Biology Commons^™

Gmr36a08, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 49927

• ID - GMR36A08
• Location - 2R: 18120673, 18124576
• Base pairs - 3903

Gmr40e08, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 41238

• ID - GMR40E08
• Location - 2R: 18162090, 18165058
• Base pairs - 2968

Gmr42a07, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 45284

• ID - GMR42A07
• Location - 2R: 18146520, 18150306
• Base pairs - 3786

Gmr36a10, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 49373

• ID - GMR36A10
• Location - 2R: 18116788, 18120701
• Base pairs - 3913

Gmr40c09, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer

• ID - GMR40C09
• Location - 2R: 18132203, 18134987
• Base pairs - 2784

Gmr41f05, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 50133

• ID - GMR41F05
• Location - 2R: 18139042, 18142672
• Base pairs - 3630

Gmr35a04, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer

• ID - GMR35A04
• Location - 2R: 18125755, 18128365
• Base pairs - 2610

Gmr39h01, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 50066

• ID - GMR39H01
• Location - 2R: 18153797, 18156108
• Base pairs - 2311

Gmr42e10, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer

• ID - GMR42E10
• Location - 2R: 18133506, 18137474
• Base pairs - 3968

Gmr41c04, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer

• ID - GMR41C04
• Location -2R: 18143594, 18147064
• Base pairs - 3470

Gmr40c05, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 45682

• ID - GMR40C05
• Location - 2R: 18141630, 18144381
• Base pairs - 2751

Gmr41h07, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 46241

• ID - GMR41H07
• Location - 2R: 18150920, 18154671
• Base pairs - 3751

Gmr42h01, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 48150

• ID - GMR42H01
• Location - 2R: 18158419, 18162751
• Base pairs - 4332

Updating Molecular Diagnostics For Detecting Methicillin- Susceptible And Methicillin-Resistant Staphylococcus Aureus Isolates In Blood Culture Bottles, Fred C. Tenover, Isabella A. Tickler, Victoria M. Le, Scott Dewell, Rodrigo E. Mendes, Richard V. Goering, Mrsa Consortium

Biology Faculty Publications

Molecular diagnostic tests can be used to provide rapid identification of staphylococcal species in blood culture bottles to help improve antimicrobial stewardship. However, alterations in the target nucleic acid sequences of the microorganisms or their antimicrobial resistance genes can lead to false-negative results. We determined the whole-genome sequences of 4 blood culture isolates of Staphylococcus aureus and 2 control organisms to understand the genetic basis of genotypephenotype discrepancies when using the Xpert MRSA/SA BC test (in vitro diagnostic medical device [IVD]). Three methicillin-resistant S. aureus (MRSA) isolates each had a different insertion of a genetic element in the staphylococcal cassette …

Total Rna Extraction From Transgenic Flies Misexpressing Foreign Genes To Perform Next Generation Rna Sequencing, Abijeet Singh Mehta, Agustin Luz-Madrigal, Jian-Liang Li, Panagiotis A. Tsonis, Amit Singh

Biology Faculty Publications

Due to absence of transgenic approaches in Notopthalmus Viridescens (newt), and conservation of genetic machinery across species, we generated transgenic Drosophila melanogaster to misexpress unique genes from newt. Novel newt genes cloned, and inserted at attP site in Drosophila were misexpressed ubiquitously using tubulin Gal-4. Sample (total RNA) for RNA sequencing was collected at 3rd instar larval stage during which major developmental events takes place in Drosophila. Total RNA was extracted, and purified using RNA clean and ConcentratorTM. RNA quality was quantitated by calculating absorbance at 260 nm (A260) and 280 nm (A280) wavelengths using Nanodrop 2000 spectrophotometer. Good quality …

Comparative Transcriptomic Analysis And Structure Prediction Of Novel Newt Proteins, Abijeet Singh Mehta, Agustin Luz-Madrigal, Jian-Liang Li, Panagiotis A. Tsonis, Amit Singh

Biology Faculty Publications

Notophthalmus viridescens (Red-spotted Newt) possess amazing capabilities to regenerate their organs and other tissues. Previously, using a de novo assembly of the newt transcriptome combined with proteomic validation, our group identified a novel family of five protein members expressed in adult tissues during regeneration in Notophthalmus viridescens. The presence of a putative signal peptide suggests that all these proteins are secretory in nature. Here we employed iterative threading assembly refinement (I-TASSER) server to generate three-dimensional structure of these novel Newt proteins and predicted their function. Our data suggests that these proteins could act as ion transporters, and be involved …

Assessing The Efficacy Of Seedling Planting As A Forest Restoration Technique In Temperate Hardwood Forests Impacted By Invasive Species, Michaela J. Woods, Meredith Cobb, Katie Hickle

