Life Sciences Commons^™

The Drug Discovery Of Potential Anti-Cancer Agents To Inhibit The Demethylation Catalytic Activity Of The Jmjc Domain Of Kdm3a, Balgees Alshanqeti

Electronic Theses & Dissertations

Lysine demethylase 3A (KDM3A) is an enzyme that specifically catalyzes the removal of 2 or three methyl groups from lysine 9 of histone 3 (KH3). It belongs to the family of histone demethylases that contain the Jumonji C (JmjC) domain, which means cruciform in Japanese. KDM3A also belongs to a family of hydroxylases that are alpha-ketoglutarate dependent. The role of KDM3A in the cell is not yet understood, however, and based on its demethylation of studies have showed that its expression is elevated in embryonic stem cells in humans and in mice. In general, patterns of elevated expression of KDM3A …

Atmospheric Cold Plasma Inactivation Of Salmonella And Escherichia Coli On The Surface Of Golden Delicious Apples, Agnes Kilonzo-Nthenge, Siqin Liu, Sudheer K. Yannam, Ankit Patras

Agricultural and Environmental Sciences Faculty Research

The contamination of fruits with human pathogens is a reoccurring concern in the fresh produce industry. Atmospheric cold plasma (ACP) is a potential alternate to customary approaches for non-thermal decontamination of foods. In this study, the efficacy of a dielectric barrier discharge ACP system against Salmonella (Salmonella Typhimurium, ATCC 13311; Salmonella Choleraesuis, ATCC 10708) and Escherichia coli (ATCC 25922, ATCC 11775) was explored. For each bacteria, a two-strain mixture at 8 log10 CFU/ml was spot inoculated on the surface of Golden Delicious apples, air dried, and exposed to ACP at a fixed distance of 35 mm, input power of 200 …

Modeling The Effect Of Post-Dispersal Seed Predation On Tropical Tree Species In Panama, Justin Tirrell

Fall Student Research Symposium 2018

Palm trees provide a unique opportunity to study what conditions optimize the probability that a seed will grow successfully. The seeds of palm trees, endocarps, are large and easy to locate. When they don't grow, predators leave marks on them that tell the story of their fate. The focus of my experiment is to determine how the current distribution pattern of parent palm trees in Panama Palm trees affects the the future distribution of seedlings. I have programmed a versatile model that takes the assumption that bruchid beetles are the sole predators acting on the seeds, and that these fall …

Review: Using Physiologically Based Models To Predict Population Responses To Phytochemicals By Wild Vertebrate Herbivores, J. S. Forbey, T. T. Caughlin

Biology Faculty Publications and Presentations

To understand how foraging decisions impact individual fitness of herbivores, nutritional ecologists must consider the complex in vivo dynamics of nutrient–nutrient interactions and nutrient–toxin interactions associated with foraging. Mathematical modeling has long been used to make foraging predictions (e.g. optimal foraging theory) but has largely been restricted to a single currency (e.g. energy) or using simple indices of nutrition (e.g. fecal nitrogen) without full consideration of physiologically based interactions among numerous co-ingested phytochemicals. Here, we describe a physiologically based model (PBM) that provides a mechanistic link between foraging decisions and demographic consequences. Including physiological mechanisms of absorption, digestion and metabolism …

Ncer Assistance Agreement Annual Progress Report For Grant #83582401 - Assessment Of Stormwater Harvesting Via Manage Aquifer Recharge (Mar) To Develop New Water Supplies In The Arid West: The Salt Lake Valley Example, Ryan Dupont, Joan E. Mclean, Richard C. Peralta, Sarah E. Null, Douglas B. Jackson-Smith

Civil and Environmental Engineering Faculty Publications

The goals of the original proposed project remain the same, that is, to test the hypothesis that Managed Aquifer Recharge (MAR) for stormwater harvesting is a technically feasible, socially and environmentally acceptable, economically viable, and legally feasible option for developing new water supplies for arid Western urban ecosystems experiencing increasing population, and climate change pressures on existing water resources. The project is being carried out via three distinct but integrated components that include: 1) Monitoring of existing distributed MAR harvesting schemes involving a growing number of demonstration Green Infrastructure (GI) test sites; 2) Integrated stormwater/vadose zone/groundwater/ ecosystem services modeling; and …

Modeling In The Physiology Classroom, Sowmya Anjur

Faculty Publications & Research

Physiology and Disease is a Biology elective at IMSA that has been developed to be mostly student-centered. Some examples of student projects include modeling heart structure to reflect function and creating LED arduino monitors to measure heart rate. Students also measure their lung capacity and blood pressure to demonstrate correlation of these values with heart rate, and trace the correlation back to neuronal controls. Projects such as these integrate other disciplines such as engineering and conform to NGSS Science and Engineering standards and NGSS Cross cutting Concepts standards. Students take responsibility for their own learning and articulate better on tests.

