Biology Commons^™

Are Morphology And Performance Predation-Related? Swimming Speed And Ontological Shape Comparisons Between Populations Of A Live-Bearing Fish, Elizabeth Hassell, Dr. Mark Belk

Journal of Undergraduate Research

I used my ORCA grant for my honors thesis in biology, which has been a great success. The results are not yet complete because the depth of this project goes beyond the one-year time frame of a typical ORCA project; however, our planned schedule is still in place and the final results of this study will be submitted for publication in the coming months.

An Objective Diagnosis Of Eating Disorders Stable Isotope Analysis Of Hair, Brooke Allen, Beverly Roeder

Journal of Undergraduate Research

Eating disorders (EDs) are a group of mental illnesses that afflict up to two percent of the population . The group of illnesses consists of anorexia, bulimia, and EDNOS (Eating Disorders Not Otherwise Specified). The diagnostic methods for eating disorders that are currently accepted by the American Psychiatric Association are problematic, because they rely mainly upon patient responses to self-report or physician-administered examinations. These assessments do not always return accurate diagnoses, because they are primarily subjective in nature . Thus, a more objective method for diagnosis, one which is more focused on physiological measures than on subjective questions, is needed …

Comparisons Of Genetic Diversity Among Disjunct Populations Of Magnolia Tripetala, Victoria A. Gilkison

Mahurin Honors College Capstone Experience/Thesis Projects

Plant ranges are often made up of core areas where the distribution is continuous and the population density is high with small disjunct populations at the margins of the core. One well-studied type of disjunct population is formed by long distance dispersal as plants migrate away from disjunct Pleistocene refugial populations. The retreat of the Wisconsinan glaciation resulted in the outward dispersal of many plant species from their refugial locations to areas with suitable habitat. Many plants expanded their ranges through rare-long-distance dispersal.

This study used microsatellites to compare the genetic diversity, inbreeding levels, and gene flow frequency of disjunct …

Signatures Of Rapid Evolution In Urban And Rural Transcriptomes Of White-Footed Mice (Peromyscus Leucopus) In The New York Metropolitan Area, Stephen Edward Harris, Jason Munshi-South, Craig Oberfell, Rachel O'Neill

Publications and Research

Urbanization is a major cause of ecological degradation around the world, and human settlement in large cities is accelerating. New York City (NYC) is one of the oldest and most urbanized cities in North America, but still maintains 20% vegetation cover and substantial populations of some native wildlife. The white-footed mouse, Peromyscus leucopus, is a common resident of NYC’s forest fragments and an emerging model system for examining the evolutionary consequences of urbanization. In this study, we developed transcriptomic resources for urban P. leucopus to examine evolutionary changes in protein-coding regions for an exemplar “urban adapter.” We used Roche 454 …

Thinking Aloud In The Science Classroom: Can A Literacy Strategy Increase Student Learning In Science?, Lindsey Joan Mockel

Dissertations and Theses

This research study investigated the effect of using the think aloud protocol while reading informational text on students' ability to learn from text in a secondary science classroom. The participants in this study were high school students (n=47) in three classes of a mixed-grade Integrated Biology, Chemistry, and Physics course. The study tracked student achievement during a four-week curriculum unit on the theory of evolution and evidence for biological evolution. All students received instruction on using the think aloud protocol, and all students practiced the think aloud protocol when reading short articles related to scientific evidence for evolution. The researcher …

Intraspecific Life History Variation In The Knife-Edged Livebearer Alfaro Cultratus (Cyprinodontiformes: Poeciliidae) From Costa Rica, Lacey Nay, Dr. Jerry Johnson

Journal of Undergraduate Research

A species’ life history traits, including growth and reproduction, follow patterns of natural selection. Evolution is driven by natural selection which, in short, can be described as the ability of an organism to conform to its environment (Pianka 2000). Individuals possessing those traits that are more favorable in a specific environment tend to have higher rates of survival and reproduction, causing those traits to become more prevalent in the population. In this manner, a trait is “selected for” by nature. Life history evolution is based on the concept of trade-offs. The more energy an individual expends on growth, the less …