Biology Faculty Publications

The emerald ash borer (Agrilus planipennis Fairmaire; EAB) is an invasive insect that causes mortality of trees in the genus Fraxinus, creating canopy gaps that may facilitate invasion by exotic plants. Planting native tree seedlings under EAB-infested Fraxinus may accelerate succession and preclude invasive plant expansion; however, the effectiveness of this approach has not been experimentally tested. We assessed understory seedling planting of Quercus rubra, Carya laciniosa, and Juglans cinerea in EAB-infested forests, where the invasive shrub Lonicera maackii (Amur honeysuckle) was removed. We tested whether the use of plastic tree shelters (“tree tubes”) or planting season (fall versus spring) …

Emergence Of Oxacillin Resistance In Stealth Methicillin-Resistant Staphylococcus Aureus Due To Meca Sequence Instability, Richard V. Goering, Erin A. Swartzendriber, Anne E. Obradovich, Isabella A. Tickler, Fred C. Tenover

Biology Faculty Publications

Staphylococcus aureus strains that possess a mecA gene but are phenotypically susceptible to oxacillin and cefoxitin (OS-MRSA) have been recognized for over a decade and are a challenge for diagnostic laboratories. The mechanisms underlying the discrepancy vary from isolate to isolate. We characterized seven OS-MRSA clinical isolates of six different spa types from six different states by whole-genome sequencing to identify the nucleotide sequence changes leading to the OS-MRSA phenotype. The results demonstrated that oxacillin susceptibility was associated with mutations in regions of nucleotide repeats within mecA. Subinhibitory antibiotic exposure selected for secondary mecA mutations that restored oxacillin resistance. …

Hippo Signaling In Cancer: Lessons From Drosophila Models, Kirti Snigdha, Karishma Sanjay Gangwani, Gauri Vijay Lapalikar, Amit Singh, Madhuri Kango-Singh

Biology Faculty Publications

Hippo pathway was initially identified through genetic screens for genes regulating organ size in fruitflies. Recent studies have highlighted the role of Hippo signaling as a key regulator of homeostasis, and in tumorigenesis. Hippo pathway is comprised of genes that act as tumor suppressor genes like hippo (hpo) and warts (wts), and oncogenes like yorkie (yki). YAP and TAZ are two related mammalian homologs of Drosophila Yki that act as effectors of the Hippo pathway. Hippo signaling deficiency can cause YAP- or TAZ-dependent oncogene addiction for cancer cells. YAP and TAZ are often activated …

The Effects Of Sublethal Antibiotics On Listeria Monocytogenes, Marlena Rae Merling

Honors Theses

Antibiotics can be found in sublethal levels environmentally as pollution and within the body when used as medication. Antibiotics induce stress responses and sometimes act as signaling molecules in bacteria. In order to better understand the relationship between antibiotics and bacterial infections, the effects of sublethal antibiotic exposure on the ability of Listeria monocytogenes to infect macrophages was studied. Listeria monocytogenes is an intracellular pathogen of the gastrointestinal tract that is facultatively anaerobic. Two strains of Listeria monocytogenes were tested: a lab strain and a clinical cardiotropic strain. The strains were grown in liquid media overnight aerobically or anaerobically with …

The Effects Of L. Rhamnosus Consumption On Male Long Evans Rat Anxiety-Like Behavior, Amanda Marie Schleper

Honors Theses

Adolescent stress in humans has been correlated with an increased likelihood of an individual to develop an alcohol use disorder later in life. Literature has demonstrated that rats subjected to adolescent stress tend to show an increased preference and consumption of ethanol. Adolescence is a critical time of development. The link between adolescent stressors and alcohol use disorders is not fully understood yet. This study examined the relationship between adolescent stress and alcohol consumption and preference in rats. Probiotics are bacteria with potential health benefits and have been well accepted as a dietary supplement. Literature shows that probiotics could decrease …

Pathogenic Differences In Listeria Monocytogenes 10403s And Cardiotropic Strains Grown Under Aerobic And Anaerobic Conditions, Alexander Hayes

Honors Theses

Listeria monocytogenes is a gram-positive bacillus that is commonly associated with foodborne illness. It is a facultative intracellular pathogen responsible for causing the listeriosis infection in humans which is particularly dangerous to immunocompromised individuals. L. monocytogenes pathogenesis occurs through a series of complex interactions between host and bacterial cellular machinery. The wild-type strain as well as a cardiotropic strain with high affinity for infecting cardiac tissue were used to investigate pathogenesis in L. monocytogenes. Specifically, the Listeriolysin O protein that is critical for virulence was investigated. Aerobic and anaerobic growth environments as well as short-chain fatty acid supplementation were utilized …

Flourishing The Urban Environment: How Urban Gardens Affect Pollinators, Emily Ann Rickert

Honors Theses

The order of Hymenoptera is classified as bees, wasps, and ants and are widely recognized as pollinators. Some species of bees (family Apoidea) and hoverflies tend to focus on certain types of flowers and are attracted to patterns and colors. Native plants and crops that are specifically bee-friendly can encourage bees and other pollinators that are decreasing in biodiversity and population to come back. Urban gardens work to provide vegetables and organic produce to its communities and subsequently are also growing pollinator-friendly food. This study focuses on whether the biodiversity of Hymenoptera, hoverflies, and other significant pollinators are affected by …

