Biology Commons^™

A Simulation Of Anthropogenic Mammoth Extinction, Matthew Klapman

Undergraduate Honors Papers

There are multiple hypotheses as to why the Columbian Mammoth (Mammuthus columbi) and other megafauna in North America went extinct relatively recently and relatively quickly. The most popular of which are disease, climate change, meteorite strikes, and over hunting by humans [2, 9]. There is evidence to show that a combination of factors contributed to the megafaunal extinction, but ”overkill” explores the idea that early humans migrated onto the continent and then hunted the mammoths and other megafauna to extinction. The overkill hypothesis was first proposed by anthropologist Paul Martin in 1973 [8]. Evidence from radiocarbon dating shows that the …

Uv Irradiation Of Thymine Molecules And Gas Chromatography – Mass Spectrometry, Kelsey Elaine Mauk

CUP Undergraduate Research

Cyclobutane pyrimidine dimers (CPDs) are products of a photochemical reaction caused by ultraviolet (UV) irradiation of adjacent pyrimidine molecules. Thymine dimers, the most common form of CPDs in the body, are of particular interest because they are the cause of the majority of UV-induced mutations in mammals, often resulting in the development of skin cancers. Because of the photochemical properties of the reactions of thymine dimers, and the relation of these dimers to cancer pathogenesis, the formation and analysis of thymine dimers in a laboratory setting could be a useful educational tool for pre-medicine students learning about organic and photochemistry. …

Spinal Cord Injuries And Evaluation Of Treatments, Amanda Nelson

Biology: Student Scholarship & Creative Works

Spinal cord injuries (SCI) are common injuries that do not currently have a fully successful treatment. These injuries cause many physical, psychological, and social burdens for the injured person and any close friends or family members. Older treatment options include surgery, pharmacotherapy, and physical therapy, while newer treatment options include stem cell therapy, bionics, and electrical stimulation. After a full evaluation of the treatments, it was concluded that the best treatment for today is pharmacotherapy, but with more research, stem cell therapy will become the ideal treatment for SCI in the future.

Trap-Neuter-Return Programs And The Importance Of Associated Public Awareness, Nicolette Sliwa

Biology: Student Scholarship & Creative Works

The focus of this paper is to describe a typical Trap-Neuter-Return (TNR) program and highlight the major pros and cons surrounding this somewhat controversial method of managing the overwhelming free-roaming cat population. The effects of the species’ overabundance on the environment and human health are also discussed. Citing studies completed on TNR programs around the globe as well as mathematical models, the effectiveness of this method is compared to other, currently used alternatives. Finally, it has been suggested that the general awareness level a neighborhood possesses about the true goals of TNR programs has a potentially significant impact on the …

Developing New Tools For The Old Tree Of Life, Kenneth Parnow, William Lambeth, Kelsi Jackson, Jesse Florendo, Jin Mao, Hong Cui, Carrine Blank

Thinking Matters Symposium Archive

Millions of species reside in the Tree of Life, making the task of resolving the evolutionary origin of many organisms difficult. Biologists draw on genetic and phenotypic information to sort the Tree of Life, but the study can be slow and complex. Phenomic data (such as cell shape, metabolism and ecology), particularly for microorganisms, is often found in scientific publications and has little digital presence outside of being scanned into an online database. This has been aided by a new text mining computer program, MicroPIE (Microbial Phenomics Information Extractor), that sifts through relevant phenomic data and creates a matrix of …

Effects Of Size On Dominance Behavior In Male Fiddler Crabs, Uca Pugnax, Heather T. Bondeson

Thinking Matters Symposium Archive

Individuals in many group-living species form dominance hierarchies, and higher ranked individuals have more access to resources or mates. Rank often depends on size. Dominance rank is settled quickly between different -sized individuals, but animals that are similar in size exchange behaviors that escalate until one individual withdraws. Dominance displays in male fiddler crabs include waving the large claw and arm wrestling. My objective was to determine if dominance behavior between male fiddler crabs varies between pairs that are similar or different in size. Because size can indicate dominance for fiddler crabs, I predicted that pairs of different-sized crabs would …

Innate Food Preference In The Larval Tobacco Hornworm, Manduca Sexta, Michael Morrison

