Digital Commons Network^™

Bio-Optics In Integrated Ocean Observing Networks: Potential For Studying Harmful Algal Blooms, Oscar Schofield, J. Bosch, Scott Glenn, Gary Kirkpatrick, John Kerfoot, Steven Lohrenz, Mark A. Moline, Matthew Oliver, Paul Bissett

Biological Sciences

Ships have a difficult time sampling the time and space scales relevant for understanding how the physics and chemistry regulates marine ecosystems (National Research Council 2000, 2003, Figure 3.1); therefore the biology in the oceans is chronically under-sampled. This is a major problem for policy makers and local governments charged with managing coastal resources who are increasingly being asked to develop ‘ecosystem-based management’ plans (US Ocean Commission on Ocean Policy, 2004). Th is is especially true in regions where Harmful Algal Blooms (HABs) are present (Hallegraeff, 1993). Ecosystem-based management requires a quantitative understanding of the processes controlling marine food webs. …

The Role Of Estrogen Receptor Alpha In Neonatal Oocyte Development, Jemella C. Raymore

Renée Crown University Honors Thesis Projects - All

The development of primordial germ cells into oocytes is important for mammalian reproduction. Female germ cells first undergo a number of cell divisions resulting in the formation of cysts. Germ cell cysts are clusters of cells connected by intercellular bridges, formed by incomplete cytokinesis. The cysts breakdown after birth, resulting in individual oocytes that become surrounded by somatic pre-granulosa cells to form primordial follicles. During cyst breakdown two thirds of the original population of oocytes die. However, the processes by which cells within the cyst are designated to survive or die is not yet known. In addition, it is not …

Lack Of Respiratory Effects Of Nicotine Applied To The Caudal Medullary Raphã©, Nicole Bates

Biology Theses - Archive

Breathing is an involuntary and automatic process initiated by a network of neurons within the brainstem. These neurons are affected by a number of factors (mechanical, electrical and chemical) that help modulate the frequency and pattern of breathing. Three respiratory chemosensitive sites have traditionally been described on the ventral medullary surface. These sites are affected by the pH of the cerebrospinal fluid (CSF) bathing the brain and by chemicals dissolved within the CSF. More recently, additional sites have been described with chemosensitive activity and of these the medullary raphé has received the most attention. Although the dangers of smoking is …

The Shapley Value Of Phylogenetic Trees, Claus-Jochen Haake, Akemi Kashiwada '05, Francis E. Su

All HMC Faculty Publications and Research

Every weighted tree corresponds naturally to a cooperative game that we call a tree game; it assigns to each subset of leaves the sum of the weights of the minimal subtree spanned by those leaves. In the context of phylogenetic trees, the leaves are species and this assignment captures the diversity present in the coalition of species considered. We consider the Shapley value of tree games and suggest a biological interpretation. We determine the linear transformation M that shows the dependence of the Shapley value on the edge weights of the tree, and we also compute a null space …

Transposon Exaptation In Mammalian Evolution, Donald Hucks

Biology Theses - Archive

A growing body of work suggests that the exaptation of transposon-derived sequences to perform beneficial cellular functions has played a significant role in eukaryotic evolution. In chapter 1, we present an analysis of 10 exapted pogo transposons in the human genome. We present evidence that all 10 are restricted to tetrapods, and that 8 of the 10 arose early in mammalian evolution, in several independent exaptation events involving diverse pogo lineages. We show that all 10 have been subject to stringent selection throughout mammalian evolution, with pseudogenization having occurred only infrequently. In 4 of these genes, we observed no cases …

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 …

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.

The Dynamic Nature Of Eukaryotic Genomes, Laura Wegener Parfrey, Daniel J.G. Lahr, Laura A. Katz

Biological Sciences: Faculty Publications

Analyses of diverse eukaryotes reveal that genomes are dynamic, sometimes dramatically so. In numerous lineages across the eukaryotic tree of life, DNA content varies within individuals throughout life cycles and among individuals within species. Discovery of examples of genome dynamism is accelerating as genome sequences are completed from diverse eukaryotes. Though much is known about genomes in animals, fungi, and plants, these lineages represent only 3 of the 60-200 lineages of eukaryotes. Here, we discuss diverse genomic strategies in exemplar eukaryotic lineages, including numerous microbial eukaryotes, to reveal dramatic variation that challenges established views of genome evolution. For example, in …

Mojave Applied Ecology Notes Spring 2008, Lesley Defalco, E. Cayenne Engel, Scott R. Abella, Jessica E. Spencer, Jill E. Craig

