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Anthropogenics: Human Influence On Global And Genetic Homogenization Of Parasite Populations, Dante S. Zarlenga, Eric P. Hoberg, Benjamin Rosenthal, Simonetti Mattiucci, Giuseppe Nascetti

Harold W. Manter Laboratory of Parasitology: Faculty Publications

The distribution, abundance, and diversity of life on Earth have been greatly shaped by human activities. This includes the geographic expansion of parasites; however, measuring the extent to which humans have influenced the dissemination and population structure of parasites has been challenging. In-depth comparisons among parasite populations extending to landscape-level processes affecting disease emergence have remained elusive. New research methods have enhanced our capacity to discern human impact, where the tools of population genetics and molecular epidemiology have begun to shed light on our historical and ongoing influence. Only since the 1990s have parasitologists coupled morphological diagnosis, long considered the …

Further Characterization Of A Secreted Lipase From The Human Pathogen Leishmania Donovani By Determining The Effect Of Various Metal Ions On Its Enzymatic Activity., Lana Hoertz

Pell Scholars and Senior Theses

Leishmania donovani, a protozoan parasite, is the causative agent of the often fatal disease visceral leishmaniasis. The current treatments available are minimal and toxic to the patient. It has been shown that these organisms exhibit lipolytic activity during their growth in vitro. Lipases are enzymes that are known to aid in the development and virulence of several pathogenic organisms such as Candida albicans and Staphylococcus warneri. Little information is known, however, about the role of lipases in Leishmania species. We hypothesize that lipase may play a part in Leishmania's ability to survive within the human host as well as its …

Two-Photon Microscopy For Biomedical Studies, Yassel Acosta

Open Access Theses & Dissertations

Fluorescence optical microscopy is one of the most important tools to investigate biological samples and to observe structures in living cells. Based on the principle of the simultaneous absorption of two-photons and subsequent emission of fluorescent light we have developed a Two-Photon Laser Scanning Fluorescence Microscope that allow us to perform optical sectioning and three-dimensional reconstructions of structures in biological samples such as dopaminergic clusters of neurons and tracheal branches in Drosophila brain. The spatial confinement of the excitation light to the focal plane combined with the temporal compression of photons into short packets during femtosecond pulses make our system …

Spingolipid Metabolism In A Reptillian Protozoan, Entamoeba Invadens, Duran Dogan Debons

Open Access Theses & Dissertations

Entamoeba invadens (hereinafter E. invadens) is an anaerobic parasitic protozoan that can be found in water and soil. Although the host organisms for this parasite are snakes, lizards, and other reptile species, the parasite is morphologically identical to Entamoeba histolytica, a causative agent of human amebiasis. Entamoeba inavdens exists in two morphological forms--(1) a replicative trophozoite, and (2) a relatively dormant cyst. While the transformation of cyst to trophozoites (called "excystation") takes place in the stomach, the differentiation of trophozoites to cyst (known as "encystation"), occurs in the small intestine. Unlike the cyst, a trophozoite is unable to survive …

Risk Assessment Of Waterborne Cryptosporidium, Victoria Norma Ochoa

Open Access Theses & Dissertations

In an effort to update the risk assessment of waterborne Cryptosporidium an additional and more complete human dose-response dataset of the parasite was used to calculate the risk of infection. The complete data studied contains larger human outcomes than the initial prior risk assessment evaluated by Haas et. al. in 1999. Quantitative analysis of the complete dose-response indicates that it no longer follows the Exponential Model used to estimate the risk for the initial data. The complete dataset appears to provide a better fit with the Beta-Poisson Model and even a dose independent constant risk model, which shows a considerable …

Mapreduce-Based Restmd: Enabling Large-Scale Sampling Tasks With Distributed Hpc Systems, Praveenkumar Kondikoppa, Richard Platania, Seung Jong Park, Tom Keyes, Jaegil Kim, Nayong Kim, Joohyun Kim, Shuju Bai

Computer Science Faculty Research & Creative Works

A novel implementation of Replica Exchange Statistical Temperature Molecular Dynamics (RESTMD), belonging to a generalized ensemble method and also known as parallel tempering, is presented. Our implementation employs the MapReduce (MR)-based iterative framework for launching RESTMD over high performance computing (HPC) clusters including our test bed system, Cyber-infrastructure for Reconfigurable Optical Networks (CRON) simulating a network-connected distributed system. Our main contribution is a new implementation of STMD plugged into the well-known CHARMM molecular dynamics package as well as the RESTMD implementation powered by the Hadoop that scales out in a cluster and across distributed systems effectively. To address challenges for …

