Biology Commons^™

Secondary Structure, A Missing Component Of Sequence- Based Minimotif Definitions, David P. Sargeant, Michael R. Gryk, Mark W. Maciejewsk, Vishal Thapar, Vamsi Kundeti, Sanguthevar Rajasekaran, Pedro Romero, Keith Dunker, Shun-Cheng Li, Tomonori Kaneko, Martin Schiller

Life Sciences Faculty Research

Minimotifs are short contiguous segments of proteins that have a known biological function. The hundreds of thousands of minimotifs discovered thus far are an important part of the theoretical understanding of the specificity of protein-protein interactions, posttranslational modifications, and signal transduction that occur in cells. However, a longstanding problem is that the different abstractions of the sequence definitions do not accurately capture the specificity, despite decades of effort by many labs. We present evidence that structure is an essential component of minimotif specificity, yet is not used in minimotif definitions. Our analysis of several known minimotifs as case studies, analysis …

Effect Of Rising Temperature Due To Ozone Depletion On The Dynamics Of A Prey-Predator System: A Mathematical Model, O. P. Misra, Preety Kalra

Applications and Applied Mathematics: An International Journal (AAM)

It is well recognized that the greenhouse gas such as Chlorofluoro Carbon (CFC) is responsible directly or indirectly for the increase in the average global temperature of the Earth. The presence of CFC is responsible for the depletion of ozone concentration in the atmosphere due to which the heat accompanied with the sun rays are less absorbed causing increase in the atmospheric temperature of the Earth. The increase in the temperature level directly or indirectly affects the dynamics of interacting species systems. Therefore, in this paper a mathematical model is proposed and analyzed using stability theory to asses the effects …

Restoration Of Biological Soil Crust On Disturbed Gypsiferous Soils In Lake Mead National Recreation Area, Eastern Mojave Desert, Lindsay P. Chiquoine

UNLV Theses, Dissertations, Professional Papers, and Capstones

Biological soil crusts (BSCs) are sensitive to anthropogenic disturbances. Natural recovery takes many years. Active restoration decreases recovery time. Native BSC inocula, which included lichens and mosses, salvaged from gypsiferous soil habitats in Lake Mead National Recreation Area (LMNRA) in the eastern Mojave Desert were stored dry for two years and applied to disturbed soil after a road reconstruction in LMNRA and also used in laboratory experiments to test inoculation technique effectiveness. After 18 months, field results revealed positive relationships between inoculation and the presence of macroscopic BSC cover, cyanobacteria abundance, soil stability, and ammonium concentrations. Chlorophyll fluorescence monitoring of …

A Time Series Analysis Method Using Hidden Variables For Gene Network Reconstruction, Xi Wu

Dissertations

The DNA microarray technology can be applied to obtain time series data which contains thousands of genes and tens of time points. When confront the great amount of data points a fast and effective method must be constructed to extract useful information. The assumption that the interactions between genes are static in the time series data is made. After made the assumption how to reconstruct those interactions becomes a difficulty problem. Since the underlying interactions between genes are complicated, which involve transcription, translation and protein-protein interaction, to construct a model from physicochemistry is almost impossible/effortless. The popular methods constructed from …

Characterization Of Biofilm Formation By Borrelia Burgdorferi In Vitro, Eva Sapi, Scott L. Bastian, Cedric L. Mpoy, Shernea Scott, Amy Rattelle, Namrata Pabbati, Akhila Poruri, Divya Burugu, Priyanka A. Theophilus, Truc V. Pham, Akshita Datar, Navroop K. Dhaliwal, Alan Macdonald, Michael J. Rossi, Saion K. Sinha, David F. Luecke

Biology and Environmental Science Faculty Publications

Borrelia burgdorferi, the causative agent of Lyme disease, has long been known to be capable of forming aggregates and colonies. It was recently demonstrated that Borrelia burgdorferi aggregate formation dramatically changes the in vitro response to hostile environments by this pathogen. In this study, we investigated the hypothesis that these aggregates are indeed biofilms, structures whose resistance to unfavorable conditions are well documented. We studied Borrelia burgdorferi for several known hallmark features of biofilm, including structural rearrangements in the aggregates, variations in development on various substrate matrices and secretion of a protective extracellular polymeric substance (EPS) matrix using several modes …

Heavy Metal Chemistry Of Sediments In Caves Of The Springfield Plateau, Missouri-Arkansas-Oklahoma: A Link To Subterranean Biodiversity, Travis M. Doughty, Aaron W. Johnson

