Digital Commons Network^™

Who's Hiding On The Savanna?, Amanda Morgan

Children's Book and Media Review

From sunset to sunrise, the savannah is full of interesting animals. In the morning, female lions can be found in the shade with two or three cubs. In the afternoon, hippos hold their breath for up to five minutes underwater. In the evening, vervet monkeys eat leaves and flowers as they lurk in branches. At night, superb starlings gather in large groups to sleep in trees.

Animal Atlas, Amanda Morgan

Children's Book and Media Review

There are animals from every continent and ocean. In North America, monarch butterflies migrate from Canada and the US to Mexico. The bee hummingbird lives in what little remains of the Cuba tropical forest. In Asia, the Baikal seal can be found in Lake Baikal, where two-thirds of the plants and animals are unique to the lake. In Australia, kiwis roam among the kauri trees, and saltwater crocodiles live in the brackish rivers leading to the Indian Ocean. Deep in the Mid-Atlantic Ridge, find mysterious animals like Murray’s abyssal anglerfish, and in the seagrass meadows of the Indian Ocean, leafy …

Simulating Polistes Dominulus Nest-Building Heuristics With Deterministic And Markovian Properties, Benjamin Pottinger

Undergraduate Honors Theses

European Paper Wasps (Polistes dominula) are social insects that build round, symmetrical nests. Current models indicate that these wasps develop colonies by following simple heuristics based on nest stimuli. Computer simulations can model wasp behavior to imitate natural nest building. This research investigated various building heuristics through a novel Markov-based simulation. The simulation used a hexagonal grid to build cells based on the building rule supplied to the agent. Nest data was compared with natural data and through visual inspection. Larger nests were found to be less compact for the rules simulated.

Validation Of Rotoscoping Method For Two-Marker Bones In The Alligator Forearm, Nina Pitre

Biology Student Scholarship

Nina Pitre ’22
Majors: Biology and Psychology
Faculty Mentor: Dr. David Baier, Biology

XROMM methods "re-animate" 3D skeletal motion of living animals by aligning digital bone models to X-ray videos. Surgically implanted markers permit automatic alignment of bone models if three or more markers are used. However, one of our specimens only had two markers implanted. These bones could be automatically positioned and partially oriented using the two markers, but then required manual alignment to the X-ray images to orient about the axis passing between the two markers. Here, we validated the method by digitally removing a marker from a …

Spring 2022: Pre-Veterinary Grad Moves On Toward The Career Of Her Dreams, St. Norbert College

St. Norbert College Magazine 2019-2023

Alicia Gehlhoff ’22, a biology major with a pre-veterinary focus at St. Norbert College, has achieved her lifelong dream of being accepted to veterinary school at UW-Madison, thanks to her dedication, research experience, and hands-on work with animals.

How Social Behavior And Interactions Scale With Group Size In Drosophila Melanogaster, Leigh Paradis

Biology Student Scholarship

Leigh Paradis ’23
Majors: Biology and Neuroscience
Faculty Mentor: Dr. James Waters, Biology

The goal of this research project was to quantify interaction patterns in groups of fruit flies and determine if flies show evidence for a linear or non-linear effect of group size on their behavior. Specifically, I tested whether flies interact with each other at a constant rate, whether this depends on density or group size, and whether their interaction patterns correlate with overall energy use and metabolic rates. This research questions common assumptions about the differences between eusocial societies such as ants and bees and the solitary …

Aeromonas Phage Research And The Public Health Impact Of Antibiotics In Aquaculture Workers, Madelyn Merchant

Honors Projects

One of the most common fish diseases in aquaculture is Aeromonas infection. The most common way to treat this infection is through antibiotics. The bacteria in the fish can become antibiotic-resistant and perpetuate the disease. The diseases in fish create a huge financial loss and the industry loses $6 billion per year due to diseases in fish. An alternative to antibiotics is bacteriophage which causes less environmental degradation and is better for human gut flora. In aquaculture there have been examples of aquaculture workers becoming sick from the water in aquaculture ponds as well as from people eating the fish. …