Thinking Matters Symposium Archive

Food preference can drive an organism to seek a specific food source even if another food, which can provide needed nutrition, is easier to obtain. Food preference can develop in different ways, including innate preference, i.e., organisms display food preference at birth, or learned preference, i.e., organisms develop food preference after previous experience with that food. The tobacco hornworm, Manduca sexta, shows learned preference; however, we lack information about innate food preference in Manduca. Manduca sexta larvae eat many different foods until they feed on a solanaceous plant, when they become more specific in their diet. This study focused on …

Dna Barcoding Reveals A New Morphotype Of The Sugar Kelp, Saccharina Latissima, Dallin Brimley, Zakery Ford, Travis Gould, Brandon Guerra, Emily Haggett, Ian Jones, Elyse Johnson, Ken Peterson, Matthew Prout

Thinking Matters Symposium Archive

Phytoplankton blooms follow predictable annual cycles in the Gulf of Maine, characterized by a large spring bloom and a smaller bloom in the fall. Marine phytoplankton form the foundation of primary production in Gulf of Maine waters, and thus community changes in composition, and abundance could have cascading effects on our coastal ecosystems.

We set out to monitor the community composition, diversity, and abundance of the spring micro-phytoplankton bloom, at a Friends of Casco Bay water quality monitoring site, in South Portland, Maine. The Gulf of Maine is experiencing accelerated warming rates, and this type of monitoring can aid in …

The Alpine Vascular Plants Of Baxter State Park, Maine, Usa, Abigail J. Urban, Glen H. Mittelhauser, Matthew Dickinson, N. Rajakaruna

Biological Sciences

We conducted 12 days of field surveys on five mountains over 1100 m in elevation (Katahdin, North Brother, South Brother, Mount Coe, and The Owl) in Baxter State Park (BSP), Maine during the summers of 2013–14. In addition, we examined historic manuscripts, unpublished data, and herbarium records for plant records from the five mountains. Katahdin, the largest and tallest of the five mountains, has a rich history of botanical exploration and we documented 1559 herbarium vouchers that were collected from the mountain, primarily before the mid-1900s. Combining all data sources, we documented 38 families, 87 genera, and 131 taxa of …

Finally, The Molecular Characterization Of Geitleria: Results In The Formation Of A Newly Described Nostocales (Cyanobacteria) Clade Geitleriaceae Fam. Prov., Sp. Prov, Jonathan Kilgore

Masters Theses

Geitleria was described from a limestone cave in Israel, and subsequently reported from caves of France, Romania, Spain, and Florida, Costa Rica, and Cook Islands. It is morphologically unusual in that it has true-branching, but no heterocytes. A morphologically distinct species of Geitleria was recently collected from a limestone cave in Great Smoky Mountains National Park, Tennessee, and is herein described as G. appalachiana sp. prov. Sequence data for 16S-rRNA and rpoC1 loci for the species were obtained from field material using single filament PCR. Phylogenetic evidence indicates that Geitleria does not belong to any family in the Nostocales containing …

Comparing The Middle And C-Terminal Domains Of The Soxe Proteins, Abigail Beer

Senior Honors Projects

Osteoarthritis is the most common form of arthritis and affects millions of adults in the United States. Osteoarthritis is a degenerative joint disease that is characterized by irreversible loss of cartilage. Cartilage develops when stem cells differentiate into chondrocytes, the cells found in cartilage, through a process called chondrogenesis. Several proteins are needed for chondrogenesis, including the SOXE family of proteins. The SOXE proteins act as transcriptional activators and consist of three members: SOX8, SOX9, and SOX10. The three proteins share the same basic structure consisting of two transactivation domains. A transactivation domain is a region of a protein that …

Effects Of Type 1 Interferon Deficiency On B-Cells In Lupus Prone Mice, Teddy Nemunaitis

Celebration of Scholarship 2012-2017

Systemic Lupus Erythematosus (SLE) is an autoimmune disease characterized by the production of autoantibodies that target nuclear and cytoplasmic agents. Lupus manifests an array of symptoms and is estimated to affect more females than males. This study analyzed the effects of type 1 interferon deficiency on B-cells in lupus prone mice. Data indicates that specific B-cell IFNAR deficiency in lupus prone mice results in significantly lower spleen weight, splenocyte count, and anti-chromatin IgG levels. Funded by the Cleveland Clinic Summer Research Program.