Mojave Applied Ecology Notes

Post-fire restoration, fire chronosequence study, Joint Fire Science update, Weed Sentry program and DNWR surveys

Volume 01, Jessica Fields, Stephanie Neeley, Derek W. Hambright, Mary E. Lehman, Andrew R. Grzankowski, Zachary Johnson, Boone M. Prentice, Ashley M. Swandby, Victoria Morgan, Katie Williamson, Kristine G. Bender, Katelyn N. Romaine, D. Nicole Swann, Jessica Fox, Mike Mcateer, Alex Grabiec, Laura Nodtvedt, Nick Costa, Rachel Wolfe, Zack Dalton

Incite: The Journal of Undergraduate Scholarship

Introduction from Dean Dr. Charles Ross

Three Decades of Digging: Undergraduate Archeology at Longwood by Jessica Fields and Stephanie Neeley

Interactions of Allelopathy and Heat Stress in Plants by Derek W. Hambright and Mary E. Lehman

Inertial Electrostatic Confinement D-D Fusion Device: Construction and Simulation by Andrew R. Grzankowski

Shackled Nim by Zachary Johnson

Development of GC-MS and Chemometric Methods for the Analysis of Accelerants in Arson Cases by Boone M. Prentice

A Comparison of Image Analysis Methods in cDNA Microarrays by Ashley M. Swandby

Perceived Sexual Activity of Short and Long-Term Relationships by Victoria Morgan and Katie Williamson

Elderly …

Polyphasic Taxonomy Of A Group Of Globally Dispersed, Desiccation-Resistant Strains Of The Microvirga/Balneimonas Cluster, Bradley Tolar

Honors Capstones

No abstract provided.

The Effects Of Epidermal Growth Factor And Basic Fibroblast Growth Factor On Cryopreserved Human Adipose Derived Stem Cells In Culture: Proliferation, Adipogenesis, And Osteogenesis, Teddi Leigh Hebert

Honors Capstones

No abstract provided.

Responses Of The Sea Catfish, Ariopsis Felis, To Chemical Defenses From The Sea Hare, Aplysia Californica, Sheybani Arman

Honors Capstones

No abstract provided.

Chromosomes And Expression Mechanisms: Bringing Together The Roles Of Dna, Rna And Proteins, Moshe Yaniv, Sarah C.R. Elgin

Biology Faculty Research

No abstract provided.

The Homodimeric Kinesin, Kif17, Is Essential For Vertebrate Photoreceptor Sensory Outer Segment Development, Christine Insinna, Narendra Pathak, Brian Perkins, Iain Drummond, Joseph C. Besharse

Neuroscience: Faculty Publications

Sensory cilia and intraflagellar transport (IFT), a pathway essential for ciliogenesis, play important roles in embryonic development and cell differentiation. In vertebrate photoreceptors IFT is required for the early development of ciliated sensory outer segments (OS), an elaborate organelle that sequesters the many proteins comprising the phototransduction machinery. As in other cilia and flagella, heterotrimeric members of the kinesin 2 family have been implicated as the anterograde IFT motor in OS. However, in Caenorhabditis elegans, OSM-3, a homodimeric kinesin 2 motor, plays an essential role in some, but not all sensory cilia. Kif17, a vertebrate OSM-3 homologue, is known for …

Extant Or Extinct? White-Tailed Jack Rabbits And Yellowstone's Food Web, Joel Berger

Biological Sciences Faculty Publications

No abstract provided.

Novel Weapons: Invasive Plant Suppresses Fungal Mutualists In America But Not In Its Native Europe, Ragan M. Callaway, Don Cipollini, Kathryn Barto, Giles C. Thelen, Steven G. Hallett, Daniel Prati, Kristina Stinson, John Klironomos

Biological Sciences Faculty Publications

Why some invasive plant species transmogrify from weak competitors at home to strong competitors abroad remains one of the most elusive questions in ecology. Some evidence suggests that disproportionately high densities of some invaders are due to the release of biochemicals that are novel, and therefore harmful, to naïve organisms in their new range. So far, such evidence has been restricted to the direct phytotoxic effects of plants on other plants. Here we found that one of North America's most aggressive invaders of undisturbed forest understories, Alliaria petiolata (garlic mustard) and a plant that inhibits mycorrhizal fungal mutualists of North …

Requirement Of A Plasmid-Encoded Catalase For Survival Of Rhizobium Etli Cfn42 In A Polyphenol-Rich Environment, Alejandro García-De Los Santos, Erika López, Ciro A. Cubillas, K. Dale Noel, Susana Brom, David Romero

