Digital Commons Network^™

Visualizing Early Frog Development With Motion-Sensitive 3-D Optical Coherence Microscopy, Richard C. Haskell, Mary E. Williams, Daniel C. Petersen, Barbara M. Hoeling, Andrew J. Schile, J. D. Pennington, M. G. Seetin, J. M. Castelaz, Scott E. Fraser, Cyrus Papan, Hongwu Ren, Johannes F. De Boer, Zhongping Chen

All HMC Faculty Publications and Research

A motion-sensitive en-face-scanning 3-D optical coherence microscope (OCM) has been designed and constructed to study critical events in the early development of plants and animals. We describe the OCM instrument and present time-lapse movies of frog gastrulation, an early developmental event in which three distinct tissue layers are established that later give rise to all major organ systems. OCM images constructed with fringe-amplitude data show the mesendoderm migrating up along the blastocoel roof, thus forming the inner two tissue layers. Motion-sigma data, measuring the random motion of scatterers, is used to construct complementary images that indicate the presence of Brownian …

Immunogold Labeling To Enhance Contrast In Optical Coherence Microscopy Of Tissue Engineered Corneal Constructs, Chris B. Raub, Elizabeth J. Orwin, Richard C. Haskell

All HMC Faculty Publications and Research

Our lab has used an optical coherence microscope (OCM) to assess both the structure of tissue-engineered corneal constructs and their transparency. Currently, we are not able to resolve cells versus collagen matrix material in the images produced. We would like to distinguish cells in order to determine if they are viable while growing in culture and also if they are significantly contributing to the light scattering in the tissue. In order to do this, we are currently investigating the use of immunogold labeling. Gold nanoparticles are high scatterers and can create contrast in images. We have conjugated gold nanoparticles to …

The Bvg Virulence Control System Regulates Biofilm Formation In Bordetella Bronchiseptica, Yasuhiko Irie, Seema Mattoo, Ming H. Yuk

Biology Faculty Publications

Bordetella species utilize the BvgAS (Bordetella virulence gene) two-component signal transduction system to sense the environment and regulate gene expression among at least three phases: a virulent Bvg⁺ phase, a nonvirulent Bvg⁻ phase, and an intermediate Bvgⁱ phase. Genes expressed in the Bvg⁺ phase encode known virulence factors, including adhesins such as filamentous hemagglutinin (FHA) and fimbriae, as well as toxins such as the bifunctional adenylate cyclase/hemolysin (ACY). Previous studies showed that in the Bvgⁱ phase, FHA and fimbriae continue to be expressed, but ACY expression is significantly downregulated. In this report, we determine …

Response Of Brood-Parasitic Bronzed Cowbird To Playback Of The Song Of Audubon's Oriole, Steven G. Monk, Timothy Brush

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

ABSTRACT—In the Lower Rio Grande Valley of South Texas, Audubon’s orioles (Icterus graduacauda) have declined substantially in the past 50 y, probably due to habitat loss, fragmentation, and brood parasitism by bronzed cowbirds (Molothrus aeneus). Tape playback of the song of Audubon’s oriole, originally intended to better survey the oriole, also attracted bronzed cowbirds. Bronzed cowbirds flew silently into the nearest tree in 14.1% of 234 playbacks, whereas Audubon’s orioles responded vocally or flew toward the recorder in 15.8% of playbacks. Bronzed cowbirds might use vocalizations of Audubon’s oriole as a cue to find breeding pairs or nests of this …

Cholinergic Modulation Of The Locomotor Network In The Lamprey Spinal Cord, Katharina A. Quinlan, Peter G. Placas, James T. Buchanan

Biological Sciences Faculty Research and Publications

Acetylcholine (ACh) was found here to be a strong modulator of swimming activity in the isolated spinal cord preparation of the adult lamprey (Ichthyomyzon unicuspis). During fictive swimming induced with either D-glutamate or N-methyl-D-aspartate, addition of ACh (200 µM) significantly reduced the cycle period of ventral root bursts to 54%, intersegmental phase lag to 32%, and ventral root burst proportion to 80% of control levels. Effects of ACh were apparent at concentrations as low as 1 µM. Both nicotinic and muscarinic receptors are involved, in that application of either nicotinic or muscarinic agonists alone significantly reduced cycle …

