Biology Commons^™

Genetic Variations In The Regulation And Biosynthesis Of Polycyclic Tetramate Macrolactams, Yunci Qi

Arts & Sciences Graduate Student Theses and Dissertations

Streptomyces are Gram-positive and filamentous bacteria with high-G+C genomes, which have yielded over half of all clinically used antibiotics plus many other useful compounds. Genome analyses indicate that these bacteria possess biosynthetic gene clusters (BGCs) encoding for many more antibiotic-like compounds than they are known to produce. The apparent silence of many BGCs poses a significant roadblock to genome-mining efforts for novel drugs. To understand BGC silence, I compared several Streptomyces that harbor the widespread BGC for polycyclic tetramate macrolactam (PTM) antibiotics to explore the genetic variations that differentiate robustly expressed BGCs from silent BGCs. To test the prevalent hypothesis …

The Role Of Enampt-Mediated Systemic Nad+ Biosynthesis In Aging And Lifespan, Mitsukuni Yoshida

Arts & Sciences Graduate Student Theses and Dissertations

Aging is a systemic decline in tissue functions that occurs during the course of our life leading to the development of age-associated health deteriorations and ultimately to the expiration of life. Over the past few decades, population aging has become increasingly evident in many parts of the world, leading to increased prevalence of age-related disabilities and diseases. Because age is a major risk factor for many chronic diseases, extensive research effort has been spent to identify common age-associated molecular changes contributing to the pathogenesis and progression of these health issues. One such molecule identified to play a central role in …

Apolipoprotein E Immunotherapy For The Preclinical Treatment Of Alzheimer Disease And Cerebral Amyloid Angiopathy, Monica Xiong

Arts & Sciences Graduate Student Theses and Dissertations

The ε4 allele of the apolipoprotein E (APOE) gene is the strongest genetic risk factor for late-onset Alzheimer disease (AD), a neurodegenerative disorder that leads to cognitive dysfunction and dementia. One copy of APOE ε4 increases AD risk by 3.7-fold and two copies by 12-fold, whereas APOE ε2 is protective relative to the more prevalent ε3 allele. APOE4 accelerates the progression of AD by markedly impairing amyloid-β (Aβ) clearance and promoting excess Aβ aggregation, ultimately resulting in downstream neuroinflammation, tau pathology, and neurodegeneration. Aggregated Aβ can co-deposit with the APOE protein in the brain parenchyma as neuritic plaques and in …

Social Communication Across Reproductive Boundaries: Hormones And The Auditory Periphery Of Songbirds And Frogs, M. D. Gall, Alexander T. Baugh, J. R. Lucas, M. A. Bee

Biology Faculty Works

Most animals experience reproductive transitions in their lives; for instance, reaching reproductive maturity or cycling in and out of breeding condition. Some reproductive transitions are abrupt, while others are more gradual. In most cases, changes in communication between the sexes follow the time course of these reproductive transitions and are typically thought to be coordinated by steroid hormones. We know a great deal about hormonal control of communication behaviors in birds and frogs, as well as the central neural control of these behaviors. There has also been significant interest in the effects of steroid hormones on central nervous system structures …

Effect Of Nitrogen Addition On Selection Of Germination Trait In An Alpine Meadow On The Tibet Plateau, Kun Liu, Yang Liu, Zhilong Zhang, Shiting Zhang, Carol C. Baskin, Jerry M. Baskin, Ting Liang, Haiyan Bu, Shuxia Li, Tingting Zhang, Xianliang Cui, Sa Xiao

Biology Faculty Publications

Seed germination requirements may determine the kinds of habitat in which plants can survive. We tested the hypothesis that nitrogen (N) addition can change seed germination trait-environmental filter interactions and ultimately redistribute seed germination traits in alpine meadows. We determined the role of N addition on germination trait selection in an alpine meadow after N addition by combining a 3-year N addition experiment in an alpine meadow and laboratory germination experiments. At the species level, germination percentage, germination rate (speed) and breadth of temperature niche for germination (BTN) were positively related to survival of a species in the fertilized community. …

Nest Site Selection And Nesting Behavior Of The Mud Turtle Kinosternon Scorpiodes (Testudines, Kinosternidae) In Palo Verde National Park, Costa Rica: Implications For Management, José M. Mora, Franklin E. Castañeda

