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Full Issue-- Volume 3 Issue 1, 2020, Issue 1 Volume 3

Pursue: Undergraduate Research Journal

PURSUE: Undergraduate Research Journal

Volume 3 Issue 1, 2020

Article 1 - Harvesting Electrical Energy Produced by Electrogenic Bacteria in Microbial Fuel Cells

Article 2 – The Effects of Fertilizer Rate on the Growth of Egyptian Spinach in a Greenhouse

Article 3 – Exploring the Association Between Nutrition and Mental Health in Adolescence: A Systematic Literature Review

Article 4— Biological Pathways Associated with Wild and Domestic Animals

Validation And Optimization Of Hyperspectral Reflectance Analysis-Based Predictive Models For The Determination Of Plant Functional Traits In Cornus, Rhododendron, And Salix, Milton I. Valdiviezo

Honors Undergraduate Theses

Near infrared spectroscopy (NIR) has become increasingly widespread throughout various fields as an alternative method for efficiently phenotyping crops and plants at rates unparalleled by conventional means. With growing reliability, the convergence of NIR spectroscopy and modern machine learning represent a promising methodology offering unprecedented access to rapid, high throughput phenotyping at negligible costs, representing prospects that excite agronomists and plant physiologists alike. However, as is true of all emergent methodologies, progressive refinement towards optimization exposes potential flaws and raises questions, one of which is the cornerstone of this study. Spectroscopic determination of plant functional traits utilizes plants' morphological and …

Baseline And Stress-Induced Corticosterone Levels Across Birds And Reptiles Do Not Reflect Urbanication Levels, A. S. Injaian, C. D. Francis, J. Q. Ouyang, D. M. Dominoni, Jeremy W. Donald, M. J. Fuxjager, W. Goymann, M. Hau, Jerry F. Husak, Michele A. Johnson, Bonnie K. Kircher, R. Knapp, L. B. Martin, E. T. Miller, L. A. Schoenle, T. D. Williams, Maren N. Vitousek

Biology Faculty Research

Rates of human-induced environmental change continue increasing with human population size, potentially altering animal physiology and negatively affecting wildlife. Researchers often use glucocorticoid concentrations (hormones that can be associated with stressors) to gauge the impact of anthropogenic factors (e.g. urbanization, noise and light pollution). Yet, no general relationships between human-induced environmental change and glucocorticoids have emerged. Given the number of recent studies reporting baseline and stress-induced corticosterone (the primary glucocorticoid in birds and reptiles) concentrations worldwide, it is now possible to conduct large-scale comparative analyses to test for general associations between disturbance and baseline and stress-induced corticosterone across species. Additionally, …

A Literature Review Of Horn And Horn-Like Structures In Vertebrates To Correlate Placement To Function, Behavior, And Niche., J T. Cottingham

Biology Papers and Presentations

In this paper, the true horns of bovids are compared to the many horn-like structures found throughout the animal kingdom. Literary sources were reviewed for a variety of horn-like structures. The review was limited to extinct and extant terrestrial vertebrates. 3D models of these organisms' skulls and “horns” were created or acquired and 3D printed at the same scale to illustrate their differences and similarities and to analysis of their comparative size easier between large and small genera.

A Look At Gene Control: Tracking The Ccnd1 Gene, Bryan Anders

Mahurin Honors College Capstone Experience/Thesis Projects

Cancer occurs when the cell does not properly control its own cell cycle. It then replicates in an out of control fashion leading to the death of various organs and then the demise of the organism as a whole. As it seems to have always been a problem for cell-based life, certain safeguards against cancer have been evolved over time. One such method comes in the form of prevention via cyclin proteins, which are encoded from cyclin genes. The gene that is the focus of this research is the CCND1, or cyclin D1, gene that controls the progression through various …

Seedling Survival Declines With Increasing Conspecific Density In A Common Temperate Tree, Fiona V. Jevon, Sydne Record, John Grady, Ashley K. Lang, David A. Orwig, Matthew P. Ayres, Jaclyn H. Matthes

