Biology Commons^™

The Diet Of The Cumberland Plateau Salamander (Plethodon Kentucki) In An Old Growth Forest Of Southeastern Kentucky, Jacob M. Hutton, Steven J. Price, Stephen C. Richter

EKU Faculty and Staff Scholarship

Examining the diet of salamanders is important for understanding their effects on invertebrate communities and the interactions among sympatric salamander species. We

examined the diet of the Cumberland Plateau Salamander, Plethodon kentucki (Mittleman), in an old growth forest in southeastern Kentucky. A total of 763 prey items were recovered from 73 salamanders with an average of 10.75 prey items per stomach. The four most important prey groups were Formicidae (ants), Araneae (spiders), Coleoptera (beetles), and Collembola (springtails). Overall, we found a total of 58 different prey types in the stomach contents from 20 invertebrate orders. This study represents one of …

Draft Genome Sequence Of Escherichia Coli K-12 (Atcc 10798), Catherine Putonti, Daniela Dimitrova, Kathleen C. Engelbrecht, David W. Koenig, Alan J. Wolfe

Biology: Faculty Publications and Other Works

Here, we present the draft genome sequence of Escherichia coli ATCC 10798. E. coli ATCC 10798 is a K-12 strain, one of the most well-studied model microorganisms. The size of the genome was 4,685,496 bp, with a G+C content of 50.70%. This assembly consists of 62 contigs and the F plasmid.

Draft Genome Sequence Of Enterococcus Faecalis Atcc Baa-2128, Catherine Putonti, Laurynas Kalesinskas, Evan Cudone, Kathleen C. Engelbrecht, David W. Koenig, Alan J. Wolfe

Biology: Faculty Publications and Other Works

While a part of the native gut microflora, the Gram-positive bacterium Enterococcus faecalis can lead to serious infections elsewhere in the body. The draft genome of E. faecalis strain ATCC BAA-2128, isolated from piglet feces, was examined. This draft genome consists of 42 contigs, 12 of which exhibit homology to annotated plasmids.

Draft Genome Sequence Of Micrococcus Luteus (Schroeter) Cohn (Atcc 12698), Catherine Putonti, Evan Cudone, Laurynas Kalesinskas, Kathleen C. Engelbrecht, David W. Koenig, Alan J. Wolfe

Biology: Faculty Publications and Other Works

The actinobacterium Micrococcus luteus can be found in a wide variety of habitats. Here, we report the 2,411,958-bp draft genome sequence of the type strain M. leuteus (Schroeter) Cohn (ATCC 12698). Characteristic of this taxa, the genome sequence has a high G+C content, 73.14%.

Bacterial Community Ecology Of The Colon In Mus Musculus, Rachel Marie Nettles

Theses and Dissertations

The gut microbiome is a community of closely interacting microbes living in the gastrointestinal tract. Its structure has direct relevance to health. Disturbances to the microbiome, such as due to antibiotic use, have been implicated in various diseases. The goal of this study was to determine how the gut microbiome reacts to and recovers from disturbance caused by antibiotics. Because diet also influences the microbiome, this study included the interaction between diet and antibiotics. Half of the mice in each diet treatment were given antibiotics to disturb their microbiomes. After cessation of antibiotics, mice were paired in combinations within diets …

The Chondrocyte Channelome: A Novel Ion Channel Candidate In The Pathogenesis Of Pectus Deformities, Anthony J. Asmar

Biological Sciences Theses & Dissertations

Costal cartilage is a type of rod-like hyaline cartilage connecting the ribs to the sternum. The chest wall deformities pectus excavatum (PE) and pectus carinatum (PC) involve displacement of the sternum causing a depression or protrusion of the chest. There is little knowledge about costal cartilage and pectus deformities with much of its understanding based on assumptions from articular cartilage. Chondrocytes are subjected to a constantly changing environment with fluctuations in pH and osmolarity. Ion channels detect these changes and in turn regulate proliferation, differentiation, and extracellular matrix production. Using ion channel qPCR arrays, we produced expression profiles for normal, …

Central Precocious Puberty Alters The Mammary Gland Epithelial Landscape In Female Rats, Alina M. Hamilton