Even More Lesser Spotted Animals, Amanda Morgan

Children's Book and Media Review

Meet the underdogs of the animal kingdom. they're not as praised as lions, tigers and other big shot mammals, but this book is here to show you why they should be. The dingiso basically looks like a living breathing teddy bear and can jump to the ground from a 60 foot tree without receiving injury. The forest musk deer, unlike real deer, hangs out in trees. The little yellow-throated marten which, as the name suggests, has bright yellow fur, can take down an entire deer. The gerenuk and the dibatags are antelope with necks like giraffes. In learning about all …

Chromatin Architecture: Mechanisms Of Gene Regulation, Logan O'Donnell

Honors Projects in Science and Technology

The rapid growth and division of cells as they proliferate and penetrate to surrounding tissues defines the collection of disease states known as cancer. Abnormal gene expression drives this uncontrollable replication of cells. In recent studies, aberrant HOX gene expression has been noted in a multitude of cancer types such as myeloid leukemia, prostate cancer, and breast cancer [1]. Within cancerous cells with aberrant HOX expression, late expressing HOX genes are suppressed while early expressing HOX genes are reactivated. HOX genes are significant in controlling early phases of organismal development such as cell cycle, cell movement, and gene expression. Likewise, …

Food For Thought: The Relationship Between Nutrition And Academic Performance, Sarah Freeman

Honors Projects in Science and Technology

Nutrition has been shown to impact the level of cognitive function in individuals. Through the analysis of nutritional diets, this new research will aim to uncover the impact that diet has on cognitive function of Bryant University students by analyzing their ability to perform on a variety of cognitive assessments. This study will provide recommendations to students at Bryant University on what they should eat so they can perform their best academically. This research will also investigate whether Bryant University is offering the best food for students to eat setting them up for success.

Something Rotten: A Fresh Look At Roadkill, Rebecca Lambert

Children's Book and Media Review

Have you ever wondered what happens to those animals that meet an unfortunate end on the highway? Heather Montgomery, a writer and biologist from Alabama, answers every question you never knew you had about roadkill. Did you know that Tasmanian Devils are endangered, in part because of a contagious cancer? Scientists learned that from roadkill. Did you know that an invasive species of python has brought parasites to the native snakes of Florida? Scientists learned that from roadkill, too. This book explains how flattened animals are used for all sorts of bizarre purposes. Scientists study roadkill to learn more about …

A Preliminary Comparative Study Of Molecular Visualization Software For Education, Ruoming Shen

Modeling, Simulation and Visualization Student Capstone Conference

Chemistry and biology are sciences vital for understanding metabolic processes, developing disease treatments, and improving environmental conditions. With extensive knowledge of biochemistry, we can take advantage of a material’s unique chemical composition and properties in various applications. Visualization software is essential for analyzing complex chemical and biological structures and predicting their interactions with each other. This paper presents a preliminary study of three open source molecular visualization software tools - Visual Molecular Dynamics (VMD), Jmol, and Mol*, and evaluates their strengths and deficiencies. This paper utilizes the March Molecule of the Month, Vascular Endothelial Growth Factor (VEGF), from the Protein …

A Multi-Spatial Analysis Of Land Use Effects On Freshwater Mussels In The Upper Cuyahoga River And Tinkers Creek, Tamar Atwell

ETD Archive

Mussels are considered one indicator of good water quality in rivers, but over the past 20 years mussel populations have continued to decline, while water quality improves. According to the Ohio Environmental Protection Agency (OEPA), water quality in the Cuyahoga River is now within safe levels for all parameters. However, what are safe levels for humans may not be safe for mussels. An analysis of freshwater mussel populations in two similarly sized watersheds, the Upper Cuyahoga River and Tinkers Creek was conducted. Correlations of mussel abundance and diversity were assessed by multivariate GIS/remote sensing tools to contrast water flow rates, …

