Biology Commons^™

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

Functional Analysis Of Stn1 Winged-Helix (Wh) Domains, Anna Bazell

Senior Theses

CST (CTC1-STN1-TEN1) is a heterotrimeric RPA-like protein complex that preferentially binds to single-stranded DNA (ssDNA). CST is conserved from yeast to humans and has been found to play a role in telomere maintenance, DNA replication, and DNA repair. Mutations in CST, specifically in the subunits of CTC1 and STN1, have been implicated in the development of the genetic diseases Coats plus and dyskeratosis congenita. Despite the known functions of CST, the mechanistic relationship between its structure and function has yet to be characterized, particularly with respect to its protein-protein interactions and DNA binding. An X-ray crystallography structure of CST revealed …

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 …

Bacteriophage That Infect Gordonia Species Show Varying Host Specificity And Infection, Lindsay Birge

Honors Program: Senior Projects (Public)

Bacteriophage (phage) are an incredibly abundant species of virus that infect bacteria. One major characteristic of phage is their small host range- many phage are known to infect only one or a few hosts. This phage and host relationship has led to phage therapy recently becoming highlighted as a possible alternative to traditional antibiotics in light of the growing antibiotic resistance crisis. The study of phage host specificity has risen in line with this concept, as a phage with a more extensive host range can provide more opportunities for use as an antibiotic. Samples of phage previously isolated on a …

An Exploration Of Trex1 Variants Of Uncertain Significance And Their Potential Impact On Autoimmunity In Systemic Lupus Erythematosus And Aicardi-Goutieres Syndrome, Jordan Peters

JSU Student Symposium 2022

TREX1 is a gene responsible for encoding a 3'-to-5' DNA exonuclease in human cells. Under normal conditions TREX1 removes bases from the free 3' end to enhance DNA damage and prevent DNA end reannealing and rapid repair. Mutations in TREX1, which result in the absence of the 3'-to-5' DNA exonuclease and the intracellular accumulation of unneeded DNA and RNA, have been shown to trigger immune dysfunction leading to diseases such as systemic lupus erythematosus (SLE) and Aicardi-Goutières Syndrome (AGS). The goal of this study is to determine the potential impact of a TREX1 missense mutation with uncertain clinical significance (VUS). …

Effects Of Specific Blocking Buffers On Histone H2b Antibodies, Noha Al-Saadi, Grace Mix, Mardasia Thompson, Elin Zaman

JSU Student Symposium 2022

Mammalian histones have been known to be one of the most highly alkaline proteins found in the nuclei. Their main function is to organize DNA into chromosomes and regulate transcription. An example of a histone would be Histone H2B, which this project focuses heavily on. Histone H2B has been seen to bind poorly to antibodies and result in a weak signal. The goal of this project is to test a multitude of blocking buffers, in triplicate, in order to find a blocking buffer that can obtain the strongest signal from the antibodies being tested. Through the use of protein gel …

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 …

Genetic Assessment Of Congenital Stationary Night Blindness-Associated Trpm1 Variants Of Uncertain Significance In C. Elegans, Sara Morris

JSU Student Symposium 2022

Congenital stationary night blindness (CSNB) is a disorder of the eye that impacts the ability to see in low to no light conditions. It occurs in horses and humans. TRPM1 encodes for a member of the transient receptor potential melastatin subfamily of transient receptor potential ion channels. Mutations in TRPM1 have been identified by previous researchers in horses with leopard complex pattern (LCP) suffering also from CSNB. Phenotypic changes in these horses are a loss of spotted coat pattern. An attempt was made to locate variants of uncertain significance (VUS) in TRPM1 that had been previously identified in horses with …

Using Ecological Niche Modeling To Predict The Response Of Hydrocotyle Bonariensis To Global Climate Change, Rachel Bonner, Laura K. Dease, Elizabeth A. Hughston

JSU Student Symposium 2022

Coastal dune habitats provide valuable ecosystem services but are declining globally due to the interacting effects of multiple stressors, including global climate change (GCC). To explore the potential severity of the effects of GCC on dune plant communities of the Northern Gulf of Mexico and surrounding areas, we modeled the fundamental bioclimatic niche of a dune plant species, largeleaf pennywort (Hydrocotyle bonariensis Comm. ex Lam.), in this region. We then projected its niche to estimate habitat suitability under current and future environmental conditions. Occurrence records were mined from the Global Biodiversity Information Facility, cleaned, then thinned by spatial filtering, …