Reticulospinal Neurons Receive Direct Spinobulbar Inputs During Locomotor Activity In Lamprey, James F. Einum, James T. Buchanan

Biological Sciences Faculty Research and Publications

Reticulospinal neurons of the lamprey brain stem receive rhythmic input from the spinal cord during locomotor activity. The goal of the present study was to determine whether such spinal input has a direct component to reticulospinal neurons or depends on brain stem interneurons. To answer this question, an in vitro lamprey brain stem-spinal cord preparation was used with a diffusion barrier placed caudal to the obex, separating the experimental chamber into two baths. Locomotor activity was induced in the spinal cord by perfusion of D-glutamate or N-methyl-DL-aspartate into the spinal cord bath. The brain stem bath was first perfused …

Genesis: The Evolution Of Biology, Michael Dietrich

Dartmouth Scholarship

Review of Genesis: The Evolution of Biology by Jan Sapp, 2003.

Multiple Kh Domains Of Poly C Binding Protein Are Required For Its Trans-Activation On The Proximal Promoter Of The Mu-Opioid Receptor Gene, Adnan K. Malik

Seton Hall University Dissertations and Theses (ETDs)

The mu-opioid receptor (MOR) has been shown to mediate morphine induced analgesia, addiction, and tolerance. The expression of the major product of the MOR (MOR-1) gene has been found to be driven by two promoters, a distal promoter and a proximal promoter. The proximal promoter region has been shown in previous studies to be the major promoter for the regulation of MOR gene transcription in the adult mouse brain and embryonic development. Recent studies have shown that single-stranded DNA binding proteins (such as Poly C Binding Protein) are involved in transcriptional regulation of mouse MOR gene. Poly C binding protein …

Testing Species Boundaries In An Ancient Species Complex With Deep Phylogeographic History: Genus Xantusia (Squamata: Xantusiidae), Keith A. Crandall, Elizabeth A. Sinclair, Robert L. Bezy, Kathryn Bolles, Jose L. Camarillo, Jack W. Sites

Faculty Publications

Identification of species in natural populations has recently received increased attention with a number of investigators proposing rigorous methods for species delimitation. Morphologically conservative species (or species complexes) with deep phylogenetic histories (and limited gene flow) are likely to pose particular problems when attempting to delimit species, yet this is crucial to comparative studies of the geography of speciation. We apply two methods of species delimitation to an ancient group of lizards (genus Xantusia) that occur throughout southwestern North America. Mitochondrial cytochrome b and nicotinamide adenine dinucleotide dehydrogenase subunit 4 gene sequences were generated from samples taken throughout the geographic …

Woodland Amphibian Distribution In Parks And Greenspaces Of The Portland, Oregon Metropolitan Area: A Multiple Scale Investigation, Laura A. Roberts

Dissertations and Theses

Loss of biodiversity due to habitat fragmentation is worldwide problem. With growing human populations and increasing urbanization, it is a necessity to conduct studies on wildlife occurring in urban areas. Currently there is a deficit of research investigating woodland amphibians in urban environments. My objectives were to describe amphibian species richness and abundance in the Portland, Oregon, Metropolitan region, and relate patterns of variation to variables at three increasingly large spatial scales: 1) local microenvironmental (i.e. amphibian/substrate interaction), (2) macrohabitat/patch (i.e. park or greenspace), and 3) landscape (surrounding parks and greenspaces). Environmental variables occurring within the three spatial scales were …

Chloroplast Dna Rearrangements In Campanulaceae: Phylogenetic Utility Of Highly Rearranged Genomes, Mary E. Cosner, Linda A. Raubeson, Robert K. Jansen

All Faculty Scholarship for the College of the Sciences

Background

The Campanulaceae (the "hare bell" or "bellflower" family) is a derived angiosperm family comprised of about 600 species treated in 35 to 55 genera. Taxonomic treatments vary widely and little phylogenetic work has been done in the family. Gene order in the chloroplast genome usually varies little among vascular plants. However, chloroplast genomes of Campanulaceae represent an exception and phylogenetic analyses solely based on chloroplast rearrangement characters support a reasonably well-resolved tree.