The Compass: Earth Science Journal of Sigma Gamma Epsilon

We used X-ray fluorescence (XRF) to compare the heavy metal chemistry of sediments in caves in rural and urban areas to the chemistry of sediments from a control cave in a relatively undisturbed watershed in the Springfield (MO) Plateau. Sediment from Smallin Cave near Ozark, MO, the control cave, has the smallest peak sizes for Zn and Mn and a moderately-sized Pb peak. Sediment from the rural cave exhibited larger peaks of Zn and Mn and a smaller Pb peak. Sediment from the urban cave had the largest Zn, Mn and Pb peaks. Interestingly, smaller peak sizes appear to correlate …

Achieving High Accuracy Prediction Of Minimotifs, Tian Mi, Sanguthevar Rajasekaran, Jerlin Camilus Merlin, Michael R. Gryk, Martin Schiller

Life Sciences Faculty Research

The low complexity of minimotif patterns results in a high false-positive prediction rate, hampering protein function prediction. A multi-filter algorithm, trained and tested on a linear regression model, support vector machine model, and neural network model, using a large dataset of verified minimotifs, vastly improves minimotif prediction accuracy while generating few false positives. An optimal threshold for the best accuracy reaches an overall accuracy above 90%, while a stringent threshold for the best specificity generates less than 1% false positives or even no false positives and still produces more than 90% true positives for the linear regression and neural network …

Modeling And Mathematical Analysis Of Plant Models In Ecology, Eric A. Eager

Department of Mathematics: Dissertations, Theses, and Student Research

Population dynamics tries to explain in a simple mechanistic way the variations of the size and structure of biological populations. In this dissertation we use mathematical modeling and analysis to study the various aspects of the dynamics of plant populations and their seed banks.

In Chapter 2 we investigate the impact of structural model uncertainty by considering different nonlinear recruitment functions in an integral projection model for Cirsium canescens. We show that, while having identical equilibrium populations, these two models can elicit drastically different transient dynamics. We then derive a formula for the sensitivity of the equilibrium population to …

Correlation Between Morphological, Optical And Electrical Properties Of Zno:Al/Zno Double Layers And The Cu(In,Ga)Se2 Solar Cell Efficiencies, Pd Nsimama

Tanzania Journal of Science

The morphological, optical and electrical properties of magnetron sputtered ZnO:Al/ZnO double layers are reported and their correlations with their respective Cu(In,Ga)Se2 (CIGS) solar cell efficiencies are presented. The ZnO:Al/ZnO double layers were produced by using the established baseline RF process and plasma emission monitoring (PEM) DC reactive sputtering. The scanning electron microscope (SEM) and atomic force microscope (AFM) were employed for the surface morphological measurements. The charge carrier concentrations, mobilities and AC resistivities were deduced from Drude’s model. The DC resistivities were determined from the four-point probe measurements. Transmittance and reflectance measurements were done by using the UV-VIS-NIR Lambda 900 …

A Study Of The Eastern Oyster, Crassostrea Virginica, In Tampa Bay: Effects Of Perkinsus Marinus On Reproduction And Condition, Bridgit Melora Mccrickard

USF Tampa Graduate Theses and Dissertations

Abstract

Five sites in Tampa Bay, Florida, were sampled monthly from February 2006 to January 2007. These sites were located at the mouth of the Alafia River, in an inlet of Cross Bayou, on the easement of Gandy Bridge, near mangrove in Manatee County, and an inlet of Salt Creek, off Bayboro Harbor. Standard methods were used to determine shell height and Condition Index (CI). Intensity and prevalence of Perkinsus marinus were analyzed using Ray's Thioglycollate medium test, while Haplosporidium nelsoni was studied by histological examination. Histological methods were also used to determine sex ratios, reproductive phases, and egg diameters. …

Transcendental Thermodynamics, Richard E. Morel, George Fleck

Kahn Institute Projects

Thermodynamics is often viewed as a narrow, introspective discipline, trapped by its origins in the 18th and 19th centuries. By dramatic contrast, we show that the Fourth Law of Thermodynamics provides explanations and interpretations of all natural events, extending across artificial boundaries of tradition- al academic disciplines. The Fourth Law of Thermodynamics states that far-from-equilibrium systems increase entropy at the maximum rate available to them. This broadly inclusive paradigm applies to systems from molecules, to organisms, to the biosphere. The Fourth Law is the Law of Evolution. All systems that communicate with their environment exhibit self-organization and self-optimization, enabling the …

