Biology Commons^™

Fecal Findings: Investigating Eastern Massasauga Rattlesnake Diet Using Dna Metabarcoding, Alyssa Swinehart

Masters Theses

Characterizing the diet of imperiled species using minimally invasive methods is crucial to understanding their conservation requirements. DNA metabarcoding methods have been used to characterize the diet primarily in mammalian systems, while reptiles are heavily underrepresented in this literature. Here, we apply a DNA metabarcoding approach to study the diet of the eastern massasauga rattlesnake (Sistrurus catenatus); a Federally Threatened snake found throughout the Great Lakes Region. Eighty-three fecal samples collected across 10 different massasauga populations located in Michigan were sequenced. We use universal metazoan primers and develop a host-specific oligonucleotide blocker to uncover the full potential diet …

Spatial And Demographic Patterns Of Two Threatened Turtle Species In An Urban Environment, Carly E. Brouwers

Masters Theses

Urban development is a global threat to native wildlife. The process of urbanization reduces and degrades the useable habitat of a region, and creates novel “urban ecosystems” that possess new threats and stressors to local species. Turtles are one of the most threatened vertebrate groups worldwide, and are particularly at risk of decline in urban ecosystems due to reduced nesting success, increased road mortality events, altered movement patterns, and increased predation rates. Eastern box and Blanding’s turtles are two at-risk turtle species in the state of Michigan, USA, primarily due to land use change. Presently, there are urban populations of …

Evaluation Of Lake Sturgeon (Acipenser Fulvescens) Spawning Success On An Artificial Reef Constructed In The Kalamazoo River, Michigan, Jason P. Lorenz

Masters Theses

Since lake sturgeon Acipenser fulvescens monitoring began on the Kalamazoo River in 2009, there has been no documentation of survival past the egg stage. Spawning has occurred directly below Calkins Dam and, in 2016, an artificial spawning reef was constructed 275-m downstream to improve habitat and increase survival to the larval stage. The site was monitored with egg mats and larval drift nets to document evidence of successful natural reproduction of lake sturgeon one year prior to construction (2016) and three years post-construction of the artificial reef (2017-2019). Fertilized lake sturgeon eggs were captured all four years of the study …

Use Of Imaging Flow Cytometry To Assess The Hematology Of Eastern Massasauga Rattlesnakes (Sistrurus Catenatus), Jennifer H. Kovach

Masters Theses

The federally threatened eastern massasauga rattlesnake is faced with many threats, including the newly recognized snake fungal disease. Unfortunately, the immune response to the disease is unknown. Leukocyte profiles are used as health assessment tools for many species, and imaging flow cytometry can be used as an application to characterize leukocyte profiles. Our goal was to use imaging flow cytometry to identify leukocyte profiles of eastern massasauga rattlesnakes and determine differences in profiles between sexes, reproductive status, ages, location, and individuals with clinical signs of snake fungal disease. Blood samples from 201 individuals were collected from ten locations throughout the …

Male-Biased Dispersal In A Fungus-Gardening Ant Symbiosis, Alix E. Matthews, Katrin Kellner, Jon N. Seal

Biology Faculty Publications and Presentations

For nearly all organisms, dispersal is a fundamental life-history trait that can shape their ecology and evolution. Variation in dispersal capabilities within a species exists and can influence population genetic structure and ecological interactions. In fungus-gardening (attine) ants, co-dispersal of ants and mutualistic fungi is crucial to the success of this obligate symbiosis. Female-biased dispersal (and gene flow) may be favored in attines because virgin queens carry the responsibility of dispersing the fungi, but a paucity of research has made this conclusion difficult. Here, we investigate dispersal of the fungus-gardening ant Trachymyrmex septentrionalis using a combination of maternally (mitochondrial DNA) …

A Mathematical Model Of Pancreatic Cancer Growth And Response To Treatment, Allison Cruikshank

