Life Sciences Commons^™

Phylogeny, Taxonomy And Morphological Evolution In Conostegia (Melastomataceae: Miconieae), Ricardo Kriebel

Dissertations, Theses, and Capstone Projects

The genus Conostegia comprises 77 species of shrubs and trees ranging from Central America to northern South America and the Caribbean. They are ecologically important as they provide pollen for native bees and fruits for birds. One of the main questions of this study is if the genus Conostegia is actually monophyletic. I address this question for the first time by gathering genetic data from four chloroplast regions and two nuclear ribosomal regions of DNA. Phylogenetic analyses of these data revealed that Conostegia is not monophyletic and that a group of species in the genera Clidemia and Miconia fall within …

An Ethnobotanical, Ecological And Lc-Ms-Based Chemometric Investigation Of Phaleria Nisidai, A Traditional Adaptogen Containing Diterpene Esters From Palau, Micronesia, Daniel Kulakowski

Dissertations, Theses, and Capstone Projects

An ethnobotanical, ecological and LC-MS-based chemometric investigation of Phaleria nisidai, a traditional adaptogen containing diterpene esters from Palau, Micronesia

Palau is a country with a rich heritage of traditional medicine still being practiced. One of the most popular and respected remedies in Palau is a tea made from fresh leaves of Phaleria nisidai Kaneh. (Thymelaeaceae). Interviews conducted to determine the use of this plant revealed that it is employed non-specifically to treat a variety of general health concerns. Its use as a prophylactic to keep away sickness, as a 'system cleaner', as well as for strength and energy indicate …

The Interplay Of Visual Attention And Saccade Planning In Active Vision, Afsheen Khan

Dissertations, Theses, and Capstone Projects

Vision is a highly active process. When we view the world, we do not hold our eyes still, but constantly move them around in order to view the object or area of interest with the fovea (the region of the retina with the highest acuity). Saccades are the step-like movements that we most often employ for this purpose. In addition, our attention is constantly being covertly attracted or directed to points of interest. Combining these different aspects of viewing: visual processing, the orienting of attention, and eye movements can be referred to as `active vision'.

Most work on active vision …

Vegf Treatment During Status Epilepticus Alters Long-Term Hippocampal Astrocyte Morphology: A Detailed Description Of Astrocyte Morphology And Glutamate Transporter Patterns With And Without Administration Of Vegf And Seizure Induction, Janice Rene Lenzer

Dissertations, Theses, and Capstone Projects

VEGF treatment during pilocarpine-induced status epilepticus (SE) causes enduring preservation of behavioral function in rats in the absence of enduring neuroprotection (Nicoletti et al., 2010). In addition, VEGF treatment reduces hyperexcitability in hippocampal slices without altering neuronal membrane properties (McCloskey et al, 2005). Combined, these data suggest the possibility that other cells or mechanisms could be involved in the beneficial effects of VEGF during SE. Our laboratory is interested in the potential contribution of astrocytes to these effects. Astrocytes are not only reported to contribute to epileptiform discharges in the hippocampus (Tian et al., 2005; Kang et al., 2005) but …

Analysis Of Dna Motifs In The Human Genome, Yupu Liang

Dissertations, Theses, and Capstone Projects

DNA motifs include repeat elements, promoter elements and gene regulator elements, and play a critical role in the human genome. This thesis describes a genome-wide computational study on two groups of motifs: tandem repeats and core promoter elements.

Tandem repeats in DNA sequences are extremely relevant in biological phenomena and diagnostic tools. Computational programs that discover tandem repeats generate a huge volume of data, which can be difficult to decipher without further organization. A new method is presented here to organize and rank detected tandem repeats through clustering and classification. Our work presents multiple ways of expressing tandem repeats using …

Psychological Contracts In Information Exchanges, Stanislav Mamonov

Dissertations, Theses, and Capstone Projects

Information assets continue to grow in importance of contribution to economic activity. Many emergent businesses, including Google, Amazon and Facebook, leverage crowd-sourced information assets as essential pillars supporting their business models. The appropriation of rights to information assets is commonly done through legal contracts. In practice this approach often fails to prevent conflicts between the information contributors and the companies claiming information rights. In research presented here I attempt to understand when and why the conflicts arise. I draw on psychological contract theory and I develop the framework of psychological contracts in information exchanges. I propose that intellectual property and …

