Biology Commons^™

Response Of The Salt Gland Of The Insectivorous Lizard Novoeumeces Schneideri To Ionic And Osmotic Challenges, Claudia Lechuga

Theses, Dissertations and Culminating Projects

The reptilian kidney can only produce isoosmotic waste. To supplement renal ion excretion and maintain ionic and osmoregulation, some reptile species rely on extrarenal salt glands that can secrete a hyperosmotic solution. Extrarenal glands among reptile taxa include the cranial gland in lizards, lacrimal gland of marine turtles, and sublingual gland of the estuarine crocodile and sea snakes. Secretion composition varies among these taxa, depending on diet, osmotic load and phylogeny. The salt glands of lizards are unique among reptiles in their ability to vary composition of the secreted fluid, secreting cations (potassium and/or sodium) and anions (chloride and/or bicarbonate). …

Production Of Cftr-Null And Cftr-Δf508 Heterozygous Pigs By Adeno-Associated Virus - Mediated Gene Targeting And Somatic Cell Nuclear Transfer, Christopher S. Rogers, Yanhong Hao, Tatiana Rokhlina, Melissa Samuel, David A. Stoltz, Yuhong Li, Elena Petroff, Daniel W. Vermeer, Amanda C. Kabel, Ziying Yan, Lee Spate, David Wax, Clifton N. Murphy, August Rieke, Kristin Whitworth, Michael L. Linville, Scott W. Korte, John F. Engelhardt, Michael J. Welsh, Randall S. Prather

Department of Biology Faculty Scholarship and Creative Works

Progress toward understanding the pathogenesis of cystic fibrosis (CF) and developing effective therapies has been hampered by lack of a relevant animal model. CF mice fail to develop the lung and pancreatic disease that cause most of the morbidity and mortality in patients with CF. Pigs may be better animals than mice in which to model human genetic diseases because their anatomy, biochemistry, physiology, size, and genetics are more similar to those of humans. However, to date, gene-targeted mammalian models of human genetic disease have not been reported for any species other than mice. Here we describe the first steps …

Acid-Sensing Ion Channels Interact With And Inhibit Bk K+ Channels, Elena Petroff, Margaret P. Price, Vladislav Snitsarev, Huiyu Gong, Victoria Korovkina, Francois M. Abboud, Michael J. Welsh

Department of Biology Faculty Scholarship and Creative Works

Acid-sensing ion channels (ASICs) are neuronal non-voltage-gated cation channels that are activated when extracellular pH falls. They contribute to sensory function and nociception in the peripheral nervous system, and in the brain they contribute to synaptic plasticity and fear responses. Some of the physiologic consequences of disrupting ASIC genes in mice suggested that ASIC channels might modulate neuronal function by mechanisms in addition to their H+-evoked opening. Within ASIC channel's large extracellular domain, we identified sequence resembling that in scorpion toxins that inhibit K+ channels. Therefore, we tested the hypothesis that ASIC channels might inhibit K+ channel function by coexpressing …

Computational Prediction And Molecular Confirmation Of Helitron Transposons In The Maize Genome, Chunguang Du, Jason Caronna, Limei He, Hugo K. Dooner

Department of Biology Faculty Scholarship and Creative Works

Background: Helitrons represent a new class of transposable elements recently uncovered in plants and animals. One remarkable feature of Helitrons is their ability to capture gene sequences, which makes them of considerable potential evolutionary importance. However, because Helitrons lack the typical structural features of other DNA transposable elements, identifying them is a challenge. Currently, most researchers identify Helitrons manually by comparing sequences. With the maize whole genome sequencing project underway, an automated computational Helitron searching tool is needed. The characterization of Helitron activities in maize needs to be addressed in order to better understand the impact of Helitrons on the …

Comparative Study Between Wild Rice (Oryza Rufipogon) And Domesticated Rice (Oryza Sativa Ssp Japonica) Chromosome 8 Centromere, Soham Aso

