Biology Commons^™

Novel Bioinformatic Approaches For Analyzing Next-Generation Sequencing Data, Yan Peng

Dissertations

In general, DNA reconstruction is deemed as the key of molecular biology since it makes people realize how genotype affects phenotypes. The DNA sequencing technology emerged exactly towards this and has greatly promoted molecular biology’s development. The traditional method, "Sanger," is effective but extremely expensive on a cost-per-base basis. This shortcoming of Sanger method leads to the rapid development of next-generation sequencing technologies. The NGS technologies are widely used by virtue of their low-cost, high-throughput, and fast nature. However, they still face major drawbacks such as huge amounts of data as well as relatively short read length compared with traditional …

Comparative Phylogeography And Demographic Histories Of West Indian Birds, Maria Wilhelmina Barbosa De Oliveira Pil

Dissertations

My dissertation investigates the demographic history of multiple island populations of several Caribbean bird species through an assessment of contemporary genetic diversity, while inferring relationships between the comparative demography of individual island populations and characteristics of the islands and species. The sizes and distributions of populations vary over time, and episodes of expansion and contraction create characteristic patterns of genetic variation within and among populations. Consequently, contemporary patterns of genetic diversity open a window onto demographic and phylogeographic history. The strength of the study lies in the scale and comprehensiveness of the analysis, encompassing most of the West Indian islands …

Development Of A Therapeutic Model Of Early Liver Cancer Using Crocin-Coated Magnetite Nanoparticles, Rkia El-Kharrag

Dissertations

Hepatocellular carcinoma is one of the most common health problems that is difficult to treat. As a result of the side effects frequently experienced with conventional cancer treatments, there has been a growing interest to develop controlled drug delivery system that can reduce the mortality rate of liver cancer patients and un-harm healthy tissues. Magnetite nanoparticles are potentially important in hepatocellular carcinoma treatment, since they can be used as delivery system. Pure and coated magnetite nanoparticles were synthesized via modified co-precipitation method in air at low temperature. Various reaction parameters and coating materials have been investigated and characterized. Among these …

E Pluribus Unum: What Individual Whales Can Tell Us About Enigmatic Species Distribution And Social Organization, Tanya Marie Lubansky

Dissertations

Large whales have historically been difficult to study and many aspects of their ecology remain unknown especially at the long -term population level. The ability to identify individual whales based on natural markings provides the opportunity to track individuals over time and space; this data may offer more insight into the ecology of whales than previously imagined. This study demonstrates use of photo-identification data to model both social structure and habitat selection, minimizing the need for invasive research and greatly increasing the sample size used in such endeavors. A conditional logistic model is written for a 20-year sightings dataset on …

Galapagos Seabirds' Lice Community: Host Hetero-Specific Interactions And Parasite Evolution, Jose Luis Rivera

Dissertations

My dissertation focused on understanding the factors behind host-parasite specificity and parasite diversification, using Galapagos seabirds and their ectoparasites as the study system. This system comprised the seabird hosts (magnificent and great frigatebirds, Nazca, blue-footed and red-footed boobies) and nine species of ectoparasitic lice (one Pectinopygus ischnoceran louse species infecting each host, two species of Colpocephalum amblyceran lice, one on each frigatebird species, and two shared amblyceran lice, Eidmanniella albescens found on Nazca and blue-footed boobies and Fregatiella aurifasciata found on the two frigatebirds). Using as focal species Eidmanniella albescens and Fregatiella aurifasciata, which infect multiple hosts, I analyzed how …

Evolution And Ecology Of Two Iconic Australian Clades: The Meliphagidae (Birds) And The Hakeinae (Plants), Eliot Trimarchi Miller

Dissertations

The first part of this dissertation explores the evolution of two iconic groups of species through Australian climate space: the Meliphagidae, or honeyeaters, which are primarily nectar-feeding birds, and the Hakeinae, a section of the plant family Proteaceae. Both groups are inferred to have had their origins in Gondwanan rainforests that were widespread across Australia 45 million years ago and then diversified into more arid environments as the continent’s climate became more arid. Accordingly, dry environments are inhabited by closely related (phylogenetically clustered) sets of species, although, in contrast to the honeyeaters, Hakeinae communities are characterized by more localized diversification. …

Amyloid Precursor Protein (App) Regulates G0/G1 Transition And Cell Growth, Anna Sobol

Dissertations

Non-small cell lung cancer (NSCLC) originates in the epithelia of the lung and persists as the leading cause of cancer-related death in the United States. Many studies have shown that hypoxia is prevalent in NSCLC tissue and negatively influences treatment outcome.