Mscs-Like Mechanosensitive Channels In Plants And Microbes, Margaret E. Wilson, Grigory Maksaev, Elizabeth S. Haswell

Biology Faculty Research

The challenge of osmotic stress is something all living organisms must face as a result of environmental dynamics. Over the past three decades, innovative research and cooperation across disciplines have irrefutably established that cells utilize mechanically gated ion channels to release osmolytes and prevent cell lysis during hypoosmotic stress. Early electrophysiological analysis of the inner membrane of Escherichia coli identified the presence of three distinct mechanosensitive activities. The subsequent discoveries of the genes responsible for two of these activities, the mechanosensitive channels of large (MscL) and small (MscS) conductance, led to the identification of two diverse families of mechanosensitive channels. …

Subset Of Heat-Shock Transcription Factors Required For The Early Response Of Arabidopsis To Excess Light, Hou-Sung Jung, Peter A. Crisp, Gonzalo M. Estavillo, Benjamin Cole

Dartmouth Scholarship

Sunlight provides energy for photosynthesis and is essential for nearly all life on earth. However, too much or too little light or rapidly fluctuating light conditions cause stress to plants. Rapid changes in the amount of light are perceived as a change in the reduced/oxidized (redox) state of photosynthetic electron transport components in chloroplasts. However, how this generates a signal that is relayed to changes in nuclear gene expression is not well understood. We modified redox state in the reference plant, Arabidopsis thaliana, using either excess light or low light plus the herbicide DBMIB (2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone), a well-known inhibitor of photosynthetic …

Dirigent Domain-Containing Protein Is Part Of The Machinery Required For Formation Of The Lignin-Based Casparian Strip In The Root, Prashant S. Hosmani, Takehiro Kamiya, John Danku, Sadaf Naseer, Niko Geldner, Mary Lou Guerinot, David Salt

Dartmouth Scholarship

The endodermis acts as a "second skin" in plant roots by providing the cellular control necessary for the selective entry of water and solutes into the vascular system. To enable such control, Casparian strips span the cell wall of adjacent endodermal cells to form a tight junction that blocks extracellular diffusion across the endodermis. This junction is composed of lignin that is polymerized by oxidative coupling of monolignols through the action of a NADPH oxidase and peroxidases. Casparian strip domain proteins (CASPs) correctly position this biosynthetic machinery by forming a protein scaffold in the plasma membrane at the site where …

Comparing Riparian Fly Diversity (Diptera) To Environmental And Human Pressures In Mongolia, Joss R. Wertz, Dr. C. Riley Nelson

Journal of Undergraduate Research

Mongolia is as large as the eastern United States with the lowest population density in Asia. This has kept development and its effects at a minimum. Thus, Mongolia retains much of the biota that has been lost in the surrounding countries. In the past 15 years, Mongolia has begun the difficult process of transitioning to a free market system. With this transition have come many pressures to exploit Mongolia’s extensive natural resources, while the number of scientists to monitor the effects of these developments is small. These pressures make an immediate need for biomonitoring methods to be developed. In addition, …

Identifying Selection In The Angptl4 Gene Using Treesaap, Jeffrey Staples, Dr. Keith Crandall

Journal of Undergraduate Research

Geneticists have successfully identified the sources of many diseases that are inherited according to Mendelian rules (e.g. cystic fibrosis and Huntington’s disease). However, not all diseases are caused by one faulty gene; these so-called complex diseases (e.g. asthma, obesity, and diabetes) result from any number of mutated genes, faulty pathways, or environmental conditions. Association studies have identified a particular gene family (Angiopoietin-like proteins or ANGPTL) to be correlated with several of these complex diseases, namely diabetes, obesity, and heart disease1, 2; however, the function and contribution of these genes to these complex diseases is not completely understood.

An Analysis Of Genetic Complexity, Gabriel Proulx, Dr. Keith Crandall

Journal of Undergraduate Research

Sequencing genomes still requires considerable equipment and resources. While a full sequencing of all known species is obviously the end goal, analyzing ESTs, short sequences of expressed genes, can suffice in the meantime as an easier and less resource-intensive method to mapping out a species’ expressed genes. ESTs, however, are limited in both length and quality.