Biology Faculty Publications and Presentations

Habitat selection is the process whereby individuals preferentially use, or occupy, a non-random set of available habitats. At the same time, nest site selection is defined as the placement of eggs by females at sites differing from random sites within a delimited area. We located 59 nests of the mud turtle Kinosternon scorpioides in Palo Verde National Park (PVNP) in Northwestern Costa Rica. We compared eight microhabitat variables at nest sites against those at random sites. Females significantly placed their eggs at sites with more understory, leaf litter cover, and greater leaf litter depth than in random sites. Additionally, females …

The Spread Of Batrachochytrium Dendrobatidis And Its Effect On The Global Amphibian Ecosystem, Mars Pinkelman

COD Library Student Research and Award Symposium

The Spread of Batrachochytrium Dendrobatidis and its Effect on the Global Amphibian Ecosystem, discusses the deadly amphibian pathogen Batrachochytrium Dendrobatidis. My work aimed to answer the question, "How did the spread of batrachochytrium dendrobatidis, affect amphibian populations from its discovery in 1993 to modern day, and how could it affect biodiversity in the future?" It first covers a brief history of the disease and its discovery as well as the impacts it has on individual hosts. I then discuss the effects that the parasitic fungus has on biodiversity, concluding with ways for individuals and communities to mitigate the impacts that …

The Effects Of Covid-19 On Heart Function, Samiha Syed

COD Library Student Research and Award Symposium

Student will investigate the heart function of heart patients who suffer from COVID-19 from a biological and physics-based lens and identify innovative treatment options to alleviate symptoms and blood flow. Students will seek faculty advising one-on-one with Dr. Purcell and additional, from other faculty members in the biology and physics departments at the College of DuPage. Student will also research ways to study heart function in the classroom and develop a model for further study.

Faculty Sponsor: Susan Purcell

Soil Macroinvertebrates Responses To Wildfires In The Blue Ridge Mountains, Usa, Madeline Olliff

Biology Theses

Fire has been a prevalent disturbance on Earth for millions of years. Around the globe there are several regions that have become fire adapted, including the Southeastern United States. There have been few studies examining the effects of wildland fires on soil macroinvertebrates in the Blue Ridge Mountains, in spite of the importance of these animals to soil processes and their contributions to the biodiversity of these ecosystems. During the fall of 2016, the Southeastern USA experienced numerous, large wildfires. These fires offered an opportunity to study the effects of wildland fire on soil macroinvertebrates. We sampled sites from three …

Evaluation Of The Effect Of The Humic Acid Inhibitor On Forensic Genetic Investigations Of Human Skeletal Remains, Madeline King

Honors Theses

Postmortem survival of DNA in human skeletal remains occurs due to the compact microstructure of the skeleton and its ability to provide a strong, protective physical barrier to environmental insults. On a molecular level, DNA preservation in bones/teeth involves electrostatic interactions between the negatively-charged DNA backbone and positively charged calcium residues in hydroxyapatite, the latter of which is one of the main components of bone microstructure. Despite these protections, over time endogenous DNA becomes damaged, limiting our ability to detect it and affecting its utility in making a positive identification. Hence, forensic genetic investigations of unidentified human remains (UHRs) are …

Physiological And Metabolic Strain Differences In Response To Constant Light In Male Mice, Hannah V. Deane

Honors Program Theses and Projects

Circadian rhythms, located in all organisms, is an innate natural clock system driving daily cycles in behavior and metabolism. This clock entrains to daily cycles via regular exposure to light:dark cycles. When light exposure is altered, it is known to cause alterations behavior and metabolism because of its role in regulating bodily function. Constant light (LL) is emerging as a predominant circadian disruption due to prolonged exposure to light at night during night-shift work, and the use of TVs and smartphones at night and throughout the night. To understand how different organisms respond to constant light, two comparative studies were …

Factors Affecting Pubertal Timing And Perceptions Of Birth Control, Ashley L. Gomm

Honors Program Theses and Projects

Menarche is the occurrence of a first menstrual period in the female adolescent. The age of menarche has been decreasing over the past 150 years. While some factors have been identified, like increased body mass index (BMI), such factors alone cannot account for the overall decrease in age.