Honors Program: Senior Projects (Public)

Pancreatic cancer is one of the leading causes of death due to cancer in the United States. Analyzing the effects of radiation is extremely valuable in determining when a patient is allowed surgical resection, which is, presently, the only potentially curative treatment for pancreatic cancer. This study examines pancreatic tumor growth and shrinkage to predict tumor response and change of resectability for pancreatic cancer patients undergoing radiation therapy. This is done using ordinary differential equations as a mathematical model. Mathematical models have increasingly been applied to various biological systems/processes to analyze the principles involved. In our project, a population dynamical …

Safety Assessment Of Aconitum-Derived Bulleyaconitine A: A 91-Day Oral Toxicity Study And A Tissue Accumulation Study In Rats, Shi Liang Yin, Feng Xu, Hao Wu, Fei Li, Ge Jin, Zu Qian Wu, Ran Meng, Si Man Ma, Fan Zhou, Peter W. Breslin, Chun Fu Wu, Hong Zhang

Biology: Faculty Publications and Other Works

Background: Bulleyaconitine A (BLA) is a diterpenoid alkaloid from the rhizomes of Aconitum bulleyanum Diels and has been clinically used for chronic pain treatment in China for many years. However, the newly reported adverse events of BLA indicated that BLA still has potential safety issues. Materials and Methods: To assess the safety of BLA, analgesic tests, acute toxicity studies, repeated-dose oral toxicity studies, and tissue distribution studies after single and repeated administration of BLA were carried out. Results: Administration of 0.14 mg/kg BLA showed potent analgesic effects in both analgesic tests. In acute toxicity study, the LD50value of BLA was …

Neurofibromatosis 1: Discovery, Treatment And Social Impact, Betsua Garcia, Arsen Khachatryan

Undergraduate Research Symposium Posters

The purpose of this timeline research project is to provide an outline of the discovery of Neurofibromatosis 1 to identify gaps in knowledge. Frederick von Recklinghausen is credited with the disease’s classification in 1882 when he observed two different cases of patients with neurofibromas. Current research of the disease involves its characterization at a molecular and genetic level. The symptoms of the disease include non-cancerous tumors in the nervous system (neurofibromas) and optic nerves (optic nerve gliomas), as well as cafe-au-lait spots around the axillary and groin areas. It tends to occur in 1 out of 3,000 births globally without …

The Effect Of A Folate Free Diet On Tumor Burden And Chemotherapy Effectiveness, Kendall E. Stalls

Senior Theses

Our research is to understand the effect of the microbiota on colorectal cancer. Evidence has been shown that the microbiota is linked to the development and progression of colorectal cancer. The research focuses on how the gut microbiome influences the effectiveness of colorectal cancer treatments. Specifically, how the composition of the microbiota and the metabolites that it secretes changes the response to chemotherapy. We also research how tumor burden can be altered through changing the composition of the gut bacteria. Our experiments are performed on APC/Min+ mice, that have been genetically altered to have colon cancer. We conducted an experiment …

Responses Of Soil Surface Greenhouse Gas Emissions To Nitrogen And Sulfur Fertilizer Rates To Brassica Carinata Grown As A Bio-Jet Fuel, Dwarika Bhattarai, Gandura O. Abagandura, Thandiwe Nleya, Sandeep Kumar

Agronomy, Horticulture and Plant Science Faculty Publications

Carinata (Brassica carinata A. Braun), a non-food oilseed crop and an alternative bio-jet fuel feedstock, has received attention for its potential as a low-input option for production in the semi-arid region of the Northern Great Plains of the United States. Research addressing the impacts of nitrogen (N) and sulfur (S) fertilizers on soils and greenhouse gas (GHG; CO₂, N₂O, and CH₄) emissions from carinata production are limited. Thus, objective of this study was to evaluate the impact of different rates of N and S fertilizers applied to carinata on soil properties and GHG …