Biology Faculty Research and Scholarship

Feedbacks between plants and their soil microbial communities often drive negative density dependence in rare, tropical tree species, but their importance to common, temperate trees remains unclear. Additionally, whether negative density dependence is driven by natural enemies (e.g., soil pathogens) or by high densities of seedlings has rarely been assessed. Density dependence may also depend on seedling size, as smaller and/or younger seedlings may be more susceptible to mortality agents. We monitored seedlings of Quercus rubra, a common, canopy‐dominant temperate tree, to investigate how the density of neighboring adults and seedlings influenced their survival over two years. We assessed …

Reflections On Implementing Active Learning Techniques In A Large Lecture, Elisabeth Anderson

Q2S Enhancing Pedagogy

Engaging students in lectures of 200+ students presents unique challenges. Here I provide reflections of a several techniques I have implemented. In addition to a description of how the technique was applied are thoughts on which aspects could be modified to provide a more effective learning outcome.

A Rubric For Grading Laboratory Research Paper Writing Assignments In Plant Biology, David Rhoads

Q2S Enhancing Pedagogy

Writing a research paper based on a course laboratory research project is challenging for many students. In addition to providing a 3 page summary on how to write the paper (with details on the type and format of the content to be included for each section), I provide a detailed grading rubric that also contains an outline of the topics to be included in the paper. This rubric was further refined in the Winter 2020 (Q2S) Writing Intensive Faculty Learning Community (WI FLC).

What Are The Most Appropriate Treatments, Preventions And Family Planning Options For Patients With Factor V Leiden?, Simha Wolf

The Science Journal of the Lander College of Arts and Sciences

The management of Venous Thromboembolism in terms of treatments and prevention has been well researched for patients who have been discovered as positive for Factor V Leiden genetic clotting disorder, in either the homozygous or the heterozygous genotype. In fact, the research and development of new agents called Direct oral anticoagulants aim to treat and prevent clotting events while minimizing the risks of bleeding. Although several risk factors have been identified in relation to VTE, Factor V Leiden mutation presents a seemingly higher risk due to its unpredictable incidences of clotting events, even in patients with optimal health characteristics. Yet, …

Diatom Community Responses To Development And Climate Change In Lake George, An Oligotrophic Lake In The Adirondack Mountains, Adam T. Ruka

Masters Theses

Lake George is a highly monitored, oligotrophic lake that experiences widespread tourism in the summer months. The southern basin is more developed than the northern basin, suggesting a north-south gradient of anthropogenic impairment. This study aimed to assess differences in nearshore diatom communities regarding gradients of water chemistry and watershed development throughout the lake. Using Redundancy analyses, water chemistry was found to explain more variation within diatom assemblages than watershed variables. Weighted averaging optima and tolerances specified taxa of concern, F. gracilis and A. formosa, that indicate increased phosphorus (μg/L) and conductivity (μS/cm), respectively. Two hypotheses related to the effect …

Variation In The Maternal Provisioning Of Alkaloids In The Strawberry Poison Frog Oophaga Pumilio: The Relationship Between Mothers And Their Tadpole Offspring, Olivia L. Brooks

Masters Theses

Within and among populations, alkaloid defenses of strawberry poison frogs (Oophaga pumilio) vary spatially, temporally, and with life history stage. Natural variation in defense has been implicated as a critical factor in determining the level of protection afforded to an individual from predators and pathogens. Oophaga pumilio tadpoles sequester defenses from nutritive eggs and are thus entirely dependent on their mothers for their alkaloids. However, it remains unclear how the alkaloid composition of a tadpole relates to that of its mother and if maternally provisioned defenses are effective against predators. Here, I demonstrate that natural variation in the alkaloid composition …

Cereus Fun: An Introduction To Microbiological Techniques, Holly Ahern, Jessica Habashi

Course Materials

Microbiology is a field of science devoted to the study of organisms that are too small to see; therefore, an engaging laboratory experience is often the key to capturing students' interest. It was with this in mind that this book was first conceived and developed. The goal was to provide undergraduate microbiology students with an engaging and meaningful laboratory experience that nurtured a sense of discovery and encouraged greater interest in microbiology as a topic, a field of study, or a career.

