Digital Commons Network^™

A Search For Genetic Modifiers Responsible For Congenital Heart Disease Variability In The Presence Of Nkx2-5 Haploinsufficiency, Julia Brandeis Winston Honold

All Theses and Dissertations (ETDs)

While a clear heritable risk has been observed for congenital heart disease, there is considerable variation in penetrance and presentation likely due to multiple genetic and environmental risk factors. To identify causative factors and interactions responsible for variability in heart development, greater than 4,200 hearts from Nkx2-5 heterozygous knockout mice have been collected and examined. Nkx2-5+/- mice in the inbred strain background C57Bl/6 frequently have atrial and ventricular septal defects. The incidences are substantially reduced in the Nkx2-5+/- progeny of first-generation: F1) outcrosses to the strains FVB/N or A/J. Defects recur in the second generation: F2) of the F1xF1 intercross …

Spotted Ash Looper, Abraxas Pantaria (L.) (Lepidoptera: Geometridae), A New Ash Pest In Turkey, Hi̇kmet Özbek, Önder Çalmaşur

Turkish Journal of Zoology

Abraxas pantaria (L.) (Lepidoptera: Geometridae), the spotted ash looper (Light Magpie), is recognized as a new pest of common ash, Fraxinus excelsior (L.) in the eastern part of Turkey. Description of different developmental stages of A. pantaria is given. Its development, biology, damage, and parasitoids were studied in the field (Aras Valley, Karakurt, Sarıkamış, Kars Province) and partly in the laboratory during 2004-2006. In the field adults started to appear at the end of June and were seen until the middle of August. The eggs were laid mostly on the lower sides of leaves adjacent to the midrib in single …

Mathematical Biology At An Undergraduate Liberal Arts College, Stephen C. Adolph, Lisette G. De Pillis

All HMC Faculty Publications and Research

Since 2002 we have offered an undergraduate major in Mathematical Biology at Harvey Mudd College. The major was developed and is administered jointly by the mathematics and biology faculty. In this paper we describe the major, courses, and faculty and student research and discuss some of the challenges and opportunities we have experienced.

Full Issue: Volume 3, Number 1

The Science Journal of the Lander College of Arts and Sciences

No abstract provided.

Effects Of Uv Light On Local Stream Frog Behavior, John Buie, Eiichiro Uemura, Candy Hwang, D. Lee, Craig Sutter, Evan Mattiasen, Thomas Vandergon, Rodney Honeycutt, Lee Kats

Featured Research

Amphibian declines have been well documented throughout the world. Several studies have examined whether UV radiation from the sun is a possible contributing cause to declining populations. In Southern California, two closely related species of treefrogs, Pseudacris hypochondriaca and Pseudacris cadaverina, coexist in many perennial streams. P. hypochondriaca is primarily nocturnal while P. cadaverina is known to bask in direct sunlight. The purpose of the study is to determine how the two different species of frogs will react under different types of light emitted by a portable flashlight. The light was emitting either UV radiation or visible light, or …

Effects Of Physical And Chemical Disturbance On Stream Ecosystem Structure And Function, Elena M. Traister

Doctoral Dissertations

A variety of natural and anthropogenic disturbances influence the structure and function of stream ecosystems. While past investigations have focused on the response of community indicators to stream disturbances, functional indicators may also be helpful for assessing stream ecosystem health. To date, few studies have compared the response of structural and functional indicators to ecosystem-level disturbances. I separately measured the effects of long-term acidification, a large-scale avulsion, and the individual and combined effects of physical streambed disturbance and altered refugia availability on stream structural and functional metrics.

I found that acidification was associated with changes in macroinvertebrate communities including reduced …

Updated Life History And Population Structure Assessment Of Spiny Dogfish, Squalus Acanthias, In The Gulf Of Maine, Walter Bubley

Doctoral Dissertations

Spiny dogfish (Squalus acanthias) are considered to be the most abundant shark species in the Western North Atlantic, but recently there was a decline in biomass estimates following a nearly ten-fold increase in fishery landings. Because fishing pressure has been shown to affect population dynamics in targeted species, an update of previous life history parameters is warranted to effectively manage the population. Although updated and accurate life history parameters are important, it is crucial that these parameters are applied to the correct populations, especially when there is evidence of population structuring in the Western Atlantic. This comprehensive study addressed the …

