performed to obtain detailed characteristics of Gasoline-Ethanol blends with respect to Laminar Flame Speed (LFS), autoignition and Flame-Wall interactions. The one-dimensional premixed flame code CHEMKIN® was applied to simulate the burning velocity and autoignition characteristics using the freely propagating model and closed homogeneous reactor model respectively. Computational Fluid Dynamics (CFD) was used to obtain detailed flow, temperature, and species fields for Flame-wall interactions. A semi-detailed validated chemical kinetic model for a gasoline surrogate fuel developed by Andrae and Head4 was used for the study of LFS and Autoignition. For the quenching study, a skeletal chemical kinetic mechanism of gasoline surrogate, having 50 species and 174 reactions was used. The surrogate fuel was defined as a mixture of pure n-heptane, isooctane, and toluene. For LFS study, the ethanol volume fraction was varied from 0 to 85%, initial pressure from 4 to 8 bar, initial temperature from 300 to 900K, and dilution from 0 to 32%. Whereas for Autoignition study, the ethanol volume fraction was varied between 0 to 85%, initial pressure was varied between 20 to 60 bar, initial temperature was varied between 800 to 1200K, and the dilution was varied between 0 to 32% at equivalence ratios of 0.5, 1.0 and 1.5 to represent the in-cylinder conditions of a SI engine. For quenching study three Ethanol blends, namely E0, E25 and E85 are described in detail at an initial pressure of 8 atm and 17 atm. Initial wall temperature was taken to be 400 K. Quenching thicknesses and heat fluxes to the wall were computed. The laminar flame speed was found to increase with ethanol concentration and temperature but decrease with pressure and dilution. The autoignition time was found to increase with ethanol concentration at lower temperatures but was found to decrease marginally at higher temperatures. The autoignition time was also found to decrease with pressure and equivalence ratio but increase with dilution. The average quenching thickness was found to decrease with an increase in Ethanol concentration in the blend. Heat flux to the wall increased with increase in ethanol percentage in the blend and at higher initial pressures. Whereas the wall heat flux decreased with an increase in dilution. Unburned Hydrocarbon (UHC) and CO % was also found to decrease with ethanol concentration in the blend.

THE DISPERSION AND SELECTIVE FLOCCULATION OF HEMATITE ORE

Iron ore is one of the most important ores in the world. Over the past century, most mining of iron ore has been focused on magnetite (Fe3O4). As the name suggests, magnetite is magnetic in nature and is easily separated from gangue (unwanted) minerals through magnetic separation processes. Unfortunately, the magnetite ore bodies are diminishing. Because of this, there has been a recent drive to pursue technology that can economically separate hematite (Fe2O3) from its gangue minerals as hematite is a much more abundant source of iron. Most hematite ore has a very small liberation size that is frequently less than 25μm. Beneficiation of any ore with this fine of a liberation size requires advanced processing methods and is seldom pursued. A single process, known as selective flocculation and dispersion, has been successfully implemented at a plant scale for the beneficiation of fine liberation size hematite ore. Very little is known about this process as it was discovered by the U.S. Bureau of Mines by accident. The process is driven by water chemistry and surface chemistry modifications that enhance the separation of the hematite from its gangue minerals. This dissertation focuses on the role of water chemistry and process reagents in this hematite beneficiation process. It has been shown that certain ions, including calcium and magnesium, play a significant role in the process. These ions have a significant effect on the surface chemistry as reported by zeta potential studies. It was shown that magnesium ions within the process water have a more significant impact on surface chemistry than calcium ions due to steric hindrance effects at the hematite surface. It has also been shown that polyacrylic acid dispersants, if used in the process, can increase product quality (increase iron content, decrease phosphorus content, decrease silica content) substantially. Water, surface and reagent chemistry experiments were performed at a laboratory, pilot, and full plant scale during the course of this work. Many of the conclusions developed in the laboratory and pilot scale were found to be true at the full plant scale as well. These studies are the first published in history to develop theories of water chemistry and surface chemistry interactions at a full plant scale.