This lab manual – which has been field-tested by hundreds of microbiology students over several years – builds …

Bias And Misrepresentation Of Science Undermines Productive Discourse On Animal Welfare Policy: A Case Study, Kelly Jaakkola, Jason N. Bruck, Richard C. Connor, Stephen H. Montgomery, Stephanie L. King

Faculty Publications

Reliable scientific knowledge is crucial for informing legislative, regulatory, and policy decisions in a variety of areas. To that end, scientific reviews of topical issues can be invaluable tools for informing productive discourse and decision-making, assuming these reviews represent the target body of scientific knowledge as completely, accurately, and objectively as possible. Unfortunately, not all reviews live up to this standard. As a case in point, Marino et al.’s review regarding the welfare of killer whales in captivity contains methodological flaws and misrepresentations of the scientific literature, including problematic referencing, overinterpretation of the data, misleading word choice, and biased argumentation. …

Can The Fut 2 Gene Variant Have An Effect On The Body Weight Of Patients Undergoing Bariatric Surgery? - Preliminary, Exploratory Study, Natalia Komorniak, Alexandra Martynova-Van Kley, Armen Nalian, Wiktoria Wardziukiewicz, Karolina Skoniecznaa-Zydecka, Daniel Styburski, Joanna Palma, Bartosz Kowalewski, Krzysztof Kaseja, Ewa Stachowska

Faculty Publications

Background: The FUT2 gene (Se gene) encoding the enzyme α-1,2-L-fucosyltransferase 2 seems to have a significant effect on the number and type of bacteria colonizing the intestines. Methods: In a group of 19 patients after bariatric surgery, the polymorphism (rs601338) of FUT2 gene was analyzed in combination with body mass reduction, intestinal microbiome (16S RNA sequencing), and short chain fatty acids (SCFA) measurements in stools. Results: Among the secretors (Se/Se polymorphism of the FUT2 gene rs601338, carriers of GG variant), correlations between waist-hip ratio (WHR) and propionate content and an increase in Prevotella, Escherichia, Shigella, and Bacteroides were observed. On …

Reassessment Of The Triassic Archosauriform Scleromochlus Taylori: Neither Runner Nor Biped, But Hopper, S. Christopher Bennett Ph.D.

Biological Sciences Faculty Publications

The six known specimens of Scleromochlus taylori and casts made from their negative impressions were examined to reassess the osteological evidence that has been used to interpret Scleromochlus’s locomotion and phylogenetic relationships. It was found that the trunk was dorsoventrally compressed. The upper temporal fenestra was on the lateral surface of skull and two-thirds the size of the lower, the jaw joint posteriorly placed with short retroarticular process, and teeth short and subconical, but no evidence of external nares or antorbital fossae was found. The posterior trunk was covered with ~20 rows of closely spaced transversely elongate dorsal osteoderms. The …

Topography And Disturbance Influence Trait‐Based Composition And Productivity Of Adjacent Habitats In A Coastal System, Joseph K. Brown, Julie C. Zinnert

Biology Publications

Coastal systems experience frequent disturbance and multiple environmental stressors over short spatial and temporal scales. Investigating functional traits in coastal systems has the potential to inform how variation in disturbance frequency and environmental variables influence differences in trait‐based community composition and ecosystem function. Our goals were to (1) quantify trait‐based communities on two barrier islands divergent in topography and long‐term disturbance response and (2) determine relationships between community trait‐based composition and ecosystem productivity. We hypothesized that locations documented with high disturbance would have habitats with similar environmental conditions and trait‐based communities, with the opposite relationship in low‐disturbance locations. Furthermore, we …

Gut Microbiome And Opioid-Induced Analgesic Tolerance, Sach D. Thakker, Karan H. Muchhala

Biology Publications

The gut microbiome plays an important role in maintaining health and homeostasis. Chronic usage of opioids leads to microbial dysbiosis in the gut. This dysbiosis leads to several severe diseases such as irritable bowel syndrome (IBS), diabetes, cancer, and obesity. Here, we discuss the literature on how opioids affect the gut-microbiome axis and how these changes alter the ability of morphine to produce analgesic tolerance. Chronic morphine exposure leads to increases in gut permeability due to disruption of tight junction proteins and increases in inflammation due to release of proinflammatory cytokines, both of which promote tolerance to morphine. Additionally, it …