In The Face Of Antimicrobialsfactors Contributing To Listeria Monocytogenes Survival And Development Of Resistance, Andrea M. Vietti

Honors Theses

Bacterial antibiotic resistance is on an alarming rise worldwide, thus posing an urgent threat to human health. The rise in antibiotic resistance can be attributed to the overuse and misuse of antibiotics in both the healthcare and agricultural industries. In order to address this concern, this research aimed to identify environmental conditions that may lead to the development of antibiotic resistance in Listeria monocytogenes. L. monocytogenes is a foodborne pathogen capable of causing the disease listeriosis and is especially dangerous for immunocompromised populations. Although infected individuals are treated with antibiotics, an alarmingly high mortality rate of 20 percent still persists; …

Propionate Enhances The Antimicrobial Defenses In Macrophages Against Listeria Monocytogenes, John Weis

Honors Theses

Propionate is a short chain fatty acid produced by the bacteria in the human gut. It has a wide range of nutritional functions in the human body. Several studies have also reported the effects of propionate on immune cell activation. In this study, we used Listeria monocytogenes as a model pathogen to determine how and what the effects of propionate on immune cells influence cell susceptibility to infections. Listeria is a dangerous intracellular pathogen that can replicate inside immune cells such as macrophages. Therefore, we can assess the impact of propionate on infection susceptibility by performing cell culture infections. We …

Analysis Of Change In The Biodiversity Of Fish And Macroinvertebrates Following Low Dam Modification And Kayak Chute Installation In The Great Miami River In Downtown Dayton, Ohio, Madison E. Conway

Honors Theses

Over two years, from 2015-2017, the Miami Conservancy District and Five Rivers Metroparks completed a project to modify the low dam above Monument Avenue into a kayak chute and constructed a second, entirely new kayak chute about one-half mile upstream near Riverscape Metropark in downtown Dayton, Ohio. Low dams have a negative impact on river habitat by decreasing water velocity in the impoundment behind the dam. Physical habitat, which should consist of alternating pools and riffles, is disturbed and replaced by deeper, slower-moving water that accumulates deposits of sediment on the river bottom degrading its value as habitat. The conditions …

Establishing The Effect Of Ethanol On Listeria Infection, Ryan Evan Restrepo

Honors Theses

Excessive alcohol consumption is common in the United States, particularly among college campuses. Previous studies have shown that excessive drinking increases the risk of drug dependency, sexual assault and liver damage. Heavy drinking has also proven to impact immune capabilities. Immune cell function and numbers have been shown to be negatively impacted by alcohol treatment. This research project used different cell cultures to model human cells and investigated how exposure to alcohol affects susceptibility to bacterial infection. Listeria monocytogenes, a common foodborne bacterium, was used as a model pathogen. A high alcohol preferring mouse model was also used to examine …

The Vascular Flora Of Bill Yeck Park: Supporting The Conservation Of Local Biodiversity, Taylor Sparbanie

Honors Theses

Maintaining and fostering biodiversity is a critical component of natural areas management and conservation because of its known links to ecosystem function and stability. Identifying and documenting species through a floristic inventory is an important strategy for detecting the presence of rare or unique species, as well as invasive species that pose a threat to biodiversity. Bill Yeck Park is a 194-acre nature park maintained by Centerville-Washington Park District and is largely surrounded by residential areas. The goal of this project was to generate list of vascular plant species for Bill Yeck Park, a large park within the Centerville-Washington Township …

Modulation Of Listeria Monocytogenes Carbon Metabolism By Short Chain Fatty Acids, Diksha Bedi

Honors Theses

Listeria monocytogenes, a bacterial pathogen, is associated with foodborne infections in humans. Listeria encounters short chain fatty acids (SCFAs) during its transit through the intestine but its metabolic responses to SCFAs are not fully understood. To determine how Listeria metabolism is affected by SCFAs, I performed basic microbiology assays, including monitoring optical density, determining acetoin production, and measuring culture pH levels. I also performed preliminary 13C-NMR assays to provide a more in-depth look into carbon metabolism in SCFA-treated Listeria. I found that propionate-supplemented Listeria produced significantly more acetoin compared to no supplemented controls. Because acetoin is a product of central …

The Prickly Problem Of Pears Potential Effects Of Native Orthopteran Herbivory On An Invasive Woody Plant, Kaitlin Gawkins

Honors Theses

Across the United States, land managers are struggling to cope with a relatively new invasive species, Callery pear (Pyrus calleryana). Callery pear is currently one of the most important invasive species threatening prairies and early successional habitats in Ohio and the Midwest, and yet, no viable means of control exists for this species. This species is relatively resistant to herbicides and resilient against prescribed cutting and burning. One potential management of invasive species is biocontrol, or the intentional introduction of natural enemies to control the growth and propagation of a target organism. Previous experiments with Callery Pear have examined herbivory …