Phenotypic Divergence In Boldness/Shyness In Brachyraphis Fishes, Scott Miller, Dr. Jerry Johnson

Journal of Undergraduate Research

Among some of the most exciting research in evolutionary biology involves animal social behavior. Of particular interest is whether social behaviors are inheritable. If social behaviors are inheritable, they become a selective force and are capable of shaping the life history of an animal. Dr. Culum Brown has pioneered much of the research in this field with fishes. My research is based on his preliminary research and supplemented with work by Dr. Jerry Johnson. The goal of my research was to test if behaviors evolve in response to differences in mortality pressures in the environment. A greater understanding of how …

Evaluating The Fitness Costs Of Rnai Resistance In C. Elegans, Stephen Jenkins, Dr. Byron Adams

Journal of Undergraduate Research

Plant-parasitic nematodes cause an estimated $125 billion worth of crop losses globally each year. Fifteen percent of nematode species are plant-parasitic nematodes, and the most significant species parasitize roots. While the parasites don’t always kill the plants, they disrupt water transport and divert nutrients to themselves, causing considerable impact on crop yields. The most significant contributors are root-knot nematodes and cyst nematodes.

Isolation And Characterization Of A North American Species Of Phasmarhabditis Sp., Nate Keplinger, Dr. Byron Adams

Journal of Undergraduate Research

Slugs and snails are pests that destroy various food crops throughout the entire world. To control their outbreak, Europeans have utilized the nematode Phasmarhabditis hermaphrodita, a mollusc pathogen. This nematode has not been introduced into US agriculture because it has not been found in a mollusc pathogenic stage in the United States and could have detrimental non-target effects. Thus, slug and snail control methods in the US are currently limited to petrochemical methods of pest management. I have recently discovered an unidentified species of the genus Phasmarhabditis. that rapidly and consistently kills slugs, snails and grubs. I propose a more …

Antarctic Plectus Biodiversity: A Molecular And Morphological Analysis, Adam Clayton, Dr. Byron Adams

Journal of Undergraduate Research

Nematodes are known to play important roles in ecosystem functioning, however their specific roles may vary across different taxonomic levels. Correct identification of nematode species is necessary when analyzing their diversity in order to effectively assign their functional role(s).

Molecular Identification Of Nematode Gut Contents, Quinn Martin, Dr. Byron Adams

Journal of Undergraduate Research

Species-specific food web relationships involving free-living microbivorous nematodes are not well established, yet critical to our understanding of their involvement in nutrient cycling and ecosystem function. Antarctic soil ecosystems are the simplest on earth and serve as a model system for exploring the role of biodiversity in ecosystem function. To establish which bacteria are involved in trophic relationships with nematodes, we surface-sterilized nematodes and extracted their DNA, including bacterial DNA from the gut contents of the nematodes. From this bacterial DNA we PCR amplified the 16S gene and sequenced the product in order to determine the identity of the gut …

Meloidogyne Phylogeny: A Supertree Approach, Camille Finlinson Porter, Dr. Byron Adams

Journal of Undergraduate Research

Meloidogyne nematodes are agricultural pests that cause approximately 5% of global crop loss each year. In order to develop more effective control strategies, a clearer image of how the many species of Meloidogyne are related is needed.

A Survey Of Dance Flies (Diptera: Empididae) In Mongolia, Paul Frandsen, Dr. C. Riley Nelson

Journal of Undergraduate Research

Dance flies from the super family Empidoidea (Diptera:Empididae, Hybotidae) were collected from western Mongolia in June and July 2009. Historical published records of Empididae in Mongolia along with unpublished, more recently collected records from the Selenge River Basin were compared with the samples from western Mongolia. Thirteen genera were identified from western Mongolia in 2009, with eight of these new for the country. Although 23 genera are now know for Empedoidea in Mongolia, only five were found in both the Selenge River and the 2009 collection from western Mongolia, suggesting distinct differences in faunal composition between the two areas.