In previous studies, we investigated the efficacy of gamma-secretase inhibitor (GSI) treatment in an orthotopic mouse NSCLC model. Analysis of hypoxic areas of tumors from GSI treated animals showed reappearance of 4E-BP1 phosphorylation at threonine 37/46 residues (T37/46). 4E-BP1 phosphorylation is primarily mediated by mechanistic target of rapamycin complex 1 (mTORC-1), a major cell integrator of growth factors stimulation, …

The Expression Pattern Of Death Associated Protein Kinase1 In Normal Dorsal Root Ganglion Neurons And Following Peripheral Nerve Injury, Maryam Sulaiman Mohammed Al Saadi

Dissertations

Death-associated protein kinase1 (DAPK1) is a calcium/calmodulin (Ca2+/CaM) regulated serine/threonine kinase. An increasing body of evidence supports the significance of DAPK1 protein in cancer and CNS diseases. The role of DAPK in peripheral nerve regeneration and neuropathic pain remains completely unexplored. The aim of this study is to investigate the expression pattern of DAPK1 along with key proand anti-apoptotic cell signaling molecules (p53, Bax, Akt, ERK5, p38) and to verify the possibilities of DAPK1-NMDA NR2B relationship in dorsal root ganglion neurons (DRG) after 2 hours, 7 days and 14 days following a sciatic nerve injury. Gene expression analysis and immunohistochemistry …

Mechanisms Of Condition-Specific Regulation Of Mrna Stability By Puf Proteins: From Yeast To Humans, Joseph Russo

Dissertations

RNA binding proteins regulate mRNA decay and translation, two key steps in the control of gene expression in cells. Controlling mRNA metabolism allows cells to respond rapidly to altering conditions by utilizing already available mRNA, bypassing the wait for newly transcribed mRNA. The Puf family of RNA binding proteins bind specific mRNAs through interactions with sequences located in the 3’ untranslated region (UTR). Puf proteins are conserved throughout eukaryotes and have diverse roles including stem cell maintenance, neuronal development, stress response and organelle biogenesis. In Saccharomyces cerevisiae, Puf proteins are conditionally regulated in response to the cells metabolic. Specifically, in …

Clarification Of The Systematics Of The Haploporoidea (Trematoda) With Descriptions Of New Genera And Species, Michael Jay Andres

Dissertations

The superfamily Haploporoidea Nicoll, 1914 comprises two families, the Atractotrematidae Yamaguti, 1939 and the Haploporidae Nicoll, 1914, and the subfamily Cadenatellinae Gibson et Bray, 1982. All members are parasites of the alimentary tract or gall bladder of marine, estuarine, and freshwater herbivorous fishes. Overstreet and Curran (2005a) provided a review of the Haploporidae and recognized four subfamilies, the Chalcinotrematinae Overstreet et Curran, 2005, Haploporinae Nicoll, 1914, Megasoleninae Manter, 1935, and Waretrematinae Srivastava, 1937. In a series of five publications, Blasco-Costa et al. (2009a-e) revised the Haploporinae and erected a fifth subfamily, the Forticulcitinae Blasco-Costa, Balbuena, Kostadinova, et Olson, 2009. The …

Online Versus Face-To-Face Biology: A Comparison Of Student Transactional Distance, Approach To Learning, And Knowledge Outcomes, Mary Erin Riggins

Dissertations

Community colleges are among many other institutions increasing course offerings online, but there is still some concern about the quality of online learning. Educator concerns, a lack of empirical evidence on biology courses offered online, and the need for an equal opportunity for education support the need for clarification of the quality of distance education in biology, especially in the community college setting. Student attitudes, approaches to learning, and performance should all be studied in order to formulate a better evaluation of the quality and effectiveness of online courses (Svirko & Mellanby, 2008).