Modeling The Effect Of Environmental Factors On The Spread Of Bacterial Disease In An Economically Structured Population, Ram Naresh, Surabhi Pandey

Applications and Applied Mathematics: An International Journal (AAM)

We have proposed and analyzed a nonlinear mathematical model for the spread of bacterial disease in an economically structured population (rich and poor) including the role of vaccination. It is assumed that rich susceptible get infected through direct contact with infectives in the same class and with infectives from the poor class who work as service providers in the houses of rich people, living in much cleaner environment. The susceptible in the poor class are assumed to become infected through direct contact with infectives in the same class as well as by bacteria present in their own environment, degraded due …

A Mathematical Study On The Dynamics Of An Eco-Epidemiological Model In The Presence Of Delay, T. K. Kar, Prasanta K. Mondal

Applications and Applied Mathematics: An International Journal (AAM)

In the present work a mathematical model of the prey-predator system with disease in the prey is proposed. The basic model is then modified by the introduction of time delay. The stability of the boundary and endemic equilibria are discussed. The stability and bifurcation analysis of the resulting delay differential equation model is studied and ranges of the delay inducing stability as well as the instability for the system are found. Using the normal form theory and center manifold argument, we derive the methodical formulae for determining the bifurcation direction and the stability of the bifurcating periodic solution. Some numerical …

Will Extreme Climatic Events Facilitate Biological Invasions?, Jeffrey M. Diez, Carla M. D'Antonio, Jeffrey S. Dukes, Edwin D. Grosholz, Julian D. Olden, Cascade J.B. Sorte, Dana M. Blumenthal, Bethany A. Bradley, Regan I. Early, Inés Ibáñez, Sierra J. Jones, Joshua J. Lawler, Luke P. Miller

Faculty Publications, Biological Sciences

Extreme climatic events (ECEs) – such as unusual heat waves, hurricanes, floods, and droughts – can dramatically affect ecological and evolutionary processes, and these events are projected to become more frequent and more intense with ongoing climate change. However, the implications of ECEs for biological invasions remain poorly understood. Using concepts and empirical evidence from invasion ecology, we identify mechanisms by which ECEs may influence the invasion process, from initial introduction through establishment and spread. We summarize how ECEs can enhance invasions by promoting the transport of propagules into new regions, by decreasing the resistance of native communities to establishment, …

The Importance Of Isolated Wetlands As Habitat For Rare And Endangered Species In Comparison To Riparian Wetlands, Hillary K. Ballantine

Honors Theses

In this paper, I will review the literature on the factors contributing to the presence of rare or endangered species, the species found in each wetland type and what threatens them, and the views on how to and why we should conserve these habitats. I will also provide data analyses on the importance of isolated wetlands as habitats for rare and endangered species in comparison to riparian wetlands, and present my own views on the topic.

Aggressive Acoustic Behavior In Yasuhikotakia Modesta: Does The Lombard Effect Hold Water?, Bethany Coffey

Mahurin Honors College Capstone Experience/Thesis Projects

The Lombard effect is the automatic and involuntary change in the intensity of vocalizations in the presence of background noise in order to maintain a constant signal to noise ratio. While this phenomenon is commonly found in vocalizing terrestrial vertebrates, it had not previously been examined in aquatic vertebrates such as fishes. This experiment tests the presence of the Lombard effect in the red-finned loach, Yasuhikotakia modesta, which make two types of sounds: butting and clicking. I recorded three pairs of Y. modesta during aggressive interactions over territory and compared the sounds produced in silence with sounds produced …

Oxaliplatin And Oxaliplatin Derivatives: Synthesis, Characterization, And Reactivity With Biologically Relevant Ligands, Amy Poynter

Mahurin Honors College Capstone Experience/Thesis Projects

Oxaliplatin is a third generation anticancer drug that has proven to be successful in fighting ovarian and testicular cancer. We are interested in determining how oxaliplatin and oxaliplatin derivatives interact with proteins, as well as how that interaction is affected by the size and shape of these platinum compounds. We have synthesized oxaliplatin as it is used in cancer treatment, as well as similar platinum compounds with the same diaminocyclohexane ligand as oxaliplatin but with additional bulk added to the nitrogen atoms. We are reacting oxaliplatin with key amino acids, including methionine, and will be comparing the kinetics of this …