Results

Chloroplast DNA physical maps were constructed for eighteen representatives of the family. So many gene order changes have occurred among the genomes that characterizing individual mutational …

Synaptic Transformations Underlying Highly Selective Auditory Representations Of Learned Birdsong, Melissa J. Coleman, Richard Mooney

WM Keck Science Faculty Papers

Stimulus-specific neuronal responses are a striking characteristic of several sensory systems, although the synaptic mechanisms underlying their generation are not well understood. The songbird nucleus HVC (used here as a proper name) contains projection neurons (PNs) that fire temporally sparse bursts of action potentials to playback of the bird's own song (BOS) but are essentially silent when presented with other acoustical stimuli. To understand how such remarkable stimulus specificity emerges, it is necessary to compare the auditory-evoked responsiveness of the afferents of HVC with synaptic responses in identified HVC neurons. We found that inactivating the interfacial nucleus of the nidopallium …

Sinusoidal Length Oscillation- And Receptor-Mediated Mrna Expression Of Myosin Isoforms And Α-Sm Actin In Airway Smooth Muscle, Melissa Wahl, Thomas J. Eddinger, Chi-Ming Hai

Biological Sciences Faculty Research and Publications

We tested the hypothesis that sinusoidal length oscillation and receptor activation interactively regulate the abundance of mRNA encoding α-smooth muscle (α-SM) actin and myosin isoforms in intact bovine tracheal smooth muscle. We found that sinusoidal length oscillation significantly downregulated abundance of mRNA encoding α-SM actin mRNA in unstimulated tissues but not in histamine- and carbachol-activated tissues. This observation suggests antagonistic interactions between mechanical stretch and receptor-mediated signal transduction in regulating the abundance of mRNA encoding α-SM actin in intact airway smooth muscle. This pattern of antagonistic interaction was also observed in cholinergic receptor activation experiments. Whereas carbachol significantly upregulated myosin …

Characterization Of A Catechol-Type Siderophore And The Detection Of A Possible Outer Membrane Receptor Protein From Rhizobium Leguminosarum Strain Iari 312., Brianne Lee Clark

Electronic Theses and Dissertations

Many gram-negative bacteria produce and secrete siderophores under iron-deficient conditions. Siderophores are low molecular weight compounds (600-1500 Daltons), which chelate ferric iron with an extremely high affinity, and the complex is actively transported across the outer and inner membranes of gram-negative bacteria. There are two main classes of siderophores: catechol and hydroxamate. Catechol-type siderophores chelate ferric iron via hydroxyl groups, and hydroxamate-type siderophores chelate ferric iron via a carbonyl group with an adjacent nitrogen. Rhizobia fix atmospheric nitrogen symbiotically in leguminous plants using the iron-containing enzyme nitrogenase. To satisfy their iron requirements, many rhizobia are known to produce siderophores. Rhizobium …

From Biomedicine To Natural History Research: Est Resources For Ambystomatid Aalamanders, Srikrishna Putta, Jeramiah J. Smith, John A. Walker, Mathieu Rondet, David W. Weisrock, James Monaghan, Amy K. Samuels, D. Kevin Kump, David C. King, Nicholas J. Maness, Bianca Habermann, Elly Tanaka, Susan V. Bryant, David M. Gardiner, David M. Parichy, S. Randal Voss

Biology Faculty Publications

BACKGROUND: Establishing genomic resources for closely related species will provide comparative insights that are crucial for understanding diversity and variability at multiple levels of biological organization. We developed ESTs for Mexican axolotl (Ambystoma mexicanum) and Eastern tiger salamander (A. tigrinum tigrinum), species with deep and diverse research histories.