Theses, Dissertations and Culminating Projects

Rice has one of the simplest of the monocotyledonous genomes analyzed to date. The Oryza sativa genome is made of 12 chromosomes and has a total length of 430 MB. It is highly syntenic amongst other cereals. Therefore, genetic distances of these organisms are surprisingly very similar, meaning that genomic recombinations in each cereal occur at much the same frequency despite the differences in their genome size. The reason for this synchrony in recombinations may be due to similar lengths of gene-rich and gene-rare regions. This study focuses on the gene-rare repetitive centromeric region of rice chromosome 8. Although the …

Evidence For Low Levels Of Genetic Variation Among Zostera Marina Populations From The Atlantic West Coast, Eric Rosenzweig

Theses, Dissertations and Culminating Projects

Zoster a marina (eelgrass), can be found in the North Atlantic on the coast of Europe and the North Arctic, as well as the Pacific. On the Atlantic west coast this species grows as far south as North Carolina and into northern Canada. The cold waters of these regions support the habitat needed for the species. Eelgrass is vital to coastal communities. It serves as a food source for many organisms, hatching ground for fish species, absorbent of water pollutants, and soil stabilizer. Over the last 30 years, the once robust populations of Atlantic west coast eelgrass have withered into …

In-Vitro Investigations On Ultrasonic Control Of Water Chestnut, Meiyin S Wu, J. Wu

Department of Biology Faculty Scholarship and Creative Works

Water chestnut (Trapa natans L.) is native to southern Europe and tropical Africa and Asia and was first introduced into North America in 1874. Since then, wild populations have quickly become established in many locations in the northeastern United States. T. natans is referred to as a noxious aquatic weed since its aggressive growth usually results in complete coverage of the water surface with floating rosettes of leaves. This study investigated the potential of the ultrasonic control of water chestnut since ultrasound has been documented to effectively damage plant cells and tissues. Various frequencies and amplitudes of ultrasound waves generated …

The Effects Of Testosterone On The Induction Of Experimental Autoimmune Thyroiditis In Sprague-Dawley Rats, Travis William Reed

Theses, Dissertations and Culminating Projects

Experimental Autoimmune Thyroiditis (EAT) could not be induced in young, immature Sprague-Dawley rats (150-200g). EAT was successfully induced in the same group of animals when they weighed 400g. The animals developed the disease every time. Sexual immaturity or immaturity of the immune system may be responsible for these results (Fernandez, 2006). It has been proven that pharmacologic doses of testosterone have shown immunosuppressive effects on the severity of EAT in the PVG/c strain of rats (Ahmed et al, 1982). In this current thesis research, it appears that normal physiologic levels of testosterone have no effect on the development and severity …

An Analysis Of Enzymatic Activity In Truncated And Wild-Type Auxin Conjugate Hydrolases In Medicago Trunculata (Barrel Clover) And Implications In Structural Modeling, Scott Sigethy

Theses, Dissertations and Culminating Projects

Auxins are plant phytohormones that play an important part in plant growth and development. The level of active auxins in plants is regulated by enzymes known as hydrolases that release inactive bound forms of auxins, known as conjugates, as the active free form. We have previously isolated and enzymatically characterized the auxin conjugate hydrolase family from the model legume Medicago truncatula (barrel clover). In the process of cloning the cDNA for the genes MtIAR31, -32, -33, -34, and -36, we also cloned a truncated version of MtIAR33 (AMtIAR33) that apparently expresses an alternative hydrolase protein from a secondary, internal AUG …

A Population Genetic Study Of The Zostera Marina (Eelgrass) Ecotypes Of Barnegat Bay, New Jersey And Implications For Grass Bed Restoration, Stephanie Marie Smith

Theses, Dissertations and Culminating Projects

Zostera marina is a species of seagrass widely found in the northern Atlantic and northern Pacific Oceans. It is primarily a cold-water adapted plant that is capable of both sexual and asexual reproduction. Zostera marina serves many ecological roles, including stabilizing sediments, reducing current velocity, preventing erosion and providing food and shelter to many organisms. Eelgrass populations have suffered numerous large-scale declines due to both natural as well as human-induced causes. Specifically within Bamegat Bay, New Jersey, the Z. marina populations have declined by over 62% within the past 20 years. Restoration efforts have had diverse growth and survival rates, …