A New Method For Extracting Alkaloid Defenses From Poison Frog Skins, Noemi Becza

Celebration of Scholarship 2012-2017

Poison frogs possess a diversity of skin alkaloids that serve as defense against predation and inhibit microbial infection. These alkaloid defenses are exclusively obtained from a diet of alkaloid-containing arthropods and differ significantly with species, geographic location, sex, size, and age. Previous research on the chemical ecology of these defenses has been largely dependent on sacrificing frogs to extract and chemically analyze alkaloids. Recently, a new non-destructive method of extracting alkaloids has been developed, using a Transcutaneous Amphibian Stimulator (TAS). This device delivers mild electrical pulses to the frog skin, causing it to release its alkaloids unharmed. The alkaloids can …

Genetics Research Paper: The Inheritance Of Schizophrenia, Kolbi Holmes

Academic Symposium of Undergraduate Scholarship

Schizophrenia is a spectrum of disorders defined by abnormalities in one or more areas including delusions, hallucinations, disorganized thinking or speech, grossly disorganized or abnormal motor behaviors including catatonia and other negative symptoms (American Psychology Association, 2013). Schizophrenia is inherited on autosomal chromosome 8p12. Neuregulin 1 (NRG1), an epithelial growth factor protein, located at 8p12, has been identified as being a nucleotide variation of the single-nucleotide polymorphism (SNP), rs833497 located on chromosome 18q21.1 that is associated with schizophrenia.

Mtorc1 Signaling Is Involved In Nephron Size Control In The Metanephric Kidney, Carolyn Stierhoff

Celebration of Scholarship 2012-2017

The nephron is the functional unit of the kidney that uses channels and transporters to regulate water concentration and recover essential biomolecules. Previous studies in mouse have shown that the proximal tubules, which are primarily responsible for biomolecule recovery, undergo a rapid burst of cell proliferation. Other studies suggest that the development and growth of proximal tubules in Xenopus is regulated by the developmental signaling pathway mTORC1. Here we now identified that various mTORC1 signaling molecules are expressed in mouse kidneys and that they follow a pattern that mimics the previously identified growth cycle. Additionally, comparing mouse kidneys lacking mTORC1 …

Aggressive Displays In Male Betta Splendens Based On Color Patterns, Julian Bones, Thomas Johnson

Thinking Matters Symposium Archive

The traits of an opponent can influence how an individual uses aggressive displays to dissuade the opponent from physical conflict. Whereas one previous study found that conspecific aggression was less intense between differently-colored Siamese fighting fish (Betta splendens), we felt that more evidence was needed to corroborate or dispute their findings. We hypothesized that B. splendens act less aggressively towards similarly- colored fish than to differently-colored fish, based on the notion that males would avoid conflict with a phenotypically similar opponent due to the costs of displaying. To test for differences in aggression due to coloration, we paired …

Cyanobacterial Blooms In Highland Lake, Me, William Lambeth, Rachel Henson, Michael Morrison

Thinking Matters Symposium Archive

Cyanobacterial blooms, like algal blooms, are a much studied phenomena; and many triggers that cause these blooms are well understood. Usually, excess nutrients (such as soluble nitrogen or phosphate) are prerequisite for a bloom to occur. Since 2013, annual summer cyanobacterial blooms have been observed at Highland Lake (HL), located in Cumberland County, Maine. Data going back more than 15 years, collected by the Highland Lake Association, shows this is a new phenomenon in this body of water. Other investigators have shown HL water chemistry to have high aluminum to phosphorous and aluminum to iron ratios. These metals bind phosphate …

Thermal Preference And Performance In A Sub-Antarctic Caterpillar: A Test Of The Coadaptation Hypothesis And Its Alternatives., Tanya M Haupt, Brent J Sinclair, Steven L Chown

Biology Publications

Physiological ecologists have long assumed that thermoregulatory behaviour will evolve to optimise physiological performance. The coadaptation hypothesis predicts that an animal's preferred body temperature will correspond to the temperature at which its performance is optimal. Here we use a strong inference approach to examine the relationship between thermal preference and locomotor performance in the caterpillars of a wingless sub-Antarctic moth, Pringleophaga marioni Viette (Tineidae). The coadaptation hypothesis and its alternatives (suboptimal is optimal, thermodynamic effect, trait variation) are tested. Compared to the optimal movement temperature (22.5°C for field-fresh caterpillars and 25, 20, 22.5, 25 and 20°C following seven day acclimations …

