Life Sciences Commons^™

Forest Regeneration On The Osa Peninsula, Costa Rica, Manette E. Sandor

Master's Theses

Woody species diversity of secondary forest has the potential to converge with that found in old growth forest. This study is the first to examine multiple aspects of species and reproductive trait diversity, and their relationship to each other, across a successional chronosequence. Species richness and species diversity increases with increasing age of forest. Diaspore size and diversity as well as fruit size generally increased with increasing age of forest, but fruit size diversity did not. Abundance of animal-dispersed species increased whereas wind-dispersed species decreased in abundance over succession. Insect-pollinated individuals were most abundant overall. Diaspore diversity, pollination diversity, and …

Detection Of Genomic Inversion From Single End Read, Pankaj Ghimire

Master's Theses

Structural Variations (SVs) are genomic rearrangements that include both copy-number variants,such as insertion,deletions, duplications and balanced variants like inversion and translocations. These SVs are getting more attentions for research and investigation because of their role on human phenotype, genetic diseases and genomic rearrangements. Evolution of Next-generation Sequencing has provided golden opportunities to investigate these variants and make their wider and clear spectrum in human genome. This investigation includes identification of type of SVs and their breakpoints at base pair level. For their effective identification and breakpoint resolution, many techniques are devised mainly based on paired end read. With relatively low …

Effects Of Neonatal Hypoxic Ischemic Brain Injury On Spatial Working Memory, Amanda L. Smith

Master's Theses

Children born prematurely or at very low birth weight (VLBW) have an increased risk for hypoxic ischemic brain injury (HI). HI refers to a lack of adequate blood and oxygen flow in the brain. HI can also occur in the term infant due to birth complications such as prolonged labor, placental dysfunction, or cord prolapse. In both populations (though exact patterns of neuropathology vary) brain damage is likely to occur in the form of decreased hippocampal and cortical volume, and enlargement of the ventricles (Kesler et al., 2004, Nagy et al., 2009). Resulting neuropathology can in turn lead to cognitive …

Tremulous Jaw Movements Induced By The Vmat2 Inhibitor Tetrabenazine, Samantha J. Podurgiel

Master's Theses

Parkinsonism is a movement disorder characterized by several cardinal motor symptoms: resting tremor, akinesia, bradykinesia, rigidity, and postural instability. Parkinsonian resting tremor can be modeled in rodents using the tremulous jaw movement model. Tremulous jaw movements (TJMs) are defined as “rapid vertical deflections of the lower jaw that resemble chewing but are not directed at any particular stimulus.” TJMs occur in a frequency range of 3-7 Hz and are induced by a number of pharmacological manipulations that parallel those seen in human Parkinsonism including dopamine (DA) depleting agents, DA antagonists, and cholinomimetic administration. Additionally, TJMs can be attenuated using antiparkinsonian …

Theta Dynamics: Speed, Acceleration And Contribution To Cognition, Lauren L. Long

Master's Theses

No abstract provided.

Annual Glyphosate Treatments Alter Growth Of Unaffected Bentgrass ( Agrostis ) Weeds And Plant Community Composition, Collin W. Ahrens, Carol A. Auer

Open Access Author Fund Awardees' Articles

Herbicide resistance is becoming more common in weed ecotypes and crop species including turfgrasses, but current gaps in knowledge limit predictive ecological risk assessments and risk management plans. This project examined the effect of annual glyphosate applications on the vegetative growth and reproductive potential of two weedy bentgrasses, creeping bentgrass (CB) and redtop (RT), where the glyphosate resistance (GR) trait was mimicked by covering the bentgrass plants during glyphosate application. Five field plots were studied in habitats commonly inhabited by weedy bentgrasses including an agricultural hayfield, natural meadow, and wasteland. Results showed that annual glyphosate treatment improved bentgrass survivorship, vegetative …

Distinct Mechanisms Mediate Naïve And Memory Cd8 T-Cell Tolerance, Evan R. Jellison, Elizabeth G. Lingenheld, Li Zu, Lynn Puddington, Leo Lefrancois

UCHC Articles - Research

Peripheral tolerance to developmentally regulated antigens is necessary to sustain tissue homeostasis. We have now devised an inducible and reversible system that allows interrogation of T-cell tolerance induction in endogenous naïve and memory CD8 T cells. Our data show that peripheral CD8 T-cell tolerance can be preserved through two distinct mechanisms, antigen addiction leading to anergy for naïve T cells and ignorance for memory T cells. Induction of antigen in dendritic cells resulted in substantial expansion and maintenance of endogenous antigen-specific CD8 T cells. The self-reactive cells initially exhibited effector activity but eventually became unresponsive. Upon antigen removal, the antigen-specific …

Logic Modeling And The Ridiculome Under The Rug, Michael L. Blinov, Ion I. Moraru

UCHC Articles - Research

Logic-derived modeling has been used to map biological networks and to study arbitrary functional interactions, and fine-grained kinetic modeling can accurately predict the detailed behavior of well-characterized molecular systems; at present, however, neither approach comes close to unraveling the full complexity of a cell. The current data revolution offers significant promises and challenges to both approaches - and could bring them together as it has spurred the development of new methods and tools that may help to bridge the many gaps between data, models, and mechanistic understanding.