Biological Sciences Faculty Research and Publications

Nitrogen-fixing bacteria collectively called rhizobia are adapted to live in polyphenol-rich environments. The mechanisms that allow these bacteria to overcome toxic concentrations of plant polyphenols have not been clearly elucidated. We used a crude extract of polyphenols released from the seed coat of the black bean to simulate a polyphenol-rich environment and analyze the response of the bean-nodulating strain Rhizobium etli CFN42. Our results showed that the viability of the wild type as well as that of derivative strains cured of plasmids p42a, p42b, p42c, and p42d or lacking 200 kb of plasmid p42e was not affected in this environment. …

Exploring The Role Of Iscsua And Suf Operon In Shigella Flexneri Invasion And Resistance To Oxidative Stress, Benjamin R. Lloyd

Honors Theses

Shigella flexneri is a facultative intracellular pathogen capable of causing dysentery, a condition that afflicts many around the world, especially in developing countries. There are several aspects of Shigella pathogenesis that are not well understood, including a number of genetic and cellular changes that allow Shigella to adapt to stresses encountered while invading and replicating within the eukaryotic cytosol. It was the goal of this research to examine the roles of iscSUA and suf, gene systems predicted to encode for iron-sulfur cluster biosynthesis proteins, in Shigella surviving exposure to oxidative stress agents and during Shigella invasion and plaque formation …

Characterization Of Sox Family Members In Sponge Stem Cells And During Development, Karen E. Leeds

Honors Theses

Sponges are considered the oldest and most basal part of the metazoan lineage and therefore possess a unique set of gene families that are highly conserved among all animals. One of these gene families is known as Sox transcription factors. Sox genes are known to play important roles in complex animals such as the specification of the primary layers of the body, determination of sex, and most recently induction of induced pluirpotent stem cells (iPS cells) from both human and mouse fibroblasts with the help of three other transcription factors. We have found that two different demosponge species Halichondria bowerbanki …

A New Reproductive Mode In The Genus Melanzophryniscus Gallardo, 1961 (Anura: Bufonidae) With Description Of A New Species From The State Of Paraná, Brazil, José A. Langone, Magno V. Segallo, Marcos Bornschein, Rafael O. De Sá

Biology Faculty Publications

A new species of bufonid toad of the genus Melanophryniscus is described from a mountaintop that is part of the Serra do Mar in the northeastern State of Paraná, Brazil. Melanophryniscus alipioi sp. nov. is distinguished from other known species by its uniformly dark brown dorsal color and a unique breeding site. The new species reproduces in bromeliads, a reproductive mode previously unknown for this genus. This species might be susceptible to current habitat lost.

Use Of Phylogenetic Stains To Determine The Feeding Preferences Of Microbivorous Soil Nematodes, E. Harlan Michelle

Honors Theses

Due to their numerous and diverse roles in soil ecological processes – most notably decomposition and nutrient mineralization – nematodes have long been recognized as important biotic indicators of soil health (Ekschmitt et al., 2001; Ritz and Trudgill, 1999). The predominate means of assessing the information that these organisms might contain has been through nematode community analyses, a methodology that seeks to convert the vast amount of data regarding features such as diversity, maturity and richness into a series of indices which can be used to evaluate soil health and make comparisons across samples. Performance of these analyses typically involves …

The Effect Of Dexmedetomidine On The Mini-Cog Score And High-Mobility Group Box 1 Levels In Elderly Patients With Postoperative Neurocognitive Disorders Undergoing Orthopedic Surgery, Joan M Mastrobattista, Mark A Klebanoff, J Christopher Carey, John C Hauth, Cora A Macpherson, J Ernest, Margaret Cotroneo, Kenneth J Leveno, Ronald Wapner, Michael Varner, Jay D Iams, Atef Moawad, Baha M Sibai, Menachem Miodovnik, Mitchell Dombrowski, Mary J O'Sullivan, J Peter Vandorsten, Oded Langer

Faculty, Staff and Student Publications

Our objective was to determine the effect of body mass index (BMI) on response to bacterial vaginosis (BV) treatment. A secondary analysis was conducted of two multicenter trials of therapy for BV and TRICHOMONAS VAGINALIS. Gravida were screened for BV between 8 and 22 weeks and randomized between 16 and 23 weeks to metronidazole or placebo. Of 1497 gravida with asymptomatic BV and preconceptional BMI, 738 were randomized to metronidazole; BMI was divided into categories: < 25, 25 to 29.9, and > or = 30. Rates of BV persistence at follow-up were compared using the Mantel-Haenszel chi square. Multiple logistic regression was used to evaluate the effect …