The purpose of this study was to …

Fungal Contribution To Carbon And Nutrient Cycling In A Subtropical Freshwater Marsh, Rong Su

Dissertations

Despite the well-known occurrence of emergent standing litter in freshwater marshes, very little quantitative data is available concerning the functional role and contribution of fungal decomposers to litter decomposition or their impact on ecosystem scale carbon and nutrient cycling. In the present study, microbial respiration and seasonal biomass and production rates of fungal decomposers associated with standing plant litter were examined to assess the quantitative contribution of fungi to both fine scale litter decay processes and large-scale ecosystem carbon flow pathways in a subtropical Typha domingensis and mixed Cladium jamaicense/Juncus roemarianus freshwater marsh, respectively. In addition, the growth …

Elucidation Of The Role Of Auxin-Input Pathways In Auxin Homeostasis., Gretchen Spiess

Dissertations

Auxin is a phytohormone involved in cell elongation and division. Levels of indole-3-acetic acid (IAA), the most abundant auxin, are tightly regulated through biosynthesis, degradation, sequestration, and transport. Sequestration of IAA occurs in reversible processes by adding amino acids, polyol or simple alcohols, or sugars, forming IAA conjugates, or via a two-carbon elongation forming indole-3-butyric acid (IBA). These forms of auxin have decreased activity and are located in multiple organelles. Using a combination of molecular and genetic tools, I examined how these storage forms are working together to contribute to overall IAA levels and IAA response in both the model …

Community Organization Of Avian Malaria Parasites In Lowland Amazonia: Prevalence, Diversity, And Specialization In A Local Assemblage, Linda Maria Elenor Svensson

Dissertations

I characterized a lowland Amazonian assemblage of haemosporidian (“malaria”) parasites (Haemoproteus and Plasmodium) of understory birds by analyzing variation in prevalence (proportion of infected host individuals) among years and host species, documenting diversity of haemosporidian evolutionary lineages, and quantifying host specialization. Using standard molecular methods to screen for haemosporidia in 2488 individual birds from 104 species in the Tiputini Biodiversity Station, Ecuador, I found 21.7% to be infected. Prevalence ranged significantly among years and host species. Forty-five putative evolutionary lineages of haemosporidia were identified, by sequencing part of the cytochrome b (cyt b) gene. Based on a comparative analysis, among …

Relative Roles Of Host Exposure And Parasite Establishment In Producing Patterns Of Infection Using Eptesicus Fuscus (Chiroptera: Vespertilionidae) And Its Helminths As A Model System, Elizabeth Warburton

Dissertations

Parasite abundance and community structure could vary depending on conditions that are both extrinsic and intrinsic to the host. Variation in parasite burden, resulting from heterogeneous exposure to parasites or heterogeneous establishment of parasites in the host, often drives transmission dynamics. Changes in parasite community structure influence parasite species diversity and thus, diversity of infection within a single host or entire host population. I sought to quantify relative roles of exposure and establishment in producing patterns of infection using bats, Eptesicus fuscus, and their helminths. I utilized subsets of data from bats captured in 16 colonies from three states …

Population Genetics And Microbial Communities Of The Gopher Tortoise (Gopherus Polyphemus), Daniel Lyle Gaillard

Dissertations

The gopher tortoise, Gopherus polyphemus, is an endangered species living in the southeastern United States. The recent and drastic decline in tortoise numbers has resulted in a multi-faceted approach to conserve this species. I used a population genetic approach to determine the population structure, genetic diversity and barriers to gene flow at a broad, regional and local scale. Tortoises are divided into five distinct genetic populations at the broad scale, the central populations have the highest levels of genetic diversity and the Tombigbee, Mobile, Apalachicola, Suwannee and St. John’s Rivers appear to be barriers to gene flow. At the regional …

The Delivery, Speciation, And Fate Of Trace Elements In St. Louis Bay, Mississippi, Gopal Bera

Dissertations

Estuaries are dynamic regions in which there can be significant modification of the riverine flux of trace elements to the open ocean due to various geochemical, physical, and biological processes. Additionally, estuaries are often subject to anthropogenic inputs of trace elements. The first portion of this study investigated the source, behavior, and sediment interaction of anthropogenic stable cesium (Cs) in St. Louis Bay (SLB), MS. A consistent increase in stable Cs concentration was noticed in sediment cores starting from a period when a titanium dioxide refinery on SLB started operations. Weak correlation between Cs and clay percentage and strong correlations …

Identification Of Novel Natural Compounds With Anti-Breast Cancer Activities, Yusra Saif Al Dhaheri