Have you used logic modeling in your research? It would not be surprising …

Unique Small Rna Signatures Uncovered In The Tammar Wallaby Genome, James Lindsay, Dawn M. Carone, Judy Brown, Laura Hall, Sohaib Qureshi, Sarah E. Mitchell, Nicholas Jannetty, Andrew Pask, Michael O’Neill, Rachel O’Neill

Open Access Author Fund Awardees' Articles

Background

Small RNAs have proven to be essential regulatory molecules encoded within eukaryotic genomes. These short RNAs participate in a diverse array of cellular processes including gene regulation, chromatin dynamics and genome defense. The tammar wallaby, a marsupial mammal, is a powerful comparative model for studying the evolution of regulatory networks. As part of the genome sequencing initiative for the tammar, we have explored the evolution of each of the major classes of mammalian small RNAs in an Australian marsupial for the first time, including the first genome-scale analysis of the newest class of small RNAs, centromere repeat associated short …

Analyzing Self-Similar And Fractal Properties Of The C. Elegans Neural Network, Tyler M. Reese, Antoni Brzoska, Daniel J. Kelleher

Open Access Author Fund Awardees' Articles

The brain is one of the most studied and highly complex systems in the biological world. While much research has concentrated on studying the brain directly, our focus is the structure of the brain itself: at its core an interconnected network of nodes (neurons). A better understanding of the structural connectivity of the brain should elucidate some of its functional properties. In this paper we analyze the connectome of the nematode Caenorhabditis elegans. Consisting of only 302 neurons, it is one of the better-understood neural networks. Using a Laplacian Matrix of the 279-neuron “giant component” of the network, we …

Setting The Sound Up For Success, Hillary Kenyon

Wrack Lines

Deploying remotely-set disease-resistant oyster seed in biodegradable netting on a natural bed in Connecticut. The eastern oyster, Crassostrea virginica, is a keystone species in Connecticut's coastal environment.

Ken Beatrice: A Volunteer For All Seasons, Peg Vanpatten

Wrack Lines

"It was really interesting, and as I read, I wondered how I could personally get involved in efforts to conserve the Sound," Ken said. One of the listings in the box titled "What Can I Do to Help?" was the NOAA volunteer Phytoplankton Monitoring Network.

Of Gardens, Microorganisms, And Long Island Sound, Judy Preston

Wrack Lines

How healthy soil can make an environmental difference.

"I happened to turn over a large rounded stone in my garden to find a mesmerizing world of organisms that had, just moments earlier, been going about their business before being exposed to the sunlit world, and me."

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

UCHC Articles - 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 …

Herpes Simplex Viruses: Mechanisms Of Dna Replication, Sandra K. Weller

UCHC Articles - Research

Herpes simplex virus (HSV) encodes seven proteins necessary for viral DNA synthesis—UL9 (origin-binding protein), ICP8 (single-strand DNA [ssDNA]-binding protein), UL30/UL42 (polymerase), and UL5/UL8/UL52 (helicase/primase). It is our intention to provide an up-to-date analysis of our understanding of the structures of these replication proteins and how they function during HSV replication. The potential roles of host repair and recombination proteins will also be discussed.

Nf-Κb Contributes To The Detrimental Effects Of Social Isolation After Experimental Stroke, Venugopal Reddy Venna, Gillian Weston, Sharon E. Benashski, Sami Tarabishy, Fudong Liu, Jun Li, Lisa H. Conti, Louise D. Mccullough

UCHC Articles - Research

Social isolation (SI) is increasingly recognized as a risk factor for stroke. Individuals with lack of social support systems have an increased incidence of stroke, poorer recovery, and greater functional decline after injury compared to individuals with social support. Attesting to the importance of social factors in stroke outcome is that these same effects can be reproducibly demonstrated in animals; social interaction improves behavioral deficits and reduces damage after experimental stroke, whereas SI enhances injury. The mechanism by which SI exacerbates injury is unclear. We investigated the role of nuclear factor-kappaB (NF-κB) signaling in male mice that were pair housed …