Iron Regulates Mrna Translation Initiation Through Rna Iron Responsive Element (Ire), Jia Ma

Dissertations, Theses, and Capstone Projects

The non-coding IRE-RNA structure, a 30 nt stem loop structure, regulates synthesis of proteins in iron trafficking, cell cycling, and nervous system function. IRE-RNA binding with iron regulatory protein (IRP) proteins inhibits ribosome accessing mRNA. Increasing iron concentration decreases IRP binding with IRE-RNA. Previous models of IRE-mRNA translation regulation concentrate on Fe-S binding to IRP and IRP degradation after release from IRE-RNA. These models lack information on the details of decreasing IRE-RNA/IRP protein binding with iron concentration elevation. This research shows 1. Eukaryotic initiation factor 4F (eIF4F) binds to IRE-RNA with high affinity and works as a positive control element …

The Characterization Of Pb2+ Toxicity In Rat Neural Development: An Assessment Of Pb2+ Effects On The Gaba Shift In Neural Networks And Implications For Learning And Memory Disruption, Lorenz Simon Neuwirth

Dissertations, Theses, and Capstone Projects

The toxic effects of Pb2+ on the developing rat nervous system has been investigated to assess early developmental GABAergic disruption and its implications with altering inhibitory learning and memory. This goal was achieved using a multi-systems approach: blood lead levels (clinical physiology), qRT-PCR (molecular genetics), brain and primary neuronal culture immunology (immunohistochemical and cellular approaches), physiological cellular components (synaptosomes and protein expression) and finally through learning and memory assessment with GABA mimetic drug manipulations in the intact animal (behavioral pharmacology). The influence of a 956ppm Pb2+ gestational diet (i.e. from birth to sacrifice) resulted in pup mean blood lead levels …

Intracellular Mechanisms Associated With Cocaine Induced Conditioned Place Preference, Stephanie K. Nygard

Dissertations, Theses, and Capstone Projects

The aim of this dissertation was to investigate the intracellular responses associated with the acquisition and expression of cocaine-context associations. ERK (extracellular regulated kinase), CREB (cAMP responsive element binding protein), FosB and deltaFosB proteins were of particular interest due to their involvement in cocaine reward and in synaptic plasticity underlying learning and memory. We used the conditioned place preference (CPP) paradigm, which employs a Pavlovian conditioning procedure to establish an association between a drug-paired environment and the drug's rewarding effects, to study the role of these signaling pathways in cocaine-context associations. N-methyl-D-aspartate receptor (NMDAR) antagonism prior to cocaine administration during …

On The Role Of Neuronal Oscillations In Auditory Cortical Processing, Monica Noelle O'Connell

Dissertations, Theses, and Capstone Projects

Although it has been over 100 years since William James stated that "everyone knows what attention is", its underlying neural mechanisms are still being debated today. The goal of this research was to describe the physiological mechanisms of auditory attention using direct electrophysiological recordings in macaque primary auditory cortex (A1). A major focus of my research was on the role ongoing neuronal oscillations play in attentional modulation of auditory responses in A1.

For all studies, laminar profiles of synaptic activity, (indexed by current source density analysis) and concomitant firing patterns in local neurons (multiunit activity) were acquired simultaneously via linear …

The Sex Of The Cell Dictates Its Response, Carlos Ganesh Penaloza

Dissertations, Theses, and Capstone Projects

Male and female differences in frequency of occurrence in disease have perplexed scientists for some time. This in part derives from limitations in the systems in which one can evaluate sex differences. At the organismal level, differences can be hidden by a myriad of extensive and complex factors. Additional limitations exist since most biomedical studies are performed almost exclusively on male subjects, as the female hormonal milieu is intrinsically more variable and too troublesome for routine inclusion in research protocols. Research documenting sex differences continues to grow, and while most researchers suggests that sex hormones are at the core of …

Comparative Modeling And Functional Characterization Of Two Enzymes Of The Cyclooxygenase Pathway In Drosophila Melanogaster, Yan Qi

