Digital Commons Network^™

The Impact Of Environmental Factors On The Physiology Of The Atlantic Surfclam, Spisula Solidissima, Jesse Hornstein

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The Atlantic surfclam supports a multi-million dollar fishery in New York. Between 2002 and 2008, surfclam abundance in New York State waters along the south shore of Long Island has decreased by 63% in biomass and 75% in the total number of clams. Population age structure has drastically shifted since 2002 indicating the lack of recruitment. Only 3% of the population was made up of clams that were 6 years old and younger in 2006, compared to 21% in 2002. In 2008, 15% of the population was composed of clams less than 6 years in age. It is hypothesized that …

Role Of Serotonin (5-Ht) In Hypoxic And Hypercapnic Ventilatory Responses, Tejus A. Bale

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Breathing is fundamental to life, and responding appropriately to hypercapnic and hypoxic conditions is essential to survival. Abberant respiratory behavior is a feature of a wide variety of clinical conditions, and appears to be central and causative to the progression and outcome of some diseases, including Sudden Infant Death Syndrome (SIDS). Evidence of serotonergic (5-HT) abnormalities within the medulla are amongst the most robust and consistent pathological findings in SIDS victims. It is hypothesized that these underlying brainstem abnormalities precipitate the failure of normal, protective homeostatic responses to physiological stressors. Understanding the mechanisms by which 5-HT modulates the responses to …

Annexin A2 And Microglia/Macrophages In Glioma Progression, Haiyan Zhai

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Gliomas are highly invasive brain tumors with the occurrence of numerous microglia/macrophages (MG/MP) in and around the tumor. Annexin A2 is overexpressed in many cancers and correlates with increased plasmin activity on the tumor cell surface. Plasmin mediates degradation of extracellular matrix and angiogenesis to facilitate tumor growth. In this study, we used a mouse glioma cell line, GL261-EGFP, and stable clones transfected with an annexin A2 knockdown (annA2KD) construct, GL261-EGFP-annA2KD. We found that the annA2KD decreased glioma cell migration in vitro and decreased membrane-bound plasmin activity. In vivo we injected GL261-EGFP cells into the mouse brain and the glioma …

The Role Of Phospholipase D2 In Golgi-Architecture Maintenance, Vesicular Trafficking And Glucose- Stimulated Insulin Release & Validation Of A Novel Non- Invasive Approach To Functional Β-Cell Mass Quantification, Oladapo Olumoroti Yeku

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Phospholipase D (PLD) is essential for different aspects of vesicle trafficking and regulated exocytosis in a variety of biological models. PLD1 and PLD2 are the two major mammalian isoforms and both isoforms localize to different organelles where they generate phosphatidic acid (PA), the effector molecule of PLD activity. The role of PLD1 in glucose-stimulated insulin release (GSIR), a form of regulated exocytosis, has been well characterized. Additionally, the role of PLD1 in anterograde vesicle trafficking from the ER to the cis-golgi and from the trans-golgi to the plasma membrane has also been described. The role of PLD2 in GSIR and …

Physical Characteristics Of Bering Sea Zooplankton And Their Use To Parameterize An Acoustic Scattering Model For Euphausiids, Joy Nicole Smith

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Acoustic assessment of Bering Sea euphausiids and their predators can provide useful data for ecosystem studies if the acoustic scattering characteristics of these animals are known. The amount of acoustic energy that is scattered by different marine zooplankton taxa is strongly affected by the contrast of the animal's density (g) and sound speed (h) with the surrounding seawater. Density and sound speed contrast were measured in the Bering Sea during the summer of 2008 for several different zooplankton and nekton taxa including: euphausiids (Thysanoessa inermis, Thysanoessa raschii, and Thysanoessa spinifera), copepods, amphipods, chaetognaths, gastropods, fish larvae, jellyfish, and squid. Density …

Tissue Plasminogen Activator & Plasminogen System In Chondroitinase-Mediated Axonal Plasticity, Noreen Bukhari