Nuclear Dna Content And Genome Size Of American Ginseng, Samuel G. Obae

Open Access Author Fund Awardees' Articles

Flow cytometry analysis of propidium iodide (PI) stained nuclei isolated from leaf tissues was used to estimate the genome size of American ginseng (Panax quinquefolius L.) and evaluate inhibitor y effects of its secondary compounds on PI intercalation. American ginseng nuclear DNA content was estimated to be 10.05 ± 0.04 pg/2C, and therefore its haploid (1C) genome size is 4914 Mbp. There was no significant inhibition of PI fluorescence of reference standard nuclei co-processed with American ginseng. This indicates that secondary compounds of American ginseng do not interfere with PI intercalation. By comparison, the genome size of American ginseng is …

The Relationship Between Liv-1 And E-Cadherin (Cdh1) In Prostate Cancer Cells, Lei Cao

Master's Theses

BACKGROUND

The zinc importer LIV-1 is widely distributed, mainly in hormonally controlled tissues. Attention has focused on its role in breast cancer, especially its regulation by estrogen and epidermal growth factor (EGF) and its link to the Epithelial–Mesenchymal Transition (EMT) marker, E-cadherin (CDH1). EMT is important for tumor progression and metastasis. CDH1 expression is under complex control, including by two transcriptional repressors, Snail and Slug. Contrast to CDH1, elevated MMP-9 expression has been linked to increased metastasis and tumor stage.

METHODS

The role of LIV-1 in prostate cancer cell lines, LNCaP and DU145 was investigated. Cells were treated with or …

Green Tea Extract Protects Against Fibrogenesis Associated With Nonalcoholic Fatty Liver Disease In Diet-Induced Obese Rats, Allyson M. Bower

Master's Theses

No abstract provided.

The Breathing Of The Bays, Jamie Vaudrey, Margaret (Peg) A. Van_Patten (Editor)

Wrack Lines

Bays in Long Island Sound and beyond have natural rhythms like breathing. Stress can impact the health of these natural ecosystems. While Long Island Sound has been examined for the extent of hypoxia in the summer, small embayments have not been examined carefully. In this article, two researchers investigate the oxygen, or lack of, in small bays of Long Island Sound.

Discovering The Light Bulb Tunicate, James F. Reinhardt Phd, Margaret (Peg) A. Van_Patten (Editor) Ms.

Wrack Lines

An article by a former UCONN marine sciences graduate student about a new invasive tunicate in Long Island Sound, the light bulb tunicate.

Fast Rebinding Increases Dwell Time Of Src Homology 2 (Sh2)-Containing Proteins Near The Plasma Membrane, Dongmyung Oh, Mari Ogiue-Ikeda, Joshua A. Jadwin, Kazuya Machida, Bruce J. Mayer, Ji Yu

UCHC Articles - Research

Receptor tyrosine kinases (RTKs) control a host of biological functions by phosphorylating tyrosine residues of intracellular proteins upon extracellular ligand binding. The phosphotyrosines (p-Tyr) then recruit a subset of ∼100 Src homology 2 (SH2) domain-containing proteins to the cell membrane. The in vivo kinetics of this process are not well understood. Here we use total internal reflection (TIR) microscopy and single-molecule imaging to monitor interactions between SH2 modules and p-Tyr sites near the cell membrane. We found that the dwell time of SH2 modules within the TIR illumination field is significantly longer than predictions based on chemical dissociation rate constants, …

Interleukin-1Β In Central Nervous System Injury And Repair, Nicole A. Jackman, Sandra J. Hewett, Robert J. Claycomb

UCHC Articles - Research

Acute inflammation is a self-limiting, complex biological response mounted to combat pathogen invasion, to protect against tissue damage, and to promote tissue repair should it occur. However, unabated inflammation can be deleterious and contribute to injury and pathology. Interleukin-1β (IL-1β), a prototypical “pro-inflammatory” cytokine, is essential to cellular defense and tissue repair in nearly all tissues. With respect to brain, however, studies suggest that IL-1β has pleiotrophic effects. It acts as a neuromodulator in the healthy central nervous system (CNS), has been implicated in the pathogenic processes associated with a number of CNS maladies, but may also provide protection to …

Dietary Protein Influences Paracellular Calcium Transport: Two Molecular Targets, Belinda M. Kotler

Master's Theses

The effect of dietary protein on bone health remains controversial. We have shown that increasing dietary protein increases calcium absorption in both humans and rats with no change in bone resorption. We used a rat model in which dietary protein increases intestinal calcium absorption and whole body calcium retention, to explore the molecular basis for this effect. Female Sprague-Dawley rats were fed a low (5%) or high (40%) protein diet for 7 days. On day 7, duodenal mucosa was harvested and total RNA isolated. Microarray analyses using these RNA samples identified 208 genes whose expression was at least 1.5 fold …