Dissertations

Breast cancer continues to be the leading cause of cancer-related death in women worldwide. In this dissertation, natural compounds with anti-breast cancer activities were identified. We investigated the effect of Salinomycin, a potassium ionophore isolated from Streptomyces albus, on the survival of three human breast cancer cell lines MCF-7, T47D and MDA-MB-231. High concentrations of Salinomycin induced a G2 arrest, down regulation of survivin and triggered apoptosis. Interestingly, treatments with low concentrations of Salinomycin induced a transient G1 arrest at an earlier time and G2 arrest and senescence, associated with enlarged cell morphology, at a later time. There was also …

Assessing The Fishery And Ecology Of Sharks In The United Arab Emirates, Rima W. Jabado

Dissertations

Large scale shark population declines have been documented worldwide due to overexploitation and the lack of adequate management frameworks to conserve shark stocks. This study aimed at gaining an understanding of the national shark fishery and the trade in shark products from the United Arab Emirates (UAE). Data were collected from June 2010 to October 2012 through interviews with local fishermen, market and landing site surveys, fishery independent surveys, and stomach content analysis. Interviews with local fishermen (n=126) provided information on the fishery characteristics and established that sharks were increasingly targeted due to their high value in the global fin …

Phospholipase D- And Phosphatidic Acid-Mediated Signaling In Plant Response To Abscisic Acid And Reactive Oxygen Species, Liang Guo

Dissertations

The Arabidopsis genome has 12 phospholipase D (PLD) genes that are classified into six types, PLDα, PLDβ, PLDγ, PLDδ, PLDε, and PLDζ, based on sequence similarities, domain structures, and biochemical properties. Phosphatidic acids (PA) produced by PLDs have been identified as important lipid signaling molecules in cell growth, development, and stress responses. This study was undertaken to determine the role of PLD and PA in plant response to abscisic acid (ABA) and reactive oxygen species (ROS). The lipid mediator PA was found to interact with sphingosine kinases (SPHKs) in Arabidopsis. Two unique SPHK cDNAs were cloned and expressed. Both SPHKs …

The Evolution Of Floral Symmetry Across The Plant Order Lamiales, Jinshun Zhong

Dissertations

Bilaterally symmetrical corollas have evolved independently numerous times from radially symmetrical ancestors and are thought to represent adaptation to specific pollinators. However, evolutionary losses of bilateral symmetry have occurred sporadically in different lineages. CYC2-like and RAD-like are genes needed for the normal development of bilateral symmetry in snapdragon corollas. However, exactly how changes in the floral symmetry patterning genes correlate with the origin and loss of floral bilateral remains poorly known. To address this question, a densely sampled phylogeny of CYC2-like genes across the order Lamiales was inferred and calibrated. The expression patterns of these genes in early diverging and …

Elucidating The Factors That Modulate The Distribution Of Avian Haemosporida Parasites Across A Community Of Hosts, Matthew Christopher Ikaika Medeiros

Dissertations

Parasites are heterogeneously distributed across host species, host populations, and host individuals within populations. A primary aim of infectious disease ecology seeks to uncover the factors that drive this heterogeneity. At a fundamental level, host infection is determined by exposure and susceptibility to a pathogen. My dissertation explores how evolutionary and ecological forces associated with these fundamental determinates of infection shape variation in parasite host breadth and host infection status. Here, I focus on a community of vector-borne avian Haemosporida parasites among suburban birds of Chicago, IL. These parasites exhibit strong variation in their distribution among available hosts, and provide …

Exploring The Local And Regional Effects Of Plant Diversity On Plant Herbivore Interactions, Diego Salazar

Dissertations

The study of biological diversity and its effects on ecosystem functioning and species interactions has always been a fundamental part of biology. The accelerating loss of species in conjunction with an increasing change in the natural environment has underlined the importance of the role that biodiversity has on the evolutionary and ecological dynamics of natural systems. In this dissertation I explore the effect of local and regional patterns of plant diversity in plant-herbivore interactions. Furthermore, this work goes beyond the classical concepts of taxonomical diversity and investigates the role of phylogenetic and chemical diversity on plant-herbivore interactions. In chapter one …

Connecting The Dots: Understanding Migration In The Context Of Other Periods Of The Annual Cycle, Kristina Lee Paxton

Dissertations

Migration is a fundamental characteristic of the life history of many organisms. Large-scale seasonal movements expose migratory species to an array of differing environmental conditions such that the ecology, behavior, and life history strategies of migratory species must balance selection pressures associated with each phase of the annual cycle. Therefore, scientists increasingly realize that to understand the ecology of a migratory species in any one phase of the annual cycle requires an understanding of how other phases may interact with and influence the period of interest. That said, following individuals throughout the year poses a serious challenge.