RESULTS: Approximately 40,000 quality cDNA sequences were isolated for these species from various tissues, including regenerating limb and tail. These sequences and an existing set of 16,030 cDNA sequences for A. mexicanum were processed to yield 35,413 and 20,599 high quality ESTs for A. mexicanum and A. t. tigrinum, respectively. Because the …

Determining Rates Of Change And Evaluating Group-Level Resiliency Differences In Hyporheic Microbial Communities In Response To Fluvial Heavy-Metal Deposition, Kevin P. Feris, Philip W. Ramsey, Matthias Rillig, Johnnie N. Moore, James E. Gannon, William E. Holben

Biological Sciences Faculty Publications

Prior field studies by our group have demonstrated a relationship between fluvial deposition of heavy metals and hyporheic-zone microbial community structure. Here, we determined the rates of change in hyporheic microbial communities in response to heavy-metal contamination and assessed group-level differences in resiliency in response to heavy metals. A controlled laboratory study was performed using 20 flowthrough river mesocosms and a repeated-measurement factorial design. A single hyporheic microbial community was exposed to five different levels of an environmentally relevant metal treatment (0, 4, 8, 16, and 30% sterilized contaminated sediments). Community-level responses were monitored at 1, 2, 4, 8, and …

The Mayfly Newsletter, Peter M. Grant

The Mayfly Newsletter

The Mayfly Newsletter is the official newsletter of the Permanent Committee of the International Conferences on Ephemeroptera.

Mechanism Of Chromium Reduction Of Benzo[A]Pyrene Diolepoxide Mutagenesis In Human Fibroblasts, Cara Suzanne Kriss

Masters Theses

Environmental agents can cause an increase in cellular stress and damage DNA which can lead to diseases such as cancer. Chromium produces cellular stress by increasing the reactive oxygen species through a Fenton-like reaction, where chromium reacts with hydrogen peroxide to form hydroxyl radicals. Benzo[ a ]pyrene is an environmental carcinogen that is metabolized by cytochrome p450 enzymes into benzo[a]pyrene diolepoxide (BPDE). BPDE is highly reactive with DNA producing large DNA-adducts primarily on guanine nucleotides. The primary intracellular pathway by which mammalian cells remove damaged DNA caused by bulky mutagens is nucleotide excision repair. We have found that, in BPDE …

Pf15p Is The Chlamydomonas Homologue Of The Katanin P80 Subunit And Is Required For Assembly Of Flagellar Central Microtubules, Erin E. Dymek, Paul A. Lefebvre, Elizabeth F. Smith

Dartmouth Scholarship

Numerous studies have indicated that the central apparatus plays a significant role in regulating flagellar motility, yet little is known about how the central pair of microtubules or their associated projections assemble. Several Chlamydomonas mutants are defective in central apparatus assembly. For example, mutant pf15 cells have paralyzed flagella that completely lack the central pair of microtubules. We have cloned the wild-type PF15 gene and confirmed its identity by rescuing the motility and ultrastructural defects in two pf15 alleles, the original pf15a mutant and a mutant generated by insertional mutagenesis. Database searches using the 798-amino-acid polypeptide predicted from the complete …

Prevalence Of Teleological And Lamarckian Misconceptions Of Natural Selection Among College Students, Bryce T. Battisti

Theses and Dissertations

Science teachers and researchers note that students must correctly understand the role of natural selection in evolution to make sense of biology. The level of understanding of natural selection can be assessed using the Conceptual Inventory of Natural Selection (CINS) which is a 20-item multiple-choice test that incorporates student misconceptions as distractors. In the present study, Item Response Theory (IRT) was used to analyze the occurance of misconceptions on the CINS among 1192 students in an introductory non-majors biology course. The four most difficult topics in the CINS are: (a) how change occurs in a population; (b) origin of variation; …

The Magnolia Warbler Dendroica Magnolia On Unaka Mountain, Unicoi County, Tn: Possible Breeding And Habitat Analysis., Kevin Patrick Elam

Electronic Theses and Dissertations

The chief purpose of this study is to provide information on the habitat and breeding information of Magnolia Warblers on Unaka Mountain. Magnolia Warblers breed in Canada and the Northeastern United States. There are no current breeding records for this species in Tennessee.