The Effects Of Didemnum Vexillum Overgrowth On Mytilus Edulis Biology And Ecology, Linda Ann Auker

Doctoral Dissertations

Didemnum vexillum is an invasive colonial ascidian in the Gulf of Maine that readily colonizes hard substrates. These substrates include hard-shelled organisms, such as the common blue mussel Mytilus edulis. Preliminary observations and short-term studies showed potential effects of epibiosis on M. edulis growth, specifically lip thickness and tissue index. This dissertation study further examined the effects of D. vexillum on growth and reproduction of, and predation on, M. edulis. Shell thickness index, tissue index, shell mass to tissue mass ratio, lip thickness and mussel length were measured throughout a 12-month period in control and overgrown mussels. Additionally, histological preparations …

Movement And Behavior Of Ocean Sunfish, Mola Mola, In The Northwest Atlantic, Inga F. Potter

Doctoral Dissertations

The ocean sunfish, Mola mola, has a worldwide distribution and is a common resident of the NW Atlantic Ocean. Notable for its unusual anatomy and large size, the biology of the species is largely unknown. I examined the movement and behavior of M. mola using pop-up satellite archival tags (PSAT's). In addition, analysis of aerial survey data was conducted to determine the distribution of ocean sunfish (Family Molidae) in NW Atlantic shelf waters. Data was analyzed from twenty-five PSAT's deployed on M. mola in the northwest Atlantic between 2005 and 2008. Tags were attached from 7-242 days. Results indicate that …

Factors Regulating The Production Of Stx-2 In Escherichia Coli O157:H7, Kate P. Stefani

Doctoral Dissertations

The severity of Escherichia coli O157:H7 disease is due in part to a major virulence factor produced by the microbe, the shiga-like toxin 2 (Stx-2). Antibiotic treatment to reduce pathogen numbers is controversial, as it is thought that antibiotics may increase the levels of Stx-2 released from the pathogen. Currently, recommended treatment for E. coli O157:H7 is palliative The purpose of this study was to examine three critical factors potentially important to disease outcomes, and to determine their effect on expression of the stx2 gene and on release of Stx-2 from the pathogen. Those factors selected for study were: (i) …

Population Genetics, Species Boundaries, And Conservation Of The Jollyville Plateau Salamander, Eurycea Tonkawae, Paul T. Chippindale

KIP Data Sets and Technical Reports

Report submitted to the Texas Parks and Wildlife Department in fulfillment of contract 184467. The report was prepared while the author was affiliated with the University of Texas at Arlington. The author evaluated the genetics variation and population structure of the Jollyville Plateau salamander, Eurycea tonkawae. This information was used to recommend conservation strategies for this species and others found in similar environments. Open Access See Extended description for more information.

Introduction: Protistan Biology, Horizontal Gene Transfer, And Common Descent Uncover Faulty Logic In Intelligent Design, Avelina Espinosa

Arts & Sciences Faculty Publications

THE International Society of Protistologists (ISOP) organized a pre-meeting workshop entitled ‘‘Horizontal Gene Transfer and Phylogenetic Evolution Debunk Intelligent Design,’’ as part of the 1st North American Section meeting held June 11–13, 2009, at Roger Williams University, Bristol, RI, USA. This workshop focused on the acceptance of Darwinian evolution in the United States and the role of intelligent design (ID) in the ongoing controversy between scientific knowledge and popular belief. Intelligent design, a doctrine born in the 1980s, proposes that a ‘‘Designer’’ is responsible for the complexity in biological systems and that Darwinism cannot explain holistically the origin and evolution …

Bacterial Acquisition In Juveniles Of Several Broadcast Spawning Coral Species, Koty H. Sharp, Kim B. Ritchie

Arts & Sciences Faculty Publications

Coral animals harbor diverse microorganisms in their tissues, including archaea, bacteria, viruses, and zooxanthellae. The extent to which coral-bacterial associations are specific and the mechanisms for their maintenance across generations in the environment are unknown. The high diversity of bacteria in adult coral colonies has made it challenging to identify species-specific patterns. Localization of bacteria in gametes and larvae of corals presents an opportunity for determining when bacterial-coral associations are initiated and whether they are dynamic throughout early development. This study focuses on the early onset of bacterial associations in the mass spawning corals Montastraea annularis, M. franksi, M. faveolata, …