It’S All About Relationships: Amf-Plant Associations, The Rhizosphere, And Our Changing World, Joel Velasco

McNair Scholars Research Journal

Arbuscular mycorrhizal fungi are obligate biotrophic organisms that facilitate nutrient uptake in exchange for organic carbon as part of a symbiotic association with their host plants. This symbiotic relationship is among the oldest known and has been important for the coevolution of both symbionts. This review explores the relationship between Arbuscular mycorrhizal fungi and their hosts, the role AMF play in the invasive strategies of certain plants, and how severe pressure affects the reciprocal relationship. This review hopes to add to the body of knowledge and to the conversation about these dynamic relationships and the timescale on which they operate, …

Exploring The Diversity Of Bacillus Whole Genome Sequencing Projects Using Peasant, The Prokaryotic Assembly And Annotation Tool, Jonathon Brenner, Laurynas Kalesinskas, Catherine Putonti

Biology: Faculty Publications and Other Works

The persistent decrease in cost and difficulty of whole genome sequencing of microbial organisms has led to a dramatic increase in the number of species and strains characterized from a wide variety of environments. Microbial genome sequencing can now be conducted by small laboratories and as part of undergraduate curriculum. While sequencing is routine in microbiology, assembly, annotation and downstream analyses still require computational resources and expertise, often necessitating familiarity with programming languages. To address this problem, we have created a light-weight, user-friendly tool for the assembly and annotation of microbial sequencing projects. The Prokaryotic Assembly and Annotation Tool, Peasant, …

Improvement Of Fluorescence-Based Microfluidic Dna Analyzers, Collin Tranter

Doctoral Dissertations

A tremendous effort continues in the development of micro-total-analysis-systems; in support of this, many chemical passivation methods have been developed to enhance the biocompatibility of such microfluidic systems. However, the suitability of these passivation techniques to many fluorescence-based assays still remains inconsistent. This part of this work is focused on the performance of a third generation intercalating DNA dye when used within microfluidic devices treated with a select variety of passivating coatings. The results of these tests indicate that passivation coatings which are intended to shed DNA based on electrostatic repulsion will in fact imbibe the fluorescent DNA intercalating dye …

The Coastal Monitor: Vol 2. No 1., John Tanacredi Ph.D.

The Coastal Monitor

There is something enchanting and vibrant about viewing the coast. Every day at CERCOM we are welcomed by either a vivid sunrise, a view of the barrier island Fire Island and a blending of the sky across the horizon, ultimately flooding the Great South Bay with either clouds or sunshine that reveals the Bay’s surface as either shimmering with sunlight, or an integration of sky and water as an endless ocean. I don’t normally wax poetic but the varying sights along the near shore ocean and this embayment beckon our scientific inquisitiveness. What’s below the surface water? How do animals …

Lake Powell Food Web Structure: Predicting Effects Of Quagga Mussel, Joshua A. Verde

Theses and Dissertations

Food webs in aquatic ecosystems can be dramatically altered by invasive species. Quagga mussels are prevalent invaders that compete with existing species and disrupt nutrient cycling. In 2012, the Quagga Mussel (Dreissena rostriformus bugensis) was introduced into Lake Powell and is expected to move throughout the reservoir in the near future. Stable isotope analysis is a powerful tool for characterizing food webs and trophic interactions. To predict the long-term effects of Quagga Mussels, we used stable isotope analysis of primary producers, primary consumers, prey fish species, and predator fish species in Lake Powell to determine food web structure. …

Phylogenetics, Biogeography, And Patterns Of Diversification Of Geckosacross The Sunda Shelf With An Emphasis On The Genuscnemaspis (Strauch, 1887), Perry Lee Wood

Theses and Dissertations

In my dissertation I investigate two genera of geckos (Cyrtodactylus and Cnemaspis) that are distributed across Southeast Asia with an emphasis on Cnemaspis. In Chapter 1 I use a multilocus dataset, ancestral area analyses, and molecular clock dating to generate a species level time calibrated phylogeny to test the monophyly of Cyrtodactylus and to identify major biogeographical patterns. I identified that Cyrtodactylus is monophyletic only if the the Sri Lankan genus often recognized as Geckoella is included. The results of the Biogeographical analyses reveal a west to east pattern of diversification. Chapter 2 I use a traditional morphological dataset to …