New Methods To Improve Protein Structure Modeling, Maha Abdelrasoul

Computer Science Theses & Dissertations

Proteins are considered the central compound necessary for life, as they play a crucial role in governing several life processes by performing the most essential biological and chemical functions in every living cell. Understanding protein structures and functions will lead to a significant advance in life science and biology. Such knowledge is vital for various fields such as drug development and synthetic biofuels production.

Most proteins have definite shapes that they fold into, which are the most stable state they can adopt. Due to the fact that the protein structure information provides important insight into its functions, many research efforts …

Modeling Habitat Of Freshwater Mussels (Bivalvia:Unionidae) In The Lower Great Lakes 25 Years After The Dreissena Invasion, Jonathan M. Bossenbroek, Lyubov E. Burlakova, Todd C. Crail, Alexander Y. Karatayev, Robert A. Krebs, David T. Zanatta

Biological, Geological, and Environmental Faculty Publications

Finding remnant populations of species that are of conservation concern can be difficult, particularly in aquatic habitats. Models of ecological niches can aid in the discovery of refuges. Remnant populations of native freshwater mussels (unionids) have been found in Lakes Erie and St Clair. Our goals were to predict undiscovered refuges in Lake Ontario based on habitat analysis from Lake Erie and to conduct surveys to test those predictions. We built a presence-only model on environmental data including attributes of the benthic zone and shoreline where mussels occurred in Lake Erie. We found a link between small- and large-scale variables …

Modeling Wind-Induced Waves In The Salish Sea, Zhaoqing Yang, Wei-Cheng Wu, Taiping Wang, Guillaume Mauger, Ruby Leung

Salish Sea Ecosystem Conference

There have been on-going efforts for increasing coastal resilience to the risk of coastal inundation as a result of sea-level rise in Washington. Accurate coastal risk projection depends on detailed and accurate information of sea level rise, including waves and storm surge induced by windstorms. This paper presents a modeling study simulating wind-induced waves in the Salish Sea. A nested-grid modeling approach was used to provide accurate and robust model simulations at various scales. The NOAA NCEP’s WaveWatch III (WW3) model is configured at global and regional scales with wind forcing obtained from the Climate Forecast System Reanalysis (CFSR). For …

An Integrated Environmental And Human Systems Modeling Framework For Puget Sound Restoration Planning, Robert Mckane, Jonathan Halama, Paul Bryce Pettus, Bradley Barnhart, Allen Brookes, Kevin Djang, Tarang Khangaonkar, Isaac Kaplan, Christopher James Harvey, Emily Howe, Phillip S. Levin, Michael W. Schmidt, Raphael Girardin

Salish Sea Ecosystem Conference

Local, state, federal, tribal and private stakeholders have committed significant resources to restoring Puget Sound’s terrestrial-marine ecosystem. Though jurisdictional issues have promoted a fragmented approach to restoration planning, there is growing recognition that a more coordinated systems-based restoration approach is needed to achieve recovery goals. This presentation describes our collaborative effort to develop and apply an integrated environmental and human systems modeling framework for the Puget Sound Basin, inclusive of all marine and land areas (1,020 and 12,680 sq. mi.). Our goal is to establish a whole-basin systems modeling framework that dynamically simulates biophysical interactions and transfers (water, nutrients, contaminants, …

Big Sharks In The Salish Sea: Combining Passive Acoustics With The Salish Sea Model To Predict Sixgill Shark (Hexanchus Griseus) Presence, Alli Cramer, Steve Katz, Kelly Andrews, Daniel H. Thornton