Antioxidant Potential Of Sutherlandia Frutescens And Its Protective Effects Against Oxidative Stress In Various Cell Cultures, Shakila Tobwala, Weili Fan, Connor J. Hines, William Robert Folk, Nuran Ercal

Chemistry Faculty Research & Creative Works

Sutherlandia frutescens (L.) R.Br. (SF) is a South African plant that is widely used to treat stress, infections, cancer, and chronic diseases, many of which involve oxidative stress. The aim of the study was to quantitatively assess the antioxidant potential of SF extracts in cell-free system as well as in cell lines. Dried SF vegetative parts were extracted using six different solvents, and the extracts were assessed for total phenolic and flavonoid contents, total reducing power, iron chelating capacity, and free radical scavenging power, including, scavenging of hydroxyl radicals, superoxide anions, nitric oxide, and hydrogen peroxide. We further investigated the …

Vanadium Complexes Are In Vitro Inhibitors Of Leishmania Secreted Acid Phosphatases, Richard Mendez, Benjamin M. Dorsey, Craig C. Mclauchlan, Matt Beio, Timothy L. Turner, Victoria H. Nguyen, Alexander Su, William Beynon, Jon A. Friesen, Marjorie A. Jones

Faculty Publications – Chemistry

Leishmaniasis is a parasitic disease caused by the protozoa Leishmania. These organisms secrete acid phosphatases during their growth cycle as an important part of cell targeting to host macrophage cells thus allowing for a successful infection. Secreted acid phosphatases (SAP) are reported to play a significant role in the survival of Leishmania cells, thus evaluation of these enzymes is of interest. The inhibition of SAP can be the focus of a new drug therapy. We tested for SAP activity from Leishmania tarentolae following the addition of a series of vanadium complexes including decavanadate. Cell cultures at different stages in their …

Design, Synthesis, And Evaluation Of Small Molecule-Based, Profluorogenic Activatable Substrate Probes For Detection And Visualization Of Human Cancer Enzyme Nad(P)H:Quinone Oxidoreductase-1, Suraj Uditha Hettiarachchi

LSU Doctoral Dissertations

Cancer comprises many specific diseases, and it is currently responsible for millions of deaths worldwide. This broad disease profile is a great challenge for personalized oncology. Critical for the success of cancer therapy is the exploration of improved methodologies for the early detection of localized and disseminated tumor cells in patients, where bio-molecular imaging has become an indispensable tool. Being one of many different imaging techniques, optical fluorescence imaging has been translated over the years from the bench to clinical research, and it is now on the verge of being able to address some of the pressing challenges in molecular …

Gumbos- And Ionic Liquid-Coated Quartz Crystal Microbalance Sensors For Detection And Molecular Weight Determination Of Organic Vapors, Bishnu Prasad Regmi

LSU Doctoral Dissertations

There has been an ever-increasing demand for the development of high-performance sensing devices for detection and discrimination of volatile organic compounds (VOCs) present in different environments. Among a number of sensing devices currently available, sorption-based sensors are particularly attractive because they are simple and inexpensive, require low power, and are appropriate for fabrication of multisensor arrays. A sorption-based sensor is comprised of a chemically active coating immobilized on the surface of a physical transducer. The chemically active film interacts with analytes, and the transducer converts the binding event into an electrical signal. This dissertation is focused on a sorption-based sensor …

Multi-State Models For Natural History Of Disease, Amy Laird, Rebecca A. Hubbard, Lurdes Y. T. Inoue

UW Biostatistics Working Paper Series

Longitudinal studies are a useful tool for investigating the course of chronic diseases. Many chronic diseases can be characterized by a set of health states. We can improve our understanding of the natural history of the disease by modeling the sequence of visited health states and the duration in each state. However, in most applications, subjects are observed only intermittently. This observation scheme creates a major modeling challenge: the transition times are not known exactly, and in some cases the path through the health states is not known.

In this manuscript we review existing approaches for modeling multi-state longitudinal data. …

Simulating Bipartite Networks To Reflect Uncertainty In Local Network Properties, Ravi Goyal, Joseph Blitzstein, Victor De Gruttola

Harvard University Biostatistics Working Paper Series

No abstract provided.

Scitech Book News Reviews, Susan Fingerman

Sci-Tech News

No abstract provided.