Is Hyperbaric Oxygen Therapy Effective For Treating Autism?, Malky Meyer

The Science Journal of the Lander College of Arts and Sciences

Autism spectrum disorder (ASD) is characterized as a developmental disability caused by abnormalities in brain function. Studies link ASD with various physiological abnormalities, such as cerebral hypoperfusion, oxidative stress, inflammation, and mitochondrial dysfunction. Studies show that diminished blood flow to the brain demonstrates a connection between several core autistic behaviors, and the hypoperfusion generally worsen with age, growing more prevalent in older children. Although hyperbaric oxygen therapy (“HBOT”) is not yet approved by the United States Food and Drug Administration ) (“FDA”), several studies performed internationally have proven its efficacy in treating people with autism. Even so, the FDA does …

Parkinson’S Disease: Causes, Symptoms, Research, And Interventions, Alexander Labkowsky

The Science Journal of the Lander College of Arts and Sciences

This paper covers several pathogenic theories of Parkinson’s disease (PD); the physiology and biological pathways involved. This includes a mitochondrial DNA (mtDNA) route, a nuclear DNA route, and other hypotheses about idiopathic PD. The subsequent discussion of PD symptoms utilizes a neurological perspective, analyzing the neuroanatomical systems involved, and how they are treated. This includes medications and surgical techniques that are employed in an effort to manage symptomatology and increase health-related quality of life.

Robert Gordon Jaeger, Caitlin R. Gabor, Carl D. Anthony

2020 Faculty Bibliography

No abstract provided.

Gosodesmine, A 7-Substituted Hexahydroindolizine From The Millipede Gosodesmus Claremontus, Madeline F. Hassler, Daniel P. Harrison, Tappey H. Jones, Casey H. Richart, Ralph Saporito

2020 Faculty Bibliography

Millipedes (Diplopoda) are well known for their toxic or repellent defensive secretions. Here we describe gosodesmine (1), 7-(4-methylpent-3-en-1-yl)-1,2,3,5,8,8a-hexahydroindolizine, a unique alkaloid with some terpene character found in the chemical defense secretions of the millipede Gosodesmus claremontus Chamberlin (Colobognatha, Platydesmida, Andrognathidae). The structure of 1 was suggested by its mass spectra and GC-FTIR spectra and established from its 1H, 13C, and 2D NMR spectra and 1D NOE studies. The 7-substituted indolizidine carbon skeleton of 1 was confirmed by unambiguous synthesis. This is the first report of an alkaloid from a platydesmid millipede and the first report of a 7-substituted indolizidine from …

Defensive Behaviour Exhibited By The Yellow-Striped Poison Frog (Dendrobates Truncatus) In Response To Simulated Predation, Nina Savastano, Koary Lutz, Andrew Britton, Ralph Saporito

2020 Faculty Bibliography

No abstract provided.

Use Of Whole-Body Cryosectioning And Desorption Electrosprayionization Mass Spectrometry Imaging To Visualize Alkaloiddistribution In Poison Frogs, Adriana M. Jeckel, Kunihiro Matsumura, Keisuke Nishikawa, Yoshiki Morimoto, Ralph Saporito, Taran Grant, Demian R. Ifa

2020 Faculty Bibliography

Ambient mass spectrometry is useful for analyzing compounds that would beaffected by other chemical procedures. Poison frogs are known to sequester alkaloidsfrom their diet, but the sequestration pathway is unknown. Here, we describemethods for whole-body cryosectioning of frogs and use desorption electrosprayionization mass spectrometry imaging (DESI-MSI) to map the orally administeredalkaloid histrionicotoxin 235A in a whole-body section of the poison frog Den-drobates tinctorius. Our results show that whole-body cryosectioning coupled withhistochemical staining and DESI-MSI is an effective technique to visualize alkaloiddistribution and help elucidate the mechanisms involved in alkaloid sequestration inpoison frogs.