For the habitat analysis, trees were identified on individual subplots. Shrubs were analyzed using the point-intercept method. Most of the major tree and shrub species were different than those found in Maine, which is a major breeding region for this species. Therefore, it's the structure of the habitat that is important for nesting. Fledglings were seen, giving …

Use Of 16s Rrna, 23s Rrna, And Gyrb Gene Sequence Analysis To Determine Phylogenetic Relationships Of Bacillus Cereus Group Microorganisms, Sergei G. Bavykin, Yuri P. Lysov, Vladimir Zakhariev, John J. Kelly, Joany Jackman, David A. Stahl, Alexey Cherni

Biology: Faculty Publications and Other Works

In order to determine if variations in rRNA sequence could be used for discrimination of the members of the Bacillus cereus group, we analyzed 183 16S rRNA and 74 23S rRNA sequences for all species in the B. cereus group. We also analyzed 30 gyrB sequences for B. cereus group strains with published 16S rRNA sequences. Our findings indicated that the three most common species of the B. cereus group, B. cereus, Bacillus thuringiensis, and Bacillus mycoides, were each heterogeneous in all three gene sequences, while all analyzed strains of Bacillus anthracis were found to be homogeneous. Based on analysis …

Size And Organic Content Of Eggs Of Marine Annelids, And The Underestimation Of Egg Energy Content By Dichromate Oxidation, William Jaeckle, Bruno Pernet

Scholarship

Dichromate oxidation is a simple technique that is often used to estimate the energy content of eggs in studies of marine invertebrate life histories (1). We used this method to measure the energy contents of the eggs of 12 species of marine annelids. In combination with measures of egg ash-free dry weight (AFDW), these data yielded estimates of AFDW-specific energy density that were mostly lower than the average weight-specific energy density of carbohydrates. This seemed unlikely to be correct, as invertebrate eggs typically contain little carbohydrate and instead are composed primarily of energy-dense protein and lipid (1, 2). After validating …

Agribusiness Sheep Updates - 2004 Part 3, Ken Hart, Keith Croker, Rob Davidson, Mario D'Antuono, Evan Burt, Tanya Kilminster, Diana Fedorenko, Darryl Mcclements, Robert Beard, Sandy Turton, Martin Atwell, Robert Beard

Sheep Updates

Posters Can Merino Ewes be Teased to Synchronise Oestrus for a Summer/Autumn Mating? Ken Hart, Keith Croker, Department of Agriculture Western Australia, Rob Davidson, School of Animal Biology, University of Western Australia. Mario D'Antuono, Department of Agriculture Western Australia Damara Sheep: Now Looking Domestic Evan Burt and Tanya Kilminster, Department of Agriculture Western Australia Production and Water Use of Lucerne and French Serradella Under Three Sowing Rates Diana Fedorenko1,4, Darryl McClements1,4 , Robert Beard3,4 1Department of Agriculture, 3 Farmer, Meckering, 4CRC for Plant-based Management of Dryland Salinity. E-SHEEP - Individual Animal Management is here Sandy Turton & Martin Atwell, Department …

A Modeling Study Of Benthic Detritus Flux's Impacts On Heterotrophic Processes In Lake Michigan, Changsheng Chen, Lixia Wang, Jianhua Qi, Hedong Liu, Judith Wells Budd, David J. Schwab, Dmitry Beletsky, Henry Vanderploeg, Brian Eadie, Thomas Johengen, James Cotner, Peter J. Lavrentyev