Dual Capture Of A Piñon Deer Mouse And A Silky Pocket Mouse Resulting In Consumption Of The Smaller Animal, Jon C. Pigage, Roger D. Peyton

The Prairie Naturalist

Intraspecific dual captures of rodents are uncommon, but not rare. There are several reports of brown rats (Rattus norvegicus), white-footed deer mice (Peromyscus leucopus), North American deer mice (P. maniculatus), western harvest mice (Reithrodontomys megalotis) and meadow voles (Microtus pennsylvanicus) caught simultaneously in the same trap (i.e. a door-closing live-trap; Davis 1955, Getz 1961, Blaustein and Rothstein 1978, Jenkins and Llewellyn 1981, Novak 1983). Some reports are incidental whereas others are interpreted as social associations or bonding between conspecifics. Interspecific dual captures are rarely reported in the literature. The earliest report of …

A Hybrid Agent-Based And Differential Equations Model For Simulating Antibiotic Resistance In A Hospital Ward, Lester Caudill, Barry Lawson

Department of Math & Statistics Faculty Publications

Serious infections due to antibiotic-resistant bacteria are pervasive, and of particular concern within hospital units due to frequent interaction among health-care workers and patients. Such nosocomial infections are difficult to eliminate because of inconsistent disinfection procedures and frequent interactions among infected persons, and because ill-chosen antibiotic treatment strategies can lead to a growth of resistant bacterial strains. Clinical studies to address these concerns have several issues, but chief among them are the effects on the patients involved. Realistic simulation models offer an attractive alternative. This paper presents a hybrid simulation model of antibiotic resistant infections in a hospital ward, combining …

Can Inhibitor-Resistant Substitutions In The Mycobacterium Tuberculosis Β-Lactamase Blac Lead To Clavulanate Resistance?: A Biochemical Rationale For The Use Of Β-Lactam–Β-Lactamase Inhibitor Combinations, Sebastian G. Kurz, Kerstin A. Wolff, Saugata Hazra, Christopher R. Bethel, Andrea M. Hujer, Kerri M. Smith, Yan Xu, Lee W. Tremblay, John S. Blanchard, Liem Nguyen, Robert A. Bonomo

Chemistry Faculty Publications

The current emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis calls for novel treatment strategies. Recently, BlaC, the principal β-lactamase of Mycobacterium tuberculosis, was recognized as a potential therapeutic target. The combination of meropenem and clavulanic acid, which inhibits BlaC, was found to be effective against even extensively drug-resistant M. tuberculosis strains when tested in vitro. Yet there is significant concern that drug resistance against this combination will also emerge. To investigate the potential of BlaC to evolve variants resistant to clavulanic acid, we introduced substitutions at important amino acid residues of M. tuberculosis BlaC (R220, A244, S130, and …

Research: South Dakota State University, Winter 2013, Christie Delfanian, Matt Landwehr

State of Discovery South Dakota State University's Research Magazine

CONTENTS:

South Dakota expertise integral part of Landsat [Page] 1
West Nile: Researchers help public health officials combat West Nile virus [page] 2
Health care: arteries, corticosteroids, concussions, and preemies [Page] 4
Oilseeds [Page] 6
Undergraduate Research [Page] 8
Organ donation key to helping Native Americans on dialysis [Page] 10
Researchers meet challenge of increased competition: 2012 measurements [Page] 11

Spread Of Malicious Objects In Computer Network: A Fuzzy Approach, Bimal K. Mishra, Apeksha Prajapati

Applications and Applied Mathematics: An International Journal (AAM)

We propose an e-epidemic fuzzy SEIQRS (Susceptible-Exposed-Infectious-Quarantine- Recovered-Susceptible) model for the transmission of malicious codes in a computer network. We have simulated the result for various parameters and analyzed the stability of the model. The efficiency of antivirus software and crashing of the nodes due to attack of malicious code is analyzed. Furthermore, initial simulation results illustrate the behavior of different classes for minimizing the infection in a computer network. It also reflects the positive impact of anti-virus software on malicious code propagation in a computer network. The basic reproduction number R0 f and its formulation is also discussed.