Genome-Wide Analyses Of Shavenbaby Target Genes Reveals Distinct Features Of Enhancer Organization, Delphine Menoret, Marc Santolini, Isabelle Fernandes, Rebecca Spokony, Jennifer Zanet, Ignacio Gonzalez, Yvan Latapie, Pierre Ferrer, Hervé Rouault, Kevin P. White, Philippe Besse, Vincent Hakim, Stein Aerts, Francois Payre, Serge Plaza

Publications and Research

Background: Developmental programs are implemented by regulatory interactions between Transcription Factors (TFs) and their target genes, which remain poorly understood. While recent studies have focused on regulatory cascades of TFs that govern early development, little is known about how the ultimate effectors of cell differentiation are selected and controlled. We addressed this question during late Drosophila embryogenesis, when the finely tuned expression of the TF Ovo/Shavenbaby (Svb) triggers the morphological differentiation of epidermal trichomes.

Results: We defined a sizeable set of genes downstream of Svb and used in vivo assays to delineate 14 enhancers driving their specific expression in trichome …

Cardiac Myocyte Diversity And A Fibroblast Network In The Junctional Region Of The Zebrafish Heart Revealed By Transmission And Serial Block-Face Scanning Electron Microscopy, Pascal J. Lafontant

Biology Faculty publications

The zebrafish has emerged as an important model of heart development and regeneration. While the structural characteristics of the developing and adult zebrafish ventricle have been previously studied, little attention has been paid to the nature of the interface between the compact and spongy myocardium. Here we describe how these two distinct layers are structurally and functionally integrated. We demonstrate by transmission electron microscopy that this interface is complex and composed primarily of a junctional region occupied by collagen, as well as a population of fibroblasts that form a highly complex network. We also describe a continuum of uniquely flattened …

Traversing Swanton Road, 13th Ed., James A. West

Academic, Government & Associated Organizational Research Resources

Situated at the northwest end of Santa Cruz County and occupying circa 30 square miles of sharply contrasted terrain, the Scott Creek Watershed concentrates within its geomorphological boundaries, at least 10-12% of California's flora, both native and introduced. Paradoxically, the use/abuse that the watershed has sustained over the past 140+ years, has not necessarily diminished the biodiversity and perhaps parallels the naturally disruptive but biologically energizing processes (fire, flooding, landslides and erosion), which have also been historically documented for the area for +60 years. This is an early edition of an extensive document by James A. West. Please visit the …

An Acid Test For G Proteins, Stephen R. Sprang

Biological Sciences Faculty Publications

Heterotrimeric G proteins are cytoplasmic transducers of signals generated by ligandactivated 7-transmembrane receptors (G protein-coupled receptors, or GPCRs) embedded in the plasma membranes of cells. GPCRs activate G proteins by catalyzing exchange of GDP for GTP at the alpha subunit (Gα) with the concomitant release of the Gβγ heterodimer. Separately or together Gα•GTP and Gβγ stimulate enzymes that produce second messengers (e.g. cyclic AMP), control ion channels, Ras-family G proteins and regulate transcription (Cabrera-Vera et al., 2003). In yeast, GPCRs intercept mating pheromones and monitor extracellular glucose concentration, and so generate intracellular signals either to arrest growth or to proliferate. …

Autism As The Early Closure Of A Neuroplastic Critical Period Normally Seen In Adolescence, Julia Marie Berger, Troy T. Rohn, Julia Thom Oxford

Biology Faculty Publications and Presentations

The most severe cases of autism are diagnosed by extreme social dysfunction and other behavioral abnormalities. A number of genetic studies have been conducted to correlate behavioral phenotypes to genetic dysfunctions, but no “autism gene” has yet been discovered. In addition, environmental factors have been found to influence the development of autistic traits with high probability. This review will examine the role of a shortened period of neuroplasticity as a unifying feature of the autistic phenotype. The neuroplastic period of interest normally extends into adolescence, allowing for neural integration and the development of language and social skills. Early closure of …

The Phage Genomics Research Program - Authentic Research For First Year Students, Aaron Best, Joseph Stukey