Characterization Of Anti-Microbial Properties Of Excrement And Functional Microbiome Of New World Vultures In Alabama, Bridgette Gray

JSU Student Symposium 2022

Two distinct species of New World vultures are native to North America and inhabit Alabama, black vultures (Coragyps atratus) and turkey vultures (Cathartes aura). They are scavengers that consume decaying carcasses or carrion, which helps reduce the spread of disease. Vultures are susceptible to declining population numbers as they have been trapped and killed due to the belief that they spread disease, additionally contact with poisons and habitat destruction have also led to their decline. Currently, these two vultures are one of the seven vulture species with least concern and stable in Alabama and the world. However, it is important …

Diving Into The Unknown: A Genetic Investigation Of Type-2 Diabetes-Associated Insr Variants Of Uncertain Significance, Trinity Elston

JSU Student Symposium 2022

Type 2 diabetes is a complex metabolic disorder with interactions between genetic and environmental factors, making it more complicated to understand the clinical implications of identified genetic variants and disease pathology. Many of the diabetes-associated variants are currently classified as VUS and occur within the genes involved in insulin signaling and regulation, so we turned our focus on the human INSR gene. INSR encodes the insulin receptor protein that plays a major role in insulin signaling. Furthermore, C. elegans provides a simple model system to examine the functional consequences of these diabetes-associated VUS. We examined INSR diabetes-associated VUS through the …

Introduction To Epigenetics, Yevgeniy Grigoryev

Open Educational Resources

Syllabus for Bio481 Introduction to Epigenetics

Predicting Gene Function Of Unknown Yeast Orfs Through Phylogenetic Comparative Analysis, Lewis Barr

Graduate Research Showcase

Yeast (Saccharomyces cerevisiae) has been an instrumental model system for an extraordinary diverse array of research applications for over a century now. The S. cerevisiae genome was fully sequenced in 1996, and, as a result, 6,753 potential proteins were identified. These putative proteins were established by investigating likely open reading frames within the genome. Over the past few decades, nearly 5,000 open reading frames (ORFs) and their expressed proteins have been described, and the remaining undefined open reading frames are labeled as open reading frames of unknown function (ORFans). To better understand the remaining gaps within the S. …

Inhibition Of Staphylococcus Aureus Biofilm By Variovorax Paradoxus, Esther Gomez

University of the Pacific Theses and Dissertations

Staphylococcus aureus is one of the leading causes of fatal nosocomial infections. Often, S. aureus can grow as a biofilm which protects the population from the surrounding environment. Strains of S. aureus are resistant to virtually all known antibiotics on the market. Variovorax paradoxus is a soil microbe with many unusual metabolic activities. It has been previously observed that, V. paradoxus can inhibit the growth of S. aureus when in co-culture. In this work we report on inhibition of S. aureus biofilm formation by V. paradoxus due to a suspected inhibitory soluble factor.

Patterns And Process Of Sandbar Revegetation On The Missouri National Recreational Rive, Amena Begum Ruma

Dissertations and Theses

Decades of flow regulation have reduced sandbar area and recruitment of cottonwood and willow along the Missouri River. Conflicts exist between managing sandbars for habitat (removing vegetation) for threatened sandbar-nesting birds (i.e., Piping Plover) and allowing natural recruitment of early successional riparian woodland (set-aside bars) that may support other species and ecological values. Recent changes in topography, geomorphology, and vegetation were examined on sandbars that have been “set aside” from management within seven reaches of the Missouri National Recreational River (MNRR) in southeastern South Dakota, USA. An existing time series of maps of sandbar landcover, derived from satellite imagery, was …

Final Report Floating Upwelling System Harvest Road Oceans, Robert Michael, Scott Bennett

Fisheries Occasional Publications

A Floating Upwelling System or FLUPSY is a mechanical system for the culture of seed stock during the nursery stage of commercial bivalve production.