Activation Of Extracellular Signal-Regulated Kinase 5 Reduces Cardiac Apoptosis And Dysfunction Via Inhibition Of A Phosphodiesterase 3a/Inducible Camp Early Repressor Feedback Loop, Chen Yan, Bo Ding, Tetsuro Shishido, Chang Hoon Woo, Seigo Itoh, Kye Im Jeon, Weimin Liu, Haodong Xu, Carolyn Mcclain, Carlos Molina, Burns C. Blaxall, Jun Ichi Abe

Department of Biology Faculty Scholarship and Creative Works

Substantial evidence suggests that the progressive loss of cardiomyocytes caused by apoptosis significantly contributes to the development of heart failure. β-Adrenergic receptor activation and subsequent persistent phosphodiesterase 3A (PDE3A) downregulation and concomitant inducible cAMP early repressor (ICER) upregulation (PDE3A/ICER feedback loop) has been proposed to play a key role in the pathogenesis of cardiomyocyte apoptosis. In contrast, insulin-like growth factor-1 can activate cell survival pathways, providing protection against cell death and restoring muscle function. In this study, we found that insulin-like growth factor-1 activates extracellular signal-regulated kinase 5 (ERK5) and inhibits PDE3A/ICER feedback loop. Insulin-like growth factor-1 normalized isoproterenol-mediated PDE3A …

Use Of Diadema Antillarum Spines By Juvenile Fish And Mysid Shrimp, Taryn Townsend, Paul Ax Bologna

Department of Biology Faculty Scholarship and Creative Works

This research has the following objectives: 1) identify the size structure of D. antillarum among 3 coastal bays of St. John, United States Virgin Islands and 2) determine relationships between urchin presence and spine utilization by fish and mysid shrimp.

Utilization Of Sea Scallop (Placopecten Magellanicus Gmelin) Microsatellite Markers For Phylogenetic Applications In Bay Scallops (Argopecten Irradians Lamarck), Lilliana E.J. Kim, James J. Campanella, Paul Ax Bologna

Department of Biology Faculty Scholarship and Creative Works

In previous research, microsatellite markers have been used to geographically and phylogenetically characterize and identify populations of sea scallops (Placopecten magellanicus Gmelin). Given that sea scallops are a closely related species to bay scallops (Argopecten irradians Lamarck), we have investigated whether the flanking DNA sequences of sea scallop microsatellite loci have been conserved in the bay scallop. We found that in all seven sets of published sea scallop PCR primers (Pma130, -132, -135, -180, -200, -212, and -275) that were tested with bay scallop DNA, there was sequence conservation and amplification of microsatellite regions. Our initial phylogenetic analyses, …

Retrotranspositions In Orthologous Regions Of Closely Related Grass Species, Chunguang Du, Zuzana Swigoňová, Joachim Messing

Department of Biology Faculty Scholarship and Creative Works

Background: Retrotransposons are commonly occurring eukaryotic transposable elements (TEs). Among these, long terminal repeat (LTR) retrotransposons are the most abundant TEs and can comprise 50-90% of the genome in higher plants. By comparing the orthologous chromosomal regions of closely related species, the effects of TEs on the evolution of plant genomes can be studied in detail. Results: Here, we compared the composition and organization of TEs within five orthologous chromosomal regions among three grass species: maize, sorghum, and rice. We identified a total of 132 full or fragmented LTR retrotransposons in these regions. As a percentage of the total cumulative …

A Minimally Invasive Method Of Piscine Tissue Collection And An Analysis Of Long-Term Field-Storage Conditions For Samples, James Campanella, John V. Smalley

Department of Biology Faculty Scholarship and Creative Works

Background: The acquisition of high-quality DNA for use in phylogenetic and molecular population genetic studies is a primary concern for evolutionary and genetic researchers. Many non-destructive DNA sampling methods have been developed and are used with a variety of taxa in applications ranging from genetic stock assessment to molecular forensics. Results: The authors have developed a field sampling method for obtaining high-quality DNA from sunfish (Lepomis) and other freshwater fish that employs a variation on the buccal swab method and results in the collection of DNA suitable for PCR amplification and polymorphism analysis. Additionally, since the circumstances of storage are …