Theses and Dissertations

Precocious puberty (PP) is a serious endocrine disorder associated with an increased risk for development of breast cancer (BC) later in life. However, the lack of a strong in vivo model has made it difficult to study this relationship. Our group has established manganese (Mn) as a non-toxic activator of the pubertal process. Recently we demonstrated that Mn-induced precocious puberty (MnPP) accelerates E2-regulated mammary gland (MG) development in prepubertal female rats, resulting in persistent proliferation and adult hyperplasia. Using this model, I demonstrate that precocious puberty alters steroidal regulation of proliferation in both the prepubertal and adult virgin MG, altering …

Linking Plant Hydraulics And Beta Diversity In Tropical Forests, Bradley O. Christoffersen, Patrick Meir, Nate G. Mcdowell

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

This article is a Commentary on Cosme et al., 215: 113–125.

Solvent Based 3d Printing Of Biopolymer/Bioactive Glass Composite And Hydrogel For Tissue Engineering Applications, Krishna Kolan, Yong Liu, Jakeb Baldridge, Caroline Murphy, Julie A. Semon, D. E. Day, Ming-Chuan Leu

Biological Sciences Faculty Research & Creative Works

Three-dimensional (3D) bioprinting is an emerging technology in which scaffolding materials and cell-laden hydrogels may be deposited in a pre-determined fashion to create 3D porous constructs. A major challenge in 3D bioprinting is the slow degradation of melt deposited biopolymer. In this paper, we describe a new method for printing poly-caprolactone (PCL)/bioactive borate glass composite as a scaffolding material and Pluronic F127 hydrogel as a cell suspension medium. Bioactive borate glass was added to a mixture of PCL and organic solvent to make an extrudable paste using one syringe while hydrogel was extruded and deposited in between the PCL/borate glass …

Determining Critical Internesting And Foraging Habitats For The Conservation Of Sea Turtles In Gabon, Africa Using Satellite Tracking And Stable Isotope Analysis, Tiffany M. Dawson

Biological Sciences Theses & Dissertations

Understanding the horizontal and vertical habitat of olive ridley sea turtles (Lepidochelys olivacea), a threatened species, is critical for determining regions of protection that may effectively reduce bycatch, the largest threat to this species. Satellite transmitters were used to determine the movement and dive behavior of 21 female olive ridley turtles tagged in Pongara National Park, Gabon during the 2012, 2013, and 2015 nesting seasons. A switching state space model was used to filter the tracking data and categorize the internesting and post-nesting movements. Gridded utilization distribution (UD) home range analysis of tracking data revealed that the entire core habitat …

The Roles Of Diffusion And Bulk Flow In Neural Function And Alzheimer's Disease, Wade N. Dauberman

Theses and Dissertations

Alzheimer’s disease (AD) is a neurodegenerative disorder affecting close to 5.1 million Americans and its incidence is expected to rise with the higher number of people in the aging population. A hallmark of the disease is the production of the amyloid-beta (Aß) peptides and eventual self-assembly of these peptides into fibrils and extracellular Aß plaques. Both plaques and oligomers are proposed to be the direct cause of AD, but it remains unclear how these structures affect neuronal function and pathogenesis. While a direct toxic effect is currently the favored hypothesis, biomolecule aggregation is also known to play a role in …

Profiling Bat Activity And Species Presence In Managed Longleaf Pine Landscapes, Margaret Hunt

Master of Science in Integrative Biology Theses

Restoration of native flora or reintroduction of at-risk fauna includes management practices that while encouraging presence and proliferation of target species, may adversely affect non-focal species. An endemic ecosystem undergoing restoration within the southeastern U.S. is that of the longleaf pine (Pinus palustris). Bats inhabit key ecological niches in forest ecosystems, including the longleaf pine ecosystem, and can be indicators of ecosystem condition. This study investigated the effects of current forest management practices and landscape management history on bat species presence and activity levels within habitat undergoing longleaf pine restoration. We deployed bat detectors in two wildlife management …

Investment In Territorial Defence Relates To Recent Reproductive Success In Common Loons (Gavia Immer), Jeremy A. Spool, Lauren V. Riters, Walter H. Piper