Diffusion Barriers Of The Lateral Ventricular System, Anitha Saravanakumar

Master's Theses

Adult neurogenesis in mammalian brain has become a well-accepted phenomenon. The neural stem cells in the sub ventricular zone (SVZ) along the lateral wall of the lateral ventricle, the largest germinal center of adult neurogenesis, are maintained by the neural stem cell niche. One prominent feature of the niche is its close proximity to the cerebral spinal fluid (CSF). The role of micromolecules (such as ions, water and gases) present in the CSF and diffusing through the lateral ventricular wall and how the stem cell micro-environment is maintained is poorly understood. The cytoarchitecture of the lateral ventricular wall with a …

Dietary Analysis And Epigenetic Comparisons Of Drosphila Melanogaster Through Multiple Generations, Xu (Kevin) F. Zheng

Holster Scholar Projects

Nutrition and the lack thereof has been a demanding issue in both the undeveloped and developed country. The unbalance diet between healthy and unhealthy diet has led to many of the problems presented in society such as obesity, heart disorders, and loss of longevity. It is now known that calorie may not provide the most accurate information in terms of the lifestyle and the well-being of humans. Rather the composition of the calorie is what becomes integral in people's understanding of the effect of food physiologically. With this knowledge, we seek to use a Drosophila melanogaster as a model organism …

Striped Bass Consumption Of Blueback Herring During Vernal Riverine Migrations: Does Relaxing Harvest Restrictions On A Predator Help Conserve A Prey Species Of Concern?, Justin P. Davis, Eric T. Schultz, Jason C. Vokoun

Open Access Author Fund Awardees' Articles

Anadromous blueback herring Alosa aestivalis are declining throughout much of their range, and fishery closures in some systems have failed to produce population recovery. A potential contributing factor is increased predation pressure from sympatric striped bass Morone saxatilis. We integrated data on the predator–prey interaction between striped bass and blueback herring during vernal migrations into the Connecticut River with data on the in-river striped bass fishery to assess the potential for mitigation of blueback herring mortality via increased striped bass harvest. Striped bass abundance, size structure, diets, and angler catches were assessed within a river segment during spring 2005–2008. …

Global Approaches To The Role Of Mirnas In Drug-Induced Changes In Gene Expression, Jodi E. Eipper-Mains, Betty A. Eipper, Richard E. Mains

UCHC Articles - Research

Neurons modulate gene expression with subcellular precision through excitation-coupled local protein synthesis, a process that is regulated in part through the involvement of microRNAs (miRNAs), a class of small non-coding RNAs. The biosynthesis of miRNAs is reviewed, with special emphasis on miRNA families, the subcellular localization of specific miRNAs in neurons, and their potential roles in the response to drugs of abuse. For over a decade, DNA microarrays have dominated genome-wide gene expression studies, revealing widespread effects of drug exposure on neuronal gene expression. We review a number of recent studies that explore the emerging role of miRNAs in the …

Expression And Putative Function Of Innate Immunity Genes Under In Situ Conditions In The Symbiotic Hydrothermal Vent Tubeworm Ridgeia Piscesae, Spencer V. Nyholm, Corey Bunce

Open Access Author Fund Awardees' Articles

The relationships between hydrothermal vent tubeworms and sulfide-oxidizing bacteria have served as model associations for understanding chemoautotrophy and endosymbiosis. Numerous studies have focused on the physiological and biochemical adaptations that enable these symbioses to sustain some of the highest recorded carbon fixation rates ever measured. However, far fewer studies have explored the molecular mechanisms underlying the regulation of host and symbiont interactions, specifically those mediated by the innate immune system of the host. To that end, we conducted a series of studies where we maintained the tubeworm, Ridgeia piscesae, in high-pressure aquaria and examined global and quantitative changes in …

Using High Throughput Sequencing To Explore The Biodiversity In Oral Bacterial Communities, Patricia I. Diaz, A. K. Dupuy, L. Abusleme, B. Reese, C. Obergfell, Linda E. Choquette, Anna Dongari-Bagtzoglou, Douglas E. Peterson, Linda D. Strausbaugh

UCHC Articles - Research

High throughput sequencing of 16S ribosomal RNA gene amplicons is a cost-effective method for characterization of oral bacterial communities. However, before undertaking large-scale studies, it is necessary to understand the technique-associated limitations and intrinsic variability of the oral ecosystem. In this work we evaluated bias in species representation using an in vitro-assembled mock community of oral bacteria. We then characterized the bacterial communities in saliva and buccal mucosa of five healthy subjects to investigate the power of high throughput sequencing in revealing their diversity and biogeography patterns. Mock community analysis showed primer and DNA isolation biases and an overestimation …