The focus of …

Middle Mississippi River Islands: Historical Distribution, Restoration Planning, And Biological Importance, Teresa Cecilia Allen

Dissertations

The Middle Mississippi River’s (MMR’s) hydrology and sedimentation patterns have been altered. These activities contribute to loss of backwaters, islands, secondary channels, and reduced biodiversity. The Fish and Wildlife Service included reasonable and prudent alternatives (RPAs) in its Biological Opinion for the Operation and Maintenance of the Nine-Foot Channel Navigation Project. These RPAs mandate dike notching and island building to increase habitat diversity. My first goal was to examine changes in the number and relative location of islands from 1797 to 2003. I found that the total number of islands increased, the number of central islands decreased, and the number …

Colonization History And Origin Of The Galapagos Flycatcher (Myiarchus Magnirostris) And Its Parasites, Eloisa Helena Reis Sari

Dissertations

The Galápagos flycatcher (Myiarchus magnirostris) is an endemic species to the Galápagos Islands, Ecuador, and is among the least studied Galápagos terrestrial birds. In this work I unveiled the origin and colonization history of the Galápagos flycatcher, and also the origin of the parasites that are currently found in/on this bird species. To determine the origin of the Galápagos flycatcher, I rebuilt the phylogeny of the Myiarchus genus using cytb and ND2, and applied a Bayesian approach to estimate its colonization time. I discovered that the closest living relative of the Galápagos flycatcher is Myiarchus tyrannulus (Brown-crested flycatcher) …

Population Demographics And Genetics Of Spix's Disk-Winged Bat: Insights Regarding Survival, Mate Choice, Gene Flow And Effective Population Size, Michael Buchalski

Dissertations

Simultaneous study of the demographics and genetics of populations are relatively rare within the literature, despite insights their combined use offers regarding the life history, ecology, and evolution of species. Here I take a comprehensive approach, using capture-recapture data, polymorphic microsatellite markers, and various modeling techniques to examine the demographics and genetics of multiple local populations of Spix’s disk-winged bat (Thyroptera tricolor) in southwestern Costa Rica. T. tricolor is a highly gregarious, neotropical bat species known to form kin-based social groups with high retention of offspring of both sexes. The implications of this highly unusual social structure for …

Role Of Msa In Immune Evasion, Persistence, And Protease Regulation In The Human Pathogenic Strains Of Staphylococcus Aureus, Maria Deepa Basco

Dissertations

Opportunistic pathogens like Staphylococcus aureus on entering the host can stay colonized at the foci of infection or evade the immune system to disseminate to other sites. In this study we investigated the regulatory influence of the modulator of sarA (msa) on immune evasion and host persistence, employing the hospital-acquired strain S. aureus UAMS-1 and community-acquired strain S. aureus USA300 LAC. In the murine sepsis model, mutation of the msa gene in LAC showed no change in dissemination of infection; however, in UAMS-1 a decrease in microbial load was observed in the lungs. Differential regulation by the msa gene was …

Science Fair: Is It Worth The Work? A Qualitative Study On Deaf Students' Perceptions And Experiences Regarding Science Fair In Primary And Secondary School, Vivian Lee Smith

Dissertations

Science fairs have a long history in American education. They play an important role for establishing inquiry-based experiences in a science classroom. Students may be more motivated to learn science content when they are allowed to choose their own science fair topics. The purpose of this study was to examine Deaf college students’ perceptions and experiences regarding science fair participation during primary and/or secondary school and determine the influence of science fair involvement on the development of language skills, writing skills, and higher order thinking skills as well as its impact on choice of a STEM major.

This study examined …

Discovery And Characterization Of A Tanapoxvirus Encoded Human Neuregulin Mimetic, David Jeng

Dissertations

Studies on large dsDNA viruses such as poxviruses have been helpful in identifying a number of viral and cellular growth factors that contribute to our broad understanding of virus-host interaction. Orthopoxviruses and leporipoxviruses are among the most studied viruses in this aspect. However, tanapoxvirus (TPV) a member of the genus Yatapoxvirus, still remains largely unexplored, as the only known hosts for this virus are humans and monkeys. Here, we describe the initial characterization of an EGF-like growth factor mimicking human neuregulin from TPV, expressed by the TPV-15L gene. Assays using a baculovirus expressed and tagged TPV-15L protein demonstrated the ability …