Analysis Of Invasive Aedes Japonicus Populations And Bloodmeals In Rural, Suburban, And Urban Land-Use Conditions, Matthew Oberholtzer Ms

Student Scholarship

Adult female mosquitoes were collected at six sites with differing land-use and

livestock characteristics to characterize populations and bloodmeal habits of the invasive

vector mosquito species, Aedes japonicus in Southern Maine. Mosquitoes were collected

and DNA was extracted for PCR amplification of cytochrome C oxidase I (COi)

mitochondrial DNA for barcoding analysis of vertebrate bloodmeals. A total of 7460

adult female mosquitoes were collected, with 444 being Ae. japonicus (5.6%). This

indicates an established breeding population of Ae. japonicus in Southern Maine. The

rural site adjacent to livestock had the highest yield of total mosquitoes as well as the

catch …

Targeted Nucleic Acid Delivery To The Endothelium, Melanie Reschke

Yale Graduate School of Arts and Sciences Dissertations

The human endothelium extends throughout nearly all tissues in the body, and has an estimated total surface area of up to seven thousand square meters [1]. This expansive monolayer of endothelial cells (ECs) serves as the interface between materials circulating in the bloodstream and the internal tissues of the body. Even in its quiescent state, the endothelium is actively signaling and reacting in order to support the basic functions of the vascular system – transporting oxygen, nutrients, and waste. A closer look reveals that the cells that make up this endothelial lining are diverse in their phenotypes and functions, dependent …

Studying Disease Dynamics With Manifold Learning, Manik Razdan Kuchroo

Yale Graduate School of Arts and Sciences Dissertations

In an effort to computationally predict causal genetic networks and derive biological pathways empirically, biomedical scientists have begun to design increasingly complicated single cell experiments. A single study can now sequence millions of cells from hundreds of patient samples across different chronological timepoints or stages of disease progression with multiple measurement modalities. None of these additional complexities, however, are adequately addressed by the current state-of-the-art computational tools. Current machine learning techniques ignore these valuable sources of information by either downsampling the number of cells to a computationally tractable number or discarding experimental information, like stage of disease, modality or timepoint, …

Identification And Characterization Of Epigenetic Regulators Of Breast Cancer Metastasis, Jocelyn Fang-Yi Chen

Yale Graduate School of Arts and Sciences Dissertations

Cancer metastasis remains a major clinical challenge for cancer treatment. It is therefore crucial to understand how cancer cells establish and maintain their metastatic traits. Emerging evidence suggests that key steps of metastasis are controlled by reversible epigenetic mechanisms, which can be targeted to prevent and treat the metastatic disease. Although a variety of epigenetic mechanisms were identified to regulate cancer metastasis, including the well-studied DNA methylation and histone modifications, there are very few epigenetic drugs for cancer treatment and currently none of them was approved specifically for metastasis. Thus, we aim to uncover novel epigenetic regulators and identify the …

Β-Catenin Nuclear Transport In Wnt Signaling: Kap-Β2/Transportin Mediates Nuclear Import Of Β-Catenin Via A Py-Nls Motif In A Ran Gtpase Dependent Manner, Woong Y. Hwang

Yale Graduate School of Arts and Sciences Dissertations

Wnt signaling is essential for embryonic development and adult tissue homeostasis; mutations in Wnt pathway components are major drivers of multiple diseases especially cancer. β-catenin is a key effector in this pathway that translocates into the nucleus and activates Wnt responsive genes. However, due to our lack of understanding of β-catenin nuclear transport, therapeutic modulation of Wnt signaling has been challenging. Here, we took an unconventional approach to address this long-standing question by exploiting a heterologous model system, the budding yeast Saccharomyces cerevisiae, which contains a conserved nuclear transport machinery. In contrast to prior work, we demonstrate that β-catenin accumulates …