Alkylamides from Echinacea are a new class of cannabinomimetics. Cannabinoid type 2 receptor-dependent and -independent immunomodulatory effects

Alkylamides (alkamides) from Echinacea modulate tumor necrosis factor alpha mRNA expression in human monocytes/macrophages via the cannabinoid type 2 (CB2) receptor (Gertsch, J., Schoop, R., Kuenzle, U., and Suter, A. (2004) FEBS Lett. 577, 563-569). Here we show that the alkylamides dodeca-2E,4E,8Z,10Z-tetraenoic acid isobutylamide (A1) and dodeca-2E,4E-dienoic acid isobutylamide (A2) bind to the CB2 receptor more strongly than the endogenous cannabinoids. The Ki values of A1 and A2 (CB2 approximately 60 nM; CB1 >1500 nM) were determined by displacement of the synthetic high affinity cannabinoid ligand [3H]CP-55,940. Molecular modeling suggests that alkylamides bind in the solvent-accessible cavity in CB2, directed by H-bonding and pi-pi interactions. In a screen with 49 other pharmacologically relevant receptors, it could be shown that A1 and A2 specifically bind to CB2 and CB1. A1 and A2 elevated total intracellular Ca2+ in CB2-positive but not in CB2-negative promyelocytic HL60 cells, an effect that was inhibited by the CB2 antagonist SR144528. At 50 nM, A1, A2, and the endogenous cannabinoid anandamide (CB2 Ki >200 nM) up-regulated constitutive interleukin (IL)-6 expression in human whole blood in a seemingly CB2-dependent manner. A1, A2, anandamide, the CB2 antagonist SR144528 (Ki <10 nM), and also the non-CB2-binding alkylamide undeca-2E-ene,8,10-diynoic acid isobutylamide all significantly inhibited lipopolysaccharide-induced tumor necrosis factor alpha, IL-1beta, and IL-12p70 expression (5-500 nM) in a CB2-independent manner. Alkylamides and anandamide also showed weak differential effects on anti-CD3-versus anti-CD28-stimulated cytokine expression in human whole blood. Overall, alkylamides, anandamide, and SR144528 potently inhibited lipopolysaccharide-induced inflammation in human whole blood and exerted modulatory effects on cytokine expression, but these effects are not exclusively related to CB2 binding.

Laser wavelengths and oral implantology

In modern implant dentistry there are several clinical indications for laser surgery. Different laser systems have a considerable spectrum of application in soft and hard peri-implant tissues. The literature was searched for clinical application of different laser wavelengths in peri-implant tissues: second-stage surgery of submerged implants, treatment of infrabony defects, removal of peri-implant hyperplastic overgrowths, and, possibly, the preparation of bone cavities for implant placement. This report describes the state-of-the-art application of different laser systems in modern implant dentistry for the treatment of peri-implant lesions and decontamination of implant surfaces. Our study evaluated in vitro examinations, clinical experience and long-term clinical studies. The exact selection of the appropriate laser system and wavelength was dependent on the scientific evaluation of recent literature and the level of changes in implant and tissue temperatures during laser application. The significant reduction in bacteria on the implant surface and the peri-implant tissues during irradiation and the cutting effects associated with the coagulation properties of the lasers are the main reasons for laser application in the treatment of peri-implant lesions and the successful long-term prognosis of failing oral implants. The various applications of lasers in implant dentistry are dependent on the wavelength and laser-tissue interactions.

The annexins: spatial and temporal coordination of signaling events during cellular stress

Annexins are a family of structurally related, Ca2+-sensitive proteins that bind to negatively charged phospholipids and establish specific interactions with other lipids and lipid microdomains. They are present in all eukaryotic cells and share a common folding motif, the "annexin core", which incorporates Ca2+- and membrane-binding sites. Annexins participate in a variety of intracellular processes, ranging from the regulation of membrane dynamics to cell migration, proliferation, and apoptosis. Here we focus on the role of annexins in cellular signaling during stress. A chronic stress response triggers the activation of different intracellular pathways, resulting in profound changes in Ca2+ and pH homeostasis and the production of lipid second messengers. We review the latest data on how these changes are sensed by the annexins, which have the ability to simultaneously interact with specific lipid and protein moieties at the plasma membrane, contributing to stress adaptation via regulation of various signaling pathways.