The Journey To Reach Herd Immunity: The United State's Efforts Towards Controlling Sars-Cov-2, Natalina Mastroianni

Senior Honors Projects

COVID-19 is a respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which emerged in December of 2019 and has been the leading global health concern since. SARS-CoV-2 is a positive sense single-stranded RNA virus coated with viral spike proteins that has led to over 500,000 deaths in the United States and is approaching 3,000,000 deaths worldwide. As COVID-19 persists globally in such high numbers, the virus has been able to undergo mutations, leading to three prominent variants: the United Kingdom variant (B.1.1.7), the South Africa variant (B.1.351), and the Brazil variant (P.1). These variants are more transmissible, …

The Journey To Reach Herd Immunity: The United State's Efforts Towards Controlling Sars-Cov-2, Natalina Mastroianni

Senior Honors Projects

COVID-19 is a respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which emerged in December of 2019 and has been the leading global health concern since. SARS-CoV-2 is a positive sense single-stranded RNA virus coated with viral spike proteins that has led to over 500,000 deaths in the United States and is approaching 3,000,000 deaths worldwide. As COVID-19 persists globally in such high numbers, the virus has been able to undergo mutations, leading to three prominent variants: the United Kingdom variant (B.1.1.7), the South Africa variant (B.1.351), and the Brazil variant (P.1). These variants are more transmissible, …

Laboratory Techniques In Public Health: Bi-520 Introduction To Public Health Lab Manual, Anuradha Srivastava

Open Educational Resources

This laboratory manual for a foundations course Public Health is unique in the sense that very rarely, a foundations course in the field has a lab component offered with the lecture. This lab manual provides basic laboratory exercises that could be useful to introduce undergraduate students to the basics of public health laboratory practices.

Mrna Vaccinations For The Prevention Of Viral Infections, Isaac Underhill

Senior Honors Theses

mRNA vaccines for the prevention of infection disease have gained significant traction in the last three decades, specifically with the recent emergency approval of two COVID-19 vaccines (Oliver, Sara E et al., 2020; Rauch et al., 2018a). mRNA vaccines occupy a unique space in immunology because of their utilization of cellular mechanisms to produce viral proteins, and their simplicity and ease of manufacture (Cullis & Hope, 2017). These vaccines have shown strong humoral and cell-mediated adaptive immune responses (Rauch et al., 2018b) . In addition, side effects of the vaccines have been limited and subject response is manipulatable by varying …

Genomic Analysis Enlightens Agaricales Lifestyle Evolution And Increasing Peroxidase Diversity, Francisco J. Ruiz-Dueñas, José M. Barrasa, Marisol Sánchez-García, Susana Camarero, Shingo Miyauchi, Ana Serrano, Dolores Linde, Rashid Babiker, Elodie Drula, Iván Ayuso-Fernández, Remedios Pacheco, Guillermo Padilla, Patricia Ferreira, Jorge Barriuso, Harald Kellner, Raúl Castanera, Manuel Alfaro, Lucía Ramírez, Antonio G. Pisabarro, Robert Riley, Alan Kuo, William Andreopoulos, Kurt Labutti, Jasmyn Pangilinan, Andrew Tritt, Anna Lipzen, Guifen He, Mi Yan, Vivian Ng, Igor V. Grigoriev, Daniel Cullen, Francis Martin, David Hibbett

Biology

As actors of global carbon cycle, Agaricomycetes (Basidiomycota) have developed complex enzymatic machineries that allow them to decompose all plant polymers, including lignin. Among them, saprotrophic Agaricales are characterized by an unparalleled diversity of habitats and lifestyles. Comparative analysis of 52 Agaricomycetes genomes (14 of them sequenced de novo) reveals that Agaricales possess a large diversity of hydrolytic and oxidative enzymes for lignocellulose decay. Based on the gene families with the predicted highest evolutionary rates - namely cellulose-binding CBM1, glycoside hydrolase GH43, lytic polysaccharide monooxygenase AA9, class-II peroxidases, glucose-methanol-choline oxidase/dehydrogenases, laccases, and unspecific peroxygenases - we reconstructed the lifestyles of …