Challenging Disciplinary Boundaries In The First Year: A New Introductory Integrated Science Course For Stem Majors, Lisa Gentile, Lester Caudill, Mirela Fetea, April L. Hill, Kathy Hoke, Barry Lawson, Ovidiu Z. Lipan, Michael Kerckhove, Carol A. Parish, Krista J. Stenger, Doug Szajda

Biology Faculty Publications

To help undergraduates make connections among disciplines so they are able to approach, evaluate, and contribute to the solutions of important global problems, our campus has been focused on interdisciplinary research and education opportunities across the science, technology, engineering, and mathematics (STEM) disciplines. This paper describes the mobilization, planning, and implementation of a first-year interdisciplinary course for STEM majors that integrates key concepts found in traditional first-semester biology, chemistry, computer science, mathematics, and physics courses. This team-taught course, Integrated Quantitative Science (IQS), is half of a first-year student’s schedule in both semesters and is composed of a double lecture and …

Investigation Of Autoregulation Of Icer And Electrochemical Properties Of Tryptophan, Mark Demilio

Theses, Dissertations and Culminating Projects

A relatively new development in the field of research-based chemistry is to study biomolecules, their interactions, and a biochemical mechanisms by examination of their physical properties and application of laboratory techniques rooted in concepts of physical chemistry. Both projects that are encompassed within this master's thesis indeed fall under the umbrella of biophysical chemistry, as they apply physical chemical techniques study particular biomolecular interactions.

The first of these two projects is the study of a leucine zipper protein, Inducible cAMP Early Repressor [ICER], which is a product of the cAMP Responsive Element Modulator [CREM] gene. ICER functions as a transcriptional …

Challenging Disciplinary Boundaries In The First Year: A New Introductory Integrated Science Course For Stem Majors, Lisa Gentile, Lester Caudill, Mirela Fetea, April L. Hill, Kathy Hoke, Barry Lawson, Ovidiu Z. Lipan, Michael Kerckhove, Carol A. Parish, Krista J. Stenger, Doug Szajda

Department of Math & Statistics Faculty Publications

To help undergraduates make connections among disciplines so they are able to approach, evaluate, and contribute to the solutions of important global problems, our campus has been focused on interdisciplinary research and education opportunities across the science, technology, engineering, and mathematics (STEM) disciplines. This paper describes the mobilization, planning, and implementation of a first-year interdisciplinary course for STEM majors that integrates key concepts found in traditional first-semester biology, chemistry, computer science, mathematics, and physics courses. This team-taught course, Integrated Quantitative Science (IQS), is half of a first-year student’s schedule in both semesters and is composed of a double lecture and …

Biomass Assisted Synthesis Of Antibacterial Gold Nanoparticles And Commentary On Its Future Potential And Applications In Medicine, Chad Willis

Mahurin Honors College Capstone Experience/Thesis Projects

Xylose is a natural monosaccharide found in biomass such as straw, pecan shells, cottonseed hulls, and corncobs. Using this monosaccharide, we report the green synthesis and characterization of biocompatible, biodegradable xylose encapsulated gold nanoparticles (Xyl-GNPs) with potential antibacterial activity. GNPs were synthesized using the bioreduction property of xylose on the chloroaurate anions in an aqueous solution at room temperature and at atmospheric pressure. The characterization of synthesized GNPs was examined by UV-vis spectroscopy; transmission electron microscopy (TEM), energy-dispersive x-ray spectroscopy (EDS) and fourier transform infrared spectroscopy (FTIR). Results indicate that the particles were stable; near spherical in shape with an …

Terrestrial Vertebrate Families On Noah's Ark, Seth J. Beech

Senior Honors Theses

One of the central challenges faced by young-Earth creation researchers who believe the Bible to be the inerrant Word of God is defending the Biblical claim that two of every kind of nephesh animal was saved from the great flood on Noah’s ark. Recently, Answers in Genesis became involved in the design and construction of a full-sized, authentic replica of Noah’s ark. They have endeavored to be as accurate as possible in presenting the number of kinds that would have needed to be on the ark in order to have the diversity in species that we observe today. In order …

The Influence Of Aliphatic Side Chain Of Anacardic Acid On Molecular Recognition Properties Of Imprinted Polymers, Jyn Philip, J Buchweishaija, Ll Mkayula, L Ye