Dissertations, Theses, and Capstone Projects

Eicosanoids are biologically active molecules oxygenated from twenty carbon polyunsaturated fatty acids. Natural eicosanoids exert potent biological effects in humans, and a great deal of pharmaceutical research has led to the discovery of compounds for selective inhibition of specific enzymes in eicosanoid biosynthesis. Coupled with different receptors, eicosanoids mediate various physiological and pathophysiological processes, including fever generation, pain response, vasoconstriction, vasodilation, platelet aggregation, platelet declumping, body temperature maintenance and sleep-wake cycle regulation. In mammals, the eicosanoid biosynthesis has three pathways: the cyclooxygenase (COX) pathway, the lipoxygenase (LOX) pathway and the epoxygenase pathway. The COX pathway synthesizes prostanoids, which are important …

Long-Term Warming And The Size And Phenology Of Long Island Sound Plankton, Edward Rice

Dissertations, Theses, and Capstone Projects

In coastal ecosystems with decades of eutrophication and other anthropogenic stressors, the impact of climate change on planktonic communities can be difficult to detect. A time-series of monthly surface water temperatures in the Central Basin of Long Island Sound (LIS) from the late 1940s until 2012 indicates a warming rate of 0.03°C per year, with recent summer temperatures increasing most consistently. During this warming trend, the proportion of chlorophyll produced by smaller phytoplankton and flagellates appears to be higher during warmer summer and fall months, enabling an increase in annual chlorophyll despite static nutrient levels. The phenology of phytoplankton and …

Neurophysiological Bases Of Frequency Discrimination In Children With Auditory Processing Disorder Or Specific Language Impairment, Christine Rota-Donahue

Dissertations, Theses, and Capstone Projects

The purpose of this study was to determine if 10-12 year old children with Auditory Processing Disorder (APD) or Specific Language Impairment (SLI) could discriminate three different frequency changes behaviorally and electrophysiologically. Behavioral frequency discrimination and event-related potentials were examined using a 1000Hz pure tone base frequency. Typically developing children and children with APD or SLI differed in in their detection of frequency changes: behavioral results were below chance level and the MMN amplitude was smaller in the impaired population. Slight differences between children with APD and children with SLI were also found that might shed light on the controversy …

Lipid Dependence In Ras-Driven Tumors, Darin Salloum

Dissertations, Theses, and Capstone Projects

Over past decade, metabolic alterations in cancer cells have received a substantial amount of interest. It had been established that cancer cells undergo a significant amount of metabolic alterations, and some of these alterations are similar to those in normal highly proliferative cells. However, it is becoming more apparent that many of the metabolic alterations are specific to particular oncogenic signaling pathways. Although altered metabolic machinery makes cancer cells more efficient at promoting growth when nutrients are supplied at the sufficient amounts, the dependency of cancer cells on particular metabolic reprogramming deems cancer cells susceptible to disruptions within metabolic network. …

Neuroimmune Crosstalk: A Role For Neuropeptide Y In Inflammatory Bowel Disease, Henry H. Ruiz

Dissertations, Theses, and Capstone Projects

Neuropeptide Y (NPY) is a 36-amino acid peptide widely expressed in the central and peripheral nervous systems. In addition to other cells, NPY is also synthesized and co-released from sympathetic nerve fibers functioning as a potent sympathetic neuromodulator. NPY has been implicated in playing important roles in the regulation of energy balance, appetite, anxiety, vascular tone, and immune cell functioning. In addition, immune cells of both the innate and adaptive immune systems express functional NPY receptors. Some immune cells can produce and secrete NPY, and genetic alteration of these receptors results in altered immune cell functioning. Its direct association with …

Metabolic Checkpoints In Cancer Cell Cycle, Mahesh Saqcena

Dissertations, Theses, and Capstone Projects

Growth factors (GFs) as well as nutrient sufficiency regulate cell division in metazoans. The vast majority of mutations that contribute to cancer are in genes that regulate progression through the G1 phase of the cell cycle. A key regulatory site in G1 is the growth factor-dependent Restriction Point (R), where cells get permissive signals to divide. In the absence of GF instructions, cells enter the quiescent G0 state. Despite fundamental differences between GF signaling and nutrient sensing, they both have been confusingly referred to as R and therefore by definition considered to be a singular event in G1. Autonomy from …