Plant-Derived Drug Discovery In An Introductory Biology Laboratory Course, Tatiana Kuzmenko, Ashwarya Sharma, Demian A. Willette

Biology Faculty Works

Hands-on, inquiry-based laboratory activities are excellent opportunities to introduce first-year undergraduate students to the lab environment and to catalyze new interest in topics they may not yet know or be as enthusiastic about studying. We describe a multisession introductory laboratory activity that couples the research areas of medicinal drug discovery and plant biology. Selecting from a diversity of native California plants and broadly recognized medicinal plants, students learn and apply an assortment of basic phytochemical assays, analyze preliminary data, and then formulate hypothesis-driven follow-up experiments. Working in small groups, students develop shared project management and collaboration skills, and present activity …

Wolf Selection Of Human-Modified Linear Features And Cover Types When Hunting And Killing White-Tailed Deer Fawns, Austin T. Homkes

All NMU Master's Theses

Predators must optimize and adapt foraging behavior for multiple spatial scales to take advantage of abundant and vulnerable prey. Wolves (Canis lupus) live in human-modified landscapes where anthropogenic disturbances and landscape alterations can influence predator-prey dynamics. In southern boreal ecosystems, wolves rely heavily on seasonally abundant white-tailed deer (Odocoileus virginianus) fawns, which are highly susceptible to predation in their first weeks of life. My objective was to understand how anthropogenic disturbances—specifically timber harvest areas and linear features—and cover types influence where wolves hunt and kill fawns. During 2016–2019, I fit wolves with 20-min-fix-interval Global Positioning System …

Anaplasma Phagocytophilum Modulates Mammalian And Arthropod Signaling For Its Survival And Transmission, Supreet Khanal

Biomedical Sciences Theses & Dissertations

Vector-borne diseases (VBDs) are illnesses transmitted to humans and other animals by arthropods such as ticks, mosquitoes, and fleas. These arthropod vectors transmit infectious pathogens such as viruses, bacteria, and protozoa, to humans during blood-feeding. We have very few control strategies to treat or control these diseases. Human anaplasmosis, caused by the bacterium Anaplasma phagocytophilum, is the second most common tick-borne disease in the United States. This work defines three studies elucidating Anaplasma phagocytophilum-mediated modulation of cell signaling in mammalian cells and arthropod vector Ixodes scapularis ticks.

The first study focused on mammalian PI3 kinases signaling in regulating …

Determination Of The Presence Of Rickettsia Spp. And Borrelia Spp. Carried By Tortoise Ticks From Madagascar, Anna Phan

Biological Sciences Theses & Dissertations

Ticks were removed from three species of Malagasy tortoises, Astrochelys yniphora, A. radiata, and Pyxis arachnoides (comprising two subspecies P. a. arachnoides and P. a. oblonga), between 2012 and 2015. The ticks were presumed to be from the genus Amblyomma. Ticks were morphologically identified and then checked molecularly to confirm their classification or identify any ticks that could not be morphologically identified. Molecular identification was done via end-point PCR that amplified tick cytochrome oxidase (CO1) and tick 12S rRNA genes. Ticks were screened via a real-time polymerase chain reaction assay for the presence of Rickettsia spp. …

The Role Of Backreef Soundscapes And Their Spatial Structure For Recruitment Of Tropical Marine Larvae, Emily R. Anderson