Impacts Of Plastic Pollution On A Pelagic Marine Mammal, The Northern Elephant Seal, Lauren M. Kashiwabara

University of the Pacific Theses and Dissertations

As plastic pollution increases, top marine predators such as marine mammals are becoming increasingly susceptible to plastic particles and their additives. Plastic particles have been found in gastrointestinal tracts and scat of many marine mammals, and quantifying plastic pollution in those that are pelagic can provide insight into plastic pollution in mesopelagic ecosystems that are just beginning to be analyzed. Adapting well-developed laboratory techniques for microplastic (MP) isolation (i.e. density separation and chemical digestion), I isolated MPs from the scat of the deepest diving pinniped, the northern elephant seal (NES), and found that100% of scat samples (n=11) contained high counts …

The Bgs 13 Mutant Of Pichia Pastoris And Its Effect On Structural Changes Of The Reporter Protein B-Lactogolbulin, Bushra Irshad

University of the Pacific Theses and Dissertations

Pichia pastoris, a methylotrophic yeast, is an ideal host for recombinant protein expression. It has the capability of performing many eukaryotic post-translational modifications and grows to high cell densities. However, P. pastoris’s secretion properties are not always efficient, and its secretory pathway mechanisms have not been thoroughly elucidated. A previously identified mutant strain, bgs13, was found to efficiently secrete most recombinant proteins tested, raising the possibility that this bgs13 mutant is a universal super secreter and understanding its secretion process is needed. In this study, we used a reporter protein, ?-lactoglobulin (b-LG), to perform structural analysis and comparisons of protein …

Chemosensitivity Of Locus Coeruleus Neurons Decreases With Postnatal Development, Yasmeen Samar

Browse all Theses and Dissertations

The locus coeruleus (LC) is a chemosensory area partially responsible for ventilation. Control over ventilation relies on inter-network communication via chemical and electrical synapses and chemosensitivity to CO2/pH. As the LC develops, it’s neural control over ventilation changes. This study investigates the chemosensitivity of the locus coeruleus over the course of development in postnatal rats. We hypothesize that 1) the CO2 sensitivity of LC neurons is highest at birth and declines with development 2) LC neurons are intrinsically chemosensitive and this chemosensitivity does not decrease with development and 3) the presence of gap junctions is highest at the beginning of …

Cpf1-Based Crispr Genome Editing In The Cyanobacterium N. Punctiforme, Soohan Woo

University of the Pacific Theses and Dissertations

CRISPR systems have been growing in their utility and their application throughout the biological field as researchers continue to grow in their understanding of the relatively novel genome editing technology. However, despite the potential of CRISPR as a genome editing tool, the complexity of applying this technology to a specific organism calls for custom modifications to the system to improve its success rate. In this project, a CRISPR-Cpf1 system that can be effectively employed in the cyanobacterium Nostoc punctiforme was designed, with a focus on the hormogonium development of this species. Multiple plasmids containing the CRISPR system and targeting different …

Land-Use And Ant Biodiversity In California’S Central Valley, Laura L. Navarro

University of the Pacific Theses and Dissertations

The growing human population results in growing demand for land allocated to urban development and agricultural production (Godfray et al. 2010; Tilman et al. 2011; McDonnell and Hahs 2013; Alexander et al. 2015; Erlwein and Pauleit 2021). Changes to land allocation associated with agricultural and urban development will increasingly alter terrestrial ecosystems impacting biodiversity (Ricketts et al. 2001; McDonald et al. 2008). Ants are an ideal organism for monitoring changes in biodiversity related to land-use change due to their ubiquitous nature, high diversity, and their role as bioindicators. The goal of this study was to assess the diversity of the …

Exploring The Host Range, Impacts, And Distribution Of Black Rot Disease On Alliaria Petiolata, Gabriela Ivette Harney-Davila

Browse all Theses and Dissertations

Garlic mustard is an invasive Eurasian biennial spreading in deciduous forests of North America. Garlic mustard plants in Ohio can be infected with a strain of Xanthomonas campestris, the causal agent of black rot disease in brassicas. I examined variation in susceptibility to X. campestris among garlic mustard populations, several native wild species, and agricultural crop varieties. Twenty-four garlic mustard populations were universally susceptible to X. campestris, though disease severity varied. Cardamine concatenata and Cardamine diphylla were susceptible but can phenologically escape infection in the field. Of the 14 agricultural crops tested, three cultivars (Raphanus sativus, Brassica rapa var. Rapa …

The Impact Of Sentiment And Misinformation Cycling Through The Social Media Platform, Twitter, During The Initial Phase Of The Covid-19 Vaccine Rollout, Emily Grace Burwell

Browse all Theses and Dissertations

This study assesses the underlying topics, sentiment, and types of information regarding COVID-19 vaccines on Twitter during the initiation of the vaccine rollout. Tweets about the COVID-19 vaccine were collected and the relevant tweets were then filtered out using a relevancy classifier. Latent Dirichlet Allocation (LDA) was used to uncover topics of discussion within the relevant tweets. The NRC lexicon was used to assess positive and negative sentiment within tweets. The type of information (information, misinformation, opinion, or question) in tweets was evaluated. The relevancy classifier resulted in a dataset of 210,657 relevant tweets. Eight topics provided the best representation …