Biology Faculty Research

Effects of sediment resuspension-induced benthic detrital flux on the heterotrophic part of the microbial food web in Lake Michigan were examined using a three-dimensional (3-D) coupled biological and physical model. The model was driven by the realistic meteorological forcing observed in March 1999. Wind-induced surface wave dynamics were incorporated into the physical model to generate the bottom flux. The model-generated benthic detrital flux was assumed to be proportional to the difference between model-calculated and critical stresses at the bottom. The model results indicate that detrital flux at the bottom was a key factor causing a significant increase of phosphorus and …

Deriving In Situ Phytoplankton Absorption For Bio-Optical Productivity Models In Turbid Waters, Christina Orrico, Matthew J. Oliver, Oscar Schofield, Trisha Bergmann, Scott Glenn, Mark A. Moline

Biological Sciences

As part of Hyperspectral Coupled Ocean Dynamics Experiment, a high-resolution hydrographic and bio-optical data set was collected from two cabled profilers at the Long-Term Ecosystem Observatory (LEO). Upwelling-and downwelling-favorable winds and a buoyant plume from the Hudson River induced large changes in hydrographic and optical structure of the water column. An absorption inversion model estimated the relative abundance of phytoplankton, colored dissolved organic matter (CDOM) and detritus, as well as the spectral exponential slopes of CDOM and detritus from in situ WET Labs nine-wavelength absorption/attenuation meter (ac-9) absorption data. Derived optical weights were proportional to the parameter concentrations and allowed …

The Assessment Of Antibiotic Resistance And Detection Of Class 1 And Class 2 Integrons In Fecal Coliform Bacteria Isolated From The Triplett Creek Watershed, Rowan County, Kentucky, Tina Howard Ousley

Morehead State Theses and Dissertations

A thesis presented to the faculty of the College of Science and Technology at Morehead State University in partial fulfillment of the requirements for the Degree of Master of Science by Tina Howard Ousley on July 15, 2004.

Genetic Diversity Of Peanut (Arachis Hypogaea L.) And Its Wild Relatives Based On The Analysis Of Hypervariable Regions Of The Genome, Marcio De Carvalho Moretzsohn, Mark S. Hopkins, Sharon E. Mitchell, Stephen Kresovich, Jose Francisco Montenegro Valls, Marcio Elias Ferreira

Faculty Publications

Background: The genus Arachis is native to a region that includes Central Brazil and neighboring countries. Little is known about the genetic variability of the Brazilian cultivated peanut (Arachis hypogaea, genome AABB) germplasm collection at the DNA level. The understanding of the genetic diversity of cultivated and wild species of peanut (Arachis spp.) is essential to develop strategies of collection, conservation and use of the germplasm in variety development. The identity of the ancestor progenitor species of cultivated peanut has also been of great interest. Several species have been suggested as putative AA and BB genome donors …

Zapus Princeps, E. Blake Hart, Mark C. Belk, Eralee Jordan, Malinda W. Gonzalez

Faculty Publications

Zapus princeps Allen, 1893:71. Type locality “Florida, La Plata Co., Colorado.”
Zapus pacificus Merriam, 1897:104. Type locality “Prospect, Rogue River Valley, Jackson Co., Oregon.”
Zapus saltator Allen, 1899:3. Type locality “Telegraph Creek, British Columbia.”

Responses Of Nesting Bobolinks (Dolichonyx Oryzivorus) To Habitat Edges, Eric K. Bollinger, Thomas A. Gavin

Faculty Research & Creative Activity

T.-Avoidance of habitat edges may be contributing to reduced densities of grass- land birds in small habitat patches. Nest densities for grassland-nesting Bobolinks (Dolichonyx oryzivorus) were much lower than expected within 25 m of forest edges at three sites in New York, and that pattern ("edge avoidance") extended to 100 m at one site. Nests located within 50 m of forest or wooded hedgerow edges had lower daily survival rates, compared with nests >100 m from any habitat edge. Bobolinks tended to move away from forest edges when renest- ing after nest failure; that pattern was especially evident in females …