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

As the value of a limited resource such as a territory increases, animals should invest more in the defence of that resource. Because reproductive success often depends on the quality of a breeding territory, reproductive success or failure may alter the perceived value of territory and affect an animal's investment in territorial defence. We used common loons (Gavia immer) to test the hypothesis that animals with recent breeding success would show stronger territorial defence than those with no recent breeding success. Surprisingly, successful loons responded less, not more, to a simulated intrusion. However, birds with success in the …

Multiple Opening Closing Net Environmental Sensing System (Mocness) Instrument Data For Cruise Dp05 R/V Point Sur In-Situ Deep Seawater And Associated Fauna, May 1-11, 2017, Viosca Knoll Gom, Gray Lawson, Travis Richards

DEEPEND Datasets

The Multiple Opening Closing Net and Environmental Sensing System(s) (MOCNESS) deployed during the DEEPEND field program collects data (e.g., pressure, temperature, conductivity, volume filtered, horizontal and vertical velocity, latitude, and longitude) from several sensors while the instrument is in use. These data help characterize the environment and assess the orientation and speed of the MOCNESS. The flow and net angle can be used to calculate the volume of water filtered for each net. The biological data and ship data collected during this cruise are available in GRIIDC datasets R4.x257.226:0005 and R4.x257.226:0014 respectively.

Symbiosis With Nitrogen-Fixing Rhizobia Influences Plant Defense Strategy And Plant-Predator Interactions, Adrienne Louise Godschalx

Dissertations and Theses

As sessile organisms, plants evolved a plethora of defenses against their attackers. Given the role of plants as a primary food source for many organisms, plant defense has important implications for community ecology. Surprisingly, despite the potential to alter entire food webs and communities, the factors determining plant investment in defense are not well-understood, and are even less understood considering the numerous symbiotic interactions in the same plant. Legume-rhizobia symbioses engineer ecosystems by fixing nitrogen from the atmosphere in trade for plant photosynthates, yet connecting symbiotic resource exchange to food web interactions has yet to be established. Here I test …

Effects Of Mycorrhizal Fungi On Vigna Radiata Growth In Soil Differing In Fertilizer Concentration, Ming Sum Jessica Cheng

Pursuit - The Journal of Undergraduate Research at The University of Tennessee

Mycorrhizal fungi form mutualistic relationships with the roots of some plants, allowing the plant access to nutrients and minerals while the fungi obtain food from the plant. Given that this relationship is beneficial to the plant, this paper investigates the nature of the impact of presence of mycorrhizal fungi on the growth of Vigna radiata (mung beans) in soil of differing chemical environments. Through comparing the stem lengths of plants seven days after germination, it is found that in soil with 0.0% fertilizer, the presence of locally collected, unclassified mycorrhizal fungi impacts the growth of Vigna radiata negatively; in intermediate …

Evaluating The Social Behavior And Activity Patterns Of Clouded Leopards (Neofelis Nebulosa) At The Nashville Zoo: Research And Literature Review, Meghan Ryckeley

Mahurin Honors College Capstone Experience/Thesis Projects

The behavior of the elusive clouded leopard (Neofelis nebulosa) is not well understood. In captivity, they are prone to exhibit stress-related behaviors and are often aggressive to conspecifics when paired. The present study built on past research by examining clouded leopards at the Nashville Zoo at Grassmere (NZG) to determine their activity patterns and temperament. Twelve leopards were exposed to familiar and unfamiliar objects and people, as well as their reflection in a mirror over nine trials. The males were often more reactive than the females, and the 5-year olds more reactive than their younger counterparts. The mirror …

Finding A Link Between Circadian Rhythms And The Immune System Of Captive Zebra Finches (Taeniopygia Guttata), Amber Bishop

Mahurin Honors College Capstone Experience/Thesis Projects

Circadian rhythms are commonplace in organisms and are normally controlled by a master clock. More recent evidence suggests that autonomous clocks operate in various systems in the body, including the immune system. This study looks for such a connection between the circadian rhythm and the immune system. In this study, captive zebra finches (Taeniopygia guttata) were exposed to different light and dark cycles and blood samples were taken every six hours. Birds were exposed to 12 hours of light and then 12 hours of darkness (LD), 24 hours of darkness (DD), or 48 hours of DD. After collecting …