Truncated Mortalin In Animal Cancer, Katrina K. Olson

Master's Theses and Capstones

Hematopoetic neoplasia or clam hemocyte cancer (a leukemia-like disease) has been studied in a number of bivalve molluscs for the last 20 years. Recent molecular studies of the hemocytes of the soft shell clam, Mya arenaria, have demonstrated an interaction between p53 and mortalin, the mitochondrial Hsp70. The former protein is intimately involved in the initiation of cell-cycle arrest, apoptosis, DNA repair, and cell differentiation. In cancerous clams, wild-type p53 is sequestered in hemocyte cytoplasm by mortalin and cannot be translocated to the nucleus. This is critical because although p53 is functions properly, it is unable to enter the nucleus …

Landscape Genetics Of The New England Cottontail: Effects Of Habitat Fragmentation On Population Genetic Structure And Dispersal, Lindsey E. Fenderson

Master's Theses and Capstones

The New England cottontail (Sylvilagus transitionalis) is a species of conservation concern. Population recovery will require knowledge of genetic structure and dispersal patterns. To this end, I used microsatellite loci to assess genetic structure at two spatial scales: across the entire range (broadscale) and within the northernmost population (finescale).

Range-wide, cottontails are separated into five distinct populations. There was little evidence of gene flow among populations and they have experienced extensive genetic drift. Several populations had comparatively reduced genetic diversity.

Intensive fine-scale surveys revealed four genetically differentiated populations. Interstate-95 is a dispersal barrier, though other major roads did not impact …

Genomic Resource Development For A Diploid Mint: Mentha Longifolia, Zahra Hadadian

Master's Theses and Capstones

This research project aimed to develop genomic resources needed to enable construction of a genetic linkage map of the diploid mint species Mentha longifolia. Such a map would facilitate identification of plant genes involved in resistance to Verticillium fungal infection. For this purpose, a small genomic library was constructed from germplasm accession CMEN 585, 279 genomic inserts were sequenced and annotated and 19 PCR primer pairs were designed and tested on two resistant and two susceptible accessions. The Cleaved Modified Polymorphic Sequence (CAPS) method of molecular marker genotyping was found to detect little variation between crossing parents CMEN 585 (resistant) …

Regulation Of Photoreceptor Phosphodiesterase By Prenyl Binding Protein And By Other Interacting Proteins In Photoreceptor Cells, Hannah J. Gitschier

Master's Theses and Capstones

Photoreceptor phosphodiesterase (PDE6) is a central component of the visual pathway. While initial PDE6 activation following light stimulation of photoreceptors is well understood, regulation of PDE6 during recovery and light adaptation may require additional components that interact with PDE6. Two approaches were taken to characterize these potential interactions. The first explored the interaction of PDE6 with prenyl binding protein (PrBP/delta) and demonstrated that changes in membrane localization of PDE6 may occur during light adaptation as a result of association with PrBP/delta. The second approach characterized the PDE6 "interactome" by a mass spectrometric identification of 75 proteins that co-purify with PDE6 …

The Genetics Of Sex Determination In Fragaria Virginiana: A Candidate Gene Approach, Benjamin Bryant Orcheski

Master's Theses and Capstones

The evolutionary genetics of plant reproduction is a fascinating aspect of plant biology, involving an astounding diversity of reproductive strategies. While the majority of flowering plants are hermaphroditic (monoecy), many species have opted for an alternate mode, whereby male and female gametes originate on different plants (dioecy).