The chemokine CCL20 and its receptor CCR6 in human malignancy with focus on colorectal cancer

Chemokines are a superfamily of small chemotactic cytokines, which interact with their G-protein-coupled receptors. These interactions regulate multiple physiological functions, particularly tissue architecture and compartment-specific migration of white blood cells. It has been found that the chemokine/chemokine receptor system has been utilized by cancer cells for migration and metastasis. The chemokine receptor CCR6 is expressed in colorectal cancer and several other cancer types, and stimulation by its physiological chemokine ligand CCL20 has been reported to promote cancer cell proliferation and migration in vitro. Moreover, CCR6/CCL20 interactions apparently play a role in organ selective liver metastasis of colorectal cancer. Here, we review the literature on expression patterns of CCL20 and CCR6 and their physiological interactions as well as the currently presumed role of CCR6 and CCL20 in the formation of colorectal cancer liver metastasis, providing a potential basis for novel treatment strategies.

Endothelial cell protection and complement inhibition in xenotransplantation: a novel in vitro model using whole blood

BACKGROUND: Studying the interactions between xenoreactive antibodies, complement and coagulation factors with the endothelium in hyperacute and acute vascular rejection usually necessitates the use of in vivo models. Conventional in vitro or ex vivo systems require either serum, plasma or anti-coagulated whole blood, making analysis of coagulation-mediated effects difficult. Here a novel in vitro microcarrier-based system for the study of endothelial cell (EC) activation and damage, using non-anticoagulated whole blood is described. Once established, the model was used to study the effect of the characterized complement- and coagulation inhibitor dextran sulfate (DXS, MW 5000) for its EC protective properties in a xenotransplantation setting. METHODS: Porcine aortic endothelial cells (PAEC), grown to confluence on microcarrier beads, were incubated with non-anticoagulated whole human blood until coagulation occurred or for a maximum of 90 min. PAEC-beads were either pre- or co-incubated with DXS. Phosphate buffered saline (PBS) experiments served as controls. Fluid phase and surface activation markers for complement and coagulation were analyzed as well as binding of DXS to PAEC-beads. RESULTS: Co- as well as pre-incubation of DXS, followed by washing of the beads, significantly prolonged time to coagulation from 39 +/- 12 min (PBS control) to 74 +/- 23 and 77 +/- 20 min, respectively (P < 0.005 vs. PBS). DXS treatment attenuated surface deposition of C1q, C4b/c, C3b/c and C5b-9 without affecting IgG or IgM deposition. Endothelial integrity, expressed by positivity for von Willebrand Factor, was maintained longer with DXS treatment. Compared with PBS controls, both pre- and co-incubation with DXS significantly prolonged activated partial thromboplastin time (>300 s, P < 0.05) and reduced production of thrombin-antithrombin complexes and fibrinopeptide A. Whilst DXS co-incubation completely blocked classical pathway complement activity (CH50 test) DXS pre-incubation or PBS control experiments showed no inhibition. DXS bound to PAEC-beads as visualized using fluorescein-labeled DXS. CONCLUSIONS: This novel in vitro microcarrier model can be used to study EC damage and the complex interactions with whole blood as well as screen ''endothelial protective'' substances in a xenotransplantation setting. DXS provides EC protection in this in vitro setting, attenuating damage of ECs as seen in hyperacute xenograft rejection.

Calibration and analysis of the 2007 data

he physics program of the NA61/SHINE (SHINE = SPS Heavy Ion and Neutrino Experiment) experiment at the CERN SPS consists of three subjects. In the first stage of data taking (2007-2009) measurements of hadron production in hadron-nucleus interactions needed for neutrino (T2K) and cosmic-ray (Pierre Auger and KASCADE) experiments will be performed. In the second stage (2009-2010) hadron production in proton-proton and proton-nucleus interactions needed as reference data for a better understanding of nucleus-nucleus reactions will be studied. In the third stage (2009-2013) energy dependence of hadron production properties will be measured in p+p, p+Pb interactions and nucleus-nucleus collisions, with the aim to identify the properties of the onset of deconfinement and find evidence for the critical point of strongly interacting matter. The NA61 experiment was approved at CERN in June 2007. The first pilot run was performed during October 2007. Calibrations of all detector components have been performed successfully and preliminary uncorrected spectra have been obtained. High quality of track reconstruction and particle identification similar to NA49 has been achieved. The data and new detailed simulations confirm that the NA61 detector acceptance and particle identification capabilities cover the phase space required by the T2K experiment. This document reports on the progress made in the calibration and analysis of the 2007 data.