The Use Of Molecular Dynamics Simulations To Predict Thymine Dimer Formation In Histone Bound Dna, Emily Ann Brune Heinsen

CUP Undergraduate Research

Thymine dimers are the major lesions in DNA that are caused by environmental conditions that can lead to apoptosis or can become carcinogenic (Schreier, et al., 2007). These dimers form when the pi electrons of one thymine in a neighboring thymine pair is excited by a photon from UV light, and occurs on the picosecond time scale (Schreier, et al., 2007). Due to the ultrafast nature of this reaction, the thymines must be in proper conformation prior to excitation in order for the reaction to take place. The proper conformation for the reaction has been found to occur when the …

Effects Of Ph20 Hyaluronidase Inhibition In Vivo Following Cerebral White Matter Injury, Rachel E. Siltman

CUP Undergraduate Research

Human infants born prematurely between 23-32 weeks have a predisposition toward sustaining white matter injury (WMI). In survivors of preterm birth, hypoxic-ischemic (H-I) damage to the cerebral white matter is the leading cause of a spectrum of neurological and motor deficits and in severe cases, cerebral palsy (CP). H-I triggers extracellular matrix (ECM) breakdown leading to production of inhibitory ECM components. H-I also induces vigorous proliferation of oligodendrocyte progenitor cells (OPCs) leading to accumulation of the pre-oligodendrocytes (preOLs). However, these preOLs fail to differentiate and generate myelin producing oligodendrocytes (OLs). Mechanistically, ECM breakdown blocks repair and regeneration of myelin following …

Student Misconceptions About Plants – A First Step In Building A Teaching Resource, April N. Wynn, Irvin L. Pan, Elizabeth E. Rueschhoff, Maryann A B Herman, E Kathleen Archer

Biological Sciences Research

Plants are ubiquitous and found in virtually every ecosystem on Earth, but their biology is often poorly understood, and inaccurate ideas about how plants grow and function abound. Many articles have been published documenting student misconceptions about photosynthesis and respiration, but there are substantially fewer on such topics as plant cell structure and growth; plant genetics, evolution, and classification; plant physiology (beyond energy relations); and plant ecology. The available studies of misconceptions held on those topics show that many are formed at a very young age and persist throughout all educational levels. Our goal is to begin building a central …

Monitoring Anuran Populations In Bosque Protector Candelaria: A Multi-Year Comparison Of Frog Populations In An Ecuadorian Cloud Forest, Mindee Goodrum

Independent Study Project (ISP) Collection

For many years, amphibian populations around the world have been declining due to climate change, habitat loss or change, and diseases such as Ranavirus or the Chytrid fungus. However, there is still a great lack of information regarding the diversity of frogs, especially in the cloud forests of Ecuador where this study was conducted. This study was conducted in April and May of 2017 in the Ecominga Reserve of Cerro Candelaria in El Placer, Ecuador. The objective was to conduct visual-encounter surveys of several sites in the reserve and compare the results to studies that have been conducted in the …

Understanding The Effects Of Propionic Acid On Listeria Monocytogenes Growth, Survival, And Virulence, Elizabeth A. Abrams

Honors Theses

Listeria monocytogenes is a foodborne pathogen that causes illnesses with a high fatality rate immunocompromised and elderly individuals. It colonizes the human intestine, which contains low levels of oxygen but high levels of fermentation acids. This work investigates how that environment affects various aspects of Listeria pathogenesis. Based on these results, we can ascertain whether propionate supplementation can be explored as an effective method of protecting individuals from Listeria infection.

Black Bugbane & The Blues: Interactions Between Our Wildflower Of The Year And The Insect World, W. John Hayden

Biology Faculty Publications

No, this article has nothing to do with American Roots music. Black Bugbane is one of several common names for the 2017 VNPS Wildflower of the Year, Actaea racemosa. And Blues refers to a subfamily of lycaenid butterflies, commonly referred to as Blues or Azures. The interactions between Black Bugbane, a.k.a., Black Cohosh, Appalachian Azure butterflies (Celastrina neglectamajor), and ants was recently summarized by VNPS charter member and past president Nicky Staunton (2015). In brief, Black Bugbane is the sole food source for caterpillars of Appalachian Azure butterflies, a situation that, superficially, might seem like any other caterpillar and host …