Wild strawberry, Fragaria virginiana, is a particularly interesting species, as its members can be female, male, or hermaphroditic. Its female flowers display arrested development of male reproductive organs (stamens), evidently conditioned by a single dominant allele of an unknown genetic locus. My aim was to isolate and characterize the gene(s) responsible for male …

Review Of The Species Of Gugolzia Delucchi And Steffan (Hymenoptera: Pteromalidae) In Europe And Turkey, With Descriptions Of New Species, Mi̇kdat Doğanlar, Oğuzhan Doğanlar

Turkish Journal of Zoology

The species of Gugolzia (Hymenoptera: Chalcidoidea, Pteromalidae) in Europe and Turkey were reviewed, and an identification key for differentiating the species is provided. Newly discovered diagnostic characters of the genus were added to the diagnoses given by earlier authors. Species were recorded as parasitoids of phytophagous Eurytomidae (Hymenoptera: Chalcidoidea). New host and distributions are for Gugolzia harmolitae, which was reared from Tetramesa romana feeding on shoots of Arundo donax (Poaceae), Gugolzia karadagae n.sp. from Eurytoma plotnikovi feeding on fruits of Pistacia vera together with Megastigmus pistaciae (Chalcidoidea: Torymidae) in Gaziantep province, and Gugolzia melengicia n.sp. from fruits of Pistacia terebinthi …

Characterization Of The Role For Nmnat, Kinase Cascades, And Purines In Axonal Degeneration, Craig Press

All Theses and Dissertations (ETDs)

Axonal degeneration is a prominent feature of many neurological disorders including Parkinson's disease: PD), motor neuron disease, inherited, diabetic, and drug-induced peripheral neuropathies. It is now thought that axonal degeneration is an active process, due in large part to studies of the Wlds mutant mouse, which undergoes delayed Wallerian degeneration in response to axonal injury. Wlds mice have slower disease progression in numerous models of neurodegenerative diseases. The Wlds mutation results in the production of a chimeric protein that containing nicotinamide mononucleotide adenylyltransferase 1: Nmnat1). Increased expression of Nmnat isoforms are sufficient for axonal protection in vitro and in vivo. …

The Role Of The Clock Gene Bmal1 In Female Fertility And Parturition, Christine Ratajczak

All Theses and Dissertations (ETDs)

Successful reproduction is essential for survival of species. For humans, reproductive problems can cause large emotional and medical burdens. Evidence in both humans and rodents indicates that circadian rhythmicity is important for supporting reproductive function. A molecular clock orchestrates circadian rhythmicity. Impairment in fertility and parturition are observed in female mice expressing a mutant form of Clock, suggesting critical roles for clock genes in reproduction. Since the clock gene Bmal1, but not Clock, is necessary for the generation of circadian rhythmicity, exploring the role of Bmal1 in reproduction may yield a better understanding of the importance of the molecular clock …

The Role Of Aerobic Glycolysis In The Resting Human Brain, Sanjeev Vaishnavi

All Theses and Dissertations (ETDs)

The human brain accounts for 2% of total body weight, though it consumes 20% of the body's energy supply. Most of this energy is provided by the complete oxidation of glucose to carbon dioxide and water, though some fraction of glucose undergoes aerobic glycolysis without concomitant oxidative phosphorylation. Elevation in neuronal activity increases aerobic glycolysis due to the disproportionate increase in blood flow and glucose utilization greater than oxygen consumption. Since aerobic glycolysis produces significantly less energy than complete oxidation of glucose, its role in cellular activities has been overlooked, though its presence in the resting brain has been known …

Role Of The Ajuba Lim Proteins In Epithelial Growth Regulation, Meghna Das Thakur

All Theses and Dissertations (ETDs)

The mammalian Ajuba LIM proteins: Ajuba, LIMD1, WTIP) are cytosolic adapter proteins recruited to nascent epithelial adherens junctions, where they are thought to contribute to junctional assembly and/or stability. They also shuttle into the nucleus acting as corepressors of the Snail family of transcriptional repressors, thereby contributing to epithelial mesenchymal transition. As such they have the potential to communicate cell adhesive events with nuclear responses to remodel epithelia. Determining their role(s) in vivo, however, has been challenging due to shared interacting proteins, overlapping tissue expression and functional redundancy in cells. Thus, we turned to the Drosophila model system where a …

Brain Insulin Action Regulates Hypothalamic Glucose Sensing And The Counterregulatory Response To Hypoglycemia, Kelly Diggs-Andrews

All Theses and Dissertations (ETDs)