Drosophila Chemoreception And Threats Of The Anthropocene, Shuke Xiao

Yale Graduate School of Arts and Sciences Dissertations

The term ‘odorant-binding proteins (Obps)’ is used to refer to a large family of insect proteins that are exceptional in their number, abundance and diversity. The name derives from the expression of many family members in the olfactory system of insects and their ability to bind odorants in vitro. However, an increasing body of evidence reveals a much broader role for this family of proteins. Recent results also provoke interesting questions about their mechanisms of action, both within and outside the olfactory system. Here we describe the identification of the first Obps and some cardinal properties of these proteins. We …

Ecological Stressors Impact Soil Biodiversity, Kaleb Frierson, John Carlile

Transformations: Presentation Slides

Soil biodiversity serves ecologically important roles like nutrient cycling and is used as an indicator of community disturbance. North American forests host a multitude of ecological stressors, including invasive plants, earth worms, and deer abundance. While relationships between deer and invasive species, as well as relationships between macroinvertebrates and worms have been heavily investigated, the effects of invasive plant species like Pale Swallowwort on soil biodiversity are unknown. To test our hypothesis that Pale Swallowwort affects soil biodiversity, we collected leaf litter from three state parks throughout Central New York at sites with and without the invasive plant. Samples were …

Life Line Spring 2022, Otterbein Biology And Earth Science Department

Life Line - The Biology Department Newsletter

In this Issue:

A CURE for the Typical STEM Classroom; Attracting Cardinals; Svitana Provides Training to IHS; The Cardinal Science Scholar Program; Mornings with Manatees; Viewing the Department from a New Perspective; Science Lecture Series Features Dr. Tyrone Hayes; Internship with Beinhower Brothers Drilling Company; New Student Chapter: The Botanical Society of America; STEM Art Show 2021; Got Bones?; The Robert and Ann Harting Endowed Award; Grossology Returns; Class Flocks to National Aviary

Tumor-Associated Macrophages In Multiple Myeloma: Advances In Biology And Therapy, Jennifer Sun, Chaelee Park, Nicole Guenthner, Shannon Gurley, Luna Zhang, Berit Lubben, Ola Adebayo, Hannah Bash, Yixuan Chen, Mina Maksimos, Barbara Muz, Abdel Kareem Azab

Open Access Publications

Multiple myeloma (MM) is a cancer of plasma cells in the bone marrow (BM) and represents the second most common hematological malignancy in the world. The MM tumor microenvironment (TME) within the BM niche consists of a wide range of elements which play important roles in supporting MM disease progression, survival, proliferation, angiogenesis, as well as drug resistance. Together, the TME fosters an immunosuppressive environment in which immune recognition and response are repressed. Macrophages are a central player in the immune system with diverse functions, and it has been long established that macrophages play a critical role in both inducing …

“Pandemias Políticas: The Effects Of Political And Social Instability On Infectious Disease Epidemiology In Latin America"”, Sarah H. Noonan

Senior Theses

This paper seeks to analyze the relationship between political and social unrest and conflict and infectious disease epidemiology in Latin America. An analysis of published literature regarding epidemiological, biomedical, political, and historical content was conducted to highlight potential connections between infectious disease epidemics and sociopolitical conflict in the region. Specific analyses of Smallpox, Venezuelan Equine Encephalitis, Chagas disease, Cholera, Dengue, and COVID-19 were conducted, in an effort to uncover potential causations and context of epidemics of these conditions. Results of this analysis depict a necessity for further research into public health and disease control mechanisms during times of conflict and …

Socio-Economic Factors Of Environmental Problems, Manzura Kamalova, D. Shakenov

Karakalpak Scientific Journal

People consciously and intensively rebuild their nature according to their own needs, creating rural and urban areas in which they live. People care about the quality of life in the context of the unity of nature and culture. Social is a relatively new discipline that deals with urban space and environmental issues. One way to imagine what is beneficial to people is to find out what is economically best for the person. The article examines the economic factors that form the attitude towards social ecology in Kazakhstan. The article concludes that society should cooperate to achieve common things, both for …