Nostoc Oromo Sp. Nov. (Nostocales, Cyanophyceae) From Ethiopia: A New Species Based On Morphological And Molecular Evidence, Melaku Mesfin, Jeffrey R. Johansen, Nicole Pietrasiak, Lauren M. Bardarelli

2020 Faculty Bibliography

In the course of study of the cyanobacterial flora of Ethiopian soil crusts, we isolated a distinctive strain most closely resembling Chroococcidiopsis kashayi, and at first considered it to be a new Chroococcidiopsis species. However, when placed in nitrogen-free medium for an extended time period this strain developed heterocytes, and consequently was placed in the genus Nostoc. It is morphologically distinct from all other Nostoc species due to its consistent formation of microscopic few-celled colonies lacking clear filamentous organization, which release smaller colonies from the mother colony, leaving behind a persistent thin firm sheath that resembles cell wall material in …

Reptodigitus Chapmanii (Nostocales, Hapalosiphonaceae) Gen. Nov.: A Unique Nostocalean (Cyanobacteria) Genus Based On A Polyphasic Approach1, Dale A. Casamatta, Chelsea D. Villanueva, Alyssa D. Garvey, Holly S. Stocks, Melissa Vaccarino, Petr Dvorak, Petr Hasler, Jeffrey R. Johansen

2020 Faculty Bibliography

The Nostocales is a monophyletic, heterocytous lineage of cyanobacteria capable of akinete production and division in multiple planes, depending upon family‐level clade. While present in a variety of ecosystems, the diversity of the Nostocales has been poorly elucidated. Due to environmentally ‐induced phenotypic plasticity, morphology alone is often insufficient to determine the true phylogenetic placement of these taxa. In order to bridge this gap, taxonomists now employ the polyphasic approach, combining methods such as morphological analysis, phylogenetic analysis based on DNA sequence and genetic identity based on ribosomal genes, and secondary structure of the 16S‐23S ITS and 16S rRNA gene …

Using Crispr-Cas9 As A Restriction Enzyme, Zack Crawley

Master's Theses

Restriction digests are a commonly utilized process for cleaving DNA at specific, but relatively common sites. Restriction enzymes have widespread use in DNA manipulation. CRISPR/Cas9 is a recently identified endonuclease which utilizes a customizable guide sequence to recognize and cut specific ~20 bp sites located in a DNA sequence. This preliminary research aimed to exploit the potential benefit of DNA restriction using the CRISPR/Cas9 procedure through alterations of different components involved in that system. We sought to refine existing CRISPR/Cas9 protocols and make a budget friendly, user-selectable CRISPR/Cas9 restriction digest protocol. The motivation for this research was to simplify and …

Electrophysiological And Motor Responses To Chemosensory Stimuli In Isolated Cephalopod Arms, Kaitlyn E. Fouke, Heather J. Rhodes

Faculty Publications

No abstract provided.

The Influences Of Green Infrastructure On Levels Of Somatic And Male-Specific Coliphages At Shadyside Park, Oula Salih

Student Papers and Reports

Microbial contamination is still considered one of the major causes of diminished function and quality of urban rivers and streams in Michigan. Floodplains, a type of green infrastructure used to reduce flooding after large amounts of rainfall, were reported to have variable effects of reducing levels of stormwater runoff within these bodies of water ( Hubbart et al., 2011 ). Viral indicators of fecal contamination in bodies of water include male-specific and somatic coliphages. Water samples from Plaster Creek were collected before and after the floodplain in order to identify the levels of somatic and male-specific coliphages during dry and …

A Method For Removing Eggs Or Embryos From Preserved, Gravid Snakes That Minimizes Damage To Museum Specimens, Christopher Sheil, Luke J. Welton

2020 Faculty Bibliography

No abstract provided.

A Spatiotemporal Assessment Of Dietary Partitioning Between Color Morphs Of A Terrestrial Salamander, Maggie M. Hantak, Kyle M. Brooks, Cari-Ann M. Hickerson, Carl D. Anthony, Shawn R. Kuchta

2020 Faculty Bibliography

When color pattern variation is co-adapted with other biological features, distinct color morphs may be separated along divergent niche axes, and data on niche partitioning can provide insight into how distinct color morphs are maintained over spatiotemporal scales. The Eastern Red-backed Salamander, Plethodon cinereus, contains two common color morphs (striped and unstriped) that differ along several trait axes in addition to coloration. Previous studies from a single population have suggested that dietary composition represents an important axis of ecological differentiation between morphs of P. cinereus. To determine if morphs partition prey resources over space and time, we collected stomach contents …