The brain is the primary organ that senses blood glucose levels and initiates a stress response when blood glucose levels are too low: hypoglycemia). Insulin-dependent people with Type 1 diabetes: T1DM) have an impaired ability to sense hypoglycemia and an impaired ability to activate this counterregulatory response: CRR) to hypoglycemia. As a result, T1DM are at a greater risk of experiencing insulin induced severe hypoglycemic episodes, which can result in seizures, brain damage, or even death. Since hypoglycemia is a major barrier that limits intensive blood glucose control, important research initiatives are needed to prevent or reduce the burden of …

An Evaluation Of Habitat Models For The Common Loon (Gavia Immer), Alexis M. Rudko

Master's Theses and Capstones

The Loon Preservation Committee (LPC) has been collecting field data for the common loon (Gavia immer) in New Hampshire for thirty-six years. A habitat model for lakes throughout New Hampshire was created by Dr. Mark Brennan for the time period 1980--2002. This project re-evaluates Brennan's habitat model using new data from 2003--2008. Two additional models, one with all lakes and another with the three largest lakes excluded, were created and compared to Brennan's model to see if the overall accuracy improved. These models show which lakes have high and low potential for loon habitat. The results of the re-evaluation of …

The Effects Of Habitat Corridors And Edges On Sources Of Seed Mortality: Implications For Restoring A Threatened Legume, Melissa Simon

All Theses and Dissertations (ETDs)

No abstract provided.

Novel Algorithms For Structural Alignment Of Non-Coding Rnas, Diana Kolbe

All Theses and Dissertations (ETDs)

Non-coding RNAs are biologically important molecules, with a variety of catalytic and regulatory activities mediated by their secondary and tertiary structures. Base-pairing interactions, particularly at the secondary structure level, are an important tool for identifying and studying these structural RNAs, but also present some unique challenges for sequence analysis. Probabilistic covariance models are effective representations of structural RNAs, with generally high sensitivity and specificity but slow computational speed. New algorithms for dealing with structural RNAs are developed to address some of the practical deficiencies of covariance models. A new model of local alignment improves accuracy for fragmentary data, such as …

The Role Of Mda5 And Tlr3 In Response To Dsrna And Viral Infection, Stephen Mccartney

All Theses and Dissertations (ETDs)

The innate immune system consists of a number of genetically encoded receptors that detect the products of viral replication and initiate signaling cascades leading to activation of the antiviral response. During the course of infection, many viruses produce dsRNA that can be recognized by two major arms of the innate immune system: the toll-like receptors: TLR) and the Rig-I-like receptors: RLR). Among the TLRs, TLR3 binds dsRNA within the endosomal compartment and initiates signaling through its downstream adapter TRIF. Melanoma differentiation-induced gene 5: MDA5) is a member of the RLR family that recognizes dsRNA within the cytosolic compartment and signals …

Regulation Of Human T-Cell Leukemia Virus Type 1 Infection And Replication, Gunjan Choudhary

All Theses and Dissertations (ETDs)

Retroviruses have evolved complex mechanisms to regulate their cellular tropism and gene expression. It is generally accepted that productive infections proceed via interactions between viral envelope molecules and specific receptors on the host cell surface. Currently, there is no known receptor for HTLV-1, though a number of factors that enhance entry have been identified. In an effort to identify a cellular receptor or attachment factor for HTLV-1, we carried out a retroviral cDNA library screen, in which cDNA from permissive HeLa S3 cells was introduced into poorly susceptible NIH 3T3 cells. These cells were selected after infection with HTLV-1 envelope …

P38 Phoshporylates Rb On Ser567 By A Novel, Cell Cycle-Independent Mechanism That Triggers Rb-Hdm2 Interaction And Apoptosis, Rachel Delston

All Theses and Dissertations (ETDs)

The retinoblastoma protein: Rb) inhibits both cell division and apoptosis, but the mechanism by which Rb alternatively regulates these divergent outcomes remains poorly understood. Cyclin dependent kinases: Cdks) promote cell division by phosphorylating and reversibly inactivating Rb by a hierarchical series of phosphorylation events and sequential conformational changes. The stress-regulated mitogen activated protein kinase: MAPK) p38 also phosphorylates Rb, but it does so in a cell cycle-independent manner that is associated with apoptosis rather than with cell division. Here, we show that p38 phosphorylates Rb by a novel mechanism that is distinct from that of Cdks. p38 bypasses the cell …