Biological Sciences Theses & Dissertations

Underwater sound is a cue used by many marine larvae to orient to coastal habitats including backreef, sponge-dominated hardbottom habitat in the Florida Keys (Florida, USA) – a particularly “noisy” coastal habitat. However, the distance over which acoustic cues are attractive to settlement-stage larvae - is generally unknown. I examined this phenomenon in a region of the Florida Keys where mass sponge die-offs have diminished both underwater soundscapes and larval settlement. The absence of pronounced hardbottom-associated sound over such a large area allowed me to experimentally test in situ the response of fish and invertebrate larvae to broadcasted sounds at …

Moderate Heat-Assisted Gene Electrotransfer For Intradermal Dna Vaccination And Protein Replacement Therapy In The Skin, Chelsea Marie Edelblute

Biomedical Sciences Theses & Dissertations

Gene electrotransfer (GET) holds great promise for the delivery of therapeutic agents. The skin serves as an attractive target for GET due to its availability and unique cellular composition. Protein replacement therapy and DNA vaccination are potential applications for intradermal GET. The combination of moderate tissue preheating and GET has been shown to achieve elevated gene expression levels while reducing the necessary applied voltage. In the current work, we utilized a 16-pin multi-electrode array (MEA) and incorporated nine optical fibers, connected to an infrared laser, to pre-heat the tissue to 43°C before application of GET. In a guinea pig model, …

Genes Related To Redox And Cell Curvature Facilitate Interactions Between Caulobacter Strains And Arabidopsis, Louis Berrios, Bert Ely

Faculty Publications

Bacteria play an integral role in shaping plant growth and development. However, the genetic factors that facilitate plant-bacteria interactions remain largely unknown. Here, we demonstrated the importance of two bacterial genetic factors that facilitate the interactions between plant-growth-promoting (PGP) bacteria in the genus Caulobacter and the host plant Arabidopsis. Using homologous recombination, we disrupted the cytochrome ubiquinol oxidase (cyo) operon in both C. vibrioides CB13 and C. segnis TK0059 by knocking out the expression of cyoB (critical subunit of the cyo operon) and showed that the mutant strains were unable to enhance the growth of …

Seed Rain–Successional Feedbacks In Wet Tropical Forests, Nohemi Huanca Nuñez, Robin L. Chazdon, Sabrina E. Russo

School of Biological Sciences: Faculty Publications

Abstract

Tropical forest regeneration after abandonment of former agricultural land depends critically on the input of tree seeds, yet seed dispersal is increasingly disrupted in contemporary human-modified landscapes. Here, we introduce the concept of seed rain–successional feedbacks as a deterministic process in which seed rain is shaped by successional dynamics internal to a forest site and that acts to reinforce priority effects. We used a combination of time series and chronosequence approaches to investigate how the quantity and taxonomic and functional composition of seed rain change during succession and to evaluate the strength of seed rain–successional feedbacks, relative to other …

Exploring Effects Of Sample Storage, Preparation, And Tissue Type On Fourier Transform-Near Infrared Spectroscopy (Ft-Nirs) Ageing Across Fish Taxa, Keith Fuller

Theses and Dissertations

The accurate determination of age for fish is a vital part of both populationmanagement and ichthyological research. However, the methods which are primarily employed to age fish can be difficult, time consuming, inaccurate, or some combination thereof. Most ageing is currently done via hard parts (such as otoliths, vertebrae, or scales) which are read in a manner similar to tree rings with markings corresponding to known or presumed periods of time. Recently, Fourier transform-near infrared spectroscopy (FT-NIRS) has been investigated as a novel tool to age fish more quickly and objectively. This method works by recording the vibrational frequencies of …

Investigating The Dynamic Interactions Of Rapidly Growing Precocial Shorebird Chicks, Luke R. Wilde

Theses and Dissertations

Organisms in dynamic environments must continually reassess the cost-benefit trade-offs of their interactions and adjust their behaviors accordingly. Nevertheless, ecological research often takes a ‘snapshot’ approach to studying interactions across sample locations and timepoints. Investigating ecological interactions in this way can miss important information about the influence spatiotemporal context has on the scale and direction of their effects. Longitudinal studies that follow individuals can elucidate how changing contexts affect an individual’s ecology while deepening our understanding of adaptive behavior. However, determining how context influences the effect of an interaction requires it be measured across a range of spatiotemporal conditions. Studying …