Due to the decreased age of menarche and as additional uses for oral contraceptive pills (OCPs) have been identified, it is becoming clear that females no longer use “birth control” or “oral contraceptives” primarily to prevent pregnancy, but instead for a myriad other reasons including “menstrual suppression.” Menstrual suppression is …

Tuning Polymorphs And Morphology Of Microbially Induced Calcium Carbonate: Controlling Factors And Underlying Mechanisms, Maryam Khanjani, David J. Westenberg, Aditya Kumar, Hongyan Ma

Biological Sciences Faculty Research & Creative Works

Microbially precipitated calcium carbonate (CaCO₃) has drawn broad attention due to its potential applications in various areas, for example, biocementation, medicine, and soil reinforcement. Sporosarcina pasteurii (S. pasteurii), formerly known as Bacillus pasteurii, has been investigated for CaCO₃ biomineralization due to its high ureolytic activity. A high degree of supersaturation with respect to the presence of bacterial cell wall, extracellular polymeric substances, and organic byproducts of bacterial activity plays an important role in the formation and stabilization of CaCO₃ polymorphs. Although microbially induced CaCO₃ and its polymorphs have been investigated broadly, the …

Identification Of Haloarchaea In Gypsum From Great Salt Lake, Zhantao Du

Utah Space Grant Consortium

Gypsum (CaSO4·2H2O) is a common precipitate at Great Salt Lake (GSL). On Earth, gypsum is formed in hypersaline environments, in minerals left behind when water evaporates. In the Autumn, as the water cools, mineral precipitation is favored since solubility is lowered. In this process, newly formed gypsum will trap microorganisms in fluid and clay inclusions. This study is to cultivate haloarchaea preserved in gypsum, and identify the species using PCR technique.

Characterization Of Halophyte Rhizosphere Microbiomes At Great Salt Lake, Utah, Haley K. Nate

Utah Space Grant Consortium

The saline soils comprising the shoreline of Great Salt Lake, Utah (GSL) provide a unique habitat for both halophytes (salt-tolerant plants) and the microorganisms that inhabit their rhizosphere. While plant diversity has been well documented at GSL, little is known about the microbial diversity in the rhizosphere. Here we present preliminary data characterizing the halophyte rhizosphere microbiome at two GSL locations; the more saline North Arm near the artwork, Robert Smithson's Spiral Jetty (SJ), and the less saline South Arm on Antelope Island (Al). The rhizosphere of several plants along the shoreline at both SJ and Al locations was sampled. …

Connecting Land Cover To Benthic Cover Within The Watershed: Quantifying Impacts Of Terrigenous Sediment On Coral Reef Health And Morphology Using Remote Sensing And Machine Learning, L. Kalai Ellis

Utah Space Grant Consortium

Erosion, with associated sedimentation of reefs and loss of habitat for marine and coastal species, is one of the most pressing environmental challenges in Hawaii. Identifying hotspots of soil erosion guides management on land, but limited work has been done connecting land cover to coral reef health and morphology. Current reef survey methods overgeneralize the spatial variation of benthic cover and this has been reflected in incorrect Geographic Information System (GIS) layers of the reef. We propose a novel and more holistic approach to improve accuracy by connecting sedimentation from source to sink using Unmanned Aerial Vehicles (UAVs), Unmanned Surface …

Selenium Burdens In Painted Turtles (Chrysemys Picta), Holly A. Gerberding

Honors Thesis

Tile drain systems are a critical advancement in agriculture that move excess water from crop fields to streams, ditches, and wetlands. Selenium is a necessary mineral but is considered toxic at high levels. Previous research indicates that wetlands with tile drains are at a higher risk for elevated selenium concentrations. Selenium enters the aquatic ecosystem via these tile systems and us taken up by invertebrates and continues to bioaccumulate mainly via direct transfer in higher trophic level taxa such as fish, amphibians, reptiles, birds, and mammals. For this study, painted turtles (Chrysemys picta) served as a model organism to …

Probing Interactions Between Canonical Nox Domains, Akua Acheampong

Master of Science in Integrative Biology Theses

NAPDH oxidase enzymes (NOXes) reduce molecular oxygen to superoxide and other ROS. NOXes contain a catalytic core comprising a heme-containing transmembrane (TM) domain and a cytoplasmic dehydrogenase (DH) domain that binds the substrate NADPH and the cofactor. Previously, NOXes were only characterized in eukaryotes, but have recently been identified in prokaryotes, namely bacteria. Due to their constitutive activity and solubility in detergent, bacterial NOXes, such as Streptococcus Pneumoniae NOX, have emerged as a model for studying NOXes. Past research studies in NOXes have identified conserved, putative interacting regions at the interface of the TM and DH domains: the TM B-loop, …