Induction Of Experimental Autoimmune Thyroiditis (Eat) In Sprague-Dawley Rats And Measurements Of Severity Of Eat Using Scanning Electron Microscopy, Claudio Miguel Fernandez

Theses, Dissertations and Culminating Projects

As early as the 1950’s it was shown that animals as mice, rats, guinea pigs, and monkeys that received one injection of xenogeneic thyroglobulin emulsified in Complete Freund’s Adjuvant (CFA) developed Experimental Autoimmune Thyroiditis (EAT) (Voller et al., 1980). The damage reported was destruction of the thyroid follicles, and infiltration of the thyroid by macrophages, neutrophils, and lymphocytes. An injection of Bordetella pertussis proved to enhance the incidence and severity of EAT in animal models. Bordetella pertussis is no longer manufactured in large quantities, and it is extremely difficult to purchase. Therefore, a different procedure had to be developed that …

Site Directed Gene Disruption Of Rpfa In Xylella Fastidiosa : Non-Biofilm Producing Mutants As An Approach To Eradication Of Pierce's Disease In Grapevine, Janice Diane Thomas

Theses, Dissertations and Culminating Projects

Xylella fastidious a, a gram-negative, rod shaped bacterium, causes disease in many economically important plants including citrus, coffee, and grapevine. Xylella fastidiosa is xylem limited and is dependent on insect vectors for transmission. Pierce’s Disease of Vitis vinifere grape, transmitted by an insect vector, poses a serious threat to California vineyards today. The glassy-winged sharp-shooter, Homalodisca coagulata, has caused millions of dollars of damage to the California wine industry in just a few years. There is evidence that Xylella fastidiosa may share the molecular mechanisms through which the bacterium establishes infection with a closely related species, Xanthomonas campestris. A cluster …

Ret Dependent Changes In Gene Expression, Christian Anne Burr

Theses, Dissertations and Culminating Projects

RET is a mammalian receptor tyrosine kinase required for proper kidney and neuronal development. RET is expressed as three splice variants named RET9, RET43 and RET51 based on the splice variations at the 3’ end of the gene. All three splice variants of RET are activated by a complex of proteins including a ligand (GFL) and a co-receptor (GFR[alpha]l-4). Although there has been a great deal of work looking at the early stages of RET activation, less is known about the long-term effects, including transcriptional changes that occur in response to RET activation. In this study, transcriptional changes following RET …

Induction Of Temperate Cyanophage As-1 By Heavy Metal - Copper, Lee H. Lee, Doris Lui, Patricia J. Platner, Shi Fang Hsu, Tin Chun Chu, John J. Gaynor, Quinn C. Vega, Bonnie K. Lustigman

Department of Biology Faculty Scholarship and Creative Works

Background: It has been reported that some marine cyanophage are temperate and can be induced from a lysogenic phase to a lytic phase by different agents such as heavy metals. However, to date no significant reports have focused on the temperate nature of freshwater cyanophage/cyanobacteria. Previous experiments with cyanophage AS-1 and cyanobacteria Anacystis nidulans have provided some evidence that AS-1 may have a lysogenic life cycle in addition to the characterized lytic cycle. Results: In this study, the possible temperate A. nidulans was treated with different concentrations of heavy metal-copper. CuSO4 with concentrations of 3.1 × 10^-3 M, 3.1 …

The Antiviral Action Of Common Household Disinfectants And Antiseptics Against Murine Hepatitis Virus, Christine Bernadette Dellanno

Theses, Dissertations and Culminating Projects

The 2003 outbreak of Severe Acute Respiratory Syndrome (SARS) infected over 8,000 people and killed 784 leaving many questions concerning the effectiveness of common household disinfectants and antiseptics at preventing viral transmission. In order to determine how well standard disinfectants and detergents were at eliminating viral particles from surfaces, the antiviral action of triclosan, pine oil, bleach, chloroxylenol and quaternary ammonium compound/ethanol based products were assayed against Murine Hepatitis Virus (MHV), a virus genetically similar to SARS. Using the Environmental Protection Agency (EPA) guidelines for the virucidal assay, it was determined that alkyl dimethyl benzyl ammonium saccharinate in 79% ethanol …