Modeling Als-Associated Matrin-3 Toxicity In Yeast, Widad El-Zein

Browse all Theses and Dissertations

ALS is a neurodegenerative disease characterized by degeneration of upper and lower motor neurons in the brain and spinal cord leading to progressive paralysis and ultimately death. Perturbations in RNA metabolism and RNA binding proteins have emerged as underlying defects in ALS pathogenesis. Matrin-3 is a multifunctional RNA binding protein that has been linked to familial and sporadic ALS. Matrin-3 is normally found in the nucleus, but mutations in the gene cause mislocalization of the protein from the nucleus into the cytoplasm of neuronal cells where it forms protein aggregates. In this study, we show that over-expressing human MATR3 in …

Urban Insect Biodiversity - Effects Of Native Landscaping, Caedmon Morgret, Dave Warners

Student Papers and Reports

Urban development comes with the cost of destroyed natural habitats. Urban infrastructure flattens entire ecosystems, replacing them with impervious, life-inhibiting constructions.

Alleviating the impacts of urbanization is possible. Green infrastructure mitigates habitat loss by restoring native habitats within urbanized areas. One benefit of green infrastructure is the reestablishment of biodiversity, benefitting plants, animals, and insects alike. Biodiversity creates a healthier habitat and location than urban infrastructure –and lack of biodiversity –does.

To investigate this benefit we performed a pilot study, sampling lawns and curb-cut rain gardens (CCRGs). We compared biodiversity between restored and unrestored urban habitats.

Observing Gravitropism In Brassica Rapa Roots, Trang Ly, Maya O'Callagham, Lan Poeschl, Adil Saeed, George Zorn

UROP Posters

The objective of this experiment is to observe the effect of gravitropism on the orientation of Brassica rapa (B. rapa) roots. Specifically, amyloplasts that reside at the bottom of root tips act as gravity sensors. As plants are disturbed from upright orientation, roots automatically grow according to the downward pull of gravity. It is hypothesized that as the angle of rotation increases, the angle of root growth is inversely proportional. Five plants containing four seeds of B. rapa were grown over the course of 10 days. Each plates, aside from the control, were rotated once 90°, 80°, and 270° to …

Can Gdp Be Predictive Of Fertility Rates In Sweden?, Hannah Coleman

Honors Program: Senior Projects (Public)

Fertility rates in a country vary and can be influenced by numerous different aspects of an individual’s life and the society in which they live. One aspect that may influence fertility rates at the national level is the gross domestic product (GDP). GDP is an indicator of a country’s economic productivity. Because fertility is linked to both economic development and individual resources, GDP may be a useful indicator of fertility rates. If so, knowing or predicting GDP could be used to project the fertility rates of a population years into the future. To determine if a reasonable connection between GDP …

Beyond Cortisol: Indicators Of Stress And Negative Feedback In Plasma And Blubber Of Marine Mammals, Jessica Avalos

University of the Pacific Theses and Dissertations

Marine mammals play an important role in ecosystem stability. However, anthropogenic activity is compounding pressure on many already vulnerable populations. A potential consequence of anthropogenic disturbance is physiological stress, which can impact metabolism, immunity, and reproduction, especially if it occurs repeatedly. Previous studies on marine mammals have focused on acute stress, but the impacts of repeated stress are poorly understood. Due to its accessibility on land during haul-outs, the northern elephant seal (Mirounga angustirostris) is a good system in which to study the effects of stress in marine mammals. Stress stimulates the release of glucocorticoid hormones, primarily cortisol. Elevated cortisol …

How Do They Do It? Using Omics Approaches To Explore Metabolic Responses Associated With Hypoxia And Exercise Tolerance In The Deepest Diving Pinniped, Elizabeth R. Piotrowski

University of the Pacific Theses and Dissertations

Marine mammals such as northern elephant seals (NES) routinely experience hypoxemia and ischemia-reperfusion events to many tissues during deep dives with no apparent adverse effects. Adaptations to diving include increased antioxidants and elevated oxygen storage capacity associated with high hemoprotein content in blood and muscle. Despite experiencing decreased oxygen tensions during diving, NES likely rely on the mobilization of large lipids stores and catabolism of fatty acids to provide energy to exercising muscle while diving. To identify potential regulatory mechanisms that may underly hypoxia and exercise tolerance in diving mammals, this study used system-wide approaches to characterize changes in genes …