Quantitative Evaluation Of Microglial Activation And Vascularization In Suicide, Tatiana Pavlovna Schnieder

Dissertations, Theses, and Capstone Projects

Accumulated evidence points to immunological factors in psychiatric disorders. In a variety of chronic neurological disorders, exacerbation is associated with inflammation and a loss of integrity of the blood-brain barrier. Microglia, the principal brain immunological cells in the healthy state, respond to changes in the internal environment of the brain through a sequence of activated states. This study compared microglial phenotypes in the white matter of autopsy brains from 11 suicide victims and 25 subjects who died involuntarily. Both groups included cases with and without major psychiatric disorders, which were determined by PA interviews. Cases were matched for sex, age, …

Phylogeny And Population Genetics Of The Endangered Dwarf Bear-Poppy, Arctomecon Humilis Coville (Papaveraceae) Using Microsatellite Markers, Joshua Simpson

Dissertations, Theses, and Capstone Projects

The genus Arctomecon (Papaveraceae) is comprised of three narrowly endemic rare species that are largely restricted to gypsum soils of the eastern Mojave Desert. The small, remaining populations of these species have become increasingly isolated by urban development and habitat fragmentation. Arctomecon humilis is federally listed as endangered due to its limited distribution within a ~15 km radius of an actively expanding city. Organizations involved with land management and conservation have called for greater insight into the genetic variation and population structure of the remaining subpopulations as they make important decisions regarding where to focus their efforts and resources.

The …

An Experimental Investigation Into The Mechanisms Of Bacterial Evolution, Zhenmao Wan

Dissertations, Theses, and Capstone Projects

This thesis studies the two fundamental mechanisms of bacterial evolution — horizontal gene transfer and spontaneous mutation, in the bacterium Escherichia coli through novel experimental assays and mathematical simulations. First, I will develop a growth assay utilizing the quantitative polymerase chain reaction (qPCR) to provide real-time enumeration of genetic marker abundance within bacterial populations. Second, I will focus on horizontal gene transfer in E. coli occurring through a process called conjugation. By fitting the qPCR data to a resource limited, logistic growth model, I will obtain estimated values of several key parameters governing the dynamics of DNA transfer through conjugation …

Identification And Characterization Of Protein Phopshatases Regulating The Sma/Mab Pathway In C. Elegans, Sheng Xiong

Dissertations, Theses, and Capstone Projects

TGF-beta signaling is a conserved signaling pathway among eukaryotes, which controls various normal cellular responses from cell proliferation to cell death. The mutations in its components are found in developmental disorders and cancer. Therefore, this signaling pathway is extensively investigated so that new therapeutic targets could be discovered and novel drugs could be developed. Previous studies suggested the involvement of phosphatases in regulation of TGF-beta signaling, but these studies were performed in cell culture rather than intact organisms. C. elegans is a tractable organism in which to study signaling in vivo. In C. elegans, growth is controled by a conserved …

Mechanisms Of Deadenylation Regulation Under Different Cellular Conditions, Xiaokan Zhang

Dissertations, Theses, and Capstone Projects

Control of gene expression by regulating mRNA stability after DNA damage has the potential to contribute to the cells rapid response to stress. The main focus of this dissertation is to elucidate the role(s) of nuclear PARN deadenylase in controlling mRNA stability, hence gene expression, of factors in the p53 signaling pathway during the DNA damage response (DDR). Understanding the mechanisms of these regulatory pathways will provide new insights on how the control of gene expression upon DNA damage decides cellular fate, offering new opportunities for therapeutics. In Chapter II, I presented evidence that PARN along with the cleavage factor …

The Developmental Trajectory Of Contour Integration In Autism Spectrum Disorders, Ted S. Altschuler