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Following Spinal Cord Injury (SCI) the injured neurons are unable to regenerate as they face an inhibitory external environment and the lack of guidance cues for direct regrowth of severed axons. A component of the inhibitory extracellular environment is the glial scar. Chondroitinase ABC (ChABC) is an enzyme able to degrade the sugar chains of chondroitin sulfate proteoglycans (CSPGs), a major constituent of the glial scar, and thus allow for improvements in SCI functional repair. The mechanism underlying this repair remains unclear. Our group has previously reported that ChABC enhances the interaction of the extracellular serine protease, tissue plasminogen activator …

Determining The Role Of Natural Selection In Plant Invasion: A Study Of Introduced Japanese Knotweed (Fallopia Japonica) And A Native Relative, Woodland Knotweed (Persicaria Virginiana), Kelly L. O'Donnell

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The ecological and evolutionary study of plant invasion processes is of exceeding importance in today's changing environment. However, few studies have addressed the impact of natural selection on invasive plant species. While scientists have been able to detect selection in natural populations, most studies are not replicated in space or time leading to unreliable statistical estimates and tentative causal analyses. My objective was to further our knowledge of selection dynamics in the wild by working in the area of invasion biology through studies that combine both field and controlled settings. It has been suggested that plant invasion affords us the …

Estimating The Reliability Of Concept Map Ratings Using A Scoring Rubric Based On Three Attributes, Laura Jimenez

Theses and Dissertations

Concept maps provide a way to assess how well students have developed an organized understanding of how the concepts taught in a unit are interrelated and fit together. However, concept maps are challenging to score because of the idiosyncratic ways in which students organize their knowledge (McClure, Sonak, & Suen, 1999). The construct a map or C-mapping" task has been shown to capture students' organized understanding. This "C-mapping" task involves giving students a list of concepts and asking them to produce a map showing how these concepts are interrelated. The purpose of this study was twofold: (a) to determine to …

A Kinesin Motor In A Force-Producing Conformation, Elisabeth Heuston, C. Eric Bronner, F Jon Kull, Sharyn A. Endow

Dartmouth Scholarship

Kinesin motors hydrolyze ATP to produce force and move along microtubules, converting chemical energy into work by a mechanism that is only poorly understood. Key transitions and intermediate states in the process are still structurally uncharacterized, and remain outstanding questions in the field. Perturbing the motor by introducing point mutations could stabilize transitional or unstable states, providing critical information about these rarer states.

Distribution And Ecology Of Invasive Ants, Chad Tillberg, Frank Andrews, Carson Moscoso, Lily Ratliff, Claire Steele, Chris Turpin, Ben Edmonds, Alex Freauff, Erik Grimstad, Sara Grusing

2010 Projects

This project examines exactly how invasive specific types of ants are, and what effect that has on the ecosystem. To do so, most of the research must be compiled for the first time, as there is a lack of knowledge and research on this subject. Through former research, Tillberg finds that there are invasive pavement ants in Oregon state parks, but due to a lack of research on the species, their impact is unknown. The research will follow a paired design, comparing similar areas with and without pavement ants, to discover what differences this invasive species has on habitats.

Lps-Induced Production Of Inflammatory Mediators In The Liver Of Postnatal Animals, Valerie P. Le Rouzic

Seton Hall University Dissertations and Theses (ETDs)

Lipopolysaccharide (LPS) is the primary component of the outer membrane of Gram-negative bacteria and is responsible for the majority of inflammatory effects of infections from Gram-negative bacteria. To gain better understanding of the effects that postnatal age has on the inflammatory response, pups were randomly assigned to be treated with 250 µg/kg of LPS or saline at postnatal day (P) 1, P21, and P70. Two hours post stimulation, the pups were sacrificed and their livers were harvested for total RN A extraction. Relative mRNA levels of inflammatory genes and �-actin were determined using RT-PCR analysis with appropriate rat sense and …

Mechanism Of Yeast Prion Portein Aggregation And Strain Formation, Tejas Baba Kalastavadi

All Theses and Dissertations (ETDs)