Tanzania Journal of Science

The objective of this work was to determine the influence of the aliphatic side chain of anacardic acid on molecular recognition properties of imprinted polymers made from anacardanyl methacrylate (AnMcr). Salicylic methacrylate (SaMcr), a structural analog of AnMcr, was synthesized and used as a functional monomer to prepare imprinted polymers for comparison with AnMcr-based polymers. Using divinylbenzene (DVB) as a cross linker and racemic propranolol as a model template, irregular monolithic particles of poly(SaMcr-co-DVB)m were synthesized in toluene, and spherical beads of poly(SaMcr-co-DVB)b and poly(AnMcr-co-DVB)b weresynthesized in acetonitrile by precipitation polymerization. Although imprinted irregular monolithic particles, poly(SaMcr-co-DVB)m, tested in toluene …

Tracing The Transport Of Colored Dissolved Organic Matter In Water Masses Of The Southern Beaufort Sea: Relationship With Hydrographic Characteristics, A. Matsuoka, A. Bricaud, Ronald Benner, J. Para, R. Sempéré, L. Prieur, S. Bélanger, M. Babin

Faculty Publications

Light absorption by colored dissolved organic matter (CDOM) [aCDOM(λ)] plays an important role in the heat budget of the Arctic Ocean, contributing to the recent decline in sea ice, as well as in biogeochemical processes. We investigated aCDOM(λ) in the Southern Beaufort Sea where a significant amount of CDOM is delivered by the Mackenzie River. In the surface layer, aCDOM(440) showed a strong and negative correlation with salinity, indicating strong river influence and conservative transport in the river plume. Below the mixed layer, a weak but positive correlation between aCDOM(440) and salinity was observed above the upper halocline, resulting from …

Research, Monitoring, Assessment And Development Plan 2011 – 2012, Department Of Fisheries

Fisheries Occasional Publications

No abstract provided.

Phenotypic Characterization And 16s Rdna Identification Of Culturable Non-Obligate Halophilic Bacterial Communities From A Hypersaline Lake, La Sal Del Rey, In Extreme South Texas (Usa), Kristen Phillips, Frederic Zaidan, Omar R. Elizondo, Kristine L. Lowe

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

Background

La Sal del Rey ("the King's Salt") is one of several naturally-occurring salt lakes in Hidalgo County, Texas and is part of the Lower Rio Grande Valley National Wildlife Refuge. The research objective was to isolate and characterize halophilic microorganisms from La Sal del Rey. Water samples were collected from the lake and a small creek that feeds into the lake. Soil samples were collected from land adjacent to the water sample locations. Sample salinity was determined using a refractometer. Samples were diluted and cultured on a synthetic saline medium to grow halophilic bacteria. The density of halophiles was …

Two New Species Of Trigonotylus (Hemiptera: Heteroptera: Miridae: Stenodemini) From Western Canada And Northwestern United States, G G.E. Scudder, Michael D. Schwartz

Green Canyon Environmental Research Area, Logan Utah

No abstract provided.

Chemical And Isotopic Evaluation Of Sulfur Sources And Cycling In The Pecos River, New Mexico, Usa, Fasong Yuan, Bernhard Mayer

Biological, Geological, and Environmental Faculty Publications

The use of stable isotopes in studies of watershed biogeochemical processes has increased greatly throughout the last several decades. Much of the sulfur cycling research has addressed the influence of changes in atmospheric acid deposition on sulfur dynamics in temperate ecosystems. Little is known about sulfur cycling in dryland ecosystems such as those in the American Southwest. To identify the sources and assess the cycling of sulfur in dryland ecosystems, chemical and isotopic compositions of water were measured on samples collected from the Pecos River (New Mexico, USA) during a reconnaissance survey in spring 2010. Based on the chemical and …

A Natural Language Interface Plug-In For Cooperative Query Answering In Biological Databases, Hasan M. Jamil

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

One of the many unique features of biological databases is that the mere existence of a ground data item is not always a precondition for a query response. It may be argued that from a biologist's standpoint, queries are not always best posed using a structured language. By this we mean that approximate and flexible responses to natural language like queries are well suited for this domain. This is partly due to biologists' tendency to seek simpler interfaces and partly due to the fact that questions in biology involve high level concepts that are open to interpretations computed …

The Role Of Fine-Scale Habitat Associations In Structuring Spider Assemblages: Determinants Of Spatial Patterns In Community Compostion, Stephanie M. Cobbold

Green Canyon Environmental Research Area, Logan Utah

No abstract provided.