Serum Biochemical Profile Of Captive-Bred Philippine Crocodiles (Crocodylus Mindorensis Schmidt, 1935) Sub-Adults, Janice A. Ragaza, Stephanie F. Velasquez, Marian Samantha M. Asuncion, Elyssa Marie F. Torres, Rainier Manalo, Hendrik Freitag

Biology Faculty Publications

The Philippine crocodiles Crocodylus mindorensis Schmidt; 1935 are a critically endangered species that necessitate minimally invasive diagnostic tools for their physiological state and health assessment. In the current study; we determined the reference ranges for the serum biochemistry of male and female captive-bred C. mindorensis sub-adults. We collected blood samples from the post-occipital venous sinus of six male and seven female captive-bred crocodile sub-adults at the Palawan Wildlife Rescue and Conservation Center and quantified the serum biochemical values for cholesterol; triglycerides; uric acid; glucose; creatinine; aspartate aminotransferase (AST); alanine aminotransferase (ALT); albumin; total protein; and globulin. We defined reference ranges …

Rhythm Of The Night: Brain Activity And Performance On A Sustained Attention Task Is Modulated By Circadian Typology And Time Of Day, Carly R. Cooper

Honors Thesis

The human circadian system plays an important role in biological and psychological processes in both health and disease. Circadian typology refers to individual differences in circadian rhythm and is categorized into three general chronotypes: morning, evening, and neither. Research suggests that an individual’s diurnal preference may be associated with differences in cognitive abilities, personality traits, and incidence of psychiatric disorders. In the present study, we utilized a Sustained Attention to Response Task (SART) and an electroencephalogram (EEG) in a desynchrony protocol. Morning-type and evening-type participants completed a SART task on two separate occasions during which brain activity was recorded. This …

Optimizing The Delivery Of A Gfp Gene Via A Biocompatible Nanocarrier In Daphnia And A Chironomid, Alexandra R. Job

Honors Thesis

Current pest control methods impose risks including pest resistance to insecticides, bioaccumulation of the insecticide, and ecosystem impact. There is a need for a better and more sustainable method of pest control in order to protect the environment and the populations reliant on it. Currently, an alternative method of pest control uses RNA interference (RNAi), that exploits heterologous protein expression to disable the insect pest, delivered by the use of nanoparticles. Nanocarriers show great promise in this method of use, but concerns of cytotoxicity, biodegradability, and transfer to off target organisms require careful consideration. This study focuses on optimizing a …

Biomedical Porcine Models For The Study Of Surgical Hemostasis, Hindlimb Ischemia, And Pancreatic Cancer, Shruthishree Aravind

Theses & Dissertations

Murine models have dominated the world of biomedical research and comparative medicine since their development in the early 1900s. [1] While they may be suitable models to study proteomics and genomics, they may not serve as effective translational models. [2-4] Murine models do not accurately model the pathophysiology of human disease and are limited by their size, application of medical imaging and intervention, which reduces their overall preclinical predictive value. [2-4]

Porcine models on the other hand, are slowly and steadily bridging the gap between murine models and human patients. [5] Pigs …

Manduca Sexta As An Animal Model Of Muscle Aging, David Melanson

Honors Thesis

Aging has a multisystemic effect on an organism’s functional physiology and quality of life. One such effect is the progressive loss of muscle mass, strength, and function, known as sarcopenia. A thorough investigation to the multiple factors that contribute to sarcopenia is required. Models are used to dissect the mechanistic understanding of the muscle aging process. Manduca sexta is emerging as a novel and complementary muscle aging model because their flight muscles are metabolically and functionally similar to vertebrate skeletal muscle. Manduca sexta is already a prominent invertebrate model organism in neurobiology, immunology, developmental research, and flight mechanics because of …

Evaluation Of Chili Pepper (Capsicum Annuum), Tiger Nuts (Cyperus Esculentus), And Turmeric (Curcuma Longa) As Sources Of Antioxidant Compounds For The Potential Of Antiaging-Like Activity, Chelsea Toyer

Theses

Aging is a natural process that living organisms go through as they become older. In humans and other animals, aging is accompanied by several morphological changes, including the formation of wrinkles. Wrinkles are also caused by various environmental factors such as excessive exposure to sun or pollution, and continuous sleep deprivation. These environmental factors cause oxidation of skin cells and the degradation of subcutaneous fatty acids, leading to the formation of wrinkles. Skin care and wrinkle treatment products are part of a multimillion-dollar industry. Plant-based products are an alternative method for treating wrinkles and premature aging. Several antioxidants naturally found …