Why Are Incubation Periods Longer In The Tropics? A Common-Garden Experiment With House Wrens Reveals It Is All In The Egg, Given Harper, W. Robinson, John Styrsky, Brian Payne, Charles Thompson

Scholarship

Incubation periods of Neotropical birds are often longer than those of related species at temperate latitudes. We conducted a common-garden experiment to test the hypothesis that longer tropical incubation periods result from longer embryo development times rather than from different patterns of parental incubation behavior. House wrens, one of few species whose geographic range includes tropical equatorial and temperate high latitudes, have incubation periods averaging 1.2 days longer at tropical latitudes. We incubated eggs of house wrens in Illinois and Panama under identical conditions in mechanical incubators. Even after factoring out differences in egg size, tropical house wrens still required …

Alignment Of Genetic And Physical Maps Of Gibberella Zeae, Jungkwan Lee, James E. Jurgenson, John F. Leslie, Robert L. Bowden

Faculty Work

We previously published a genetic map of Gibberella zeae (Fusarium graminearum sensu lato) based on a cross between Kansas strain Z-3639 (lineage 7) and Japanese strain R-5470 (lineage 6). In this study, that genetic map was aligned with the third assembly of the genomic sequence of ₊₊ strain PH-1 (lineage 7) using seven structural genes and 108 sequenced amplified fragment length polymorphism markers. Several linkage groups were combined based on the alignments, the nine original linkage groups were reduced to six groups, and the total size of the genetic map was reduced from 1,286 to 1,140 centimorgans. Nine …

Molecular Evolution, Michael Dietrich

Dartmouth Scholarship

Comprised of essays by top scholars in the field, this volume offers detailed overviews of philosophical issues raised by biology.

An Investigation Of The Diets Of Infants Born In Ireland During The First Six Months Of Life, Roslyn Tarrant

Doctoral

Appropriate infant feeding practices play a crucial part in achieving optimal health outcomes. It is well established that the protection, promotion and support of exclusive breastfeeding during the first 6-months of life would decrease the health inequalities experienced by mothers and infants (WHO/UNICEF, 2003c). Optimal weaning practices also have significant implications for infant health, notably in relation to normal development, mineral balance and the development of obesity (Department of Health, 1994). Historically, Ireland has one of the lowest breastfeeding rates in Europe. Furthermore, prior Irish-based research indicates significant deficiencies relating to weaning practices among mothers during the first year of …

Systems Approach Identifies An Organic Nitrogen-Responsive Gene Network That Is Regulated By The Master Clock Control Gene Cca1, Rodrigo A. Gutierrez, Trevor L. Stokes, Karen Thum, Xiaodong Xu, Mariana Obertello, Manpreet S. Katari, Milos Tanurdzic, Alexis Dean, Damion C. Nero, C Robertson Mcclung, Gloria M. Coruzzi

Dartmouth Scholarship

Understanding how nutrients affect gene expression will help us to understand the mechanisms controlling plant growth and development as a function of nutrient availability. Nitrate has been shown to serve as a signal for the control of gene expression in Arabidopsis. There is also evidence, on a gene-by-gene basis, that downstream products of nitrogen (N) assimilation such as glutamate (Glu) or glutamine (Gln) might serve as signals of organic N status that in turn regulate gene expression. To identify genome-wide responses to such organic N signals, Arabidopsis seedlings were transiently treated with ammonium nitrate in the presence or absence of …

All I Really Needed To Know I Learned During Gastrulation, Scott F. Gilbert

Biology Faculty Works

No abstract provided.

Supplemental Protocol For Liana Censuses, Stefan A. Schnitzer, Suzanne Rutishauser, Salomón Aguilar

Biological Sciences Faculty Research and Publications

Lianas affect many aspects of tropical forest dynamics and thus the study of their ecology is critical for a comprehensive understanding of tropical forest ecology. Recently, we initiated a complete census of all lianas ≥1 cm diameter in the 50 ha forest dynamics plot on Barro Colorado Island, Panama using the census protocol developed by Gerwing et al. [Gerwing, J.J., Schnitzer, S.A., Burnham, R.J., Bongers, F., Chave, J., DeWalt, S.J., Ewango, C.E.N., Foster, R., Kenfack, D., Martinez-Ramos, M., Parren, M., Parthasarathy, N., Perez-Salicrup, D.R., Putz, F.E., Thomas, D.W., 2006. A standard protocol for liana censuses. Biotropica 38, 256–261]. This protocol …