Effect Of Oxidative Stress On Lifespan And Cellular Survival, Benedicth Onyeka Ukhueduan

Theses and Dissertations

When cells experience oxidative stress, the integrated stress response (ISR) signaling pathway is activated. One of the first outcomes of such ISR-activated response is to temporarily halt protein synthesis, which aids in cellular recovery. However, if cells cannot recover from the stress, they activate the cell death pathways which kills the affected cells, usually by apoptosis, which can then lead to either acquisition or prevention of diseases depending on the situation. In physiological aging, a compromised stress response is observed as an organism ages, which leads to disrupted homeostasis and elevated risk of disease. Thus, longevity of an organism is …

Applications And Mechanisms Of Near Infrared Spectroscopy For Age Estimation In Otoliths Of Red Snapper Lutjanus Campechanus, Michelle S. Passerotti

Theses and Dissertations

Near infrared spectroscopy (NIRS) is a light spectroscopy method useful for non-invasively discriminating and quantifying chemical composition of a wide variety of substances. Recently-developed applications of NIRS to fish age estimation across a range of taxa have sparked intense interest in exploring the feasibility of its use for rapid age estimation in fisheries population management. In this pursuit, development of species-specific calibration models relating traditionally-derived age estimates (i.e., those estimated from growth band counts) to NIR spectral signatures from ageing structures is required to derive predictive models that can then estimate age from rapid scans of whole ageing structures alone. …

Plasmids Bring Novel Functions To Caulobacter Genomes, Taylor Howell Carter

Theses and Dissertations

Caulobacter is a well-studied bacterial genus, but little is known about the plasmids that are found in some wild Caulobacter isolates. I identified nine plasmids from seven different Caulobacter strains and grouped them based on their size and the similarity of their repABC, parAB, and mobAB genes. Protein pathway analysis of the genes on the K31p1, and K31p2 plasmids showed many metabolic pathways that would enhance the metabolic versatility of the host strain. In contrast, the CB4 plasmid contained 21 heavy metal resistance genes organized into 9 operons. The majority of the CB4 heavy metal resistance genes code for …

Events Associated With Dna Replication Disruption Are Not Observed In Hydrogen Peroxide-Treated Escherichia Coli, Chettar A. Hoff, Sierra S. Schmidt, Brandy J. Hackert, Travis K. Worley, Justin Courcelle, Charmain Courcelle

Biology Faculty Publications and Presentations

UV irradiation induces pyrimidine dimers that block polymerases and disrupt the replisome. Restoring replication depends on the recF pathway proteins which process and maintain the replication fork DNA to allow the lesion to be repaired before replication resumes. Oxidative DNA lesions, such as those induced by hydrogen peroxide (H₂O₂), are often thought to require similar processing events, yet far less is known about how cells process oxidative damage during replication. Here we show that replication is not disrupted by H₂O₂-induced DNA damage in vivo. Following an initial inhibition, replication resumes in …

How To Get Away With Murder: The Effectiveness Of Blood Detectors On Surfaces Cleaned Of Blood, Grace Cavanaugh

Undergraduate Theses and Capstone Projects

The purpose of this experiment was to test blood detectors against household cleaners. Similar experiments have been run before, but not on the selected surfaces. It is important to understand what one is looking for at a crime scene, and what a cleaned surface may look like. Four surfaces were chosen for this experiment: ceramic tile as a control, concrete, laminated wood flooring, and drywall. For each surface, 0.5mL of pig’s blood was allowed to dry before being cleaned off with either Clorox bleach, Dawn soap and hot water, a Mr. Clean Magic Eraser, or Mrs. Meyer’s Multi-Purpose Concentrate. Bluestar …