Factors Associated With Parental Decision Making And Childhood Vaccination, Zuwen Qiu-Shultz

UNLV Theses, Dissertations, Professional Papers, and Capstones

In order to better understand factors affecting immunization status, logistic regression was used to assess the association of various socio-demographic factors and whether parents would have their child immunized if not a state mandate. Factors included in the study were race, household income, number of children in the household, number of adults in the household, if the child had a primary provider, if the child had a health check-up in the last twelve months, and medical insurance status of the child. The combined Nevada Kindergarten Health Survey Result of 2009-2010 (Year Two) and 2010-2011 (Year Three) conducted by the Nevada …

Molecular Detection Of Culture-Confirmed Bacterial Bloodstream Infections With Limited Enrichment Time, Miranda S. Moore, Chase D. Mccann, Jeanne Jordan

Epidemiology Faculty Publications

Conventional blood culturing using automated instrumentation with phenotypic identification requires a significant amount of time to generate results. This study investigated the speed and accuracy of results generated using PCR and pyrosequencing compared to the time required to obtain Gram stain results and final culture identification for cases of culture-confirmed bloodstream infections. Research and physician-ordered blood cultures were drawn concurrently. Aliquots of the incubating research blood culture fluid were removed hourly between 5 and 8 h, at 24 h, and again at 5 days. DNA was extracted from these 6 time point aliquots and analyzed by PCR and pyrosequencing for …

Substrate-Dependent Dynamics Of Udp-Galactopyranose Mutase: Implications For Drug Design, Leonardo Boechi, Cesar Augusto F. De Oliveira, Isabel Da Fonseca, Karina Kizjakina, Pablo Sobrado, John J. Tanner, J. Andrew Mccammon

Chemistry Faculty Research & Creative Works

Trypanosoma cruzi is the causative agent of Chagas disease, a neglected tropical disease that represents one of the major health challenges of the Latin American countries. Successful efforts were made during the last few decades to control the transmission of this disease, but there is still no treatment for the 10 million adults in the chronic phase of the disease. In T. cruzi, as well as in other pathogens, the flavoenzyme UDP-galactopyranose mutase (UGM) catalyzes the conversion of UDP-galactopyranose to UDP-galactofuranose, a precursor of the cell surface b-galactofuranose that is involved in the virulence of the pathogen. The fact that …

An Epidemic Model Structured By The Time Since Last Infection, Jorge Alturo Alfaro Murillo

Open Access Dissertations

Epidemiological models structured by time since infection have their origin in the seminal work of 1927 by Kermack and McKendrick. Compared to ordinary differential equations (ODE) models, they are able to capture differences in infectivity of the individuals in a more suitable manner. Their use declined in the second half of the 20th century, probably because the theory for ODE models is more robust, complete and has proved successful in providing insights and predictions for many epidemiological problems. Nevertheless, it is important to understand in what occasions the inclusion of time since infection may alter the outcomes in a significant …

Disk Diffusion Breakpoint Determination Using A Bayesian Nonparametric Variation Of The Errors-In-Variables Model, Glen Richard Depalma

Open Access Dissertations

Drug dilution (MIC) and disk diffusion (DIA) are the two most common antimicrobial susceptibility tests used by hospitals and clinics to determine an unknown pathogen's susceptibility to various antibiotics. Both tests use breakpoints to classify the pathogen as either susceptible, indeterminant, or resistant to each drug under consideration. While the determination of these drug-specific MIC classification breakpoints is straightforward, determination of comparable DIA breakpoints is not. It is this issue that motivates this research.

Traditionally, the error-rate bounded (ERB) method has been used to calibrate the two tests. This procedure involves determining DIA breakpoints which minimize the observed discrepancies between …

Antibiotic Thin Films, Timothy Jennings, Jason Nielsen, Brian Ratcliff, Nina Wallace, Xin Zhong Lai, Paul B. Savage

Journal of Undergraduate Research

Nosocomial infections lead to septicemia, a severe problem in the United States. The Savage group has developed a novel class of antibiotics (CSAs) that can be attached to polymers. Invasive medical equipment can be coated with CSA polymers, forming an antibiotic thin film. Testing has shown the ability of CSA polymers to kill bacteria, which will lead to further testing and future use in the medical field.

Feeling The Heat? Substantial Variation In Temperatures Does Not Affect The Proportion Of Males Born In Australia, Barnaby J. Dixson, John Haywood, Philip J. Lester, Diane K. Ormsby

Human Biology Open Access Pre-Prints

The global proportion of male births has been shown to vary with climate, with a higher proportion of male births documented in colder climates. Here we examined the hypothesis that ambient temperature predicts fluctuations in the proportion of male births in Australia and within seven Australian states using historical annual data spanning 1910-2009. We predicted that within states with tropical ambient temperatures the proportion of male births would decrease when ambient temperatures are higher. Considering the national composite births for the whole of Australia first, the proportion of males born ranged only from 0.510 to 0.517. We observed no relationship …