Misfolding and aggregation of the prion protein: PrP) causes fatal neurodegenerative diseases in many mammalian species, including humans. Mutations in the gene encoding PrP are associated with ~15% of the incidences, while, the vast majority of the cases are sporadic. Interestingly, prion diseases also display pathological variation, suggesting that there are multiple different strains. To elucidate the mechanism of prion protein aggregation and strain formation, I have taken advantage of the yeast prions [PSI+] and [RNQ+] and their protein determinants Sup35p and Rnq1p, respectively. Using a Sup35-PrP chimera, I have investigated the effect of the disease associated oligopeptide repeat domain: …

Student Content Knowledge Increases After Participation In A Hands-On Biotechnology Intervention, Amber L. Bigler

Theses and Dissertations

Hands-on learning is at the heart of science learning. This study examined increased changes of student content knowledge in biology, particularly biotechnology, after a hands-on biotechnology intervention was implemented into a secondary school. A traditional learning school was selected for a control. Both teachers had participated in a biotechnology professional development program called Project Crawfish. Students from both schools took the same assessment before and after their respective units (biotechnology intervention and genetics unit), and the classroom was the unit of analysis (n=5, n=6, respectively). The assessment was compared as a whole and then divided into five components, eight questions …

P53 Action In Suppressing Acute Myeloid Leukemia, Zhen Zhao

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Acute myeloid leukemia (AML) is the major form of adult acute leukemia. It is characterized by colonial expansion of malignant myeloid progenitors in bone marrow, resulting in insufficient generation of normal blood components to cause sever infection, fatigue, and hemorrhage in patients. p53 is a tumor suppressor that commonly mutates in human cancers. p53 mutations have profound effects on AML biology and are associated with the clinical aggressiveness and drug resistance. However, how p53 loss influences AML development remains to be determined. Mouse models recapitulating molecular alterations of human cancer are useful tools to dissect the in vivo roles of …

Novel Amyloid Beta-Protein Degrading Enzymes. Membrane Type 1 Matrix-Metalloproteinase And Myelin Basic Protein, Mei-Chen Liao

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The progressive accumulation of á-amyloid (Aá) in senile plaques and in the cerebral vasculature is the hallmark of Alzheimer's disease (AD) and related disorders. Several major pathways for Aá clearance include receptor-mediated cellular uptake, blood-brain barrier transport and direct proteolytic degradation. My thesis focused on two novel Aá degrading enzymes- Membrane type 1 matrix metalloproteinase (MT1-MMP) and myelin basic protein (MBP). Matrix metalloproteinase 2 (MMP2) was shown to be expressed in reactive astrocytes surrounding amyloid plaques and may contribute to Aá degradation. MT1-MMP is the physiological activator for the zymogen pro-MMP2. In addition to MMP2, its activator MT1-MMP was also …

Restoration Of The Hudson River Oyster: A Physiological And Spatial Assessment Of Crassostrea Virginica's Restoration Potential In The Hudson River, Ny, Adam Faulkner Starke

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The Hudson River was once home to abundant eastern oyster (Crassostrea virginica, (Gremlin 1791) populations which catered to an enormous fishery and supplied a number of vital ecological services to the estuary. Since this time, oysters have become depleted and the estuary's vitality has been compromised. Recognizing the current state of the Hudson, a comprehensive restoration plan has been implemented and targets the recovery of oysters and oyster reefs. To begin moving forward with these plans, a two year study investigating the physiological responses of the oyster to New York's Hudson River was made. The results have provided useful insights …

The Invasion Of The Colonial Ascidian Didemnum Vexillum, Into South Shore Bays Of Long Island, New York-Feeding And Metabolic Characteristics, Carlene Theresa Harrington

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The invasive ascidian, Didemnum vexillum, has recently spread into south shore bays of Long Island, New York including Great South Bay and Shinnecock Bay. In order to determine the impact this invasive species will have on these bays, colonies from Shinnecock Bay were studied, due to easiest accessibility. D. vexillum currently forms extensive mats on the pillars of Ponquogue Bridge located in Shinnecock Bay. These mats have the potential to drastically alter the structure of the ecosystem; an effect which has been observed in other waters that the species has invaded. Thus, in order to predict the impact D. vexillum …

A Role For The Transcriptional Repressor Rest In Patterning The Zebrafish Neural Tube, Keith Pendleton Gates