Comparison of Round and Square Cores in the Determination of Beef Tenderness by Warner- Bratzler and Instron

Seven rib-eye rolls, lip on (112A), were each cut into eight 2.54 centimeter thick steaks starting from the blade end. Steaks were randomly assigned to one of four treatment groups; 1) round versus square cores using Instron [inst1], 2) round versus square cores using Warner- Bratzler [inst2], 3) Instron versus Warner-Bratzler using round cores [rdsq1], and 4) Instron versus Warner- Bratzler using square cores [rdsq2]. Subsequently, steaks from each group were broiled in a General Electric industrial broiler grill to an internal temperature of 63 §C. Steaks were held overnight at 2 §C. Two steaks from each rib were placed into each instrument/core treatment group. Steaks were then divided into three sections identified as: a) lateral, b) medial, and c) central. Three 1.27 centimeter cores from each section were taken from each steak for a total of nine cores per steak and sheared once through the center. The results indicated that there was a significant difference ( p> .05) between round and square cores for both Warner- Bratzler and Instron. In all mean groups tested, square cores had higher shear values than did round cores. There was no indication of differences between instruments, and no significant interactions between instruments and core types.

Pelvic lymph node dissection in the context of radical cystectomy: a thorough insight into the connection between patient, surgeon, pathologist and treating institution

Pelvic lymph node dissection (PLND) in patients with bladder cancer varies widely in extent, technique employed, and pathological workup of specimens. The present paper provides an overview of the existing evidence regarding the effectiveness of PLND and elucidates the interactions between patient, surgeon, pathologist, and treating institution as well as their cumulative impact on the final postoperative lymph node (LN) staging. Bladder cancer patients undergoing radical cystectomy with extended PLND appear to have better oncologic outcomes compared to patients undergoing radical cystectomy and limited PLND. Attempts have been made to define and assess the quality of PLND according to the number of lymph nodes identified. However, lymph node counts depend on multiple factors such as patient characteristics, surgical template, pathological workup, and institutional policies; hence, meticulous PLND within a defined and uniformly applied extended template appears to be a better assurance of quality than absolute lymph node counts. Nevertheless, the prognosis of the patients can be partially predicted with findings from the histopathological evaluation of the PLND specimen, such as the number of positive lymph nodes, extracapsular extension, and size of the largest LN metastases. Therefore, particular prognostic parameters should be addressed within the pathological report to guide the urologist in terms of patient counseling.

Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies.

A wealth of genetic associations for cardiovascular and metabolic phenotypes in humans has been accumulating over the last decade, in particular a large number of loci derived from recent genome wide association studies (GWAS). True complex disease-associated loci often exert modest effects, so their delineation currently requires integration of diverse phenotypic data from large studies to ensure robust meta-analyses. We have designed a gene-centric 50 K single nucleotide polymorphism (SNP) array to assess potentially relevant loci across a range of cardiovascular, metabolic and inflammatory syndromes. The array utilizes a "cosmopolitan" tagging approach to capture the genetic diversity across approximately 2,000 loci in populations represented in the HapMap and SeattleSNPs projects. The array content is informed by GWAS of vascular and inflammatory disease, expression quantitative trait loci implicated in atherosclerosis, pathway based approaches and comprehensive literature searching. The custom flexibility of the array platform facilitated interrogation of loci at differing stringencies, according to a gene prioritization strategy that allows saturation of high priority loci with a greater density of markers than the existing GWAS tools, particularly in African HapMap samples. We also demonstrate that the IBC array can be used to complement GWAS, increasing coverage in high priority CVD-related loci across all major HapMap populations. DNA from over 200,000 extensively phenotyped individuals will be genotyped with this array with a significant portion of the generated data being released into the academic domain facilitating in silico replication attempts, analyses of rare variants and cross-cohort meta-analyses in diverse populations. These datasets will also facilitate more robust secondary analyses, such as explorations with alternative genetic models, epistasis and gene-environment interactions.