Spatial And Temporal Variation In Mangrove Distribution (1950-2014) In Tampa, Florida Usa, Carolyn Cheatham Rhodes

USF Tampa Graduate Theses and Dissertations

I carried out an observational study of historic high resolution aerial imagery spanning six decades (1950-2014) to identify recent and historic spatial extent of mangrove forests, within the municipal boundaries of the City of Tampa, Florida USA. My objectives were to map mangrove distribution and spatial extent and any change or patterns of change discernable. I observed variable patterns of change and rates of expansion varied between sites spatially as well as within sites between time intervals. I found notable changes in mangrove extent in the Tampa from historic and modern aerial imagery for the ~64-year period between 1950 and …

Bio-Docklets: Virtualization Containers For Single-Step Execution Of Ngs Pipelines, Baekdoo Kim, Thahmina Ali, Carlos Lijeron, Enis Afgan, Konstantinos Krampis

Publications and Research

Processing of next-generation sequencing (NGS) data requires significant technical skills, involving installation, configuration, and execution of bioinformatics data pipelines, in addition to specialized postanalysis visualization and data mining software. In order to address some of these challenges, developers have leveraged virtualization containers toward seamless deployment of preconfigured bioinformatics software and pipelines on any computational platform. We present an approach for abstracting the complex data operations of multistep, bioinformatics pipelines for NGS data analysis. As examples, we have deployed 2 pipelines for RNA sequencing and chromatin immunoprecipitation sequencing, preconfigured within Docker virtualization containers we call Bio-Docklets. Each Bio-Docklet exposes a single …

Comparison Of The Neuroprotective And Anti-Inflammatory Effects Of The Anthocyanin Metabolites, Protocatechuic Acid And 4-Hydroxybenzoic Acid, Aimee N. Winter, Matthew C. Brenner, Noelle Punessen, Michael Snodgrass, Caleb Byars, Yingyot Arora, Daniel A. Linseman

Biological Sciences: Faculty Scholarship

Anthocyanins are being increasingly investigated for their neuroprotective and antineuroinflammatory effects; however, the overall bioavailability of many anthocyanins is relatively low. In contrast, phenolic acids, metabolites of many polyphenols, including anthocyanins, have been shown to accumulate in tissue at higher concentrations than those of parent compounds, suggesting that these metabolites may be the bioactive components of anthocyanin-rich diets. We examined the neuroprotective capacity of two common phenolic acids, 4-hydroxybenzoic acid (HBA) and protocatechuic acid (PCA), in primary cultures of cerebellar granule neurons. Both HBA and PCA are capable of mitigating oxidative stress induced by hydrogen peroxide, which is thought to …

A Study Of Ticks And Tick-Borne Livestock Pathogens In Pakistan, Shahid Karim, Khemraj Budachetri, Nabanita Mukherjee, Jaclyn Williams, Asma Kausar, Muhammad Jawadul Hassan, Steven W. Adamson, Scot E. Dowd, Dmitry Apanskevich, Abdullah Arijo, Zia Uddin Sindhu, Muhammad Azam Kakar, Raja Muhammad Dilpazir Khan, Shafiq Ullah, Muhammad Sohail Sajid, Abid Ali, Zafar Iqbal

Faculty Publications

Background

As obligate blood-feeding arthropods, ticks transmit pathogens to humans and domestic animals more often than other arthropod vectors. Livestock farming plays a vital role in the rural economy of Pakistan, and tick infestation causes serious problems with it. However, research on tick species diversity and tick-borne pathogens has rarely been conducted in Pakistan. In this study, a systematic investigation of the tick species infesting livestock in different ecological regions of Pakistan was conducted to determine the microbiome and pathobiome diversity in the indigenous ticks.