Salish Sea Ecosystem Conference

Examination of species-environment relationships that determine broad-scale distribution patterns is a key focus of ecological research. Characterizing animal-habitat associations in the marine environment is particularly challenging given the opacity of the ocean, and addressing this question in marine systems has consequently lagged behind terrestrial systems. In this project, we have leveraged existing data on locations of a large marine predator, the Sixgill Shark, Hexanchus griseus, and linked that with the PNNL’s Salish Sea Model over the domain of shark movement in Puget Sound, Washington state. Twenty-nine Sixgill sharks were tracked from 2005-2009 across 130 hydrophone receivers with tags that reported …

A Modeling Study Of Storm Surge In The Salish Sea, Zhaoqing Yang, Taiping Wang, Ian Miller

Salish Sea Ecosystem Conference

The Pacific Northwest coasts are subject to the threat of coastal inundation as a result of storm surge. This snapshot presentation provides an overview of a modeling study of storm surge in the Salish Sea using a high resolution coastal hydrodynamic model. A series of historical storm surge events were identified based on non-tidal residual (NTR) water levels observed at Seattle tide gage. Model simulations corresponding to selected storm surge events were conducted. The Salish Sea storm surge model was validated with both observed tidal and NTR data at NOAA tide gauges in the Salish Sea. Sensitivity analysis on the …

Effects Of Elevated Temperature, Elevated Co2 And Photoperiod On Conifer Carbon Fluxes, Joseph R. Stinziano

Electronic Thesis and Dissertation Repository

Increasing temperatures due to rising atmospheric CO₂ concentrations will have direct effects on plant physiology, specifically photosynthetic carbon uptake. Changes in photosynthetic carbon uptake will alter feedbacks between vegetation and atmospheric CO₂, and changes in forest carbon dynamics will be important in determining whether vegetation amplifies or attenuates the effects of anthropogenic CO₂ emissions on climate. Coniferous trees, which are a large component of the boreal forest, are understudied in relation to thermal acclimation of photosynthesis and temperature effects on growth. In the present work, I assess the impact of rising temperatures on carbon fluxes in …

A Systems Modeling Approach To Forecast Corn Economic Optimum Nitrogen Rate, Laila A. Puntel, John E. Sawyer, Daniel W. Barker, Peter J. Thorburn, Michael J. Castellano, Kenneth J. Moore, Andy Vanloocke, Emily A. Heaton, Sotirios V. Archontoulis

Department of Agronomy and Horticulture: Faculty Publications

Historically crop models have been used to evaluate crop yield responses to nitrogen (N) rates after harvest when it is too late for the farmers to make in-season adjustments. We hypothesize that the use of a crop model as an in-season forecast tool will improve current N decision-making. To explore this, we used the Agricultural Production Systems sIMulator (APSIM) calibrated with long-term experimental data for central Iowa, USA (16-years in continuous corn and 15-years in soybean-corn rotation) combined with actual weather data up to a specific crop stage and historical weather data thereafter. The objectives were to: (1) evaluate the …

Vesicle Biomechanics In A Time-Varying Magnetic Field, Hui Ye, Austen Curcuru

Hui Ye

Background Cells exhibit distortion when exposed to a strong electric field, suggesting that the field imposes control over cellular biomechanics. Closed pure lipid bilayer membranes (vesicles) have been widely used for the experimental and theoretical studies of cellular biomechanics under this electrodeformation. An alternative method used to generate an electric field is by electromagnetic induction with a time-varying magnetic field. References reporting the magnetic control of cellular mechanics have recently emerged. However, theoretical analysis of the cellular mechanics under a time-varying magnetic field is inadequate. We developed an analytical theory to investigate the biomechanics of a modeled vesicle under a …

Learning From Disorder And Noise In Physical Biology, Taylor Emil Firman

Electronic Theses and Dissertations

Stochasticity, disorder, and noise play crucial roles in the functioning of many biological systems over many different length scales. On the molecular scale, most proteins are envisioned as pristinely folded structures, but intrinsically disordered proteins (IDPs) have no such folded state and still serve distinct purposes within the cell. At the scale of gene regulation, realistic in vivo conditions produce stochastic fluctuations in gene expression that can lead to advantageous bet-hedging strategies, but can be difficult to characterize using a deterministic framework. Even at the organismal scale, germband extension (GBE) in Drosophila melanogaster embryos systematically elongates the epithelial tissue using …