Faculty Presentations

The Hope College Department of Biology is entering its 6th year of the Phage Genomics Research Honors Laboratory course offered to first-year college students as an alternative to the standard Hope College Introductory Biology lab. This course is part of a national experiment to improve education in the sciences led by the Howard Hughes Medical Institute; Hope College was selected as one of 12 institutions nationwide to pilot this program. Students for the honors laboratory course at Hope College were selected from a restricted pool of applicants earning high scores on the ACT and/or SAT college entrance exams and showing …

Experimental Demonstration Of Accelerated Extinction In Source-Sink Metapopulations, John M. Drake, Blaine D. Griffen

Faculty Publications

Population extinction is a fundamental ecological process which may be aggravated by the exchange of organisms between productive (source) and unproductive (sink) habitat patches. The extent to which such source-sink exchange affects extinction rates is unknown. We conducted an experiment in which metapopulation effects could be distinguished from source-sink effects in laboratory populations of Daphnia magna. Time-to-extinction in this experiment was maximized at intermediate levels of habitat fragmentation, which is consistent with a minority of theoretical models. These results provided a baseline for comparison with experimental treatments designed to detect effects of concentrating resources in source patches. These treatments showed …

Low Seroprevalent Species D Adenovirus Vectors As Influenza Vaccines, Eric A. Weaver, Michael A. Barry

School of Biological Sciences: Faculty Publications

Seasonal and pandemic influenza remains a constant threat. While standard influenza vaccines have great utility, the need for improved vaccine technologies have been brought to light by the 2009 swine flu pandemic, highly pathogenic avian influenza infections, and the most recent early and widespread influenza activity. Species C adenoviruses based on serotype 5 (AD5) are potent vehicles for gene-based vaccination. While potent, most humans are already immune to this virus. In this study, low seroprevalent species D adenoviruses Ad26, 28, and 48 were cloned and modified to express the influenza virus A/PR/8/34 hemagglutinin gene for vaccine studies. When studied in …

Recruitment And Survival Of Post-Parasitic Juvenile Mussels In An East Texas River, David S. Bakkin

Biology Theses

Freshwater mussels (order Unionoida) are the most imperiled group of fauna in North America. The factors driving this decline chiefly affect juvenile recruitment and survival, rather than adult mortality. However, our present knowledge generally consists of inferences from studies of adult distributions. Juvenile mussels are rarely collected in the field, leaving our understanding of this critical period in the mussel life cycle incomplete. Popular hypotheses, most notably that shear stress during floods scours small mussels from the substrate and largely confines mussel beds to sheltered areas, are supported by circumstantial evidence and have rarely been tested directly. The role of …

The Uropathogenic Escherichia Coli Effector Ybcl Modulates The Innate Immune Response In The Urinary Tract, Megan Elizabeth Lau

Arts & Sciences Graduate Student Theses and Dissertations

Uropathogenic Escherichia coli (UPEC) are the primary etiology of urinary tract infections (UTIs), one of the most common bacterial infections afflicting the human population. While UPEC cause disease throughout the urinary tract, bladder infection, or cystitis, is most prevalent. A key aspect of UPEC pathogenesis in the bladder is the modulation of the host inflammatory response. At acute time points, UPEC delay the arrival of immune cells, such as neutrophils, to the bladder. The lack of neutrophils in the bladder lumen enables UPEC to replicate freely in the urine and invade the bladder epithelium, a requirement for bacterial persistence, in …

Taxonomic Revision Of The Olingos (Bassaricyon), With Description Of A New Species, The Olinguito, Kristofer M. Helgen, C. Miguel Pinto, Roland Kays, Laura E. Helgen, Mirian T. N. Tsuchiya, Aleta Quinn, Don E. Wilson, Jesús E. Maldonado

Publications and Research

We present the first comprehensive taxonomic revision and review the biology of the olingos, the endemic Neotropical procyonid genus Bassaricyon, based on most specimens available in museums, and with data derived from anatomy, morphometrics, mitochondrial and nuclear DNA, field observations, and geographic range modeling. Species of Bassaricyon are primarily forest-living, arboreal, nocturnal, frugivorous, and solitary, and have one young at a time. We demonstrate that four olingo species can be recognized, including a Central American species (B. gabbii), lowland species with eastern, cis-Andean (B. alleni) and western, trans- Andean (B. medius) distributions, and a species endemic to cloud forests in …