Methodology/Principal findings A total of 3,866 tick specimens were morphologically identified as 19 different tick …

The General Amino Acid Permease Gap1 Is Regulated Differentially By Torc1 Activation And Inhibition, Ray Bowman

D.U.Quark

How does cell signaling in response to extracellular stressors impact the trafficking of membrane proteins? In particular, the TORC1 complex plays a key role in this process and while some details of this system have reported, in a recent Journal of Biological Chemistry publication, Andre’s group has revealed new details of this pathway focusing on the general amino acid permease Gap1 as a model cargo. Andre et al. describe a novel and distinct pathway wherein ubiquitylation and downregulation of Gap1 is regulated not only by amino acid-induced activation of TORC1, but also by numerous sources of TORC1 inhibition and cellular …

Spatiotemporal Regulation Of Atg1 Kinase Activation In Selective Autophagy, Ning Sun

D.U.Quark

Autophagy is a potent intracellular degradation system and thus its activation requires exquisite regulation to maintain cellular homeostasis. Atg1, a serine-threonine protein kinase, is essential in both selective and non-selective autophagy. New findings suggest that in selective autophagy, Atg1 is activated at the vacuole by convergence of two independent recruitment pathways to prevent aberrant autophagy induction.

Hsp70 Conformational Plasticity Allows For Expansive Chaperone Role, Megan Bean

D.U.Quark

The Hsp70 system is an essential component of chaperone activity in many organisms. Hsp70 functions include: protein folding, aggregation prevention, trafficking, and enzyme regulation. Hsp70’s ability to bind such a vast array of substrates suggests wide range of conformational plasticity. By utilizing a single mode optical tweezers technique, Mashaghi1 et al., confirms previous theories Hsp70 binds and stabilizes extended peptide segments but also partially folded and near-native protein.

Plasmodium Falciparum 26s Proteasome Network: A Mystery Solved, Christina Grogan

D.U.Quark

One ofthe most devastating diseases thatthreatens the world population is malaria. The 26S proteasome complex of the malaria parasite Plasmodium falciparum, which was previously unknown, was characterized by the authors through an affinity purification protocol that isolated functional 26S proteasome complexes. This allowed for the identification of subunit composition and PfUSP14, a proteasomeassociated deubiquitinase. This new understanding presents a potential target to disrupt protein regulation in thequest for effective antimalarial strategies.

Autophagy Inhibition In Pain: Role Of A Microrna, Andrea Stevens

D.U.Quark

Neuropathic pain caused by peripheral nerve injury (PNI) leads to the activation and infiltration of microglial cells and to a neuroinflammatory-induced pain state. miRNAs and autophagy are two main factors and/or mechanisms which have the ability to alter the pain state. In this study, miR-195 was shown to be markedly increased after PNI and associated with the pain phenotype. In addition, inhibition of autophagy in vivo led to p62 accumulation, decreased production of LC3, and inhibition of ATG14.

The Ethical Considerations Of Physician-Assisted Suicide, Madeline Jordan

Dialogue & Nexus

With respect to physician-assisted suicide, several approaches to adjudicate an ethical position can be processed from the theories of utilitarianism, Kantian deontology, and virtue ethics. This paper will explore these three positions with respect to physician-assisted suicide and the pros and cons of each. In conclusion, based on my research and Christian beliefs, I will define why I reside with virtue ethics and why it leads me to a position that is against physician-assisted suicide at this particular point in my life.

From Beginning To The End: Humans As Caretakers And Co-Creators Of Nature, Amber Grothe

Dialogue & Nexus

Followers of the Christian faith ought to reconsider their role as being created in the ‘image of God,’ their interpretation of the Apocalyptic literature, and the relationship between the two. Different interpretations of these two narratives in Biblical literature (the Creation and the End Times) can create and support the view of humans as care-takers of Earth. A different perspective of the Creation story and Apocalyptic literature can lead to a different view of humans and their role in nature. By realizing their equivalence with nature and nature’s true ownership by God, humans are demoted from nature’s tyrannical kings to …

The Origins Of Morality, Paulina Sanchez

Dialogue & Nexus

In modern society, there exists a standard for moral conduct that seems to reign universal over many societies of people. Pinpointing the origins of morality, however, can become problematic because of how one approaches what morality is and what its purpose is in society. Psychologists may point out the social constructs and norms that allow for morality to unfold. Evolutionary biologists may give evidence of human-related species that have developed similar behavioral standards. A Christian theologian may look to scripture in explaining a Creator who ordained that all abide by the standards of conduct most pleasing to this deity. Which …