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The spatial and temporal control of gene expression is key to generation of specific cellular fates during development. Studies of the transcriptional repressor REST/NRSF (RE1 Silencing Transcription factor/Neural Restrictive Silencing Factor) have provided important insight into the role that epigenetic modifications play in differential gene expression. Functional studies place REST within multiple developmental pathways and transcriptional networks. However, findings between different groups are often incongruent, and little progress has been made on understanding the embryonic lethality of the Rest knockout mice. What emerges from the controversies surrounding REST function is that the cellular context of REST is paramount. Here, zebrafish …

Cooperative Learning: Attitudes, Perceptions, And Achievement In A Traditional, Online, And Hybrid Instructional Setting, Allison Hardin Duckworth

Dissertations

Cooperative learning has been sufficiently studied to be accepted as an effective method of education. Student reception of cooperative learning, and therefore the degree of its success in a given situation, will depend on the mode of delivery. New technology for delivering courses totally online challenges many aspects of traditional education, and is particularly difficult for cooperative learning that relies heavily on intense face-to-face communication among students. This study was conducted to compare cooperative learning in a traditional setting to that in hybrid and online settings. A model for delivering a cooperative learning experience has been developed utilizing concept maps …

Citrate Synthase And The Visual Interactions Hypothesis, Kristina Camarena

Senior Honors Projects

It has been shown that the metabolic rates of deep-living species of particular pelagic groups are significantly lower than those that live closer to the surface in the water column. Various theories as to why have been presented, including the visual interactions hypothesis, which states that because there is a greatly minimized ability to visually interact in the light-limited deep, predators have a reduced need for high metabolic rates because they do not actively go after their prey. Citrate synthase is a mitochondrial enzyme found at the beginning of the citric acid cycle, which plays an integral role in cellular …

Cell(F), Nicole Lynn Herden

Boise State University Theses and Dissertations

I see the human experience as composed of both objectivity and subjectivity. Objectivity in that science has helped us better understand our physicality, such as defining biological processes within our body. Empirical knowledge has provided a level of truth in explaining a foundation for our existence.

Subjective experiences materialize as we engage within the environment. Walking in the park or purchasing food seem to be similar experiences for everyone in that we can envision the process of doing it; however, that process is an individual process composed of unique characteristics and perspectives. A subjective experience is as unique as one’s …

Nutrient And Contaminant Dynamics In The Marine Food Web Of Kotzebue Sound (Alaska), Sara K. Moses

Biological Sciences

The objectives of these studies were to document nutrient and contaminant concentrations in upper trophic level organisms of the Kotzeue, Alaska marine food web; address associated risks and benefits to human consumers of these species; understand the drivers of nutrient and contaminant patterns and concentrations; and test the limitations of chemical feeding ecology tools used to trace nutrient and contaminant pathways within this food web. Tissues of subsistence harvested animals were analyzed for nutrients, contaminants and stable isotopes (delta13C and delta15N). Foods derived from sheefish (Stenodus leucicthys) and spotted seal (Phoca largha) provide numerous essential nutrients, with limited risk from …

Effects Of Mold Exposure On Immune Cells, Katrin Gorham

Honors Projects in Science and Technology

The relationship between exposure to mold spores and human disease is only beginning to be understood. While evidence exists of strong correlations between moldy environments and allergic and infectious diseases, the relationship between exposure to specific species and human immune responses to them is not fully understood. This paper seeks to clarify this relationship by analyzing the effects of exposing murine immune cells to volatile organic compounds (VOCs) produced by different mold species. Mold species studied include Stachybotrys alternans; tests performed include cell viability studies and immunoassays. Results have implications for further research and treatment of mold-related diseases.

Modulation Of L-Type Calcium Current By Gaba-B Receptor Activation In The Neonatal Rat Hippocampus, Jennifer Grace Bray

Dissertations (1934 -)

During the early postnatal period, the inhibitory neurotransmitter γ-aminobutyric acid (GABA) facilitates current through voltage-dependent L-type calcium channels by activating metabotropic GABA_B receptors in the rat hippocampus. In the present study, the effects of the GABA_B receptor agonist baclofen on L-type currents were tested using whole-cell voltage clamp recording on neurons isolated from the superior region of hippocampi obtained from pups of various ages to determine the exact time course of L-type current facilitation. The facilitation of L-type current by GABA_B receptors is more prominent during the second week of development.