Comparison Of Skin Microbial Communities Between Striped And Unstriped Morphs Of Plethodon Cinereus In Massachusetts, Alyssa St. John

Honors Program Theses and Projects

The skin-microbial community on amphibians plays a large role in maintaining the general health of the organism. One of the most common patterns found in amphibian skin microbiomes pertains to the antifungal aspect of these communities: beneficial microbes protect amphibians against harmful pathogenic fungi. The eastern red-backed salamander is one of the few amphibian species with well-documented skin microbes that produce antifungal compounds. These compounds are potentially lethal to chytrid fungus, one of the deadliest amphibian pathogens. The eastern red-backed salamander also has two primary color morphs that coexist over a large geographic range. Physiological differences between morphs have been …

Illuminating The First Bacteria, Laura A. Katz

Biological Sciences: Faculty Publications

The ability to sequence genes and, more recently, whole genomes has transformed our understanding of the tree of life by elucidating the tremendous diversity of microorganisms and by placing plants, animals, and fungi as branches nested among microbial lineages (1–3). The resulting evolutionary tree divides life into three domains: the exclusively microbial Bacteria and Archaea, and Eukarya, organisms whose cells contain nuclei (including ciliates, amoebae, and animals). Yet, the ordering of the earliest branching events on the tree and the nature of now-extinct ancestors remains unclear. On page 588 of this issue, Coleman et al. (4) provide a new estimate …

Hidden Consequences: The Effects Of Daikon Radish On The Microbial Communities Of Purple Vetch In Cover Crop Mixtures, Marcello B. Kuan

Creative Activity and Research Day - CARD

Many microbes live in and on plants. Some of these microbes are mutualists, and help the plant, while others are pathogenic and cause harm. It is not always clear which will occur, because the outcomes are influenced by the host, the microbe, and their shared environmental context. A previous study from our lab of the microbes associated with cover crops at the oldest continually-operating organic farm in California, Star Route Farms, found that leaves of cover crops were frequently inhabited by fungi in the classes Dothideomycetes, Leotiomycetes, Sordariomycetes, and Agaricomycetes. Using the recently-published FungalTraits database, I determined the commonly observed …

Development Of A Real-Time Cell Imaging Assay To Characterize The Delivery Of A Cell-Penetrating Peptide Adaptor And Its Associated Cargo, Schuyler Gentry

Master of Science in Integrative Biology Theses

Cell-penetrating peptides (CPPs) are small peptides capable of transporting molecules across the membrane. In most cases, the membrane is a blockade that prevents molecules from entering the cell, therefore CPPs have attracted much attention. Although CPPs are effective, this system is still hindered by many issues. The endosomal entrapment problem is the main rate-limiting step for cytosolic delivery and is a result of endocytosis. To combat this issue, a new CPP, TAT-CaM, that can reach the cytosol has been developed. Conventional methods involve observing these peptides in a static manner, which has hindered a complete understanding of CPPs. Therefore, a …

Big Five Personality Traits And Political Orientation: An Inquiry Into Political Beliefs, Ian E. Phillips

The Downtown Review: An Interdisciplinary Journal Written and Peer-Reviewed by Mandel Honors College Students at Cleveland State University

Personality research centered on the Big Five personality traits has heavily impacted our understanding in regards to what forces orient a person on a political spectrum. Examining how personality differences interact with political orientation, this research seeks to provide information on what makes someone either more or less likely to be liberal or conservative based on their temperament. In this paper, previous personality research is synthesized into one discussion, centered on what the effects of each trait are and how they impact political orientation, the heritability of personality, and what implications there are for such research in the realm of …

Terrestrial Soldier Crab (Coenobita Clypeatus, Fabricius 1787) And Cerion Spp. (Röding 1798) Shell Relationship On San Salvador Island, Bahamas, Harley Hunt

Biology Theses

The Caribbean terrestrial soldier crab, Coenobita clypeatus(Fabricius 1787), coexist and utilize the shells of numerous species of land and marine gastropods. Soldier crabs rely on gastropod shells for protection as the crabs have a soft abdomen, leaving them vulnerable for predation and desiccation, threatening their survival. This creates a strong pressure to obtain well-fitting shells that provide adequate protection against water loss. Cerion of Röding (1798) shells are one of the most commonly used shells among living colonies of C. clypeatuson San Salvador Island. This study is interested in the frequency of shell use by C. clypeatus crabs …