Maize And Soybean Root Front Velocity And Maximum Depth In Iowa, Usa, Raziel A. Ordóñez, Michael J. Castellano, J. L. Hatfield, M. J. Helmers, Mark A. Licht, Matt Liebman, Ranae Dietzel, Rafael Martinez-Feria, Javed Iqbal, Laila A. Puntel, S. Carolina Córdova, Kaitlin Togliatti, Emily E. Wright, Sotirios V. Archontoulis

Department of Agronomy and Horticulture: Faculty Publications

Quantitative measurements of root traits can improve our understanding of how crops respond to soil and weather conditions, but such data are rare. Our objective was to quantify maximum root depth and root front velocity (RFV) for maize (Zea mays) and soybean (Glycine max) crops across a range of growing conditions in the Midwest USA. Two sets of root measurements were taken every 10–15 days: in the crop row (in-row) and between two crop rows (center-row) across six Iowa sites having different management practices such as planting dates and drainage systems, totaling 20 replicated experimental treatments. …

He Scenario Tree Epidemiological Model In Estimation Effects Of B. Melitensis Rev 1 Vaccination On Disease Prevalence, Sabina Seric Haracic, Nihad Fejzic, Ermin Saljic, Dzenita Hadzijunuzovic Alagic, Mo Salman

Turkish Journal of Veterinary & Animal Sciences

minant brucellosis. The stochastic scenario tree model was used to simulate vaccination and surveillance implementation during 8 years. Outputs were annual proportions of true positive, true negative, false positive, and false negative flocks. Vaccination coverage was described by the Pert distribution with average 70% and min and max 50% and 80%, respectively. Effects of risk factors (high prevalence-areas and transhumance) were considered. The model was separately simulated for three levels of initial average flock prevalence (2%, 5%, and 10%). In the following years, flock prevalence arising from the fitted distribution of the false negative flocks from the previous year increased …

Effects Of Diabetes On Ovarian Cancer: Data Analysis And Modeling Study, Claire Belay

Theses and Dissertations

Ovarian cancer has one of the highest mortality rates of all gynecological cancers [13]. Further knowledge of risk factors for the growth of ovarian tumors would be beneficial in both the treatment and prevention of this type of cancer. Previous research has shown a positive correlation between diabetes and prostate tumor growth [22], The first aim of this study was to determine the effect of diabetes of ovarian tumor growth. The second aim was to develop a model to predict ovarian tumor growth based on the microenvironment within a patient’s body. The hypothesis was that there would be a positive …

Population Size And Habitat Association Of Etheostoma Nebra, The Buck Darter, Using Abundance Modeling In The Buck Creek System, Cumberland River Drainage, Kentucky, Harold Davidson Black

Online Theses and Dissertations

Etheostoma nebra (Buck Darter) is a recently described fish species confined to the Buck Creek system, Cumberland River drainage, Kentucky. A 2010-2012 survey of Buck Creek by Kentucky Department of Fish and Wildlife Resources personnel observed E. nebra at 2 of 47 historical sites. Within the entire system, individuals were found only in Flat Lick Creek around the confluence of two spring-fed tributaries, Big Spring Branch and Stewart Branch. The objectives of this study were to: (1) determine population size, demographics, and habitat association of E. nebra in Big Spring Branch and Stewart Branch, (2) evaluate habitat conditions both within …

Effects Of Standardized Ileal Digestible Histidine:Lysine Ratio On Growth Performance Of 15- To 25-Lb Pigs, H. S. Cemin, R. M. Karns, C. M. Vier, M. D. Tokach, S. S. Dritz, K. J. Touchette, J. C. Woodworth, J. M. Derouchey, R. D. Goodband

Kansas Agricultural Experiment Station Research Reports

Two experiments were conducted to determine the standardized ileal digestible (SID) His:Lys requirement of 15- to 25-lb nursery pigs. A total of 360 and 350 pigs (DNA 241 × 600), initially 15.6 and 14.5 lb body weight (BW), were used in Exp. 1 and 2, respectively. There were 5 pigs per pen and 12 and 10 replicates per treatment in Exp. 1 and 2, respectively. After weaning, pigs were fed a common pelleted diet for 10 d in Exp. 1 and 7 d in Exp. 2. Then, pens were assigned to treatments in a randomized complete block design with BW …