One developmental process that L-type current …

Legal, Moral And Biological Implications Of Poaching And Illegal Animal Trafficking On An International Scale, Meghan A. Pastor

Pell Scholars and Senior Theses

Poaching and animal trafficking is a global issue in the areas of biology, morality and politics. This paper will discuss the different areas of impact as well as consider options for the prevention and alleviation of this issue.

Part I: Evaluation Of Student Assessment Of Learning Gains (Salg)In Two Different Biology 100 Classes Part 2: What Biology Concepts Are Important In General Education?: Analysis Of Seventeen Core Concepts, Jessica Marie Rosenvall Howelle

Theses and Dissertations

The purpose of this two-part study is to examine how to improve introductory level non-majors biology courses to improve student attitude and learning gains in the sciences. The first part of this study examines the collective effect of three different pedagogies (service learning, concept mapping and guest lectures) on student attitude and learning gains in a freshman, non-majors biology course. Two classes, one with the three pedagogies, and one without, were compared. Data were collected from two classes in Fall 2008 (one treatment and one control) and two similar classes replicated in Fall 2009. Learning and attitude gains were measured …

Organismal Climatology: Analyzing Environmental Variability At Scales Relevant To Physiological Stress, Brian Helmuth, Bernardo R. Broitman, Lauren Yamane, Sarah E. Gilman, Katharine Mach, K. A.S. Mislan, Mark W. Denny

Faculty Publications

Predicting when, where and with what magnitude climate change is likely to affect the fitness, abundance and distribution of organisms and the functioning of ecosystems has emerged as a high priority for scientists and resource managers. However, even in cases where we have detailed knowledge of current species’ range boundaries, we often do not understand what, if any, aspects of weather and climate act to set these limits. This shortcoming significantly curtails our capacity to predict potential future range shifts in response to climate change, especially since the factors that set range boundaries under those novel conditions may be different …

The Effects Of Seasonality And Land Use On Microbe Populations In Three Ecological Areas, Rachel E. Hutchins

McNair Scholars Research Journal

The Huron River watershed is comprised of three primary land uses: agricultural, natural, and urban. Land usage affects the biological and chemical conditions within the watershed, therefore affecting water quality. Recent studies have provided evidence that water quality can be assessed by examining the composition of the microbial communities found in biofilms. In this study we analyzed and compared samples collected from a natural site and urban site over the course of three seasons; fall (August), winter (December), and spring (April). Microbial diversity was determined by isolating, amplifying, and genotyping the 16S rRNA gene. The results show that microbial community …

The Synergistic Effects Of Probiotic Microorganisms On The Microbial Production Of Butyrate In Vitro, Khadija A. Abbas

McNair Scholars Research Journal

Butyrate producing microbiota perform a number of activities important in supporting the normal function of the human gastrointestinal tract. The goal of this study was to determine the synergistic effects of lactate- and butyrate-producing bacteria on butyrate production in vitro co-culture. PCR was used to detect the genes butyrate kinase and butyryl-CoA transferase that contribute to butyrate production, in a panel of representative gut microbiota. Preliminary data suggested that two Clostridium sp. (ASF 500 and ASF 502) and one Eubacterium sp. (ASF492) possessed at least one of these genes for butyrate production. Co-culture experiments mixing a lactate-producer with a butyrate-producer …

Does Rac Gtpase Play A Role In Epha4 Signaling In Xenopus Embroys?, Ashley Durand

McNair Scholars Research Journal

In embryonic development, many cells migrate in order to correctly form new structures. One way that guidance of this migration occurs is via a repulsion mechanism involving the Eph family of receptors. Signaling through these receptors activates the repulsive mechanism that limits which tissues can interact with each other. The repulsion mechanism is not well understood, but involves the reorganization of the actin cytoskeleton and a loss of cell-cell adhesion. Activation of the EphA4 signaling pathway in Xenopus laevis embryos has been shown to cause the repulsion mechanism. the Rho family of GTPases consisting of Cdc42, Rho, and Rac, has …