Research On Characteristics, Development Trend And Funding Countermeasures Of Biology, Jie Chen, Jing Qu, Zhiyong Lou, Bing Zhu, Le Kang

Bulletin of Chinese Academy of Sciences (Chinese Version)

Strengthening the research in biology aimed at national strategic needs and major scientific frontier issues is conducive to giving full play to the strategic supporting role of biological research for national economic development and the promotion of international competitiveness. This article combs the basic characteristics and development trend of biology, summarizes the practical experience of international biological research funding, and analyzes the outstanding problems in biological research in China, such as incomplete layout, lack of sustainable and stable support, and insufficient funding for top talents and teams. By referring to the international practical experience, it puts forward policy suggestions to …

Of Vascular Defense, Hemostasis, Cancer, And Platelet Biology: An Evolutionary Perspective, David G Menter, Vahid Afshar-Kharghan, John Paul Shen, Stephanie L Martch, Anirban Maitra, Scott Kopetz, Kenneth V Honn, Anil K Sood

Faculty, Staff and Student Publications

We have established considerable expertise in studying the role of platelets in cancer biology. From this expertise, we were keen to recognize the numerous venous-, arterial-, microvascular-, and macrovascular thrombotic events and immunologic disorders are caused by severe, acute-respiratory-syndrome coronavirus 2 (SARS-CoV-2) infections. With this offering, we explore the evolutionary connections that place platelets at the center of hemostasis, immunity, and adaptive phylogeny. Coevolutionary changes have also occurred in vertebrate viruses and their vertebrate hosts that reflect their respective evolutionary interactions. As mammals adapted from aquatic to terrestrial life and the heavy blood loss associated with placentalization-based live birth, platelets …

Antioxidant Content In Plant-Based Diets Versus Meat-Based Diets, Lia Meadows, Peeper Walker, Reveca Tomas

JSU Student Symposium 2022

The result of naturally occurring free radicals in the body are oxidative-stress-related damages to cells, tissues, and biomolecules. Oxidative stress occurs when the balance between reactive oxygen species (ROS) outnumbers antioxidants, producing negative effects. Antioxidants exist as a natural defense mechanism utilized by the body. This defense exists in two distinct forms: enzymatic and non-enzymatic antioxidants. Non-enzymatic antioxidants consist of vitamins and bioactive compounds, such as phenols. In previous studies, plant-based diets showed promising results in reducing damage caused by oxidative-stress. The purpose of this study was to determine the extent to which antioxidant concentration differs between meat-based diet and …

Introduction To Epigenetics, Yevgeniy Grigoryev

Open Educational Resources

Syllabus for Bio481 Introduction to Epigenetics

Dna Barcoding For Molecular Prospecting Of Platyhelminthes, Logan Elkin, Will Butak

Student Presentations

DNA barcoding (Folmer et al. 1994), is an efficient method to distinguish species by short specific DNA sequences from a common region of their genome, such as the cytochrome c oxidase subunit 1 (CO1) gene. The early primers of Folmer et al. (1994) were not as universal as desired (Elias et al. 2007). Platyhelminthes (flatworms), being the fourth most speciose animal phylum, is a taxonomic group where universal barcoding primers are not very effective (Vanhove, et al. 2013). Recently, Van Steenkiste et al. (2014) and Elbrecht and Leese (2017) developed primers for parasitic and free-living flatworms that show promise as …

Interspecies Tissue Transplants In Planarians, Maddie Thorstad

Student Presentations

Planarian flatworms have many stem cells called neoblasts which makes them adept at regenerating tissue after injury. This project aims to determine if neoblasts from two different species of planarians—Schmidtea mediterranea and Dugesia japonica—can integrate into the regenerated tissue of the other species. This is done by transplantation of a donor tissue plug from one species into a host planarian of the opposite species. After the host planarian is injured, neoblasts travel to the site of injury and begin regeneration of tissue. We have worked to optimize the transplantation procedure to visually obtain a 75% success rate. Simultaneously, we have …