Ecology Of The Plankton Of Lakes Wapalanne And Ocquittunk In Sussex County, New Jersey, Malgorzata Barbara Drazek-Falah

Theses, Dissertations and Culminating Projects

The diversity of planktonic organisms was studied for seven months in Lake Wapalanne and Lake Ocquittunk (Stokes State Forest), Sussex County, New Jersey. Relative abundance and species diversity were studied as well as water quality including parameters: temperature, pH, dissolved oxygen, conductivity and depth of lakes. The data of seasonal changes in abundance of organisms and water quality was compared between both lakes.

Three stations were set up along the straight line on Lake Wapalanne, buoyed by diatometers, which were used for diatom collection. There were also three stations located along the sides of Lake Ocquittunk arbitrary picked. Plankton samples …

Determining The Phylogenetic Relationship Of A Collection Of Hydra Strains And Species Using The Mitochondrial Genes : Lrrna, Trna-Trp And Coii, Jacob Zuckman

Theses, Dissertations and Culminating Projects

The discovery of the mitochondrial DNA (mtDNA) in the early 1960’s ushered in the field of organellar genetics. Evidence from both genetic and physical techniques has demonstrated that mtDNA are generally circular in structure, and that they represent the vestigial structure of the ancestral prokaryotic endosymbiont genome (Nosek et al., 1998). The more than 90 vertebrates and invertebrates sequenced to date have been found to have a remarkably constant gene content. With few exceptions, each contains the genes for 13 energy pathway proteins, the 2 RNA components of mitochondrial ribosomes (23S and 16S rRNA), and 22 transfer RNAs (Pont-Kingdon et …

A Phylogenomic Study Of The Genus Alphavirus Employing Whole Genome Comparison, Aimée J. Luers, Sandra Adams, John V. Smalley, James Campanella

Department of Biology Faculty Scholarship and Creative Works

The phylogenetics of the genus Alphavirus have historically been characterized using partial gene, single gene or partial proteomic data. We have mined cDNA and amino acid sequences from GenBank for all fully sequenced and some partially sequenced alphaviruses and generated phylogenomic analyses of the genus Alphavirus genus, employing capsid encoding structural regions, non-structural coding regions and complete viral genomes. Our studies support the presence of the previously reported recombination event that produced the Western Equine Encephalitis clade, and confirm many of the patterns of geographic radiation and divergence of the multiple species. Our data suggest that the Salmon Pancreatic Disease …

The Effects Of Heavy Metals On The Cyanobacterium, Anacystis Nidulans, Suzen Sameer Awad

Theses, Dissertations and Culminating Projects

Anacystis nidulans is a rod-shaped, freshwater cyanobacterium. Like other cyanobacteria, it is an obligate photoautotroph that is similar to gram-negative bacteria in cell wall structure, replication and ability to harbor plasmids. Anacystis nidulans is often used as an indicator of the presence and level of pollutants in the environment. Mercury, iron, cadmium, and zinc are among the heavy metal contaminants found in the environment and in bodies of freshwater through industrial discharges, agricultural runoff and sewage treatments. In very low concentrations, they do not pose any threat to the environment, but high concentrations can be lethal. Different microorganisms vary in …

A Molecular Phylogenomic Analysis Of The Ilri-Like Family Of Iaa Amidohydrolase Genes, James Campanella, Daniel Larko, John Smalley

Department of Biology Faculty Scholarship and Creative Works

The ILR1-like family of hydrolase genes was initially isolated in Arabidopsis thaliana and is thought to help regulate levels of free indole-3-acetic-acid. We have investigated how this family has evolved in dicotyledon, monocotyledon and gymnosperm species by employing the GenBank and TIGR databases to retrieve orthologous genes. The relationships among these sequences were assessed employing phylogenomic analyses to examine molecular evolution and phylogeny. The members of the ILR1-like family analysed were ILL1, ILL2, ILL3, ILL6, ILR1. and IAR3. Present evidence suggests that IAR3 has undergone the least evolution and is most conserved. This conclusion is based on IAR3 having the …