Chimeric Rhinoviruses Displaying Mper Epitopes Elicit Anti-Hiv Neutralizing Responses, Guohua Yi, Mauro Lapelosa, Rachel Bradley, Thomas M. Mariano, Denise Elsasser Dietz, Scott Hughes, Terri Wrin, Chris Petropoulos, Emilio Gallicchio, Ronald M. Levy, Eddy Arnold, Gail Ferstandig Arnold

Publications and Research

Background: The development of an effective AIDS vaccine has been a formidable task, but remains a critical necessity. The well conserved membrane-proximal external region (MPER) of the HIV-1 gp41 glycoprotein is one of the crucial targets for AIDS vaccine development, as it has the necessary attribute of being able to elicit antibodies capable of neutralizing diverse isolates of HIV.

Methodology/Principle Findings: Guided by X-ray crystallography, molecular modeling, combinatorial chemistry, and powerful selection techniques, we designed and produced six combinatorial libraries of chimeric human rhinoviruses (HRV) displaying the MPER epitopes corresponding to mAbs 2F5, 4E10, and/or Z13e1, connected to an immunogenic …

Antimicrobial Activity And Mechanistic Study For The Poly(Phenylene Ethynylene) (Ppe)-Based Cationic Conjugated Polyelectrolytes And Oligo-Phenylene Ethynylenes, Ying Wang

Chemistry and Chemical Biology ETDs

My dissertation work focuses on recent progress made in elucidating the intermolecular interactions between a novel class of synthetic phenylene ethynylene (PPE)-based conjugated polyelectrolyte polymers (CPEs) and oligomers (OPEs) and multiscale cellular targets that give rise to their remarkable broad spectrum biocidal activity. We studied the interactions and self-assembly behaviors of the CPEs and OPEs with a set of vital biomolecules, including lipids, proteins and nucleic acids, that reveal the potential pathways by which the synthetic biocidal agents could exert toxicity. Then, we explored the antimicrobial effects and mechanisms of the CPEs and OPEs on multiple clinically relevant pathogens, with …

Cloning And Characterization Of Ef-Tu And Ef-Ts From Pseudomonas Aeruginosa, Stephanie O. Palmer, Edna Y. Rangel, Alberto E. Montalvo, Alexis T. Tran, Kate C. Ferguson, James M. Bullard

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

We have cloned genes encoding elongation factors We have cloned genes encoding elongation factors EF-Tu and EF-Ts from Pseudomonas aeruginosa and expressed and purified the proteins to greater than 95% homogeneity. Sequence analysis indicated that P. aeruginosa EF-Tu and EF-Ts are 84% and 55% identical to E. coli counterparts, respectively. P. aeruginosa EF-Tu was active when assayed in GDP exchange assays. Kinetic parameters for the interaction of EF-Tu with GDP in the absence of EF-Ts were observed to be = 33 μM, = 0.003 s−1, and the specificity constant was  s−1 μM−1. In the presence of EF-Ts, these values were …

Mining Effective Multi-Segment Sliding Window For Pathogen Incidence Rate Prediction, Lei Duan, Changjie Tang, Xiasong Li, Guozhu Dong, Xianming Wang, Jie Zuo, Min Jiang, Zhongqi Li, Yongqing Zhang

Kno.e.sis Publications

Pathogen incidence rate prediction, which can be considered as time series modeling, is an important task for infectious disease incidence rate prediction and for public health. This paper investigates the application of a genetic computation technique, namely GEP, for pathogen incidence rate prediction. To overcome the shortcomings of traditional sliding windows in GEP-based time series modeling, the paper introduces the problem of mining effective sliding window, for discovering optimal sliding windows for building accurate prediction models. To utilize the periodical characteristic of pathogen incidence rates, a multi-segment sliding window consisting of several segments from different periodical intervals is proposed and …

Predicting Unobserved Exposures From Seasonal Epidemic Data, Eric Forgoston, Ira B. Schwartz

Department of Applied Mathematics and Statistics Faculty Scholarship and Creative Works

We consider a stochastic Susceptible-Exposed-Infected-Recovered (SEIR) epidemiological model with a contact rate that fluctuates seasonally. Through the use of a nonlinear, stochastic projection, we are able to analytically determine the lower dimensional manifold on which the deterministic and stochastic dynamics correctly interact. Our method produces a low dimensional stochastic model that captures the same timing of disease outbreak and the same amplitude and phase of recurrent behavior seen in the high dimensional model. Given seasonal epidemic data consisting of the number of infectious individuals, our method enables a data-based model prediction of the number of unobserved exposed individuals over very …