Dissertations, Theses, and Capstone Projects

Sensory input is inherently ambiguous and complex, so perception is believed to be achieved by combining incoming sensory information with prior knowledge. One model envisions the grouping of sensory features (the local dimensions of stimuli) to be the outcome of a predictive process relying on prior experience (the global dimension of stimuli) to disambiguate possible configurations those elements could take. Contour integration, the linking of aligned but separate visual elements, is one example of perceptual grouping. Kanizsa-type illusory contour (IC) stimuli have been widely used to explore contour integration processing. Consisting of two conditions which differ only in the alignment …

A Kinder, Gentler Dopamine. . . Highlighting Dopamine's Role In Behavioral Flexibility, Jeff A. Beeler, Roshan Cools, Monica Luciana, Sean B. Ostlund, Giselle Petzinger

Publications and Research

No abstract provided.

2matrix: A Utility For Indel Coding And Phylogenetic Matrix Concatenation, Nelson R. Salinas, Damon P. Little

Publications and Research

Premise of the study: Phylogenetic analysis of DNA and amino acid sequences requires the creation of files formatted specifically for each analysis package. Programs currently available cannot simultaneously code inferred insertion/deletion (indel) events in sequence alignments and concatenate data sets.

Methods and Results: A novel Perl script, 2matrix, was created to concatenate matrices of non-molecular characters and/or aligned sequences and to code indels. 2matrix outputs a variety of formats compatible with popular phylogenetic programs.

Conclusions: 2matrix efficiently codes indels and concatenates matrices of sequences and non-molecular data. It is available for free download under a GPL (General Public License) open …

Insects And Humans Share A Complex History, Aldemaro Romero Jr.

Publications and Research

No abstract provided.

An Environment And Cultural Heritage Workbook For Students And Teachers, Rebecca Zarger, Kristina Baines

Open Educational Resources

The word "heritage" is one that means many things to many people. It often brings to mind things like food, language, clothing, or other traditions that are passed on from generation to generation. But it also includes places, buildings, art, values, and ways of making a living in particular environments. In Maya communities, as is the case elsewhere around the world, cultural practices and the environment are tightly connected, with one shaping the other.

With this workbook we take a broad view of heritage, one that links cultural and environmental histories, landscapes, and practices together. A term that UNESCO and …

Variance Predicts Salience In Central Sensory Processing, Ann M. Hermundstad, John J. Briguglio, Mary M. Conte, Jonathan D. Victor, Vijay Balasubramanian, Gašper Tkačik

Publications and Research

Information processing in the sensory periphery is shaped by natural stimulus statistics. In the periphery, a transmission bottleneck constrains performance; thus efficient coding implies that natural signal components with a predictably wider range should be compressed. In a different regime—when sampling limitations constrain performance—efficient coding implies that more resources should be allocated to informative features that are more variable. We propose that this regime is relevant for sensory cortex when it extracts complex features from limited numbers of sensory samples. To test this prediction, we use central visual processing as a model: we show that visual sensitivity for local multi-point …

Nest Destruction Elicits Indiscriminate Con- Versus Heterospecific Brood Parasitism In A Captive Bird, Rachel C. Shaw, William E. Feeney, Mark E. Hauber

Publications and Research

Following nest destruction, the laying of physiologically committed eggs (eggs that are ovulated, yolked, and making their way through the oviduct) in the nests of other birds is considered a viable pathway for the evolution of obligate interspecific brood parasitism. While intraspecific brood parasitism in response to nest predation has been experimentally demonstrated, this pathway has yet to be evaluated in an interspecific context. We studied patterns of egg laying following experimental nest destruction in captive zebra finches, Taeniopygia guttata, a frequent intraspecific brood parasite. We found that zebra finches laid physiologically committed eggs indiscriminately between nests containing conspecific eggs …

Spatial Gaussian Markov Random Fields: Modelling, Applications And Efficient Computations, Yu Ryan Yue, Xiao-Feng Wang

Publications and Research

A powerful modelling tool for spatial data is the framework of Gaussian Markov random fields (GMRFs), which are discrete domain Gaussian random fields equipped with a Markov property. GMRFs allow us to combine the analytical results for the Gaussian distribution as well as Markov properties, thus allow for the development of computationally efficient algorithms. Here we briefly review popular spatial GMRFs, show how to construct them, and outline their recent developments and possible future work.