Matgat: An Application That Generates Similarity/Identity Matrices Using Protein Or Dna Sequences, James Campanella, Ledion Bitincka, John Smalley

Department of Biology Faculty Scholarship and Creative Works

Background: The rapid increase in the amount of protein and DNA sequence information available has become almost overwhelming to researchers. So much information is now accessible that high-quality, functional gene analysis and categorization has become a major goal for many laboratories. To aid in this categorization, there is a need for non-commercial software that is able to both align sequences and also calculate pairwise levels of similarity/identity. Results: We have developed MatGAT (Matrix Global Alignment Tool), a simple, easy to use computer application that generates similarity/identity matrices for DNA or protein sequences without needing pre-alignment of the data. Conclusions: The …

Analysis Of Intermolecular Rna-Rna Recombination By Rubella Virus, Sandra Adams, Wen Pin Tzeng, Min Hsin Chen, Teryl K. Frey

Department of Biology Faculty Scholarship and Creative Works

To investigate whether rubella virus (RUB) undergoes intermolecular RNA-RNA recombination, cells were cotransfected with pairs of in vitro transcripts from genomic cDNA plasmid vectors engineered to contain nonoverlapping deletions: the replicative transcript maintained the 5′-proximal nonstructural (NS) ORF (which contained the replicase, making it RNA replication competent), had a deletion in the 3′-proximal structural protein (SP) ORF, and maintained the 3′ end of the genome, including the putative 3′ cis-acting elements (CSE), while the nonreplicative transcript consisted of the 3′ half of the genome including the SP-ORF and 3′ CSE. Cotransfection yielded plaque-forming virus that synthesized the standard genomic and …

Development Of A Maize Molecular Evolutionary Genomic Database, Chunguang Du, Edward Buckler, Spencer Muse

Department of Biology Faculty Scholarship and Creative Works

PANZEA is the first public database for studying maize genomic diversity. It was initiated as a repository of genomic diversity for an NSF Plant Genome project on 'Maize Evolutionary Genomics'. PANZEA is hosted at the Bioinformatics Research Center, North Carolina State University, and is open to the public (http://statgen.ncsu.edu/panzea). PANZEA is designed to capture the interrelationships between germplasm, molecular diversity, phenotypic diversity and genome structure. It has the ability to store, integrate and visualize DNA sequence, enzymatic, SSR (simple sequence repeat) marker, germplasm and phenotypic data. The relational data model is selected and implemented in Oracle. An automated DNA sequence …

Vocal Development In American Kestrel (Falco Sparverius) Nestlings, John A. Smallwood, Valerie Dudajek, Sivajini Gilchrist, Mary Anne Smallwood

Department of Biology Faculty Scholarship and Creative Works

We studied the acoustical characteristics of calls made by nestling American Kestrels (Falco sparverius). A total of 563 vocal samples was obtained from 88 chicks (49 males and 39 females) from 20 broods. Thirteen frequency, three numerical, and two temporal characteristics were measured using audio spectrography. Discriminant function analysis failed to distinguish the calls of male and female chicks, but univariate and principal component analyses suggest that vocal ontogeny proceeds more rapidly in males than in females. The acoustical characteristics of call notes changed in a consistent manner as nestlings matured, and by day 16 chicks produced calls similar to …

Mammary Gland Cell Death Also Involves Lysosomal Autophagy, Reginald Halaby

Department of Biology Faculty Scholarship and Creative Works

The mammary gland undergoes apoptosis when estrogen ablation occurs, either naturally or enforced. The gland is known to execute the apoptotic process post weaning. Although the involuting mammary gland displays the characteristic biochemical features of apoptosis, including DNA fragmentation, chromatin condensation, and the formation of apoptotic bodies, it also shows evidence of an autophagic death. In this report, apoptosis of the gland was induced by removing the pups from their nursing mothers. In particular, we show that lysosomes increased in size and number, and moved from basal to apical regions in dying rat mammary gland cells. Lysosomal enzyme activities were …